<86>Apr 14 03:13:37 userdel[66432]: delete user 'rooter' <86>Apr 14 03:13:37 userdel[66432]: removed group 'rooter' owned by 'rooter' <86>Apr 14 03:13:37 userdel[66432]: removed shadow group 'rooter' owned by 'rooter' <86>Apr 14 03:13:37 groupadd[66450]: group added to /etc/group: name=rooter, GID=639 <86>Apr 14 03:13:37 groupadd[66450]: group added to /etc/gshadow: name=rooter <86>Apr 14 03:13:37 groupadd[66450]: new group: name=rooter, GID=639 <86>Apr 14 03:13:37 useradd[66463]: new user: name=rooter, UID=639, GID=639, home=/root, shell=/bin/bash <86>Apr 14 03:13:37 userdel[66488]: delete user 'builder' <86>Apr 14 03:13:37 userdel[66488]: removed group 'builder' owned by 'builder' <86>Apr 14 03:13:37 groupadd[66506]: group added to /etc/group: name=builder, GID=640 <86>Apr 14 03:13:37 groupadd[66506]: group added to /etc/gshadow: name=builder <86>Apr 14 03:13:37 groupadd[66506]: new group: name=builder, GID=640 <86>Apr 14 03:13:37 useradd[66519]: new user: name=builder, UID=640, GID=640, home=/usr/src, shell=/bin/bash <13>Apr 14 03:13:45 rpmi: tex-common-0.2-alt4 1244804096 installed <13>Apr 14 03:13:45 rpmi: texlive-common-0.1-alt3 1244804816 installed <13>Apr 14 03:13:45 rpmi: libjpeg-2:1.3.1-alt0.1 1388074033 installed <13>Apr 14 03:13:45 rpmi: libpng15-1.5.28-alt1 1484572014 installed <13>Apr 14 03:13:45 rpmi: libtiff5-4.0.3-alt1 1348347498 installed <13>Apr 14 03:13:45 rpmi: perl-Encode-2.83-alt1 1459157776 installed <13>Apr 14 03:13:46 rpmi: libnspr-1:4.20-alt1 p8.216526.40 1542382588 installed <13>Apr 14 03:13:46 rpmi: libpng12-1.2.50-alt2 1347753407 installed <13>Apr 14 03:13:46 rpmi: liblcms2-2.8-alt1 1471601528 installed <13>Apr 14 03:13:46 rpmi: libexpat-2.2.4-alt0.M80P.1 1503871120 installed <13>Apr 14 03:13:46 rpmi: perl-Term-ANSIColor-4.05-alt1 1458575791 installed <13>Apr 14 03:13:46 rpmi: libidn2-2.0.4-alt3.M80P.1 1520307194 installed <13>Apr 14 03:13:46 rpmi: libICE-1.0.9-alt1 1409902719 installed <13>Apr 14 03:13:46 rpmi: libwayland-server-1.14.0-alt0.M80P.1 1502720500 installed <13>Apr 14 03:13:46 rpmi: libgdbm-1.8.3-alt10 1454943313 installed <13>Apr 14 03:13:46 rpmi: libkpathsea-2008.0-alt0.15.6 1449446882 installed <13>Apr 14 03:13:46 rpmi: libopenjpeg2.0-2.2.0-alt0.M80P.1 1503526491 installed <13>Apr 14 03:13:46 rpmi: ca-certificates-2016.02.25-alt1 1462368370 installed <13>Apr 14 03:13:46 rpmi: libcrypto10-1.0.2n-alt0.M80P.1 1512766129 installed <13>Apr 14 03:13:46 rpmi: perl-DBM-1:5.22.3-alt0.M80P.1 1485958065 installed <13>Apr 14 03:13:46 rpmi: libSM-1.2.2-alt1 1391072686 installed <13>Apr 14 03:13:46 rpmi: libjasper-1.900.1-alt3 1391718482 installed <13>Apr 14 03:13:46 rpmi: fonts-type1-tipa-tex-1.3-alt4 1246545601 installed <13>Apr 14 03:13:46 rpmi: texlive-doc-base-2008.0-alt0.10 1238420746 installed <13>Apr 14 03:13:46 rpmi: texmf-tex4ht-1.0.2009_06_11_1038-alt1 1328304130 installed <13>Apr 14 03:13:46 rpmi: tcsh-6.18.01-alt2 1442313244 installed <13>Apr 14 03:13:46 rpmi: t1lib-5.1.2-alt5 1326979643 installed <13>Apr 14 03:13:46 rpmi: perl-Term-Cap-1.17-alt1 1445018869 installed <13>Apr 14 03:13:46 rpmi: perl-Pod-Simple-3.32-alt1 1447205413 installed <13>Apr 14 03:13:46 rpmi: libruby-2.5.1-alt0.M80P.1 1525659669 installed <13>Apr 14 03:13:46 rpmi: ruby-2.5.1-alt0.M80P.1 1525659669 installed <13>Apr 14 03:13:47 rpmi: poppler-data-0.4.8-alt1.M80P.1 1524561858 installed <13>Apr 14 03:13:47 rpmi: publicsuffix-list-dafsa-20190329-alt1 p8+226349.100.1.1 1554128046 installed <13>Apr 14 03:13:47 rpmi: libpsl-0.18.0-alt0.M80P.1 1502785107 installed <13>Apr 14 03:13:47 rpmi: libnghttp2-1.8.0-alt1 1456818805 installed <13>Apr 14 03:13:47 rpmi: libpixman-3:0.32.8-alt1 1447610691 installed <13>Apr 14 03:13:47 rpmi: libbrotlicommon0-1.0.4-alt0.M80P.1 1528205024 installed <13>Apr 14 03:13:47 rpmi: libbrotlidec0-1.0.4-alt0.M80P.1 1528205024 installed <13>Apr 14 03:13:47 rpmi: libwayland-client-1.14.0-alt0.M80P.1 1502720500 installed <13>Apr 14 03:13:47 rpmi: libxshmfence-1.2-alt1 1420972191 installed <13>Apr 14 03:13:47 rpmi: libpciaccess-1:0.13.4-alt1 1431681688 installed <13>Apr 14 03:13:47 rpmi: libdrm-1:2.4.89-alt1.M80P.1 1516609380 installed <13>Apr 14 03:13:47 rpmi: libgbm-4:18.0.5-alt1.M80P.1 p8+226404.100.1.1 1554206332 installed <13>Apr 14 03:13:47 rpmi: libX11-locales-3:1.6.3-alt1 1431956885 installed <13>Apr 14 03:13:47 rpmi: libXdmcp-1.1.1-alt1 1334617699 installed <13>Apr 14 03:13:47 rpmi: libXau-1.0.8-alt1 1369565807 installed <13>Apr 14 03:13:47 rpmi: libxcb-1.12-alt2 p8.218219.300 1545313310 installed <13>Apr 14 03:13:47 rpmi: libX11-3:1.6.3-alt1 1431956911 installed <13>Apr 14 03:13:47 rpmi: libXext-1.3.3-alt1 1409902932 installed <13>Apr 14 03:13:47 rpmi: libXt-1.1.4-alt1 1369984716 installed <13>Apr 14 03:13:47 rpmi: libXmu-1.1.2-alt1 1391072528 installed <13>Apr 14 03:13:47 rpmi: libXpm-3.5.11-alt1 1391072398 installed <13>Apr 14 03:13:47 rpmi: libXrender-0.9.8-alt1 1371312110 installed <13>Apr 14 03:13:47 rpmi: libXaw-1.0.12-alt1 1391072621 installed <13>Apr 14 03:13:47 rpmi: libXxf86vm-1.1.3-alt1 1369984824 installed <13>Apr 14 03:13:47 rpmi: libXdamage-1.1.3-alt4 1297162596 installed <13>Apr 14 03:13:47 rpmi: libXfixes-5.0.1-alt1 1369809606 installed <13>Apr 14 03:13:47 rpmi: libGL-4:18.0.5-alt1.M80P.1 p8+226404.100.1.1 1554206332 installed <13>Apr 14 03:13:47 rpmi: libEGL-4:18.0.5-alt1.M80P.1 p8+226404.100.1.1 1554206332 installed <13>Apr 14 03:13:47 rpmi: mailx-8.1.2-alt7 1366314831 installed <13>Apr 14 03:13:47 rpmi: sharutils-4.6.3-alt1.1.qa2.1 1449219807 installed <13>Apr 14 03:13:47 rpmi: libsqlite3-3.15.2-alt1 1480432212 installed <13>Apr 14 03:13:47 rpmi: libnss-3.40.0-alt0.M80P.1 p8.216526.44 1542814585 installed <13>Apr 14 03:13:47 rpmi: nss-utils-3.40.0-alt0.M80P.1 p8.216526.44 1542814585 installed <13>Apr 14 03:13:47 rpmi: ncompress-4.2.4.4-alt1 1366160439 installed <13>Apr 14 03:13:47 rpmi: libjbig-2.1-alt1 1401380921 installed <13>Apr 14 03:13:47 rpmi: xorg-rgb-1.0.4-alt1.qa1 1366268675 installed <13>Apr 14 03:13:47 rpmi: libnetpbm-10.35.97-alt1 1447854203 installed <13>Apr 14 03:13:48 rpmi: netpbm-10.35.97-alt1 1447854203 installed <13>Apr 14 03:13:48 rpmi: libpaper-1.1.24-alt4 1315383473 installed <13>Apr 14 03:13:48 rpmi: libverto-0.2.6-alt1_6 1455633234 installed <13>Apr 14 03:13:48 rpmi: libkeyutils-1.5.10-alt0.M80P.2 p8+216694.100.6.1 1547827915 installed <13>Apr 14 03:13:48 rpmi: libcom_err-1.42.13-alt2 1449075846 installed <13>Apr 14 03:13:48 rpmi: liblz4-1:1.7.5-alt1 1488766699 installed <13>Apr 14 03:13:48 rpmi: libgpg-error-1.31-alt1.M80P.1 1529024730 installed <13>Apr 14 03:13:48 rpmi: libgcrypt20-1.8.3-alt4 p8+219793.200.6.1 1551112986 installed <13>Apr 14 03:13:48 rpmi: libsystemd-1:237-alt2.M80P.6 p8+221965.100.2.1 1550786217 installed <13>Apr 14 03:13:48 rpmi: libdbus-1.10.24-alt4.M80P.1 1518773282 installed <13>Apr 14 03:13:48 rpmi: libavahi-0.6.31-alt7.M80P.1 1526318593 installed <13>Apr 14 03:13:48 rpmi: libgraphite2-1.3.10-alt0.M80P.1 1496411360 installed <13>Apr 14 03:13:49 rpmi: texlive-base-bin-2008.0-alt0.15.6 1449446882 installed <13>Apr 14 03:13:50 rpmi: texlive-base-2008.0-alt0.15 1300007455 installed <13>Apr 14 03:13:52 rpmi: texlive-latex-base-2008.0-alt0.15 1300007455 installed <13>Apr 14 03:13:52 rpmi: texlive-font-utils-2008.0-alt0.15.6 1449446882 installed <86>Apr 14 03:13:52 groupadd[126135]: group added to /etc/group: name=_keytab, GID=499 <86>Apr 14 03:13:52 groupadd[126135]: new group: name=_keytab, GID=499 <13>Apr 14 03:13:52 rpmi: libkrb5-1.14.6-alt1.M80P.1 1525355673 installed <13>Apr 14 03:13:52 rpmi: libssl10-1.0.2n-alt0.M80P.1 1512766129 installed <13>Apr 14 03:13:52 rpmi: perl-Pod-Usage-1.68-alt1 1451923699 installed <13>Apr 14 03:13:52 rpmi: libcups-2.1.0-alt2.M80P.4 p8+223280.100.1.1 1551372192 installed <86>Apr 14 03:13:52 groupadd[126791]: group added to /etc/group: name=sasl, GID=498 <86>Apr 14 03:13:52 groupadd[126791]: group added to /etc/gshadow: name=sasl <86>Apr 14 03:13:52 groupadd[126791]: new group: name=sasl, GID=498 <13>Apr 14 03:13:52 rpmi: libsasl2-3-2.1.26-alt7 1479477445 installed <13>Apr 14 03:13:52 rpmi: libldap-2.4.45-alt1.M80P.1 1513980376 installed <13>Apr 14 03:13:52 rpmi: libcurl-7.64.0-alt1 p8+220788.100.1.1 1549495393 installed <13>Apr 14 03:13:52 rpmi: texlive-latex3-2008.0-alt0.16 1300008623 installed <13>Apr 14 03:13:52 rpmi: texlive-lang-tibetan-2008.0-alt0.14 1248958512 installed <13>Apr 14 03:13:52 rpmi: texlive-lang-polish-2008.0-alt0.14 1248958512 installed <13>Apr 14 03:13:53 rpmi: texmf-latex-tipa-1.3-alt4 1246545601 installed <13>Apr 14 03:13:53 rpmi: texlive-generic-extra-2008.0-alt0.16 1300008623 installed <13>Apr 14 03:13:53 rpmi: perl-podlators-4.07-alt1 1458574366 installed <13>Apr 14 03:13:53 rpmi: libharfbuzz-1.6.3-alt0.M80P.1 1509918814 installed <13>Apr 14 03:13:53 rpmi: libfreetype-2.8-alt0.M80P.3 1505462817 installed <13>Apr 14 03:13:53 rpmi: fontconfig-2.12.6-alt1.M80P.1 1506008910 installed Updating fonts cache: <29>Apr 14 03:13:54 fontconfig: Updating fonts cache: succeeded [ DONE ] <13>Apr 14 03:13:54 rpmi: fonts-type1-urw-3:1.0.7pre44-alt3 p8+224868.100.1.1 1552412385 installed <13>Apr 14 03:13:54 rpmi: libgs-9.20-alt1.M80P.1 1494700569 installed <13>Apr 14 03:13:54 rpmi: libXft-2.3.2-alt1 1409902650 installed <13>Apr 14 03:13:55 rpmi: perl-Tk-804.033-alt1.1 1448484960 installed <13>Apr 14 03:13:55 rpmi: libcairo-1:1.14.4-alt1 1447005495 installed <13>Apr 14 03:13:55 rpmi: libpoppler72-0.61.1-alt1.M80P.1 1524829028 installed <13>Apr 14 03:13:55 rpmi: poppler-0.61.1-alt1.M80P.1 1524829028 installed <13>Apr 14 03:13:55 rpmi: python-modules-encodings-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 14 03:13:56 rpmi: ghostscript-common-9.20-alt1.M80P.1 1494700614 installed <13>Apr 14 03:13:56 rpmi: ghostscript-classic-9.20-alt1.M80P.1 1494700569 installed <13>Apr 14 03:13:56 rpmi: latex2html-2012-alt1 1450368036 installed <13>Apr 14 03:13:56 rpmi: ghostscript-utils-9.20-alt1.M80P.1 1494700614 installed <13>Apr 14 03:13:56 rpmi: python-modules-compiler-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 14 03:13:56 rpmi: python-modules-email-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 14 03:13:56 rpmi: python-modules-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 14 03:13:56 rpmi: python-modules-unittest-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 14 03:13:59 rpmi: texlive-fonts-recommended-2008.0-alt0.15 1300007455 installed <13>Apr 14 03:14:09 rpmi: texlive-latex-recommended-2008.0-alt0.15 1300007455 installed <13>Apr 14 03:14:09 rpmi: texlive-generic-recommended-2008.0-alt0.15 1300007455 installed <13>Apr 14 03:14:09 rpmi: texlive-math-extra-2008.0-alt0.16 1300008623 installed <13>Apr 14 03:14:09 rpmi: texlive-lang-french-2008.0-alt0.14 1248958512 installed <13>Apr 14 03:14:09 rpmi: texlive-extra-utils-2008.0-alt0.15.6 1449446882 installed <13>Apr 14 03:14:10 rpmi: texlive-lang-german-2008.0-alt0.14 1248958512 installed <13>Apr 14 03:14:10 rpmi: texlive-lang-cyrillic-2008.0-alt0.14 1248958512 installed <13>Apr 14 03:14:10 rpmi: texmf-latex-xcolor-2.06-alt3 1244802289 installed <13>Apr 14 03:14:11 rpmi: texmf-pgf-3.0.1-alt1 1439012888 installed <13>Apr 14 03:14:17 rpmi: texlive-fonts-extra-2008.0-alt0.16 1300008623 installed <13>Apr 14 03:14:26 rpmi: texlive-pstricks-2008.0-alt0.16 1300008623 installed <13>Apr 14 03:14:26 rpmi: texlive-games-2008.0-alt0.16 1300008623 installed <13>Apr 14 03:14:26 rpmi: texmf-latex-obsolete-0.1-alt1 1244748792 installed <13>Apr 14 03:14:27 rpmi: texlive-lang-arab-2008.0-alt0.14 1248958512 installed <13>Apr 14 03:14:27 rpmi: texlive-xetex-2008.0-alt0.15.6 1449446882 installed <13>Apr 14 03:14:28 rpmi: texmf-latex-beamer-3.36-alt4 1451249538 installed <13>Apr 14 03:14:30 rpmi: texlive-publishers-2008.0-alt0.16 1300008623 installed <13>Apr 14 03:14:30 rpmi: texlive-pictures-2008.0-alt0.15 1300007455 installed <13>Apr 14 03:14:31 rpmi: texlive-science-2008.0-alt0.16 1300008623 installed <13>Apr 14 03:14:32 rpmi: texlive-humanities-2008.0-alt0.16 1300008623 installed <13>Apr 14 03:14:39 rpmi: texlive-latex-extra-2008.0-alt0.16 1300008623 installed <13>Apr 14 03:14:40 rpmi: texlive-bibtex-extra-2008.0-alt0.16 1300008623 installed Installing fenics-book-20130430-alt1.src.rpm Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.99234 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + rm -rf fenics-book-20130430 + echo 'Source #0 (fenics-book-20130430.tar.gz):' Source #0 (fenics-book-20130430.tar.gz): + /bin/gzip -dc /usr/src/RPM/SOURCES/fenics-book-20130430.tar.gz + /bin/tar -xf - + cd fenics-book-20130430 + /bin/chmod -c -Rf u+rwX,go-w . + install -p -m644 /usr/src/RPM/SOURCES/emptypage.sty /usr/src/RPM/SOURCES/todonotes.sty packages + exit 0 Executing(%build): /bin/sh -e /usr/src/tmp/rpm-tmp.14072 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd fenics-book-20130430 + '[' -n '' ']' + NPROCS=8 + make -j8 final make: Entering directory `/usr/src/RPM/BUILD/fenics-book-20130430' ./build.sh book --final ./build.sh manual --final This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. entering extended mode (./manual.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded. (./fenicsbook.cls Document Class: fenicsbook (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/geometry.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.styThis is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. ) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/etc/texmf/tex/xelatex/xetexconfig/geometry.cfg)) (/usr/share/texmf-texlive/tex/latex/oberdiek/bookmark.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdfescape.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.styentering extended mode (./book.tex (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded. (./fenicsbook.cls (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty Document Class: fenicsbook (/usr/share/texmf-texlive/tex/latex/base/book.cls)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/geometry.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty)) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/etc/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty) (/etc/texmf/tex/xelatex/xetexconfig/geometry.cfg) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/bookmark.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdfescape.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def (/etc/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty)) (/usr/share/texmf-texlive/tex/latex/oberdiek/auxhook.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/bkm-pdftex.def)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/emptypage.sty) (/usr/share/texmf-texlive/tex/latex/psnfss/mathpazo.sty Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty)) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/latex/psnfss/helvet.sty) (/usr/share/texmf-texlive/tex/latex/bera/beramono.sty) (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty) (/usr/share/texmf-texlive/tex/latex/base/t1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty))) (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def)) (/usr/share/texmf-texlive/tex/latex/textcase/textcase.sty) (/usr/share/texmf-texlive/tex/latex/titlesec/titlesec.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) (/usr/share/texmf-texlive/tex/latex/fancyhdr/fancyhdr.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) (/usr/share/texmf-texlive/tex/latex/tools/multicol.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/auxhook.sty)) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/natbib/natbib.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/bkm-pdftex.def)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/emptypage.sty) (/usr/share/texmf-texlive/tex/latex/psnfss/mathpazo.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty (/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf-texlive/tex/latex/psnfss/helvet.sty) (/usr/share/texmf-texlive/tex/latex/bera/beramono.sty) (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def)) (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty) (/usr/share/texmf-texlive/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf-texlive/tex/latex/amsfonts/amsfonts.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))) (/usr/share/texmf-texlive/tex/latex/textcase/textcase.sty) (/usr/share/texmf-texlive/tex/latex/titlesec/titlesec.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amscd.sty) (/usr/share/texmf-texlive/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texmf-texlive/tex/latex/stmaryrd/stmaryrd.sty) (/usr/share/texmf-texlive/tex/latex/tools/multicol.sty)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/codehighlight.sty (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty (/usr/src/RPM/BUILD/fenics-book-20130430/packages/mylistings.sty) (/usr/share/texmf-texlive/tex/latex/natbib/natbib.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty (/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) (/usr/share/texmf-texlive/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf-texlive/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texmf-texlive/tex/latex/listings/listings.cfg)) (/usr/share/texmf/tex/latex/xcolor/xcolor.sty (/etc/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def) (/usr/share/texmf-texlive/tex/latex/amsmath/amscd.sty) (/usr/share/texmf-texlive/tex/latex/stmaryrd/stmaryrd.sty) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/codehighlight.sty) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/mylistings.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty)) (/usr/share/texmf-texlive/tex/latex/listings/listings.cfg)) (/usr/share/texmf/tex/latex/xcolor/xcolor.sty (/etc/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-texlive/tex/latex/ltxmisc/import.sty) (/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty (/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def (/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) (/etc/texmf/tex/latex/config/graphics.cfg)))) (/usr/share/texmf-texlive/tex/latex/subfig/subfig.sty (/usr/share/texmf-texlive/tex/latex/caption/caption3.sty)) (/usr/share/texmf-texlive/tex/latex/ltxmisc/import.sty) (/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty (/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty (/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) (/etc/texmf/tex/latex/config/graphics.cfg)))) (/usr/share/texmf-texlive/tex/latex/subfig/subfig.sty (/usr/share/texmf-texlive/tex/latex/caption/caption3.sty) (/usr/share/texmf-texlive/tex/latex/booktabs/booktabs.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty) (/usr/share/texmf-texlive/tex/latex/tools/array.sty) (/usr/share/texmf-texlive/tex/latex/microtype/microtype.sty)) (/usr/share/texmf-texlive/tex/latex/booktabs/booktabs.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty) (/usr/share/texmf-texlive/tex/latex/tools/array.sty) (/usr/share/texmf-texlive/tex/latex/microtype/microtype.sty (/usr/share/texmf-texlive/tex/latex/microtype/microtype.cfg (/usr/share/texmf-texlive/tex/latex/microtype/microtype.cfg)) (/usr/share/texmf-texlive/tex/latex/tools/xspace.sty) (/usr/share/texmf-texlive/tex/latex/setspace/setspace.sty Package: `setspace' 6.7 <2000/12/01> ) (/usr/share/texmf-texlive/tex/latex/floatrow/floatrow.sty) (/usr/share/texmf-texlive/tex/latex/caption/caption.sty)) (/usr/share/texmf-texlive/tex/latex/tools/xspace.sty) (/usr/share/texmf-texlive/tex/latex/setspace/setspace.sty Package: `setspace' 6.7 <2000/12/01> ) (/usr/share/texmf-texlive/tex/latex/floatrow/floatrow.sty (/usr/share/texmf-texlive/tex/latex/caption/ltcaption.sty)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithm.sty Document Style `algorithm' - floating environment (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithmicx.sty Document Style algorithmicx 1.2 - a greatly improved `algorithmic' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algpseudocode.sty) (/usr/share/texmf-texlive/tex/latex/caption/caption.sty Document Style - pseudocode environments for use with the `algorithmicx' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/todonotes.sty (/usr/share/texmf-texlive/tex/latex/xkeyval/xkeyval.sty (/usr/share/texmf-texlive/tex/generic/xkeyval/xkeyval.tex)) (/usr/share/texmf/tex/latex/pgf/frontendlayer/tikz.sty (/usr/share/texmf/tex/latex/pgf/basiclayer/pgf.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfrcs.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common.tex (/usr/share/texmf-texlive/tex/latex/caption/ltcaption.sty) (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common-lists.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-latex.def (/usr/share/texmf-texlive/tex/latex/ms/everyshi.sty)) (/usr/share/texmf/tex/generic/pgf/utilities/pgfrcs.code.tex)) (/usr/share/texmf/tex/latex/pgf/basiclayer/pgfcore.sty (/usr/share/texmf/tex/latex/pgf/systemlayer/pgfsys.sty (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys.code.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex) (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeysfiltered.code.tex (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithm.sty Document Style `algorithm' - floating environment (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)))) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithmicx.sty (/usr/share/texmf/tex/generic/pgf/systemlayer/pgf.cfg) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-pdftex.def (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-common-pdf.def))) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsyssoftpath.code.tex) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsysprotocol.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcore.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathcalc.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathutil.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathparser.code.tex Document Style algorithmicx 1.2 - a greatly improved `algorithmic' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algpseudocode.sty) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.basic.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.trigonometric.code.tex Document Style - pseudocode environments for use with the `algorithmicx' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/todonotes.sty (/usr/share/texmf-texlive/tex/latex/xkeyval/xkeyval.sty (/usr/share/texmf-texlive/tex/generic/xkeyval/xkeyval.tex)) (/usr/share/texmf/tex/latex/pgf/frontendlayer/tikz.sty (/usr/share/texmf/tex/latex/pgf/basiclayer/pgf.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfrcs.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common-lists.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-latex.def) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.random.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.comparison.code.tex (/usr/share/texmf-texlive/tex/latex/ms/everyshi.sty))) (/usr/share/texmf/tex/generic/pgf/utilities/pgfrcs.code.tex)) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.base.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.round.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.misc.code.tex (/usr/share/texmf/tex/latex/pgf/basiclayer/pgfcore.sty (/usr/share/texmf/tex/latex/pgf/systemlayer/pgfsys.sty (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys.code.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.integerarithmetics.code .tex))) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfloat.code.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeysfiltered.code.tex)) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgf.cfg) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-pdftex.def (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-common-pdf.def))) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsyssoftpath.code.tex) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsysprotocol.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcore.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathcalc.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathutil.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathparser.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepoints.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathconstruct.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathusage.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.basic.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorescopes.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoregraphicstate.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransformations.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorequick.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreobjects.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathprocessing.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorearrows.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.trigonometric.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreshade.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreimage.code.tex (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreexternal.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorelayers.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransparency.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.random.code.tex)) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.comparison.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.base.code.tex (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepatterns.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.round.code.tex)))) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleshapes.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.misc.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.integerarithmetics.code .tex) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleplot.code.tex))) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfloat.code.tex) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-0-65.sty) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-1-18.sty)) (/usr/share/texmf/tex/latex/pgf/utilities/pgffor.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfkeys.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex)) (/usr/share/texmf/tex/latex/pgf/math/pgfmath.sty (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgffor.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex))) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepoints.code.tex)) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/tikz.code.tex (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryplothandlers.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathconstruct.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathusage.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorescopes.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoregraphicstate.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransformations.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorequick.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreobjects.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathprocessing.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorearrows.code.tex (/usr/share/texmf/tex/generic/pgf/modules/pgfmodulematrix.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreshade.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreimage.code.tex (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibrarytopat hs.code.tex (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreexternal.code.tex))) (/usr/share/texmf-texlive/tex/latex/tools/calc.sty))) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorelayers.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransparency.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepatterns.code.tex))) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleshapes.code.tex (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryshado ws.code.tex (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryfadin gs.code.tex (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryfadings.code.tex) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleplot.code.tex) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-0-65.sty))))) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-1-18.sty)) (/usr/share/texmf/tex/latex/pgf/utilities/pgffor.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfkeys.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex)) (/usr/share/texmf/tex/latex/pgf/math/pgfmath.sty (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgffor.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex))) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/tikz.code.tex) Writing index file book.idx No file book.aux. (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryplothandlers.code.tex (/usr/share/texmf-texlive/tex/latex/psnfss/t1pplx.fd)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (/usr/share/texmf/tex/generic/pgf/modules/pgfmodulematrix.code.tex) (/usr/share/texmf-texlive/tex/latex/microtype/mt-ppl.cfg) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibrarytopat hs.code.tex))) (/usr/share/texmf-texlive/tex/latex/floatrow/fr-subfig.sty (/usr/share/texmf-texlive/tex/latex/tools/calc.sty)) (/usr/share/texmf-texlive/tex/latex/floatrow/fr-longtable.sty) ABD: EveryShipout initializing macros (./tex/FM1.tex (/usr/share/texmf-texlive/tex/latex/psnfss/ot1pplx.fd) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryshado ws.code.tex (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryfadin gs.code.tex (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryfadings.code.tex (/usr/share/texmf-texlive/tex/latex/psnfss/omlzplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omszplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omxzplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/ot1zplm.fd) (/usr/share/texmf-texlive/tex/latex/microtype/mt-msa.cfg) (/usr/share/texmf-texlive/tex/latex/microtype/mt-msb.cfg) (/usr/share/texmf-texlive/tex/latex/stmaryrd/Ustmry.fd) (/usr/share/texmf-texlive/tex/latex/bera/t1fvm.fd) [1{/var/cache/texmf/fonts/ma p/pdftex/updmap/pdftex.map)))))} Writing index file manual.idx No file manual.aux. (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd]) (/usr/share/texmf-texlive/tex/latex/psnfss/t1pplx.fd) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) Underfull \hbox (badness 10000) in paragraph at lines 59--67 Overfull \hbox (2.20999pt too wide) in paragraph at lines 46--68 $[]$ $[]$ (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pplx.fd) [2] [3 (/usr/share/texmf-texlive/tex/latex/microtype/mt-ppl.cfg] [4]) [5]) [6] (./tex/1.tex (/usr/share/texmf-texlive/tex/latex/floatrow/fr-subfig.sty) (/usr/share/texmf-texlive/tex/latex/floatrow/fr-longtable.sty) ABD: EveryShipout initializing macros (./tex/FMmanual.tex Chapter 1. [1] [1 LaTeX Warning: Reference `langtangen:app:install' on page 2 undefined on input line 67. LaTeX Warning: Reference `langtangen:poisson1' on page 2 undefined on input lin e 109. LaTeX Warning: Reference `langtangen:poisson1' on page 2 undefined on input lin e 117. LaTeX Warning: Reference `langtangen:poisson1' on page 2 undefined on input lin e 132. LaTeX Warning: Reference `langtangen:appendix:books' on page 2 undefined on inp ut line 153. [2{/var/cache/texmf/fonts/map/pdftex/updmap/pdft ex.map] LaTeX Warning: Reference `langtangen:poisson1:eqbyparts' on page 3 undefined on input line 195. LaTeX Warning: Reference `langtangen:poisson1:multbyv' on page 3 undefined on i nput line 196. LaTeX Warning: Reference `langtangen:poisson1:eqbyparts' on page 3 undefined on input line 197. LaTeX Warning: Reference `langtangen:poisson1:weak1' on page 3 undefined on inp ut line 204. LaTeX Warning: Reference `langtangen:poisson1' on page 3 undefined on input lin e 206. LaTeX Warning: Reference `langtangen:poisson1:var' on page 3 undefined on input line 230. LaTeX Warning: Reference `langtangen:poisson1:var' on page 3 undefined on input line 235. [3]} <./png/fenics_logo_text.png LaTeX Warning: Reference `langtangen:poisson1:vard' on page 4 undefined on inpu t line 270. LaTeX Warning: Reference `langtangen:poisson1:impl:uex' on page 4 undefined on input line 315. [4] LaTeX Warning: Reference `langtangen:poisson1:impl:uex' on page 5 undefined on input line 321. (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty)>] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pplx.fd) [2] Package natbib Warning: Citation `PythonTutorial' on page 5 undefined on input line 379. LaTeX Warning: Reference `langtangen:appendix:pybooks' on page 5 undefined on i nput line 384. [5] [3] [4] (/usr/share/texmf-texlive/tex/latex/bera/t1fvm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/ot1pplx.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omlzplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omszplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omxzplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/ot1zplm.fd) (/usr/share/texmf-texlive/tex/latex/microtype/mt-msa.cfg) (/usr/share/texmf-texlive/tex/latex/microtype/mt-msb.cfg) (/usr/share/texmf-texlive/tex/latex/stmaryrd/Ustmry.fd)) [5] [6] (./tex/1.tex Chapter 1. [1] LaTeX Warning: Reference `langtangen:app:install' on page 2 undefined on input line 67. LaTeX Warning: Reference `langtangen:poisson1' on page 2 undefined on input lin e 109. LaTeX Warning: Reference `langtangen:poisson1' on page 2 undefined on input lin e 117. LaTeX Warning: Reference `langtangen:poisson1' on page 2 undefined on input lin e 132. LaTeX Warning: Reference `langtangen:appendix:books' on page 2 undefined on inp ut line 153. [2] LaTeX Warning: Reference `langtangen:poisson1:eqbyparts' on page 3 undefined on input line 195. LaTeX Warning: Reference `langtangen:poisson1:multbyv' on page 3 undefined on i nput line 196. LaTeX Warning: Reference `langtangen:poisson1:eqbyparts' on page 3 undefined on input line 197. LaTeX Warning: Reference `langtangen:poisson1:weak1' on page 3 undefined on inp ut line 204. LaTeX Warning: Reference `langtangen:poisson1' on page 3 undefined on input lin e 206. LaTeX Warning: Reference `langtangen:poisson1:var' on page 3 undefined on input line 230. LaTeX Warning: Reference `langtangen:poisson1:var' on page 3 undefined on input line 235. [3] LaTeX Warning: Reference `langtangen:poisson1:vard' on page 4 undefined on inpu t line 270. LaTeX Warning: Reference `langtangen:poisson1:impl:uex' on page 4 undefined on input line 315. [4] LaTeX Warning: Reference `langtangen:poisson1:impl:uex' on page 5 undefined on input line 321. (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) LaTeX Warning: Reference `langtangen:prepro' on page 6 undefined on input line 422. [6] Package natbib Warning: Citation `PythonTutorial' on page 5 undefined on input line 379. LaTeX Warning: Reference `langtangen:appendix:pybooks' on page 5 undefined on i nput line 384. [5] LaTeX Warning: Reference `langtangen:prepro' on page 6 undefined on input line 422. [6 LaTeX Warning: Reference `langtangen:app:cpp:functions' on page 7 undefined on input line 483. LaTeX Warning: Reference `chap:logg-2' on page 7 undefined on input line 483. [7]] [8] LaTeX Warning: Reference `langtangen:poisson:2D:fig:ex1:u' on page 9 undefined on input line 607. LaTeX Warning: Reference `langtangen:poisson:2D:fig:ex1:mesh' on page 9 undefin ed on input line 608. LaTeX Warning: Reference `langtangen:quickviz' on page 9 undefined on input lin e 632. LaTeX Warning: Reference `langtangen:quickviz' on page 9 undefined on input lin e 632. LaTeX Warning: Reference `langtangen:poisson:membrane' on page 9 undefined on i nput line 652. [9 <./chapters/langtangen/pdf/ex1_u.pdf>] LaTeX Warning: Reference `langtangen:app:solver:prec' on page 10 undefined on i nput line 682. [10 <./chapters/langtangen/png/ex1_mesh.png (PNG copy)>] LaTeX Warning: Reference `langtangen:app:cpp:functions' on page 7 undefined on input line 483. LaTeX Warning: Reference `chap:logg-2' on page 7 undefined on input line 483. [7] [11] [8] LaTeX Warning: Reference `langtangen:poisson1:impl' on page 12 undefined on inp ut line 824. [12] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) LaTeX Warning: Reference `langtangen:poisson:2D:fig:ex1:u' on page 9 undefined on input line 607. LaTeX Warning: Reference `langtangen:poisson:2D:fig:ex1:mesh' on page 9 undefin ed on input line 608. LaTeX Warning: Reference `langtangen:quickviz' on page 9 undefined on input lin e 632. LaTeX Warning: Reference `langtangen:quickviz' on page 9 undefined on input lin e 632. LaTeX Warning: Reference `langtangen:poisson:membrane' on page 9 undefined on i nput line 652. [9 <./chapters/langtangen/pdf/ex1_u.pdf>] LaTeX Warning: Reference `langtangen:app:solver:prec' on page 10 undefined on i nput line 682. [10 [13 <./chapters/langtangen/png/ex1_mesh.png (PNG copy)>]] LaTeX Warning: Reference `langtangen:poisson1:impl' on page 14 undefined on inp ut line 993. [14] LaTeX Warning: Reference `langtangen:poisson1:membrane:scaled:eq:rhs' on page 1 5 undefined on input line 1041. [15 [11]] LaTeX Warning: Reference `langtangen:poisson1:impl' on page 12 undefined on inp ut line 824. [12] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) LaTeX Warning: Reference `langtangen:poisson1:verify1' on page 16 undefined on input line 1107. LaTeX Warning: Reference `langtangen:poisson1:impl' on page 16 undefined on inp ut line 1126. LaTeX Warning: Reference `langtangen:poisson1:solve:prm' on page 16 undefined o n input line 1131. LaTeX Warning: Reference `langtangen:poisson1:solver:problem' on page 16 undefi ned on input line 1133. LaTeX Warning: Reference `langtangen:poisson1:verify1' on page 16 undefined on input line 1135. [16] Underfull \vbox (badness 1033) has occurred while \output is active [17] [13] LaTeX Warning: Reference `langtangen:poisson:membrane' on page 18 undefined on input line 1228. LaTeX Warning: Reference `langtangen:poisson:2D:fig1' on page 18 undefined on i nput line 1278. [18] Underfull \vbox (badness 10000) has occurred while \output is active [19 <./cha pters/langtangen/pdf/membrane_waxis.pdf LaTeX Warning: Reference `langtangen:poisson1:impl' on page 14 undefined on inp ut line 993. [14]>] LaTeX Warning: Reference `langtangen:poisson1:membrane:scaled:eq:rhs' on page 1 5 undefined on input line 1041. [15] LaTeX Warning: Reference `langtangen:poisson:2D:fig:ex1:gradu' on page 20 undef ined on input line 1357. [20 <./chapters/langtangen/pdf/ex1_ gradu.pdf>] LaTeX Warning: Reference `langtangen:poisson1:verify1' on page 16 undefined on input line 1107. LaTeX Warning: Reference `langtangen:poisson1:impl' on page 16 undefined on inp ut line 1126. LaTeX Warning: Reference `langtangen:poisson1:solve:prm' on page 16 undefined o n input line 1131. LaTeX Warning: Reference `langtangen:poisson1:solver:problem' on page 16 undefi ned on input line 1133. LaTeX Warning: Reference `langtangen:poisson1:verify1' on page 16 undefined on input line 1135. [16] LaTeX Warning: Reference `langtangen:poisson1:verify1' on page 21 undefined on input line 1397. LaTeX Warning: Reference `langtangen:quickviz' on page 21 undefined on input li ne 1407. LaTeX Warning: Reference `langtangen:poisson1:verify1' on page 21 undefined on input line 1451. [21] Underfull \vbox (badness 1033) has occurred while \output is active [17] LaTeX Warning: Reference `langtangen:poisson:2D:varcoeff' on page 22 undefined on input line 1462. LaTeX Warning: Reference `langtangen:poisson1:varform' on page 22 undefined on input line 1472. LaTeX Warning: Reference `langtangen:poisson1:impl' on page 22 undefined on inp ut line 1480. LaTeX Warning: Reference `langtangen:poisson:gradu' on page 22 undefined on inp ut line 1500. LaTeX Warning: Reference `langtangen:poisson:gradu' on page 22 undefined on inp ut line 1514. [22] LaTeX Warning: Reference `langtangen:poisson:membrane' on page 18 undefined on input line 1228. LaTeX Warning: Reference `langtangen:poisson:2D:fig1' on page 18 undefined on i nput line 1278. [18] Underfull \vbox (badness 10000) has occurred while \output is active [19 <./cha pters/langtangen/pdf/membrane_waxis.pdf LaTeX Warning: Reference `langtangen:poisson:gradu' on page 23 undefined on inp ut line 1535. LaTeX Warning: Reference `langtangen:structviz' on page 23 undefined on input l ine 1555. LaTeX Warning: Reference `langtangen:possion:2D:varcoeff' on page 23 undefined on input line 1583. [23]>] LaTeX Warning: Reference `langtangen:poisson:2D:fig:ex1:gradu' on page 20 undef ined on input line 1357. LaTeX Warning: Reference `langtangen:poisson1:functionals:energy' on page 24 un defined on input line 1589. LaTeX Warning: Reference `langtangen:poisson:mat:neumann' on page 24 undefined on input line 1599. LaTeX Warning: Reference `langtangen:poisson:membrane' on page 24 undefined on input line 1605. LaTeX Warning: Reference `langtangen:poisson:gradu' on page 24 undefined on inp ut line 1610. LaTeX Warning: Reference `langtangen:poisson1:functionals:error' on page 24 und efined on input line 1632. [24] [20 <./chapters/langtangen/pdf/ex1_ gradu.pdf>] [25] [26] LaTeX Warning: Reference `langtangen:poisson1:verify1' on page 21 undefined on input line 1397. LaTeX Warning: Reference `langtangen:quickviz' on page 21 undefined on input li ne 1407. LaTeX Warning: Reference `langtangen:poisson1:verify1' on page 21 undefined on input line 1451. [21] LaTeX Warning: Reference `langtangen:poisson1:verify1' on page 27 undefined on input line 1786. LaTeX Warning: Reference `langtangen:poisson1:functionals:flux' on page 27 unde fined on input line 1792. LaTeX Warning: Reference `langtangen:poisson:mat:neumann' on page 27 undefined on input line 1810. LaTeX Warning: Reference `langtangen:possion:2D:varcoeff' on page 27 undefined on input line 1851. [27] LaTeX Warning: Reference `langtangen:poisson:2D:fig2' on page 28 undefined on i nput line 1937. Underfull \vbox (badness 3536) has occurred while \output is active [28] LaTeX Warning: Reference `langtangen:poisson:2D:varcoeff' on page 22 undefined on input line 1462. LaTeX Warning: Reference `langtangen:poisson1:varform' on page 22 undefined on input line 1472. LaTeX Warning: Reference `langtangen:poisson1:impl' on page 22 undefined on inp ut line 1480. LaTeX Warning: Reference `langtangen:poisson:gradu' on page 22 undefined on inp ut line 1500. LaTeX Warning: Reference `langtangen:poisson:gradu' on page 22 undefined on inp ut line 1514. [22] LaTeX Warning: Reference `langtangen:poisson:gradu' on page 23 undefined on inp ut line 1535. LaTeX Warning: Reference `langtangen:structviz' on page 23 undefined on input l ine 1555. LaTeX Warning: Reference `langtangen:possion:2D:varcoeff' on page 23 undefined on input line 1583. [23] LaTeX Warning: Reference `langtangen:poisson:2D:fig3' on page 29 undefined on i nput line 1962. LaTeX Warning: Reference `langtangen:poisson:2D:fig2' on page 29 undefined on i nput line 2017. [29] LaTeX Warning: Reference `langtangen:poisson1:bvp' on page 30 undefined on inpu t line 2065. Underfull \vbox (badness 10000) has occurred while \output is active [30 <./cha pters/langtangen/pdf/Poisson2D_Dvc_contour1.pdf> <./chapters/langtangen/pdf/Poi sson2D_Dvc_flux_x.pdf> <./chapters/langtangen/pdf/Poisson2D_Dvc_surf1.pdf> <./c hapters/langtangen/pdf/Poisson2D_Dvc_mesh1.pdf>] LaTeX Warning: Reference `langtangen:poisson:2D:DN:weak' on page 31 undefined o n input line 2130. [31] LaTeX Warning: Reference `langtangen:poisson1:functionals:energy' on page 24 un defined on input line 1589. LaTeX Warning: Reference `langtangen:poisson:mat:neumann' on page 24 undefined on input line 1599. LaTeX Warning: Reference `langtangen:poisson:membrane' on page 24 undefined on input line 1605. LaTeX Warning: Reference `langtangen:poisson:gradu' on page 24 undefined on inp ut line 1610. LaTeX Warning: Reference `langtangen:poisson1:functionals:error' on page 24 und efined on input line 1632. [24] LaTeX Warning: Reference `langtangen:poisson1:impl' on page 32 undefined on inp ut line 2166. LaTeX Warning: Reference `langtangen:poisson1:DN' on page 32 undefined on input line 2204. [32] [25] [26] LaTeX Warning: Reference `langtangen:poisson:mat:neumann' on page 33 undefined on input line 2259. Underfull \vbox (badness 1122) has occurred while \output is active [33 LaTeX Warning: Reference `langtangen:poisson1:verify1' on page 27 undefined on input line 1786. LaTeX Warning: Reference `langtangen:poisson1:functionals:flux' on page 27 unde fined on input line 1792. LaTeX Warning: Reference `langtangen:poisson:mat:neumann' on page 27 undefined on input line 1810. LaTeX Warning: Reference `langtangen:possion:2D:varcoeff' on page 27 undefined on input line 1851. [27]] LaTeX Warning: Reference `langtangen:poisson:2D:fig2' on page 28 undefined on i nput line 1937. Underfull \vbox (badness 3536) has occurred while \output is active [28] LaTeX Warning: Reference `langtangen:poisson:multiple:Dirichlet' on page 34 und efined on input line 2310. [34] LaTeX Warning: Reference `langtangen:poisson:2D:fig3' on page 29 undefined on i nput line 1962. LaTeX Warning: Reference `langtangen:poisson:2D:fig2' on page 29 undefined on i nput line 2017. [29] LaTeX Warning: Reference `langtangen:poisson:multiple:Dirichlet' on page 35 und efined on input line 2386. LaTeX Warning: Reference `langtangen:app:solver:prec' on page 35 undefined on i nput line 2400. LaTeX Warning: Reference `langtangen:poisson1:solver:problem' on page 35 undefi ned on input line 2405. [35] LaTeX Warning: Reference `langtangen:poisson1:bvp' on page 30 undefined on inpu t line 2065. Underfull \vbox (badness 10000) has occurred while \output is active [30 <./cha pters/langtangen/pdf/Poisson2D_Dvc_contour1.pdf> <./chapters/langtangen/pdf/Poi sson2D_Dvc_flux_x.pdf> <./chapters/langtangen/pdf/Poisson2D_Dvc_surf1.pdf> <./c hapters/langtangen/pdf/Poisson2D_Dvc_mesh1.pdf>] LaTeX Warning: Reference `langtangen:timedep:diffusion1:impl' on page 36 undefi ned on input line 2440. LaTeX Warning: Reference `langtangen:timedep:diffusion1:noassemble' on page 36 undefined on input line 2441. LaTeX Warning: Reference `langtangen:poisson1:ddim' on page 36 undefined on inp ut line 2498. [36] LaTeX Warning: Reference `langtangen:poisson:2D:DN:weak' on page 31 undefined o n input line 2130. [31] LaTeX Warning: Reference `langtangen:poisson1:impl' on page 32 undefined on inp ut line 2166. LaTeX Warning: Reference `langtangen:poisson1:DN' on page 32 undefined on input line 2204. [32] LaTeX Warning: Reference `langtangen:poisson:mat:neumann' on page 33 undefined on input line 2259. Underfull \vbox (badness 1122) has occurred while \output is active [33] Underfull \vbox (badness 3646) has occurred while \output is active [37] LaTeX Warning: Reference `langtangen:poisson:nonlinear:d' on page 38 undefined on input line 2626. LaTeX Warning: Reference `langtangen:poisson1:varform' on page 38 undefined on input line 2629. [38] LaTeX Warning: Reference `langtangen:poisson:nonlinear:picard1' on page 39 unde fined on input line 2670. LaTeX Warning: Reference `langtangen:poisson:nonlinear2' on page 39 undefined o n input line 2672. [39] LaTeX Warning: Reference `langtangen:poisson:nD' on page 40 undefined on input line 2757. LaTeX Warning: Reference `langtangen:poisson:nonlinear1' on page 40 undefined o n input line 2767. LaTeX Warning: Reference `langtangen:poisson:nonlinear:d' on page 40 undefined on input line 2768. LaTeX Warning: Reference `langtangen:poisson:nonlinear:d' on page 40 undefined on input line 2771. LaTeX Warning: Reference `langtangen:nonlinear:Newton:F1' on page 40 undefined on input line 2797. LaTeX Warning: Reference `langtangen:poisson:nonlinear:dFdU' on page 40 undefin ed on input line 2810. LaTeX Warning: Reference `langtangen:poisson:nonlinear:dFdU' on page 40 undefin ed on input line 2817. Underfull \vbox (badness 1412) has occurred while \output is active [40] LaTeX Warning: Reference `langtangen:poisson:multiple:Dirichlet' on page 34 und efined on input line 2310. [34] LaTeX Warning: Reference `langtangen:nonlinear:Newton:aLF' on page 41 undefined on input line 2852. LaTeX Warning: Reference `langtangen:poisson1:varform' on page 41 undefined on input line 2869. LaTeX Warning: Reference `langtangen:poisson1:impl' on page 41 undefined on inp ut line 2870. LaTeX Warning: Reference `langtangen:poisson1:DN' on page 41 undefined on input line 2870. [41] LaTeX Warning: Reference `langtangen:poisson:multiple:Dirichlet' on page 35 und efined on input line 2386. LaTeX Warning: Reference `langtangen:app:solver:prec' on page 35 undefined on i nput line 2400. LaTeX Warning: Reference `langtangen:poisson1:solver:problem' on page 35 undefi ned on input line 2405. [35] LaTeX Warning: Reference `langtangen:timedep:diffusion1:impl' on page 36 undefi ned on input line 2440. LaTeX Warning: Reference `langtangen:timedep:diffusion1:noassemble' on page 36 undefined on input line 2441. LaTeX Warning: Reference `langtangen:poisson1:ddim' on page 36 undefined on inp ut line 2498. [36] Underfull \vbox (badness 3646) has occurred while \output is active [37] LaTeX Warning: Reference `langtangen:poisson:nonlinear:d' on page 38 undefined on input line 2626. LaTeX Warning: Reference `langtangen:poisson1:varform' on page 38 undefined on input line 2629. [38] LaTeX Warning: Reference `langtangen:nonlinear:Picard' on page 42 undefined on input line 2930. LaTeX Warning: Reference `langtangen:poisson:nD' on page 42 undefined on input line 2963. [42] LaTeX Warning: Reference `langtangen:nonlinear:Newton:algebraic' on page 43 und efined on input line 2975. LaTeX Warning: Reference `langtangen:poisson1:varform' on page 43 undefined on input line 3026. LaTeX Warning: Reference `langtangen:nonlinear:poisson:pdelevel:eqa' on page 43 undefined on input line 3041. LaTeX Warning: Reference `langtangen:nonlinear:poisson:pdelevel:eqL' on page 43 undefined on input line 3042. LaTeX Warning: Reference `langtangen:nonlinear:Newton:algebraic' on page 43 und efined on input line 3044. [43] LaTeX Warning: Reference `langtangen:poisson:nonlinear:picard1' on page 39 unde fined on input line 2670. LaTeX Warning: Reference `langtangen:poisson:nonlinear2' on page 39 undefined o n input line 2672. [39] LaTeX Warning: Reference `langtangen:poisson:nD' on page 40 undefined on input line 2757. LaTeX Warning: Reference `langtangen:poisson:nonlinear1' on page 40 undefined o n input line 2767. LaTeX Warning: Reference `langtangen:poisson:nonlinear:d' on page 40 undefined on input line 2768. LaTeX Warning: Reference `langtangen:poisson:nonlinear:d' on page 40 undefined on input line 2771. LaTeX Warning: Reference `langtangen:nonlinear:Newton:F1' on page 40 undefined on input line 2797. LaTeX Warning: Reference `langtangen:poisson:nonlinear:dFdU' on page 40 undefin ed on input line 2810. LaTeX Warning: Reference `langtangen:poisson:nonlinear:dFdU' on page 40 undefin ed on input line 2817. Underfull \vbox (badness 1412) has occurred while \output is active [40] LaTeX Warning: Reference `langtangen:nonlinear:Newton:aLF' on page 41 undefined on input line 2852. LaTeX Warning: Reference `langtangen:poisson1:varform' on page 41 undefined on input line 2869. LaTeX Warning: Reference `langtangen:poisson1:impl' on page 41 undefined on inp ut line 2870. LaTeX Warning: Reference `langtangen:poisson1:DN' on page 41 undefined on input line 2870. [41] LaTeX Warning: Reference `langtangen:nonlinear:Newton:algebraic' on page 44 und efined on input line 3054. LaTeX Warning: Reference `langtangen:nonlinear:Newton:algebraic' on page 44 und efined on input line 3058. Underfull \hbox (badness 2221) in paragraph at lines 3053--3059 []\T1/pplx/m/n/10 (+20) The im-ple-men-ta-tion is iden-ti-cal to the one in Sec -tion [] and is found in the file LaTeX Warning: Reference `langtangen:poisson:nonlinear2' on page 44 undefined o n input line 3080. [44] LaTeX Warning: Reference `langtangen:nonlinear:Picard' on page 42 undefined on input line 2930. LaTeX Warning: Reference `langtangen:poisson:nD' on page 42 undefined on input line 2963. [42] LaTeX Warning: Reference `langtangen:nonlinear:Newton:algebraic' on page 43 und efined on input line 2975. LaTeX Warning: Reference `langtangen:poisson1:varform' on page 43 undefined on input line 3026. LaTeX Warning: Reference `langtangen:nonlinear:poisson:pdelevel:eqa' on page 43 undefined on input line 3041. LaTeX Warning: Reference `langtangen:nonlinear:poisson:pdelevel:eqL' on page 43 undefined on input line 3042. LaTeX Warning: Reference `langtangen:nonlinear:Newton:algebraic' on page 43 und efined on input line 3044. [43] [45] LaTeX Warning: Reference `langtangen:nonlinear:Newton:algebraic' on page 44 und efined on input line 3054. LaTeX Warning: Reference `langtangen:nonlinear:Newton:algebraic' on page 44 und efined on input line 3058. Underfull \hbox (badness 2221) in paragraph at lines 3053--3059 []\T1/pplx/m/n/10 (+20) The im-ple-men-ta-tion is iden-ti-cal to the one in Sec -tion [] and is found in the file LaTeX Warning: Reference `langtangen:poisson:nonlinear2' on page 44 undefined o n input line 3080. [44] LaTeX Warning: Reference `langtangen:fundamentals' on page 46 undefined on inpu t line 3258. LaTeX Warning: Reference `langtangen:poisson:nonlinear' on page 46 undefined on input line 3263. LaTeX Warning: Reference `langtangen:nonlinear:Newton:auto' on page 46 undefine d on input line 3264. [46] LaTeX Warning: Reference `langtangen:diffusion:BE' on page 47 undefined on inpu t line 3319. LaTeX Warning: Reference `langtangen:diffusion:pde1:tk' on page 47 undefined on input line 3319. LaTeX Warning: Reference `langtangen:diffusion:pde1' on page 47 undefined on in put line 3325. LaTeX Warning: Reference `langtangen:diffusion:pde1:BE' on page 47 undefined on input line 3326. LaTeX Warning: Reference `langtangen:diffusion:pde1:BE' on page 47 undefined on input line 3327. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0' on page 47 undefined on input line 3341. LaTeX Warning: Reference `langtangen:diffusion:pde1:uk' on page 47 undefined on input line 3342. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0' on page 47 undefined on input line 3347. LaTeX Warning: Reference `langtangen:diffusion:pde1:uk' on page 47 undefined on input line 3348. [47] LaTeX Warning: Reference `langtangen:poisson:gradu' on page 48 undefined on inp ut line 3376. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0' on page 48 undefined on input line 3378. LaTeX Warning: Reference `langtangen:poisson1:linalg' on page 48 undefined on i nput line 3395. [48] [45] LaTeX Warning: Reference `langtangen:fundamentals' on page 46 undefined on inpu t line 3258. LaTeX Warning: Reference `langtangen:poisson:nonlinear' on page 46 undefined on input line 3263. LaTeX Warning: Reference `langtangen:nonlinear:Newton:auto' on page 46 undefine d on input line 3264. [46] LaTeX Warning: Reference `langtangen:diffusion:BE' on page 47 undefined on inpu t line 3319. LaTeX Warning: Reference `langtangen:diffusion:pde1:tk' on page 47 undefined on input line 3319. LaTeX Warning: Reference `langtangen:diffusion:pde1' on page 47 undefined on in put line 3325. LaTeX Warning: Reference `langtangen:diffusion:pde1:BE' on page 47 undefined on input line 3326. LaTeX Warning: Reference `langtangen:diffusion:pde1:BE' on page 47 undefined on input line 3327. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0' on page 47 undefined on input line 3341. LaTeX Warning: Reference `langtangen:diffusion:pde1:uk' on page 47 undefined on input line 3342. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0' on page 47 undefined on input line 3347. LaTeX Warning: Reference `langtangen:diffusion:pde1:uk' on page 47 undefined on input line 3348. [47] LaTeX Warning: Reference `langtangen:poisson:gradu' on page 48 undefined on inp ut line 3376. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0' on page 48 undefined on input line 3378. LaTeX Warning: Reference `langtangen:poisson1:linalg' on page 48 undefined on i nput line 3395. [48] LaTeX Warning: Reference `langtangen:diffusion:pde1:u0test' on page 49 undefine d on input line 3438. LaTeX Warning: Reference `langtangen:diffusion:pde1' on page 49 undefined on in put line 3439. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0test' on page 49 undefine d on input line 3440. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0test' on page 49 undefine d on input line 3445. LaTeX Warning: Reference `langtangen:poisson:membrane' on page 49 undefined on input line 3448. LaTeX Warning: Reference `langtangen:poisson:gradu' on page 49 undefined on inp ut line 3478. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0test' on page 49 undefine d on input line 3480. [49] LaTeX Warning: Reference `langtangen:diffusion:pde1:u0test' on page 49 undefine d on input line 3438. LaTeX Warning: Reference `langtangen:diffusion:pde1' on page 49 undefined on in put line 3439. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0test' on page 49 undefine d on input line 3440. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0test' on page 49 undefine d on input line 3445. LaTeX Warning: Reference `langtangen:poisson:membrane' on page 49 undefined on input line 3448. LaTeX Warning: Reference `langtangen:poisson:gradu' on page 49 undefined on inp ut line 3478. LaTeX Warning: Reference `langtangen:diffusion:pde1:u0test' on page 49 undefine d on input line 3480. [49] [50] LaTeX Warning: Reference `langtangen:diffusion:pde1:L' on page 51 undefined on input line 3567. LaTeX Warning: Reference `langtangen:poisson1:linalg' on page 51 undefined on i nput line 3572. LaTeX Warning: Reference `langtangen:diffusion:pde1:a' on page 51 undefined on input line 3617. Underfull \vbox (badness 10000) has occurred while \output is active [51] LaTeX Warning: Reference `langtangen:timedep:diffusion1:noassemble' on page 52 undefined on input line 3685. LaTeX Warning: Reference `langtangen:timedep:diffusion1:impl' on page 52 undefi ned on input line 3685. [52] LaTeX Warning: Reference `langtangen:timedep:diffusion2:sin:fig1' on page 53 un defined on input line 3703. Underfull \vbox (badness 2088) has occurred while \output is active [53 <./chap ters/langtangen/pdf/daynight.pdfError: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap >] [50] LaTeX Warning: Reference `langtangen:diffusion:pde1:L' on page 51 undefined on input line 3567. LaTeX Warning: Reference `langtangen:poisson1:linalg' on page 51 undefined on i nput line 3572. LaTeX Warning: Reference `langtangen:diffusion:pde1:a' on page 51 undefined on input line 3617. Underfull \vbox (badness 10000) has occurred while \output is active [51] LaTeX Warning: Reference `langtangen:timedep:diffusion1:noassemble' on page 52 undefined on input line 3685. LaTeX Warning: Reference `langtangen:timedep:diffusion1:impl' on page 52 undefi ned on input line 3685. [52] LaTeX Warning: Reference `langtangen:timedep:diffusion2:sin:fig1' on page 53 un defined on input line 3703. Underfull \vbox (badness 2088) has occurred while \output is active [53 <./chap ters/langtangen/pdf/daynight.pdfError: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap >] [54] [54] LaTeX Warning: Reference `langtangen:timedep:diffusion2:sin:fig1' on page 55 un defined on input line 3796. Underfull \vbox (badness 3977) has occurred while \output is active [55] LaTeX Warning: Reference `langtangen:timedep:diffusion2:sin:fig1' on page 55 un defined on input line 3796. Underfull \vbox (badness 3977) has occurred while \output is active [55] LaTeX Warning: Reference `langtangen:timedep:diffusion1:noassemble' on page 56 undefined on input line 3880. LaTeX Warning: Reference `langtangen:timedep:diffusion1:impl' on page 56 undefi ned on input line 3885. [56] [57] LaTeX Warning: Reference `langtangen:timedep:diffusion1:noassemble' on page 56 undefined on input line 3880. LaTeX Warning: Reference `langtangen:timedep:diffusion1:impl' on page 56 undefi ned on input line 3885. [56] [58] LaTeX Warning: Reference `langtangen:mesh:transform:cyl:fig1' on page 59 undefi ned on input line 4086. [57] LaTeX Warning: Reference `langtangen:possion:2D:2mat:fig1' on page 59 undefined on input line 4125. [59 <./chapters/langtangen/pdf/hollow_cylinder.pdf>] [58 [60]] LaTeX Warning: Reference `langtangen:mesh:transform:cyl:fig1' on page 59 undefi ned on input line 4086. LaTeX Warning: Reference `langtangen:possion:2D:2mat:fig1' on page 59 undefined on input line 4125. [59 <./chapters/langtangen/pdf/hollow_cylinder.pdf>] [60] Underfull \hbox (badness 1215) in paragraph at lines 4284--4288 []\T1/pplx/m/n/10 (+20) Calling \T1/fvm/m/n/10 subdomains.array() \T1/pplx/m/n/ 10 (+20) re-turns a \T1/fvm/m/n/10 numpy \T1/pplx/m/n/10 (+20) ar-ray of the su b-do-main val-ues. That is, [61] Underfull \hbox (badness 1215) in paragraph at lines 4284--4288 []\T1/pplx/m/n/10 (+20) Calling \T1/fvm/m/n/10 subdomains.array() \T1/pplx/m/n/ 10 (+20) re-turns a \T1/fvm/m/n/10 numpy \T1/pplx/m/n/10 (+20) ar-ray of the su b-do-main val-ues. That is, [61] LaTeX Warning: Reference `langtangen:poisson:multiple:Dirichlet' on page 62 und efined on input line 4332. LaTeX Warning: Reference `langtangen:possion:2D:varcoeff' on page 62 undefined on input line 4333. LaTeX Warning: Reference `langtangen:poisson:multiple:Dirichlet' on page 62 und efined on input line 4344. LaTeX Warning: Reference `langtangen:poisson:multiple:Dirichlet' on page 62 und efined on input line 4360. [62] Underfull \vbox (badness 10000) has occurred while \output is active [63] LaTeX Warning: Reference `langtangen:poisson:multiple:Dirichlet' on page 62 und efined on input line 4332. LaTeX Warning: Reference `langtangen:possion:2D:varcoeff' on page 62 undefined on input line 4333. LaTeX Warning: Reference `langtangen:poisson:multiple:Dirichlet' on page 62 und efined on input line 4344. LaTeX Warning: Reference `langtangen:poisson:multiple:Dirichlet' on page 62 und efined on input line 4360. [62] LaTeX Warning: Reference `langtangen:possion:2D:2mat:impl' on page 64 undefined on input line 4449. LaTeX Warning: Reference `langtangen:possion:2D:2mat:impl' on page 64 undefined on input line 4460. [64] Underfull \vbox (badness 10000) has occurred while \output is active [63] [65] LaTeX Warning: Reference `chap:selim' on page 66 undefined on input line 4578. LaTeX Warning: Reference `chap:narayanan' on page 66 undefined on input line 45 79. LaTeX Warning: Reference `chap:selim' on page 66 undefined on input line 4580. LaTeX Warning: Reference `chap:vynnytska' on page 66 undefined on input line 45 81. Package natbib Warning: Citation `Mortensen2011' on page 66 undefined on input line 4586. Package natbib Warning: Citation `Mortensen2011b' on page 66 undefined on input line 4586. LaTeX Warning: Reference `langtangen:poisson1:functionals' on page 66 undefined on input line 4622. [66] LaTeX Warning: Reference `langtangen:prepro' on page 67 undefined on input line 4673. Overfull \hbox (2.004pt too wide) in paragraph at lines 4672--4674 []\T1/pplx/m/n/10 (-20) generate mesh over LaTeX Warning: Reference `langtangen:poisson1:impl' on page 67 undefined on inp ut line 4700. LaTeX Warning: Reference `langtangen:possion:2D:2mat:problem' on page 67 undefi ned on input line 4708. LaTeX Warning: Reference `langtangen:poisson:mat:neumann' on page 67 undefined on input line 4709. [67] [68 LaTeX Warning: Reference `langtangen:possion:2D:2mat:impl' on page 64 undefined on input line 4449. LaTeX Warning: Reference `langtangen:possion:2D:2mat:impl' on page 64 undefined on input line 4460. [64]] [69] Package natbib Warning: Citation `Gockenbach2006' on page 70 undefined on input line 4917. Package natbib Warning: Citation `DoneaHuerta2003' on page 70 undefined on inpu t line 4918. Package natbib Warning: Citation `Hughes1987' on page 70 undefined on input lin e 4919. Package natbib Warning: Citation `Bickford1994' on page 70 undefined on input l ine 4924. Package natbib Warning: Citation `ErikssonEstepHansboEtAl1996' on page 70 undef ined on input line 4928. Package natbib Warning: Citation `BrennerScott2008' on page 70 undefined on inp ut line 4931. Package natbib Warning: Citation `Braess2007' on page 70 undefined on input lin e 4932. Package natbib Warning: Citation `ErnGuermond2004' on page 70 undefined on inpu t line 4932. Package natbib Warning: Citation `QuarteroniValli2008' on page 70 undefined on input line 4932. Package natbib Warning: Citation `Ciarlet2002' on page 70 undefined on input li ne 4933. Package natbib Warning: Citation `Lutz2007' on page 70 undefined on input line 4939. Package natbib Warning: Citation `Hetland2002' on page 70 undefined on input li ne 4939. Package natbib Warning: Citation `Lutz2006' on page 70 undefined on input line 4941. Package natbib Warning: Citation `MartelliAscher2005' on page 70 undefined on i nput line 4941. Package natbib Warning: Citation `Martelli2006' on page 70 undefined on input l ine 4942. Package natbib Warning: Citation `Langtangen2008' on page 70 undefined on input line 4946. Package natbib Warning: Citation `Langtangen20011' on page 70 undefined on inpu t line 4946. Package natbib Warning: Citation `Kiusalaas2010' on page 70 undefined on input line 4946. ) (./tex/2.tex [70] Chapter 2. (/usr/share/texmf-texlive/tex/latex/psnfss/ufplmbb.fd) LaTeX Warning: Reference `chap:terrel' on page 71 undefined on input line 57. LaTeX Warning: Reference `chap:kvs-1' on page 71 undefined on input line 57. LaTeX Warning: Reference `chap:mortensen' on page 71 undefined on input line 58 . LaTeX Warning: Reference `chap:kvs-2' on page 71 undefined on input line 59. LaTeX Warning: Reference `chap:hentschel' on page 71 undefined on input line 59 . LaTeX Warning: Reference `chap:lopes' on page 71 undefined on input line 59. LaTeX Warning: Reference `chap:hoffman-1' on page 71 undefined on input line 60 . LaTeX Warning: Reference `chap:selim' on page 71 undefined on input line 60. LaTeX Warning: Reference `eq:poisson' on page 71 undefined on input line 62. Underfull \vbox (badness 2951) has occurred while \output is active [71] LaTeX Warning: Reference `eq:testvolume' on page 72 undefined on input line 76. LaTeX Warning: Reference `eq:poisson' on page 72 undefined on input line 96. LaTeX Warning: Reference `eq:poisson,mixed' on page 72 undefined on input line 98. LaTeX Warning: Reference `eq:poisson' on page 72 undefined on input line 100. LaTeX Warning: Reference `eq:poisson' on page 72 undefined on input line 101. (./chapters/kirby-7/pdf/heat_equation_model_domain.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/heat_equation_model_domai n.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allow ed ) LaTeX Warning: Reference `eq:poisson' on page 72 undefined on input line 119. [72 <./chapters/kirby-7/pdf/heat_equation_model_domain.pdf>] LaTeX Warning: Reference `eq:poisson,varproblem' on page 73 undefined on input line 152. LaTeX Warning: Reference `eq:poisson,varproblem,discrete' on page 73 undefined on input line 167. LaTeX Warning: Reference `eq:poisson,varproblem,discrete' on page 73 undefined on input line 179. LaTeX Warning: Reference `eq:poisson,mixed' on page 73 undefined on input line 206. [73] [65] LaTeX Warning: Reference `eq:poisson,varproblem,mixed' on page 74 undefined on input line 235. LaTeX Warning: Reference `eq:poisson,varproblem' on page 74 undefined on input line 236. LaTeX Warning: Reference `eq:mixedsystem' on page 74 undefined on input line 26 9. LaTeX Warning: Reference `chap:kirby-6' on page 74 undefined on input line 277. LaTeX Warning: Reference `eq:poisson' on page 74 undefined on input line 290. LaTeX Warning: Reference `eq:poisson,mixed' on page 74 undefined on input line 290. [74] LaTeX Warning: Reference `eq:varproblem' on page 75 undefined on input line 309 . LaTeX Warning: Reference `eq:varproblem,discrete' on page 75 undefined on input line 316. LaTeX Warning: Reference `eq:varproblem,nonlinear' on page 75 undefined on inpu t line 348. LaTeX Warning: Reference `eq:system,nonlinear' on page 75 undefined on input li ne 367. Underfull \vbox (badness 7451) has occurred while \output is active [75 LaTeX Warning: Reference `chap:selim' on page 66 undefined on input line 4578. LaTeX Warning: Reference `chap:narayanan' on page 66 undefined on input line 45 79. LaTeX Warning: Reference `chap:selim' on page 66 undefined on input line 4580. LaTeX Warning: Reference `chap:vynnytska' on page 66 undefined on input line 45 81. Package natbib Warning: Citation `Mortensen2011' on page 66 undefined on input line 4586. Package natbib Warning: Citation `Mortensen2011b' on page 66 undefined on input line 4586. LaTeX Warning: Reference `langtangen:poisson1:functionals' on page 66 undefined on input line 4622. [66]] LaTeX Warning: Reference `eq:varproblem' on page 76 undefined on input line 392 . LaTeX Warning: Reference `eq:varproblem,newton' on page 76 undefined on input l ine 397. LaTeX Warning: Reference `sec:abstract,linear' on page 76 undefined on input li ne 398. LaTeX Warning: Reference `eq:system,linearization' on page 76 undefined on inpu t line 399. LaTeX Warning: Reference `eq:poisson,nonlinear' on page 76 undefined on input l ine 412. LaTeX Warning: Reference `eq:varproblem,nonlinear' on page 76 undefined on inpu t line 419. LaTeX Warning: Reference `chap:kirby-6' on page 76 undefined on input line 449. LaTeX Warning: Reference `chap:kirby-1' on page 76 undefined on input line 449. [76] LaTeX Warning: Reference `fig:shapes' on page 77 undefined on input line 464. LaTeX Warning: Reference `langtangen:prepro' on page 67 undefined on input line 4673. Overfull \hbox (2.004pt too wide) in paragraph at lines 4672--4674 []\T1/pplx/m/n/10 (-20) generate mesh over LaTeX Warning: Reference `langtangen:poisson1:impl' on page 67 undefined on inp ut line 4700. LaTeX Warning: Reference `langtangen:possion:2D:2mat:problem' on page 67 undefi ned on input line 4708. LaTeX Warning: Reference `langtangen:poisson:mat:neumann' on page 67 undefined on input line 4709. [67] Package natbib Warning: Citation `Ciarlet1976' on page 77 undefined on input li ne 494. Package natbib Warning: Citation `BrennerScott2008' on page 77 undefined on inp ut line 495. LaTeX Warning: Reference `fig:P1' on page 77 undefined on input line 501. Package natbib Warning: Citation `BrennerScott2008' on page 77 undefined on inp ut line 518. [77 <./chapters/kirby-7/pdf/cells.pdf>] Package natbib Warning: Citation `Kirby2004' on page 78 undefined on input line 596. [78 <./chapters/kirby-7/pdf/P1.pdf>] [68] LaTeX Warning: Reference `eq:nodalbasis' on page 79 undefined on input line 601 . LaTeX Warning: Reference `fig:dofmap' on page 79 undefined on input line 644. pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/dofmap.pdf): PDF inclusio n: found PDF version <1.5>, but at most version <1.4> allowed Underfull \vbox (badness 4060) has occurred while \output is active [79] LaTeX Warning: Reference `fig:femspace' on page 80 undefined on input line 685. Underfull \hbox (badness 1107) in paragraph at lines 694--694 []\T1/pplx/m/n/9 (+20) Figure 2.5: |Patch-ing to-gether a Underfull \hbox (badness 1755) in paragraph at lines 694--694 \T1/pplx/m/n/9 (+20) pair of quadratic lo-cal func-tion LaTeX Warning: Reference `eq:constraint' on page 80 undefined on input line 699 . [80 <./chapters/kirby-7/pdf/dofmap.pdf> <./chapters/kirby-7/pdf/femspace.pdf>] LaTeX Warning: Reference `chap:kirby-6' on page 81 undefined on input line 729. LaTeX Warning: Reference `fig:kirby-7:affinemap' on page 81 undefined on input line 752. (./chapters/kirby-7/pdf/affine_map.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/affine_map.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `eq:poisson,varproblem' on page 81 undefined on input line 770. LaTeX Warning: Reference `eq:poisson,varproblem,mixed' on page 81 undefined on input line 776. Package natbib Warning: Citation `RognesKirbyLogg2009' on page 81 undefined on input line 779. Underfull \vbox (badness 1810) has occurred while \output is active [81 [69 <./chap ters/kirby-7/pdf/affine_map.pdf>]] Package natbib Warning: Citation `BrennerScott2008' on page 82 undefined on inp ut line 846. Package natbib Warning: Citation `Ciarlet2002' on page 82 undefined on input li ne 855. Package natbib Warning: Citation `BrennerScott2008' on page 82 undefined on inp ut line 855. Package natbib Warning: Citation `Davis2004' on page 82 undefined on input line 875. Package natbib Warning: Citation `Li2005' on page 82 undefined on input line 87 5. Package natbib Warning: Citation `HestenesStiefel1952' on page 82 undefined on input line 880. Underfull \vbox (badness 5924) has occurred while \output is active [82] Package natbib Warning: Citation `Gockenbach2006' on page 70 undefined on input line 4917. Package natbib Warning: Citation `DoneaHuerta2003' on page 70 undefined on inpu t line 4918. Package natbib Warning: Citation `Hughes1987' on page 70 undefined on input lin e 4919. Package natbib Warning: Citation `Bickford1994' on page 70 undefined on input l ine 4924. Package natbib Warning: Citation `ErikssonEstepHansboEtAl1996' on page 70 undef ined on input line 4928. Package natbib Warning: Citation `BrennerScott2008' on page 70 undefined on inp ut line 4931. Package natbib Warning: Citation `Braess2007' on page 70 undefined on input lin e 4932. Package natbib Warning: Citation `ErnGuermond2004' on page 70 undefined on inpu t line 4932. Package natbib Warning: Citation `QuarteroniValli2008' on page 70 undefined on input line 4932. Package natbib Warning: Citation `Ciarlet2002' on page 70 undefined on input li ne 4933. Package natbib Warning: Citation `Lutz2007' on page 70 undefined on input line 4939. Package natbib Warning: Citation `Hetland2002' on page 70 undefined on input li ne 4939. Package natbib Warning: Citation `Lutz2006' on page 70 undefined on input line 4941. Package natbib Warning: Citation `MartelliAscher2005' on page 70 undefined on i nput line 4941. Package natbib Warning: Citation `Martelli2006' on page 70 undefined on input l ine 4942. Package natbib Warning: Citation `Langtangen2008' on page 70 undefined on input line 4946. Package natbib Warning: Citation `Langtangen20011' on page 70 undefined on inpu t line 4946. Package natbib Warning: Citation `Kiusalaas2010' on page 70 undefined on input line 4946. ) (./tex/Part1.tex [70] [71] Package natbib Warning: Citation `Brandt1977' on page 83 undefined on input lin e 886. Package natbib Warning: Citation `Wesseling1992' on page 83 undefined on input line 886. Package natbib Warning: Citation `FalgoutYang2002' on page 83 undefined on inpu t line 893. Package natbib Warning: Citation `HerouxBartlettHowleEtAl2005' on page 83 undef ined on input line 894. Package natbib Warning: Citation `SaadSchultz1986' on page 83 undefined on inpu t line 899. Package natbib Warning: Citation `Manteuffel1980' on page 83 undefined on input line 921. Package natbib Warning: Citation `Axelsson1986' on page 83 undefined on input l ine 921. Package natbib Warning: Citation `Saad1994' on page 83 undefined on input line 921. Package natbib Warning: Citation `BalayBuschelmanEijkhoutEtAl2004' on page 83 u ndefined on input line 932. Package natbib Warning: Citation `HerouxBartlettHowleEtAl2005' on page 83 undef ined on input line 933. LaTeX Warning: Reference `eq:varproblem' on page 83 undefined on input line 945 . LaTeX Warning: Reference `eq:varproblem' on page 83 undefined on input line 958 . LaTeX Warning: Reference `eq:poisson' on page 83 undefined on input line 970. Package natbib Warning: Citation `OdenDemkowicz1996' on page 83 undefined on in put line 973. [83 [72]) (./tex/2.tex] Chapter 2. (/usr/share/texmf-texlive/tex/latex/psnfss/ufplmbb.fd) Package natbib Warning: Citation `LaxMilgram1954' on page 84 undefined on input line 980. LaTeX Warning: Reference `eq:varproblem' on page 84 undefined on input line 981 . LaTeX Warning: Reference `eq:varproblem,discrete' on page 84 undefined on input line 985. LaTeX Warning: Reference `eq:ceaslemma' on page 84 undefined on input line 1007 . LaTeX Warning: Reference `eq:varproblem' on page 84 undefined on input line 101 6. LaTeX Warning: Reference `fig:ceaslemma' on page 84 undefined on input line 101 7. (./chapters/kirby-7/pdf/projection.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/projection.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `chap:terrel' on page 73 undefined on input line 57. LaTeX Warning: Reference `chap:kvs-1' on page 73 undefined on input line 57. LaTeX Warning: Reference `chap:mortensen' on page 73 undefined on input line 58 . LaTeX Warning: Reference `chap:kvs-2' on page 73 undefined on input line 59. LaTeX Warning: Reference `chap:hentschel' on page 73 undefined on input line 59 . LaTeX Warning: Reference `chap:lopes' on page 73 undefined on input line 59. LaTeX Warning: Reference `chap:hoffman-1' on page 73 undefined on input line 60 . LaTeX Warning: Reference `chap:selim' on page 73 undefined on input line 60. LaTeX Warning: Reference `eq:poisson' on page 73 undefined on input line 62. Underfull \vbox (badness 2951) has occurred while \output is active [73] [84 <./chapters/kirby-7/pdf/projecti on.pdf>] LaTeX Warning: Reference `eq:testvolume' on page 74 undefined on input line 76. LaTeX Warning: Reference `eq:poisson' on page 74 undefined on input line 96. LaTeX Warning: Reference `eq:poisson,mixed' on page 74 undefined on input line 98. LaTeX Warning: Reference `eq:poisson' on page 74 undefined on input line 100. LaTeX Warning: Reference `eq:poisson' on page 74 undefined on input line 101. (./chapters/kirby-7/pdf/heat_equation_model_domain.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/heat_equation_model_domai n.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allow ed LaTeX Warning: Reference `eq:apriori' on page 85 undefined on input line 1083. LaTeX Warning: Reference `eq:aposteriori' on page 85 undefined on input line 10 83. LaTeX Warning: Reference `eq:apriori' on page 85 undefined on input line 1100. LaTeX Warning: Reference `eq:aposteriori' on page 85 undefined on input line 11 00. Package natbib Warning: Citation `ErikssonEstepEtAl1995' on page 85 undefined o n input line 1117. Package natbib Warning: Citation `ErikssonEstepEtAl1995' on page 85 undefined o n input line 1117. Package natbib Warning: Citation `BeckerRannacher2001' on page 85 undefined on input line 1117. Package natbib Warning: Citation `BeckerRannacher2001' on page 85 undefined on input line 1118. Underfull \vbox (badness 10000) has occurred while \output is active [85)] LaTeX Warning: Reference `eq:poisson' on page 86 undefined on input line 1175. Package natbib Warning: Citation `ElmanSilvesterWathen2005' on page 86 undefine d on input line 1188. Package natbib Warning: Citation `Dorfler1996' on page 86 undefined on input li ne 1207. [86] LaTeX Warning: Reference `fig:refinement' on page 87 undefined on input line 12 16. Package natbib Warning: Citation `Logg2007a' on page 87 undefined on input line 1269. Package natbib Warning: Citation `LoggWells2010' on page 87 undefined on input line 1269. Package natbib Warning: Citation `Kirby2004' on page 87 undefined on input line 1269. Package natbib Warning: Citation `KirbyLogg2006' on page 87 undefined on input line 1269. Package natbib Warning: Citation `AlnaesLoggMardalEtAl2009' on page 87 undefine d on input line 1269. Package natbib Warning: Citation `AlnaesMardal2009b' on page 87 undefined on in put line 1269. Package natbib Warning: Citation `KirbyKnepleyLoggEtAl2005' on page 87 undefine d on input line 1269. Package natbib Warning: Citation `KirbyLoggScottEtAl2006' on page 87 undefined on input line 1269. Package natbib Warning: Citation `KirbyLogg2007' on page 87 undefined on input line 1269. Package natbib Warning: Citation `KirbyLogg2008' on page 87 undefined on input line 1269. Package natbib Warning: Citation `KirbyScott2007' on page 87 undefined on input line 1269. Package natbib Warning: Citation `Kirby2006a' on page 87 undefined on input lin e 1269. Package natbib Warning: Citation `OelgaardLoggWells2008' on page 87 undefined o n input line 1269. Package natbib Warning: Citation `RognesKirbyLogg2009' on page 87 undefined on input line 1269. Package natbib Warning: Citation `OelgaardWells2010' on page 87 undefined on in put line 1269. Package natbib Warning: Citation `Logg2009' on page 87 undefined on input line 1269. [87 <./chapters/kirby-7/png/refinement.png (PNG copy)>] LaTeX Warning: Reference `eq:poisson' on page 74 undefined on input line 119. [74 <./chapters/kirby-7/pdf/heat_equation_model_domain.pdf>] Package natbib Warning: Citation `Galerkin1915' on page 88 undefined on input l ine 1275. Package natbib Warning: Citation `Castigliano1879' on page 88 undefined on inpu t line 1280. Package natbib Warning: Citation `Rayleigh1870' on page 88 undefined on input l ine 1280. Package natbib Warning: Citation `Ritz1908' on page 88 undefined on input line 1281. Package natbib Warning: Citation `Courant1943' on page 88 undefined on input li ne 1285. Package natbib Warning: Citation `ZienkiewiczTaylorZhu2005firstpublishedin1967' on page 88 undefined on input line 1290. Package natbib Warning: Citation `StrangFix1973' on page 88 undefined on input line 1290. Package natbib Warning: Citation `Ciarlet1976' on page 88 undefined on input li ne 1290. Package natbib Warning: Citation `BeckerCareyOden1981' on page 88 undefined on input line 1290. Package natbib Warning: Citation `Hughes1987' on page 88 undefined on input lin e 1290. Package natbib Warning: Citation `BrennerScott2008' on page 88 undefined on inp ut line 1290. Package natbib Warning: Citation `ArnoldFalkWinther2006' on page 88 undefined o n input line 1293. Package natbib Warning: Citation `BabuvskaRheinboldt1978' on page 88 undefined on input line 1297. Package natbib Warning: Citation `BankWeiser1985' on page 88 undefined on input line 1299. Package natbib Warning: Citation `ZienkiewiczZhu1987' on page 88 undefined on i nput line 1299. Package natbib Warning: Citation `ErikssonJohnson1991' on page 88 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnson1995a' on page 88 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnsonIII' on page 88 undefined on i nput line 1299. Package natbib Warning: Citation `ErikssonJohnson1995b' on page 88 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnson1995c' on page 88 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnsonLarsson1998' on page 88 undefi ned on input line 1299. Package natbib Warning: Citation `AinsworthOden1993' on page 88 undefined on in put line 1299. Package natbib Warning: Citation `ErikssonEstepEtAl1995' on page 88 undefined o n input line 1301. Package natbib Warning: Citation `Verfurth1994' on page 88 undefined on input l ine 1301. Package natbib Warning: Citation `Verfurth1999' on page 88 undefined on input l ine 1301. Package natbib Warning: Citation `AinsworthOden2000' on page 88 undefined on in put line 1301. Package natbib Warning: Citation `BeckerRannacher2001' on page 88 undefined on input line 1301. ) (./tex/10.tex [88] LaTeX Warning: Reference `eq:poisson,varproblem' on page 75 undefined on input line 152. LaTeX Warning: Reference `eq:poisson,varproblem,discrete' on page 75 undefined on input line 167. LaTeX Warning: Reference `eq:poisson,varproblem,discrete' on page 75 undefined on input line 179. LaTeX Warning: Reference `eq:poisson,mixed' on page 75 undefined on input line 206. [75] Chapter 3. Package natbib Warning: Citation `LoggWells2010' on page 89 undefined on input line 11. LaTeX Warning: Reference `fig:logg-2:fenicsmap' on page 89 undefined on input l ine 26. LaTeX Warning: Reference `chap:alnes-1' on page 89 undefined on input line 37. LaTeX Warning: Reference `chap:logg-1' on page 89 undefined on input line 38. LaTeX Warning: Reference `chap:alnes-3' on page 89 undefined on input line 38. LaTeX Warning: Reference `chap:alnes-2' on page 89 undefined on input line 39. LaTeX Warning: Reference `chap:kirby-2' on page 89 undefined on input line 42. LaTeX Warning: Reference `chap:wilbers' on page 89 undefined on input line 43. LaTeX Warning: Reference `chap:kirby-3' on page 89 undefined on input line 44. Package natbib Warning: Citation `www:viper' on page 89 undefined on input line 45. Package natbib Warning: Citation `www:petsc' on page 89 undefined on input line 52. Package natbib Warning: Citation `www:trilinos' on page 89 undefined on input l ine 52. Package natbib Warning: Citation `www:ublas' on page 89 undefined on input line 52. Package natbib Warning: Citation `www:mtl4' on page 89 undefined on input line 52. Package natbib Warning: Citation `www:parmetis' on page 89 undefined on input l ine 53. Package natbib Warning: Citation `www:scotch' on page 89 undefined on input lin e 54. pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/fenics-map.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed [89] LaTeX Warning: Reference `eq:poisson,varproblem,mixed' on page 76 undefined on input line 235. LaTeX Warning: Reference `eq:poisson,varproblem' on page 76 undefined on input line 236. LaTeX Warning: Reference `eq:mixedsystem' on page 76 undefined on input line 26 9. LaTeX Warning: Reference `chap:kirby-6' on page 76 undefined on input line 277. LaTeX Warning: Reference `eq:poisson' on page 76 undefined on input line 290. LaTeX Warning: Reference `eq:poisson,mixed' on page 76 undefined on input line 290. [76 LaTeX Warning: Reference `fig:logg-2:uml' on page 90 undefined on input line 87 . LaTeX Warning: Reference `sec:logg-2:functionality' on page 90 undefined on inp ut line 118. [90] <./chapters/logg-2/pdf/fenics-map.pdf>] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty LaTeX Warning: Reference `eq:varproblem' on page 77 undefined on input line 309 . LaTeX Warning: Reference `eq:varproblem,discrete' on page 77 undefined on input line 316. LaTeX Warning: Reference `eq:varproblem,nonlinear' on page 77 undefined on inpu t line 348. LaTeX Warning: Reference `eq:system,nonlinear' on page 77 undefined on input li ne 367. Underfull \vbox (badness 7451) has occurred while \output is active [77]) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) LaTeX Warning: Reference `eq:varproblem' on page 78 undefined on input line 392 . LaTeX Warning: Reference `eq:varproblem,newton' on page 78 undefined on input l ine 397. LaTeX Warning: Reference `sec:abstract,linear' on page 78 undefined on input li ne 398. LaTeX Warning: Reference `eq:system,linearization' on page 78 undefined on inpu t line 399. LaTeX Warning: Reference `eq:poisson,nonlinear' on page 78 undefined on input l ine 412. LaTeX Warning: Reference `eq:varproblem,nonlinear' on page 78 undefined on inpu t line 419. LaTeX Warning: Reference `chap:kirby-6' on page 78 undefined on input line 449. LaTeX Warning: Reference `chap:kirby-1' on page 78 undefined on input line 449. [78] LaTeX Warning: Reference `fig:shapes' on page 79 undefined on input line 464. Package natbib Warning: Citation `Beazley2006' on page 91 undefined on input li ne 148. Package natbib Warning: Citation `www:swig' on page 91 undefined on input line 148. Underfull \vbox (badness 3482) has occurred while \output is active [91 Package natbib Warning: Citation `Ciarlet1976' on page 79 undefined on input li ne 494. Package natbib Warning: Citation `BrennerScott2008' on page 79 undefined on inp ut line 495. LaTeX Warning: Reference `fig:P1' on page 79 undefined on input line 501. Package natbib Warning: Citation `BrennerScott2008' on page 79 undefined on inp ut line 518. <./chap ters/logg-2/pdf/dolfin-uml.pdf>] [79 <./chapters/kirby-7/pdf/cells.pdf>] Package natbib Warning: Citation `Kirby2004' on page 80 undefined on input line 596. [80 <./chapters/kirby-7/pdf/P1.pdf>] LaTeX Warning: Reference `eq:nodalbasis' on page 81 undefined on input line 601 . LaTeX Warning: Reference `fig:dofmap' on page 81 undefined on input line 644. pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/dofmap.pdf): PDF inclusio n: found PDF version <1.5>, but at most version <1.4> allowed Underfull \vbox (badness 4060) has occurred while \output is active [81] LaTeX Warning: Reference `fig:femspace' on page 82 undefined on input line 685. Underfull \hbox (badness 1107) in paragraph at lines 694--694 []\T1/pplx/m/n/9 (+20) Figure 2.5: |Patch-ing to-gether a Underfull \hbox (badness 1755) in paragraph at lines 694--694 \T1/pplx/m/n/9 (+20) pair of quadratic lo-cal func-tion LaTeX Warning: Reference `eq:constraint' on page 82 undefined on input line 699 . [82 <./chapters/kirby-7/pdf/dofmap.pdf> <./chapters/kirby-7/pdf/femspace.pdf>] LaTeX Warning: Reference `chap:kirby-6' on page 83 undefined on input line 729. LaTeX Warning: Reference `fig:kirby-7:affinemap' on page 83 undefined on input line 752. (./chapters/kirby-7/pdf/affine_map.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/affine_map.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `eq:poisson,varproblem' on page 83 undefined on input line 770. LaTeX Warning: Reference `eq:poisson,varproblem,mixed' on page 83 undefined on input line 776. Package natbib Warning: Citation `RognesKirbyLogg2009' on page 83 undefined on input line 779. Underfull \vbox (badness 1810) has occurred while \output is active [83 <./chap ters/kirby-7/pdf/affine_map.pdf>] Package natbib Warning: Citation `BrennerScott2008' on page 84 undefined on inp ut line 846. Package natbib Warning: Citation `Ciarlet2002' on page 84 undefined on input li ne 855. Package natbib Warning: Citation `BrennerScott2008' on page 84 undefined on inp ut line 855. Package natbib Warning: Citation `Davis2004' on page 84 undefined on input line 875. Package natbib Warning: Citation `Li2005' on page 84 undefined on input line 87 5. Package natbib Warning: Citation `HestenesStiefel1952' on page 84 undefined on input line 880. Underfull \vbox (badness 5924) has occurred while \output is active [84] Package natbib Warning: Citation `Brandt1977' on page 85 undefined on input lin e 886. Package natbib Warning: Citation `Wesseling1992' on page 85 undefined on input line 886. Package natbib Warning: Citation `FalgoutYang2002' on page 85 undefined on inpu t line 893. Package natbib Warning: Citation `HerouxBartlettHowleEtAl2005' on page 85 undef ined on input line 894. Package natbib Warning: Citation `SaadSchultz1986' on page 85 undefined on inpu t line 899. Package natbib Warning: Citation `Manteuffel1980' on page 85 undefined on input line 921. Package natbib Warning: Citation `Axelsson1986' on page 85 undefined on input l ine 921. Package natbib Warning: Citation `Saad1994' on page 85 undefined on input line 921. Package natbib Warning: Citation `BalayBuschelmanEijkhoutEtAl2004' on page 85 u ndefined on input line 932. Package natbib Warning: Citation `HerouxBartlettHowleEtAl2005' on page 85 undef ined on input line 933. LaTeX Warning: Reference `eq:varproblem' on page 85 undefined on input line 945 . LaTeX Warning: Reference `eq:varproblem' on page 85 undefined on input line 958 . LaTeX Warning: Reference `eq:poisson' on page 85 undefined on input line 970. Package natbib Warning: Citation `OdenDemkowicz1996' on page 85 undefined on in put line 973. [85] Package natbib Warning: Citation `LaxMilgram1954' on page 86 undefined on input line 980. LaTeX Warning: Reference `eq:varproblem' on page 86 undefined on input line 981 . LaTeX Warning: Reference `eq:varproblem,discrete' on page 86 undefined on input line 985. LaTeX Warning: Reference `eq:ceaslemma' on page 86 undefined on input line 1007 . LaTeX Warning: Reference `eq:varproblem' on page 86 undefined on input line 101 6. LaTeX Warning: Reference `fig:ceaslemma' on page 86 undefined on input line 101 7. (./chapters/kirby-7/pdf/projection.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/projection.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) [86 <./chapters/kirby-7/pdf/projecti on.pdf>] LaTeX Warning: Reference `eq:apriori' on page 87 undefined on input line 1083. LaTeX Warning: Reference `eq:aposteriori' on page 87 undefined on input line 10 83. LaTeX Warning: Reference `eq:apriori' on page 87 undefined on input line 1100. LaTeX Warning: Reference `eq:aposteriori' on page 87 undefined on input line 11 00. Package natbib Warning: Citation `ErikssonEstepEtAl1995' on page 87 undefined o n input line 1117. Package natbib Warning: Citation `ErikssonEstepEtAl1995' on page 87 undefined o n input line 1117. Package natbib Warning: Citation `BeckerRannacher2001' on page 87 undefined on input line 1117. Package natbib Warning: Citation `BeckerRannacher2001' on page 87 undefined on input line 1118. Underfull \vbox (badness 10000) has occurred while \output is active [87] LaTeX Warning: Reference `eq:poisson' on page 88 undefined on input line 1175. Package natbib Warning: Citation `ElmanSilvesterWathen2005' on page 88 undefine d on input line 1188. Package natbib Warning: Citation `Dorfler1996' on page 88 undefined on input li ne 1207. [88] LaTeX Warning: Reference `fig:refinement' on page 89 undefined on input line 12 16. Package natbib Warning: Citation `LoggWells2010' on page 92 undefined on input line 178. [92] Package natbib Warning: Citation `Logg2007a' on page 89 undefined on input line 1269. Package natbib Warning: Citation `LoggWells2010' on page 89 undefined on input line 1269. Package natbib Warning: Citation `Kirby2004' on page 89 undefined on input line 1269. Package natbib Warning: Citation `KirbyLogg2006' on page 89 undefined on input line 1269. Package natbib Warning: Citation `AlnaesLoggMardalEtAl2009' on page 89 undefine d on input line 1269. Package natbib Warning: Citation `AlnaesMardal2009b' on page 89 undefined on in put line 1269. Package natbib Warning: Citation `KirbyKnepleyLoggEtAl2005' on page 89 undefine d on input line 1269. Package natbib Warning: Citation `KirbyLoggScottEtAl2006' on page 89 undefined on input line 1269. Package natbib Warning: Citation `KirbyLogg2007' on page 89 undefined on input line 1269. Package natbib Warning: Citation `KirbyLogg2008' on page 89 undefined on input line 1269. Package natbib Warning: Citation `KirbyScott2007' on page 89 undefined on input line 1269. Package natbib Warning: Citation `Kirby2006a' on page 89 undefined on input lin e 1269. Package natbib Warning: Citation `OelgaardLoggWells2008' on page 89 undefined o n input line 1269. Package natbib Warning: Citation `RognesKirbyLogg2009' on page 89 undefined on input line 1269. Package natbib Warning: Citation `OelgaardWells2010' on page 89 undefined on in put line 1269. Package natbib Warning: Citation `Logg2009' on page 89 undefined on input line 1269. [89 <./chapters/kirby-7/png/refinement.png (PNG copy)>] Package natbib Warning: Citation `Galerkin1915' on page 90 undefined on input l ine 1275. Package natbib Warning: Citation `Castigliano1879' on page 90 undefined on inpu t line 1280. Package natbib Warning: Citation `Rayleigh1870' on page 90 undefined on input l ine 1280. Package natbib Warning: Citation `Ritz1908' on page 90 undefined on input line 1281. Package natbib Warning: Citation `Courant1943' on page 90 undefined on input li ne 1285. Package natbib Warning: Citation `ZienkiewiczTaylorZhu2005firstpublishedin1967' on page 90 undefined on input line 1290. Package natbib Warning: Citation `StrangFix1973' on page 90 undefined on input line 1290. Package natbib Warning: Citation `Ciarlet1976' on page 90 undefined on input li ne 1290. Package natbib Warning: Citation `BeckerCareyOden1981' on page 90 undefined on input line 1290. Package natbib Warning: Citation `Hughes1987' on page 90 undefined on input lin e 1290. Package natbib Warning: Citation `BrennerScott2008' on page 90 undefined on inp ut line 1290. Package natbib Warning: Citation `ArnoldFalkWinther2006' on page 90 undefined o n input line 1293. Package natbib Warning: Citation `BabuvskaRheinboldt1978' on page 90 undefined on input line 1297. Package natbib Warning: Citation `BankWeiser1985' on page 90 undefined on input line 1299. Package natbib Warning: Citation `ZienkiewiczZhu1987' on page 90 undefined on i nput line 1299. Package natbib Warning: Citation `ErikssonJohnson1991' on page 90 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnson1995a' on page 90 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnsonIII' on page 90 undefined on i nput line 1299. Package natbib Warning: Citation `ErikssonJohnson1995b' on page 90 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnson1995c' on page 90 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnsonLarsson1998' on page 90 undefi ned on input line 1299. Package natbib Warning: Citation `AinsworthOden1993' on page 90 undefined on in put line 1299. Package natbib Warning: Citation `ErikssonEstepEtAl1995' on page 90 undefined o n input line 1301. Package natbib Warning: Citation `Verfurth1994' on page 90 undefined on input l ine 1301. Package natbib Warning: Citation `Verfurth1999' on page 90 undefined on input l ine 1301. Package natbib Warning: Citation `AinsworthOden2000' on page 90 undefined on in put line 1301. Package natbib Warning: Citation `BeckerRannacher2001' on page 90 undefined on input line 1301. ) (./tex/3.tex [90] Chapter 3. Package natbib Warning: Citation `Ciarlet1975' on page 91 undefined on input li ne 26. Package natbib Warning: Citation `Ciarlet2002' on page 91 undefined on input li ne 27. Package natbib Warning: Citation `BrennerScott2008' on page 91 undefined on inp ut line 28. LaTeX Warning: Reference `chap:kirby-7' on page 91 undefined on input line 29. Package natbib Warning: Citation `Ciarlet2002' on page 91 undefined on input li ne 32. Package natbib Warning: Citation `CiarletRaviart1972' on page 91 undefined on i nput line 39. Package natbib Warning: Citation `BrambleZlamal1970' on page 91 undefined on in put line 51. [91] LaTeX Warning: Reference `kirby-6:tab:overview' on page 92 undefined on input l ine 119. LaTeX Warning: Reference `kirby-6:fig:notation' on page 92 undefined on input l ine 163. [92] (./chapters/kirby-6/pdf/notation_new.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-6/pdf/notation_new.pdf): PDF in clusion: found PDF version <1.5>, but at most version <1.4> allowed ) [93] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 238. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 238. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 238. Package natbib Warning: Citation `Braess2007' on page 94 undefined on input lin e 245. Package natbib Warning: Citation `Courant1943' on page 94 undefined on input li ne 259. Package natbib Warning: Citation `TaylorHood1973' on page 94 undefined on input line 269. Package natbib Warning: Citation `ScottVogelius1985' on page 94 undefined on in put line 269. [94 <./chapters/kirby-6/pdf/notation_new.pdf>] pdfTeX warning: pdflatex (file ./chapters/kirby-6/pdf/P1_1d2d3d.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed [93] Package natbib Warning: Citation `Warburton2005' on page 95 undefined on input line 324. LaTeX Warning: Reference `kirby-6:fig:lagrange:dim' on page 95 undefined on inp ut line 326. LaTeX Warning: Reference `kirby-6:fig:lagrange:2d' on page 95 undefined on inpu t line 327. LaTeX Warning: Reference `kirby-6:fig:lagrange:3d' on page 95 undefined on inpu t line 327. Package natbib Warning: Citation `BrennerScott2008' on page 95 undefined on inp ut line 331. Package natbib Warning: Citation `CrouzeixRaviart1973' on page 95 undefined on input line 348. Underfull \hbox (badness 10000) in paragraph at lines 347--350 \T1/pplx/m/n/10 (+20) equa-tions. The global el-e-ment space con-sists of piece -wise lin-ear Package natbib Warning: Citation `HansboLarson2003' on page 95 undefined on inp ut line 385. Package natbib Warning: Citation `ArnoldFalk1989' on page 95 undefined on input line 386. [95 <./chapters/kirby-6/pdf/P1_1d2d3d.pdf>] [96 <./chapters/kirby-6/png/CG1_2d. png (PNG copy)> <./chapters/kirby-6/png/CG2_2d.png (PNG copy)> <./chapters/kirb y-6/png/CG3_2d.png (PNG copy)> <./chapters/kirby-6/png/CG4_2d.png (PNG copy)> < ./chapters/kirby-6/png/CG5_2d.png (PNG copy)> <./chapters/kirby-6/png/CG6_2d.pn g (PNG copy)> <./chapters/kirby-6/png/CG1_3d.png (PNG copy)> <./chapters/kirby- 6/png/CG2_3d.png (PNG copy)> <./chapters/kirby-6/png/CG3_3d.png (PNG copy)> <./ chapters/kirby-6/png/CG4_3d.png (PNG copy)> <./chapters/kirby-6/png/CG5_3d.png (PNG copy)> <./chapters/kirby-6/png/CG6_3d.png (PNG copy)>] Underfull \hbox (badness 3503) in paragraph at lines 394--394 []\T1/pplx/m/n/9 (+20) Figure 3.5: |Il-lus-tra-tion of the Package natbib Warning: Citation `Braess2007' on page 97 undefined on input lin e 418. Package natbib Warning: Citation `CrouzeixFalk1989' on page 97 undefined on inp ut line 427. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 430. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 430. [97 <./chapters/kirby-6/png/CR1_2d.png (PNG copy)> <./chapters/kirby-6/png/CR1_ 3d.png (PNG copy)>] Package natbib Warning: Citation `RaviartThomas1977' on page 98 undefined on in put line 456. Package natbib Warning: Citation `Nedelec1980' on page 98 undefined on input li ne 462. Package natbib Warning: Citation `Nedelec1980' on page 98 undefined on input li ne 467. Package natbib Warning: Citation `BrezziFortin1991' on page 98 undefined on inp ut line 467. Underfull \hbox (badness 1354) in paragraph at lines 510--510 \T1/pplx/m/n/9 (+20) mo-ments of the nor-mal com-po- Underfull \hbox (badness 1968) in paragraph at lines 510--510 \T1/pplx/m/n/9 (+20) ter-na-tively, as in-di-cated in this [98 <./chapters/kirby-6/png/RT1_2d.png (PNG copy)> <./chapters/kirby-6/png/RT2_ 2d.png (PNG copy)> <./chapters/kirby-6/png/RT3_2d.png (PNG copy)> <./chapters/k irby-6/png/RT1_3d.png (PNG copy)> <./chapters/kirby-6/png/RT2_3d.png (PNG copy) > <./chapters/kirby-6/png/RT3_3d.png (PNG copy)>] Package natbib Warning: Citation `BrezziFortin1991' on page 99 undefined on inp ut line 534. [94] Package natbib Warning: Citation `BrezziDouglasMarini1985' on page 99 undefined on input line 572. Package natbib Warning: Citation `Nedelec1986' on page 99 undefined on input li ne 575. Package natbib Warning: Citation `BrezziDouglasDuranFortin1987' on page 99 unde fined on input line 576. Package natbib Warning: Citation `Nedelec1986' on page 99 undefined on input li ne 577. Package natbib Warning: Citation `FarhloulFortin1997' on page 99 undefined on i nput line 582. Package natbib Warning: Citation `ArnoldFalkWinther2007' on page 99 undefined o n input line 582. Underfull \hbox (badness 4995) in paragraph at lines 585--587 []\T1/pplx/m/it/10 The Brezzi--Douglas--Marini el-e-ment ($[][]$) is LaTeX Warning: Reference `sec:nedelec:first' on page 99 undefined on input line 603. [99 <./chapters/kirby-6/png/BDM1_2d.png (PNG copy)> <./chapters/kirby-6/png/BDM 2_2d.png (PNG copy)> <./chapters/kirby-6/png/BDM3_2d.png (PNG copy)> <./chapter s/kirby-6/png/BDM1_3d.png (PNG copy)> <./chapters/kirby-6/png/BDM2_3d.png (PNG copy)> <./chapters/kirby-6/png/BDM3_3d.png (PNG copy)>] Package natbib Warning: Citation `BrezziFortin1991' on page 100 undefined on in put line 618. Package natbib Warning: Citation `BrezziDouglasFortinEtAl1987' on page 100 unde fined on input line 628. Package natbib Warning: Citation `BrezziFortin1991' on page 100 undefined on in put line 629. Package natbib Warning: Citation `BrezziDouglasMarini1985a' on page 100 undefin ed on input line 632. Package natbib Warning: Citation `MardalTaiWinther2002' on page 100 undefined o n input line 638. Package natbib Warning: Citation `TaiWinther2006' on page 100 undefined on inpu t line 646. Underfull \hbox (badness 3503) in paragraph at lines 677--677 []\T1/pplx/m/n/9 (+20) Figure 3.8: |Il-lus-tra-tion of the Package natbib Warning: Citation `ArnoldWinther2002' on page 100 undefined on i nput line 695. Package natbib Warning: Citation `AdamsCockburn2005' on page 100 undefined on i nput line 702. Package natbib Warning: Citation `ArnoldAwanouWinther2008' on page 100 undefine d on input line 702. [100] Overfull \hbox (1.29993pt too wide) in paragraph at lines 737--737 []\T1/pplx/m/n/9 (-20) Figure 3.9: |Illustration of the Arnold-- Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 748. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 748. Package natbib Warning: Citation `Nedelec1980' on page 101 undefined on input l ine 755. Package natbib Warning: Citation `Nedelec1986' on page 101 undefined on input l ine 755. Underfull \vbox (badness 10000) has occurred while \output is active [101 <./ch apters/kirby-6/png/MTW_2d.png (PNG copy)> <./chapters/kirby-6/png/AW_2d.png (PN G copy)>] Package natbib Warning: Citation `Nedelec1980' on page 102 undefined on input l ine 761. Package natbib Warning: Citation `Nedelec1986' on page 102 undefined on input l ine 761. Package natbib Warning: Citation `ArnoldFalkWinther2006' on page 102 undefined on input line 791. Package natbib Warning: Citation `Nedelec1980' on page 102 undefined on input l ine 794. Package natbib Warning: Citation `ArnoldFalkWinther2006c' on page 102 undefined on input line 796. Underfull \vbox (badness 10000) has occurred while \output is active [102] Package natbib Warning: Citation `Nedelec1980' on page 103 undefined on input l ine 876. Underfull \vbox (badness 10000) has occurred while \output is active [103 <./ch apters/kirby-6/png/NED1_1_2d.png (PNG copy)> <./chapters/kirby-6/png/NED1_2_2d. png (PNG copy)> <./chapters/kirby-6/png/NED1_3_2d.png (PNG copy)> <./chapters/k irby-6/png/NED1_1_3d.png (PNG copy)> <./chapters/kirby-6/png/NED1_2_3d.png (PNG copy)> <./chapters/kirby-6/png/NED1_3_3d.png (PNG copy)>] [95] Package natbib Warning: Citation `Nedelec1986' on page 104 undefined on input l ine 956. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 963. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 963. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 963. [104 <./chapters/kirby-6/png/NED2_1_2d.png (PNG copy)> <./chapters/kirby-6/png/ NED2_2_2d.png (PNG copy)> <./chapters/kirby-6/png/NED2_3_2d.png (PNG copy)> <./ chapters/kirby-6/png/NED2_1_3d.png (PNG copy)>] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 1026. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 1026. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 1026. [96] Package natbib Warning: Citation `ArgyrisFriedScharpf1968' on page 105 undefine d on input line 1072. Package natbib Warning: Citation `Ciarlet2002' on page 105 undefined on input l ine 1072. [105] [106 <./chapters/kirby-6/png/DG0_2d.png (PNG copy)> <./chapters/kirby-6/p ng/DG1_2d.png (PNG copy)> <./chapters/kirby-6/png/DG2_2d.png (PNG copy)> <./cha pters/kirby-6/png/DG3_2d.png (PNG copy)> <./chapters/kirby-6/png/DG0_3d.png (PN G copy)> <./chapters/kirby-6/png/DG1_3d.png (PNG copy)> <./chapters/kirby-6/png /DG2_3d.png (PNG copy)> <./chapters/kirby-6/png/DG3_3d.png (PNG copy)> <./chapt ers/kirby-6/pdf/dgspace.pdf>] Package natbib Warning: Citation `Braess2007' on page 107 undefined on input li ne 1103. Package natbib Warning: Citation `DominguezSayas2008' on page 107 undefined on input line 1124. Package natbib Warning: Citation `SolinSegethDolevzel2004' on page 107 undefine d on input line 1129. Package natbib Warning: Citation `Ciarlet2002' on page 107 undefined on input l ine 1136. Package natbib Warning: Citation `CiarletRaviart1972' on page 107 undefined on input line 1138. Package natbib Warning: Citation `Braess2007' on page 107 undefined on input li ne 1140. Package natbib Warning: Citation `Ciarlet2002' on page 107 undefined on input l ine 1140. Package natbib Warning: Citation `BrennerScott2008' on page 107 undefined on in put line 1142. [107 <./chapters/kirby-6/png/ARG5_2d.png (PNG copy)>] Underfull \hbox (badness 1412) in paragraph at lines 563--570 \T1/pplx/m/n/10 (+20) abled when DOLFIN is con-fig-ured. The back-end can be se t via the global pa-ram-e-ter [97] Package natbib Warning: Citation `BrennerScott2008' on page 108 undefined on in put line 1198. Package natbib Warning: Citation `Morley1968' on page 108 undefined on input li ne 1204. Package natbib Warning: Citation `Morley1968' on page 108 undefined on input li ne 1215. Package natbib Warning: Citation `Morley1971' on page 108 undefined on input li ne 1215. Package natbib Warning: Citation `LascauxLesaint1975' on page 108 undefined on input line 1216. Package natbib Warning: Citation `HuangGuoShi2008' on page 108 undefined on inp ut line 1218. Package natbib Warning: Citation `MinXu2006' on page 108 undefined on input lin e 1218. Underfull \vbox (badness 2573) has occurred while \output is active [108 <./cha pters/kirby-6/png/HER_2d.png (PNG copy)> <./chapters/kirby-6/png/HER_3d.png (PN G copy)>] [98 ] Package natbib Warning: Citation `ArnoldBrezziDouglas1984' on page 109 undefine d on input line 1271. Package natbib Warning: Citation `ArnoldBrezziFortin1984' on page 109 undefined on input line 1271. Package natbib Warning: Citation `ArnoldBrezziFortin1984' on page 109 undefined on input line 1278. [109 <./chapters/kirby-6/png/MOR_2d.png (PNG copy)>] Package natbib Warning: Citation `ArnoldBrezziDouglas1984' on page 110 undefine d on input line 1283. Package natbib Warning: Citation `ArnoldFalkWinther2006' on page 110 undefined on input line 1326. LaTeX Warning: Reference `tab:feec' on page 110 undefined on input line 1344. [110 Package natbib Warning: Citation `Logg2009' on page 99 undefined on input line 733. [99]] Overfull \hbox (2.96089pt too wide) in paragraph at lines 1410--1410 []|\T1/pplx/m/n/9 (-20) Dimension| Underfull \hbox (badness 1484) in paragraph at lines 1425--1425 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 12$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 1484) in paragraph at lines 1428--1428 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 12$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 1484) in paragraph at lines 1431--1431 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 24$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 1484) in paragraph at lines 1434--1434 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 40$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 10000) in alignment at lines 1408--1468 [] [] [] [] [] Underfull \vbox (badness 10000) detected at line 1468 Underfull \hbox (badness 10000) in alignment at lines 1468--1528 [] [] [] [] [] [111] [112] Underfull \hbox (badness 10000) in alignment at lines 1528--1544 [] [] [] [] [] [113] [114] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty [115]) (./tex/4.tex [116]) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) Chapter 4. LaTeX Warning: Reference `chap:kirby-2' on page 117 undefined on input line 14. LaTeX Warning: Reference `chap:alnes-3' on page 117 undefined on input line 15. Package natbib Warning: Citation `HughesCottrellBazilevs2005' on page 117 undef ined on input line 23. Package natbib Warning: Citation `ChessaSmolinskiBelytschko2002' on page 117 un defined on input line 24. Package natbib Warning: Citation `Schwab1998' on page 117 undefined on input li ne 25. Package natbib Warning: Citation `AinsworthCoyle2003' on page 117 undefined on input line 33. LaTeX Warning: Reference `chap:kirby-6' on page 117 undefined on input line 39. Package natbib Warning: Citation `Nedelec1980' on page 117 undefined on input l ine 45. Package natbib Warning: Citation `Nedelec1986' on page 117 undefined on input l ine 45. Package natbib Warning: Citation `BrezziFortin1991' on page 117 undefined on in put line 47. Package natbib Warning: Citation `GiraultRaviart1986' on page 117 undefined on input line 47. LaTeX Warning: Reference `chap:kirby-2' on page 117 undefined on input line 61. LaTeX Warning: Reference `chap:alnes-3' on page 117 undefined on input line 61. [117] [100] Package natbib Warning: Citation `ArnoldFalkWinther2006' on page 118 undefined on input line 80. Package natbib Warning: Citation `LoggMardal2009' on page 118 undefined on inpu t line 90. Package natbib Warning: Citation `Ciarlet2002' on page 118 undefined on input l ine 92. LaTeX Warning: Reference `chap:logg-1' on page 118 undefined on input line 97. LaTeX Warning: Reference `chap:alnes-3' on page 118 undefined on input line 97. Package natbib Warning: Citation `SzaboBabuska1991' on page 118 undefined on in put line 102. Package natbib Warning: Citation `AinsworthCoyle2003' on page 118 undefined on input line 104. Package natbib Warning: Citation `Ciarlet2002' on page 118 undefined on input l ine 117. [118] [119] LaTeX Warning: Reference `eq:singlebfA' on page 120 undefined on input line 217 . LaTeX Warning: Reference `chap:kirby-1:fedef' on page 120 undefined on input li ne 232. LaTeX Warning: Reference `chap:kirby-1:nodaldef' on page 120 undefined on input line 244. [120] Package natbib Warning: Citation `KarniadakisSherwin2005' on page 121 undefined on input line 296. Package natbib Warning: Citation `Dubiner1991' on page 121 undefined on input l ine 328. LaTeX Warning: Reference `fig:tricoord' on page 121 undefined on input line 344 . LaTeX Warning: Reference `fig:logg-2:entities' on page 101 undefined on input l ine 891. LaTeX Warning: Reference `tab:logg-2:entities' on page 101 undefined on input l ine 892. [101 [121 <./chapters/logg-2/pdf/mesh-p1-entities.pdf>]] Package natbib Warning: Citation `Kirby2009' on page 122 undefined on input lin e 402. Package natbib Warning: Citation `Kirby2010' on page 122 undefined on input lin e 402. Underfull \vbox (badness 10000) has occurred while \output is active [122 <./ch apters/kirby-1/pdf/tricoord.pdf>] LaTeX Warning: Reference `chap:kirby-6' on page 123 undefined on input line 433 . LaTeX Warning: Reference `Lagrange' on page 123 undefined on input line 446. LaTeX Warning: Reference `Hermite' on page 123 undefined on input line 474. [123 <./chapters/kirby-6/pdf/P1.pdf> <./chapters/kirby-6/pdf/P2.pdf>] Underfull \hbox (badness 2744) in paragraph at lines 495--495 []\T1/pplx/m/n/9 (+20) Figure 4.4: |Tri-an-gu-lar Raviart-- LaTeX Warning: Reference `RaviartThomas' on page 124 undefined on input line 50 0. [124 <./chapters/kirby-6/pdf/RT0.pdf>] [125] Package natbib Warning: Citation `Nedelec1980' on page 126 undefined on input l ine 578. Package natbib Warning: Citation `ArnoldWinther2002' on page 126 undefined on i nput line 578. Package natbib Warning: Citation `MardalTaiWinther2002' on page 126 undefined o n input line 579. Package natbib Warning: Citation `TaiWinther2006' on page 126 undefined on inpu t line 580. Package natbib Warning: Citation `Ciarlet2002' on page 126 undefined on input l ine 580. Package natbib Warning: Citation `KarniadakisSherwin2005' on page 126 undefined on input line 634. Package natbib Warning: Citation `Kirby2010' on page 126 undefined on input lin e 634. Package natbib Warning: Citation `Kirby' on page 126 undefined on input line 63 7. [126] Package natbib Warning: Citation `Dubiner1991' on page 127 undefined on input l ine 649. Package natbib Warning: Citation `Dunavant1985' on page 127 undefined on input line 659. Package natbib Warning: Citation `KeeganRidzalBochev2008' on page 127 undefined on input line 659. Package natbib Warning: Citation `SolinSegethDolevzel2004' on page 127 undefine d on input line 659. [127] LaTeX Warning: Reference `chap:alnes-2' on page 128 undefined on input line 728 . Package natbib Warning: Citation `RognesKirbyLogg2009' on page 128 undefined on input line 730. Package natbib Warning: Citation `Turek1999' on page 128 undefined on input lin e 732. Package natbib Warning: Citation `RannacherTurek1992' on page 128 undefined on input line 732. LaTeX Warning: Reference `fig:kirby-1:patch' on page 128 undefined on input lin e 739. LaTeX Warning: Reference `eq:geometry' on page 128 undefined on input line 746. ) (./tex/5.tex [128 <./chapters/kirby-1/pdf /patch.pdf>] Chapter 5. LaTeX Warning: Reference `chap:kirby-7' on page 129 undefined on input line 17. LaTeX Warning: Reference `chap:kirby-7' on page 129 undefined on input line 43. Underfull \vbox (badness 10000) has occurred while \output is active [129] LaTeX Warning: Reference `tab:logg-2:connectivity' on page 102 undefined on inp ut line 989. [102] LaTeX Warning: Reference `sec:kirby-5:discretizing' on page 130 undefined on in put line 68. LaTeX Warning: Reference `eq:kirby-5:canonical' on page 130 undefined on input line 73. LaTeX Warning: Reference `sec:kirby-7:mixed' on page 130 undefined on input lin e 92. LaTeX Warning: Reference `chap:alnes-1' on page 130 undefined on input line 145 . [130] (./chapters/kirby-5/pdf/lift_drag.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-5/pdf/lift_drag.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) [131] LaTeX Warning: Reference `eq:kirby-5:integrals' on page 132 undefined on input line 240. LaTeX Warning: Reference `chap:kirby-7' on page 132 undefined on input line 249 . LaTeX Warning: Reference `eq:kirby-5:canonical' on page 132 undefined on input line 251. [132 [103 <./chapters/kirby-5/pdf/lift_drag.pdf>]] LaTeX Warning: Reference `chap:logg-3' on page 133 undefined on input line 305. (./chapters/kirby-5/pdf/element_tensors.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-5/pdf/element_tensors.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `eq:kirby-5:celltensor' on page 133 undefined on input line 325. LaTeX Warning: Reference `fig:kirby-5:tensors' on page 133 undefined on input l ine 330. Package natbib Warning: Citation `OelgaardLoggWells2008' on page 133 undefined on input line 331. [133 <./chapters/kirby-5/pdf/element_tensors.pdf>] [104] LaTeX Warning: Reference `eq:kirby-5:canonical' on page 134 undefined on input line 358. Package natbib Warning: Citation `SaadSchultz1986' on page 134 undefined on inp ut line 360. Package natbib Warning: Citation `HestenesStiefel1952' on page 134 undefined on input line 361. LaTeX Warning: Reference `eq:kirby-5:canonical' on page 134 undefined on input line 385. Package natbib Warning: Citation `BagheriScott2004' on page 134 undefined on in put line 393. LaTeX Warning: Reference `eq:kirby-5:nonlinear' on page 134 undefined on input line 418. Underfull \vbox (badness 4467) has occurred while \output is active [134] Package natbib Warning: Citation `Rivara1984' on page 105 undefined on input li ne 1207. Package natbib Warning: Citation `Rivara1992' on page 105 undefined on input li ne 1207. LaTeX Warning: Reference `fig:logg-2:refinement' on page 105 undefined on input line 1209. [105 LaTeX Warning: Reference `eq:kirby-5:nonlinear' on page 135 undefined on input line 434. LaTeX Warning: Reference `eq:kirby-5:nonlinear' on page 135 undefined on input line 442. LaTeX Warning: Reference `chap:kirby-7' on page 135 undefined on input line 443 . LaTeX Warning: Reference `chap:kirby-7' on page 135 undefined on input line 463 . LaTeX Warning: Reference `chap:selim' on page 135 undefined on input line 464. LaTeX Warning: Reference `eq:kirby-5:nonlinear' on page 135 undefined on input line 466. Underfull \vbox (badness 4569) has occurred while \output is active [135]] ) (./tex/6.tex LaTeX Warning: Reference `sec:logg-2:implementation' on page 106 undefined on i nput line 1229. LaTeX Warning: Reference `chap:kirby-7' on page 106 undefined on input line 123 7. LaTeX Warning: Reference `chap:kirby-6' on page 106 undefined on input line 123 7. LaTeX Warning: Reference `chap:logg-1' on page 106 undefined on input line 1243 . LaTeX Warning: Reference `chap:alnes-3' on page 106 undefined on input line 124 3. LaTeX Warning: Reference `chap:alnes-1' on page 106 undefined on input line 125 7. [106 <./chapters/logg-2/png/refined_cube.png (PNG copy)>] [136] Chapter 6. LaTeX Warning: Reference `chap:kirby-5' on page 137 undefined on input line 21. LaTeX Warning: Reference `alg:assembly,naive' on page 137 undefined on input li ne 36. LaTeX Warning: Reference `chap:kirby-5' on page 137 undefined on input line 49. LaTeX Warning: Reference `chap:kirby-7' on page 137 undefined on input line 80. [137] LaTeX Warning: Reference `chap:kirby-6' on page 107 undefined on input line 127 8. LaTeX Warning: Reference `tab:logg-2:elements' on page 107 undefined on input l ine 1280. LaTeX Warning: Reference `chap:kirby-7' on page 107 undefined on input line 133 0. [107] LaTeX Warning: Reference `alg:assembly' on page 138 undefined on input line 126 . LaTeX Warning: Reference `fig:insertion' on page 138 undefined on input line 12 7. (./chapters/logg-3/pdf/insertion.pdf_tex pdfTeX warning: pdflatex (file ./chapters/logg-3/pdf/insertion.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `alg:assembly' on page 138 undefined on input line 164 . LaTeX Warning: Reference `fig:assembly,code' on page 138 undefined on input lin e 166. Underfull \vbox (badness 10000) has occurred while \output is active [138] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) LaTeX Warning: Reference `alg:assembly' on page 139 undefined on input line 199 . LaTeX Warning: Reference `alg:assembly' on page 139 undefined on input line 199 . LaTeX Warning: Reference `chap:oelgaard-2' on page 139 undefined on input line 207. LaTeX Warning: Reference `chap:kirby-8' on page 139 undefined on input line 207 . [139 <./chapters/logg-3/pdf/insertion.pdf>] [108] LaTeX Warning: Reference `chap:kirby-7' on page 109 undefined on input line 146 1. LaTeX Warning: Reference `fig:logg-2:femsolution' on page 109 undefined on inpu t line 1479. (./chapters/logg-2/pdf/femsolution.pdf_tex pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/femsolution.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `alg:assembly' on page 140 undefined on input line 227 . LaTeX Warning: Reference `alg:assembly:sym' on page 140 undefined on input line 266. Package natbib Warning: Citation `BalayBuschelmanGroppEtAl2001' on page 140 und efined on input line 309. Package natbib Warning: Citation `BalayBuschelmanEijkhoutEtAl2004' on page 140 undefined on input line 309. Package natbib Warning: Citation `HerouxBartlettHowleEtAl2005' on page 140 unde fined on input line 310. [140]) (./tex/7.tex [109] [141] [142] Chapter 7. LaTeX Warning: Reference `chap:kirby-8' on page 143 undefined on input line 13. LaTeX Warning: Reference `chap:logg-1' on page 143 undefined on input line 15. LaTeX Warning: Reference `oelgaard-2:eq:weightedlaplacian' on page 143 undefine d on input line 49. [143] LaTeX Warning: Reference `oelgaard-2:eq:localtensor' on page 144 undefined on i nput line 74. LaTeX Warning: Reference `chap:alnes-1' on page 144 undefined on input line 75. LaTeX Warning: Reference `chap:logg-1' on page 144 undefined on input line 77. LaTeX Warning: Reference `oelgaard-2:eq:weightedlaplacian_quadraturerepresentat ion' on page 144 undefined on input line 111. LaTeX Warning: Reference `oelgaard-2:fig:standard_code' on page 144 undefined o n input line 114. LaTeX Warning: Reference `oelgaard-2:fig:standard_code' on page 144 undefined o n input line 129. LaTeX Warning: Reference `oelgaard-2:fig:standard_code' on page 144 undefined o n input line 138. LaTeX Warning: Reference `oelgaard-2:fig:standard_code' on page 144 undefined o n input line 141. LaTeX Warning: Reference `oelgaard-2:eq:weightedlaplacian_quadraturerepresentat ion' on page 144 undefined on input line 215. Package natbib Warning: Citation `AhoSethiUllman1986' on page 144 undefined on input line 220. LaTeX Warning: Reference `oelgaard-2:fig:standard_code' on page 144 undefined o n input line 229. [144] [145] Package natbib Warning: Citation `www:cgal' on page 110 undefined on input line 1548. [110 <./chapters/logg-2/pdf/femsolution.pdf>] LaTeX Warning: Reference `oelgaard-2:fig:O_zeros_code' on page 146 undefined on input line 252. LaTeX Warning: Reference `oelgaard-2:fig:standard_code' on page 146 undefined o n input line 253. LaTeX Warning: Reference `oelgaard-2:fig:standard_code' on page 146 undefined o n input line 293. LaTeX Warning: Reference `oelgaard-2:fig:standard_code' on page 146 undefined o n input line 293. Underfull \hbox (badness 1038) in paragraph at lines 293--293 \T1/fvm/m/n/9 -f eliminate_zeros\T1/pplx/m/n/9 (+20) . The ar-rays Underfull \hbox (badness 1383) in paragraph at lines 293--293 \T1/pplx/m/n/9 (+20) of val-ues. Note how elim-i-nat- LaTeX Warning: Reference `oelgaard-2:fig:standard_code' on page 146 undefined o n input line 303. [146] LaTeX Warning: Reference `oelgaard-2:eq:weightedlaplacian_quadraturerepresentat ion' on page 147 undefined on input line 359. LaTeX Warning: Reference `oelgaard-2:fig:O_simplify_code' on page 147 undefined on input line 360. LaTeX Warning: Reference `oelgaard-2:fig:standard_code' on page 147 undefined o n input line 362. LaTeX Warning: Reference `oelgaard-2:fig:standard_code' on page 147 undefined o n input line 406. [147] [111] Package natbib Warning: Citation `OelgaardWells2010' on page 148 undefined on i nput line 419. LaTeX Warning: Reference `oelgaard-2:eq:weightedlaplacian_quadraturerepresentat ion' on page 148 undefined on input line 434. LaTeX Warning: Reference `oelgaard-2:fig:O_ip_code' on page 148 undefined on in put line 435. Underfull \vbox (badness 4805) has occurred while \output is active [148] LaTeX Warning: Reference `oelgaard-2:eq:weightedlaplacian_quadraturerepresentat ion' on page 149 undefined on input line 487. LaTeX Warning: Reference `oelgaard-2:fig:O_basis_code' on page 149 undefined on input line 488. LaTeX Warning: Reference `oelgaard-2:fig:O_ip_code' on page 149 undefined on in put line 489. LaTeX Warning: Reference `oelgaard-2:fig:O_basis_code' on page 149 undefined on input line 535. LaTeX Warning: Reference `chap:kirby-2' on page 149 undefined on input line 549 . Package natbib Warning: Citation `KarniadakisSherwin2005' on page 149 undefined on input line 551. [149] LaTeX Warning: Reference `chap:kirby-8' on page 150 undefined on input line 575 . LaTeX Warning: Reference `oelgaard-2:eq:weightedlaplacian' on page 150 undefine d on input line 583. LaTeX Warning: Reference `chap:alnes-1' on page 150 undefined on input line 584 . LaTeX Warning: Reference `alnes-1:eq:hypdefa' on page 150 undefined on input li ne 585. LaTeX Warning: Reference `oelgaard-2:tab:laplace_stats_1' on page 150 undefined on input line 611. LaTeX Warning: Reference `oelgaard-2:fig:laplace_stats_2' on page 150 undefined on input line 612. LaTeX Warning: Reference `oelgaard-2:fig:laplace_stats_2' on page 150 undefined on input line 648. [150] [151 <./chapters/oelgaard-2/pdf/runtime_laplace.pdf>] LaTeX Warning: Reference `oelgaard-2:tab:hyper_stats_1' on page 152 undefined o n input line 679. LaTeX Warning: Reference `oelgaard-2:fig:hyper_stats_2' on page 152 undefined o n input line 680. [112] LaTeX Warning: Reference `oelgaard-2:tab:hyper_stats_1' on page 152 undefined o n input line 716. [152] Package natbib Warning: Citation `OelgaardWells2010' on page 153 undefined on i nput line 770. LaTeX Warning: Reference `oelgaard-2:tab:elasticity2D_complex_comparison' on pa ge 153 undefined on input line 772. LaTeX Warning: Reference `oelgaard-2:tab:elasticity2D_complex_comparison' on pa ge 153 undefined on input line 807. Package natbib Warning: Citation `OelgaardWells2010' on page 153 undefined on i nput line 821. [153 <./chapters/oelgaard-2/pdf/runtime_hyperelasticity.pdf>] Package natbib Warning: Citation `OelgaardWells2010' on page 154 undefined on i nput line 828. Package natbib Warning: Citation `OelgaardWells2010' on page 154 undefined on i nput line 828. [154] LaTeX Warning: Reference `oelgaard-2:tab:elasticity2D_complex_comparison' on pa ge 155 undefined on input line 894. ) (./tex/8.tex [155] [156] Chapter 8. LaTeX Warning: Reference `chap:logg-3' on page 157 undefined on input line 7. LaTeX Warning: Reference `fig:affinemap' on page 157 undefined on input line 45 . [157] (./chapters/kirby-8/pdf/affinemap.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-8/pdf/affinemap.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `chap:logg-1' on page 158 undefined on input line 122. LaTeX Warning: Reference `chap:kirby-4' on page 158 undefined on input line 134 . Package natbib Warning: Citation `KirbyLogg2006' on page 158 undefined on input line 142. Underfull \vbox (badness 10000) has occurred while \output is active [158 <./ch apters/kirby-8/pdf/affinemap.pdf>] Package natbib Warning: Citation `RognesKirbyLogg2009' on page 159 undefined on input line 161. Package natbib Warning: Citation `OelgaardLoggWells2008' on page 159 undefined on input line 161. LaTeX Warning: Reference `tab:mass' on page 159 undefined on input line 171. LaTeX Warning: Reference `tab:advection' on page 159 undefined on input line 17 2. LaTeX Warning: Reference `eq:tensorcontraction' on page 159 undefined on input line 230. LaTeX Warning: Reference `tab:advection' on page 159 undefined on input line 23 7. Package natbib Warning: Citation `KirbyLogg2006' on page 159 undefined on input line 239. [159] LaTeX Warning: Reference `eq:tensorcontraction' on page 160 undefined on input line 269. LaTeX Warning: Reference `chap:oelgaard-2' on page 160 undefined on input line 292. LaTeX Warning: Reference `chap:kirby-3' on page 160 undefined on input line 292 . ) (./tex/9.tex [160] Chapter 9. LaTeX Warning: Reference `chap:kirby-8' on page 161 undefined on input line 8. Package natbib Warning: Citation `KirbyLoggScottEtAl2006' on page 161 undefined on input line 17. Package natbib Warning: Citation `KirbyScott2007' on page 161 undefined on inpu t line 17. Package natbib Warning: Citation `KirbyLogg2008' on page 161 undefined on input line 17. LaTeX Warning: Reference `chap:kirby-3' on page 161 undefined on input line 18. LaTeX Warning: Reference `chap:kirby-8' on page 161 undefined on input line 39. [161] LaTeX Warning: Reference `eq:kirby-4:contract' on page 162 undefined on input l ine 59. LaTeX Warning: Reference `eq:kirby-4:tildeag' on page 162 undefined on input li ne 72. LaTeX Warning: Reference `eq:kirby-4:ALap' on page 162 undefined on input line 86. LaTeX Warning: Reference `eq:kirby-4:ALap' on page 162 undefined on input line 118. LaTeX Warning: Reference `eq:kirby-4:ALap' on page 162 undefined on input line 130. Underfull \vbox (badness 1389) has occurred while \output is active [162] LaTeX Warning: Reference `chap:alnes-1' on page 113 undefined on input line 174 7. LaTeX Warning: Reference `chap:logg-1' on page 113 undefined on input line 1749 . LaTeX Warning: Reference `chap:alnes-3' on page 113 undefined on input line 174 9. LaTeX Warning: Reference `chap:alnes-2' on page 113 undefined on input line 175 0. LaTeX Warning: Reference `chap:alnes-1' on page 113 undefined on input line 177 5. [113 LaTeX Warning: Reference `eq:kirby-4:Aflat' on page 163 undefined on input line 165. LaTeX Warning: Reference `eq:kirby-4:Aflat' on page 163 undefined on input line 182. Package natbib Warning: Citation `WolfHeath2009' on page 163 undefined on input line 196. LaTeX Warning: Reference `sec:kirby-4:graph' on page 163 undefined on input lin e 213. Underfull \vbox (badness 10000) has occurred while \output is active [163]] Package natbib Warning: Citation `Prim1957' on page 164 undefined on input line 233. Package natbib Warning: Citation `KirbyLoggScottEtAl2006' on page 164 undefined on input line 236. LaTeX Warning: Reference `fig:kirby-4:mst' on page 164 undefined on input line 248. (./chapters/kirby-4/pdf/small_mst.pdf_tex ) LaTeX Warning: Reference `eq:kirby-4:Aflat' on page 164 undefined on input line 256. LaTeX Warning: Reference `eq:kirby-4:Aflat' on page 164 undefined on input line 256. [164 <./chapters/kirby-4/pdf/small_mst.pdf>] LaTeX Warning: Reference `eq:kirby-4:Aflat' on page 165 undefined on input line 329. LaTeX Warning: Reference `fig:kirby-4:gg' on page 165 undefined on input line 3 31. (./chapters/kirby-4/pdf/gg2.pdf_tex ) LaTeX Warning: Reference `eq:kirby-4:Aflat' on page 165 undefined on input line 343. LaTeX Warning: Reference `eq:kirby-4:Aflat' on page 165 undefined on input line 343. Package natbib Warning: Citation `KirbyScott2007' on page 165 undefined on inpu t line 371. Package natbib Warning: Citation `WolfHeath2009' on page 165 undefined on input line 380. [165 <./chapters/kirby-4/pdf/gg2.pdf>] LaTeX Warning: Reference `tab:kirby-4:geom' on page 166 undefined on input line 421. LaTeX Warning: Reference `tab:kirby-4:geom' on page 166 undefined on input line 431. Package natbib Warning: Citation `WhaleyPetitetDongarra2001' on page 166 undefi ned on input line 467. Package natbib Warning: Citation `BientinesiGunnelsMyersEtAl2005' on page 166 u ndefined on input line 468. Underfull \vbox (badness 1215) has occurred while \output is active [166] [114] LaTeX Warning: Reference `chap:kirby-8' on page 167 undefined on input line 496 . LaTeX Warning: Reference `chap:oelgaard-2' on page 167 undefined on input line 498. Package natbib Warning: Citation `KirbyLogg2008' on page 167 undefined on input line 499. ) (./tex/Part2.tex [167] [168] [169] [170]) (./tex/10.tex Chapter 10. Package natbib Warning: Citation `LoggWells2010' on page 171 undefined on input line 11. LaTeX Warning: Reference `fig:logg-2:fenicsmap' on page 171 undefined on input line 26. LaTeX Warning: Reference `chap:alnes-1' on page 171 undefined on input line 37. LaTeX Warning: Reference `chap:logg-1' on page 171 undefined on input line 38. LaTeX Warning: Reference `chap:alnes-3' on page 171 undefined on input line 38. LaTeX Warning: Reference `chap:alnes-2' on page 171 undefined on input line 39. LaTeX Warning: Reference `chap:kirby-2' on page 171 undefined on input line 42. LaTeX Warning: Reference `chap:wilbers' on page 171 undefined on input line 43. LaTeX Warning: Reference `chap:kirby-3' on page 171 undefined on input line 44. Package natbib Warning: Citation `www:viper' on page 171 undefined on input lin e 45. Package natbib Warning: Citation `www:petsc' on page 171 undefined on input lin e 52. Package natbib Warning: Citation `www:trilinos' on page 171 undefined on input line 52. Package natbib Warning: Citation `www:ublas' on page 171 undefined on input lin e 52. Package natbib Warning: Citation `www:mtl4' on page 171 undefined on input line 52. Package natbib Warning: Citation `www:parmetis' on page 171 undefined on input line 53. Package natbib Warning: Citation `www:scotch' on page 171 undefined on input li ne 54. pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/fenics-map.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed Underfull \hbox (badness 1215) in paragraph at lines 61--61 \T1/pplx/m/n/9 (+20) the main user in-ter-face of FEn- [171] LaTeX Warning: Reference `fig:logg-2:uml' on page 172 undefined on input line 8 7. LaTeX Warning: Reference `chap:logg-3' on page 115 undefined on input line 1881 . [115 LaTeX Warning: Reference `sec:logg-2:functionality' on page 172 undefined on in put line 118. [172] <./chapters/logg-2/pdf/fenics-map.pdf>] LaTeX Warning: Reference `chap:logg-3' on page 116 undefined on input line 1930 . LaTeX Warning: Reference `sec:logg-2:implementation' on page 116 undefined on i nput line 1935. LaTeX Warning: Reference `chap:kirby-7' on page 116 undefined on input line 194 5. [116] Package natbib Warning: Citation `Beazley2006' on page 173 undefined on input l ine 148. Package natbib Warning: Citation `www:swig' on page 173 undefined on input line 148. Underfull \vbox (badness 3482) has occurred while \output is active [173 <./cha pters/logg-2/pdf/dolfin-uml.pdf>] Package natbib Warning: Citation `LoggWells2010' on page 174 undefined on input line 178. [174] Package natbib Warning: Citation `www:meshbuilder' on page 117 undefined on inp ut line 2020. [117] LaTeX Warning: Reference `eq:logg-2:elasticity' on page 118 undefined on input line 2112. [118] [119 [175]] [176] Underfull \vbox (badness 1448) has occurred while \output is active [120] [177] [178] Underfull \hbox (badness 1412) in paragraph at lines 563--570 \T1/pplx/m/n/10 (+20) abled when DOLFIN is con-fig-ured. The back-end can be se t via the global pa-ram-e-ter [179] [180] Package natbib Warning: Citation `Logg2009' on page 181 undefined on input line 733. [181] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) [182] LaTeX Warning: Reference `fig:logg-2:entities' on page 183 undefined on input l ine 891. LaTeX Warning: Reference `tab:logg-2:entities' on page 183 undefined on input l ine 892. [183 <./chapters/logg-2/pdf/mesh-p1-entities.pdf>] LaTeX Warning: Reference `tab:logg-2:conversionformats' on page 121 undefined o n input line 2331. [121] LaTeX Warning: Reference `tab:logg-2:connectivity' on page 184 undefined on inp ut line 989. [184] [185] [186] LaTeX Warning: Reference `fig:logg-2:plots,mesh' on page 122 undefined on input line 2395. LaTeX Warning: Reference `fig:logg-2:plots,function' on page 122 undefined on i nput line 2395. Package natbib Warning: Citation `Rivara1984' on page 187 undefined on input li ne 1207. Package natbib Warning: Citation `Rivara1992' on page 187 undefined on input li ne 1207. LaTeX Warning: Reference `fig:logg-2:refinement' on page 187 undefined on input line 1209. [187] LaTeX Warning: Reference `sec:logg-2:implementation' on page 188 undefined on i nput line 1229. LaTeX Warning: Reference `chap:kirby-7' on page 188 undefined on input line 123 7. LaTeX Warning: Reference `chap:kirby-6' on page 188 undefined on input line 123 7. LaTeX Warning: Reference `chap:logg-1' on page 188 undefined on input line 1243 . LaTeX Warning: Reference `chap:alnes-3' on page 188 undefined on input line 124 3. LaTeX Warning: Reference `chap:alnes-1' on page 188 undefined on input line 125 7. [188 <./chapters/logg-2/png/refined_cube.png (PNG copy)>] LaTeX Warning: Reference `fig:logg-2:plots,mesh' on page 122 undefined on input line 2423. LaTeX Warning: Reference `fig:logg-2:plots,mesh' on page 122 undefined on input line 2423. Package natbib Warning: Citation `www:paraview' on page 122 undefined on input line 2438. Package natbib Warning: Citation `www:mayavi' on page 122 undefined on input li ne 2438. [122] [123 <./chapters/logg-2/png/plot_mesh.png (PNG copy)> <./chapters/logg-2/ png/plots.png (PNG copy)>] LaTeX Warning: Reference `chap:kirby-6' on page 189 undefined on input line 127 8. LaTeX Warning: Reference `tab:logg-2:elements' on page 189 undefined on input l ine 1280. LaTeX Warning: Reference `chap:kirby-7' on page 189 undefined on input line 133 0. [189] [124] Underfull \hbox (badness 1184) in paragraph at lines 2529--2532 \T1/pplx/m/n/10 (+20) One can-not read-/write \T1/fvm/m/n/10 Function \T1/pplx/ m/n/10 (+20) and \T1/fvm/m/n/10 FunctionSpace \T1/pplx/m/n/10 (+20) ob-jects si nce the rep-re-sen-ta-tion of a [125] LaTeX Warning: Reference `tab:logg-2:loglevels' on page 126 undefined on input line 2653. LaTeX Warning: Reference `tab:logg-2:loglevels' on page 126 undefined on input line 2659. [126] [190] [127] LaTeX Warning: Reference `chap:kirby-7' on page 191 undefined on input line 146 1. LaTeX Warning: Reference `fig:logg-2:femsolution' on page 191 undefined on inpu t line 1479. (./chapters/logg-2/pdf/femsolution.pdf_tex pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/femsolution.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) [128] [191] [129] Package natbib Warning: Citation `www:cgal' on page 192 undefined on input line 1548. [192 <./chapters/logg-2/pdf/femsolution.pdf>] [130] [193] [194] [131] LaTeX Warning: Reference `fig:logg-2:parallel' on page 132 undefined on input l ine 3049. LaTeX Warning: Reference `fig:logg-2:parallel' on page 132 undefined on input l ine 3051. Overfull \hbox (1.6556pt too wide) in paragraph at lines 3058--3067 [][] LaTeX Warning: Reference `fig:logg-2:parallel' on page 132 undefined on input l ine 3115. [132 <./chapters/logg-2/png/coloured.png (PNG copy)> <./chapters/logg-2/png/par tition.png (PNG copy)>] Package natbib Warning: Citation `www:pastix' on page 133 undefined on input li ne 3121. Package natbib Warning: Citation `www:parmetis' on page 133 undefined on input line 3157. Package natbib Warning: Citation `www:scotch' on page 133 undefined on input li ne 3157. LaTeX Warning: Reference `fig:logg-2:parallel' on page 133 undefined on input l ine 3171. [133] LaTeX Warning: Reference `chap:alnes-1' on page 195 undefined on input line 174 7. LaTeX Warning: Reference `chap:logg-1' on page 195 undefined on input line 1749 . LaTeX Warning: Reference `chap:alnes-3' on page 195 undefined on input line 174 9. LaTeX Warning: Reference `chap:alnes-2' on page 195 undefined on input line 175 0. LaTeX Warning: Reference `chap:alnes-1' on page 195 undefined on input line 177 5. [195] Package natbib Warning: Citation `Beazley2006' on page 134 undefined on input l ine 3187. Package natbib Warning: Citation `www:swig' on page 134 undefined on input line 3187. LaTeX Warning: Reference `chap:mardal-2' on page 134 undefined on input line 31 88. [134] [196] Underfull \hbox (badness 1533) in paragraph at lines 3274--3279 [] []\T1/pplx/m/it/10 Con-struct-ing ar-gu-ments (trial and test func-tions).[] \T1/pplx/m/n/10 (+20) The \T1/fvm/m/n/10 ufl.Argument \T1/pplx/m/n/10 (+20) cl ass (the base class of [135] LaTeX Warning: Reference `chap:logg-3' on page 197 undefined on input line 1881 . [197] LaTeX Warning: Reference `chap:logg-3' on page 198 undefined on input line 1930 . LaTeX Warning: Reference `sec:logg-2:implementation' on page 198 undefined on i nput line 1935. LaTeX Warning: Reference `chap:kirby-7' on page 198 undefined on input line 194 5. [198] [136] Package natbib Warning: Citation `www:meshbuilder' on page 199 undefined on inp ut line 2020. [199] LaTeX Warning: Reference `chap:wilbers' on page 137 undefined on input line 340 7. Underfull \vbox (badness 1377) has occurred while \output is active [137] LaTeX Warning: Reference `chap:logg-1' on page 138 undefined on input line 3519 . LaTeX Warning: Reference `chap:alnes-3' on page 138 undefined on input line 352 0. Underfull \vbox (badness 1067) has occurred while \output is active [138] LaTeX Warning: Reference `eq:logg-2:elasticity' on page 200 undefined on input line 2112. [200] Package natbib Warning: Citation `JonesOliphantPetersonEtAl2009' on page 139 un defined on input line 3592. Package natbib Warning: Citation `BellOlsonSchroder2009' on page 139 undefined on input line 3603. LaTeX Warning: Reference `chap:mardal-2' on page 139 undefined on input line 36 09. [139] [201] LaTeX Warning: Reference `chap:logg-1' on page 140 undefined on input line 3649 . ) (./tex/17.tex [140] Chapter 4. Package natbib Warning: Citation `AlnaesLogg2009' on page 141 undefined on inpu t line 54. LaTeX Warning: Reference `chap:logg-1' on page 141 undefined on input line 66. LaTeX Warning: Reference `chap:alnes-3' on page 141 undefined on input line 66. Package natbib Warning: Citation `Stroustrup1997' on page 141 undefined on inpu t line 69. LaTeX Warning: Reference `chap:alnes-2' on page 141 undefined on input line 70. LaTeX Warning: Reference `chap:logg-2' on page 141 undefined on input line 72. LaTeX Warning: Reference `chap:langtangen' on page 141 undefined on input line 75. LaTeX Warning: Reference `ufl:sec:overview' on page 141 undefined on input line 83. LaTeX Warning: Reference `ufl:sec:formtransformations' on page 141 undefined on input line 83. LaTeX Warning: Reference `ufl:sec:representation' on page 141 undefined on inpu t line 86. LaTeX Warning: Reference `ufl:sec:implementation' on page 141 undefined on inpu t line 86. Package natbib Warning: Citation `AlnaesLogg2009' on page 141 undefined on inpu t line 90. LaTeX Warning: Reference `ufl:sec:overview' on page 141 undefined on input line 96. LaTeX Warning: Reference `ufl:sec:elements' on page 141 undefined on input line 97. LaTeX Warning: Reference `ufl:sec:forms' on page 141 undefined on input line 99 . LaTeX Warning: Reference `ufl:sec:defexpr' on page 141 undefined on input line 101. LaTeX Warning: Reference `ufl:sec:formtransformations' on page 141 undefined on input line 103. LaTeX Warning: Reference `ufl:sec:representation' on page 141 undefined on inpu t line 106. LaTeX Warning: Reference `ufl:sec:ad' on page 141 undefined on input line 109. LaTeX Warning: Reference `ufl:sec:algorithms' on page 141 undefined on input li ne 111. Package natbib Warning: Citation `Rossumothers' on page 141 undefined on input line 112. LaTeX Warning: Reference `ufl:sec:implementation' on page 141 undefined on inpu t line 113. LaTeX Warning: Reference `ufl:sec:future' on page 141 undefined on input line 1 14. Package natbib Warning: Citation `Long2003' on page 141 undefined on input line 122. Package natbib Warning: Citation `Long2004a' on page 141 undefined on input lin e 122. Package natbib Warning: Citation `Long2004' on page 141 undefined on input line 122. Package natbib Warning: Citation `Prudhomme2006a' on page 141 undefined on inpu t line 125. Package natbib Warning: Citation `Prudhomme2006' on page 141 undefined on input line 125. Package natbib Warning: Citation `Cimrman2008' on page 141 undefined on input l ine 127. Package natbib Warning: Citation `DularGeuzaine2005' on page 141 undefined on i nput line 129. Package natbib Warning: Citation `Korelc1997' on page 141 undefined on input li ne 131. Package natbib Warning: Citation `Korelc2002' on page 141 undefined on input li ne 131. Underfull \vbox (badness 6493) has occurred while \output is active [141] Package natbib Warning: Citation `BauerFrinkKreckel2000' on page 142 undefined on input line 139. Package natbib Warning: Citation `SkavhaugCertik2009' on page 142 undefined on input line 140. Package natbib Warning: Citation `Certikothers2009' on page 142 undefined on in put line 140. Package natbib Warning: Citation `AlnaesMardal2009b' on page 142 undefined on i nput line 176. Package natbib Warning: Citation `OelgaardWells2010' on page 142 undefined on i nput line 176. LaTeX Warning: Reference `chap:narayanan' on page 142 undefined on input line 1 96. [142] LaTeX Warning: Reference `chap:kirby-7' on page 143 undefined on input line 223 . LaTeX Warning: Reference `ufl:eq:ppeqzero' on page 143 undefined on input line 225. LaTeX Warning: Reference `ufl:eq:elasticitynewton' on page 143 undefined on inp ut line 243. LaTeX Warning: Reference `ufl:fig:hypcode' on page 143 undefined on input line 250. LaTeX Warning: Reference `ufl:eq:hypdef' on page 143 undefined on input line 25 1. LaTeX Warning: Reference `ufl:eq:hypdefL' on page 143 undefined on input line 2 51. LaTeX Warning: Reference `alnes-1:eq:hypdefa' on page 143 undefined on input li ne 251. Underfull \vbox (badness 10000) has occurred while \output is active [143] Underfull \vbox (badness 1448) has occurred while \output is active [202] [144] [145] LaTeX Warning: Reference `ufl:sec:ad' on page 146 undefined on input line 435. [146] LaTeX Warning: Reference `tab:logg-2:conversionformats' on page 203 undefined o n input line 2331. [203] LaTeX Warning: Reference `ufl:eq:form_integrals' on page 147 undefined on input line 489. LaTeX Warning: Reference `ufl:sec:indexnotation' on page 147 undefined on input line 492. LaTeX Warning: Reference `ufl:sec:conditionals' on page 147 undefined on input line 492. LaTeX Warning: Reference `ufl:sec:arguments' on page 147 undefined on input lin e 495. LaTeX Warning: Reference `ufl:sec:indexnotation' on page 147 undefined on input line 501. LaTeX Warning: Reference `ufl:eq:Aij' on page 147 undefined on input line 534. [147] LaTeX Warning: Reference `fig:logg-2:plots,mesh' on page 204 undefined on input line 2395. LaTeX Warning: Reference `fig:logg-2:plots,function' on page 204 undefined on i nput line 2395. [148] LaTeX Warning: Reference `fig:logg-2:plots,mesh' on page 204 undefined on input line 2423. LaTeX Warning: Reference `fig:logg-2:plots,mesh' on page 204 undefined on input line 2423. Package natbib Warning: Citation `www:paraview' on page 204 undefined on input line 2438. Package natbib Warning: Citation `www:mayavi' on page 204 undefined on input li ne 2438. [204] [205 <./chapters/logg-2/png/plot_mesh.png (PNG copy)> <./chapters/logg-2/ png/plots.png (PNG copy)>] LaTeX Warning: Reference `ufl:sec:representation' on page 149 undefined on inpu t line 700. [149] LaTeX Warning: Reference `ufl:sec:indexnotation' on page 150 undefined on input line 752. LaTeX Warning: Reference `ufl:sec:derivative' on page 150 undefined on input li ne 810. LaTeX Warning: Reference `ufl:sec:ad' on page 150 undefined on input line 814. [150] Underfull \vbox (badness 10000) has occurred while \output is active [151] LaTeX Warning: Reference `ufl:sec:ad' on page 152 undefined on input line 925. [152] [206] [153] LaTeX Warning: Reference `ufl:eq:harmonic' on page 154 undefined on input line 1074. [154] [155] Underfull \hbox (badness 1184) in paragraph at lines 2529--2532 \T1/pplx/m/n/10 (+20) One can-not read-/write \T1/fvm/m/n/10 Function \T1/pplx/ m/n/10 (+20) and \T1/fvm/m/n/10 FunctionSpace \T1/pplx/m/n/10 (+20) ob-jects si nce the rep-re-sen-ta-tion of a [207] LaTeX Warning: Reference `ufl:eq:pde' on page 156 undefined on input line 1198. LaTeX Warning: Reference `ufl:eq:pde' on page 156 undefined on input line 1205. LaTeX Warning: Reference `ufl:eq:sL' on page 156 undefined on input line 1218. [156] LaTeX Warning: Reference `ufl:alg:program' on page 157 undefined on input line 1271. (/usr/share/texmf-texlive/tex/latex/microtype/mt-euf.cfg) [157] (./chapters/alnes-1/pdf/expr.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/expr.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `ufl:alg:program' on page 158 undefined on input line 1333. LaTeX Warning: Reference `ufl:fig:expr' on page 158 undefined on input line 134 2. [158 <./chapters/alnes-1/pdf/expr.pdf>] LaTeX Warning: Reference `ufl:sec:indexnotation' on page 159 undefined on input line 1368. (./chapters/alnes-1/pdf/stiffness.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/stiffness.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \hbox (badness 1668) in paragraph at lines 1415--1415 []\T1/pplx/m/n/9 (+20) Figure 4.3: |Ex-pres-sion tree for LaTeX Warning: Reference `ufl:fig:stiffness' on page 159 undefined on input lin e 1430. [159] LaTeX Warning: Reference `tab:logg-2:loglevels' on page 208 undefined on input line 2653. LaTeX Warning: Reference `tab:logg-2:loglevels' on page 208 undefined on input line 2659. [208] LaTeX Warning: Reference `ufl:eq:G' on page 160 undefined on input line 1454. LaTeX Warning: Reference `ufl:eq:E' on page 160 undefined on input line 1454. [160 <./chapters/alnes-1/pdf/stiffness.pdf>] LaTeX Warning: Reference `ufl:sec:transformer' on page 161 undefined on input l ine 1564. LaTeX Warning: Reference `ufl:alg:program' on page 161 undefined on input line 1574. [161] [162] Package natbib Warning: Citation `Griewank1989' on page 163 undefined on input line 1686. Package natbib Warning: Citation `Griewank1989' on page 163 undefined on input line 1696. Package natbib Warning: Citation `BischofCarleCorlissEtAl1992' on page 163 unde fined on input line 1707. Package natbib Warning: Citation `BischofHovlandNorris2002' on page 163 undefin ed on input line 1707. Package natbib Warning: Citation `GieringKaminski1998' on page 163 undefined on input line 1707. LaTeX Warning: Reference `ufl:sec:forwardad' on page 163 undefined on input lin e 1710. LaTeX Warning: Reference `ufl:alg:program' on page 163 undefined on input line 1717. LaTeX Warning: Reference `ufl:alg:forwardad' on page 163 undefined on input lin e 1723. LaTeX Warning: Reference `ufl:alg:program' on page 163 undefined on input line 1726. LaTeX Warning: Reference `ufl:alg:program' on page 163 undefined on input line 1726. LaTeX Warning: Reference `ufl:alg:forwardad' on page 163 undefined on input lin e 1746. LaTeX Warning: Reference `ufl:alg:forwardadprogram' on page 163 undefined on in put line 1747. LaTeX Warning: Reference `ufl:alg:program' on page 163 undefined on input line 1748. [163] LaTeX Warning: Reference `ufl:alg:program' on page 164 undefined on input line 1763. LaTeX Warning: Reference `ufl:alg:forwardadprogram' on page 164 undefined on in put line 1764. LaTeX Warning: Reference `ufl:alg:program' on page 164 undefined on input line 1765. LaTeX Warning: Reference `ufl:alg:forwardadprogram' on page 164 undefined on in put line 1766. [164] LaTeX Warning: Reference `ufl:alg:forwardad' on page 165 undefined on input lin e 1826. Package natbib Warning: Citation `Karczmarczuk2001' on page 165 undefined on in put line 1836. Package natbib Warning: Citation `PearlmutterSiskind2007' on page 165 undefined on input line 1836. Package natbib Warning: Citation `SiskindPearlmutter2008' on page 165 undefined on input line 1836. LaTeX Warning: Reference `ufl:eq:nested' on page 165 undefined on input line 18 39. LaTeX Warning: Reference `ufl:alg:forwardadprogram' on page 165 undefined on in put line 1855. LaTeX Warning: Reference `ufl:alg:forwardad' on page 165 undefined on input lin e 1866. LaTeX Warning: Reference `ufl:alg:forwardadprogram' on page 165 undefined on in put line 1867. [165] LaTeX Warning: Reference `ufl:fig:applyad' on page 166 undefined on input line 1876. [166] [209] [167] Package natbib Warning: Citation `GammaHelmJohnsonEtAl1995' on page 168 undefin ed on input line 2022. [168] [210] [169] LaTeX Warning: Reference `ufl:eq:a_before_expand' on page 170 undefined on inpu t line 2178. LaTeX Warning: Reference `ufl:eq:a_after_expand_compounds' on page 170 undefine d on input line 2190. LaTeX Warning: Reference `ufl:eq:a_after_expand_derivatives' on page 170 undefi ned on input line 2204. LaTeX Warning: Reference `ufl:eq:a_before_expand' on page 170 undefined on inpu t line 2212. [170] [211] [171] Underfull \vbox (badness 10000) has occurred while \output is active [172] [173] [212] [174] Package natbib Warning: Citation `Rossumothers' on page 175 undefined on input line 2515. Package natbib Warning: Citation `Kuchling2007' on page 175 undefined on input line 2525. [175] Package natbib Warning: Citation `ForthTadjouddinePryceEtAl2004' on page 176 un defined on input line 2574. Package natbib Warning: Citation `Tadjouddine2008' on page 176 undefined on inp ut line 2574. ) [176] Chapter 5. [177] [178] No file manual.bbl. No file manual.ind. Package natbib Warning: There were undefined citations. Package caption Warning: Unused \captionsetup[subalgorithm] on input line 8. (./manual.aux [213] LaTeX Warning: Reference `fig:logg-2:parallel' on page 214 undefined on input l ine 3049. LaTeX Warning: Reference `fig:logg-2:parallel' on page 214 undefined on input l ine 3051. ) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (\end occurred inside a group at level 1) ### simple group (level 1) entered at line 58 ({) ### bottom level (see the transcript file for additional information)pdfTeX warning (dest): name {Hfootnote.11} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.10} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.9} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.8} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.7} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.6} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.5} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.4} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.3} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.2} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.1} has been referenced but does not exist , replaced by a fixed one {/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc} Output written on manual.pdf (184 pages, 4980149 bytes). Transcript written on manual.log. Overfull \hbox (1.6556pt too wide) in paragraph at lines 3058--3067 [][] LaTeX Warning: Reference `fig:logg-2:parallel' on page 214 undefined on input l ine 3115. [214 <./chapters/logg-2/png/coloured.png (PNG copy)> <./chapters/logg-2/png/par tition.png (PNG copy)>]This is BibTeX, Version 0.99c (Web2C 7.5.7) The top-level auxiliary file: manual.aux The style file: abbrvnat.bst Database file #1: bibliography.bib Warning--empty year in www:cgal Warning--empty year in ErikssonJohnsonIII Warning--empty year in ErikssonJohnsonIII Warning--empty note in www:mayavi Warning--empty year in www:mayavi Warning--empty year in www:meshbuilder Warning--empty year in www:mtl4 Warning--empty note in www:paraview Warning--empty year in www:paraview Warning--empty year in www:parmetis Warning--empty note in www:pastix Warning--empty year in www:pastix Warning--empty year in www:scotch Warning--empty note in www:petsc Warning--empty year in www:petsc Warning--empty year in www:swig Warning--empty author in PythonTutorial Warning--empty year in PythonTutorial Warning--empty note in www:trilinos Warning--empty year in www:trilinos Warning--empty year in www:ublas Warning--empty year in Rossumothers Warning--empty year in www:viper (There were 23 warnings) This is makeindex, version 2.15 [20-Nov-2007] (kpathsea + Thai support). Scanning input file manual.idx....done (458 entries accepted, 0 rejected). Sorting entries.......done (4567 comparisons). Generating output file manual.ind....done (469 lines written, 0 warnings). Output written in manual.ind. Transcript written in manual.ilg. This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. entering extended mode (./manual.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded. (./fenicsbook.cls Document Class: fenicsbook (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/geometry.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/etc/texmf/tex/xelatex/xetexconfig/geometry.cfg)) (/usr/share/texmf-texlive/tex/latex/oberdiek/bookmark.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdfescape.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty) (/etc/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty)) (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) (/usr/share/texmf-texlive/tex/latex/oberdiek/auxhook.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/bkm-pdftex.def)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/emptypage.sty) (/usr/share/texmf-texlive/tex/latex/psnfss/mathpazo.sty) (/usr/share/texmf-texlive/tex/latex/psnfss/helvet.sty) (/usr/share/texmf-texlive/tex/latex/bera/beramono.sty) (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def)) (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def)) (/usr/share/texmf-texlive/tex/latex/textcase/textcase.sty) (/usr/share/texmf-texlive/tex/latex/titlesec/titlesec.sty) (/usr/share/texmf-texlive/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texmf-texlive/tex/latex/tools/multicol.sty) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/natbib/natbib.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty (/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf-texlive/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf-texlive/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amscd.sty) (/usr/share/texmf-texlive/tex/latex/stmaryrd/stmaryrd.sty) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/codehighlight.sty (/usr/src/RPM/BUILD/fenics-book-20130430/packages/mylistings.sty Package natbib Warning: Citation `www:pastix' on page 215 undefined on input li ne 3121. Package natbib Warning: Citation `www:parmetis' on page 215 undefined on input line 3157. Package natbib Warning: Citation `www:scotch' on page 215 undefined on input li ne 3157. LaTeX Warning: Reference `fig:logg-2:parallel' on page 215 undefined on input l ine 3171. [215 (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) (/usr/share/texmf-texlive/tex/latex/listings/listings.cfg)]) (/usr/share/texmf/tex/latex/xcolor/xcolor.sty (/etc/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))) (/usr/share/texmf-texlive/tex/latex/ltxmisc/import.sty) (/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty (/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty (/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) (/etc/texmf/tex/latex/config/graphics.cfg))) (/usr/share/texmf-texlive/tex/latex/subfig/subfig.sty (/usr/share/texmf-texlive/tex/latex/caption/caption3.sty)) (/usr/share/texmf-texlive/tex/latex/booktabs/booktabs.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty) (/usr/share/texmf-texlive/tex/latex/tools/array.sty) (/usr/share/texmf-texlive/tex/latex/microtype/microtype.sty (/usr/share/texmf-texlive/tex/latex/microtype/microtype.cfg)) (/usr/share/texmf-texlive/tex/latex/tools/xspace.sty) (/usr/share/texmf-texlive/tex/latex/setspace/setspace.sty Package: `setspace' 6.7 <2000/12/01> ) (/usr/share/texmf-texlive/tex/latex/floatrow/floatrow.sty) (/usr/share/texmf-texlive/tex/latex/caption/caption.sty (/usr/share/texmf-texlive/tex/latex/caption/ltcaption.sty)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithm.sty Document Style `algorithm' - floating environment (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithmicx.sty Document Style algorithmicx 1.2 - a greatly improved `algorithmic' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algpseudocode.sty Document Style - pseudocode environments for use with the `algorithmicx' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/todonotes.sty (/usr/share/texmf-texlive/tex/latex/xkeyval/xkeyval.sty (/usr/share/texmf-texlive/tex/generic/xkeyval/xkeyval.tex)) (/usr/share/texmf/tex/latex/pgf/frontendlayer/tikz.sty (/usr/share/texmf/tex/latex/pgf/basiclayer/pgf.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfrcs.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common-lists.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-latex.def (/usr/share/texmf-texlive/tex/latex/ms/everyshi.sty)) (/usr/share/texmf/tex/generic/pgf/utilities/pgfrcs.code.tex)) (/usr/share/texmf/tex/latex/pgf/basiclayer/pgfcore.sty (/usr/share/texmf/tex/latex/pgf/systemlayer/pgfsys.sty (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys.code.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeysfiltered.code.tex)) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgf.cfg) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-pdftex.def (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-common-pdf.def))) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsyssoftpath.code.tex) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsysprotocol.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcore.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathcalc.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathutil.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathparser.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.basic.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.trigonometric.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.random.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.comparison.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.base.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.round.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.misc.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.integerarithmetics.code .tex))) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfloat.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepoints.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathconstruct.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathusage.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorescopes.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoregraphicstate.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransformations.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorequick.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreobjects.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathprocessing.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorearrows.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreshade.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreimage.code.tex (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreexternal.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorelayers.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransparency.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepatterns.code.tex))) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleshapes.code.tex) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleplot.code.tex) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-0-65.sty) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-1-18.sty)) (/usr/share/texmf/tex/latex/pgf/utilities/pgffor.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfkeys.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex)) (/usr/share/texmf/tex/latex/pgf/math/pgfmath.sty (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgffor.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex))) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/tikz.code.tex (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryplothandlers.code.tex) (/usr/share/texmf/tex/generic/pgf/modules/pgfmodulematrix.code.tex) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibrarytopat hs.code.tex))) (/usr/share/texmf-texlive/tex/latex/tools/calc.sty) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryshado ws.code.tex (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryfadin gs.code.tex (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryfadings.code.tex))))) Package natbib Warning: Citation `Beazley2006' on page 216 undefined on input l ine 3187. Package natbib Warning: Citation `www:swig' on page 216 undefined on input line 3187. LaTeX Warning: Reference `chap:mardal-2' on page 216 undefined on input line 31 88. [216 Writing index file manual.idx (./manual.aux]) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/t1pplx.fd) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (/usr/share/texmf-texlive/tex/latex/microtype/mt-ppl.cfg) (/usr/share/texmf-texlive/tex/latex/floatrow/fr-subfig.sty) (/usr/share/texmf-texlive/tex/latex/floatrow/fr-longtable.sty) ABD: EveryShipout initializing macros (./tex/FMmanual.tex [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdft ex.map} <./png/fenics_logo_text.png>] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pplx.fd) [2] (./manual.toc (/usr/share/texmf-texlive/tex/latex/psnfss/ot1pplx.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omlzplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omszplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omxzplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/ot1zplm.fd) Underfull \hbox (badness 1533) in paragraph at lines 3274--3279 [] []\T1/pplx/m/it/10 Con-struct-ing ar-gu-ments (trial and test func-tions).[] \T1/pplx/m/n/10 (+20) The \T1/fvm/m/n/10 ufl.Argument \T1/pplx/m/n/10 (+20) cl ass (the base class of [217 (/usr/share/texmf-texlive/tex/latex/microtype/mt-msa.cfg) (/usr/share/texmf-texlive/tex/latex/microtype/mt-msb.cfg)] (/usr/share/texmf-texlive/tex/latex/stmaryrd/Ustmry.fd)) [3] [4] (/usr/share/texmf-texlive/tex/latex/bera/t1fvm.fd)) [5] [6] (./tex/1.tex Chapter 1. [1] [2] [3] [4] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) Package natbib Warning: Citation `PythonTutorial' on page 5 undefined on input line 379. [5 [218]] [6] LaTeX Warning: Reference `chap:wilbers' on page 219 undefined on input line 340 7. Underfull \vbox (badness 1377) has occurred while \output is active [219] [7] LaTeX Warning: Reference `chap:logg-1' on page 220 undefined on input line 3519 . LaTeX Warning: Reference `chap:alnes-3' on page 220 undefined on input line 352 0. Underfull \vbox (badness 1067) has occurred while \output is active [220] [8] [9 <./chapters/langtangen/pdf/ex1_u. pdf>] Package natbib Warning: Citation `JonesOliphantPetersonEtAl2009' on page 221 un defined on input line 3592. Package natbib Warning: Citation `BellOlsonSchroder2009' on page 221 undefined on input line 3603. LaTeX Warning: Reference `chap:mardal-2' on page 221 undefined on input line 36 09. [221 [10] <./chapters/langtangen/png/ex1_mesh.png (PNG copy)>] LaTeX Warning: Reference `chap:logg-1' on page 222 undefined on input line 3649 . ) (./tex/11.tex [222] Chapter 11. LaTeX Warning: Reference `chap:alnes-3' on page 223 undefined on input line 16. LaTeX Warning: Reference `chap:logg-3' on page 223 undefined on input line 29. LaTeX Warning: Reference `chap:oelgaard-2' on page 223 undefined on input line 50. LaTeX Warning: Reference `chap:kirby-8' on page 223 undefined on input line 50. LaTeX Warning: Reference `chap:kirby-4' on page 223 undefined on input line 51. LaTeX Warning: Reference `chap:alnes-1' on page 223 undefined on input line 59. LaTeX Warning: Reference `chap:alnes-2' on page 223 undefined on input line 61. LaTeX Warning: Reference `fig:logg-1:formcompiler' on page 223 undefined on inp ut line 62. LaTeX Warning: Reference `sec:logg-1:jit' on page 223 undefined on input line 7 9. [223 <./chapters/logg-1/pdf/ufl_ffc_ufc.pdf>] [11] [12] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty LaTeX Warning: Reference `fig:logg-1:python:form' on page 224 undefined on inpu t line 149. LaTeX Warning: Reference `fig:logg-1:formcode' on page 224 undefined on input l ine 156. LaTeX Warning: Reference `fig:logg-1:python:form' on page 224 undefined on inpu t line 157. [224) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty]) [13] [14] [15] [16] Underfull \vbox (badness 1033) has occurred while \output is active [17] [18] Underfull \vbox (badness 10000) has occurred while \output is active [19 <./cha pters/langtangen/pdf/membrane_waxis.pdf>] [20 <./chapters/langtangen/pdf/ex1_ gradu.pdf>] [21] [22] [23] [24] [25] LaTeX Warning: Reference `fig:logg-1:python:form' on page 225 undefined on inpu t line 230. LaTeX Warning: Reference `chap:kirby-8' on page 225 undefined on input line 230 . LaTeX Warning: Reference `fig:logg-1:python:form' on page 225 undefined on inpu t line 230. LaTeX Warning: Reference `chap:kirby-8' on page 225 undefined on input line 230 . LaTeX Warning: Reference `fig:logg-1:python:element' on page 225 undefined on i nput line 234. LaTeX Warning: Reference `fig:logg-1:elementcode' on page 225 undefined on inpu t line 242. LaTeX Warning: Reference `fig:logg-1:python:element' on page 225 undefined on i nput line 243. LaTeX Warning: Reference `fig:logg-1:python:element' on page 225 undefined on i nput line 321. LaTeX Warning: Reference `fig:logg-1:python:element' on page 225 undefined on i nput line 321. LaTeX Warning: Reference `fig:logg-1:python:form' on page 225 undefined on inpu t line 336. [225] [226 [26]] [227 [27]] Underfull \vbox (badness 3536) has occurred while \output is active [28] LaTeX Warning: Reference `sec:logg-1:representation' on page 228 undefined on i nput line 381. LaTeX Warning: Reference `chap:oelgaard-2' on page 228 undefined on input line 382. LaTeX Warning: Reference `chap:kirby-8' on page 228 undefined on input line 382 . LaTeX Warning: Reference `fig:logg-1:compilerstages' on page 228 undefined on i nput line 410. Underfull \hbox (badness 1975) in paragraph at lines 428--428 \T1/pplx/m/n/9 (+20) guage, Anal-y-sis, Rep-re-sen-ta-tion, LaTeX Warning: Reference `sec:logg-1:representation' on page 228 undefined on i nput line 449. [228] [29 [229 <./chapters/logg-1/pdf/compilerdesign.pdf]>] Underfull \vbox (badness 10000) has occurred while \output is active [30 <./cha pters/langtangen/pdf/Poisson2D_Dvc_contour1.pdf> <./chapters/langtangen/pdf/Poi sson2D_Dvc_flux_x.pdf> <./chapters/langtangen/pdf/Poisson2D_Dvc_surf1.pdf> <./c hapters/langtangen/pdf/Poisson2D_Dvc_mesh1.pdf>] [31] LaTeX Warning: Reference `chap:kirby-3' on page 230 undefined on input line 479 . LaTeX Warning: Reference `chap:oelgaard-2' on page 230 undefined on input line 480. LaTeX Warning: Reference `chap:oelgaard-2' on page 230 undefined on input line 532. LaTeX Warning: Reference `chap:kirby-8' on page 230 undefined on input line 533 . [230] LaTeX Warning: Reference `chap:kirby-8' on page 231 undefined on input line 565 . LaTeX Warning: Reference `chap:oelgaard-2' on page 231 undefined on input line 580. Package natbib Warning: Citation `OelgaardWells2010' on page 231 undefined on i nput line 586. Package natbib Warning: Citation `OelgaardWells2010' on page 231 undefined on i nput line 588. LaTeX Warning: Reference `chap:kirby-3' on page 231 undefined on input line 618 . LaTeX Warning: Reference `chap:oelgaard-2' on page 231 undefined on input line 621. [231] [32] Underfull \vbox (badness 1122) has occurred while \output is active [33] Underfull \hbox (badness 2961) in paragraph at lines 626--647 \T1/pplx/m/n/10 (+20) interface by giv-ing the ad-di-tional op-tions \T1/fvm/m/ n/10 -f eliminate_zeros\T1/pplx/m/n/10 (+20) , \T1/fvm/m/n/10 -f simplify_expre ssions\T1/pplx/m/n/10 (+20) , LaTeX Warning: Reference `chap:wilbers' on page 232 undefined on input line 684 . LaTeX Warning: Reference `fig:logg-1:jit' on page 232 undefined on input line 6 90. [34] Underfull \hbox (badness 1308) in paragraph at lines 701--701 []\T1/pplx/m/n/9 (+20) Figure 11.7: |JIT com-pi-la-tion of [232] [35] [36] Underfull \vbox (badness 3646) has occurred while \output is active [37] [38] [39] Package natbib Warning: Citation `KirbyLogg2006' on page 233 undefined on input line 732. Package natbib Warning: Citation `KirbyLogg2007' on page 233 undefined on input line 732. LaTeX Warning: Reference `fig:logg-1:poisson,before' on page 233 undefined on i nput line 738. LaTeX Warning: Reference `fig:logg-1:poisson,ufl' on page 233 undefined on inpu t line 738. Package natbib Warning: Citation `OelgaardLoggWells2008' on page 233 undefined on input line 815. Package natbib Warning: Citation `RognesKirbyLogg2009' on page 233 undefined on input line 816. Package natbib Warning: Citation `OelgaardWells2010' on page 233 undefined on i nput line 817. Package natbib Warning: Citation `RognesLogg2011' on page 233 undefined on inpu t line 821. ) (./tex/12.tex [233 Underfull \vbox (badness 1412) has occurred while \output is active [40 <./chapters/logg-1/pdf/jit.pdf>]] [234] [41] [42] [43] Underfull \hbox (badness 1331) in paragraph at lines 3053--3059 []\T1/pplx/m/n/10 (+20) The im-ple-men-ta-tion is iden-ti-cal to the one in Sec -tion [][]1.2.2[][] and is found in the file [44] [45] Chapter 12. LaTeX Warning: Reference `chap:kirby-8' on page 235 undefined on input line 9. LaTeX Warning: Reference `chap:kirby-4' on page 235 undefined on input line 13. Package natbib Warning: Citation `KirbyKnepleyLoggEtAl2005' on page 235 undefin ed on input line 17. Package natbib Warning: Citation `KirbyLoggScottEtAl2006' on page 235 undefined on input line 17. Package natbib Warning: Citation `KirbyScott2007' on page 235 undefined on inpu t line 17. Package natbib Warning: Citation `KirbyLogg2008' on page 235 undefined on input line 17. LaTeX Warning: Reference `chap:logg-1' on page 235 undefined on input line 19. LaTeX Warning: Reference `chap:kirby-5' on page 235 undefined on input line 24. LaTeX Warning: Reference `chap:kirby-8' on page 235 undefined on input line 41. LaTeX Warning: Reference `chap:kirby-8' on page 235 undefined on input line 52. LaTeX Warning: Reference `chap:kirby-4' on page 235 undefined on input line 52. LaTeX Warning: Reference `fig:code,poisson' on page 235 undefined on input line 58. LaTeX Warning: Reference `fig:code,poisson,optimized' on page 235 undefined on input line 59. Package natbib Warning: Citation `WolfHeath2009' on page 235 undefined on input line 160. Underfull \vbox (badness 1152) has occurred while \output is active [235] [236] [46] [47 LaTeX Warning: Reference `chap:oelgaard-2' on page 237 undefined on input line 177. LaTeX Warning: Reference `fig:MassH1' on page 237 undefined on input line 196. [237] [48]] LaTeX Warning: Reference `fig:Poisson' on page 238 undefined on input line 217. LaTeX Warning: Reference `fig:WeightedPoisson' on page 238 undefined on input l ine 240. Underfull \vbox (badness 1946) has occurred while \output is active [238 <./cha pters/kirby-3/pdf/MassH1.pdf>] [239 <./chapters/kirby-3/pdf/Poisson.pdf> <./cha pters/kirby-3/pdf/WeightedPoisson.pdf>] [49] LaTeX Warning: Reference `eq:MassH1' on page 240 undefined on input line 286. Package natbib Warning: Citation `RognesKirbyLogg2009' on page 240 undefined on input line 289. LaTeX Warning: Reference `fig:MassHdiv' on page 240 undefined on input line 296 . LaTeX Warning: Reference `fig:MassHcurl' on page 240 undefined on input line 29 6. Underfull \vbox (badness 10000) has occurred while \output is active [240 <./ch apters/kirby-3/pdf/NavierStokes.pdf>] [241 <./chapters/kirby-3/pdf/MassHdiv.pdf > <./chapters/kirby-3/pdf/MassHcurl.pdf>]) (./tex/13.tex [242] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] Chapter 13. Package natbib Warning: Citation `Kirby2004' on page 243 undefined on input lin e 9. Package natbib Warning: Citation `Kirby2006' on page 243 undefined on input lin e 9. LaTeX Warning: Reference `chap:kirby-1' on page 243 undefined on input line 10. Package natbib Warning: Citation `Ciarlet2002' on page 243 undefined on input l ine 23. LaTeX Warning: Reference `chap:kirby-1' on page 243 undefined on input line 29. Package natbib Warning: Citation `KarniadakisSherwin2005' on page 243 undefined on input line 48. Underfull \vbox (badness 10000) has occurred while \output is active [243] [52] Underfull \vbox (badness 2088) has occurred while \output is active [53 <./chap ters/langtangen/pdf/daynight.pdfError: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap >] Package natbib Warning: Citation `Kirby' on page 244 undefined on input line 71 . Package natbib Warning: Citation `Kirby' on page 244 undefined on input line 94 . LaTeX Warning: Reference `dubalg' on page 244 undefined on input line 95. [244] LaTeX Warning: Reference `eq:bigphi' on page 245 undefined on input line 188. Underfull \vbox (badness 10000) has occurred while \output is active [245] LaTeX Warning: Reference `eq:doteval' on page 246 undefined on input line 220. LaTeX Warning: Reference `dubalg' on page 246 undefined on input line 223. [246] [247] [54] LaTeX Warning: Reference `dubalg' on page 248 undefined on input line 387. Package natbib Warning: Citation `BrezziFortin1991' on page 248 undefined on in put line 396. Package natbib Warning: Citation `GolubVan1996' on page 248 undefined on input line 430. Underfull \hbox (badness 1371) in paragraph at lines 428--435 \T1/pplx/m/n/10 (+20) Then, a ba-sis for the null space of this ma-trix is con- structed us-ing the sin-gu-lar value [248] Package natbib Warning: Citation `Nedelec1980' on page 249 undefined on input l ine 437. Package natbib Warning: Citation `ArnoldWinther2002' on page 249 undefined on i nput line 438. Package natbib Warning: Citation `MardalTaiWinther2002' on page 249 undefined o n input line 439. Package natbib Warning: Citation `Kirby2006a' on page 249 undefined on input li ne 450. Package natbib Warning: Citation `KnepleyKarpeev2009' on page 249 undefined on input line 450. Package natbib Warning: Citation `Logg2009' on page 249 undefined on input line 451. LaTeX Warning: Reference `fig:reftri' on page 249 undefined on input line 456. LaTeX Warning: Reference `fig:p3' on page 249 undefined on input line 457. LaTeX Warning: Reference `chap:alnes-2' on page 249 undefined on input line 476 . LaTeX Warning: Reference `chap:alnes-2' on page 249 undefined on input line 476 . [249 <./chapters/kirby-2/pdf/reftri.pdf>] [250 Underfull \vbox (badness 3977) has occurred while \output is active [55 <./chapters/kirby-2/pdf/P3.pdf>] ] Package natbib Warning: Citation `Warburton2005' on page 251 undefined on input line 579. LaTeX Warning: Reference `fig:struct' on page 251 undefined on input line 583. ) (./tex/14.tex [251 <./chapters/kirby-2/p df/struct.pdf>] [252] [56] [57] [58] [59 <./chapters/langtangen/pd f/hollow_cylinder.pdf>] Chapter 14. LaTeX Warning: Reference `chap:logg-1' on page 253 undefined on input line 20. LaTeX Warning: Reference `chap:alnes-3' on page 253 undefined on input line 20. LaTeX Warning: Reference `chap:mardal-2' on page 253 undefined on input line 20 . Package natbib Warning: Citation `www:swig' on page 253 undefined on input line 23. Package natbib Warning: Citation `Beazley2006' on page 253 undefined on input l ine 23. Package natbib Warning: Citation `HansenWollman' on page 253 undefined on input line 29. [253] [60] Underfull \hbox (badness 1215) in paragraph at lines 4284--4288 []\T1/pplx/m/n/10 (+20) Calling \T1/fvm/m/n/10 subdomains.array() \T1/pplx/m/n/ 10 (+20) re-turns a \T1/fvm/m/n/10 numpy \T1/pplx/m/n/10 (+20) ar-ray of the su b-do-main val-ues. That is, [61] LaTeX Warning: Reference `chap:mardal-2' on page 254 undefined on input line 99 . [254] [62] Underfull \vbox (badness 10000) has occurred while \output is active [63] [64] [65] Package natbib Warning: Citation `Mortensen2011' on page 66 undefined on input line 4586. Package natbib Warning: Citation `Mortensen2011b' on page 66 undefined on input line 4586. [66] Overfull \hbox (2.004pt too wide) in paragraph at lines 4672--4674 []\T1/pplx/m/n/10 (-20) generate mesh over [67] LaTeX Warning: Reference `wilbers:fig:speed-up' on page 255 undefined on input line 168. Package natbib Warning: Citation `WilbersLangtangenOdegaard2009' on page 255 un defined on input line 178. LaTeX Warning: Reference `wilbers:fig:fig1' on page 255 undefined on input line 180. [68] [255] [256 <./chapters/wilbers/pdf /pressure_plot.pdf>] [69] Package natbib Warning: Citation `Gockenbach2006' on page 70 undefined on input line 4917. Package natbib Warning: Citation `DoneaHuerta2003' on page 70 undefined on inpu t line 4918. Package natbib Warning: Citation `Hughes1987' on page 70 undefined on input lin e 4919. Package natbib Warning: Citation `Bickford1994' on page 70 undefined on input l ine 4924. Package natbib Warning: Citation `ErikssonEstepHansboEtAl1996' on page 70 undef ined on input line 4928. Package natbib Warning: Citation `BrennerScott2008' on page 70 undefined on inp ut line 4931. Package natbib Warning: Citation `Braess2007' on page 70 undefined on input lin e 4932. Package natbib Warning: Citation `ErnGuermond2004' on page 70 undefined on inpu t line 4932. Package natbib Warning: Citation `QuarteroniValli2008' on page 70 undefined on input line 4932. Package natbib Warning: Citation `Ciarlet2002' on page 70 undefined on input li ne 4933. Package natbib Warning: Citation `Lutz2007' on page 70 undefined on input line 4939. Package natbib Warning: Citation `Hetland2002' on page 70 undefined on input li ne 4939. Package natbib Warning: Citation `Lutz2006' on page 70 undefined on input line 4941. Package natbib Warning: Citation `MartelliAscher2005' on page 70 undefined on i nput line 4941. Package natbib Warning: Citation `Martelli2006' on page 70 undefined on input l ine 4942. Package natbib Warning: Citation `Langtangen2008' on page 70 undefined on input line 4946. Package natbib Warning: Citation `Langtangen20011' on page 70 undefined on inpu t line 4946. Package natbib Warning: Citation `Kiusalaas2010' on page 70 undefined on input line 4946. ) (./tex/2.tex [70] Chapter 2. (/usr/share/texmf-texlive/tex/latex/psnfss/ufplmbb.fd) [71] (./chapters/kirby-7/pdf/heat_equation_model_domain.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/heat_equation_model_domai n.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allow ed ) [72 <./ch apters/kirby-7/pdf/heat_equation_model_domain.pdf>] [73] [74] [75] [76] Package natbib Warning: Citation `Ciarlet1976' on page 77 undefined on input li ne 494. Package natbib Warning: Citation `BrennerScott2008' on page 77 undefined on inp ut line 495. Package natbib Warning: Citation `BrennerScott2008' on page 77 undefined on inp ut line 518. [77 <./chapters/kirby-7/pdf/cells.pdf>] Package natbib Warning: Citation `Kirby2004' on page 78 undefined on input line 596. Underfull \vbox (badness 6348) has occurred while \output is active [78 <./chap ters/kirby-7/pdf/P1.pdf>] [257 pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/dofmap.pdf): PDF inclusio n: found PDF version <1.5>, but at most version <1.4> allowed ] [79 <./chapters/kirby-7/pdf/dofmap.pdf>] Underfull \hbox (badness 1107) in paragraph at lines 694--694 []\T1/pplx/m/n/9 (+20) Figure 2.5: |Patch-ing to-gether a Underfull \hbox (badness 1755) in paragraph at lines 694--694 \T1/pplx/m/n/9 (+20) pair of quadratic lo-cal func-tion [80 <./chapters/kirby-7/pdf/femspace.pdf>] (./chapters/kirby-7/pdf/affine_map.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/affine_map.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) Package natbib Warning: Citation `RognesKirbyLogg2009' on page 81 undefined on input line 779. Underfull \vbox (badness 10000) has occurred while \output is active [81 <./cha pters/kirby-7/pdf/affine_map.pdf>] Package natbib Warning: Citation `BrennerScott2008' on page 82 undefined on inp ut line 846. Package natbib Warning: Citation `Ciarlet2002' on page 82 undefined on input li ne 855. Package natbib Warning: Citation `BrennerScott2008' on page 82 undefined on inp ut line 855. Package natbib Warning: Citation `Davis2004' on page 82 undefined on input line 875. Package natbib Warning: Citation `Li2005' on page 82 undefined on input line 87 5. Package natbib Warning: Citation `HestenesStiefel1952' on page 82 undefined on input line 880. Underfull \vbox (badness 5924) has occurred while \output is active [82] Package natbib Warning: Citation `Brandt1977' on page 83 undefined on input lin e 886. Package natbib Warning: Citation `Wesseling1992' on page 83 undefined on input line 886. Package natbib Warning: Citation `FalgoutYang2002' on page 83 undefined on inpu t line 893. Package natbib Warning: Citation `HerouxBartlettHowleEtAl2005' on page 83 undef ined on input line 894. Package natbib Warning: Citation `SaadSchultz1986' on page 83 undefined on inpu t line 899. Package natbib Warning: Citation `Manteuffel1980' on page 83 undefined on input line 921. Package natbib Warning: Citation `Axelsson1986' on page 83 undefined on input l ine 921. Package natbib Warning: Citation `Saad1994' on page 83 undefined on input line 921. Package natbib Warning: Citation `BalayBuschelmanEijkhoutEtAl2004' on page 83 u ndefined on input line 932. Package natbib Warning: Citation `HerouxBartlettHowleEtAl2005' on page 83 undef ined on input line 933. Package natbib Warning: Citation `OdenDemkowicz1996' on page 83 undefined on in put line 973. [83] Package natbib Warning: Citation `LaxMilgram1954' on page 84 undefined on input line 980. (./chapters/kirby-7/pdf/projection.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/projection.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) [84 <./chapters/kirby-7/pdf/projecti on.pdf>] Package natbib Warning: Citation `ErikssonEstepEtAl1995' on page 85 undefined o n input line 1117. Package natbib Warning: Citation `ErikssonEstepEtAl1995' on page 85 undefined o n input line 1117. Package natbib Warning: Citation `BeckerRannacher2001' on page 85 undefined on input line 1117. Package natbib Warning: Citation `BeckerRannacher2001' on page 85 undefined on input line 1118. Underfull \vbox (badness 10000) has occurred while \output is active [85] Package natbib Warning: Citation `ElmanSilvesterWathen2005' on page 86 undefine d on input line 1188. Package natbib Warning: Citation `Dorfler1996' on page 86 undefined on input li ne 1207. [86] Package natbib Warning: Citation `Logg2007a' on page 87 undefined on input line 1269. Package natbib Warning: Citation `LoggWells2010' on page 87 undefined on input line 1269. Package natbib Warning: Citation `Kirby2004' on page 87 undefined on input line 1269. Package natbib Warning: Citation `KirbyLogg2006' on page 87 undefined on input line 1269. Package natbib Warning: Citation `AlnaesLoggMardalEtAl2009' on page 87 undefine d on input line 1269. Package natbib Warning: Citation `AlnaesMardal2009b' on page 87 undefined on in put line 1269. Package natbib Warning: Citation `KirbyKnepleyLoggEtAl2005' on page 87 undefine d on input line 1269. Package natbib Warning: Citation `KirbyLoggScottEtAl2006' on page 87 undefined on input line 1269. Package natbib Warning: Citation `KirbyLogg2007' on page 87 undefined on input line 1269. Package natbib Warning: Citation `KirbyLogg2008' on page 87 undefined on input line 1269. Package natbib Warning: Citation `KirbyScott2007' on page 87 undefined on input line 1269. Package natbib Warning: Citation `Kirby2006a' on page 87 undefined on input lin e 1269. Package natbib Warning: Citation `OelgaardLoggWells2008' on page 87 undefined o n input line 1269. Package natbib Warning: Citation `RognesKirbyLogg2009' on page 87 undefined on input line 1269. Package natbib Warning: Citation `OelgaardWells2010' on page 87 undefined on in put line 1269. Package natbib Warning: Citation `Logg2009' on page 87 undefined on input line 1269. [87 <./chapters/kirby-7/png/refinement.png (PNG copy)>] Package natbib Warning: Citation `Galerkin1915' on page 88 undefined on input l ine 1275. Package natbib Warning: Citation `Castigliano1879' on page 88 undefined on inpu t line 1280. Package natbib Warning: Citation `Rayleigh1870' on page 88 undefined on input l ine 1280. Package natbib Warning: Citation `Ritz1908' on page 88 undefined on input line 1281. Package natbib Warning: Citation `Courant1943' on page 88 undefined on input li ne 1285. Package natbib Warning: Citation `ZienkiewiczTaylorZhu2005firstpublishedin1967' on page 88 undefined on input line 1290. Package natbib Warning: Citation `StrangFix1973' on page 88 undefined on input line 1290. Package natbib Warning: Citation `Ciarlet1976' on page 88 undefined on input li ne 1290. Package natbib Warning: Citation `BeckerCareyOden1981' on page 88 undefined on input line 1290. Package natbib Warning: Citation `Hughes1987' on page 88 undefined on input lin e 1290. Package natbib Warning: Citation `BrennerScott2008' on page 88 undefined on inp ut line 1290. Package natbib Warning: Citation `ArnoldFalkWinther2006' on page 88 undefined o n input line 1293. Package natbib Warning: Citation `BabuvskaRheinboldt1978' on page 88 undefined on input line 1297. Package natbib Warning: Citation `BankWeiser1985' on page 88 undefined on input line 1299. Package natbib Warning: Citation `ZienkiewiczZhu1987' on page 88 undefined on i nput line 1299. Package natbib Warning: Citation `ErikssonJohnson1991' on page 88 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnson1995a' on page 88 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnsonIII' on page 88 undefined on i nput line 1299. Package natbib Warning: Citation `ErikssonJohnson1995b' on page 88 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnson1995c' on page 88 undefined on input line 1299. Package natbib Warning: Citation `ErikssonJohnsonLarsson1998' on page 88 undefi ned on input line 1299. Package natbib Warning: Citation `AinsworthOden1993' on page 88 undefined on in put line 1299. Package natbib Warning: Citation `ErikssonEstepEtAl1995' on page 88 undefined o n input line 1301. Package natbib Warning: Citation `Verfurth1994' on page 88 undefined on input l ine 1301. Package natbib Warning: Citation `Verfurth1999' on page 88 undefined on input l ine 1301. Package natbib Warning: Citation `AinsworthOden2000' on page 88 undefined on in put line 1301. Package natbib Warning: Citation `BeckerRannacher2001' on page 88 undefined on input line 1301. ) (./tex/10.tex [88] LaTeX Warning: Reference `speed-up2' on page 258 undefined on input line 295. [258] Chapter 3. Package natbib Warning: Citation `LoggWells2010' on page 89 undefined on input line 11. Package natbib Warning: Citation `www:viper' on page 89 undefined on input line 45. Package natbib Warning: Citation `www:petsc' on page 89 undefined on input line 52. Package natbib Warning: Citation `www:trilinos' on page 89 undefined on input l ine 52. Package natbib Warning: Citation `www:ublas' on page 89 undefined on input line 52. Package natbib Warning: Citation `www:mtl4' on page 89 undefined on input line 52. Package natbib Warning: Citation `www:parmetis' on page 89 undefined on input l ine 53. Package natbib Warning: Citation `www:scotch' on page 89 undefined on input lin e 54. pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/fenics-map.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed [89] [90 <./chapters/logg-2/pdf/fenics-map. pdf>] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) Package natbib Warning: Citation `Beazley2006' on page 91 undefined on input li ne 148. Package natbib Warning: Citation `www:swig' on page 91 undefined on input line 148. Underfull \vbox (badness 3482) has occurred while \output is active [91 <./chap ters/logg-2/pdf/dolfin-uml.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 350--357 \T1/fvm/m/n/10 /tmp/tmpZ4M_ZO2010-11-9-08-24_instant/instant_module_dff94651124 1aab327593a2d71105c5fc/\T1/pplx/m/n/10 (+20) . [259] [260] Package natbib Warning: Citation `LoggWells2010' on page 92 undefined on input line 178. [92] [261] [93] [262] [263] [264] [265] LaTeX Warning: Reference `wilbers:sec:msc' on page 266 undefined on input line 828. [266] [94 [267]] Package natbib Warning: Citation `www:weave' on page 268 undefined on input lin e 940. Package natbib Warning: Citation `EwingBradshawBehnelEtAl2009' on page 268 unde fined on input line 942. Package natbib Warning: Citation `Peterson' on page 268 undefined on input line 944. Package natbib Warning: Citation `WilbersLangtangenOdegaard2009' on page 268 un defined on input line 948. Package natbib Warning: Citation `Ewing2009' on page 268 undefined on input lin e 951. ) (./tex/15.tex [268] Chapter 15. Package natbib Warning: Citation `BauerFrinkKreckel2000' on page 269 undefined on input line 19. Package natbib Warning: Citation `SkavhaugCertik2009' on page 269 undefined on input line 20. LaTeX Warning: Reference `chap:kirby-2' on page 269 undefined on input line 21. LaTeX Warning: Reference `chap:logg-1' on page 269 undefined on input line 22. Package natbib Warning: Citation `AlnaesMardal2009a' on page 269 undefined on i nput line 23. LaTeX Warning: Reference `chap:alnes-1' on page 269 undefined on input line 26. LaTeX Warning: Reference `chap:alnes-2' on page 269 undefined on input line 27. LaTeX Warning: Reference `chap:logg-3' on page 269 undefined on input line 28. LaTeX Warning: Reference `chap:wilbers' on page 269 undefined on input line 29. Package natbib Warning: Citation `BauerFrinkKreckel2000' on page 269 undefined on input line 48. [269] LaTeX Warning: Reference `chap:kirby-6' on page 270 undefined on input line 129 . [270] [95] [271] [96] Underfull \hbox (badness 1412) in paragraph at lines 563--570 \T1/pplx/m/n/10 (+20) abled when DOLFIN is con-fig-ured. The back-end can be se t via the global pa-ram-e-ter [97] LaTeX Warning: Reference `chap:kirby-6' on page 272 undefined on input line 223 . LaTeX Warning: Reference `chap:kirby-1' on page 272 undefined on input line 224 . [272] [98] Package natbib Warning: Citation `Logg2009' on page 99 undefined on input line 733. [99] Package natbib Warning: Citation `AlnaesMardal2009b' on page 273 undefined on i nput line 318. Package natbib Warning: Citation `Fung1993' on page 273 undefined on input line 326. [273] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) [100] [274] [101 <./chapters/logg-2/pdf/mesh -p1-entities.pdf>] LaTeX Warning: Reference `SFCtest' on page 275 undefined on input line 380. Package natbib Warning: Citation `AlnaesMardal2009b' on page 275 undefined on i nput line 403. Package natbib Warning: Citation `OelgaardLoggWells2008' on page 275 undefined on input line 403. Package natbib Warning: Citation `KirbyLogg2008' on page 275 undefined on input line 403. Package natbib Warning: Citation `OelgaardWells2010' on page 275 undefined on i nput line 403. [275] [102] [103] [104] LaTeX Warning: Reference `chap:alnes-1' on page 276 undefined on input line 510 . ) (./tex/16.tex [276 Package natbib Warning: Citation `Rivara1984' on page 105 undefined on input li ne 1207. Package natbib Warning: Citation `Rivara1992' on page 105 undefined on input li ne 1207. [105] ] [106 <./chapters/logg-2/png/refined_ cube.png (PNG copy)>] [277] [107] [278] [108] Chapter 16. Package natbib Warning: Citation `AlnaesLangtangenEtAl2007' on page 279 undefin ed on input line 22. Package natbib Warning: Citation `AlnaesLoggMardalEtAl2009' on page 279 undefin ed on input line 23. LaTeX Warning: Reference `fig:alnes-2:ufc_flowdiagram' on page 279 undefined on input line 49. pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ufc_flowdiagram.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed (./chapters/logg-2/pdf/femsolution.pdf_tex pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/femsolution.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `chap:logg-3' on page 279 undefined on input line 67. Underfull \vbox (badness 10000) has occurred while \output is active [279] LaTeX Warning: Reference `chap:logg-3' on page 280 undefined on input line 89. LaTeX Warning: Reference `eq:varform' on page 280 undefined on input line 103. Underfull \vbox (badness 10000) has occurred while \output is active [280 <./ch apters/alnes-2/pdf/ufc_flowdiagram.pdf>] [109] pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ufc_classes.pdf): PDF inc lusion: found PDF version <1.5>, but at most version <1.4> allowed Package natbib Warning: Citation `www:cgal' on page 110 undefined on input line 1548. [110 <./chapters/logg-2/pdf/femsolution.pdf>] LaTeX Warning: Reference `fig:uml' on page 281 undefined on input line 158. LaTeX Warning: Reference `eq:form_integrals' on page 281 undefined on input lin e 161. [281 <./chapters/alnes-2/pdf/ufc_classes.pdf>] [111] [112] [113] [114] [115] [116] Package natbib Warning: Citation `www:meshbuilder' on page 117 undefined on inp ut line 2020. [117] LaTeX Warning: Reference `chap:logg-3' on page 282 undefined on input line 225. LaTeX Warning: Reference `fig:cellcode' on page 282 undefined on input line 233 . Underfull \vbox (badness 10000) has occurred while \output is active [282] [283] [118] [119] Underfull \vbox (badness 1448) has occurred while \output is active [120] LaTeX Warning: Reference `fig:uml' on page 284 undefined on input line 357. [284] [121] Package natbib Warning: Citation `www:paraview' on page 122 undefined on input line 2438. Package natbib Warning: Citation `www:mayavi' on page 122 undefined on input li ne 2438. [122] [123 <./chapters/logg-2/png/plot_mesh.png (PNG copy)> <./chapters/logg-2/ png/plots.png (PNG copy)>] LaTeX Warning: Reference `chap:wilbers' on page 285 undefined on input line 427 . Underfull \vbox (badness 10000) has occurred while \output is active [285] [286] [124] Underfull \vbox (badness 10000) has occurred while \output is active [287] Underfull \hbox (badness 1184) in paragraph at lines 2529--2532 \T1/pplx/m/n/10 (+20) One can-not read-/write \T1/fvm/m/n/10 Function \T1/pplx/ m/n/10 (+20) and \T1/fvm/m/n/10 FunctionSpace \T1/pplx/m/n/10 (+20) ob-jects si nce the rep-re-sen-ta-tion of a [125] [126] LaTeX Warning: Reference `chap:alnes-1' on page 288 undefined on input line 566 . [288] [289] [127 (./chapters/alnes-2/pdf/interval.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/interval.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed )] Overfull \hbox (7.96405pt too wide) in paragraph at lines 51--730 []|[]| (./chapters/alnes-2/pdf/triangle.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/triangle.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 50--753 []|[]| (./chapters/alnes-2/pdf/quadrilateral.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/quadrilateral.pdf): PDF i nclusion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 51--777 []|[]| [290 <./chapters/alnes-2/pdf/interval.pdf> <./chapters/alnes-2/pdf/triangle.pdf >] (./chapters/alnes-2/pdf/tetrahedron.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/tetrahedron.pdf): PDF inc lusion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 51--802 []|[]| (./chapters/alnes-2/pdf/hexahedron.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/hexahedron.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 53--827 []|[]| Underfull \vbox (badness 7740) has occurred while \output is active [291 <./cha pters/alnes-2/pdf/quadrilateral.pdf> <./chapters/alnes-2/pdf/tetrahedron.pdf>] LaTeX Warning: Reference `fig:numbering_example_triangles' on page 292 undefine d on input line 907. (./chapters/alnes-2/pdf/numbering_example_triangles.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/numbering_example_triangl es.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allo wed ) LaTeX Warning: Reference `fig:numbering_example_quadrilaterals' on page 292 und efined on input line 924. (./chapters/alnes-2/pdf/numbering_example_quadrilaterals.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/numbering_example_quadril aterals.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [292 <./chapte rs/alnes-2/pdf/hexahedron.pdf>] [293 <./chapters/alnes-2/pdf/numbering_example_ triangles.pdf> <./chapters/alnes-2/pdf/numbering_example_quadrilaterals.pdf>] [128] LaTeX Warning: Reference `fig:orderingexample,triangle' on page 294 undefined o n input line 948. LaTeX Warning: Reference `fig:orderingexample,tetrahedron' on page 294 undefine d on input line 963. (./chapters/alnes-2/pdf/ordering_example_triangle.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ordering_example_triangle .pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowe d ) [129] (./chapters/alnes-2/pdf/ordering_example_tetrahedron.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ordering_example_tetrahed ron.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> all owed ) [294 <./chapters/alnes-2/pdf/ordering_example_triangle.pdf> <./chapters/alnes-2 /pdf/ordering_example_tetrahedron.pdf>] LaTeX Warning: Reference `fig:orientation_example_triangles' on page 295 undefi ned on input line 1002. (./chapters/alnes-2/pdf/orientation_example_triangles.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/orientation_example_trian gles.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> al lowed ) [295 <./chapters/alnes-2/pdf/orientation_example_triangles.pdf>] [296] LaTeX Warning: Reference `chap:logg-1' on page 297 undefined on input line 1181 . LaTeX Warning: Reference `chap:alnes-3' on page 297 undefined on input line 118 2. [297]) (./tex/17.tex [298 [130]] Chapter 17. Package natbib Warning: Citation `AlnaesLogg2009' on page 299 undefined on inpu t line 54. LaTeX Warning: Reference `chap:logg-1' on page 299 undefined on input line 66. LaTeX Warning: Reference `chap:alnes-3' on page 299 undefined on input line 66. Package natbib Warning: Citation `Stroustrup1997' on page 299 undefined on inpu t line 69. LaTeX Warning: Reference `chap:alnes-2' on page 299 undefined on input line 70. LaTeX Warning: Reference `chap:logg-2' on page 299 undefined on input line 72. LaTeX Warning: Reference `chap:langtangen' on page 299 undefined on input line 75. LaTeX Warning: Reference `ufl:sec:overview' on page 299 undefined on input line 83. LaTeX Warning: Reference `ufl:sec:formtransformations' on page 299 undefined on input line 83. LaTeX Warning: Reference `ufl:sec:representation' on page 299 undefined on inpu t line 86. LaTeX Warning: Reference `ufl:sec:implementation' on page 299 undefined on inpu t line 86. Package natbib Warning: Citation `AlnaesLogg2009' on page 299 undefined on inpu t line 90. LaTeX Warning: Reference `ufl:sec:overview' on page 299 undefined on input line 96. LaTeX Warning: Reference `ufl:sec:elements' on page 299 undefined on input line 97. LaTeX Warning: Reference `ufl:sec:forms' on page 299 undefined on input line 99 . LaTeX Warning: Reference `ufl:sec:defexpr' on page 299 undefined on input line 101. LaTeX Warning: Reference `ufl:sec:formtransformations' on page 299 undefined on input line 103. LaTeX Warning: Reference `ufl:sec:representation' on page 299 undefined on inpu t line 106. LaTeX Warning: Reference `ufl:sec:ad' on page 299 undefined on input line 109. LaTeX Warning: Reference `ufl:sec:algorithms' on page 299 undefined on input li ne 111. Package natbib Warning: Citation `Rossumothers' on page 299 undefined on input line 112. LaTeX Warning: Reference `ufl:sec:implementation' on page 299 undefined on inpu t line 113. LaTeX Warning: Reference `ufl:sec:future' on page 299 undefined on input line 1 14. Package natbib Warning: Citation `Long2003' on page 299 undefined on input line 122. Package natbib Warning: Citation `Long2004a' on page 299 undefined on input lin e 122. Package natbib Warning: Citation `Long2004' on page 299 undefined on input line 122. Package natbib Warning: Citation `Prudhomme2006a' on page 299 undefined on inpu t line 125. Package natbib Warning: Citation `Prudhomme2006' on page 299 undefined on input line 125. Package natbib Warning: Citation `Cimrman2008' on page 299 undefined on input l ine 127. Package natbib Warning: Citation `DularGeuzaine2005' on page 299 undefined on i nput line 129. Package natbib Warning: Citation `Korelc1997' on page 299 undefined on input li ne 131. Package natbib Warning: Citation `Korelc2002' on page 299 undefined on input li ne 131. Underfull \vbox (badness 6493) has occurred while \output is active [299] Package natbib Warning: Citation `BauerFrinkKreckel2000' on page 300 undefined on input line 139. Package natbib Warning: Citation `SkavhaugCertik2009' on page 300 undefined on input line 140. Package natbib Warning: Citation `Certikothers2009' on page 300 undefined on in put line 140. Package natbib Warning: Citation `AlnaesMardal2009b' on page 300 undefined on i nput line 176. Package natbib Warning: Citation `OelgaardWells2010' on page 300 undefined on i nput line 176. LaTeX Warning: Reference `chap:narayanan' on page 300 undefined on input line 1 96. [300] LaTeX Warning: Reference `chap:kirby-7' on page 301 undefined on input line 223 . LaTeX Warning: Reference `ufl:eq:ppeqzero' on page 301 undefined on input line 225. LaTeX Warning: Reference `ufl:eq:elasticitynewton' on page 301 undefined on inp ut line 243. LaTeX Warning: Reference `ufl:fig:hypcode' on page 301 undefined on input line 250. LaTeX Warning: Reference `ufl:eq:hypdef' on page 301 undefined on input line 25 1. LaTeX Warning: Reference `ufl:eq:hypdefL' on page 301 undefined on input line 2 51. LaTeX Warning: Reference `alnes-1:eq:hypdefa' on page 301 undefined on input li ne 251. Underfull \vbox (badness 10000) has occurred while \output is active [301] [131] Overfull \hbox (1.6556pt too wide) in paragraph at lines 3058--3067 [][] [132 <./chapters/logg-2/png/coloured.png (PNG copy)> <./chapters/logg-2/png/par tition.png (PNG copy)>] Package natbib Warning: Citation `www:pastix' on page 133 undefined on input li ne 3121. Package natbib Warning: Citation `www:parmetis' on page 133 undefined on input line 3157. Package natbib Warning: Citation `www:scotch' on page 133 undefined on input li ne 3157. [133] Package natbib Warning: Citation `Beazley2006' on page 134 undefined on input l ine 3187. Package natbib Warning: Citation `www:swig' on page 134 undefined on input line 3187. [134] [302] Underfull \hbox (badness 1533) in paragraph at lines 3274--3279 [] []\T1/pplx/m/it/10 Con-struct-ing ar-gu-ments (trial and test func-tions).[] \T1/pplx/m/n/10 (+20) The \T1/fvm/m/n/10 ufl.Argument \T1/pplx/m/n/10 (+20) cl ass (the base class of [135] [303] [136] LaTeX Warning: Reference `ufl:sec:ad' on page 304 undefined on input line 435. [304] Underfull \vbox (badness 1377) has occurred while \output is active [137] Underfull \vbox (badness 1067) has occurred while \output is active [138] LaTeX Warning: Reference `ufl:eq:form_integrals' on page 305 undefined on input line 489. LaTeX Warning: Reference `ufl:sec:indexnotation' on page 305 undefined on input line 492. LaTeX Warning: Reference `ufl:sec:conditionals' on page 305 undefined on input line 492. LaTeX Warning: Reference `ufl:sec:arguments' on page 305 undefined on input lin e 495. LaTeX Warning: Reference `ufl:sec:indexnotation' on page 305 undefined on input line 501. LaTeX Warning: Reference `ufl:eq:Aij' on page 305 undefined on input line 534. [305] Package natbib Warning: Citation `JonesOliphantPetersonEtAl2009' on page 139 un defined on input line 3592. Package natbib Warning: Citation `BellOlsonSchroder2009' on page 139 undefined on input line 3603. [139]) (./tex/17.tex [140] Chapter 4. Package natbib Warning: Citation `AlnaesLogg2009' on page 141 undefined on inpu t line 54. Package natbib Warning: Citation `Stroustrup1997' on page 141 undefined on inpu t line 69. Package natbib Warning: Citation `AlnaesLogg2009' on page 141 undefined on inpu t line 90. Package natbib Warning: Citation `Rossumothers' on page 141 undefined on input line 112. Package natbib Warning: Citation `Long2003' on page 141 undefined on input line 122. Package natbib Warning: Citation `Long2004a' on page 141 undefined on input lin e 122. Package natbib Warning: Citation `Long2004' on page 141 undefined on input line 122. Package natbib Warning: Citation `Prudhomme2006a' on page 141 undefined on inpu t line 125. Package natbib Warning: Citation `Prudhomme2006' on page 141 undefined on input line 125. Package natbib Warning: Citation `Cimrman2008' on page 141 undefined on input l ine 127. Package natbib Warning: Citation `DularGeuzaine2005' on page 141 undefined on i nput line 129. Package natbib Warning: Citation `Korelc1997' on page 141 undefined on input li ne 131. Package natbib Warning: Citation `Korelc2002' on page 141 undefined on input li ne 131. Underfull \vbox (badness 6493) has occurred while \output is active [141] Package natbib Warning: Citation `BauerFrinkKreckel2000' on page 142 undefined on input line 139. Package natbib Warning: Citation `SkavhaugCertik2009' on page 142 undefined on input line 140. Package natbib Warning: Citation `Certikothers2009' on page 142 undefined on in put line 140. Package natbib Warning: Citation `AlnaesMardal2009b' on page 142 undefined on i nput line 176. Package natbib Warning: Citation `OelgaardWells2010' on page 142 undefined on i nput line 176. [142] Underfull \vbox (badness 10000) has occurred while \output is active [143] [306 [144]] [145] [146] [147] [148] LaTeX Warning: Reference `ufl:sec:representation' on page 307 undefined on inpu t line 700. [307] [149] [150] LaTeX Warning: Reference `ufl:sec:indexnotation' on page 308 undefined on input line 752. LaTeX Warning: Reference `ufl:sec:derivative' on page 308 undefined on input li ne 810. LaTeX Warning: Reference `ufl:sec:ad' on page 308 undefined on input line 814. [308] Underfull \vbox (badness 10000) has occurred while \output is active [151] Underfull \vbox (badness 10000) has occurred while \output is active [309] [152] [153] LaTeX Warning: Reference `ufl:sec:ad' on page 310 undefined on input line 925. [310] [154] [155] [311] [156] (/usr/share/texmf-texlive/tex/latex/microtype/mt-euf.cfg) [157] (./chapters/alnes-1/pdf/expr.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/expr.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [158 <./chapters/alnes-1/pdf/expr.pdf>] (./chapters/alnes-1/pdf/stiffness.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/stiffness.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \hbox (badness 1668) in paragraph at lines 1415--1415 []\T1/pplx/m/n/9 (+20) Figure 4.3: |Ex-pres-sion tree for [159] LaTeX Warning: Reference `ufl:eq:harmonic' on page 312 undefined on input line 1074. [312] [160 <./chapters/alnes-1/pdf/stiffness.pdf>] [161] [162] [313] Package natbib Warning: Citation `Griewank1989' on page 163 undefined on input line 1686. Package natbib Warning: Citation `Griewank1989' on page 163 undefined on input line 1696. Package natbib Warning: Citation `BischofCarleCorlissEtAl1992' on page 163 unde fined on input line 1707. Package natbib Warning: Citation `BischofHovlandNorris2002' on page 163 undefin ed on input line 1707. Package natbib Warning: Citation `GieringKaminski1998' on page 163 undefined on input line 1707. [163] [164] Package natbib Warning: Citation `Karczmarczuk2001' on page 165 undefined on in put line 1836. Package natbib Warning: Citation `PearlmutterSiskind2007' on page 165 undefined on input line 1836. Package natbib Warning: Citation `SiskindPearlmutter2008' on page 165 undefined on input line 1836. [165] LaTeX Warning: Reference `ufl:eq:pde' on page 314 undefined on input line 1198. LaTeX Warning: Reference `ufl:eq:pde' on page 314 undefined on input line 1205. LaTeX Warning: Reference `ufl:eq:sL' on page 314 undefined on input line 1218. [314] [166] [167] LaTeX Warning: Reference `ufl:alg:program' on page 315 undefined on input line 1271. (/usr/share/texmf-texlive/tex/latex/microtype/mt-euf.cfg) [315] (./chapters/alnes-1/pdf/expr.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/expr.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) Package natbib Warning: Citation `GammaHelmJohnsonEtAl1995' on page 168 undefin ed on input line 2022. [168] LaTeX Warning: Reference `ufl:alg:program' on page 316 undefined on input line 1333. LaTeX Warning: Reference `ufl:fig:expr' on page 316 undefined on input line 134 2. [316 <./chapters/alnes-1/pdf/expr.pdf>] [169] [170] LaTeX Warning: Reference `ufl:sec:indexnotation' on page 317 undefined on input line 1368. (./chapters/alnes-1/pdf/stiffness.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/stiffness.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `ufl:fig:stiffness' on page 317 undefined on input lin e 1430. [317] [171] Underfull \vbox (badness 10000) has occurred while \output is active [172] LaTeX Warning: Reference `ufl:eq:G' on page 318 undefined on input line 1454. LaTeX Warning: Reference `ufl:eq:E' on page 318 undefined on input line 1454. [318 <./chapters/alnes-1/pdf/stiffness.pdf>] [173] LaTeX Warning: Reference `ufl:sec:transformer' on page 319 undefined on input l ine 1564. LaTeX Warning: Reference `ufl:alg:program' on page 319 undefined on input line 1574. [319] [174] [320] Package natbib Warning: Citation `Rossumothers' on page 175 undefined on input line 2515. Package natbib Warning: Citation `Kuchling2007' on page 175 undefined on input line 2525. [175] Package natbib Warning: Citation `ForthTadjouddinePryceEtAl2004' on page 176 un defined on input line 2574. Package natbib Warning: Citation `Tadjouddine2008' on page 176 undefined on inp ut line 2574. ) Package natbib Warning: Citation `Griewank1989' on page 321 undefined on input line 1686. Package natbib Warning: Citation `Griewank1989' on page 321 undefined on input line 1696. Package natbib Warning: Citation `BischofCarleCorlissEtAl1992' on page 321 unde fined on input line 1707. Package natbib Warning: Citation `BischofHovlandNorris2002' on page 321 undefin ed on input line 1707. Package natbib Warning: Citation `GieringKaminski1998' on page 321 undefined on input line 1707. LaTeX Warning: Reference `ufl:sec:forwardad' on page 321 undefined on input lin e 1710. LaTeX Warning: Reference `ufl:alg:program' on page 321 undefined on input line 1717. LaTeX Warning: Reference `ufl:alg:forwardad' on page 321 undefined on input lin e 1723. LaTeX Warning: Reference `ufl:alg:program' on page 321 undefined on input line 1726. LaTeX Warning: Reference `ufl:alg:program' on page 321 undefined on input line 1726. LaTeX Warning: Reference `ufl:alg:forwardad' on page 321 undefined on input lin e 1746. LaTeX Warning: Reference `ufl:alg:forwardadprogram' on page 321 undefined on in put line 1747. LaTeX Warning: Reference `ufl:alg:program' on page 321 undefined on input line 1748. [321 [176]] LaTeX Warning: Reference `ufl:alg:program' on page 322 undefined on input line 1763. LaTeX Warning: Reference `ufl:alg:forwardadprogram' on page 322 undefined on in put line 1764. LaTeX Warning: Reference `ufl:alg:program' on page 322 undefined on input line 1765. LaTeX Warning: Reference `ufl:alg:forwardadprogram' on page 322 undefined on in put line 1766. [322 Chapter 5. [177]] [178] (./manual.bbl [179] LaTeX Warning: Reference `ufl:alg:forwardad' on page 323 undefined on input lin e 1826. Package natbib Warning: Citation `Karczmarczuk2001' on page 323 undefined on in put line 1836. Package natbib Warning: Citation `PearlmutterSiskind2007' on page 323 undefined on input line 1836. Package natbib Warning: Citation `SiskindPearlmutter2008' on page 323 undefined on input line 1836. LaTeX Warning: Reference `ufl:eq:nested' on page 323 undefined on input line 18 39. LaTeX Warning: Reference `ufl:alg:forwardadprogram' on page 323 undefined on in put line 1855. LaTeX Warning: Reference `ufl:alg:forwardad' on page 323 undefined on input lin e 1866. LaTeX Warning: Reference `ufl:alg:forwardadprogram' on page 323 undefined on in put line 1867. [323] [180] [181] LaTeX Warning: Reference `ufl:fig:applyad' on page 324 undefined on input line 1876. [324] [182] [183] [325] [184]) (./manual.ind Package natbib Warning: Citation `GammaHelmJohnsonEtAl1995' on page 326 undefin ed on input line 2022. [326 [185]] [186 [327]] LaTeX Warning: Reference `ufl:eq:a_before_expand' on page 328 undefined on inpu t line 2178. LaTeX Warning: Reference `ufl:eq:a_after_expand_compounds' on page 328 undefine d on input line 2190. LaTeX Warning: Reference `ufl:eq:a_after_expand_derivatives' on page 328 undefi ned on input line 2204. LaTeX Warning: Reference `ufl:eq:a_before_expand' on page 328 undefined on inpu t line 2212. [328] [187] [188] [329] Overfull \hbox (7.21391pt too wide) in paragraph at lines 315--317 []\T1/pplx/m/n/10 (-20) LBB con-di-tions, \T1/pplx/m/it/10 see \T1/pplx/m/n/10 (-20) Ladyzhenskaya--BabuČka--Brezzi [189] [190]) Package natbib Warning: There were undefined citations. Package caption Warning: Unused \captionsetup[subalgorithm] on input line 8. (./manual.aux Underfull \vbox (badness 10000) has occurred while \output is active [330] Package natbib Warning: Citation(s) may have changed. (natbib) Rerun to get citations correct. ) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (\end occurred inside a group at level 1) ### simple group (level 1) entered at line 58 ({) ### bottom level (see the transcript file for additional information)pdfTeX warning (dest): name {Hfootnote.11} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.10} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.9} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.8} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.7} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.6} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.5} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.4} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.3} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.2} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.1} has been referenced but does not exist , replaced by a fixed one {/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}]] Output written on manual.pdf (196 pages, 5193384 bytes). Transcript written on manual.log. Package natbib Warning: Citation `Rossumothers' on page 333 undefined on input line 2515. Package natbib Warning: Citation `Kuchling2007' on page 333 undefined on input line 2525. [333] Package natbib Warning: Citation `ForthTadjouddinePryceEtAl2004' on page 334 un defined on input line 2574. Package natbib Warning: Citation `Tadjouddine2008' on page 334 undefined on inp ut line 2574. ) (./tex/18.tex [334] Chapter 18. Package natbib Warning: Citation `HoffmanJanssonStockli2011' on page 335 undefi ned on input line 28. Underfull \hbox (badness 1442) in paragraph at lines 89--89 \T1/pplx/m/n/9 (+20) around a cylin-der with par-al-lel Package natbib Warning: Citation `Gurtin1981' on page 335 undefined on input li ne 98. [335] [336 <./chapters/hoffman-2/pdf/cube556.pdf> <./chapters/hoffman-2/pdf/com pressible3D.pdf> <./chapters/hoffman-2/pdf/Hoffman_fig3d.pdf>] LaTeX Warning: Reference `sec:hoffman-2:ale' on page 337 undefined on input lin e 115. [337] Package natbib Warning: Citation `HoffmanJanssonStockli2011' on page 338 undefi ned on input line 167. Package natbib Warning: Citation `Hoffman2005' on page 338 undefined on input l ine 179. Package natbib Warning: Citation `HoffmanJohnson2006b' on page 338 undefined on input line 179. Package natbib Warning: Citation `Hoffman2006' on page 338 undefined on input l ine 179. Package natbib Warning: Citation `HoffmanJohnson2007' on page 338 undefined on input line 179. Package natbib Warning: Citation `Hoffman2009' on page 338 undefined on input l ine 179. Package natbib Warning: Citation `HoffmanJansson2009' on page 338 undefined on input line 179. Package natbib Warning: Citation `VilelaJanssonEtAl2010' on page 338 undefined on input line 179. Package natbib Warning: Citation `ErikssonEstepHansboEtAl1996' on page 338 unde fined on input line 188. LaTeX Warning: Reference `eq:TotalModel' on page 338 undefined on input line 18 9. [338] Package natbib Warning: Citation `ErikssonEstepHansboEtAl1996' on page 339 unde fined on input line 231. Package natbib Warning: Citation `Comp`ereRemacleJanssonEtAl2009' on page 339 u ndefined on input line 274. Package natbib Warning: Citation `ErikssonEstepHansboEtAl1996' on page 339 unde fined on input line 281. Package natbib Warning: Citation `HoffmanJohnson2007' on page 339 undefined on input line 281. [339]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. entering extended mode (./manual.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded. (./fenicsbook.cls Document Class: fenicsbook (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/geometry.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/etc/texmf/tex/xelatex/xetexconfig/geometry.cfg)) (/usr/share/texmf-texlive/tex/latex/oberdiek/bookmark.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdfescape.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty LaTeX Warning: Reference `code:UCSolver' on page 340 undefined on input line 30 7. LaTeX Warning: Reference `code:FFC_UC' on page 340 undefined on input line 310. LaTeX Warning: Reference `fig:hoffman-2:sp' on page 340 undefined on input line 373. Package natbib Warning: Citation `JanssonHoffmanJansson2010' on page 340 undefi ned on input line 377. Package natbib Warning: Citation `Jansson2011' on page 340 undefined on input l ine 377. LaTeX Warning: Reference `fig:parcyl3D' on page 340 undefined on input line 379 . (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty) (/etc/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty)) (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) (/usr/share/texmf-texlive/tex/latex/oberdiek/auxhook.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/bkm-pdftex.def)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/emptypage.sty) (/usr/share/texmf-texlive/tex/latex/psnfss/mathpazo.sty Package natbib Warning: Citation `Nazarov2009' on page 340 undefined on input l ine 397. LaTeX Warning: Reference `fig:compr3D' on page 340 undefined on input line 398. LaTeX Warning: Float too large for page by 32.91196pt on input line 472. [340]) (/usr/share/texmf-texlive/tex/latex/psnfss/helvet.sty [341) (/usr/share/texmf-texlive/tex/latex/bera/beramono.sty) (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty] (/usr/share/texmf-texlive/tex/latex/base/t1enc.def [342 <./chapters/hoffman-2/pdf/speedup_solve.pdf> <./chapters/hoffm an-2/pdf/speedup_unrivara.pdf>] [343)) (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty] (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def)) (/usr/share/texmf-texlive/tex/latex/textcase/textcase.sty) (/usr/share/texmf-texlive/tex/latex/titlesec/titlesec.sty) (/usr/share/texmf-texlive/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texmf-texlive/tex/latex/tools/multicol.sty) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/natbib/natbib.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty (/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf-texlive/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf-texlive/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amscd.sty) (/usr/share/texmf-texlive/tex/latex/stmaryrd/stmaryrd.sty) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/codehighlight.sty (/usr/src/RPM/BUILD/fenics-book-20130430/packages/mylistings.sty LaTeX Warning: Reference `code:TimeDependentPDE' on page 344 undefined on input line 515. LaTeX Warning: Reference `code:time-stepping' on page 344 undefined on input li ne 559. Package natbib Warning: Citation `Jansson2009' on page 344 undefined on input l ine 618. Package natbib Warning: Citation `HoffmanJanssonStockli2011' on page 344 undefi ned on input line 618. Underfull \vbox (badness 2600) has occurred while \output is active [344] [345] (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) (/usr/share/texmf-texlive/tex/latex/listings/listings.cfg)) (/usr/share/texmf/tex/latex/xcolor/xcolor.sty (/etc/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))) (/usr/share/texmf-texlive/tex/latex/ltxmisc/import.sty) (/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty (/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty (/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) (/etc/texmf/tex/latex/config/graphics.cfg))) (/usr/share/texmf-texlive/tex/latex/subfig/subfig.sty (/usr/share/texmf-texlive/tex/latex/caption/caption3.sty)) (/usr/share/texmf-texlive/tex/latex/booktabs/booktabs.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty Package natbib Warning: Citation `Comp`ereRemacleJanssonEtAl2009' on page 346 u ndefined on input line 647. LaTeX Warning: Reference `code:ErrorEstimate' on page 346 undefined on input li ne 653. LaTeX Warning: Reference `code:SpaceTimeFunction' on page 346 undefined on inpu t line 702. [346)] (/usr/share/texmf-texlive/tex/latex/tools/array.sty [347) (/usr/share/texmf-texlive/tex/latex/microtype/microtype.sty] (/usr/share/texmf-texlive/tex/latex/microtype/microtype.cfg Package natbib Warning: Citation `Nazarov2011' on page 348 undefined on input l ine 778. )) (/usr/share/texmf-texlive/tex/latex/tools/xspace.sty) (/usr/share/texmf-texlive/tex/latex/setspace/setspace.sty Package: `setspace' 6.7 <2000/12/01> ) (/usr/share/texmf-texlive/tex/latex/floatrow/floatrow.sty) (/usr/share/texmf-texlive/tex/latex/caption/caption.sty (/usr/share/texmf-texlive/tex/latex/caption/ltcaption.sty)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithm.sty Document Style `algorithm' - floating environment (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithmicx.sty Document Style algorithmicx 1.2 - a greatly improved `algorithmic' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algpseudocode.sty Overfull \hbox (1.6596pt too wide) in paragraph at lines 807--818 [][] LaTeX Warning: Reference `code:FFC_ElasticSmoother' on page 348 undefined on in put line 860. [348] [349 <./chapters/hoffman-2/pdf/force_smooth01.pdf> <./chapters/hoffman-2/ pdf/force_hybrid01.pdf Document Style - pseudocode environments for use with the `algorithmicx' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/todonotes.sty> <./chapters/hoffman-2/pdf/force_smooth02.pdf> <./chapte rs/hoffman-2/pdf/force_hybrid02.pdf (/usr/share/texmf-texlive/tex/latex/xkeyval/xkeyval.sty (/usr/share/texmf-texlive/tex/generic/xkeyval/xkeyval.tex> <./chapters/hoffman-2/pdf/force_smooth03.p df> <./chapters/hoffman-2/pdf/force_hybrid03.pdf)>]) (/usr/share/texmf/tex/latex/pgf/frontendlayer/tikz.sty (/usr/share/texmf/tex/latex/pgf/basiclayer/pgf.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfrcs.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common-lists.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-latex.def (/usr/share/texmf-texlive/tex/latex/ms/everyshi.sty)) (/usr/share/texmf/tex/generic/pgf/utilities/pgfrcs.code.tex)) (/usr/share/texmf/tex/latex/pgf/basiclayer/pgfcore.sty (/usr/share/texmf/tex/latex/pgf/systemlayer/pgfsys.sty (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys.code.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeysfiltered.code.tex)) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgf.cfg) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-pdftex.def (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-common-pdf.def LaTeX Warning: Reference `code:ElasticSmoother' on page 350 undefined on input line 889. LaTeX Warning: Reference `fig:flag_robustness' on page 350 undefined on input l ine 893. Package natbib Warning: Citation `Rivara1992' on page 350 undefined on input li ne 909. Package natbib Warning: Citation `Rivara1992' on page 350 undefined on input li ne 936. ))) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsyssoftpath.code.tex) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsysprotocol.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcore.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathcalc.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathutil.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathparser.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.basic.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.trigonometric.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.random.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.comparison.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.base.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.round.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.misc.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.integerarithmetics.code .tex))) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfloat.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepoints.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathconstruct.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathusage.code.tex LaTeX Warning: Reference `fig:op:eswap' on page 350 undefined on input line 956 . Package natbib Warning: Citation `BangerthHartmannKanschat2007' on page 350 und efined on input line 967. Package natbib Warning: Citation `COMSOL2009' on page 350 undefined on input li ne 967. LaTeX Warning: Reference `code:MeshAdaptInterface' on page 350 undefined on inp ut line 974. [350) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorescopes.code.tex]) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoregraphicstate.code.tex) [351 <./chapters/hoffman-2/pdf/swap.pdf> <./chapters/hoffman-2/pdf/swap_c onfig1.pdf>] (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransformations.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorequick.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreobjects.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathprocessing.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorearrows.code.tex Package natbib Warning: Citation `HronTurek2005' on page 352 undefined on input line 1044. Package natbib Warning: Citation `HoffmanJanssonStockli2011' on page 352 undefi ned on input line 1046. LaTeX Warning: Reference `chap:hoffman-1' on page 352 undefined on input line 1 047. LaTeX Warning: Reference `fig:fsi2D_plot2' on page 352 undefined on input line 1048. LaTeX Warning: Reference `code:UseCasePart1' on page 352 undefined on input lin e 1067. LaTeX Warning: Reference `code:UseCasePart4' on page 352 undefined on input lin e 1067. ) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreshade.code.tex ) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreimage.code.tex (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreexternal.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorelayers.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransparency.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepatterns.code.tex LaTeX Warning: Reference `chap:hoffman-1' on page 352 undefined on input line 1 084. LaTeX Warning: Reference `fig:cube2' on page 352 undefined on input line 1085. [352))) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleshapes.code.tex] [353 <./chapters/hoffman-2/png/fsi3_vel_050.png (PNG copy)> <./chapters/h offman-2/png/fsi3_theta_050.png (PNG copy)> <./chapters/hoffman-2/png/fsi3_vel_ 250.png (PNG copy)> <./chapters/hoffman-2/png/fsi3_theta_250.png (PNG copy)) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleplot.code.tex>]) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-0-65.sty) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-1-18.sty)) (/usr/share/texmf/tex/latex/pgf/utilities/pgffor.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfkeys.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex)) (/usr/share/texmf/tex/latex/pgf/math/pgfmath.sty (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgffor.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex))) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/tikz.code.tex (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryplothandlers.code.tex) [354 <./chapters/hoffman-1/png/fig2b.png (PNG copy)> <./chapters/hoffman-1/png/ fig2c.png (PNG copy)>] (/usr/share/texmf/tex/generic/pgf/modules/pgfmodulematrix.code.tex) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibrarytopat hs.code.tex))) (/usr/share/texmf-texlive/tex/latex/tools/calc.sty) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryshado ws.code.tex (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryfadin gs.code.tex (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryfadings.code.tex))))) Writing index file manual.idx (./manual.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/t1pplx.fd) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (/usr/share/texmf-texlive/tex/latex/microtype/mt-ppl.cfg) (/usr/share/texmf-texlive/tex/latex/floatrow/fr-subfig.sty) LaTeX Warning: Float too large for page by 4.412pt on input line 1281. LaTeX Warning: Reference `chap:hoffman-1' on page 355 undefined on input line 1 370. ) (/usr/share/texmf-texlive/tex/latex/floatrow/fr-longtable.sty (./tex/19.tex) ABD: EveryShipout initializing macros (./tex/FMmanual.tex [355] [356] [357] [358] [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdft ex.map} <./png/fenics_logo_text.png Chapter 19. Overfull \hbox (1.19252pt too wide) in paragraph at lines 5--5 |[]\T1/pplx/m/it/20.74 Lessons learned in mixed lan-guage pro-gram-ming| Package natbib Warning: Citation `www:petsc' on page 359 undefined on input lin e 16. Package natbib Warning: Citation `www:hypre' on page 359 undefined on input lin e 16. Package natbib Warning: Citation `www:trilinos' on page 359 undefined on input line 16. Package natbib Warning: Citation `www:vtk' on page 359 undefined on input line 17. Package natbib Warning: Citation `www:vmtk' on page 359 undefined on input line 17. Package natbib Warning: Citation `BauerFrinkKreckel2000' on page 359 undefined on input line 17. Package natbib Warning: Citation `CertikSeoanePetersonEtAl2009' on page 359 und efined on input line 20. Package natbib Warning: Citation `JonesOliphantPetersonEtAl2009' on page 359 un defined on input line 21. Package natbib Warning: Citation `Langtangen2008' on page 359 undefined on inpu t line 27. Package natbib Warning: Citation `www:swig' on page 359 undefined on input line 30. Package natbib Warning: Citation `Langtangen2003b' on page 359 undefined on inp ut line 30. Package natbib Warning: Citation `SalaSpotzHeroux2008' on page 359 undefined on input line 31. Package natbib Warning: Citation `www:python-capi' on page 359 undefined on inp ut line 42. Package natbib Warning: Citation `Peterson' on page 359 undefined on input line 45. Package natbib Warning: Citation `SIP' on page 359 undefined on input line 45. Package natbib Warning: Citation `Siloon' on page 359 undefined on input line 4 5. Package natbib Warning: Citation `www:swig' on page 359 undefined on input line 45. Underfull \vbox (badness 1092) has occurred while \output is active [359] (./chapters/mardal-2/code/Array.h) (./chapters/mardal-2/code/Array_1.i)>] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pplx.fd) [2] (./manual.toc (/usr/share/texmf-texlive/tex/latex/psnfss/ot1pplx.fd) Package natbib Warning: Citation `www:distutils' on page 360 undefined on input line 74. (./chapters/mardal-2/code/setup.py (/usr/share/texmf-texlive/tex/latex/psnfss/omlzplm.fd) [360 (/usr/share/texmf-texlive/tex/latex/psnfss/omszplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omxzplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/ot1zplm.fd)]) (/usr/share/texmf-texlive/tex/latex/microtype/mt-msa.cfg) (/usr/share/texmf-texlive/tex/latex/microtype/mt-msb.cfg) (/usr/share/texmf-texlive/tex/latex/stmaryrd/Ustmry.fd)) [3] [4] (/usr/share/texmf-texlive/tex/latex/bera/t1fvm.fd) [361]) [5 (./chapters/mardal-2/code/segfault_test.py] [6] (./tex/1.tex) Chapter 1. [1] [362] [2] [363] [3] [4] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty [364]) [365] [5 [366]] [367] [368] [6] [369] [370] [371] [7] [372] [373] LaTeX Warning: Reference `chap:wilbers' on page 374 undefined on input line 943 . [374] [8] Package natbib Warning: Citation `www:gdb' on page 375 undefined on input line 1006. [375] Package natbib Warning: Citation `www:ddd' on page 376 undefined on input line 1017. Package natbib Warning: Citation `www:valgrind' on page 376 undefined on input line 1036. ) (./tex/Part3.tex [376] [377] [378]) (./tex/20.tex Chapter 20. LaTeX Warning: Reference `eqn:terrel:StrongStokes' on page 379 undefined on inp ut line 42. LaTeX Warning: Reference `eqn:terrel:StrongStokes_icomp' on page 379 undefined on input line 43. LaTeX Warning: Reference `eqn:stokes_momentum' on page 379 undefined on input l ine 72. LaTeX Warning: Reference `eqn:stokes_continuity' on page 379 undefined on input line 72. Package natbib Warning: Citation `BrezziFortin1991' on page 379 undefined on in put line 74. Package natbib Warning: Citation `BrennerScott2008' on page 379 undefined on in put line 75. [379] [9 <./chapters/langtangen/pdf/ex1_u. pdf>] Package natbib Warning: Citation `BrezziFortin1991' on page 380 undefined on in put line 87. Package natbib Warning: Citation `EngelmanSaniGreshoBercovier1982' on page 380 undefined on input line 92. Package natbib Warning: Citation `HughesFrancaBalestra1986' on page 380 undefin ed on input line 102. LaTeX Warning: Reference `code:terrel:var:mixed' on page 380 undefined on input line 120. LaTeX Warning: Reference `code:terrel:var:mixed' on page 380 undefined on input line 126. Package natbib Warning: Citation `TaylorHood1973' on page 380 undefined on inpu t line 150. Package natbib Warning: Citation `Boffi1997' on page 380 undefined on input lin e 150. LaTeX Warning: Reference `fig:terrel:THElements' on page 380 undefined on input line 153. LaTeX Warning: Reference `code:terrel:var:mixed' on page 380 undefined on input line 155. [10 <./chapters/langtangen/png/ex1_mesh.png (PNG copy)>] LaTeX Warning: Reference `sub@fig:terrel:THElements_P3' on page 380 undefined o n input line 169. LaTeX Warning: Reference `sub@fig:terrel:THElements_P2' on page 380 undefined o n input line 169. LaTeX Warning: Reference `sub@fig:terrel:THElements_P3' on page 380 undefined o n input line 169. LaTeX Warning: Reference `sub@fig:terrel:THElements_P2' on page 380 undefined o n input line 169. Package natbib Warning: Citation `CrouzeixRaviart1973' on page 380 undefined on input line 173. LaTeX Warning: Reference `fig:terrel:CRElements' on page 380 undefined on input line 179. LaTeX Warning: Reference `code:terrel:var:mixed' on page 380 undefined on input line 180. [380] [381 <./chapters/kirby-6/pdf/P3.pdf>] Package natbib Warning: Citation `ArnoldBrezziFortin1984' on page 382 undefined on input line 192. LaTeX Warning: Reference `fig:terrel:MINIElement' on page 382 undefined on inpu t line 194. LaTeX Warning: Reference `code:terrel:MINI' on page 382 undefined on input line 199. pdfTeX warning: pdflatex (file ./chapters/terrel/pdf/MINI.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed [11] Package natbib Warning: Citation `BrezziFortin1991' on page 382 undefined on in put line 226. Package natbib Warning: Citation `MadayPateraRonquist1992' on page 382 undefine d on input line 228. LaTeX Warning: Reference `code:terrel:var:mixed' on page 382 undefined on input line 229. [382 <./chapters/kirby-6/pdf/CR1.pdf> <./chapters/terrel/pdf/MINI.pdf>] [12] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) LaTeX Warning: Reference `tab:terrel:element_vars' on page 383 undefined on inp ut line 258. LaTeX Warning: Reference `code:terrel:var:mixed' on page 383 undefined on input line 259. Package natbib Warning: Citation `DoneaHuerta2003' on page 383 undefined on inp ut line 271. LaTeX Warning: Reference `code:terrel:var:stab' on page 383 undefined on input line 289. LaTeX Warning: Reference `code:terrel:var:mixed' on page 383 undefined on input line 291. LaTeX Warning: Reference `tab:terrel:element_vars' on page 383 undefined on inp ut line 291. LaTeX Warning: Reference `code:terrel:var:mixed' on page 383 undefined on input line 307. LaTeX Warning: Reference `code:terrel:var:mixed' on page 383 undefined on input line 307. Package natbib Warning: Citation `ScottVogelius1985' on page 383 undefined on i nput line 316. [383] [13] LaTeX Warning: Reference `eqn:terrel:IPStokes' on page 384 undefined on input l ine 337. LaTeX Warning: Reference `eqn:terrel:IPStokes_update' on page 384 undefined on input line 338. LaTeX Warning: Reference `code:terrel:var:ip' on page 384 undefined on input li ne 346. LaTeX Warning: Reference `chap:mardal-4' on page 384 undefined on input line 39 4. Package natbib Warning: Citation `ElmanSilvesterWathen2005' on page 384 undefin ed on input line 395. LaTeX Warning: Reference `tab:terrel:DOFs' on page 384 undefined on input line 397. [384] LaTeX Warning: Float too large for page by 3.70213pt on input line 417. LaTeX Warning: Reference `fig:terrel:mesh' on page 385 undefined on input line 470. Package natbib Warning: Citation `NagtegaalDeJong1974' on page 385 undefined on input line 473. Package natbib Warning: Citation `Malkus2000' on page 385 undefined on input li ne 474. Package natbib Warning: Citation `BrezziFortin1991' on page 385 undefined on in put line 476. Package natbib Warning: Citation `TerrelScott2008' on page 385 undefined on inp ut line 480. Underfull \vbox (badness 6236) has occurred while \output is active [385] [386 <./chapters/terrel/pdf/mesh.pdf> <./chapters/terrel/pdf/vel_test.pdf> <./c hapters/terrel/pdf/vel_lid.pdf>] [14] [15] LaTeX Warning: Reference `fig:terrel:vel_test' on page 387 undefined on input l ine 505. LaTeX Warning: Reference `fig:terrel:vel_lid' on page 387 undefined on input li ne 506. LaTeX Warning: Reference `code:terrel:domain:test' on page 387 undefined on inp ut line 508. LaTeX Warning: Reference `code:terrel:domain:lid' on page 387 undefined on inpu t line 508. LaTeX Warning: Reference `code:terrel:error' on page 387 undefined on input lin e 596. LaTeX Warning: Reference `tab:terrel:vel_error' on page 387 undefined on input line 631. [387] [388] LaTeX Warning: Reference `fig:terrel:4th_Order:vel' on page 389 undefined on in put line 674. LaTeX Warning: Reference `fig:terrel:4th_Order:press' on page 389 undefined on input line 677. LaTeX Warning: Reference `fig:terrel:4th_Order:div' on page 389 undefined on in put line 681. LaTeX Warning: Reference `fig:terrel:4th_Order:run' on page 389 undefined on in put line 707. LaTeX Warning: Reference `fig:terrel:4th_Order_lid' on page 389 undefined on in put line 732. LaTeX Warning: Reference `fig:terrel:lid_div_error' on page 389 undefined on in put line 737. ) (./tex/21.tex Underfull \vbox (badness 10000) has occurred while \output is active [389] [390 <./chapters/terrel/pdf/vel_4.pdf> <./chapters/terrel/pdf/press_4.pdf>] [391 <./chapters/terrel/pdf/div_4.pdf> <./chapters/terrel/pdf/run_4.pdf>] [392 <./chapters/terrel/pdf/div_4_test.pdf> <./chapters/terrel/png/lid_div_erro r.png (PNG copy)>] [393] [16 [394]] Underfull \vbox (badness 1033) has occurred while \output is active [17] Chapter 21. Package natbib Warning: Citation `Chorin1968' on page 395 undefined on input li ne 55. Package natbib Warning: Citation `Temam1969' on page 395 undefined on input lin e 56. Package natbib Warning: Citation `Goda1979' on page 395 undefined on input line 57. Package natbib Warning: Citation `GuermondMinevShen2006' on page 395 undefined on input line 58. Package natbib Warning: Citation `HoffmanJohnson2007' on page 395 undefined on input line 59. Package natbib Warning: Citation `Turek1996' on page 395 undefined on input lin e 61. Underfull \vbox (badness 1348) has occurred while \output is active [395] [18] [396] Underfull \vbox (badness 10000) has occurred while \output is active [19 <./cha pters/langtangen/pdf/membrane_waxis.pdf>] [20 <./chapters/langtangen/pdf/ex1_ gradu.pdf>] Package natbib Warning: Citation `Chorin1968' on page 397 undefined on input li ne 187. Package natbib Warning: Citation `Temam1969' on page 397 undefined on input lin e 188. LaTeX Warning: Reference `eq:ns,mom' on page 397 undefined on input line 190. LaTeX Warning: Reference `eq:ns,con' on page 397 undefined on input line 190. LaTeX Warning: Reference `fig:chorin_code' on page 397 undefined on input line 202. Package natbib Warning: Citation `Goda1979' on page 397 undefined on input line 269. LaTeX Warning: Reference `fig:IPCS' on page 397 undefined on input line 270. [397] [21 [398]] [22] Package natbib Warning: Citation `GuermondMinevShen2006' on page 399 undefined on input line 349. Package natbib Warning: Citation `GuermondShen2003' on page 399 undefined on in put line 349. LaTeX Warning: Reference `eq:ns,mom' on page 399 undefined on input line 352. LaTeX Warning: Reference `eq:ns,mom' on page 399 undefined on input line 358. LaTeX Warning: Reference `eq:ns,con' on page 399 undefined on input line 364. LaTeX Warning: Reference `eq:ns,con' on page 399 undefined on input line 372. LaTeX Warning: Reference `eq:css,laplace' on page 399 undefined on input line 3 73. [399] [23] [24] LaTeX Warning: Reference `eq:css,pn' on page 400 undefined on input line 404. LaTeX Warning: Reference `eq:css,u' on page 400 undefined on input line 404. LaTeX Warning: Reference `eq:css,pn' on page 400 undefined on input line 405. LaTeX Warning: Reference `eq:css,tmp' on page 400 undefined on input line 420. Overfull \hbox (25.00003pt too wide) detected at line 474 [] Overfull \hbox (25.00003pt too wide) detected at line 474 [] Package natbib Warning: Citation `GuermondShen2003' on page 400 undefined on in put line 488. LaTeX Warning: Reference `fig:impl_css' on page 400 undefined on input line 489 . Package natbib Warning: Citation `HoffmanJohnson2007' on page 400 undefined on input line 534. LaTeX Warning: Reference `sec:g2comment' on page 400 undefined on input line 53 7. Underfull \vbox (badness 10000) has occurred while \output is active [400] [401] [25] LaTeX Warning: Reference `fig:g2_code' on page 402 undefined on input line 579. LaTeX Warning: Reference `eq:ns,mom' on page 402 undefined on input line 666. LaTeX Warning: Reference `eq:ns,con' on page 402 undefined on input line 667. Underfull \vbox (badness 1502) has occurred while \output is active [402] [403 [26]] [27] Package natbib Warning: Citation `Turek1999' on page 404 undefined on input lin e 717. Package natbib Warning: Citation `CahouetChabard1988' on page 404 undefined on input line 725. Package natbib Warning: Citation `Turek1999' on page 404 undefined on input lin e 725. Package natbib Warning: Citation `MardalWinther2004' on page 404 undefined on i nput line 725. Package natbib Warning: Citation `MardalWinther11' on page 404 undefined on inp ut line 725. LaTeX Warning: Reference `chap:mardal-4' on page 404 undefined on input line 73 2. LaTeX Warning: Reference `fig:grpc_code' on page 404 undefined on input line 73 5. LaTeX Warning: Reference `tab:problems' on page 404 undefined on input line 796 . Underfull \vbox (badness 4303) has occurred while \output is active [404] Underfull \vbox (badness 3536) has occurred while \output is active [28] LaTeX Warning: Reference `fig:bc_drivencavity' on page 405 undefined on input l ine 856. [405] [29] Underfull \vbox (badness 10000) has occurred while \output is active [30 <./cha pters/langtangen/pdf/Poisson2D_Dvc_contour1.pdf> <./chapters/langtangen/pdf/Poi sson2D_Dvc_flux_x.pdf> <./chapters/langtangen/pdf/Poisson2D_Dvc_surf1.pdf> <./c hapters/langtangen/pdf/Poisson2D_Dvc_mesh1.pdf>] [31] Package natbib Warning: Citation `PanditKalitaDalal2007' on page 406 undefined on input line 883. Package natbib Warning: Citation `ChudanovPopkovChurbanovEtAl2007' on page 406 undefined on input line 885. Package natbib Warning: Citation `Blackburn2009' on page 406 undefined on input line 888. Package natbib Warning: Citation `Blackburn2004' on page 406 undefined on input line 888. LaTeX Warning: Reference `fig:drivencavity_CPU_and_errors' on page 406 undefine d on input line 898. Package natbib Warning: Citation `White1999' on page 406 undefined on input lin e 916. Package natbib Warning: Citation `White1991' on page 406 undefined on input lin e 917. LaTeX Warning: Reference `fig:streamfunction' on page 406 undefined on input li ne 917. LaTeX Warning: Reference `fig:drivencavity_CPU_and_errors' on page 406 undefine d on input line 944. [32] Underfull \vbox (badness 3460) has occurred while \output is active [406] [407 <./chapters/kvs-1/pdf/new_drivencavity_res.pdf>] LaTeX Warning: Reference `fig:channel_results' on page 408 undefined on input l ine 980. Package natbib Warning: Citation `CanutoHussainiQuarteroniEtAl2007' on page 408 undefined on input line 997. Underfull \vbox (badness 10000) has occurred while \output is active [408 Underfull \vbox (badness 1122) has occurred while \output is active [33 <./ch apters/kvs-1/pdf/new_channel_res.pdf>]] LaTeX Warning: Reference `fig:periodic_bcs' on page 409 undefined on input line 1008. LaTeX Warning: Reference `fig:periodic' on page 409 undefined on input line 100 9. LaTeX Warning: Reference `fig:periodic_res' on page 409 undefined on input line 1044. [34] Package natbib Warning: Citation `Turek1996' on page 409 undefined on input lin e 1071. LaTeX Warning: Reference `fig:cylinder_illustration' on page 409 undefined on i nput line 1074. Underfull \vbox (badness 3396) has occurred while \output is active [409] [410 <./chapters/kvs-1/pdf/periodic_v.pdf> <./chapters/kvs-1/pdf/periodic_p.pdf > <./chapters/kvs-1/pdf/new_periodic_res.pdf>] LaTeX Warning: Reference `fig:cylinder_res' on page 411 undefined on input line 1107. [35 ] Package natbib Warning: Citation `EthierSteinmann1994' on page 411 undefined on input line 1123. Underfull \vbox (badness 6428) has occurred while \output is active [411 <./cha pters/kvs-1/pdf/cylinderandgeoattime5nr2.pdf> <./chapters/kvs-1/pdf/new_cylinde r_res.pdf>] [36] LaTeX Warning: Reference `fig:beltrami' on page 412 undefined on input line 114 7. Package natbib Warning: Citation `EthierSteinmann1994' on page 412 undefined on input line 1149. Package natbib Warning: Citation `EthierSteinmann1994' on page 412 undefined on input line 1153. LaTeX Warning: Reference `fig:beltrami_res' on page 412 undefined on input line 1164. Underfull \vbox (badness 3646) has occurred while \output is active [37] [38 ] LaTeX Warning: Reference `chap:kvs-2' on page 412 undefined on input line 1178. LaTeX Warning: Reference `fig:aneurysm' on page 412 undefined on input line 118 4. [412 <./chapters/kvs-1/pdf/new_beltrami_illustration.pdf>] [39] Underfull \vbox (badness 1412) has occurred while \output is active [40] [41] LaTeX Warning: Reference `fig:aneurysm_res' on page 413 undefined on input line 1211. LaTeX Warning: Reference `fig:scatter' on page 413 undefined on input line 1230 . LaTeX Warning: Reference `fig:scatter' on page 413 undefined on input line 1242 . [413 <./chapters/kvs-1/pdf/new_beltrami_res.pdf>] [414 <./chapters/kvs-1/pdf/an eurysm_at_end_css1.pdf> <./chapters/kvs-1/pdf/new_aneurysm_res.pdf>] Package natbib Warning: Citation `GuermondMinevShen2006' on page 415 undefined on input line 1257. [415 <./chapters/kvs-1/pdf/new_scatter.pdf>] LaTeX Warning: Reference `sec:g2' on page 416 undefined on input line 1288. Package natbib Warning: Citation `HoffmanJohnson2007' on page 416 undefined on input line 1291. LaTeX Warning: Reference `fig:g3plots' on page 416 undefined on input line 1303 . LaTeX Warning: Reference `fig:g3scatter' on page 416 undefined on input line 13 03. [42 ] [43] LaTeX Warning: Reference `fig:scatter' on page 416 undefined on input line 1328 . ) (./tex/22.tex Underfull \vbox (badness 7558) has occurred while \output is active [416 <./cha pters/kvs-1/pdf/drivencavity-plots.pdf>] [417 <./chapters/kvs-1/pdf/drivencavit y-scatter.pdf>] [418] Underfull \hbox (badness 1331) in paragraph at lines 3053--3059 []\T1/pplx/m/n/10 (+20) The im-ple-men-ta-tion is iden-ti-cal to the one in Sec -tion [][]1.2.2[][] and is found in the file [44] Chapter 22. LaTeX Warning: Reference `chap:kvs-1' on page 419 undefined on input line 21. Package natbib Warning: Citation `Mortensen2011' on page 419 undefined on input line 37. [419] Package natbib Warning: Citation `CanutoHussainiQuarteroniEtAl2007' on page 420 undefined on input line 85. Package natbib Warning: Citation `Blackburn2009' on page 420 undefined on input line 87. Package natbib Warning: Citation `Iles' on page 420 undefined on input line 113 . LaTeX Warning: Reference `sec:mortensen:OS' on page 420 undefined on input line 150. Underfull \vbox (badness 1515) has occurred while \output is active [420] LaTeX Warning: Reference `eq:mortensen:Bu2' on page 421 undefined on input line 214. [421] [45 LaTeX Warning: Reference `eq:mortensen:conv:K' on page 422 undefined on input l ine 230. LaTeX Warning: Reference `eq:mortensen:skew' on page 422 undefined on input lin e 247. LaTeX Warning: Reference `eq:mortensen:skew' on page 422 undefined on input lin e 249. LaTeX Warning: Reference `eq:mortensen:B0' on page 422 undefined on input line 249. LaTeX Warning: Reference `eq:mortensen:NS' on page 422 undefined on input line 261. LaTeX Warning: Reference `eq:mortensen:K(u)' on page 422 undefined on input lin e 273. Package natbib Warning: Citation `SimoArmero1994' on page 422 undefined on inpu t line 277. [422]] LaTeX Warning: Reference `eq:mortensen:phi:pde' on page 423 undefined on input line 317. LaTeX Warning: Reference `eq:mortensen:phi:pde' on page 423 undefined on input line 328. LaTeX Warning: Reference `eq:mortensen:phi:pde' on page 423 undefined on input line 333. LaTeX Warning: Reference `eq:mortensen:phi:pde' on page 423 undefined on input line 354. Package natbib Warning: Citation `SimoArmero1994' on page 423 undefined on inpu t line 384. [423] [46] LaTeX Warning: Reference `eq:mortensen:EX' on page 424 undefined on input line 446. LaTeX Warning: Reference `eq:mortensen:IM1' on page 424 undefined on input line 450. LaTeX Warning: Reference `eq:mortensen:IM2' on page 424 undefined on input line 451. LaTeX Warning: Reference `eq:mortensen:IM1' on page 424 undefined on input line 452. Package natbib Warning: Citation `SimoArmero1994' on page 424 undefined on inpu t line 454. LaTeX Warning: Reference `eq:mortensen:NS_d' on page 424 undefined on input lin e 456. LaTeX Warning: Reference `eq:mortensen:cont_d' on page 424 undefined on input l ine 456. LaTeX Warning: Reference `eq:mortensen:NS_d' on page 424 undefined on input lin e 459. LaTeX Warning: Reference `eq:mortensen:cont_d' on page 424 undefined on input l ine 459. LaTeX Warning: Reference `eq:mortensen:NS_d' on page 424 undefined on input lin e 464. LaTeX Warning: Reference `eq:mortensen:NS_d' on page 424 undefined on input lin e 467. LaTeX Warning: Reference `eq:mortensen:cont_d' on page 424 undefined on input l ine 469. LaTeX Warning: Reference `eq:mortensen:NS_d' on page 424 undefined on input lin e 471. [424] [47] [48 LaTeX Warning: Reference `eq:mortensen:NS_d' on page 425 undefined on input lin e 486. LaTeX Warning: Reference `eq:mortensen:NS_FS' on page 425 undefined on input li ne 487. LaTeX Warning: Reference `eq:mortensen:NS_FS:error' on page 425 undefined on in put line 495. LaTeX Warning: Reference `eq:mortensen:NS_FS:error2' on page 425 undefined on i nput line 509. LaTeX Warning: Reference `eq:mortensen:NS_FS:cont' on page 425 undefined on inp ut line 510. LaTeX Warning: Reference `eq:mortensen:NS_FS:error2' on page 425 undefined on i nput line 517. LaTeX Warning: Reference `eq:mortensen:NS_FS' on page 425 undefined on input li ne 525. LaTeX Warning: Reference `eq:mortensen:PC' on page 425 undefined on input line 525. LaTeX Warning: Reference `eq:mortensen:vel_update' on page 425 undefined on inp ut line 526. LaTeX Warning: Reference `eq:mortensen:update' on page 425 undefined on input l ine 526. LaTeX Warning: Reference `eq:mortensen:PC' on page 425 undefined on input line 527. LaTeX Warning: Reference `eq:mortensen:NS_FS' on page 425 undefined on input li ne 528. LaTeX Warning: Reference `eq:mortensen:NS_d' on page 425 undefined on input lin e 532. LaTeX Warning: Reference `eq:mortensen:cont_d' on page 425 undefined on input l ine 532. LaTeX Warning: Reference `eq:mortensen:NS_FS' on page 425 undefined on input li ne 536. LaTeX Warning: Reference `eq:mortensen:vel_update' on page 425 undefined on inp ut line 536. LaTeX Warning: Reference `eq:mortensen:vel_update' on page 425 undefined on inp ut line 541. LaTeX Warning: Reference `eq:mortensen:vel_update' on page 425 undefined on inp ut line 543. LaTeX Warning: Reference `eq:mortensen:vel_update' on page 425 undefined on inp ut line 547. LaTeX Warning: Reference `eq:mortensen:NS_FS' on page 425 undefined on input li ne 549. LaTeX Warning: Reference `eq:mortensen:vel_update' on page 425 undefined on inp ut line 552. [425]] LaTeX Warning: Reference `eq:mortensen:PC' on page 426 undefined on input line 564. Package natbib Warning: Citation `GuermondMinevShen2006' on page 426 undefined on input line 569. LaTeX Warning: Reference `eq:mortensen:EX' on page 426 undefined on input line 591. LaTeX Warning: Reference `eq:mortensen:IM2' on page 426 undefined on input line 591. LaTeX Warning: Reference `chap:kvs-1' on page 426 undefined on input line 601. [426] [49] LaTeX Warning: Reference `sec:mortensen:Convection' on page 427 undefined on in put line 661. LaTeX Warning: Reference `chap:kvs-1' on page 427 undefined on input line 676. [427] LaTeX Warning: Reference `eq:mortensen:NS' on page 428 undefined on input line 718. LaTeX Warning: Reference `chap:langtangen' on page 428 undefined on input line 751. LaTeX Warning: Reference `tab:mortensen:speed-up' on page 428 undefined on inpu t line 766. LaTeX Warning: Reference `sec:mortensen:TG' on page 428 undefined on input line 768. LaTeX Warning: Reference `tab:mortensen:speed-up' on page 428 undefined on inpu t line 771. LaTeX Warning: Reference `sec:mortensen:impl_fenics' on page 428 undefined on i nput line 774. [428] LaTeX Warning: Reference `eq:mortensen:EX' on page 429 undefined on input line 805. LaTeX Warning: Reference `eq:mortensen:IM2' on page 429 undefined on input line 807. LaTeX Warning: Reference `sec:mortensen:Numerical' on page 429 undefined on inp ut line 818. LaTeX Warning: Reference `sec:mortensen:Convection' on page 429 undefined on in put line 823. LaTeX Warning: Reference `sec:mortensen:NS-solver' on page 429 undefined on inp ut line 826. LaTeX Warning: Reference `eq:mortensen:burgers' on page 429 undefined on input line 849. LaTeX Warning: Reference `sec:mortensen:NS-solver' on page 429 undefined on inp ut line 861. [429] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] LaTeX Warning: Reference `fig:mortensen:burgers_KE' on page 430 undefined on in put line 910. Underfull \vbox (badness 2088) has occurred while \output is active [53 <./chap ters/langtangen/pdf/daynight.pdfError: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap >] [54] LaTeX Warning: Reference `eq:mortensen:IM1' on page 430 undefined on input line 931. LaTeX Warning: Reference `eq:mortensen:IM2' on page 430 undefined on input line 931. LaTeX Warning: Reference `eq:mortensen:IM1' on page 430 undefined on input line 931. LaTeX Warning: Reference `eq:mortensen:IM2' on page 430 undefined on input line 931. Package natbib Warning: Citation `Orzag1971' on page 430 undefined on input lin e 939. [430] Underfull \vbox (badness 3977) has occurred while \output is active [55] Package natbib Warning: Citation `Trefethen2006' on page 431 undefined on input line 997. LaTeX Warning: Reference `fig:mortensen:OS_init' on page 431 undefined on input line 1001. [431 <./chapters/mortensen/pdf/Burgers_KE_IM1.pdf> <./chapters/mortensen/pdf/Bu rgers_KE_IM2.pdf>] [56] LaTeX Warning: Reference `eq:mortensen:channel' on page 432 undefined on input line 1012. LaTeX Warning: Reference `eq:mortensen:OrrS' on page 432 undefined on input lin e 1014. Package natbib Warning: Citation `MalikZangHussaini1984' on page 432 undefined on input line 1015. Package natbib Warning: Citation `Trefethen2006' on page 432 undefined on input line 1054. LaTeX Warning: Reference `eq:mortensen:channel' on page 432 undefined on input line 1060. [432] [57] LaTeX Warning: Reference `fig:mortensen:OS_init' on page 433 undefined on input line 1075. LaTeX Warning: Reference `fig:mortensen:OS_init_cfl' on page 433 undefined on i nput line 1096. [58] LaTeX Warning: Reference `eq:mortensen:error' on page 433 undefined on input li ne 1115. LaTeX Warning: Reference `eq:mortensen:EX' on page 433 undefined on input line 1115. LaTeX Warning: Reference `eq:mortensen:IM2' on page 433 undefined on input line 1115. LaTeX Warning: Reference `eq:mortensen:error' on page 433 undefined on input li ne 1115. LaTeX Warning: Reference `eq:mortensen:EX' on page 433 undefined on input line 1115. LaTeX Warning: Reference `eq:mortensen:IM2' on page 433 undefined on input line 1115. [59 LaTeX Warning: Reference `eq:mortensen:error' on page 433 undefined on input li ne 1132. LaTeX Warning: Reference `eq:mortensen:EX' on page 433 undefined on input line 1132. LaTeX Warning: Reference `eq:mortensen:IM2' on page 433 undefined on input line 1132. LaTeX Warning: Reference `eq:mortensen:error' on page 433 undefined on input li ne 1132. LaTeX Warning: Reference `eq:mortensen:EX' on page 433 undefined on input line 1132. LaTeX Warning: Reference `eq:mortensen:IM2' on page 433 undefined on input line 1132. LaTeX Warning: Reference `fig:mortensen:OS_init_cfl' on page 433 undefined on i nput line 1138. [433 <./chapters/langtangen/pd f/hollow_cylinder.pdf>] <./chapters/mortensen/pdf/OS_init.pdf> <./chapters/mortensen/pdf/OrrS_eigv als.pdf> <./chapters/mortensen/pdf/OS_init_cfl_1.pdf> <./chapters/mortensen/pdf /OS_init_cfl_0.pdf>] LaTeX Warning: Reference `fig:mortensen:OS_init_dx' on page 434 undefined on in put line 1156. LaTeX Warning: Reference `fig:mortensen:OS_init_cfl' on page 434 undefined on i nput line 1162. LaTeX Warning: Reference `fig:mortensen:OS_init_dx' on page 434 undefined on in put line 1162. LaTeX Warning: Reference `fig:mortensen:OS_long_time' on page 434 undefined on input line 1180. LaTeX Warning: Reference `eq:mortensen:IM2' on page 434 undefined on input line 1182. LaTeX Warning: Reference `eq:mortensen:EX' on page 434 undefined on input line 1183. LaTeX Warning: Reference `fig:mortensen:OS_long_time' on page 434 undefined on input line 1197. LaTeX Warning: Reference `fig:mortensen:OS_long_time' on page 434 undefined on input line 1202. LaTeX Warning: Reference `eq:mortensen:IM2' on page 434 undefined on input line 1206. Package natbib Warning: Citation `MalikZangHussaini1984' on page 434 undefined on input line 1214. Package natbib Warning: Citation `CanutoHussainiQuarteroniEtAl2007' on page 434 undefined on input line 1215. [434 <./chapters/mortensen/pdf/OS_init_dx_1.pdf> <./chapters/mortensen/pdf/OS_i nit_dx_0.pdf>] [60] LaTeX Warning: Reference `eq:mortensen:EX' on page 435 undefined on input line 1234. LaTeX Warning: Reference `eq:mortensen:IM2' on page 435 undefined on input line 1234. LaTeX Warning: Reference `eq:mortensen:EX' on page 435 undefined on input line 1234. LaTeX Warning: Reference `eq:mortensen:IM2' on page 435 undefined on input line 1234. [435 <./chapters/mortensen/pdf/OS_energy_cfl_0_1_model_1.pdf> <./chapters/morte nsen/pdf/OS_energy_cfl_0_1_model_0.pdf> <./chapters/mortensen/pdf/OS_energy_cfl _0_05_model_1.pdf> <./chapters/mortensen/pdf/OS_energy_cfl_0_05_model_0.pdf>] Package natbib Warning: Citation `Blackburn2009' on page 436 undefined on input line 1274. LaTeX Warning: Reference `fig:mortensen:dissipation' on page 436 undefined on i nput line 1284. LaTeX Warning: Reference `eq:mortensen:EX' on page 436 undefined on input line 1290. LaTeX Warning: Reference `eq:mortensen:IM2' on page 436 undefined on input line 1290. Underfull \hbox (badness 1215) in paragraph at lines 4284--4288 []\T1/pplx/m/n/10 (+20) Calling \T1/fvm/m/n/10 subdomains.array() \T1/pplx/m/n/ 10 (+20) re-turns a \T1/fvm/m/n/10 numpy \T1/pplx/m/n/10 (+20) ar-ray of the su b-do-main val-ues. That is, [61] LaTeX Warning: Reference `eq:mortensen:diss' on page 436 undefined on input lin e 1304. LaTeX Warning: Reference `eq:mortensen:q' on page 436 undefined on input line 1 304. LaTeX Warning: Reference `eq:mortensen:IM2' on page 436 undefined on input line 1304. Package natbib Warning: Citation `Blackburn2009' on page 436 undefined on input line 1304. LaTeX Warning: Reference `eq:mortensen:diss' on page 436 undefined on input lin e 1304. LaTeX Warning: Reference `eq:mortensen:q' on page 436 undefined on input line 1 304. LaTeX Warning: Reference `eq:mortensen:IM2' on page 436 undefined on input line 1304. Package natbib Warning: Citation `Blackburn2009' on page 436 undefined on input line 1304. LaTeX Warning: Reference `fig:mortensen:dissipation' on page 436 undefined on i nput line 1308. Underfull \vbox (badness 10000) has occurred while \output is active [436 <./ch apters/mortensen/pdf/TG_disserror_model_0_cfl_0_05_Re_100_dofs.pdf> <./chapters /mortensen/pdf/TG_energyerror_model_0_cfl_0_05_Re_100_dofs.pdf>]) (./tex/23.tex [437] [438] Chapter 23. Package natbib Warning: Citation `LindekleivValen-SendstadMorganEtAl2010' on pa ge 439 undefined on input line 20. Package natbib Warning: Citation `JiangJohnsonValen-SendstadEtAl2010' on page 4 39 undefined on input line 23. Package natbib Warning: Citation `Feigin2005' on page 439 undefined on input li ne 32. Package natbib Warning: Citation `MurrayLopez1997' on page 439 undefined on inp ut line 33. LaTeX Warning: Reference `fig:kvs-2:textbook-circle' on page 439 undefined on i nput line 45. LaTeX Warning: Reference `cok' on page 439 undefined on input line 53. LaTeX Warning: Reference `fig:kvs-2:circle_kent' on page 439 undefined on input line 53. Package natbib Warning: Citation `Gray1897' on page 439 undefined on input line 61. Package natbib Warning: Citation `Gray1897' on page 439 undefined on input line 61. Package natbib Warning: Citation `Weir2002' on page 439 undefined on input line 75. Package natbib Warning: Citation `Humphrey2001' on page 439 undefined on input line 77. Package natbib Warning: Citation `DAVIESREMUZZIGORDONEtAl1986' on page 439 unde fined on input line 81. Package natbib Warning: Citation `BousselRayzMcCullochEtAl2008' on page 439 und efined on input line 83. Package natbib Warning: Citation `CebralCastroBurgessEtAl2005' on page 439 unde fined on input line 85. Package natbib Warning: Citation `Humphrey2001' on page 439 undefined on input line 91. Package natbib Warning: Citation `Stehbens1975' on page 439 undefined on input line 91. Package natbib Warning: Citation `Fung1984' on page 439 undefined on input line 95. Package natbib Warning: Citation `MhurchuAndersonJamrozikEtAl2001' on page 439 undefined on input line 97. Package natbib Warning: Citation `LongstrethNelsonKoepsellEtAl1994' on page 439 undefined on input line 97. Package natbib Warning: Citation `KongableLanzinoGermansonEtAl1996' on page 439 undefined on input line 97. [439] [440 <./chapters/kvs-2/png/cow_gray_1.png (PNG copy)> <./chapters/kvs-2/p df/kentus.pdf>] [62] Underfull \vbox (badness 10000) has occurred while \output is active [63] LaTeX Warning: Reference `fig:kvs-2:stress_code' on page 441 undefined on input line 105. Package natbib Warning: Citation `FordAlperinLeeEtAl2005' on page 441 undefined on input line 156. LaTeX Warning: Reference `fig:kvs-2:ford' on page 441 undefined on input line 1 59. LaTeX Warning: Reference `cok' on page 441 undefined on input line 162. [441] [64] LaTeX Warning: Reference `resistance_coeff' on page 442 undefined on input line 192. LaTeX Warning: Reference `resistance_coeff' on page 442 undefined on input line 194. Package natbib Warning: Citation `AlastrueyParkerPeiroEtAl2007' on page 442 und efined on input line 195. LaTeX Warning: Reference `fig:kvs-2:resistance_code' on page 442 undefined on i nput line 198. LaTeX Warning: Reference `kvs-2:eq:resistancebc' on page 442 undefined on input line 214. LaTeX Warning: Reference `kvs-2:eq:resistancebc' on page 442 undefined on input line 214. LaTeX Warning: Reference `fig:kvs-2:resistance_bcs_fig' on page 442 undefined o n input line 242. LaTeX Warning: Reference `dog_study' on page 442 undefined on input line 243. [442 <./chapters/kvs-2/pdf/systolic.pdf>] LaTeX Warning: Reference `resistance_bcs' on page 443 undefined on input line 2 61. LaTeX Warning: Reference `resistance_bcs' on page 443 undefined on input line 2 61. Package natbib Warning: Citation `vmtk' on page 443 undefined on input line 278 . LaTeX Warning: Reference `fig:kvs-2:imagseg' on page 443 undefined on input lin e 282. [443 [65 <./chapters/kvs-2/png/zero_dp_vs_res.png] [66] Overfull \hbox (2.004pt too wide) in paragraph at lines 4672--4674 []\T1/pplx/m/n/10 (-20) generate mesh over [67] [68] [69]) (./tex/2.tex [70] Chapter 2. (/usr/share/texmf-texlive/tex/latex/psnfss/ufplmbb.fd) [71] (./chapters/kirby-7/pdf/heat_equation_model_domain.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/heat_equation_model_domai n.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allow ed ) [72 <./ch apters/kirby-7/pdf/heat_equation_model_domain.pdf>] [73] [74] [75] [76] [77 <./chapters/kirby-7/pdf/cells.pdf>] [78 <./chapters/kirby-7/pdf/P1.pdf>] pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/dofmap.pdf): PDF inclusio n: found PDF version <1.5>, but at most version <1.4> allowed [79 <./chapters/kirby-7/pdf/dofmap.pdf>] Underfull \hbox (badness 1107) in paragraph at lines 694--694 []\T1/pplx/m/n/9 (+20) Figure 2.5: |Patch-ing to-gether a Underfull \hbox (badness 1755) in paragraph at lines 694--694 \T1/pplx/m/n/9 (+20) pair of quadratic lo-cal func-tion [80 <./chapters/kirby-7/pdf/femspace.pdf>] (./chapters/kirby-7/pdf/affine_map.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/affine_map.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \vbox (badness 10000) has occurred while \output is active [81 <./cha pters/kirby-7/pdf/affine_map.pdf>] [82] [83] (./chapters/kirby-7/pdf/projection.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/projection.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \vbox (badness 10000) has occurred while \output is active [84 <./cha pters/kirby-7/pdf/projection.pdf>] [85] [86] [87 <./chapters/kirby-7/png/refinemen t.png (PNG copy)>]) (./tex/10.tex [88] Chapter 3. pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/fenics-map.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed [89] [90 <./chapters/logg-2/pdf/fenics-map. pdf>] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) [91 <./chapters/logg- 2/pdf/dolfin-uml.pdf>]> <./chapters/kvs-2/pdf/stacks.pdf > <./chapters/kvs-2/pdf/3d.pdf> <./chapters/kvs-2/pdf/viper3.pdf>] Package natbib Warning: Citation `LindekleivValen-SendstadMorganEtAl2010' on pa ge 444 undefined on input line 290. Package natbib Warning: Citation `EdenMeurerSanchezEtAl2008' on page 444 undefi ned on input line 298. Package natbib Warning: Citation `IngebrigtsenMorganFaulderEtAl2004' on page 44 4 undefined on input line 309. Package natbib Warning: Citation `KrejzaSzydlikLiebeskindEtAl2005' on page 444 undefined on input line 323. LaTeX Warning: Reference `bcs' on page 444 undefined on input line 324. LaTeX Warning: Reference `resistance_bcs' on page 444 undefined on input line 3 28. LaTeX Warning: Reference `bcs' on page 444 undefined on input line 332. LaTeX Warning: Reference `fig:kvs-2:mca_wss_res' on page 444 undefined on input line 337. LaTeX Warning: Reference `fig:kvs-2:ica_wss_res' on page 444 undefined on input line 338. Package natbib Warning: Citation `LindekleivValen-SendstadMorganEtAl2010' on pa ge 444 undefined on input line 344. LaTeX Warning: Reference `fig:kvs-2:bif' on page 444 undefined on input line 38 2. LaTeX Warning: Reference `fig:kvs-2:bif' on page 444 undefined on input line 38 2. [92] Package natbib Warning: Citation `JiangJohnsonValen-SendstadEtAl2010' on page 4 44 undefined on input line 407. [444] [445 <./chapters/kvs-2/pdf/bifurcation_clean.pdf> <./chapters/kvs-2/pdf/m cas_wss_II4.pdf>] Package natbib Warning: Citation `LotzMeierLeppertEtAl2002' on page 446 undefin ed on input line 424. Package natbib Warning: Citation `EvansIwaiGristEtAl1993' on page 446 undefined on input line 424. Package natbib Warning: Citation `GermanBlack1965' on page 446 undefined on inp ut line 444. LaTeX Warning: Reference `fig:kvs-2:mass_dog' on page 446 undefined on input li ne 454. LaTeX Warning: Reference `fig:kvs-2:mass_dog' on page 446 undefined on input li ne 457. Package natbib Warning: Citation `JiangJohnsonValen-SendstadEtAl2010' on page 4 46 undefined on input line 461. LaTeX Warning: Reference `fig:kvs-2:dog_mri' on page 446 undefined on input lin e 463. [446 <./chapters/kvs-2/pdf/icas_wss.pdf>] [93] LaTeX Warning: Reference `vmtk' on page 447 undefined on input line 492. LaTeX Warning: Reference `chap:kvs-1' on page 447 undefined on input line 494. LaTeX Warning: Reference `resistance_bcs' on page 447 undefined on input line 5 01. LaTeX Warning: Reference `fig:kvs-2:inflow_codeI' on page 447 undefined on inpu t line 502. LaTeX Warning: Reference `fig:kvs-2:inflow_codeII' on page 447 undefined on inp ut line 503. LaTeX Warning: Reference `fig:kvs-2:inflow_codeI' on page 447 undefined on inpu t line 505. LaTeX Warning: Reference `fig:kvs-2:mass_dog' on page 447 undefined on input li ne 506. LaTeX Warning: Reference `fig:kvs-2:inflow_codeII' on page 447 undefined on inp ut line 535. LaTeX Warning: Reference `fig:kvs-2:dog_mri' on page 447 undefined on input lin e 585. Package natbib Warning: Citation `JiangJohnsonValen-SendstadEtAl2010' on page 4 47 undefined on input line 590. Underfull \vbox (badness 1688) has occurred while \output is active [447 <./cha pters/kvs-2/pdf/mass_dog.pdf> <./chapters/kvs-2/pdf/dog_data_mr_cfd.pdf>] [448] LaTeX Warning: Reference `fig:kvs-2:mass_dog' on page 449 undefined on input li ne 597. Underfull \vbox (badness 10000) has occurred while \output is active [449] LaTeX Warning: Reference `fig:kvs-2:dog_mri' on page 450 undefined on input lin e 615. Package natbib Warning: Citation `JiangJohnsonValen-SendstadEtAl2010' on page 4 50 undefined on input line 624. Package natbib Warning: Citation `AlastrueyParkerPeiroEtAl2007' on page 450 und efined on input line 652. Package natbib Warning: Citation `Vignon-ClementelFigueroaJansenEtAl2006' on pa ge 450 undefined on input line 652. LaTeX Warning: Reference `fig:kvs-2:cok_inflow' on page 450 undefined on input line 675. LaTeX Warning: Reference `vmtk' on page 450 undefined on input line 685. [450] [451 <./chapters/kvs-2/pdf/ica.pdf> <./chapters/kvs-2/pdf/cok_inflow.pdf> ] [94] LaTeX Warning: Reference `measure_vs_comp' on page 452 undefined on input line 700. LaTeX Warning: Reference `measure_vs_comp' on page 452 undefined on input line 735. LaTeX Warning: Reference `fig:kvs-2:screenshot' on page 452 undefined on input line 743. LaTeX Warning: Reference `fig:kvs-2:area_code' on page 452 undefined on input l ine 747. LaTeX Warning: Reference `fig:kvs-2:cok_ica' on page 452 undefined on input lin e 757. ) (./tex/24.tex [452] [453 <./chapters/kvs-2/pdf/cok_top_steam_white.pdf>] [454 <./chapters/kvs -2/pdf/cok_slice.pdf> <./chapters/kvs-2/pdf/cok_ica_vel_peak_syst.pdf>] [95 Chapter 24. LaTeX Warning: Reference `chap:kvs-1' on page 455 undefined on input line 15. ] LaTeX Warning: Reference `fig:anatomy' on page 455 undefined on input line 54. LaTeX Warning: Reference `fig:anatomy' on page 455 undefined on input line 60. Package natbib Warning: Citation `OldfieldMuraszkoShawkerEtAl1994' on page 455 undefined on input line 72. Package natbib Warning: Citation `HeissPatronasDeVroomEtAl1999' on page 455 und efined on input line 75. Package natbib Warning: Citation `PinnaAlessandriniAlfieriEtAl2000' on page 455 undefined on input line 75. Package natbib Warning: Citation `HofmannWarmuth-MetzBendszusEtAl2000' on page 455 undefined on input line 75. Package natbib Warning: Citation `HaughtonKorosecMedowEtAl2003' on page 455 und efined on input line 75. Package natbib Warning: Citation `MilhoratBolognese2003' on page 455 undefined on input line 79. Package natbib Warning: Citation `OldfieldMuraszkoShawkerEtAl1994' on page 455 undefined on input line 84. Package natbib Warning: Citation `PinnaAlessandriniAlfieriEtAl2000' on page 455 undefined on input line 84. Package natbib Warning: Citation `HeissPatronasDeVroomEtAl1999' on page 455 und efined on input line 84. Package natbib Warning: Citation `Quigley2004' on page 455 undefined on input l ine 86. Package natbib Warning: Citation `HaughtonKorosecMedowEtAl2003' on page 455 und efined on input line 86. Package natbib Warning: Citation `RoldanHaughtonWiebenEtAl2009' on page 455 und efined on input line 91. Package natbib Warning: Citation `HentschelMardalLovgren2010' on page 455 undef ined on input line 91. Package natbib Warning: Citation `LingeHaughtonLovgren2010' on page 455 undefin ed on input line 91. Package natbib Warning: Citation `LingeHaughtonLovgren2011' on page 455 undefin ed on input line 91. [455] LaTeX Warning: Reference `chap:kvs-1' on page 456 undefined on input line 102. LaTeX Warning: Reference `tab:entities' on page 456 undefined on input line 125 . [456 <./chapters/hentschel/pdf/ChiariImage2.pdf>] [96] Package natbib Warning: Citation `HofmannWarmuth-MetzBendszusEtAl2000' on page 457 undefined on input line 160. Package natbib Warning: Citation `GuptaSoellingerBoesigerEtAl2009' on page 457 undefined on input line 160. Package natbib Warning: Citation `LothYardimciAlperin2001' on page 457 undefine d on input line 160. Package natbib Warning: Citation `HofmannWarmuth-MetzBendszusEtAl2000' on page 457 undefined on input line 160. Package natbib Warning: Citation `GuptaSoellingerBoesigerEtAl2009' on page 457 undefined on input line 160. Package natbib Warning: Citation `LothYardimciAlperin2001' on page 457 undefine d on input line 160. LaTeX Warning: Reference `chap:kvs-1' on page 457 undefined on input line 169. [457] Package natbib Warning: Citation `GuptaSoellingerBoesigerEtAl2009' on page 458 undefined on input line 252. Package natbib Warning: Citation `LothYardimciAlperin2001' on page 458 undefine d on input line 258. Package natbib Warning: Citation `OldfieldMuraszkoShawkerEtAl1994' on page 458 undefined on input line 261. [458] Package natbib Warning: Citation `SmithChase2ShawEtAl2006' on page 459 undefine d on input line 283. LaTeX Warning: Reference `fig:sin_pulse' on page 459 undefined on input line 28 5. LaTeX Warning: Reference `chap:kvs-1' on page 459 undefined on input line 314. [459 <./chapters/hentschel/pdf/sin_pulse.pdf>] Underfull \hbox (badness 1412) in paragraph at lines 563--570 \T1/pplx/m/n/10 (+20) abled when DOLFIN is con-fig-ured. The back-end can be se t via the global pa-ram-e-ter [97] [460] [461] Package natbib Warning: Citation `GeuzaineRemacle' on page 462 undefined on inp ut line 501. [462] LaTeX Warning: Reference `fig:Gmsh_mesh' on page 463 undefined on input line 57 1. [463] [98] LaTeX Warning: Reference `fig:case1' on page 464 undefined on input line 629. [464 <./chapters/hentschel/pdf/gmsh.pdf>] Package natbib Warning: Citation `SmithChase2ShawEtAl2006' on page 465 undefine d on input line 648. Package natbib Warning: Citation `SmithChase2ShawEtAl2006' on page 465 undefine d on input line 648. Package natbib Warning: Citation `SmithChase2ShawEtAl2006' on page 465 undefine d on input line 648. Package natbib Warning: Citation `SmithChase2ShawEtAl2006' on page 465 undefine d on input line 648. LaTeX Warning: Reference `solvers:pressurediff' on page 465 undefined on input line 660. LaTeX Warning: Reference `chap:kvs-1' on page 465 undefined on input line 665. [465 <./chapters/hentschel/pdf/pulse_f1_08_sysmax_nmb7.pdf> <./chapters/hentsch el/pdf/pulse_f1_08_sysdia_nmb18.pdf> <./chapters/hentschel/pdf/pulse_f1_08_diam in1_nmb25.pdf>] LaTeX Warning: Reference `fig:sin_pulse' on page 466 undefined on input line 73 1. LaTeX Warning: Reference `fig:case2' on page 466 undefined on input line 734. Package natbib Warning: Citation `LothYardimciAlperin2001' on page 466 undefine d on input line 754. Package natbib Warning: Citation `AlperinMazdaLichtorEtAl2006' on page 466 unde fined on input line 754. [466] LaTeX Warning: Reference `fig:case3' on page 467 undefined on input line 769. LaTeX Warning: Reference `fig:case3b' on page 467 undefined on input line 783. LaTeX Warning: Reference `fig:case4' on page 467 undefined on input line 813. LaTeX Warning: Reference `tab:Re_We' on page 467 undefined on input line 841. [467 <./chapters/hentschel/pdf/sin_sysmax_nmb2.pdf> <./chapters/hentschel/pdf/s in_sysdia_nmb4.pdf> <./chapters/hentschel/pdf/sin_diamin_nmb6.pdf>] [468 <./cha pters/hentschel/pdf/pulse_f1_08_elliptic_sysmax_nmb7.pdf> <./chapters/hentschel /pdf/pulse_f1_08_elliptic_sysdia_nmb18.pdf> <./chapters/hentschel/pdf/pulse_f1_ 08_elliptic_diamin1_nmb25.pdf> <./chapters/hentschel/pdf/pulse_f1_08_elliptic_e ccentric_sysmax_nmb7.pdf> <./chapters/hentschel/pdf/pulse_f1_08_elliptic_eccent ric_sysdia_nmb18.pdf> <./chapters/hentschel/pdf/pulse_f1_08_elliptic_eccentric_ diamin1_nmb25.pdf> <./chapters/hentschel/pdf/pulse_syrinx_f1_08_syrinx05_sysmax _nmb7.pdf> <./chapters/hentschel/pdf/pulse_syrinx_f1_08_syrinx05_sysdia_nmb18.p df> <./chapters/hentschel/pdf/pulse_syrinx_f1_08_syrinx05_diamin1_nmb25.pdf>]) (./tex/25.tex [469] [470] Chapter 25. Package natbib Warning: Citation `ZhaoTengCheng2004' on page 471 undefined on i nput line 10. Package natbib Warning: Citation `Peregrine1967' on page 471 undefined on input line 32. Package natbib Warning: Citation `Wu1981' on page 471 undefined on input line 3 2. Package natbib Warning: Citation `MadsenEtAl1991' on page 471 undefined on inpu t line 34. Package natbib Warning: Citation `Nwogu1993' on page 471 undefined on input lin e 34. Package natbib Warning: Citation `ChenLiu1994' on page 471 undefined on input l ine 34. Package natbib Warning: Citation `BejiNadaoka1996' on page 471 undefined on inp ut line 35. LaTeX Warning: Reference `fig:lopes:harbor' on page 471 undefined on input line 40. LaTeX Warning: Reference `sec:lopes:dolfwave' on page 471 undefined on input li ne 52. LaTeX Warning: Reference `sec:lopes:modelderivation' on page 471 undefined on i nput line 58. Package natbib Warning: Citation `WalkleyBerzins2002' on page 471 undefined on input line 62. Package natbib Warning: Citation `WooLiu2004a' on page 471 undefined on input l ine 62. Package natbib Warning: Citation `WooLiu2004b' on page 471 undefined on input l ine 63. Package natbib Warning: Citation `LangtangenPedersen1998' on page 471 undefined on input line 66. [471] [99 Package natbib Warning: Citation `ZhaoTengCheng2004' on page 472 undefined on i nput line 76. LaTeX Warning: Reference `lopes:i' on page 472 undefined on input line 81. LaTeX Warning: Reference `sec:lopes:dispersionproperties' on page 472 undefined on input line 89. LaTeX Warning: Reference `sec:lopes:numericalmethods' on page 472 undefined on input line 94. LaTeX Warning: Reference `chap:kirby-6' on page 472 undefined on input line 98. LaTeX Warning: Reference `sec:lopes:wavegeneration' on page 472 undefined on in put line 101. LaTeX Warning: Reference `sec:lopes:boundaryconditions' on page 472 undefined o n input line 102. Package natbib Warning: Citation `WeiKirbySinha1999' on page 472 undefined on i nput line 107. LaTeX Warning: Reference `sec:lopes:linearanalysis' on page 472 undefined on in put line 112. Package natbib Warning: Citation `LovholtPedersen2009' on page 472 undefined on input line 116. LaTeX Warning: Reference `sec:lopes:numericaltests' on page 472 undefined on in put line 119. LaTeX Warning: Reference `fig:lopes:harbor' on page 472 undefined on input line 124. Package natbib Warning: Citation `Kirby1998' on page 472 undefined on input lin e 130. Package natbib Warning: Citation `LynettLiu2004' on page 472 undefined on input line 131. Package natbib Warning: Citation `PedersenLovholt2008' on page 472 undefined on input line 132. Package natbib Warning: Citation `WeiKirby1995' on page 472 undefined on input line 133. [472 <./chapters/lopes/pdf/nazare1.pdf>]] Package natbib Warning: Citation `PedersenLovholt2008' on page 473 undefined on input line 157. Package natbib Warning: Citation `LovholtPedersen2009' on page 473 undefined on input line 159. LaTeX Warning: Reference `lopes:list_i' on page 473 undefined on input line 192 . [473] Package natbib Warning: Citation `ChenLiu1994' on page 474 undefined on input l ine 216. Package natbib Warning: Citation `LopesPereiraTrabucho' on page 474 undefined o n input line 223. LaTeX Warning: Reference `chap:alnes-1' on page 474 undefined on input line 239 . LaTeX Warning: Reference `fig:lopes:schematic' on page 474 undefined on input l ine 276. LaTeX Warning: Reference `fig:lopes:schematic' on page 474 undefined on input l ine 278. (./chapters/lopes/pdf/graph.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/graph.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `eq:lopes:euler-b' on page 474 undefined on input line 292. LaTeX Warning: Reference `eq:lopes:bern' on page 474 undefined on input line 30 3. LaTeX Warning: Reference `eq:lopes:euler-c' on page 474 undefined on input line 305. [474pdfTeX warning (ext4): destination with the same identifier (name{equation. 25.3.1}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.307 \begin{equation} pdfTeX warning (ext4): destination with the same identifi er (name{equation.25.3.2}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.307 \begin{equation} ] Package natbib Warning: Citation `DutykhDias2007' on page 475 undefined on inpu t line 342. LaTeX Warning: Reference `eq:lopes:lap' on page 475 undefined on input line 355 . LaTeX Warning: Reference `eq:lopes:diss' on page 475 undefined on input line 35 6. Underfull \vbox (badness 10000) has occurred while \output is active [475pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.3}) h as been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.361 <./chapters/lopes/pdf/graph.pdf>] Package natbib Warning: Citation `Whitham1974' on page 476 undefined on input l ine 363. Package natbib Warning: Citation `Johnson1997' on page 476 undefined on input l ine 364. LaTeX Warning: Reference `eq:lopes:bern' on page 476 undefined on input line 37 0. LaTeX Warning: Reference `eq:lopes:diss' on page 476 undefined on input line 37 0. LaTeX Warning: Reference `fig:lopes:schematic' on page 476 undefined on input l ine 372. Package natbib Warning: Citation `ChenLiu1994' on page 476 undefined on input l ine 413. Package natbib Warning: Citation `ZhaoTengCheng2004' on page 476 undefined on i nput line 414. LaTeX Warning: Reference `eq:lopes:ursell' on page 476 undefined on input line 428. pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3 .1}) has been already used, duplicate ignored \relax l.461 \end{align} pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.2}) has been already used, duplicate ignored \relax l.461 \end{align} Underfull \vbox (badness 10000) has occurred while \output is active [476] LaTeX Warning: Reference `eq:lopes:phi_1' on page 477 undefined on input line 4 87. Package natbib Warning: Citation `DutykhDias2007' on page 477 undefined on inpu t line 489. LaTeX Warning: Reference `eq:lopes:kindyn' on page 477 undefined on input line 498. LaTeX Warning: Reference `eq:lopes:phi_1' on page 477 undefined on input line 4 98. pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3 .1}) has been already used, duplicate ignored \relax l.512 \end{align} pdfTeX warning (ext4): destination with the same identifier (n ame{equation.25.3.2}) has been already used, duplicate ignored \relax l.512 \end{align} pdfTeX warning (ext4): destination with the same identifier (n ame{equation.25.3.1}) has been already used, duplicate ignored \relax l.545 \end{align} pdfTeX warning (ext4): destination with the same identifier (n ame{equation.25.3.2}) has been already used, duplicate ignored \relax l.545 \end{align} [477] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) LaTeX Warning: Reference `eq:lopes:ztcdimensionless' on page 478 undefined on i nput line 556. pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3 .1}) has been already used, duplicate ignored \relax l.571 \end{align} pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.2}) has been already used, duplicate ignored \relax l.571 \end{align} LaTeX Warning: Reference `eq:lopes:phitransdimensionless' on page 478 undefined on input line 574. Package natbib Warning: Citation `ZhaoTengCheng2004' on page 478 undefined on i nput line 583. Package natbib Warning: Citation `ChenLiu1994' on page 478 undefined on input l ine 588. Package natbib Warning: Citation `Nwogu1993' on page 478 undefined on input lin e 589. Package natbib Warning: Citation `DutykhDias2007' on page 478 undefined on inpu t line 604. LaTeX Warning: Reference `eq:lopes:linwave' on page 478 undefined on input line 624. LaTeX Warning: Reference `eq:lopes:linairy' on page 478 undefined on input line 643. [478] [100] LaTeX Warning: Reference `eq:lopes:dissdisp' on page 479 undefined on input lin e 647. LaTeX Warning: Reference `fig:lopes:dispersion' on page 479 undefined on input line 656. [101 <./chapters/logg-2/pdf/mesh -p1-entities.pdf>] Underfull \hbox (badness 5681) in paragraph at lines 667--667 []\T1/pplx/m/n/9 (+20) Figure 25.3: |Pos-i-tive part of LaTeX Warning: Reference `fig:lopes:dispersion' on page 479 undefined on input line 671. LaTeX Warning: Reference `eq:lopes:linairy' on page 479 undefined on input line 677. LaTeX Warning: Reference `eq:lopes:phasevel' on page 479 undefined on input lin e 686. LaTeX Warning: Reference `eq:lopes:nu1' on page 479 undefined on input line 696 . Package natbib Warning: Citation `DutykhDias2007' on page 479 undefined on inpu t line 698. LaTeX Warning: Reference `fig:lopes:dispersion' on page 479 undefined on input line 699. Underfull \vbox (badness 10000) has occurred while \output is active [479 <./ch apters/lopes/pdf/phase_velocity_simple.pdf>] LaTeX Warning: Reference `eq:lopes:phitrans' on page 480 undefined on input lin e 709. Package natbib Warning: Citation `BinghamMadsenFuhrman2008' on page 480 undefin ed on input line 711. Package natbib Warning: Citation `MadsenAgnon2003' on page 480 undefined on inp ut line 711. Package natbib Warning: Citation `MadsenBinghamSchaffer2003' on page 480 undefi ned on input line 712. Package natbib Warning: Citation `Lopes2007' on page 480 undefined on input lin e 720. LaTeX Warning: Reference `eq:lopes:ztc' on page 480 undefined on input line 723 . Overfull \hbox (0.95473pt too wide) in paragraph at lines 771--777 \T1/pplx/m/n/10 (-20) Corr and RungeKutta classes (see \T1/fvm/m/n/10 dolfwave/ src/predictorcorrector \T1/pplx/m/n/10 (-20) and \T1/fvm/m/n/10 dolfwave/src/ru ngekutta\T1/pplx/m/n/10 (-20) ). LaTeX Warning: Reference `eq:lopes:varform' on page 480 undefined on input line 778. LaTeX Warning: Reference `eq:lopes:varform' on page 480 undefined on input line 788. LaTeX Warning: Reference `eq:lopes:pc-b' on page 480 undefined on input line 81 1. Package natbib Warning: Citation `HairerWanner1991a' on page 480 undefined on i nput line 813. Package natbib Warning: Citation `Lambert1991' on page 480 undefined on input l ine 814. LaTeX Warning: Reference `eq:lopes:varform' on page 480 undefined on input line 817. LaTeX Warning: Reference `chap:kirby-6' on page 480 undefined on input line 818 . [480pdfTeX warning (ext4): destination with the same identifier (name{equation. 25.5.1}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.820 pdfTeX warning (ext4): destination with the same identifier (name{equatio n.25.5.2}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.820 ] [102] [481] LaTeX Warning: Reference `sec:lopes:wavegeneration' on page 482 undefined on in put line 888. LaTeX Warning: Reference `sec:lopes:boundaryconditions' on page 482 undefined o n input line 889. LaTeX Warning: Reference `eq:lopes:ztc-b' on page 482 undefined on input line 9 30. LaTeX Warning: Reference `eq:lopes:solita' on page 482 undefined on input line 934. LaTeX Warning: Reference `eq:lopes:solitb' on page 482 undefined on input line 934. Package natbib Warning: Citation `Walkley1999' on page 482 undefined on input l ine 936. Package natbib Warning: Citation `WeiKirby1995' on page 482 undefined on input line 936. LaTeX Warning: Reference `eq:lopes:dissdisp' on page 482 undefined on input lin e 963. [482] Package natbib Warning: Citation `WeiKirbySinha1999' on page 483 undefined on i nput line 975. Package natbib Warning: Citation `Peregrine1967' on page 483 undefined on input line 979. Package natbib Warning: Citation `Nwogu1993' on page 483 undefined on input lin e 980. Package natbib Warning: Citation `WeiKirbySinha1999' on page 483 undefined on i nput line 1000. LaTeX Warning: Reference `eq:lopes:ztc-a' on page 483 undefined on input line 1 001. LaTeX Warning: Reference `eq:lopes:fullrefl' on page 483 undefined on input lin e 1028. LaTeX Warning: Reference `eq:lopes:ztc-b' on page 483 undefined on input line 1 031. [483] Package natbib Warning: Citation `Walkley1999' on page 484 undefined on input l ine 1060. Package natbib Warning: Citation `LovholtPedersen2009' on page 484 undefined on input line 1068. Package natbib Warning: Citation `LovholtPedersen2009' on page 484 undefined on input line 1072. Package natbib Warning: Citation `LovholtPedersen2009' on page 484 undefined on input line 1091. LaTeX Warning: Reference `eq:lopes:varform' on page 484 undefined on input line 1092. LaTeX Warning: Reference `eq:lopes:varform' on page 484 undefined on input line 1101. LaTeX Warning: Reference `eq:lopes:eigenvalue' on page 484 undefined on input l ine 1108. Underfull \vbox (badness 10000) has occurred while \output is active [484] Package natbib Warning: Citation `LovholtPedersen2009' on page 485 undefined on input line 1175. LaTeX Warning: Reference `eq:lopes:exp' on page 485 undefined on input line 117 9. LaTeX Warning: Reference `eq:lopes:eigenvalue' on page 485 undefined on input l ine 1179. LaTeX Warning: Reference `fig:lopes:spikeshelf' on page 485 undefined on input line 1195. (./chapters/lopes/pdf/spike_shelf.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/spike_shelf.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `fig:lopes:spectrum1' on page 485 undefined on input l ine 1207. LaTeX Warning: Reference `fig:lopes:spectrum3' on page 485 undefined on input l ine 1207. LaTeX Warning: Reference `fig:lopes:spectrumhm1' on page 485 undefined on input line 1218. LaTeX Warning: Reference `fig:lopes:spectrumhm3' on page 485 undefined on input line 1218. [485] [103 Package natbib Warning: Citation `LovholtPedersen2009' on page 486 undefined on input line 1229. Package natbib Warning: Citation `LovholtPedersen2009' on page 486 undefined on input line 1236. LaTeX Warning: Reference `fig:lopes:spectrum1' on page 486 undefined on input l ine 1241. LaTeX Warning: Reference `fig:lopes:spectrumhm3' on page 486 undefined on input line 1241. ] Underfull \hbox (badness 1377) in paragraph at lines 1290--1290 \T1/pplx/m/n/9 (+20) pan-els) and ZTC (lower pan-els) Underfull \hbox (badness 1377) in paragraph at lines 1305--1305 \T1/pplx/m/n/9 (+20) pan-els) and ZTC (lower pan-els) Underfull \hbox (badness 1377) in paragraph at lines 1319--1319 \T1/pplx/m/n/9 (+20) pan-els) and ZTC (lower pan-els) Package natbib Warning: Citation `Walkley1999' on page 486 undefined on input l ine 1343. Package natbib Warning: Citation `HairerWanner1991b' on page 486 undefined on i nput line 1345. [486 <./chapters/lopes/pdf/spike_shelf.pdf> <./chapters/lopes/png/L2_spike_stab ility.png> <./chapters/lopes/png/L2_shelf_stability.png [104]> <./chapters/lopes/png/ L1_spike_stability.png> <./chapters/lopes/png/L1_shelf_stability.png [105>]] [487 <./ chapters/lopes/png/L0_5_spike_stability.png [106 <./chapters/logg-2/png/refined_ cube.png (PNG copy)>] [107]> <./chapters/lopes/png/L0_5_shelf_s tability.png> <./chapters/lopes/png/L2_dx_0_02_hm_spike_spectrum_StdPot.png [108] (./chapters/logg-2/pdf/femsolution.pdf_tex pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/femsolution.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed )> <. /chapters/lopes/png/L2_dx_0_02_hm_shelf_spectrum_StdPot.png [109] [110 <./chapters/logg-2/pdf/fe msolution.pdf>]> <./chapters/lopes/ png/L2_dx_0_02_hm_spike_spectrum_Zhao.png [111] [112]> <./chapters/lopes/png/L2_dx_0_02_hm_ shelf_spectrum_Zhao.png [113] [114]> <./chapters/lopes/png/L1_dx_0_1_hm_spike_spectrum_StdP ot.png [115]> <./chapters/lopes/png/L1_dx_0_1_hm_shelf_spectrum_StdPot.png [116]> <./chapte rs/lopes/png/L1_dx_0_1_hm_spike_spectrum_Zhao.png [117]> <./chapters/lopes/png/L1_dx_ 0_1_hm_shelf_spectrum_Zhao.png [118]>] [119] LaTeX Warning: Reference `eq:lopes:solita' on page 488 undefined on input line 1356. LaTeX Warning: Reference `eq:lopes:solitp' on page 488 undefined on input line 1375. [488 <./chapters/lopes/png/L0_5_dx_0_25_hm_spike_spectrum_StdPot.png> <./chapte rs/lopes/png/L0_5_dx_0_25_hm_shelf_spectrum_StdPot.png Underfull \vbox (badness 1448) has occurred while \output is active [120]> <./chapters/lopes/png/L 0_5_dx_0_25_hm_spike_spectrum_Zhao.png> <./chapters/lopes/png/L0_5_dx_0_25_hm_s helf_spectrum_Zhao.png [121] >] [122] [123 <./chapters/logg-2/png/plot_mesh .png (PNG copy)> <./chapters/logg-2/png/plots.png (PNG copy)>] [124] LaTeX Warning: Reference `eq:lopes:varform' on page 489 undefined on input line 1436. LaTeX Warning: Reference `chap:langtangen' on page 489 undefined on input line 1437. [489] Underfull \hbox (badness 1184) in paragraph at lines 2529--2532 \T1/pplx/m/n/10 (+20) One can-not read-/write \T1/fvm/m/n/10 Function \T1/pplx/ m/n/10 (+20) and \T1/fvm/m/n/10 FunctionSpace \T1/pplx/m/n/10 (+20) ob-jects si nce the rep-re-sen-ta-tion of a [125] [126] [127] [128] LaTeX Warning: Reference `eq:lopes:pc' on page 490 undefined on input line 1498 . [490] LaTeX Warning: Reference `fig:lopes:submergedbar' on page 491 undefined on inpu t line 1520. [129] LaTeX Warning: Reference `fig:lopes:zhaonwogu' on page 491 undefined on input l ine 1533. LaTeX Warning: Reference `eq:lopes:solita' on page 491 undefined on input line 1535. LaTeX Warning: Reference `eq:lopes:solitb' on page 491 undefined on input line 1535. LaTeX Warning: Reference `fig:lopes:spikes' on page 491 undefined on input line 1546. LaTeX Warning: Reference `fig:lopes:znspike01' on page 491 undefined on input l ine 1548. LaTeX Warning: Reference `fig:lopes:znspike025' on page 491 undefined on input line 1554. LaTeX Warning: Reference `fig:lopes:zn05' on page 491 undefined on input line 1 556. LaTeX Warning: Reference `fig:lopes:zn05' on page 491 undefined on input line 1 556. LaTeX Warning: `!h' float specifier changed to `!ht'. LaTeX Warning: `!h' float specifier changed to `!ht'. [491 <./chapters/lopes/pdf/submergedbar.pdf>] [130] [492 <./chapters/lopes/pdf/ZhaoNw ogu.pdf> <./chapters/lopes/pdf/deptheps.pdf>] [493 <./chapters/lopes/pdf/epsilo n0_1.pdf> <./chapters/lopes/pdf/epsilon0_25.pdf>] [131] Package natbib Warning: Citation `WeiKirby1995' on page 494 undefined on input line 1638. Package natbib Warning: Citation `WooLiu2004a' on page 494 undefined on input l ine 1638. LaTeX Warning: Reference `eq:lopes:fullrefl' on page 494 undefined on input lin e 1643. Package natbib Warning: Citation `Kirby1998' on page 494 undefined on input lin e 1658. LaTeX Warning: Reference `fig:lopes:symmetry' on page 494 undefined on input li ne 1663. Overfull \hbox (1.6556pt too wide) in paragraph at lines 3058--3067 [][] [132 <./chapters/logg-2/png/coloured.png (PNG copy)> <./chapters/logg-2/png/par tition.png (PNG copy)>] LaTeX Warning: Reference `fig:lopes:unstmesh' on page 494 undefined on input li ne 1684. LaTeX Warning: Reference `fig:lopes:unstdetail' on page 494 undefined on input line 1692. [133] [494 <./chapters/lopes/pdf/epsilon0_5. pdf>] [134] [495 <./chapters/lopes/pdf/eta000000.pdf> <./chapters/lopes/pdf/eta002000 .pdf> <./chapters/lopes/pdf/eta004000.pdf> <./chapters/lopes/pdf/eta006000.pdf> <./chapters/lopes/pdf/eta007972.pdf> <./chapters/lopes/pdf/eta009946.pdf>] [496 <./chapters/lopes/pdf/unstr.pdf> <./chapters/lopes/pdf/unstrcorner.pdf>] LaTeX Warning: Reference `fig:lopes:harbor' on page 497 undefined on input line 1751. LaTeX Warning: Reference `eq:lopes:varform' on page 497 undefined on input line 1752. LaTeX Warning: Reference `sec:lopes:numericalmethods' on page 497 undefined on input line 1753. LaTeX Warning: Reference `fig:lopes:harbor_depth' on page 497 undefined on inpu t line 1758. LaTeX Warning: Reference `fig:lopes:potential1' on page 497 undefined on input line 1758. LaTeX Warning: Reference `fig:lopes:scale' on page 497 undefined on input line 1759. LaTeX Warning: Reference `fig:lopes:harbor_depth' on page 497 undefined on inpu t line 1761. LaTeX Warning: Reference `fig:lopes:sponge' on page 497 undefined on input line 1762. LaTeX Warning: Reference `eq:lopes:sponge' on page 497 undefined on input line 1765. LaTeX Warning: Reference `fig:lopes:sponge' on page 497 undefined on input line 1769. LaTeX Warning: Reference `eq:lopes:dirichleteta' on page 497 undefined on input line 1771. LaTeX Warning: Reference `eq:lopes:dirichletphi' on page 497 undefined on input line 1772. Underfull \vbox (badness 4048) has occurred while \output is active [497 <./cha pters/lopes/pdf/detail_unstr.pdf>] LaTeX Warning: Reference `fig:lopes:elevation' on page 498 undefined on input l ine 1796. LaTeX Warning: Reference `fig:lopes:potential1' on page 498 undefined on input line 1802. LaTeX Warning: Reference `fig:lopes:etap' on page 498 undefined on input line 1 803. LaTeX Warning: Reference `fig:lopes:velp' on page 498 undefined on input line 1 803. (./chapters/lopes/pdf/scale_tex.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/scale_tex.pdf): PDF inclusi on: found PDF version <1.5>, but at most version <1.4> allowed ) (./chapters/lopes/pdf/sponge_tex.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/sponge_tex.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \hbox (badness 1533) in paragraph at lines 3274--3279 [] []\T1/pplx/m/it/10 Con-struct-ing ar-gu-ments (trial and test func-tions).[] \T1/pplx/m/n/10 (+20) The \T1/fvm/m/n/10 ufl.Argument \T1/pplx/m/n/10 (+20) cl ass (the base class of [135 ] LaTeX Warning: Reference `eq:lopes:varform' on page 498 undefined on input line 1885. LaTeX Warning: Reference `sec:lopes:numericalmethods' on page 498 undefined on input line 1886. [498 <./chapters/lopes/pdf/scale_tex.pdf> <./chapters/lopes/pdf/depth.pdf>] [499 <./chapters/lopes/pdf/sponge_tex.pdf> <./chapters/lopes/pdf/eta.pdf> <./ch apters/lopes/pdf/pvel2.pdf>] [500 <./chapters/lopes/pdf/etaprofile.pdf> <./chap ters/lopes/pdf/velprofile.pdf>] LaTeX Warning: Reference `fig:lopes:objectbottom' on page 501 undefined on inpu t line 1918. LaTeX Warning: Reference `fig:lopes:objectbottom2' on page 501 undefined on inp ut line 1918. pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/depth0.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/depth6.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed [136 LaTeX Warning: Reference `fig:lopes:objectsurface0' on page 501 undefined on in put line 1941. LaTeX Warning: Reference `fig:lopes:objectsurface3' on page 501 undefined on in put line 1941. LaTeX Warning: Reference `fig:lopes:scale' on page 501 undefined on input line 1945. [501 <./chapters/lopes/pdf/depth0.pdf]> <./chapters/lopes/pdf/depth6.pdf>] pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/eta3.pdf): PDF inclusion: f ound PDF version <1.5>, but at most version <1.4> allowed [502 <./chapters/lopes/pdf/eta1.pdf> <./chap ters/lopes/pdf/eta3.pdf> <./chapters/lopes/pdf/eta45.pdf>] pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/eta6.pdf): PDF inclusion: f ound PDF version <1.5>, but at most version <1.4> allowed Underfull \vbox (badness 1377) has occurred while \output is active [137] LaTeX Warning: Reference `eq:lopes:bottom1' on page 503 undefined on input line 1989. LaTeX Warning: Reference `eq:lopes:bottom4' on page 503 undefined on input line 1989. Package natbib Warning: Citation `LopesPereiraTrabucho' on page 503 undefined o n input line 1996. Package natbib Warning: Citation `ZhaoTengCheng2004' on page 503 undefined on i nput line 2009. [503 <./chapters/lopes/pdf/eta6.pdf>] Package natbib Warning: Citation `LopesPereiraTrabucho' on page 504 undefined o n input line 2083. ) (./tex/26.tex [504] Chapter 26. [505] LaTeX Warning: Reference `eq:oelgaard-1:gov_generic' on page 506 undefined on i nput line 119. LaTeX Warning: Reference `eq:oelgaard-1:gov_jacobian' on page 506 undefined on input line 135. LaTeX Warning: Reference `eq:oelgaard-1:gov_residual' on page 506 undefined on input line 136. LaTeX Warning: Reference `eq:oelgaard-1:linear_weak_form' on page 506 undefined on input line 138. LaTeX Warning: Reference `eq:oelgaard-1:gov_generic' on page 506 undefined on i nput line 140. Underfull \vbox (badness 10000) has occurred while \output is active [506] LaTeX Warning: Reference `eq:oelgaard-1:gov_balance_momentum' on page 507 undef ined on input line 180. LaTeX Warning: Reference `eq:oelgaard-1:gov_balance_momentum' on page 507 undef ined on input line 187. LaTeX Warning: Reference `eq:oelgaard-1:gov_neumann_bc' on page 507 undefined o n input line 198. Package natbib Warning: Citation `Holzapfel2000' on page 507 undefined on input line 222. Underfull \vbox (badness 1917) has occurred while \output is active [507 Underfull \vbox (badness 1067) has occurred while \output is active [138]] LaTeX Warning: Reference `eq:oelgaard-1:gov_potential_energy' on page 508 undef ined on input line 253. LaTeX Warning: Reference `eq:oelgaard-1:gov_generic' on page 508 undefined on i nput line 263. Package natbib Warning: Citation `Lubliner2008' on page 508 undefined on input line 330. [508] LaTeX Warning: Reference `sec:oelgaard-1:examples_plasticity' on page 509 undef ined on input line 404. Underfull \vbox (badness 10000) has occurred while \output is active [509] LaTeX Warning: Reference `eq:oelgaard-1:elas_stress_def' on page 510 undefined on input line 422. LaTeX Warning: Reference `eq:oelgaard-1:gov_energy_variation' on page 510 undef ined on input line 424. LaTeX Warning: Reference `eq:oelgaard-1:elas_stress_def' on page 510 undefined on input line 426. LaTeX Warning: Reference `eqn:oelgaard-1:F' on page 510 undefined on input line 427. Package natbib Warning: Citation `bonet1997' on page 510 undefined on input lin e 432. LaTeX Warning: Reference `eq:oelgaard-1:hyp_small_strain_energy' on page 510 un defined on input line 450. LaTeX Warning: Reference `chap:alnes-1' on page 510 undefined on input line 476 . Underfull \vbox (badness 10000) has occurred while \output is active [510] LaTeX Warning: Reference `eq:oelgaard-1:time_u_n1' on page 511 undefined on inp ut line 516. LaTeX Warning: Reference `eq:oelgaard-1:time_v_n1' on page 511 undefined on inp ut line 517. LaTeX Warning: Reference `eq:oelgaard-1:time_a_n1' on page 511 undefined on inp ut line 541. LaTeX Warning: Reference `eq:oelgaard-1:time_v(u)_n1' on page 511 undefined on input line 542. LaTeX Warning: Reference `eqn:oelgaard-1:F' on page 511 undefined on input line 552. Package natbib Warning: Citation `SimoTaylor1985' on page 511 undefined on inpu t line 557. LaTeX Warning: Reference `chap:logg-1' on page 511 undefined on input line 568. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_F' on page 511 undefined on i nput line 589. [511] [139] LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_f' on page 512 undefined on i nput line 605. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_f' on page 512 undefined on i nput line 608. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_linearised_stiffness' on page 512 undefined on input line 616. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_stress' on page 512 undefined on input line 637. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_strain' on page 512 undefined on input line 638. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_linearised_stiffness' on page 512 undefined on input line 639. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_f' on page 512 undefined on i nput line 647. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_F' on page 512 undefined on i nput line 649. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_k_star' on page 512 undefined on input line 669. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_k' on page 512 undefined on i nput line 670. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_k' on page 512 undefined on i nput line 672. LaTeX Warning: Reference `eq:oelgaard-1:lin_issue_F' on page 512 undefined on i nput line 673. LaTeX Warning: Reference `eq:oelgaard-1:hyp_neo_hookean' on page 512 undefined on input line 680. [512]) [513 (./tex/17.tex] [140] Chapter 4. Underfull \vbox (badness 1092) has occurred while \output is active [141] [142] Underfull \vbox (badness 10000) has occurred while \output is active [143] [144] [145] [146] LaTeX Warning: Reference `eq:oelgaard-1:quad_elem_mass_form' on page 514 undefi ned on input line 802. LaTeX Warning: Reference `fig:oelgaard-1:plas_nonlinear_poisson_code' on page 5 14 undefined on input line 823. LaTeX Warning: Reference `tab:oelgaard-1:plas_nonlinear_poisson_convergence' on page 514 undefined on input line 826. LaTeX Warning: Reference `eq:oelgaard-1:plas_nonlinear_poisson' on page 514 und efined on input line 891. LaTeX Warning: Reference `eq:oelgaard-1:plas_nonlinear_poisson' on page 514 und efined on input line 891. LaTeX Warning: Reference `fig:oelgaard-1:plas_nonlinear_poisson_code' on page 5 14 undefined on input line 902. LaTeX Warning: Reference `fig:oelgaard-1:plas_nonlinear_poisson_code' on page 5 14 undefined on input line 902. [514] [515 [147]] [148] [149] [150] [151] [152] LaTeX Warning: Reference `chap:langtangen' on page 516 undefined on input line 942. LaTeX Warning: Reference `chap:logg-2' on page 516 undefined on input line 942. LaTeX Warning: Reference `eq:oelgaard-1:elas_stress_def' on page 516 undefined on input line 949. LaTeX Warning: Reference `eqn:oelgaard-1:F' on page 516 undefined on input line 950. LaTeX Warning: Reference `fig:oelgaard-1:elas_code' on page 516 undefined on in put line 952. LaTeX Warning: Reference `fig:oelgaard-1:elas_code' on page 516 undefined on in put line 953. LaTeX Warning: Reference `fig:oelgaard-1:elas_code' on page 516 undefined on in put line 958. LaTeX Warning: Reference `fig:oelgaard-1:elas_code' on page 516 undefined on in put line 960. LaTeX Warning: Reference `sec:oelgaard-1:plasticity' on page 516 undefined on i nput line 1014. LaTeX Warning: Reference `eq:oelgaard-1:plas_yield_function' on page 516 undefi ned on input line 1017. Package natbib Warning: Citation `SimoHughes1998' on page 516 undefined on inpu t line 1020. LaTeX Warning: Reference `eq:oelgaard-1:plas_stress_def' on page 516 undefined on input line 1024. LaTeX Warning: Reference `eq:oelgaard-1:plas_strain_decomposed' on page 516 und efined on input line 1025. [516] [517] [153] [154] LaTeX Warning: Reference `eq:oelgaard-1:rm_stress_strain' on page 518 undefined on input line 1046. LaTeX Warning: Reference `eq:oelgaard-1:rm_plas_strain' on page 518 undefined o n input line 1047. LaTeX Warning: Reference `eq:oelgaard-1:rm_trial_stress' on page 518 undefined on input line 1058. LaTeX Warning: Reference `eq:oelgaard-1:rm_stress_strain' on page 518 undefined on input line 1059. LaTeX Warning: Reference `eq:oelgaard-1:rm_plas_strain' on page 518 undefined o n input line 1060. LaTeX Warning: Reference `eq:oelgaard-1:rm_trial_stress' on page 518 undefined on input line 1071. LaTeX Warning: Reference `eq:oelgaard-1:plas_yield_function' on page 518 undefi ned on input line 1072. LaTeX Warning: Reference `fig:oelgaard-1:plasticity_interface' on page 518 unde fined on input line 1134. [518] [155] [156] (/usr/share/texmf-texlive/tex/latex/microtype/mt-euf.cfg) [157] (./chapters/alnes-1/pdf/expr.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/expr.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [158 <./chapters/alnes-1/pdf/expr.pdf>] (./chapters/alnes-1/pdf/stiffness.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/stiffness.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \hbox (badness 1668) in paragraph at lines 1415--1415 []\T1/pplx/m/n/9 (+20) Figure 4.3: |Ex-pres-sion tree for [159] LaTeX Warning: Reference `chap:logg-2' on page 519 undefined on input line 1188 . LaTeX Warning: Reference `fig:oelgaard-1:plas_ufl_code' on page 519 undefined o n input line 1193. LaTeX Warning: Reference `fig:oelgaard-1:plas_ufl_code' on page 519 undefined o n input line 1197. LaTeX Warning: Reference `sec:oelgaard-1:linearization' on page 519 undefined o n input line 1199. LaTeX Warning: Reference `fig:oelgaard-1:plas_ufl_code' on page 519 undefined o n input line 1202. Underfull \vbox (badness 2181) has occurred while \output is active [519] [160 <./chapters/alnes-1/pdf/stiffness.pdf>] LaTeX Warning: Reference `fig:oelgaard-1:plas_cpp_code' on page 520 undefined o n input line 1237. LaTeX Warning: Reference `fig:oelgaard-1:plasticity_interface' on page 520 unde fined on input line 1248. LaTeX Warning: Reference `chap:logg-2' on page 520 undefined on input line 1256 . LaTeX Warning: Reference `sec:oelgaard-1:minimization' on page 520 undefined on input line 1328. LaTeX Warning: Reference `eq:oelgaard-1:hyp_neo_hookean' on page 520 undefined on input line 1329. LaTeX Warning: Reference `fig:oelgaard-1:hyperelastic_solver_code' on page 520 undefined on input line 1337. LaTeX Warning: Reference `fig:oelgaard-1:hyperelastic_solver_code' on page 520 undefined on input line 1343. LaTeX Warning: Reference `sec:oelgaard-1:minimization' on page 520 undefined on input line 1344. LaTeX Warning: Reference `sec:oelgaard-1:hyperelasticity' on page 520 undefined on input line 1345. [520] [521] [161] Underfull \vbox (badness 10000) has occurred while \output is active [162] [163] [164] [165] [166 Underfull \hbox (badness 1178) in paragraph at lines 1410--1410 []\T1/pplx/m/n/9 (+20) Figure 26.6: |Com-plete DOLFIN Underfull \hbox (badness 1102) in paragraph at lines 1410--1410 \T1/pplx/m/n/9 (+20) solver for the com-press-ible neo- LaTeX Warning: Reference `fig:oelgaard-1:hyperelastic_solver_code' on page 522 undefined on input line 1414. LaTeX Warning: Reference `sec:oelgaard-1:time_integration' on page 522 undefine d on input line 1428. LaTeX Warning: Reference `eq:oelgaard-1:elas_stress_def' on page 522 undefined on input line 1430. LaTeX Warning: Reference `fig:oelgaard-1:time_ufl_code' on page 522 undefined o n input line 1442. LaTeX Warning: Reference `fig:oelgaard-1:time_ufl_code2' on page 522 undefined on input line 1443. LaTeX Warning: Reference `sec:oelgaard-1:time_integration' on page 522 undefine d on input line 1444. LaTeX Warning: Reference `fig:oelgaard-1:time_ufl_code2' on page 522 undefined on input line 1530. LaTeX Warning: Reference `fig:oelgaard-1:time_ufl_code2' on page 522 undefined on input line 1530. LaTeX Warning: Float too large for page by 23.41197pt on input line 1532. ) (./tex/27.tex] [522] [523] [524] [525] [526] Chapter 27. Package natbib Warning: Citation `Holzapfel2000' on page 527 undefined on input line 41. Package natbib Warning: Citation `TruesdellNoll1965' on page 527 undefined on i nput line 42. Package natbib Warning: Citation `LoggWells2010' on page 527 undefined on input line 64. Package natbib Warning: Citation `AlnaesLogg2009' on page 527 undefined on inpu t line 65. Package natbib Warning: Citation `TruesdellToupin1960' on page 527 undefined on input line 88. Package natbib Warning: Citation `TruesdellNoll1965' on page 527 undefined on i nput line 88. Package natbib Warning: Citation `Gurtin1981' on page 527 undefined on input li ne 89. Package natbib Warning: Citation `Ogden1997' on page 527 undefined on input lin e 89. Package natbib Warning: Citation `Holzapfel2000' on page 527 undefined on input line 90. [527] LaTeX Warning: Reference `fig:narayanan:continuumpotato' on page 528 undefined on input line 142. [528 <./chapter s/narayanan/images/pdf/continuumpotato.pdf>] [167] LaTeX Warning: Reference `eq:narayanan:balance-of-momentum' on page 529 undefin ed on input line 172. Package natbib Warning: Citation `SimoHughes1998' on page 529 undefined on inpu t line 194. LaTeX Warning: Reference `eq:narayanan:balance-of-momentum' on page 529 undefin ed on input line 202. Package natbib Warning: Citation `Holzapfel2000' on page 529 undefined on input line 213. LaTeX Warning: Reference `tab:narayanan:straindefs' on page 529 undefined on in put line 296. LaTeX Warning: Reference `tab:narayanan:straindefs' on page 529 undefined on in put line 296. Underfull \hbox (badness 4316) in paragraph at lines 296--296 []\T1/pplx/m/n/9 (+20) Figure 27.2: |Sam-ples of how LaTeX Warning: Reference `tab:narayanan:straindefs' on page 529 undefined on in put line 301. LaTeX Warning: Reference `code:narayanan:kinematics.py' on page 529 undefined o n input line 303. [529] [530] [168] LaTeX Warning: Reference `eq:narayanan:secondpk' on page 531 undefined on input line 345. LaTeX Warning: Reference `tab:narayanan:straindefs' on page 531 undefined on in put line 350. LaTeX Warning: Reference `code:narayanan:material_model_base.py' on page 531 un defined on input line 353. LaTeX Warning: Reference `code:narayanan:svk' on page 531 undefined on input li ne 402. LaTeX Warning: Reference `code:narayanan:mr' on page 531 undefined on input lin e 402. Package natbib Warning: Citation `MarckmannVerron2006' on page 531 undefined on input line 409. [531] Underfull \hbox (badness 1019) in paragraph at lines 449--449 \T1/pplx/m/n/9 (+20) en-ergy func-tion for a two term Package natbib Warning: Citation `SimoHughes1998' on page 532 undefined on inpu t line 461. LaTeX Warning: Reference `eq:narayanan:balance-of-momentum' on page 532 undefin ed on input line 466. [532] [169] LaTeX Warning: Reference `eq:narayanan:weakform' on page 533 undefined on input line 501. LaTeX Warning: Reference `eq:narayanan:weakform' on page 533 undefined on input line 510. LaTeX Warning: Reference `eq:narayanan:staticweakform' on page 533 undefined on input line 528. LaTeX Warning: Reference `chap:alnes-1' on page 533 undefined on input line 549 . LaTeX Warning: Reference `code:narayanan:staticmomentumsolver' on page 533 unde fined on input line 551. Underfull \hbox (badness 10000) in paragraph at lines 597--597 []\T1/pplx/m/n/9 (+20) Figure 27.6: |The rel-e- Underfull \hbox (badness 10000) in paragraph at lines 597--597 \T1/pplx/m/n/9 (+20) vant sec-tion of the class Underfull \hbox (badness 10000) in paragraph at lines 597--597 \T1/fvm/m/n/9 StaticMomentumBalanceSolver\T1/pplx/m/n/9 (+20) , LaTeX Warning: Reference `eq:narayanan:weakform' on page 533 undefined on input line 607. Package natbib Warning: Citation `ErikssonEstepHansboEtAl1996' on page 533 unde fined on input line 608. LaTeX Warning: Reference `eq:narayanan:weakform' on page 533 undefined on input line 609. Underfull \vbox (badness 1571) has occurred while \output is active [533] [170] LaTeX Warning: Reference `code:narayanan:cg1' on page 534 undefined on input li ne 662. LaTeX Warning: Reference `eq:narayanan:cg1weakformapprox' on page 534 undefined on input line 664. LaTeX Warning: Reference `eq:narayanan:cg1weakformapprox' on page 534 undefined on input line 722. LaTeX Warning: Reference `fig:narayanan:energies' on page 534 undefined on inpu t line 725. [534] [535] Package natbib Warning: Citation `HilberHughesTaylor1977' on page 536 undefined on input line 733. Package natbib Warning: Citation `Hughes1987' on page 536 undefined on input li ne 735. LaTeX Warning: Reference `eq:narayanan:hhtdefs' on page 536 undefined on input line 778. LaTeX Warning: Reference `eq:narayanan:newaccn' on page 536 undefined on input line 791. LaTeX Warning: Reference `eq:narayanan:hhtdefs' on page 536 undefined on input line 792. LaTeX Warning: Reference `code:narayanan:dynamicrelease' on page 536 undefined on input line 800. [536] LaTeX Warning: Reference `code:narayanan:statictwist' on page 537 undefined on input line 841. LaTeX Warning: Reference `code:narayanan:statictwist' on page 537 undefined on input line 860. [537 <./chapters/narayanan/images/png/twistedcube.png (PNG copy)>] LaTeX Warning: Reference `code:narayanan:solveproblem' on page 538 undefined on input line 907. LaTeX Warning: Reference `tab:narayanan:residualnorms' on page 538 undefined on input line 909. LaTeX Warning: Reference `fig:narayanan:twistedcube' on page 538 undefined on i nput line 911. LaTeX Warning: Reference `code:narayanan:dynamicrelease' on page 538 undefined on input line 963. [538] [171] LaTeX Warning: Reference `fig:narayanan:releasedcube' on page 539 undefined on input line 1020. LaTeX Warning: Reference `fig:narayanan:energies' on page 539 undefined on inpu t line 1020. Underfull \vbox (badness 1681) has occurred while \output is active [172] [173] LaTeX Warning: Reference `code:narayanan:fishyflow' on page 539 undefined on in put line 1084. LaTeX Warning: Reference `code:narayanan:manualstep' on page 539 undefined on i nput line 1127. LaTeX Warning: Reference `chap:selim' on page 539 undefined on input line 1156. LaTeX Warning: Reference `code:narayanan:manualstep' on page 539 undefined on i nput line 1159. [539] [540] [541 <./chapters/narayanan/images/png/release_000.png (PNG copy)> < ./chapters/narayanan/images/png/release_100.png (PNG copy)> <./chapters/narayan an/images/png/release_200.png (PNG copy)> <./chapters/narayanan/images/png/rele ase_300.png (PNG copy)> <./chapters/narayanan/images/png/release_400.png (PNG c opy)> <./chapters/narayanan/images/png/release_500.png (PNG copy)>] [542 <./cha pters/narayanan/images/pdf/energies.pdf>] LaTeX Warning: Reference `fig:narayanan:tumblingdolphin' on page 543 undefined on input line 1166. [174] [175] ) [176] Chapter 5. [177] [178] (./manual.bbl [179] [180] [181] [182 ] [183] [184] ) (./manual.ind [185]) (./tex/28.tex [543] [544 <./chapters/narayanan/images/png/dolphin_000.png (PNG copy)> <./chapters/n arayanan/images/png/dolphin_001.png (PNG copy)> <./chapters/narayanan/images/pn g/dolphin_002.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_003.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_004.png (PNG copy)> <./cha pters/narayanan/images/png/dolphin_005.png (PNG copy)> <./chapters/narayanan/im ages/png/dolphin_006.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_0 07.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_008.png (PNG copy)> ] Chapter 28. LaTeX Warning: Reference `chap:hoffman-2' on page 545 undefined on input line 1 9. Package natbib Warning: Citation `Sagaut2005' on page 545 undefined on input li ne 56. [545] [186] Package natbib Warning: Citation `Sagaut2005' on page 546 undefined on input li ne 69. Package natbib Warning: Citation `HoffmanJohnson2007' on page 546 undefined on input line 71. Package natbib Warning: Citation `HoffmanJohnson2007' on page 546 undefined on input line 78. Package natbib Warning: Citation `SagautDeckTerracol2006' on page 546 undefined on input line 101. Package natbib Warning: Citation `PiomelliBalaras2002' on page 546 undefined on input line 101. Package natbib Warning: Citation `Schumann1975' on page 546 undefined on input line 104. Package natbib Warning: Citation `ErikssonEstepEtAl1995' on page 546 undefined on input line 134. Package natbib Warning: Citation `BeckerRannacher2001' on page 546 undefined on input line 134. Package natbib Warning: Citation `GilesSuli2002' on page 546 undefined on input line 134. [546] [187 Package natbib Warning: Citation `HoffmanJohnson2007' on page 547 undefined on input line 150. Package natbib Warning: Citation `Hoffman2005' on page 547 undefined on input l ine 161. Package natbib Warning: Citation `HoffmanJohnson2006b' on page 547 undefined on input line 161. Package natbib Warning: Citation `Hoffman2006' on page 547 undefined on input l ine 161. Package natbib Warning: Citation `Hoffman2009' on page 547 undefined on input l ine 161. Package natbib Warning: Citation `HoffmanJansson2009' on page 547 undefined on input line 161. Package natbib Warning: Citation `VilelaJanssonEtAl2010' on page 547 undefined on input line 161. Package natbib Warning: Citation `HoffmanJanssonStockli2011' on page 547 undefi ned on input line 178. Package natbib Warning: Citation `Hansbo2000' on page 547 undefined on input li ne 195. Package natbib Warning: Citation `HoffmanJanssonStockli2011' on page 547 undefi ned on input line 195. [547]] [188] LaTeX Warning: Reference `hoffman-1:fig:cube1' on page 548 undefined on input l ine 216. Package natbib Warning: Citation `Mccormick1995' on page 548 undefined on input line 221. Package natbib Warning: Citation `Mccormick1995' on page 548 undefined on input line 226. LaTeX Warning: Reference `hoffman-1:fig:cube2' on page 548 undefined on input l ine 229. LaTeX Warning: Reference `hoffman-1:fig:cube3' on page 548 undefined on input l ine 230. LaTeX Warning: Reference `hoffman-1:fig:cube3' on page 548 undefined on input l ine 236. Package natbib Warning: Citation `HoffmanJansson2011' on page 548 undefined on input line 246. Overfull \hbox (7.21391pt too wide) in paragraph at lines 315--317 []\T1/pplx/m/n/10 (-20) LBB con-di-tions, \T1/pplx/m/it/10 see \T1/pplx/m/n/10 (-20) Ladyzhenskaya--BabuČka--Brezzi [189] [190 ]) Package caption Warning: Unused \captionsetup[subalgorithm] on input line 8. (./manual.aux ) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (\end occurred inside a group at level 1) ### simple group (level 1) entered at line 58 ({) ### bottom level (see the transcript file for additional information)pdfTeX warning (dest): name {Hfootnote.11} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.10} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.9} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.8} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.7} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.6} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.5} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.4} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.3} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.2} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.1} has been referenced but does not exist , replaced by a fixed one { Package natbib Warning: Citation `HoffmanJansson2009' on page 548 undefined on input line 289. Package natbib Warning: Citation `Zdravkovich2003' on page 548 undefined on inp ut line 296. Package natbib Warning: Citation `Zdravkovich2003' on page 548 undefined on inp ut line 299. LaTeX Warning: Reference `hoffman-1:fig:1' on page 548 undefined on input line 302. LaTeX Warning: Reference `hoffman-1:fig:3' on page 548 undefined on input line 302. Package natbib Warning: Citation `HoffmanJohnson2008b' on page 548 undefined on input line 305. Package natbib Warning: Citation `HoffmanJansson2009' on page 548 undefined on input line 305. [548/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc} <./chapters/hoffman-1/png/ fig1b.png (PNG copy)>]> <./ chapters/hoffman-1/png/fig3b.png (PNG copy)>]> > > > Package natbib Warning: Citation `HoffmanJansson2009' on page 550 undefined on input line 315. Package natbib Warning: Citation `HoffmanJansson2009' on page 550 undefined on input line 315. Output written on manual.pdf (196 pages, 5247013 bytes). Transcript written on manual.log. Package natbib Warning: Citation `HoffmanJansson2009' on page 550 undefined on input line 327. Package natbib Warning: Citation `HoffmanJansson2009' on page 550 undefined on input line 327. Package natbib Warning: Citation `HoffmanJansson2009' on page 550 undefined on input line 339. Package natbib Warning: Citation `HoffmanJansson2009' on page 550 undefined on input line 339. Package natbib Warning: Citation `VilelaJanssonEtAl2010' on page 550 undefined on input line 352. Package natbib Warning: Citation `SpalartMejia2011' on page 550 undefined on in put line 355. [550 <./chapters/hoffman-1/png/Hoffman_fig2a.png (PNG copy)> <./chapters/hoffma n-1/png/Hoffman_fig2b.png (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig2c.p ng (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig2d.png (PNG copy)> <./chapt ers/hoffman-1/png/Hoffman_fig3a.png (PNG copy)> <./chapters/hoffman-1/png/Hoffm an_fig3b.png (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig3c.png (PNG copy) > <./chapters/hoffman-1/png/Hoffman_fig3d.png (PNG copy)>] LaTeX Warning: Reference `hoffman-1:rlg' on page 551 undefined on input line 36 7. LaTeX Warning: Reference `hoffman-1:tab:hoffman-1-rlg' on page 551 undefined on input line 374. Package natbib Warning: Citation `SpalartMejia2011' on page 551 undefined on in put line 403. Package natbib Warning: Citation `SpalartMejia2011' on page 551 undefined on in put line 403. Package natbib Warning: Citation `HronTurek2005' on page 551 undefined on input line 411. Package natbib Warning: Citation `HronTurek2005' on page 551 undefined on input line 414. Package natbib Warning: Citation `DunneRannacher2006' on page 551 undefined on input line 414. LaTeX Warning: Reference `hoffman-1:fig:flustruk' on page 551 undefined on inpu t line 417. Package natbib Warning: Citation `HoffmanJanssonStockli2011' on page 551 undefi ned on input line 422. [551 <./chapters/hoffman-1/png/Hoffman_fig5a.png (PNG copy)> <./chapters/hoffma n-1/png/Hoffman_fig5b.png (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig5c.p ng (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig5d.png (PNG copy)> <./chapt ers/hoffman-1/png/rlg_vorticity.png (PNG copy)> <./chapters/hoffman-1/png/oilfi lm_back_sim.png (PNG copy)>] Underfull \hbox (badness 1584) in paragraph at lines 431--431 \T1/pplx/m/n/9 (+20) benchmark prob-lem FLUSTRUK- Underfull \hbox (badness 1783) in paragraph at lines 431--431 \T1/pplx/m/n/9 (+20) uni-formly re-fined meshes us-ing LaTeX Warning: Reference `hoffman-1:fig:flag' on page 552 undefined on input li ne 436. Underfull \vbox (badness 10000) has occurred while \output is active [552 <./ch apters/hoffman-1/png/fsi_bench3D_displacement_aligned.pdf>] Package natbib Warning: Citation `HoffmanJanssonStockli2011' on page 553 undefi ned on input line 469. Package natbib Warning: Citation `HoffmanJanssonStockli2011' on page 553 undefi ned on input line 469. [553 <./chapters/hoffman-1/png/cube000.png (PNG copy)> <./chapters/hoffman-1/pn g/cube115.png (PNG copy)> <./chapters/hoffman-1/png/cube125.png (PNG copy)> <./ chapters/hoffman-1/png/cube168.png (PNG copy)> <./chapters/hoffman-1/png/cube18 7.png (PNG copy)> <./chapters/hoffman-1/png/cube405.png (PNG copy)> <./chapters /hoffman-1/png/cube550.png (PNG copy)> <./chapters/hoffman-1/png/cube649.png (P NG copy)>]) (./tex/29.tex [554] Chapter 29. Package natbib Warning: Citation `SelimLogg2011a' on page 555 undefined on inpu t line 76. Package natbib Warning: Citation `Dunne2007' on page 555 undefined on input lin e 76. Package natbib Warning: Citation `Dunne2006' on page 555 undefined on input lin e 76. Package natbib Warning: Citation `GratschBathe2006' on page 555 undefined on in put line 76. Package natbib Warning: Citation `BengzonLarson2010' on page 555 undefined on i nput line 76. Package natbib Warning: Citation `ZeeBrummelenBorst2008a' on page 555 undefined on input line 76. Package natbib Warning: Citation `Van2009' on page 555 undefined on input line 76. LaTeX Warning: Reference `selim:eq:momentum' on page 555 undefined on input lin e 92. LaTeX Warning: Reference `selim:eq:continuity' on page 555 undefined on input l ine 93. LaTeX Warning: Reference `selim:eq:traction' on page 555 undefined on input lin e 108. [555] LaTeX Warning: Reference `selim:eq:SVKcon' on page 556 undefined on input line 161. Package natbib Warning: Citation `Gurtin1981' on page 556 undefined on input li ne 164. Package natbib Warning: Citation `Holzapfel2000' on page 556 undefined on input line 164. Underfull \vbox (badness 1603) has occurred while \output is active [556] Package natbib Warning: Citation `Batchelor1967' on page 557 undefined on input line 197. Package natbib Warning: Citation `Panton1984' on page 557 undefined on input li ne 197. LaTeX Warning: Reference `selim:eq:NSmom' on page 557 undefined on input line 2 05. LaTeX Warning: Reference `selim:eq:NScon' on page 557 undefined on input line 2 05. LaTeX Warning: Reference `selim:eq:SVKmom' on page 557 undefined on input line 206. LaTeX Warning: Reference `selim:eq:SVKcon' on page 557 undefined on input line 206. Package natbib Warning: Citation `DoneaGiulianiHalleux1982' on page 557 undefin ed on input line 218. Package natbib Warning: Citation `DoneaHuertaPonthotEtAl2004' on page 557 undef ined on input line 218. LaTeX Warning: Reference `selim:fig:mapping' on page 557 undefined on input lin e 251. pdfTeX warning: pdflatex (file ./chapters/selim/pdf/mapping.pdf): PDF inclusion : found PDF version <1.5>, but at most version <1.4> allowed [557 <./chapters/selim/pdf/mapping.pdf>] Package natbib Warning: Citation `HermanssonHansbo2003' on page 558 undefined o n input line 286. Package natbib Warning: Citation `LopezNigroStorti2008' on page 558 undefined o n input line 286. LaTeX Warning: Reference `selim:eq:ALEtraction-1' on page 558 undefined on inpu t line 341. LaTeX Warning: Reference `selim:eq:ALEtraction-2' on page 558 undefined on inpu t line 341. LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 558 undefined on in put line 342. LaTeX Warning: Reference `selim:eq:FSIsystem-M' on page 558 undefined on input line 342. LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 558 undefined on in put line 358. LaTeX Warning: Reference `selim:eq:FSIsystem-M' on page 558 undefined on input line 358. LaTeX Warning: Reference `selim:eq:ALEtraction-1' on page 558 undefined on inpu t line 360. LaTeX Warning: Reference `selim:eq:ALEtraction-2' on page 558 undefined on inpu t line 360. LaTeX Warning: Reference `selim:fig:fp' on page 558 undefined on input line 362 . [558] LaTeX Warning: Reference `selim:eq:ALEtraction-1' on page 559 undefined on inpu t line 367. LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 559 undefined on in put line 419. LaTeX Warning: Reference `selim:eq:FSIsystem-M' on page 559 undefined on input line 419. LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 559 undefined on in put line 425. LaTeX Warning: Reference `selim:eq:FSIsystem-f-con' on page 559 undefined on in put line 425. Package natbib Warning: Citation `Goda1979' on page 559 undefined on input line 430. LaTeX Warning: Reference `selim:fig:fluidsolver' on page 559 undefined on input line 439. LaTeX Warning: Reference `chap:kvs-1' on page 559 undefined on input line 442. [559 <./chapters/selim/pdf/primal.pdf>] Package natbib Warning: Citation `ErikssonEstepHansboEtAl1996' on page 560 unde fined on input line 503. Package natbib Warning: Citation `HilberHughesTaylor1977' on page 560 undefined on input line 504. LaTeX Warning: Reference `selim:eq:FSIsystem-S' on page 560 undefined on input line 507. LaTeX Warning: Reference `selim:fig:structuresolver' on page 560 undefined on i nput line 512. LaTeX Warning: Reference `chap:narayanan' on page 560 undefined on input line 5 15. LaTeX Warning: Reference `selim:eq:FSIsystem-S' on page 560 undefined on input line 561. LaTeX Warning: Reference `selim:eq:FSIsystem-S' on page 560 undefined on input line 561. Package natbib Warning: Citation `FormaggiaNobile1999' on page 560 undefined on input line 574. [560] [561] LaTeX Warning: Reference `selim:fig:meshsolver' on page 562 undefined on input line 577. Package natbib Warning: Citation `ErikssonEstepEtAl1995' on page 562 undefined on input line 610. Package natbib Warning: Citation `BeckerRannacher2001' on page 562 undefined on input line 610. LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 562 undefined on in put line 622. LaTeX Warning: Reference `selim:eq:FSIsystem-M' on page 562 undefined on input line 622. LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 562 undefined on in put line 634. LaTeX Warning: Reference `selim:eq:FSIsystem-M' on page 562 undefined on input line 634. Underfull \vbox (badness 2608) has occurred while \output is active [562] LaTeX Warning: Reference `selim:eq:monolithic' on page 563 undefined on input l ine 658. LaTeX Warning: Reference `selim:eq:dual' on page 563 undefined on input line 66 9. LaTeX Warning: Reference `selim:eq:dual' on page 563 undefined on input line 67 7. LaTeX Warning: Reference `selim:eq:dual' on page 563 undefined on input line 69 2. LaTeX Warning: Reference `selim:eq:representation' on page 563 undefined on inp ut line 700. LaTeX Warning: Reference `selim:eq:dual' on page 563 undefined on input line 70 5. LaTeX Warning: Reference `selim:eq:dual' on page 563 undefined on input line 70 7. LaTeX Warning: Reference `selim:eq:dualsystem' on page 563 undefined on input l ine 729. Underfull \vbox (badness 10000) has occurred while \output is active [563] LaTeX Warning: Reference `selim:eq:representation' on page 564 undefined on inp ut line 742. LaTeX Warning: Reference `selim:fig:strong_residuals' on page 564 undefined on input line 771. Package natbib Warning: Citation `SelimLogg2011a' on page 564 undefined on inpu t line 825. [564] LaTeX Warning: Reference `selim:eq:aposteriori-Eh' on page 565 undefined on inp ut line 832. LaTeX Warning: Reference `selim:eq:aposteriori-Ec' on page 565 undefined on inp ut line 832. LaTeX Warning: Reference `selim:eq:goalTOL' on page 565 undefined on input line 834. LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 565 undefined on in put line 844. LaTeX Warning: Reference `selim:eq:FSIsystem-M' on page 565 undefined on input line 844. Package natbib Warning: Citation `Dorfler1996' on page 565 undefined on input l ine 850. Package natbib Warning: Citation `Logg2004' on page 565 undefined on input line 871. LaTeX Warning: Reference `selim:eq:timestep1' on page 565 undefined on input li ne 871. LaTeX Warning: Reference `selim:fig:adaptiveMAP' on page 565 undefined on input line 883. LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 565 undefined on in put line 884. LaTeX Warning: Reference `selim:eq:FSIsystem-M' on page 565 undefined on input line 884. LaTeX Warning: Reference `selim:eq:dual' on page 565 undefined on input line 89 1. LaTeX Warning: Reference `selim:eq:aposteriori-Eh' on page 565 undefined on inp ut line 893. LaTeX Warning: Reference `selim:eq:aposteriori-Ec' on page 565 undefined on inp ut line 893. LaTeX Warning: Reference `selim:fig:FSISolver-1' on page 565 undefined on input line 895. LaTeX Warning: Reference `selim:fig:FSISolver-2' on page 565 undefined on input line 895. LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 565 undefined on in put line 900. LaTeX Warning: Reference `selim:eq:FSIsystem-M' on page 565 undefined on input line 900. LaTeX Warning: Reference `selim:eq:timestep2' on page 565 undefined on input li ne 903. LaTeX Warning: Reference `selim:eq:dual' on page 565 undefined on input line 90 5. LaTeX Warning: Reference `selim:eq:aposteriori-Eh' on page 565 undefined on inp ut line 908. LaTeX Warning: Reference `selim:eq:aposteriori-Ec' on page 565 undefined on inp ut line 908. [565] LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 566 undefined on in put line 929. LaTeX Warning: Reference `selim:eq:FSIsystem-M' on page 566 undefined on input line 929. LaTeX Warning: Reference `selim:eq:timestep2' on page 566 undefined on input li ne 929. LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 566 undefined on in put line 929. LaTeX Warning: Reference `selim:eq:FSIsystem-M' on page 566 undefined on input line 929. LaTeX Warning: Reference `selim:eq:timestep2' on page 566 undefined on input li ne 929. LaTeX Warning: Reference `selim:eq:aposteriori-Eh' on page 566 undefined on inp ut line 941. LaTeX Warning: Reference `selim:eq:aposteriori-Ec' on page 566 undefined on inp ut line 941. LaTeX Warning: Reference `selim:eq:dorfler' on page 566 undefined on input line 941. LaTeX Warning: Reference `selim:eq:aposteriori-Eh' on page 566 undefined on inp ut line 941. LaTeX Warning: Reference `selim:eq:aposteriori-Ec' on page 566 undefined on inp ut line 941. LaTeX Warning: Reference `selim:eq:dorfler' on page 566 undefined on input line 941. LaTeX Warning: Reference `selim:fig:primal_channel' on page 566 undefined on in put line 1044. LaTeX Warning: Reference `selim:fig:dual_channel_1' on page 566 undefined on in put line 1045. LaTeX Warning: Reference `selim:fig:dual_channel_2' on page 566 undefined on in put line 1046. LaTeX Warning: Reference `selim:eq:goalfunctional_channel' on page 566 undefine d on input line 1074. LaTeX Warning: Reference `selim:eq:goalfunctional_channel' on page 566 undefine d on input line 1074. LaTeX Warning: Reference `selim:eq:goalfunctional_channel' on page 566 undefine d on input line 1074. LaTeX Warning: Reference `selim:eq:goalfunctional_channel' on page 566 undefine d on input line 1074. [566 <./chapters/selim/pdf/adaptive.pdf> ] [567] LaTeX Warning: Reference `selim:fig:primal_cavity' on page 568 undefined on inp ut line 1124. LaTeX Warning: Reference `selim:fig:cavity_timestep' on page 568 undefined on i nput line 1126. LaTeX Warning: Reference `selim:eq:FSIsystem-f-mom' on page 568 undefined on in put line 1157. LaTeX Warning: Reference `selim:eq:FSIsystem-M' on page 568 undefined on input line 1157. LaTeX Warning: Reference `selim:eq:dual' on page 568 undefined on input line 11 59. Underfull \vbox (badness 10000) has occurred while \output is active [568]) (./tex/30.tex [569 <./chapters/selim/png/new_channel.png (PNG copy)> <./chapter s/selim/png/channel_test_zoom.png (PNG copy)>] [570 <./chapters/selim/png/chann elZF.png (PNG copy)> <./chapters/selim/png/channelZS.png (PNG copy)> <./chapter s/selim/png/channelZM.png (PNG copy)>] [571 <./chapters/selim/png/new_cavity.pn g> <./chapters/selim/png/zoom_cavity.png (PNG copy)> <./chapters/selim/pdf/plot .pdf>] [572] Chapter 30. Package natbib Warning: Citation `BelytschkoBlack1999' on page 573 undefined on input line 52. Package natbib Warning: Citation `MoesDolbowBelytschko1999' on page 573 undefin ed on input line 52. Package natbib Warning: Citation `WellsSluys2001' on page 573 undefined on inpu t line 52. Package natbib Warning: Citation `BabuskaBanerjeeOsborn2003' on page 573 undefi ned on input line 54. Package natbib Warning: Citation `NikbakhtWells2009' on page 573 undefined on i nput line 66. [573] LaTeX Warning: Reference `fig:nikbakht:domain' on page 574 undefined on input l ine 87. (./chapters/nikbakht/pdf/domain.pdf_tex ) Underfull \vbox (badness 5908) has occurred while \output is active [574 <./cha pters/nikbakht/pdf/domain.pdf>] LaTeX Warning: Reference `eqn:nikbakht:u_decomp' on page 575 undefined on input line 156. LaTeX Warning: Reference `eqn:nikbakht:poisson_discontinuous_variational' on pa ge 575 undefined on input line 167. LaTeX Warning: Reference `sec:nikbakht:examples' on page 575 undefined on input line 186. LaTeX Warning: Reference `eqn:nikbakht:u_h_decomp' on page 575 undefined on inp ut line 198. [575] LaTeX Warning: Reference `chap:alnes-1' on page 576 undefined on input line 238 . LaTeX Warning: Reference `chap:logg-1' on page 576 undefined on input line 244. LaTeX Warning: Reference `chap:logg-2' on page 576 undefined on input line 249. LaTeX Warning: Reference `eqn:nikbakht:u_decomp' on page 576 undefined on input line 269. [576] LaTeX Warning: Reference `sec:nikbakht:examples' on page 577 undefined on input line 320. [577] Package natbib Warning: Citation `JagerSteinmannKuhl2008' on page 578 undefined on input line 443. [578] LaTeX Warning: Reference `code:nikbakht:Poisson' on page 579 undefined on input line 506. LaTeX Warning: Reference `fig:nikbakht:poisson_c++' on page 579 undefined on in put line 595. LaTeX Warning: Reference `fig:nikbakht:poisson_c++' on page 579 undefined on in put line 601. LaTeX Warning: Reference `fig:nikbakht:poisson_contours' on page 579 undefined on input line 616. LaTeX Warning: Reference `fig:nikbakht:poisson_contours_b' on page 579 undefine d on input line 620. LaTeX Warning: Reference `sub@fig:nikbakht:poisson_contours_a' on page 579 unde fined on input line 630. LaTeX Warning: Reference `sub@fig:nikbakht:poisson_contours_b' on page 579 unde fined on input line 630. LaTeX Warning: Reference `sub@fig:nikbakht:poisson_contours_a' on page 579 unde fined on input line 630. LaTeX Warning: Reference `sub@fig:nikbakht:poisson_contours_b' on page 579 unde fined on input line 630. [579] Package natbib Warning: Citation `RognesKirbyLogg2009' on page 580 undefined on input line 639. Package natbib Warning: Citation `BrezziDouglasMarini1985' on page 580 undefine d on input line 642. LaTeX Warning: Reference `chap:kirby-6' on page 580 undefined on input line 643 . LaTeX Warning: Reference `code:nikbakht:mixed-Poisson' on page 580 undefined on input line 677. Package natbib Warning: Citation `OelgaardLoggWells2008' on page 580 undefined on input line 722. [580] [581] [582 <./chapters/nikbakht/png/mesh.png> <./chapters/nikbakht/png/re sult.png>] LaTeX Warning: Reference `code:nikbakht:dg-elasticity' on page 583 undefined on input line 766. LaTeX Warning: Reference `eqn:nikbakht:compact_discontinuous_space' on page 583 undefined on input line 838. [583] [584] LaTeX Warning: Reference `eqn:nikbakht:nonlinear_poisson' on page 585 undefined on input line 872. LaTeX Warning: Reference `fig:nikbakht:ufl_nonlinear_poisson' on page 585 undef ined on input line 873. LaTeX Warning: Reference `eqn:nikbakht:nonlinear_poisson_J' on page 585 undefin ed on input line 877. LaTeX Warning: Reference `fig:nikbakht:c++_nonlinear_poisson' on page 585 undef ined on input line 887. ) (./tex/31.tex [585] [586] Chapter 31. Package natbib Warning: Citation `vanderMeer2010' on page 587 undefined on inpu t line 35. Package natbib Warning: Citation `Jarvis2007' on page 587 undefined on input li ne 38. Package natbib Warning: Citation `McNamaraZhong2005' on page 587 undefined on i nput line 43. Package natbib Warning: Citation `McNutt1998' on page 587 undefined on input li ne 46. Package natbib Warning: Citation `Burke2008' on page 587 undefined on input lin e 49. Package natbib Warning: Citation `McNamara2010' on page 587 undefined on input line 54. LaTeX Warning: Reference `vynnytska:sec:results' on page 587 undefined on input line 68. LaTeX Warning: Reference `vynnytska:sec:results' on page 587 undefined on input line 68. [587] LaTeX Warning: Reference `vynnytska:fig:IC' on page 588 undefined on input line 89. Package natbib Warning: Citation `KekenEtAl1997' on page 588 undefined on input line 95. Package natbib Warning: Citation `Ricard2009' on page 588 undefined on input li ne 102. Package natbib Warning: Citation `TanGurnis2005' on page 588 undefined on input line 104. LaTeX Warning: Reference `vynnytska:sec:results' on page 588 undefined on input line 125. Package natbib Warning: Citation `KennettBunge2008' on page 588 undefined on in put line 131. [588 <./chapters/vynnytska/png/layout.png>] Package natbib Warning: Citation `MontagueKelloggManga1998' on page 589 undefin ed on input line 143. Package natbib Warning: Citation `KekenEtAl1997' on page 589 undefined on input line 155. Package natbib Warning: Citation `HansenYuen1988' on page 589 undefined on inpu t line 155. LaTeX Warning: Reference `vynnytska:eq:trans' on page 589 undefined on input li ne 156. Package natbib Warning: Citation `BlankenbachBusse1989' on page 589 undefined o n input line 169. LaTeX Warning: Reference `vynnytska:eq:momentum' on page 589 undefined on input line 183. Underfull \vbox (badness 10000) has occurred while \output is active [589] LaTeX Warning: Reference `vynnytska:fig:IC' on page 590 undefined on input line 210. Package natbib Warning: Citation `KekenEtAl1997' on page 590 undefined on input line 212. Package natbib Warning: Citation `BergKekenYuen1993' on page 590 undefined on i nput line 246. Package natbib Warning: Citation `HansenEbel1988' on page 590 undefined on inpu t line 246. LaTeX Warning: Reference `vynnytska:eq:energy' on page 590 undefined on input l ine 249. LaTeX Warning: Reference `vynnytska:eq:transdif' on page 590 undefined on input line 250. LaTeX Warning: Reference `vynnytska:eq:momentum' on page 590 undefined on input line 253. LaTeX Warning: Reference `vynnytska:eq:incompress' on page 590 undefined on inp ut line 253. LaTeX Warning: Reference `vynnytska:eq:momentum' on page 590 undefined on input line 270. LaTeX Warning: Reference `vynnytska:eq:incompress' on page 590 undefined on inp ut line 270. LaTeX Warning: Reference `vynnytska:eq:bcs' on page 590 undefined on input line 271. [590] Package natbib Warning: Citation `TaylorHood1973' on page 591 undefined on inpu t line 290. LaTeX Warning: Reference `vynnytska:eq:energy' on page 591 undefined on input l ine 298. LaTeX Warning: Reference `vynnytska:eq:transdif' on page 591 undefined on input line 299. Package natbib Warning: Citation `Lin2006' on page 591 undefined on input line 306. Package natbib Warning: Citation `ZienkiewiczTaylor2000' on page 591 undefined on input line 306. LaTeX Warning: Reference `vynnytska:eq:transdif' on page 591 undefined on input line 312. LaTeX Warning: Reference `vynnytska:eq:energy' on page 591 undefined on input l ine 314. LaTeX Warning: Reference `vynnytska:eq:trans' on page 591 undefined on input li ne 315. LaTeX Warning: Reference `vynnytska:eq:trans' on page 591 undefined on input li ne 321. Package natbib Warning: Citation `PietroLoForteParolini2006' on page 591 undefi ned on input line 322. LaTeX Warning: Reference `vynnytska:eq:transdif' on page 591 undefined on input line 352. Package natbib Warning: Citation `Arnold1982' on page 591 undefined on input li ne 354. Underfull \vbox (badness 3049) has occurred while \output is active [591] LaTeX Warning: Reference `vynnytska:eq:dgadv' on page 592 undefined on input li ne 369. LaTeX Warning: Reference `vynnytska:eq:dgdiff' on page 592 undefined on input l ine 370. LaTeX Warning: Reference `vynnytska:eq:transdif' on page 592 undefined on input line 372. LaTeX Warning: Reference `vynnytska:eq:momentum' on page 592 undefined on input line 390. LaTeX Warning: Reference `vynnytska:eq:incompress' on page 592 undefined on inp ut line 390. LaTeX Warning: Reference `vynnytska:eq:energy' on page 592 undefined on input l ine 391. LaTeX Warning: Reference `vynnytska:eq:transdif' on page 592 undefined on input line 391. Package natbib Warning: Citation `BergKekenYuen1993' on page 592 undefined on i nput line 393. Package natbib Warning: Citation `HansenEbel1988' on page 592 undefined on inpu t line 393. Package natbib Warning: Citation `LenardicKaula1993' on page 592 undefined on i nput line 398. LaTeX Warning: Reference `vynnytska:eq:semi_composition' on page 592 undefined on input line 401. LaTeX Warning: Reference `vynnytska:eq:semi_composition' on page 592 undefined on input line 403. LaTeX Warning: Reference `vynnytska:eq:dgadv' on page 592 undefined on input li ne 427. LaTeX Warning: Reference `vynnytska:eq:dgdiff' on page 592 undefined on input l ine 428. Underfull \vbox (badness 10000) has occurred while \output is active [592] LaTeX Warning: Reference `vynnytska:alg:algorithm' on page 593 undefined on inp ut line 442. LaTeX Warning: Reference `vynnytska:eq:mixed' on page 593 undefined on input li ne 448. LaTeX Warning: Reference `vynnytska:eq:timestep' on page 593 undefined on input line 450. LaTeX Warning: Reference `vynnytska:eq:predictor' on page 593 undefined on inpu t line 452. LaTeX Warning: Reference `vynnytska:eq:predictor' on page 593 undefined on inpu t line 454. LaTeX Warning: Reference `vynnytska:eq:mixed' on page 593 undefined on input li ne 457. LaTeX Warning: Reference `vynnytska:eq:corrector' on page 593 undefined on inpu t line 459. LaTeX Warning: Reference `vynnytska:eq:mixed' on page 593 undefined on input li ne 460. LaTeX Warning: Reference `vynnytska:eq:timestep' on page 593 undefined on input line 463. Package natbib Warning: Citation `LenardicKaula1993' on page 593 undefined on i nput line 484. LaTeX Warning: Reference `vynnytska:alg:algorithm' on page 593 undefined on inp ut line 509. LaTeX Warning: Reference `vynnytska:fig:mainalgorithm' on page 593 undefined on input line 510. LaTeX Warning: Reference `vynnytska:alg:filtering' on page 593 undefined on inp ut line 513. Underfull \vbox (badness 6157) has occurred while \output is active [593] LaTeX Warning: Reference `vynnytska:alg:filtering' on page 594 undefined on inp ut line 522. LaTeX Warning: Reference `chap:mardal-4' on page 594 undefined on input line 55 3. LaTeX Warning: Reference `vynnytska:eq:timestep' on page 594 undefined on input line 561. [594] LaTeX Warning: Reference `vynnytska:fig:stokes' on page 595 undefined on input line 585. LaTeX Warning: Reference `vynnytska:eq:mixed' on page 595 undefined on input li ne 588. LaTeX Warning: Reference `vynnytska:eq:dgadv' on page 595 undefined on input li ne 611. LaTeX Warning: Reference `vynnytska:eq:dgdiff' on page 595 undefined on input l ine 611. LaTeX Warning: Reference `vynnytska:eq:thetascheme' on page 595 undefined on in put line 612. LaTeX Warning: Reference `vynnytska:fig:advection' on page 595 undefined on inp ut line 615. LaTeX Warning: Reference `vynnytska:fig:diffusion' on page 595 undefined on inp ut line 616. LaTeX Warning: Reference `vynnytska:fig:temperaturecorrection' on page 595 unde fined on input line 621. LaTeX Warning: Reference `vynnytska:eq:timestep' on page 595 undefined on input line 635. LaTeX Warning: Reference `vynnytska:eq:viscosity' on page 595 undefined on inpu t line 636. LaTeX Warning: Reference `vynnytska:sec:maths' on page 595 undefined on input l ine 638. LaTeX Warning: Reference `vynnytska:table:variables' on page 595 undefined on i nput line 640. LaTeX Warning: Reference `vynnytska:alg:algorithm' on page 595 undefined on inp ut line 766. LaTeX Warning: Reference `vynnytska:alg:algorithm' on page 595 undefined on inp ut line 766. LaTeX Warning: Reference `vynnytska:alg:algorithm' on page 595 undefined on inp ut line 766. LaTeX Warning: Reference `vynnytska:alg:algorithm' on page 595 undefined on inp ut line 766. Underfull \hbox (badness 2027) in paragraph at lines 766--766 \T1/pplx/m/n/8.5 main predictor--corrector al-go-rithm, Underfull \hbox (badness 1253) in paragraph at lines 766--766 \T1/pplx/m/n/8.5 ini-tial-iza-tion is not in-cluded here). LaTeX Warning: Float too large for page by 15.77048pt on input line 768. LaTeX Warning: Reference `vynnytska:eq:dgadv' on page 595 undefined on input li ne 825. LaTeX Warning: Reference `vynnytska:eq:dgadv' on page 595 undefined on input li ne 825. LaTeX Warning: Reference `vynnytska:eq:dgdiff' on page 595 undefined on input l ine 854. LaTeX Warning: Reference `vynnytska:eq:dgdiff' on page 595 undefined on input l ine 854. LaTeX Warning: Reference `vynnytska:eq:corrector' on page 595 undefined on inpu t line 915. LaTeX Warning: Reference `vynnytska:eq:corrector' on page 595 undefined on inpu t line 915. LaTeX Warning: Reference `vynnytska:eq:corrector' on page 595 undefined on inpu t line 915. LaTeX Warning: Reference `vynnytska:eq:corrector' on page 595 undefined on inpu t line 915. [595] [596] [597] [598] LaTeX Warning: Reference `vynnytska:fig:rms_velocity' on page 599 undefined on input line 932. LaTeX Warning: Reference `vynnytska:fig:BG' on page 599 undefined on input line 935. LaTeX Warning: Reference `vynnytska:fig:HM' on page 599 undefined on input line 935. Underfull \hbox (badness 1038) in paragraph at lines 975--975 []\T1/pplx/m/n/9 (+20) Figure 31.7: |Di-men-sion-less root Overfull \hbox (1.66838pt too wide) in paragraph at lines 981--1019 [][] LaTeX Warning: Reference `vynnytska:table:variables' on page 599 undefined on i nput line 1019. LaTeX Warning: Reference `vynnytska:table:variables' on page 599 undefined on i nput line 1019. Overfull \hbox (1.66838pt too wide) in paragraph at lines 1025--1053 [][] LaTeX Warning: Reference `vynnytska:fig:BG' on page 599 undefined on input line 1053. LaTeX Warning: Reference `vynnytska:fig:BG' on page 599 undefined on input line 1053. [599] LaTeX Warning: Reference `vynnytska:eq:transdif' on page 600 undefined on input line 1089. Package natbib Warning: Citation `IsmailZadehTackley2010' on page 600 undefined on input line 1093. [600 <./chapters/vynnytska/png/u_rms.png>] [601 <./chapters/vynnytska/png/tmB.p ng (PNG copy)> <./chapters/vynnytska/png/visB.png (PNG copy)> <./chapters/vynny tska/png/tmC.png (PNG copy)> <./chapters/vynnytska/png/visC.png (PNG copy)> <./ chapters/vynnytska/png/tmD.png (PNG copy)> <./chapters/vynnytska/png/visD.png ( PNG copy)> <./chapters/vynnytska/png/tmE.png (PNG copy)> <./chapters/vynnytska/ png/visE.png (PNG copy)> <./chapters/vynnytska/png/tmF.png (PNG copy)> <./chapt ers/vynnytska/png/visF.png (PNG copy)> <./chapters/vynnytska/png/tmG.png (PNG c opy)> <./chapters/vynnytska/png/visG.png (PNG copy)> <./chapters/vynnytska/png/ tmleg.png (PNG copy)> <./chapters/vynnytska/png/visleg.png (PNG copy)>] [602 <./chapters/vynnytska/png/tmH.png (PNG copy)> <./chapters/vynnytska/png/vi sH.png (PNG copy)> <./chapters/vynnytska/png/tmI.png (PNG copy)> <./chapters/vy nnytska/png/visI.png (PNG copy)> <./chapters/vynnytska/png/tmJ.png (PNG copy)> <./chapters/vynnytska/png/visJ.png (PNG copy)> <./chapters/vynnytska/png/tmK.pn g (PNG copy)> <./chapters/vynnytska/png/visK.png (PNG copy)> <./chapters/vynnyt ska/png/tmL.png (PNG copy)> <./chapters/vynnytska/png/visL.png (PNG copy)> <./c hapters/vynnytska/png/tmM.png (PNG copy)> <./chapters/vynnytska/png/visM.png (P NG copy)>]) (./tex/32.tex Chapter 32. Package natbib Warning: Citation `Rivenaes1992' on page 603 undefined on input line 63. Package natbib Warning: Citation `Rivenaes1993' on page 603 undefined on input line 63. [603] Package natbib Warning: Citation `ImhofSharma2007' on page 604 undefined on inp ut line 109. Package natbib Warning: Citation `Landweber1951' on page 604 undefined on input line 132. [604] LaTeX Warning: Reference `eq:schroll:ansatz' on page 605 undefined on input lin e 176. LaTeX Warning: Reference `eq:schroll:approx' on page 605 undefined on input lin e 177. LaTeX Warning: Reference `eq:schroll:b' on page 605 undefined on input line 181 . LaTeX Warning: Reference `eq:schroll:projection' on page 605 undefined on input line 181. LaTeX Warning: Reference `eq:schroll:gamma' on page 605 undefined on input line 187. Package natbib Warning: Citation `ChaventLemmonier1974' on page 605 undefined o n input line 210. Underfull \vbox (badness 1496) has occurred while \output is active [605] LaTeX Warning: Reference `eq:schroll:A' on page 606 undefined on input line 246 . LaTeX Warning: Reference `eq:schroll:model' on page 606 undefined on input line 267. LaTeX Warning: Reference `eq:schroll:output' on page 606 undefined on input lin e 276. Underfull \vbox (badness 10000) has occurred while \output is active [606] Package natbib Warning: Citation `Schroll2008' on page 607 undefined on input l ine 294. Package natbib Warning: Citation `LoggWells2010' on page 607 undefined on input line 310. LaTeX Warning: Reference `eq:schroll:dual' on page 607 undefined on input line 315. [607] LaTeX Warning: Reference `eq:schroll:trapez' on page 608 undefined on input lin e 350. LaTeX Warning: Reference `eq:schroll:trapez' on page 608 undefined on input lin e 354. LaTeX Warning: Reference `eq:schroll:output' on page 608 undefined on input lin e 377. LaTeX Warning: Reference `eq:schroll:model' on page 608 undefined on input line 378. LaTeX Warning: Reference `eq:schroll:model' on page 608 undefined on input line 380. [608] LaTeX Warning: Reference `fig1' on page 609 undefined on input line 404. LaTeX Warning: Reference `fig2' on page 609 undefined on input line 422. LaTeX Warning: Reference `fig2' on page 609 undefined on input line 432. LaTeX Warning: Reference `fig3' on page 609 undefined on input line 455. LaTeX Warning: Reference `fig7' on page 609 undefined on input line 464. LaTeX Warning: Reference `fig7' on page 609 undefined on input line 466. LaTeX Warning: Reference `fig3' on page 609 undefined on input line 469. LaTeX Warning: Reference `fig4' on page 609 undefined on input line 484. LaTeX Warning: Reference `fig7' on page 609 undefined on input line 492. [609 <./chapters/schroll/pdf/h0_typical.pdf> <./chapters/schroll/pdf/h_typical. pdf>] [610 <./chapters/schroll/pdf/a1a2scan4.pdf> <./chapters/schroll/pdf/a1a2s can4-5.pdf> <./chapters/schroll/pdf/b1b2scan4.pdf> <./chapters/schroll/pdf/b1b2 scan4-5.pdf> <./chapters/schroll/pdf/4Dscan3.pdf> <./chapters/schroll/pdf/4Dsca n3-5.pdf>] LaTeX Warning: Reference `fig6' on page 611 undefined on input line 528. [611 <./chapters/schroll/pdf/4Dscan 3b.pdf> <./chapters/schroll/pdf/4Dscan3b-5.pdf> <./chapters/schroll/pdf/4Dsampl e3-5.pdf> <./chapters/schroll/pdf/4Dsample3b-5.pdf> <./chapters/schroll/pdf/4D- 1scan4b.pdf> <./chapters/schroll/pdf/4D-1scan4b-5.pdf>]) (./tex/33.tex [612] Chapter 33. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 23. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 23. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 23. Package natbib Warning: Citation `AlbertsBrayLewisEtAl2002' on page 613 undefin ed on input line 29. Package natbib Warning: Citation `Bers2001' on page 613 undefined on input line 78. [613] Package natbib Warning: Citation `SoellerCannell1999' on page 614 undefined on input line 122. LaTeX Warning: Reference `fig:hake:morphology' on page 614 undefined on input l ine 123. Package natbib Warning: Citation `PeskoffPostLanger1992' on page 614 undefined on input line 131. Package natbib Warning: Citation `SoellerCannell1997' on page 614 undefined on input line 131. Package natbib Warning: Citation `KohSrinivasanChingEtAl2006' on page 614 undef ined on input line 131. Package natbib Warning: Citation `TanskanenGreensteinChenEtAl2007' on page 614 undefined on input line 131. LaTeX Warning: Reference `fig:hake:morphology' on page 614 undefined on input l ine 133. Package natbib Warning: Citation `LangerPeskoff1996' on page 614 undefined on i nput line 145. Package natbib Warning: Citation `McLaughlinSzaboEisenman1971' on page 614 unde fined on input line 148. Package natbib Warning: Citation `LangnerCafisoMarceljaEtAl1990' on page 614 un defined on input line 148. Package natbib Warning: Citation `Grahame1947' on page 614 undefined on input l ine 152. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [614 <./chapters/hake/pdf/morphology.pdf>] Package natbib Warning: Citation `LangnerCafisoMarceljaEtAl1990' on page 615 un defined on input line 185. Package natbib Warning: Citation `SoellerCannell1997' on page 615 undefined on input line 186. Package natbib Warning: Citation `SoellerCannell1997' on page 615 undefined on input line 197. LaTeX Warning: Reference `fig:hake:morphology' on page 615 undefined on input l ine 209. LaTeX Warning: Reference `fig:hake:morphology' on page 615 undefined on input l ine 213. LaTeX Warning: Reference `fig:hake:morphology' on page 615 undefined on input l ine 220. Package natbib Warning: Citation `GuiaSternLakattaEtAl2001' on page 615 undefin ed on input line 232. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [615] Package natbib Warning: Citation `JafriRiceWinslow1998' on page 616 undefined o n input line 273. Package natbib Warning: Citation `JafriRiceWinslow1998' on page 616 undefined o n input line 273. Package natbib Warning: Citation `SternSongEtAl1999' on page 616 undefined on i nput line 273. Package natbib Warning: Citation `JafriRiceWinslow1998' on page 616 undefined o n input line 273. Package natbib Warning: Citation `JafriRiceWinslow1998' on page 616 undefined o n input line 273. Package natbib Warning: Citation `SternSongEtAl1999' on page 616 undefined on i nput line 273. Package natbib Warning: Citation `JafriRiceWinslow1998' on page 616 undefined o n input line 273. Package natbib Warning: Citation `JafriRiceWinslow1998' on page 616 undefined o n input line 273. Package natbib Warning: Citation `SternSongEtAl1999' on page 616 undefined on i nput line 273. Package natbib Warning: Citation `JafriRiceWinslow1998' on page 616 undefined o n input line 273. Package natbib Warning: Citation `JafriRiceWinslow1998' on page 616 undefined o n input line 273. Package natbib Warning: Citation `SternSongEtAl1999' on page 616 undefined on i nput line 273. Package natbib Warning: Citation `Hille2001' on page 616 undefined on input lin e 306. Package natbib Warning: Citation `JafriRiceWinslow1998' on page 616 undefined o n input line 309. Package natbib Warning: Citation `GreensteinWinslow2002' on page 616 undefined on input line 309. LaTeX Warning: Reference `fig:hake:markov-models' on page 616 undefined on inpu t line 310. Package natbib Warning: Citation `GreensteinWinslow2002' on page 616 undefined on input line 314. Package natbib Warning: Citation `BeuckelmannWier1988' on page 616 undefined on input line 323. Package natbib Warning: Citation `Franzini-ArmstrongProtasiRamesh1999' on page 616 undefined on input line 323. Package natbib Warning: Citation `SternSongEtAl1999' on page 616 undefined on i nput line 327. LaTeX Warning: Reference `fig:hake:markov-models' on page 616 undefined on inpu t line 328. Package natbib Warning: Citation `SternSongEtAl1999' on page 616 undefined on i nput line 332. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [616 <./chapters/hake/pdf/markov_models.pdf>] LaTeX Warning: Reference `eq:hake:advection-diffusion' on page 617 undefined on input line 349. LaTeX Warning: Reference `eq:hake:conc-dependent-flux' on page 617 undefined on input line 349. LaTeX Warning: Reference `eq:hake:no-flux' on page 617 undefined on input line 367. LaTeX Warning: Reference `eq:hake:conc-dependent-flux' on page 617 undefined on input line 367. LaTeX Warning: Reference `eq:hake:full_system' on page 617 undefined on input l ine 370. LaTeX Warning: Reference `eq:hake:full_system' on page 617 undefined on input l ine 378. LaTeX Warning: Reference `eq:hake:advection-diffusion-weak-form' on page 617 un defined on input line 387. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [617] LaTeX Warning: Reference `eq:hake:no-flux' on page 618 undefined on input line 415. LaTeX Warning: Reference `eq:hake:conc-dependent-flux' on page 618 undefined on input line 415. LaTeX Warning: Reference `eq:hake:matrices' on page 618 undefined on input line 438. LaTeX Warning: Reference `eq:hake:vector' on page 618 undefined on input line 4 38. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [618] Package natbib Warning: Citation `BalayBuschelmanGroppEtAl2001' on page 619 und efined on input line 495. Package natbib Warning: Citation `Vorst1992' on page 619 undefined on input lin e 496. Package natbib Warning: Citation `FalgoutYang2002' on page 619 undefined on inp ut line 497. LaTeX Warning: Reference `eq:hake:algebraic-equation' on page 619 undefined on input line 498. LaTeX Warning: Reference `eq:hake:algebraic-equation' on page 619 undefined on input line 511. LaTeX Warning: Reference `eq:hake:matrices' on page 619 undefined on input line 514. Package natbib Warning: Citation `BrooksHughes1982' on page 619 undefined on in put line 516. LaTeX Warning: Reference `eq:hake:advection-diffusion-weak-form-0' on page 619 undefined on input line 518. LaTeX Warning: Reference `eq:hake:element-tau' on page 619 undefined on input l ine 539. LaTeX Warning: Reference `eq:hake:peclet' on page 619 undefined on input line 5 39. Package natbib Warning: Citation `ChristieGriffithsMitchellEtAl1976' on page 61 9 undefined on input line 541. Package natbib Warning: Citation `BrooksHughes1982' on page 619 undefined on in put line 541. Package natbib Warning: Citation `JohnKnobloch2007' on page 619 undefined on in put line 546. Package natbib Warning: Citation `TezduyarPark1986' on page 619 undefined on in put line 547. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [619] Package natbib Warning: Citation `Si2007' on page 620 undefined on input line 5 94. LaTeX Warning: Reference `eq:hake:algebraic-equation' on page 620 undefined on input line 612. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [620 <./chapters/hake/pdf/error_plot.pdf>] LaTeX Warning: Reference `fig:hake:error_plot' on page 621 undefined on input l ine 681. LaTeX Warning: Reference `fig:hake:error_plot' on page 621 undefined on input l ine 681. LaTeX Warning: Reference `fig:hake:error_plot' on page 621 undefined on input l ine 681. LaTeX Warning: Reference `fig:hake:error_plot' on page 621 undefined on input l ine 681. LaTeX Warning: Reference `fig:hake:error_plot' on page 621 undefined on input l ine 704. LaTeX Warning: Reference `fig:hake:error_plot' on page 621 undefined on input l ine 704. LaTeX Warning: Reference `fig:hake:error_plot' on page 621 undefined on input l ine 704. LaTeX Warning: Reference `fig:hake:error_plot' on page 621 undefined on input l ine 704. LaTeX Warning: Reference `eq:hake:algebraic-equation' on page 621 undefined on input line 714. LaTeX Warning: Reference `eq:hake:nernst-planck' on page 621 undefined on input line 719. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [621] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [622 <./chapters/hake/pdf/traces_mesh_1.pdf> <./chapters/hake/pdf/traces_mesh_2 .pdf>] LaTeX Warning: Reference `eq:hake:electric_potential' on page 623 undefined on input line 725. LaTeX Warning: Reference `fig:hake:error_plot' on page 623 undefined on input l ine 732. LaTeX Warning: Reference `fig:hake:error_plot' on page 623 undefined on input l ine 744. LaTeX Warning: Reference `fig:hake:traces_mesh_1' on page 623 undefined on inpu t line 748. LaTeX Warning: Reference `fig:hake:traces_mesh_3' on page 623 undefined on inpu t line 748. LaTeX Warning: Reference `fig:hake:error_plot' on page 623 undefined on input l ine 752. Underfull \vbox (badness 10000) has occurred while \output is active Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [623] LaTeX Warning: Reference `fig:hake:error_plot' on page 624 undefined on input l ine 774. LaTeX Warning: Reference `fig:hake:traces_mesh_2' on page 624 undefined on inpu t line 774. LaTeX Warning: Reference `fig:hake:error_plot' on page 624 undefined on input l ine 774. LaTeX Warning: Reference `fig:hake:error_plot' on page 624 undefined on input l ine 774. LaTeX Warning: Reference `fig:hake:traces_mesh_2' on page 624 undefined on inpu t line 774. LaTeX Warning: Reference `fig:hake:error_plot' on page 624 undefined on input l ine 774. LaTeX Warning: Reference `fig:hake:traces_mesh_1' on page 624 undefined on inpu t line 778. LaTeX Warning: Reference `fig:hake:traces_mesh_2' on page 624 undefined on inpu t line 787. LaTeX Warning: Reference `fig:hake:traces_mesh_1' on page 624 undefined on inpu t line 790. LaTeX Warning: Reference `fig:hake:traces_mesh_3' on page 624 undefined on inpu t line 796. LaTeX Warning: Reference `fig:hake:traces_mesh_2' on page 624 undefined on inpu t line 799. LaTeX Warning: Reference `eq:hake:full_system' on page 624 undefined on input l ine 814. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [624 <./chapters/hake/pdf/traces_mesh_3.pdf>] Underfull \hbox (badness 3965) in paragraph at lines 844--844 []\T1/pplx/m/n/9 (+20) Figure 33.7: |Di-a-gram for the Underfull \hbox (badness 6316) in paragraph at lines 844--844 \T1/pplx/m/n/9 (+20) time step-ping al-go-rithm us-ing Underfull \hbox (badness 3769) in paragraph at lines 844--844 \T1/pplx/m/n/9 (+20) 3 dis-crete ob-jects: \T1/fvm/m/n/9 DtExpander\T1/pplx/m/n /9 (+20) , LaTeX Warning: Reference `eq:hake:matrices' on page 625 undefined on input line 853. LaTeX Warning: Reference `sec:hake:stochastic-models' on page 625 undefined on input line 876. Package natbib Warning: Citation `Gillespie1977' on page 625 undefined on input line 877. Package natbib Warning: Citation `RudigerShuaiHuisingaEtAl2007' on page 625 und efined on input line 878. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [625 <./chapters/hake/pdf/timeline.pdf>] LaTeX Warning: Reference `fig:hake:time-line' on page 626 undefined on input li ne 955. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [626] LaTeX Warning: Reference `sec:hake:ca-diffusion' on page 627 undefined on input line 988. Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [627] LaTeX Warning: Reference `sec:hake:stochastic-models' on page 628 undefined on input line 1039. ) (./tex/34.tex Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [628] Chapter 34. Package natbib Warning: Citation `Silvester1969' on page 629 undefined on input line 20. Package natbib Warning: Citation `Pozar2005' on page 629 undefined on input lin e 25. Package natbib Warning: Citation `LeeSunCendes1991' on page 629 undefined on in put line 30. Package natbib Warning: Citation `Lee1994' on page 629 undefined on input line 31. Package natbib Warning: Citation `Davidson2011' on page 629 undefined on input line 33. Package natbib Warning: Citation `Pozar2005' on page 629 undefined on input lin e 38. LaTeX Warning: Reference `lezar:sec:formulation' on page 629 undefined on input line 52. LaTeX Warning: Reference `lezar:sec:Implementation' on page 629 undefined on in put line 55. LaTeX Warning: Reference `lezar:sec:Examples' on page 629 undefined on input li ne 57. Package natbib Warning: Citation `Jin2002' on page 629 undefined on input line 68. Package natbib Warning: Citation `Smith1997' on page 629 undefined on input lin e 68. Package natbib Warning: Citation `Jin2002' on page 629 undefined on input line 76. Underfull \vbox (badness 10000) has occurred while \output is active [629] Package natbib Warning: Citation `RamoWhinneryVanDuzer1994' on page 630 undefin ed on input line 96. Package natbib Warning: Citation `PolycarpouLyonsBalanis1996' on page 630 undef ined on input line 98. LaTeX Warning: Reference `eq:lezar:vector_helmholtz' on page 630 undefined on i nput line 100. Package natbib Warning: Citation `Jin2002' on page 630 undefined on input line 109. Package natbib Warning: Citation `Jin2002' on page 630 undefined on input line 121. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 630 undefi ned on input line 122. Package natbib Warning: Citation `LeeSunCendes1991' on page 630 undefined on in put line 123. LaTeX Warning: Reference `eq:lezar:standard_functional' on page 630 undefined o n input line 127. LaTeX Warning: Reference `fig:lezar:long_waveguide' on page 630 undefined on in put line 132. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 630 undefi ned on input line 136. Package natbib Warning: Citation `Pozar2005' on page 630 undefined on input lin e 136. [630] (./chapters/lezar/svg/arbitrary_waveguide_cross_section.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/arbitrary_waveguide_cross_s ection.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `eq:lezar:field_components' on page 631 undefined on i nput line 177. LaTeX Warning: Reference `eq:lezar:nabla_components' on page 631 undefined on i nput line 178. LaTeX Warning: Reference `eq:lezar:standard_functional' on page 631 undefined o n input line 179. LaTeX Warning: Reference `eq:lezar:standard_functional' on page 631 undefined o n input line 189. LaTeX Warning: Reference `eq:lezar:functional' on page 631 undefined on input l ine 192. LaTeX Warning: Reference `eq:lezar:functional' on page 631 undefined on input l ine 193. Package natbib Warning: Citation `LeeSunCendes1991' on page 631 undefined on in put line 194. Package natbib Warning: Citation `Jin2002' on page 631 undefined on input line 194. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 631 undefi ned on input line 195. LaTeX Warning: Reference `eq:lezar:field_components' on page 631 undefined on i nput line 196. LaTeX Warning: Reference `eq:lezar:vector_helmholtz' on page 631 undefined on i nput line 197. Package natbib Warning: Citation `Nedelec1980' on page 631 undefined on input l ine 202. Package natbib Warning: Citation `Webb1993' on page 631 undefined on input line 202. Package natbib Warning: Citation `Monk2003' on page 631 undefined on input line 202. Package natbib Warning: Citation `Jin2002' on page 631 undefined on input line 204. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 631 undefi ned on input line 204. LaTeX Warning: Reference `eq:lezar:field_components' on page 631 undefined on i nput line 205. Package natbib Warning: Citation `Jin2002' on page 631 undefined on input line 206. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 631 undefi ned on input line 206. LaTeX Warning: Reference `chap:kirby-6' on page 631 undefined on input line 220 . Package natbib Warning: Citation `ItohPelosiSilvester1996' on page 631 undefine d on input line 226. Package natbib Warning: Citation `DillonWebb1994' on page 631 undefined on inpu t line 227. Package natbib Warning: Citation `ZhuCangellaris2006' on page 631 undefined on input line 231. [631 <./chapters/lezar/svg/arbitrary_waveguide_cross_section.pdf>] LaTeX Warning: Reference `eq:lezar:field_components' on page 632 undefined on i nput line 240. Package natbib Warning: Citation `Pozar2005' on page 632 undefined on input lin e 240. LaTeX Warning: Reference `eq:lezar:functional' on page 632 undefined on input l ine 241. LaTeX Warning: Reference `eq:lezar:E_t_discretized' on page 632 undefined on in put line 256. LaTeX Warning: Reference `eq:lezar:E_z_discretized' on page 632 undefined on in put line 256. LaTeX Warning: Reference `eq:lezar:functional_cutoff' on page 632 undefined on input line 257. Package natbib Warning: Citation `Davidson2011' on page 632 undefined on input line 259. LaTeX Warning: Reference `eq:lezar:matrix_equation_cutoff' on page 632 undefine d on input line 297. Package natbib Warning: Citation `Davidson2011' on page 632 undefined on input line 302. Package natbib Warning: Citation `Jin2002' on page 632 undefined on input line 302. LaTeX Warning: Reference `eq:lezar:matrix_equation_cutoff' on page 632 undefine d on input line 304. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 632 undefi ned on input line 305. Package natbib Warning: Citation `Jin2002' on page 632 undefined on input line 305. LaTeX Warning: Reference `eq:lezar:matrix_equation_cutoff' on page 632 undefine d on input line 319. LaTeX Warning: Reference `eq:lezar:E_t_discretized' on page 632 undefined on in put line 322. LaTeX Warning: Reference `eq:lezar:E_z_discretized' on page 632 undefined on in put line 323. LaTeX Warning: Reference `eq:lezar:E_t_discretized' on page 632 undefined on in put line 327. LaTeX Warning: Reference `eq:lezar:E_z_discretized' on page 632 undefined on in put line 327. Package natbib Warning: Citation `Pozar2005' on page 632 undefined on input lin e 332. LaTeX Warning: Reference `lezar:sec:cutoff_formulation' on page 632 undefined o n input line 339. Package natbib Warning: Citation `Jin2002' on page 632 undefined on input line 343. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 632 undefi ned on input line 343. LaTeX Warning: Reference `eq:lezar:functional' on page 632 undefined on input l ine 345. [632] Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 633 undefi ned on input line 361. LaTeX Warning: Reference `eq:lezar:S_tt_ij' on page 633 undefined on input line 382. LaTeX Warning: Reference `eq:lezar:T_tt_ij' on page 633 undefined on input line 382. LaTeX Warning: Reference `eq:lezar:S_zz_ij' on page 633 undefined on input line 383. LaTeX Warning: Reference `eq:lezar:T_zz_ij' on page 633 undefined on input line 383. Package natbib Warning: Citation `Jin2002' on page 633 undefined on input line 399. Package natbib Warning: Citation `Davidson2011' on page 633 undefined on input line 400. LaTeX Warning: Reference `eq:lezar:vector_helmholtz' on page 633 undefined on i nput line 402. Package natbib Warning: Citation `Bossavit1998' on page 633 undefined on input line 402. Package natbib Warning: Citation `FernandesRaffetto2002' on page 633 undefined on input line 404. Package natbib Warning: Citation `Webb1993' on page 633 undefined on input line 410. Package natbib Warning: Citation `Davidson2011' on page 633 undefined on input line 412. Package natbib Warning: Citation `Jin2002' on page 633 undefined on input line 412. Package natbib Warning: Citation `VardapetyanDemkowicz2002' on page 633 undefin ed on input line 414. LaTeX Warning: Reference `eq:lezar:standard_functional' on page 633 undefined o n input line 416. Package natbib Warning: Citation `ConstableDauge2002' on page 633 undefined on input line 416. Package natbib Warning: Citation `BuffaHoustonPerugia2007' on page 633 undefine d on input line 418. [633] Package natbib Warning: Citation `Jin2002' on page 634 undefined on input line 439. LaTeX Warning: Reference `fig:lezar:rectangular_fenics_mesh' on page 634 undefi ned on input line 444. (./chapters/lezar/svg/rectangular_fenics_mesh.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/rectangular_fenics_mesh.pdf ): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [634 <./chapters/le zar/svg/rectangular_fenics_mesh.pdf>] LaTeX Warning: Reference `eq:lezar:S_tt_ij' on page 635 undefined on input line 505. LaTeX Warning: Reference `eq:lezar:T_zz_ij' on page 635 undefined on input line 505. LaTeX Warning: Reference `eq:lezar:A_tt' on page 635 undefined on input line 50 6. LaTeX Warning: Reference `eq:lezar:B_zt_ij' on page 635 undefined on input line 506. LaTeX Warning: Reference `eq:lezar:matrix_equation_cutoff' on page 635 undefine d on input line 508. LaTeX Warning: Reference `eq:lezar:matrix_equation_dispersion' on page 635 unde fined on input line 509. LaTeX Warning: Reference `eq:lezar:electric_wall_BC' on page 635 undefined on i nput line 532. Package natbib Warning: Citation `Smith1997' on page 635 undefined on input lin e 534. LaTeX Warning: Reference `eq:lezar:magnetic_wall_BC' on page 635 undefined on i nput line 552. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 635 undefi ned on input line 555. Package natbib Warning: Citation `Jin2002' on page 635 undefined on input line 558. LaTeX Warning: Reference `chap:rognes' on page 635 undefined on input line 564. [635] Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 636 undefi ned on input line 592. Package natbib Warning: Citation `Davidson2011' on page 636 undefined on input line 624. Package natbib Warning: Citation `Jin2002' on page 636 undefined on input line 624. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 636 undefi ned on input line 624. Package natbib Warning: Citation `Pozar2005' on page 636 undefined on input lin e 624. LaTeX Warning: Reference `fig:lezar:hollow_rectangular_guide' on page 636 undef ined on input line 637. Package natbib Warning: Citation `Pozar2005' on page 636 undefined on input lin e 642. [636] Package natbib Warning: Citation `Pozar2005' on page 637 undefined on input lin e 651. (./chapters/lezar/svg/hollow_rectangular_waveguide.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_rectangular_waveguid e.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allow ed ) LaTeX Warning: Reference `eq:lezar:electric_wall_BC' on page 637 undefined on i nput line 664. LaTeX Warning: Reference `eq:lezar:electric_wall_BC' on page 637 undefined on i nput line 664. Package natbib Warning: Citation `Pozar2005' on page 637 undefined on input lin e 669. LaTeX Warning: Reference `eq:lezar:rect:E_x analytical' on page 637 undefined o n input line 678. LaTeX Warning: Reference `eq:lezar:rect:E_y analytical' on page 637 undefined o n input line 678. LaTeX Warning: Reference `eq:lezar:rect_E_z_analytical' on page 637 undefined o n input line 679. LaTeX Warning: Reference `eq:lezar:operating_wavenumber' on page 637 undefined on input line 689. LaTeX Warning: Reference `fig:lezar:rectangular_cutoff_TE' on page 637 undefine d on input line 701. LaTeX Warning: Reference `fig:lezar:rectangular_cutoff_TM' on page 637 undefine d on input line 702. LaTeX Warning: Reference `fig:lezar:hollow_rectangular_guide' on page 637 undef ined on input line 704. (./chapters/lezar/svg/hollow_cutoff_TE.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_cutoff_TE.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `fig:lezar:hollow_rectangular_guide' on page 637 undef ined on input line 712. LaTeX Warning: Reference `fig:lezar:hollow_rectangular_guide' on page 637 undef ined on input line 712. (./chapters/lezar/svg/hollow_cutoff_TM.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_cutoff_TM.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `fig:lezar:hollow_rectangular_guide' on page 637 undef ined on input line 724. LaTeX Warning: Reference `fig:lezar:hollow_rectangular_guide' on page 637 undef ined on input line 724. LaTeX Warning: Reference `tab:lezar:rectangular_cutoff_comparison' on page 637 undefined on input line 727. LaTeX Warning: Reference `lezar:sec:propagation_curves' on page 637 undefined o n input line 759. LaTeX Warning: Reference `fig:lezar:hollow_rectangular_dispersion_curves' on pa ge 637 undefined on input line 761. Package natbib Warning: Citation `Davidson2011' on page 637 undefined on input line 764. LaTeX Warning: Reference `eq:lezar:rectangular_propagation' on page 637 undefin ed on input line 765. LaTeX Warning: Reference `eq:lezar:rectangular_cutoff' on page 637 undefined on input line 766. (./chapters/lezar/svg/hollow_rectangular_waveguide_dispersion_curve.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_rectangular_waveguid e_dispersion_curve.pdf): PDF inclusion: found PDF version <1.5>, but at most ve rsion <1.4> allowed ) LaTeX Warning: Reference `fig:lezar:hollow_rectangular_guide' on page 637 undef ined on input line 781. LaTeX Warning: Reference `fig:lezar:hollow_rectangular_guide' on page 637 undef ined on input line 781. [637 <./chapters/lezar/svg/hollow_rectangular_waveguide.pdf>] [638 <./chapters/ lezar/svg/hollow_cutoff_TE.pdf> <./chapters/lezar/svg/hollow_cutoff_TM.pdf>] Package natbib Warning: Citation `Pozar2005' on page 639 undefined on input lin e 798. LaTeX Warning: Reference `fig:lezar:half_filled_rectangular_guide' on page 639 undefined on input line 800. (./chapters/lezar/svg/half_filled_rectangular_waveguide.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_rectangular_wav eguide.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `eq:lezar:electric_wall_BC' on page 639 undefined on i nput line 813. LaTeX Warning: Reference `eq:lezar:electric_wall_BC' on page 639 undefined on i nput line 813. LaTeX Warning: Reference `fig:lezar:half_filled_rectangular_cutoff_TE' on page 639 undefined on input line 820. LaTeX Warning: Reference `fig:lezar:half_filled_rectangular_cutoff_TM' on page 639 undefined on input line 821. LaTeX Warning: Reference `fig:lezar:half_filled_rectangular_guide' on page 639 undefined on input line 823. Package natbib Warning: Citation `Pozar2005' on page 639 undefined on input lin e 827. Package natbib Warning: Citation `Smith1997' on page 639 undefined on input lin e 827. (./chapters/lezar/svg/half_filled_cutoff_TE.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_cutoff_TE.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `fig:lezar:half_filled_rectangular_guide' on page 639 undefined on input line 836. LaTeX Warning: Reference `fig:lezar:half_filled_rectangular_guide' on page 639 undefined on input line 836. [639 <./chapters/lezar/svg/hollow_rectangular_waveguide_dispersion_curve.pdf> < ./chapters/lezar/svg/half_filled_rectangular_waveguide.pdf>] (./chapters/lezar/svg/half_filled_cutoff_TM.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_cutoff_TM.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `fig:lezar:half_filled_rectangular_guide' on page 640 undefined on input line 848. LaTeX Warning: Reference `fig:lezar:half_filled_rectangular_guide' on page 640 undefined on input line 848. Underfull \hbox (badness 2698) in paragraph at lines 848--848 []\T1/pplx/m/n/9 (+20) Figure 34.9: |The fourth cal-cu- LaTeX Warning: Reference `fig:lezar:half_loaded_rectangular_dispersion_curves' on page 640 undefined on input line 857. Package natbib Warning: Citation `Jin2002' on page 640 undefined on input line 858. Package natbib Warning: Citation `Pozar2005' on page 640 undefined on input lin e 873. LaTeX Warning: Reference `fig:lezar:shielded_microstrip' on page 640 undefined on input line 877. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 640 undefi ned on input line 880. Package natbib Warning: Citation `Pozar2005' on page 640 undefined on input lin e 885. Package natbib Warning: Citation `Jin2002' on page 640 undefined on input line 887. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 640 undefi ned on input line 887. Package natbib Warning: Citation `Pozar2005' on page 640 undefined on input lin e 891. [640 <./chapters/lezar/svg/half_filled_cutoff_TE.pdf> <./chapters/lezar/svg/hal f_filled_cutoff_TM.pdf>] (./chapters/lezar/svg/half_filled_rectangular_waveguide_dispersion_curve.pdf_te x pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_rectangular_wav eguide_dispersion_curve.pdf): PDF inclusion: found PDF version <1.5>, but at mo st version <1.4> allowed ) LaTeX Warning: Reference `fig:lezar:half_filled_rectangular_guide' on page 641 undefined on input line 902. Package natbib Warning: Citation `Jin2002' on page 641 undefined on input line 902. LaTeX Warning: Reference `fig:lezar:half_filled_rectangular_guide' on page 641 undefined on input line 902. Package natbib Warning: Citation `Jin2002' on page 641 undefined on input line 902. (./chapters/lezar/svg/shielded_microstrip_waveguide.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/shielded_microstrip_wavegui de.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allo wed ) [641 <./chapters/lezar/svg/half_filled_rectangular_waveguide_dispersion_curve.p df> <./chapters/lezar/svg/shielded_microstrip_waveguide.pdf>] (./chapters/lezar/svg/boxed_microstrip_dispersion_curves.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/boxed_microstrip_dispersion _curves.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) LaTeX Warning: Reference `fig:lezar:shielded_microstrip' on page 642 undefined on input line 932. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 642 undefi ned on input line 932. LaTeX Warning: Reference `fig:lezar:shielded_microstrip' on page 642 undefined on input line 932. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 642 undefi ned on input line 932. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 642 undefi ned on input line 941. LaTeX Warning: Reference `fig:lezar:shielded_microstrip_dispersion_curves' on p age 642 undefined on input line 943. Package natbib Warning: Citation `HuangItoh1988' on page 642 undefined on input line 950. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 642 undefi ned on input line 953. Package natbib Warning: Citation `Jin2002' on page 642 undefined on input line 966. Package natbib Warning: Citation `PelosiCoccioliSelleri1998' on page 642 undefi ned on input line 967. ) (./tex/35.tex [642 <./chapters/lezar/svg/boxed_microstrip_dispersion_curves.p df>] Chapter 35. Package natbib Warning: Citation `MardalWinther11' on page 643 undefined on inp ut line 43. Underfull \vbox (badness 3281) has occurred while \output is active [643] LaTeX Warning: Reference `fig:mardal-4:block:dag' on page 644 undefined on inpu t line 112. (./chapters/mardal-4/pdf/block.pdf_tex pdfTeX warning: pdflatex (file ./chapters/mardal-4/pdf/block.pdf): PDF inclusio n: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \vbox (badness 2443) has occurred while \output is active [644 <./cha pters/mardal-4/pdf/block.pdf>] Package natbib Warning: Citation `Bramble1993' on page 645 undefined on input l ine 167. Package natbib Warning: Citation `Hackbusch1994' on page 645 undefined on input line 167. Package natbib Warning: Citation `TrottenbergOosterleeSchuller2001' on page 645 undefined on input line 167. [645] Package natbib Warning: Citation `Saad2003' on page 646 undefined on input line 244. [646] LaTeX Warning: Reference `tabel:neumann' on page 647 undefined on input line 30 5. [647] Package natbib Warning: Citation `Brezzi1974' on page 648 undefined on input li ne 358. Package natbib Warning: Citation `BrezziFortin1991' on page 648 undefined on in put line 358. Package natbib Warning: Citation `MardalWinther11' on page 648 undefined on inp ut line 371. Package natbib Warning: Citation `ElmanSilvesterWathen2005' on page 648 undefin ed on input line 380. Package natbib Warning: Citation `RustenWinther1992' on page 648 undefined on i nput line 380. Package natbib Warning: Citation `SilvesterWathen1993' on page 648 undefined on input line 380. Package natbib Warning: Citation `SilvesterWathen1994' on page 648 undefined on input line 380. LaTeX Warning: Reference `stokes:ex' on page 648 undefined on input line 382. LaTeX Warning: Reference `chap:rognes' on page 648 undefined on input line 398. Underfull \vbox (badness 2384) has occurred while \output is active [648] [649] Package natbib Warning: Citation `MardalWinther2004' on page 650 undefined on i nput line 529. Package natbib Warning: Citation `MardalTaiWinther2002' on page 650 undefined o n input line 531. Package natbib Warning: Citation `MardalWinther2004' on page 650 undefined on i nput line 531. [650] Package natbib Warning: Citation `MardalWinther11' on page 651 undefined on inp ut line 552. Package natbib Warning: Citation `CahouetChabard1988' on page 651 undefined on input line 556. Package natbib Warning: Citation `ElmanSilvesterWathen2005' on page 651 undefin ed on input line 556. Package natbib Warning: Citation `MardalWinther2004' on page 651 undefined on i nput line 556. Package natbib Warning: Citation `MardalWinther11' on page 651 undefined on inp ut line 556. Package natbib Warning: Citation `Turek1999' on page 651 undefined on input lin e 556. LaTeX Warning: Reference `timestokes:ex' on page 651 undefined on input line 59 5. [651] Package natbib Warning: Citation `ArnoldFalkWinther1997a' on page 652 undefined on input line 624. Package natbib Warning: Citation `ArnoldFalkWinther2000' on page 652 undefined on input line 624. Package natbib Warning: Citation `Hiptmair1997' on page 652 undefined on input line 624. Package natbib Warning: Citation `Hiptmair1999' on page 652 undefined on input line 624. Package natbib Warning: Citation `GeeSiefertHuEtAl2006' on page 652 undefined o n input line 629. Package natbib Warning: Citation `HuTuminaroBochevEtAl2006' on page 652 undefin ed on input line 629. LaTeX Warning: Reference `mixed:hodge1' on page 652 undefined on input line 649 . LaTeX Warning: Reference `mixed:hodge2' on page 652 undefined on input line 649 . Underfull \vbox (badness 10000) has occurred while \output is active [652] LaTeX Warning: Reference `table:hodge' on page 653 undefined on input line 713. Package natbib Warning: Citation `Nedelec1980' on page 653 undefined on input l ine 715. [653] Package natbib Warning: Citation `BellOlsonSchroder2009' on page 654 undefined on input line 753. Package natbib Warning: Citation `MardalWinther11' on page 654 undefined on inp ut line 758. Package natbib Warning: Citation `BenziGolubLiesen2005' on page 654 undefined o n input line 762. Package natbib Warning: Citation `ElmanSilvesterWathen2005' on page 654 undefin ed on input line 762. Package natbib Warning: Citation `Hiptmair2006' on page 654 undefined on input line 762. Package natbib Warning: Citation `Kirby2010' on page 654 undefined on input lin e 762. ) (./tex/36.tex [654] Chapter 36. Package natbib Warning: Citation `Babuvska1972/73' on page 655 undefined on inp ut line 44. Package natbib Warning: Citation `Brezzi1974' on page 655 undefined on input li ne 45. Package natbib Warning: Citation `ArnoldFalkWinther2006' on page 655 undefined on input line 52. Package natbib Warning: Citation `BrezziDouglasMarini1985' on page 655 undefine d on input line 52. Package natbib Warning: Citation `BrezziFalk1991' on page 655 undefined on inpu t line 52. Package natbib Warning: Citation `BrezziFortin1991' on page 655 undefined on in put line 52. Package natbib Warning: Citation `RaviartThomas1977' on page 655 undefined on i nput line 52. Package natbib Warning: Citation `TaylorHood1973' on page 655 undefined on inpu t line 52. Package natbib Warning: Citation `BrezziFalk1991' on page 655 undefined on inpu t line 54. Package natbib Warning: Citation `Stenberg1984' on page 655 undefined on input line 54. Package natbib Warning: Citation `TaylorHood1973' on page 655 undefined on inpu t line 54. Package natbib Warning: Citation `BoffiBrezziGastaldi2000' on page 655 undefine d on input line 58. Package natbib Warning: Citation `ArnoldRognes2009' on page 655 undefined on in put line 67. Package natbib Warning: Citation `ChapelleBathe1993' on page 655 undefined on i nput line 67. Package natbib Warning: Citation `Qin1994' on page 655 undefined on input line 67. Package natbib Warning: Citation `ArnoldRognes2009' on page 655 undefined on in put line 84. [655] LaTeX Warning: Reference `rognes:sec:motivation' on page 656 undefined on input line 88. LaTeX Warning: Reference `rognes:sec:automation' on page 656 undefined on input line 92. Package natbib Warning: Citation `Rognes2009' on page 656 undefined on input li ne 94. Package natbib Warning: Citation `LoggWells2010' on page 656 undefined on input line 95. LaTeX Warning: Reference `rognes:sec:examples' on page 656 undefined on input l ine 100. LaTeX Warning: Reference `rognes:sec:conclusion' on page 656 undefined on input line 101. LaTeX Warning: Reference `rognes:eq:mixedlaplace' on page 656 undefined on inpu t line 126. LaTeX Warning: Reference `rognes:eq:mixedlaplace' on page 656 undefined on inpu t line 133. LaTeX Warning: Reference `rognes:fig:example' on page 656 undefined on input li ne 164. LaTeX Warning: Reference `sub@rognes:fig:cg' on page 656 undefined on input lin e 164. LaTeX Warning: Reference `rognes:eq:mixedlaplace' on page 656 undefined on inpu t line 192. LaTeX Warning: Reference `sub@rognes:fig:cg' on page 656 undefined on input lin e 192. LaTeX Warning: Reference `sub@rognes:fig:rt' on page 656 undefined on input lin e 192. LaTeX Warning: Reference `rognes:eq:mixedlaplace' on page 656 undefined on inpu t line 192. LaTeX Warning: Reference `sub@rognes:fig:cg' on page 656 undefined on input lin e 192. LaTeX Warning: Reference `sub@rognes:fig:rt' on page 656 undefined on input lin e 192. Package natbib Warning: Citation `RaviartThomas1977' on page 656 undefined on i nput line 200. LaTeX Warning: Reference `rognes:fig:example' on page 656 undefined on input li ne 202. LaTeX Warning: Reference `sub@rognes:fig:rt' on page 656 undefined on input lin e 202. [656] LaTeX Warning: Reference `rognes:sec:examples' on page 657 undefined on input l ine 211. Package natbib Warning: Citation `Babuvska1972/73' on page 657 undefined on inp ut line 223. Package natbib Warning: Citation `Brezzi1974' on page 657 undefined on input li ne 223. Package natbib Warning: Citation `BrezziFortin1991' on page 657 undefined on in put line 223. LaTeX Warning: Reference `rognes:eq:infsup' on page 657 undefined on input line 258. LaTeX Warning: Reference `rognes:eq:canonical' on page 657 undefined on input l ine 260. Package natbib Warning: Citation `Babuvska1972/73' on page 657 undefined on inp ut line 260. LaTeX Warning: Reference `rognes:eq:canonical' on page 657 undefined on input l ine 264. [657 <./chapters/rognes/pdf/CG.pdf> <./chapters/rognes/pdf/RT.pdf>] LaTeX Warning: Reference `rognes:eq:infsup' on page 658 undefined on input line 274. LaTeX Warning: Reference `rognes:eq:discrete' on page 658 undefined on input li ne 275. Package natbib Warning: Citation `Babuvska1972/73' on page 658 undefined on inp ut line 286. LaTeX Warning: Reference `rognes:eq:infsup:discrete' on page 658 undefined on i nput line 288. LaTeX Warning: Reference `rognes:eq:discrete' on page 658 undefined on input li ne 292. LaTeX Warning: Reference `rognes:eq:infsup:discrete' on page 658 undefined on i nput line 304. LaTeX Warning: Reference `rognes:eq:infsup:discrete' on page 658 undefined on i nput line 311. LaTeX Warning: Reference `rognes:eq:saddlepoint' on page 658 undefined on input line 325. LaTeX Warning: Reference `rognes:eq:canonical' on page 658 undefined on input l ine 326. LaTeX Warning: Reference `rognes:eq:infsup' on page 658 undefined on input line 332. LaTeX Warning: Reference `rognes:eq:saddlepoint' on page 658 undefined on input line 336. LaTeX Warning: Reference `rognes:eq:discrete' on page 658 undefined on input li ne 339. LaTeX Warning: Reference `rognes:eq:infsup:discrete' on page 658 undefined on i nput line 348. LaTeX Warning: Reference `rognes:eq:saddlepoint' on page 658 undefined on input line 348. Underfull \vbox (badness 2608) has occurred while \output is active [658] LaTeX Warning: Reference `rognes:eq:saddlepoint' on page 659 undefined on input line 365. LaTeX Warning: Reference `rognes:eq:saddlepoint' on page 659 undefined on input line 366. Package natbib Warning: Citation `Brezzi1974' on page 659 undefined on input li ne 369. Package natbib Warning: Citation `Brezzi1974' on page 659 undefined on input li ne 391. Package natbib Warning: Citation `Qin1994' on page 659 undefined on input line 421. [659] Package natbib Warning: Citation `ArnoldRognes2009' on page 660 undefined on in put line 468. Package natbib Warning: Citation `Malkus1981' on page 660 undefined on input li ne 468. LaTeX Warning: Reference `rognes:eq:eigenvalue:kernel' on page 660 undefined on input line 490. LaTeX Warning: Reference `rognes:eq:eigenvalue:kernel' on page 660 undefined on input line 502. Package natbib Warning: Citation `ArnoldRognes2009' on page 660 undefined on in put line 503. LaTeX Warning: Reference `rognes:eq:eigenvalue:coercivity' on page 660 undefine d on input line 505. LaTeX Warning: Reference `rognes:eq:eigenvalue:coercivity' on page 660 undefine d on input line 506. LaTeX Warning: Reference `rognes:eq:eigenvalue:coercivity' on page 660 undefine d on input line 510. LaTeX Warning: Reference `rognes:eq:eigenvalue:coercivity' on page 660 undefine d on input line 511. Package natbib Warning: Citation `Malkus1981' on page 660 undefined on input li ne 517. Package natbib Warning: Citation `Qin1994' on page 660 undefined on input line 517. LaTeX Warning: Reference `rognes:eq:eigenvalue:infsup' on page 660 undefined on input line 524. Package natbib Warning: Citation `Qin1994' on page 660 undefined on input line 528. LaTeX Warning: Reference `rognes:eq:eigenvalue:babuska' on page 660 undefined o n input line 535. LaTeX Warning: Reference `rognes:eq:eigenvalue:coercivity' on page 660 undefine d on input line 536. LaTeX Warning: Reference `rognes:eq:eigenvalue:infsup' on page 660 undefined on input line 537. LaTeX Warning: Reference `rognes:eq:eigenvalue:infsup' on page 660 undefined on input line 539. Package natbib Warning: Citation `Qin1994' on page 660 undefined on input line 541. Package natbib Warning: Citation `ChapelleBathe1993' on page 660 undefined on i nput line 541. Underfull \vbox (badness 3861) has occurred while \output is active [660] LaTeX Warning: Reference `rognes:eq:saddlepoint' on page 661 undefined on input line 550. LaTeX Warning: Reference `rognes:def:stable' on page 661 undefined on input lin e 551. LaTeX Warning: Reference `rognes:eq:saddlepoint' on page 661 undefined on input line 563. LaTeX Warning: Reference `rognes:eq:canonical' on page 661 undefined on input l ine 564. LaTeX Warning: Reference `rognes:def:stable' on page 661 undefined on input lin e 581. LaTeX Warning: Reference `rognes:def:reduced_stable' on page 661 undefined on i nput line 582. Package natbib Warning: Citation `Rognes2009' on page 661 undefined on input li ne 591. [661] LaTeX Warning: Reference `rognes:eq:mixedlaplace:discrete' on page 662 undefine d on input line 621. [662] LaTeX Warning: Reference `rognes:eq:eigenvalue:infsup' on page 663 undefined on input line 701. LaTeX Warning: Reference `rognes:eq:eigenvalue:infsup' on page 663 undefined on input line 705. [663] Package natbib Warning: Citation `HernandezRomanVidal2005' on page 664 undefine d on input line 752. Package natbib Warning: Citation `HernandezRomanRomeroEtAl2009' on page 664 und efined on input line 752. Package natbib Warning: Citation `HernandezRomanRomeroEtAl2009' on page 664 und efined on input line 768. LaTeX Warning: Reference `rognes:sec:motivation' on page 664 undefined on input line 823. Underfull \vbox (badness 7522) has occurred while \output is active [664] LaTeX Warning: Reference `rognes:sec:motivation' on page 665 undefined on input line 831. LaTeX Warning: Reference `rognes:subsec:input' on page 665 undefined on input l ine 838. LaTeX Warning: Reference `rognes:sec:motivation' on page 665 undefined on input line 874. [665] LaTeX Warning: Reference `rognes:sec:motivation' on page 666 undefined on input line 905. LaTeX Warning: Reference `rognes:fig:example' on page 666 undefined on input li ne 908. LaTeX Warning: Reference `sub@rognes:fig:cg' on page 666 undefined on input lin e 908. Package natbib Warning: Citation `RaviartThomas1977' on page 666 undefined on i nput line 926. Package natbib Warning: Citation `ArnoldRognes2009' on page 666 undefined on in put line 930. LaTeX Warning: Reference `rognes:fig:example' on page 666 undefined on input li ne 932. LaTeX Warning: Reference `sub@rognes:fig:rt' on page 666 undefined on input lin e 932. [666] Package natbib Warning: Citation `Qin1994' on page 667 undefined on input line 958. Package natbib Warning: Citation `ArnoldRognes2009' on page 667 undefined on in put line 963. LaTeX Warning: Reference `rognes:eq:stokes' on page 667 undefined on input line 1010. [667] LaTeX Warning: Reference `rognes:fig:stokeslist' on page 668 undefined on input line 1041. Package natbib Warning: Citation `TaylorHood1973' on page 668 undefined on inpu t line 1047. Package natbib Warning: Citation `Stenberg1984' on page 668 undefined on input line 1047. Package natbib Warning: Citation `BrezziFalk1991' on page 668 undefined on inpu t line 1047. Package natbib Warning: Citation `CrouzeixRaviart1973' on page 668 undefined on input line 1050. Package natbib Warning: Citation `Qin1994' on page 668 undefined on input line 1059. Package natbib Warning: Citation `ArnoldRognes2009' on page 668 undefined on in put line 1122. ) [668] [669] [670] (./tex/BM1.tex LaTeX Warning: Reference `chap:wilbers' on page 671 undefined on input line 28. LaTeX Warning: Reference `chap:alnes-3' on page 671 undefined on input line 28. LaTeX Warning: Reference `chap:alnes-2' on page 671 undefined on input line 28. LaTeX Warning: Reference `chap:alnes-1' on page 671 undefined on input line 28. LaTeX Warning: Reference `chap:vynnytska' on page 671 undefined on input line 3 4. LaTeX Warning: Reference `chap:lezar' on page 671 undefined on input line 42. LaTeX Warning: Reference `chap:hoffman-1' on page 671 undefined on input line 4 8. LaTeX Warning: Reference `chap:hoffman-2' on page 671 undefined on input line 5 4. LaTeX Warning: Reference `chap:mardal-4' on page 671 undefined on input line 64 . Underfull \vbox (badness 10000) has occurred while \output is active [671] LaTeX Warning: Reference `chap:logg-2' on page 672 undefined on input line 77. LaTeX Warning: Reference `chap:mardal-2' on page 672 undefined on input line 77 . LaTeX Warning: Reference `chap:hake' on page 672 undefined on input line 77. LaTeX Warning: Reference `chap:hoffman-2' on page 672 undefined on input line 8 3. LaTeX Warning: Reference `chap:hoffman-1' on page 672 undefined on input line 8 3. LaTeX Warning: Reference `chap:hoffman-2' on page 672 undefined on input line 8 9. LaTeX Warning: Reference `chap:hoffman-1' on page 672 undefined on input line 8 9. LaTeX Warning: Reference `chap:hoffman-2' on page 672 undefined on input line 9 5. LaTeX Warning: Reference `chap:hoffman-1' on page 672 undefined on input line 9 5. LaTeX Warning: Reference `chap:hoffman-1' on page 672 undefined on input line 1 01. LaTeX Warning: Reference `chap:kirby-7' on page 672 undefined on input line 116 . LaTeX Warning: Reference `chap:kirby-6' on page 672 undefined on input line 116 . LaTeX Warning: Reference `chap:kirby-1' on page 672 undefined on input line 116 . LaTeX Warning: Reference `chap:kirby-5' on page 672 undefined on input line 116 . LaTeX Warning: Reference `chap:kirby-8' on page 672 undefined on input line 116 . LaTeX Warning: Reference `chap:kirby-4' on page 672 undefined on input line 116 . LaTeX Warning: Reference `chap:kirby-3' on page 672 undefined on input line 116 . LaTeX Warning: Reference `chap:kirby-2' on page 672 undefined on input line 116 . LaTeX Warning: Reference `chap:terrel' on page 672 undefined on input line 116. LaTeX Warning: Reference `chap:terrel' on page 672 undefined on input line 125. Underfull \vbox (badness 10000) has occurred while \output is active [672] LaTeX Warning: Reference `chap:langtangen' on page 673 undefined on input line 135. LaTeX Warning: Reference `chap:lezar' on page 673 undefined on input line 143. LaTeX Warning: Reference `chap:hentschel' on page 673 undefined on input line 1 52. LaTeX Warning: Reference `chap:kirby-7' on page 673 undefined on input line 176 . LaTeX Warning: Reference `chap:kirby-6' on page 673 undefined on input line 176 . LaTeX Warning: Reference `chap:kirby-5' on page 673 undefined on input line 176 . LaTeX Warning: Reference `chap:logg-3' on page 673 undefined on input line 176. LaTeX Warning: Reference `chap:kirby-8' on page 673 undefined on input line 176 . LaTeX Warning: Reference `chap:kirby-4' on page 673 undefined on input line 176 . LaTeX Warning: Reference `chap:logg-2' on page 673 undefined on input line 176. LaTeX Warning: Reference `chap:logg-1' on page 673 undefined on input line 176. LaTeX Warning: Reference `chap:kirby-3' on page 673 undefined on input line 176 . LaTeX Warning: Reference `chap:alnes-2' on page 673 undefined on input line 176 . LaTeX Warning: Reference `chap:kvs-1' on page 673 undefined on input line 176. LaTeX Warning: Reference `chap:kvs-2' on page 673 undefined on input line 176. LaTeX Warning: Reference `chap:lopes' on page 673 undefined on input line 186. Underfull \vbox (badness 10000) has occurred while \output is active [673] LaTeX Warning: Reference `chap:hentschel' on page 674 undefined on input line 1 95. LaTeX Warning: Reference `chap:kirby-1' on page 674 undefined on input line 210 . LaTeX Warning: Reference `chap:logg-3' on page 674 undefined on input line 210. LaTeX Warning: Reference `chap:wilbers' on page 674 undefined on input line 210 . LaTeX Warning: Reference `chap:alnes-3' on page 674 undefined on input line 210 . LaTeX Warning: Reference `chap:alnes-2' on page 674 undefined on input line 210 . LaTeX Warning: Reference `chap:mardal-2' on page 674 undefined on input line 21 0. LaTeX Warning: Reference `chap:kvs-1' on page 674 undefined on input line 210. LaTeX Warning: Reference `chap:mortensen' on page 674 undefined on input line 2 10. LaTeX Warning: Reference `chap:kvs-2' on page 674 undefined on input line 210. LaTeX Warning: Reference `chap:hentschel' on page 674 undefined on input line 2 10. LaTeX Warning: Reference `chap:mardal-4' on page 674 undefined on input line 21 0. LaTeX Warning: Reference `chap:kvs-1' on page 674 undefined on input line 216. LaTeX Warning: Reference `chap:mortensen' on page 674 undefined on input line 2 16. LaTeX Warning: Reference `chap:kvs-1' on page 674 undefined on input line 227. LaTeX Warning: Reference `chap:narayanan' on page 674 undefined on input line 2 27. LaTeX Warning: Reference `chap:hoffman-2' on page 674 undefined on input line 2 33. LaTeX Warning: Reference `chap:nikbakht' on page 674 undefined on input line 24 3. Underfull \vbox (badness 10000) has occurred while \output is active [674] LaTeX Warning: Reference `chap:lopes' on page 675 undefined on input line 252. LaTeX Warning: Reference `chap:kirby-6' on page 675 undefined on input line 275 . LaTeX Warning: Reference `chap:logg-1' on page 675 undefined on input line 275. LaTeX Warning: Reference `chap:vynnytska' on page 675 undefined on input line 2 75. LaTeX Warning: Reference `chap:rognes' on page 675 undefined on input line 275. LaTeX Warning: Reference `chap:schroll' on page 675 undefined on input line 282 . LaTeX Warning: Reference `chap:terrel' on page 675 undefined on input line 290. LaTeX Warning: Reference `chap:selim' on page 675 undefined on input line 302. Underfull \vbox (badness 10000) has occurred while \output is active [675] LaTeX Warning: Reference `chap:hentschel' on page 676 undefined on input line 3 11. LaTeX Warning: Reference `chap:kirby-6' on page 676 undefined on input line 320 . LaTeX Warning: Reference `chap:kirby-4' on page 676 undefined on input line 320 . LaTeX Warning: Reference `chap:terrel' on page 676 undefined on input line 320. LaTeX Warning: Reference `chap:lopes' on page 676 undefined on input line 328. LaTeX Warning: Reference `chap:kvs-1' on page 676 undefined on input line 337. LaTeX Warning: Reference `chap:kvs-2' on page 676 undefined on input line 337. LaTeX Warning: Reference `chap:vynnytska' on page 676 undefined on input line 3 43. LaTeX Warning: Reference `chap:logg-3' on page 676 undefined on input line 356. LaTeX Warning: Reference `chap:oelgaard-2' on page 676 undefined on input line 356. LaTeX Warning: Reference `chap:logg-2' on page 676 undefined on input line 356. LaTeX Warning: Reference `chap:logg-1' on page 676 undefined on input line 356. LaTeX Warning: Reference `chap:terrel' on page 676 undefined on input line 356. LaTeX Warning: Reference `chap:oelgaard-1' on page 676 undefined on input line 356. LaTeX Warning: Reference `chap:nikbakht' on page 676 undefined on input line 35 6. LaTeX Warning: Reference `chap:wilbers' on page 676 undefined on input line 364 . [676] LaTeX Warning: Reference `chap:oelgaard-2' on page 677 undefined on input line 376. LaTeX Warning: Reference `chap:logg-1' on page 677 undefined on input line 376. LaTeX Warning: Reference `chap:oelgaard-1' on page 677 undefined on input line 376. [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] No file book.ind. ) [713] Package natbib Warning: There were undefined citations. Package caption Warning: Unused \captionsetup[subalgorithm] on input line 14. (./book.aux Package natbib Warning: Citation(s) may have changed. (natbib) Rerun to get citations correct. ) LaTeX Font Warning: Size substitutions with differences (Font) up to 0.43996pt have occurred. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Hfootnote.38} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.37} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.36} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.35} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.34} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.33} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.32} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.31} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.30} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.29} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.28} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.27} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.26} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.25} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.24} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.23} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.22} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.21} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.20} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.19} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.18} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.17} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.16} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.15} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.14} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.13} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.12} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.11} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.10} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.9} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.8} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.7} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.6} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.5} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.4} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.3} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.2} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.1} has been referenced but does not exist , replaced by a fixed one {/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc} Output written on book.pdf (719 pages, 65527804 bytes). Transcript written on book.log. This is BibTeX, Version 0.99c (Web2C 7.5.7) The top-level auxiliary file: book.aux I found no \bibdata command---while reading file book.aux I found no \bibstyle command---while reading file book.aux (There were 2 error messages) This is makeindex, version 2.15 [20-Nov-2007] (kpathsea + Thai support). Scanning input file book.idx....done (776 entries accepted, 0 rejected). Sorting entries.........done (7953 comparisons). Generating output file book.ind....done (713 lines written, 1 warning). Output written in book.ind. Transcript written in book.ilg. This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. entering extended mode (./book.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded. (./fenicsbook.cls Document Class: fenicsbook (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/geometry.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/etc/texmf/tex/xelatex/xetexconfig/geometry.cfg)) (/usr/share/texmf-texlive/tex/latex/oberdiek/bookmark.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdfescape.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty) (/etc/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty)) (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) (/usr/share/texmf-texlive/tex/latex/oberdiek/auxhook.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/bkm-pdftex.def)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/emptypage.sty) (/usr/share/texmf-texlive/tex/latex/psnfss/mathpazo.sty) (/usr/share/texmf-texlive/tex/latex/psnfss/helvet.sty) (/usr/share/texmf-texlive/tex/latex/bera/beramono.sty) (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def)) (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def)) (/usr/share/texmf-texlive/tex/latex/textcase/textcase.sty) (/usr/share/texmf-texlive/tex/latex/titlesec/titlesec.sty) (/usr/share/texmf-texlive/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texmf-texlive/tex/latex/tools/multicol.sty) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/natbib/natbib.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty (/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf-texlive/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf-texlive/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amscd.sty) (/usr/share/texmf-texlive/tex/latex/stmaryrd/stmaryrd.sty) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/codehighlight.sty (/usr/src/RPM/BUILD/fenics-book-20130430/packages/mylistings.sty (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) (/usr/share/texmf-texlive/tex/latex/listings/listings.cfg)) (/usr/share/texmf/tex/latex/xcolor/xcolor.sty (/etc/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))) (/usr/share/texmf-texlive/tex/latex/ltxmisc/import.sty) (/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty (/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty (/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) (/etc/texmf/tex/latex/config/graphics.cfg))) (/usr/share/texmf-texlive/tex/latex/subfig/subfig.sty (/usr/share/texmf-texlive/tex/latex/caption/caption3.sty)) (/usr/share/texmf-texlive/tex/latex/booktabs/booktabs.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty) (/usr/share/texmf-texlive/tex/latex/tools/array.sty) (/usr/share/texmf-texlive/tex/latex/microtype/microtype.sty (/usr/share/texmf-texlive/tex/latex/microtype/microtype.cfg)) (/usr/share/texmf-texlive/tex/latex/tools/xspace.sty) (/usr/share/texmf-texlive/tex/latex/setspace/setspace.sty Package: `setspace' 6.7 <2000/12/01> ) (/usr/share/texmf-texlive/tex/latex/floatrow/floatrow.sty) (/usr/share/texmf-texlive/tex/latex/caption/caption.sty (/usr/share/texmf-texlive/tex/latex/caption/ltcaption.sty)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithm.sty Document Style `algorithm' - floating environment (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithmicx.sty Document Style algorithmicx 1.2 - a greatly improved `algorithmic' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algpseudocode.sty Document Style - pseudocode environments for use with the `algorithmicx' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/todonotes.sty (/usr/share/texmf-texlive/tex/latex/xkeyval/xkeyval.sty (/usr/share/texmf-texlive/tex/generic/xkeyval/xkeyval.tex)) (/usr/share/texmf/tex/latex/pgf/frontendlayer/tikz.sty (/usr/share/texmf/tex/latex/pgf/basiclayer/pgf.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfrcs.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common-lists.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-latex.def (/usr/share/texmf-texlive/tex/latex/ms/everyshi.sty)) (/usr/share/texmf/tex/generic/pgf/utilities/pgfrcs.code.tex)) (/usr/share/texmf/tex/latex/pgf/basiclayer/pgfcore.sty (/usr/share/texmf/tex/latex/pgf/systemlayer/pgfsys.sty (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys.code.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeysfiltered.code.tex)) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgf.cfg) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-pdftex.def (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-common-pdf.def))) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsyssoftpath.code.tex) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsysprotocol.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcore.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathcalc.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathutil.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathparser.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.basic.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.trigonometric.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.random.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.comparison.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.base.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.round.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.misc.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.integerarithmetics.code .tex))) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfloat.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepoints.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathconstruct.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathusage.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorescopes.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoregraphicstate.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransformations.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorequick.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreobjects.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathprocessing.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorearrows.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreshade.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreimage.code.tex (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreexternal.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorelayers.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransparency.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepatterns.code.tex))) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleshapes.code.tex) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleplot.code.tex) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-0-65.sty) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-1-18.sty)) (/usr/share/texmf/tex/latex/pgf/utilities/pgffor.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfkeys.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex)) (/usr/share/texmf/tex/latex/pgf/math/pgfmath.sty (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgffor.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex))) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/tikz.code.tex (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryplothandlers.code.tex) (/usr/share/texmf/tex/generic/pgf/modules/pgfmodulematrix.code.tex) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibrarytopat hs.code.tex))) (/usr/share/texmf-texlive/tex/latex/tools/calc.sty) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryshado ws.code.tex (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryfadin gs.code.tex (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryfadings.code.tex))))) Writing index file book.idx (./book.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/t1pplx.fd) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (/usr/share/texmf-texlive/tex/latex/microtype/mt-ppl.cfg) (/usr/share/texmf-texlive/tex/latex/floatrow/fr-subfig.sty) (/usr/share/texmf-texlive/tex/latex/floatrow/fr-longtable.sty) ABD: EveryShipout initializing macros (./tex/FM1.tex (/usr/share/texmf-texlive/tex/latex/psnfss/ot1pplx.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omlzplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omszplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omxzplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/ot1zplm.fd) (/usr/share/texmf-texlive/tex/latex/microtype/mt-msa.cfg) (/usr/share/texmf-texlive/tex/latex/microtype/mt-msb.cfg) (/usr/share/texmf-texlive/tex/latex/stmaryrd/Ustmry.fd) (/usr/share/texmf-texlive/tex/latex/bera/t1fvm.fd) [1{/var/cache/texmf/fonts/ma p/pdftex/updmap/pdftex.map}] Underfull \hbox (badness 10000) in paragraph at lines 59--67 Overfull \hbox (2.20999pt too wide) in paragraph at lines 46--68 $[]$ $[]$ (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pplx.fd) [2] (./book.toc [3] [4] [5] [6] [7] [8]) [9] [10]) [11] [12] (./tex/1.tex Chapter 1. [1] [2] [3] [4] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) [5] [6] [7] [8] [9 <./chapters/langtangen/pdf/ex1_u. pdf>] [10 <./chapters/langtangen/png/ex1_mesh.png (PNG copy)>] [11] [12] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) [13] [14] [15] [16] Underfull \vbox (badness 1033) has occurred while \output is active [17] [18] Underfull \vbox (badness 10000) has occurred while \output is active [19 <./cha pters/langtangen/pdf/membrane_waxis.pdf>] [20 <./chapters/langtangen/pdf/ex1_ gradu.pdf>] [21] [22] [23] [24] [25] [26] [27] Underfull \vbox (badness 3536) has occurred while \output is active [28] [29] Underfull \vbox (badness 10000) has occurred while \output is active [30 <./cha pters/langtangen/pdf/Poisson2D_Dvc_contour1.pdf> <./chapters/langtangen/pdf/Poi sson2D_Dvc_flux_x.pdf> <./chapters/langtangen/pdf/Poisson2D_Dvc_surf1.pdf> <./c hapters/langtangen/pdf/Poisson2D_Dvc_mesh1.pdf>] [31] [32] Underfull \vbox (badness 1122) has occurred while \output is active [33] [34] [35] [36] Underfull \vbox (badness 3646) has occurred while \output is active [37] [38] [39] Underfull \vbox (badness 1412) has occurred while \output is active [40] [41] [42] [43] Underfull \hbox (badness 1331) in paragraph at lines 3053--3059 []\T1/pplx/m/n/10 (+20) The im-ple-men-ta-tion is iden-ti-cal to the one in Sec -tion [][]1.2.2[][] and is found in the file [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] Underfull \vbox (badness 2088) has occurred while \output is active [53 <./chap ters/langtangen/pdf/daynight.pdfError: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap >] [54] Underfull \vbox (badness 3977) has occurred while \output is active [55] [56] [57] [58] [59 <./chapters/langtangen/pd f/hollow_cylinder.pdf>] [60] Underfull \hbox (badness 1215) in paragraph at lines 4284--4288 []\T1/pplx/m/n/10 (+20) Calling \T1/fvm/m/n/10 subdomains.array() \T1/pplx/m/n/ 10 (+20) re-turns a \T1/fvm/m/n/10 numpy \T1/pplx/m/n/10 (+20) ar-ray of the su b-do-main val-ues. That is, [61] [62] Underfull \vbox (badness 10000) has occurred while \output is active [63] [64] [65] [66] Overfull \hbox (2.004pt too wide) in paragraph at lines 4672--4674 []\T1/pplx/m/n/10 (-20) generate mesh over [67] [68] [69]) (./tex/Part1.tex [70] [71] [72]) (./tex/2.tex Chapter 2. (/usr/share/texmf-texlive/tex/latex/psnfss/ufplmbb.fd) Underfull \vbox (badness 2951) has occurred while \output is active [73] (./chapters/kirby-7/pdf/heat_equation_model_domain.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/heat_equation_model_domai n.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allow ed ) [74 <./ch apters/kirby-7/pdf/heat_equation_model_domain.pdf>] [75] [76] Underfull \vbox (badness 7451) has occurred while \output is active [77] [78] [79 <./chapters/kirby-7/pdf/cells.pdf>] [80 <./chapters/kirby-7/pdf/P1.pdf>] pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/dofmap.pdf): PDF inclusio n: found PDF version <1.5>, but at most version <1.4> allowed Underfull \vbox (badness 4060) has occurred while \output is active [81] Underfull \hbox (badness 1107) in paragraph at lines 694--694 []\T1/pplx/m/n/9 (+20) Figure 2.5: |Patch-ing to-gether a Underfull \hbox (badness 1755) in paragraph at lines 694--694 \T1/pplx/m/n/9 (+20) pair of quadratic lo-cal func-tion [82 <./chapters/kirby-7/pdf/dofmap.pdf> <./chapters/kirby-7/pdf/femspace.pdf>] (./chapters/kirby-7/pdf/affine_map.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/affine_map.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) [83 <./chapters/kirby-7/pdf/affine_m ap.pdf>] [84] [85] (./chapters/kirby-7/pdf/projection.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/projection.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \vbox (badness 10000) has occurred while \output is active [86 <./cha pters/kirby-7/pdf/projection.pdf>] [87] [88] [89 <./chapters/kirby-7/png/refinemen t.png (PNG copy)>]) (./tex/3.tex [90] Chapter 3. [91] [92] (./chapters/kirby-6/pdf/notation_new.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-6/pdf/notation_new.pdf): PDF in clusion: found PDF version <1.5>, but at most version <1.4> allowed ) [93] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 238. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 238. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 238. [94 <./chapters/kirby-6/pdf/notation_new.pdf>] pdfTeX warning: pdflatex (file ./chapters/kirby-6/pdf/P1_1d2d3d.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed [95 <./chapters/kirby-6/pdf/P1_1d2d3d.pdf >] [96 <./chapters/kirby-6/png/CG1_2d.png (PNG copy)> <./chapters/kirby-6/png/C G2_2d.png (PNG copy)> <./chapters/kirby-6/png/CG3_2d.png (PNG copy)> <./chapter s/kirby-6/png/CG4_2d.png (PNG copy)> <./chapters/kirby-6/png/CG5_2d.png (PNG co py)> <./chapters/kirby-6/png/CG6_2d.png (PNG copy)> <./chapters/kirby-6/png/CG1 _3d.png (PNG copy)> <./chapters/kirby-6/png/CG2_3d.png (PNG copy)> <./chapters/ kirby-6/png/CG3_3d.png (PNG copy)> <./chapters/kirby-6/png/CG4_3d.png (PNG copy )> <./chapters/kirby-6/png/CG5_3d.png (PNG copy)> <./chapters/kirby-6/png/CG6_3 d.png (PNG copy)>] Underfull \hbox (badness 3503) in paragraph at lines 394--394 []\T1/pplx/m/n/9 (+20) Figure 3.5: |Il-lus-tra-tion of the Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 430. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 430. [97 <./chapters/kirby-6/png/CR1_2d.png (PNG copy)> <./chapters/kirby-6/png/CR1_ 3d.png (PNG copy)>] Underfull \hbox (badness 1354) in paragraph at lines 510--510 \T1/pplx/m/n/9 (+20) mo-ments of the nor-mal com-po- Underfull \hbox (badness 1968) in paragraph at lines 510--510 \T1/pplx/m/n/9 (+20) ter-na-tively, as in-di-cated in this [98 <./chapters/kirby-6/png/RT1_2d.png (PNG copy)> <./chapters/kirby-6/png/RT2_ 2d.png (PNG copy)> <./chapters/kirby-6/png/RT3_2d.png (PNG copy)> <./chapters/k irby-6/png/RT1_3d.png (PNG copy)> <./chapters/kirby-6/png/RT2_3d.png (PNG copy) > <./chapters/kirby-6/png/RT3_3d.png (PNG copy)>] Underfull \hbox (badness 4995) in paragraph at lines 585--587 []\T1/pplx/m/it/10 The Brezzi--Douglas--Marini el-e-ment ($[][]$) is [99 <./chapters/kirby-6/png/BDM1_2d.png (PNG copy)> <./chapters/kirby-6/png/BDM 2_2d.png (PNG copy)> <./chapters/kirby-6/png/BDM3_2d.png (PNG copy)> <./chapter s/kirby-6/png/BDM1_3d.png (PNG copy)> <./chapters/kirby-6/png/BDM2_3d.png (PNG copy)> <./chapters/kirby-6/png/BDM3_3d.png (PNG copy)>] Underfull \hbox (badness 3503) in paragraph at lines 677--677 []\T1/pplx/m/n/9 (+20) Figure 3.8: |Il-lus-tra-tion of the [100] Overfull \hbox (1.29993pt too wide) in paragraph at lines 737--737 []\T1/pplx/m/n/9 (-20) Figure 3.9: |Illustration of the Arnold-- [101 <./chapters/kirby-6/png/MTW_2d.png (PNG copy)> <./chapters/kirby-6/png/AW_ 2d.png (PNG copy)>] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 748. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 748. Underfull \vbox (badness 10000) has occurred while \output is active [102] Underfull \vbox (badness 10000) has occurred while \output is active [103 <./ch apters/kirby-6/png/NED1_1_2d.png (PNG copy)> <./chapters/kirby-6/png/NED1_2_2d. png (PNG copy)> <./chapters/kirby-6/png/NED1_3_2d.png (PNG copy)> <./chapters/k irby-6/png/NED1_1_3d.png (PNG copy)> <./chapters/kirby-6/png/NED1_2_3d.png (PNG copy)> <./chapters/kirby-6/png/NED1_3_3d.png (PNG copy)>] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 963. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 963. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 963. [104 <./chapters/kirby-6/png/NED2_1_2d.png (PNG copy)> <./chapters/kirby-6/png/ NED2_2_2d.png (PNG copy)> <./chapters/kirby-6/png/NED2_3_2d.png (PNG copy)> <./ chapters/kirby-6/png/NED2_1_3d.png (PNG copy)>] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 1026. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 1026. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 1026. [105] [106 <./chapters/kirby-6/png/DG0_2 d.png (PNG copy)> <./chapters/kirby-6/png/DG1_2d.png (PNG copy)> <./chapters/ki rby-6/png/DG2_2d.png (PNG copy)> <./chapters/kirby-6/png/DG3_2d.png (PNG copy)> <./chapters/kirby-6/png/DG0_3d.png (PNG copy)> <./chapters/kirby-6/png/DG1_3d. png (PNG copy)> <./chapters/kirby-6/png/DG2_3d.png (PNG copy)> <./chapters/kirb y-6/png/DG3_3d.png (PNG copy)> <./chapters/kirby-6/pdf/dgspace.pdf>] [107 <./chapters/kirby-6/png/ARG5_2d.png (PNG copy)>] Underfull \vbox (badness 1092) has occurred while \output is active [108 <./cha pters/kirby-6/png/HER_2d.png (PNG copy)> <./chapters/kirby-6/png/HER_3d.png (PN G copy)>] [109 <./chapters/kirby-6/png/MOR_2d.png ( PNG copy)>] [110] Overfull \hbox (2.96089pt too wide) in paragraph at lines 1410--1410 []|\T1/pplx/m/n/9 (-20) Dimension| Underfull \hbox (badness 1484) in paragraph at lines 1425--1425 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 12$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 1484) in paragraph at lines 1428--1428 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 12$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 1484) in paragraph at lines 1431--1431 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 24$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 1484) in paragraph at lines 1434--1434 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 40$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 10000) in alignment at lines 1408--1468 [] [] [] [] [] Underfull \vbox (badness 10000) detected at line 1468 Underfull \hbox (badness 10000) in alignment at lines 1468--1528 [] [] [] [] [] [111] [112] Underfull \hbox (badness 10000) in alignment at lines 1528--1544 [] [] [] [] [] [113] [114] [115]) (./tex/4.tex [116] Chapter 4. [117] [118] [119] [120] [121] [122 <./chapters/kirby-1/pdf/tricoord.p df>] [123 <./chapters/kirby-6/pdf/P1.pdf> <./chapters/kirby-6/pdf/P2.pdf>] Underfull \hbox (badness 2744) in paragraph at lines 495--495 []\T1/pplx/m/n/9 (+20) Figure 4.4: |Tri-an-gu-lar Raviart-- [124 <./chapters/kirby-6/pdf/RT0.pdf>] [125] [126] [127] ) (./tex/5.tex [128 <./chapters/kirby-1/pdf /patch.pdf>] Chapter 5. Underfull \vbox (badness 10000) has occurred while \output is active [129] Underfull \vbox (badness 3219) has occurred while \output is active [130] (./chapters/kirby-5/pdf/lift_drag.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-5/pdf/lift_drag.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) [131] [132 <./chapters/kirby-5/pdf/li ft_drag.pdf>] (./chapters/kirby-5/pdf/element_tensors.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-5/pdf/element_tensors.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [133 <./chapters/kirby-5/pdf/el ement_tensors.pdf>] [134] [135]) (./tex/6.tex [136] Chapter 6. [137] (./chapters/logg-3/pdf/insertion.pdf_tex pdfTeX warning: pdflatex (file ./chapters/logg-3/pdf/insertion.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \vbox (badness 10000) has occurred while \output is active [138] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) [139 <./chapters/logg -3/pdf/insertion.pdf>] [140]) (./tex/7.tex [141] [142] Chapter 7. [143] [144] [145] Underfull \hbox (badness 1430) in paragraph at lines 293--293 \T1/pplx/m/n/9 (+20) from Fig-ure [][]7.1[][] with one ta-ble [146] [147] Underfull \vbox (badness 4805) has occurred while \output is active [148] [149] [150] [151 <./chapters/oelgaa rd-2/pdf/runtime_laplace.pdf>] [152] [153 <./chapter s/oelgaard-2/pdf/runtime_hyperelasticity.pdf>] [154]) (./tex/8.tex [155] [156] Chapter 8. [157] (./chapters/kirby-8/pdf/affinemap.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-8/pdf/affinemap.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \vbox (badness 10000) has occurred while \output is active [158 <./ch apters/kirby-8/pdf/affinemap.pdf>] [159]) (./tex/9.tex [160] Chapter 9. [161] Underfull \vbox (badness 1389) has occurred while \output is active [162] Underfull \vbox (badness 4981) has occurred while \output is active [163] (./chapters/kirby-4/pdf/small_mst.pdf_tex ) [164 <./chapters/kirby-4/pdf/small_ms t.pdf>] (./chapters/kirby-4/pdf/gg2.pdf_tex ) [165 <./chapters/kirby-4/pdf/gg2.pdf>] Underfull \vbox (badness 1215) has occurred while \output is active [166]) (./tex/Part2.tex [167] [168] [169] [170]) (./tex/10.tex Chapter 10. pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/fenics-map.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed Underfull \hbox (badness 1215) in paragraph at lines 61--61 \T1/pplx/m/n/9 (+20) the main user in-ter-face of FEn- [171] [172 <./chapters/logg-2/pdf/fenics-map .pdf>] [173 <./chapters/logg-2/pdf/dolfin-uml.pdf>] [174] [175] [176] [177] [178] Underfull \hbox (badness 1412) in paragraph at lines 563--570 \T1/pplx/m/n/10 (+20) abled when DOLFIN is con-fig-ured. The back-end can be se t via the global pa-ram-e-ter [179] [180] [181] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) [182] [183 <./chapters/logg-2/pdf/mesh -p1-entities.pdf>] [184] [185] [186] [187] [188 <./chapters/logg-2/png/refined_ cube.png (PNG copy)>] [189] [190] (./chapters/logg-2/pdf/femsolution.pdf_tex pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/femsolution.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) [191] [192 <./chapters/logg-2/pdf/fe msolution.pdf>] [193] [194] [195] [196] [197] [198] [199] [200] [201] Underfull \vbox (badness 1448) has occurred while \output is active [202] [203] [204] [205 <./chapters/logg-2/png/plot_mesh .png (PNG copy)> <./chapters/logg-2/png/plots.png (PNG copy)>] [206] Underfull \hbox (badness 1184) in paragraph at lines 2529--2532 \T1/pplx/m/n/10 (+20) One can-not read-/write \T1/fvm/m/n/10 Function \T1/pplx/ m/n/10 (+20) and \T1/fvm/m/n/10 FunctionSpace \T1/pplx/m/n/10 (+20) ob-jects si nce the rep-re-sen-ta-tion of a [207] [208] [209] [210] [211] [212] [213] Overfull \hbox (1.6556pt too wide) in paragraph at lines 3058--3067 [][] [214 <./chapters/logg-2/png/coloured.png (PNG copy)> <./chapters/logg-2/png/par tition.png (PNG copy)>] [215] [216] Underfull \hbox (badness 1533) in paragraph at lines 3274--3279 [] []\T1/pplx/m/it/10 Con-struct-ing ar-gu-ments (trial and test func-tions).[] \T1/pplx/m/n/10 (+20) The \T1/fvm/m/n/10 ufl.Argument \T1/pplx/m/n/10 (+20) cl ass (the base class of [217] [218] [219] Underfull \vbox (badness 1067) has occurred while \output is active [220] [221]) (./tex/11.tex [222] Chapter 11. [223 <./chapters/logg-1/pdf/ufl_ffc_u fc.pdf>] [224] [225] [226] [227] Underfull \hbox (badness 1975) in paragraph at lines 428--428 \T1/pplx/m/n/9 (+20) guage, Anal-y-sis, Rep-re-sen-ta-tion, [228] [229 <./chapters/logg-1/pdf/compilerdesign.pdf>] [230] [231] Underfull \hbox (badness 2961) in paragraph at lines 626--647 \T1/pplx/m/n/10 (+20) interface by giv-ing the ad-di-tional op-tions \T1/fvm/m/ n/10 -f eliminate_zeros\T1/pplx/m/n/10 (+20) , \T1/fvm/m/n/10 -f simplify_expre ssions\T1/pplx/m/n/10 (+20) , Underfull \hbox (badness 1308) in paragraph at lines 701--701 []\T1/pplx/m/n/9 (+20) Figure 11.7: |JIT com-pi-la-tion of [232]) (./tex/12.tex [233 <./chapters/logg-1/pdf/jit.pdf>] [234] Chapter 12. [235] [236] [237] Underfull \vbox (badness 1946) has occurred while \output is active [238 <./cha pters/kirby-3/pdf/MassH1.pdf>] [239 <./chapters/kirby-3/pdf/Poisson.pdf> <./cha pters/kirby-3/pdf/WeightedPoisson.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active [240 <./ch apters/kirby-3/pdf/NavierStokes.pdf>] [241 <./chapters/kirby-3/pdf/MassHdiv.pdf > <./chapters/kirby-3/pdf/MassHcurl.pdf>]) (./tex/13.tex [242] Chapter 13. Underfull \vbox (badness 10000) has occurred while \output is active [243] [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] [247] Underfull \hbox (badness 1371) in paragraph at lines 428--435 \T1/pplx/m/n/10 (+20) Then, a ba-sis for the null space of this ma-trix is con- structed us-ing the sin-gu-lar value [248] [249 <./chapters/kirby-2/pdf/reftri.pdf>] [250 <./chapters/kirby-2/pdf/P3.pdf>] ) (./tex/14.tex [251 <./chapters/kirby-2/p df/struct.pdf>] [252] Chapter 14. [253] [254] [255] [256 <./chapters/wilbers/pdf /pressure_plot.pdf>] [257] [258] Underfull \hbox (badness 10000) in paragraph at lines 350--357 \T1/fvm/m/n/10 /tmp/tmpZ4M_ZO2010-11-9-08-24_instant/instant_module_dff94651124 1aab327593a2d71105c5fc/\T1/pplx/m/n/10 (+20) . [259] [260] [261] [262] [263] [264] [265] [266] [267]) (./tex/15.tex [268] Chapter 15. [269] [270] [271] [272] [273] Underfull \vbox (badness 10000) has occurred while \output is active [274] [275]) (./tex/16.tex [276] [277] [278] Chapter 16. pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ufc_flowdiagram.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed Underfull \vbox (badness 10000) has occurred while \output is active [279] Underfull \vbox (badness 2181) has occurred while \output is active [280 <./cha pters/alnes-2/pdf/ufc_flowdiagram.pdf>] pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ufc_classes.pdf): PDF inc lusion: found PDF version <1.5>, but at most version <1.4> allowed [281 <./chapters/alnes-2/pdf/ufc_cla sses.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active [282] [283] [284] Underfull \vbox (badness 10000) has occurred while \output is active [285] [286] Underfull \vbox (badness 10000) has occurred while \output is active [287] [288] [289] (./chapters/alnes-2/pdf/interval.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/interval.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 51--730 []|[]| (./chapters/alnes-2/pdf/triangle.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/triangle.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 50--753 []|[]| (./chapters/alnes-2/pdf/quadrilateral.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/quadrilateral.pdf): PDF i nclusion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 51--777 []|[]| [290 <./chapters/alnes-2/pdf/interval.pdf> <./chapters/alnes-2/pdf/triangle.pdf >] (./chapters/alnes-2/pdf/tetrahedron.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/tetrahedron.pdf): PDF inc lusion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 51--802 []|[]| (./chapters/alnes-2/pdf/hexahedron.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/hexahedron.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 53--827 []|[]| Underfull \vbox (badness 7740) has occurred while \output is active [291 <./cha pters/alnes-2/pdf/quadrilateral.pdf> <./chapters/alnes-2/pdf/tetrahedron.pdf>] (./chapters/alnes-2/pdf/numbering_example_triangles.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/numbering_example_triangl es.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allo wed ) (./chapters/alnes-2/pdf/numbering_example_quadrilaterals.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/numbering_example_quadril aterals.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [292 <./chapte rs/alnes-2/pdf/hexahedron.pdf>] [293 <./chapters/alnes-2/pdf/numbering_example_ triangles.pdf> <./chapters/alnes-2/pdf/numbering_example_quadrilaterals.pdf>] (./chapters/alnes-2/pdf/ordering_example_triangle.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ordering_example_triangle .pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowe d ) (./chapters/alnes-2/pdf/ordering_example_tetrahedron.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ordering_example_tetrahed ron.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> all owed ) [294 <./chapters/alnes-2/pdf/ordering_example_triangle.pdf> <./chapters/alnes-2 /pdf/ordering_example_tetrahedron.pdf>] (./chapters/alnes-2/pdf/orientation_example_triangles.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/orientation_example_trian gles.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> al lowed ) [295 <./chapters/alnes-2/pdf/orientation_example_triangles.pdf>] [296] [297]) (./tex/17.tex [298] Chapter 17. Underfull \vbox (badness 1092) has occurred while \output is active [299] [300] Underfull \vbox (badness 10000) has occurred while \output is active [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] (/usr/share/texmf-texlive/tex/latex/microtype/mt-euf.cfg) [315] (./chapters/alnes-1/pdf/expr.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/expr.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [316 <./chapters/alnes-1/pdf/expr.pdf>] (./chapters/alnes-1/pdf/stiffness.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/stiffness.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) [317] [318 <./chapters/alnes-1/pdf/st iffness.pdf>] [319] Underfull \vbox (badness 10000) has occurred while \output is active [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] Underfull \vbox (badness 1681) has occurred while \output is active [330] [331] [332] [333]) (./tex/18.tex [334] Chapter 18. Underfull \hbox (badness 1442) in paragraph at lines 89--89 \T1/pplx/m/n/9 (+20) around a cylin-der with par-al-lel [335] [336 <./chapters/hoffman-2/pdf/cube556.pdf> <./chapters/hoffman-2/pdf/com pressible3D.pdf> <./chapters/hoffman-2/pdf/Hoffman_fig3d.pdf>] [337] [338] [339] LaTeX Warning: Float too large for page by 32.91196pt on input line 472. [340] [341] [342 <./chapters/hoffman-2/pdf/speedup_solve.pdf> <./chapters/hoffm an-2/pdf/speedup_unrivara.pdf>] [343] [344] [345] [346] [347] Overfull \hbox (1.6596pt too wide) in paragraph at lines 807--818 [][] [348] [349 <./chapters/hoffman-2/pdf/force_smooth01.pdf> <./chapters/hoffman-2/ pdf/force_hybrid01.pdf> <./chapters/hoffman-2/pdf/force_smooth02.pdf> <./chapte rs/hoffman-2/pdf/force_hybrid02.pdf> <./chapters/hoffman-2/pdf/force_smooth03.p df> <./chapters/hoffman-2/pdf/force_hybrid03.pdf>] [350] [351 <./chapters/hoffman-2/pdf/ swap.pdf> <./chapters/hoffman-2/pdf/swap_config1.pdf>] [352] [353 <./chapters/hoffman-2/png/fsi 3_vel_050.png (PNG copy)> <./chapters/hoffman-2/png/fsi3_theta_050.png (PNG cop y)> <./chapters/hoffman-2/png/fsi3_vel_250.png (PNG copy)> <./chapters/hoffman- 2/png/fsi3_theta_250.png (PNG copy)>] [354 <./chapters/hoffman-1/png/fig2b.png (PNG copy)> <./chapters/hoffman-1/png/fig2c.png (PNG copy)>] LaTeX Warning: Float too large for page by 4.412pt on input line 1281. ) (./tex/19.tex [355] [356] [357] [358] [359] [360] Chapter 19. Overfull \hbox (1.19252pt too wide) in paragraph at lines 5--5 |[]\T1/pplx/m/it/20.74 Lessons learned in mixed lan-guage pro-gram-ming| [361] (./chapters/mardal-2/code/Array.h) (./chapters/mardal-2/code/Array_1.i) (./chapters/mardal-2/code/setup.py [362]) [363] (./chapters/mardal-2/code/segfault_test.py) [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] [376] [377]) (./tex/Part3.tex [378] [379] [380]) (./tex/20.tex Chapter 20. [381] [382] [383 <./chapters/kirby-6/pdf/P3.pdf>] pdfTeX warning: pdflatex (file ./chapters/terrel/pdf/MINI.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed [384 <./chapters/kirby-6/pdf/CR1.pdf> <./cha pters/terrel/pdf/MINI.pdf>] [385] Underfull \vbox (badness 10000) has occurred while \output is active [386] LaTeX Warning: Float too large for page by 3.70213pt on input line 417. [387] [388 <./chapters/terrel/pdf/mesh.pdf> <./chapters/terrel/pdf/vel_test.pdf > <./chapters/terrel/pdf/vel_lid.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active [389] [390] [391] [392 <./chapters/terrel/pdf/vel_ 4.pdf> <./chapters/terrel/pdf/press_4.pdf>] [393 <./chapters/terrel/pdf/div_4.p df> <./chapters/terrel/pdf/run_4.pdf>] ) (./tex/21.tex [394 <./chapters/ter rel/pdf/div_4_test.pdf> <./chapters/terrel/png/lid_div_error.png (PNG copy)>] Chapter 21. [395] [396] [397] [398] Underfull \vbox (badness 10000) has occurred while \output is active [399] Overfull \hbox (25.00003pt too wide) detected at line 474 [] Overfull \hbox (25.00003pt too wide) detected at line 474 [] [400] [401] Underfull \vbox (badness 10000) has occurred while \output is active [402] [403] Underfull \vbox (badness 10000) has occurred while \output is active [404] [405] Underfull \vbox (badness 2126) has occurred while \output is active [406] Underfull \vbox (badness 1515) has occurred while \output is active [407] [408 <./chapters/kvs-1/pdf/new_drivencavity_res.pdf> <./chapters/kvs-1/pdf/new_ channel_res.pdf>] Underfull \vbox (badness 3396) has occurred while \output is active [409] [410 <./chapters/kvs-1/pdf/periodic_v.pdf> <./chapters/kvs-1/pdf/periodic_p.pdf > <./chapters/kvs-1/pdf/new_periodic_res.pdf>] Underfull \vbox (badness 6428) has occurred while \output is active [411 <./cha pters/kvs-1/pdf/cylinderandgeoattime5nr2.pdf> <./chapters/kvs-1/pdf/new_cylinde r_res.pdf>] [412 <./chapters/kvs-1/pdf/new_be ltrami_illustration.pdf>] [413 <./chapters/kvs-1/pdf/new_beltram i_res.pdf>] [414 <./chapters/kvs-1/pdf/aneurysm_at_end_css1.pdf> <./chapters/kv s-1/pdf/new_aneurysm_res.pdf>] [415 <./chapters/kvs-1/pdf/new_scatter.pdf>] ) (./tex/22.tex Underfull \vbox (badness 4108) has occurred while \output is active [416 <./cha pters/kvs-1/pdf/drivencavity-plots.pdf>] [417 <./chapters/kvs-1/pdf/drivencavit y-scatter.pdf>] [418] Chapter 22. [419] Underfull \vbox (badness 1515) has occurred while \output is active [420] Underfull \vbox (badness 1038) has occurred while \output is active [421] Underfull \vbox (badness 2662) has occurred while \output is active [422] [423] [424] Underfull \vbox (badness 2351) has occurred while \output is active [425] [426] [427] [428] [429] [430] [431 <./chapters/mortensen/pd f/Burgers_KE_IM1.pdf> <./chapters/mortensen/pdf/Burgers_KE_IM2.pdf>] [432] Underfull \hbox (badness 1331) in paragraph at lines 1115--1115 []\T1/pplx/m/n/9 (+20) Figure 22.3: |Ac-cu-mu-lated er-ror Underfull \hbox (badness 1331) in paragraph at lines 1132--1132 []\T1/pplx/m/n/9 (+20) Figure 22.4: |Ac-cu-mu-lated er-ror [433 <./chapters/mortensen/pdf/OS_init.pdf> <./chapters/mortensen/pdf/OrrS_eigv als.pdf>] [434 <./chapters/mortensen/pdf/OS_init_cfl_1.pdf> <./chapters/mortens en/pdf/OS_init_cfl_0.pdf> <./chapters/mortensen/pdf/OS_init_dx_1.pdf> <./chapte rs/mortensen/pdf/OS_init_dx_0.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active [435] [436 <./chapters/mortensen/pdf/OS_energy_cfl_0_1_model_1.pdf> <./chapters/morte nsen/pdf/OS_energy_cfl_0_1_model_0.pdf> <./chapters/mortensen/pdf/OS_energy_cfl _0_05_model_1.pdf> <./chapters/mortensen/pdf/OS_energy_cfl_0_05_model_0.pdf>] [437 <./chapters/mortensen/pdf/TG_disserror_model_0_cfl_0_05_Re_100_dofs.pdf> < ./chapters/mortensen/pdf/TG_energyerror_model_0_cfl_0_05_Re_100_dofs.pdf>]) (./tex/23.tex [438] Chapter 23. [439] [440 <./chapters/kvs-2/png/cow_gray_1 .png (PNG copy)> <./chapters/kvs-2/pdf/kentus.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active [441] [442 <./cha pters/kvs-2/pdf/systolic.pdf>] [443 <./chapters/kvs-2/png/zero_dp_vs_res.png>] [444 <./chapters/kvs-2/pdf/stacks.pdf> <./chapters/kvs-2/pdf/3d.pdf> <./chapter s/kvs-2/pdf/viper3.pdf>] [445 <./chapters/kvs-2/pdf/bifurcation_cl ean.pdf>] [446 <./chapters/kvs-2/pdf/mcas_wss_II4.pdf> <./chapters/kvs-2/pdf/ic as_wss.pdf>] [447 <./chapters/kvs-2/pdf/mass_do g.pdf>] [448 <./chapters/kvs-2/pdf/dog_data_mr_cfd.pdf>] [449] [450 <./chapters/kvs-2/pdf/ica.pdf> <./ chapters/kvs-2/pdf/cok_inflow.pdf>] ) (./tex/24.tex [451] [452 <./chapters/kvs-2/pdf/cok_top_steam_white.pdf>] [453 <./chapters/kvs -2/pdf/cok_slice.pdf> <./chapters/kvs-2/pdf/cok_ica_vel_peak_syst.pdf>] [454] Chapter 24. [455] Underfull \vbox (badness 4391) has occurred while \output is active [456 <./cha pters/hentschel/pdf/ChiariImage2.pdf>] [457] [458] [459 <./chapters/hentschel/pdf/sin_p ulse.pdf>] [460] [461] [462] [463] [464 <./chapters/hentschel/pdf/gmsh.pdf>] [465 <./chapters/hen tschel/pdf/pulse_f1_08_sysmax_nmb7.pdf> <./chapters/hentschel/pdf/pulse_f1_08_s ysdia_nmb18.pdf> <./chapters/hentschel/pdf/pulse_f1_08_diamin1_nmb25.pdf>] [466] [467 <./chapters/hentschel/pdf/sin_sysmax_nmb2.pdf> <./chapters/hentschel/pdf/s in_sysdia_nmb4.pdf> <./chapters/hentschel/pdf/sin_diamin_nmb6.pdf>] [468 <./cha pters/hentschel/pdf/pulse_f1_08_elliptic_sysmax_nmb7.pdf> <./chapters/hentschel /pdf/pulse_f1_08_elliptic_sysdia_nmb18.pdf> <./chapters/hentschel/pdf/pulse_f1_ 08_elliptic_diamin1_nmb25.pdf> <./chapters/hentschel/pdf/pulse_f1_08_elliptic_e ccentric_sysmax_nmb7.pdf> <./chapters/hentschel/pdf/pulse_f1_08_elliptic_eccent ric_sysdia_nmb18.pdf> <./chapters/hentschel/pdf/pulse_f1_08_elliptic_eccentric_ diamin1_nmb25.pdf>]) (./tex/25.tex [469 <./chapters/hentschel/pdf/pulse_syrinx_ f1_08_syrinx05_sysmax_nmb7.pdf> <./chapters/hentschel/pdf/pulse_syrinx_f1_08_sy rinx05_sysdia_nmb18.pdf> <./chapters/hentschel/pdf/pulse_syrinx_f1_08_syrinx05_ diamin1_nmb25.pdf>] [470] Chapter 25. [471] [472 <./chapters/lopes/pdf/nazare1.p df>] [473] (./chapters/lopes/pdf/graph.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/graph.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [474pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.1}) has been already used, duplicate i gnored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.290 \end{figure} ]pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.2}) has been already used, duplicate ignored \relax l.295 \begin{equation} pdfTeX warning (ext4): destination with the same identifi er (name{equation.25.3.3}) has been already used, duplicate ignored \relax l.307 \begin{equation} [475 <./chapters/lopes/pdf/graph.pdf>]pdfTeX warning (ex t4): destination with the same identifier (name{equation.25.3.1}) has been alre ady used, duplicate ignored \relax l.461 \end{align} pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.2}) has been already used, duplicate ignored \relax l.461 \end{align} Underfull \vbox (badness 2744) has occurred while \output is active [476]pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.1}) h as been already used, duplicate ignored \relax l.512 \end{align} pdfTeX warning (ext4): destination with the same identifier (n ame{equation.25.3.2}) has been already used, duplicate ignored \relax l.512 \end{align} pdfTeX warning (ext4): destination with the same identifier (n ame{equation.25.3.1}) has been already used, duplicate ignored \relax l.545 \end{align} pdfTeX warning (ext4): destination with the same identifier (n ame{equation.25.3.2}) has been already used, duplicate ignored \relax l.545 \end{align} [477]pdfTeX warning (ext4): destination with the same identif ier (name{equation.25.3.1}) has been already used, duplicate ignored \relax l.571 \end{align} pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.2}) has been already used, duplicate ignored \relax l.571 \end{align} [478] Underfull \hbox (badness 5681) in paragraph at lines 667--667 []\T1/pplx/m/n/9 (+20) Figure 25.3: |Pos-i-tive part of [479 <./chapters/lopes/pdf/phase_velocity_simple.pdf>] Overfull \hbox (0.95473pt too wide) in paragraph at lines 771--777 \T1/pplx/m/n/10 (-20) Corr and RungeKutta classes (see \T1/fvm/m/n/10 dolfwave/ src/predictorcorrector \T1/pplx/m/n/10 (-20) and \T1/fvm/m/n/10 dolfwave/src/ru ngekutta\T1/pplx/m/n/10 (-20) ). [480pdfTeX warning (ext4): destination with the same identifier (name{equation. 25.5.1}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.820 pdfTeX warning (ext4): destination with the same identifier (name{equatio n.25.5.2}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.820 ] Underfull \vbox (badness 10000) has occurred while \output is active [481] [482] [483] Underfull \vbox (badness 10000) has occurred while \output is active [484] (./chapters/lopes/pdf/spike_shelf.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/spike_shelf.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) [485] Underfull \hbox (badness 1377) in paragraph at lines 1290--1290 \T1/pplx/m/n/9 (+20) pan-els) and ZTC (lower pan-els) Underfull \hbox (badness 1377) in paragraph at lines 1305--1305 \T1/pplx/m/n/9 (+20) pan-els) and ZTC (lower pan-els) Underfull \hbox (badness 1377) in paragraph at lines 1319--1319 \T1/pplx/m/n/9 (+20) pan-els) and ZTC (lower pan-els) [486 <./chapters/lopes/pdf/spike_shelf.pdf> <./chapters/lopes/png/L2_spike_stab ility.png> <./chapters/lopes/png/L2_shelf_stability.png> <./chapters/lopes/png/ L1_spike_stability.png> <./chapters/lopes/png/L1_shelf_stability.png>] [487 <./ chapters/lopes/png/L0_5_spike_stability.png> <./chapters/lopes/png/L0_5_shelf_s tability.png> <./chapters/lopes/png/L2_dx_0_02_hm_spike_spectrum_StdPot.png> <. /chapters/lopes/png/L2_dx_0_02_hm_shelf_spectrum_StdPot.png> <./chapters/lopes/ png/L2_dx_0_02_hm_spike_spectrum_Zhao.png> <./chapters/lopes/png/L2_dx_0_02_hm_ shelf_spectrum_Zhao.png> <./chapters/lopes/png/L1_dx_0_1_hm_spike_spectrum_StdP ot.png> <./chapters/lopes/png/L1_dx_0_1_hm_shelf_spectrum_StdPot.png> <./chapte rs/lopes/png/L1_dx_0_1_hm_spike_spectrum_Zhao.png> <./chapters/lopes/png/L1_dx_ 0_1_hm_shelf_spectrum_Zhao.png>] [488 <./chapters/lopes/png/L0_5_dx_0_25_hm_spi ke_spectrum_StdPot.png> <./chapters/lopes/png/L0_5_dx_0_25_hm_shelf_spectrum_St dPot.png> <./chapters/lopes/png/L0_5_dx_0_25_hm_spike_spectrum_Zhao.png> <./cha pters/lopes/png/L0_5_dx_0_25_hm_shelf_spectrum_Zhao.png>] [489] [490] LaTeX Warning: `!h' float specifier changed to `!ht'. LaTeX Warning: `!h' float specifier changed to `!ht'. [491 <./chapters/lopes/pdf/submergedbar.pdf>] [492 <./chapters/lopes/pdf/ZhaoNw ogu.pdf> <./chapters/lopes/pdf/deptheps.pdf>] [493 <./chapters/lopes/pdf/epsilo n0_1.pdf> <./chapters/lopes/pdf/epsilon0_25.pdf>] [494 <./chapters/lopes/pdf/epsilon0_5. pdf>] [495 <./chapters/lopes/pdf/eta000000.pdf> <./chapters/lopes/pdf/eta002000 .pdf> <./chapters/lopes/pdf/eta004000.pdf> <./chapters/lopes/pdf/eta006000.pdf> <./chapters/lopes/pdf/eta007972.pdf> <./chapters/lopes/pdf/eta009946.pdf>] [496 <./chapters/lopes/pdf/unstr.pdf> <./chapters/lopes/pdf/unstrcorner.pdf>] Underfull \vbox (badness 4048) has occurred while \output is active [497 <./cha pters/lopes/pdf/detail_unstr.pdf>] (./chapters/lopes/pdf/scale_tex.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/scale_tex.pdf): PDF inclusi on: found PDF version <1.5>, but at most version <1.4> allowed ) (./chapters/lopes/pdf/sponge_tex.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/sponge_tex.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed ) [498 <./chapters/lopes/pdf/scale_tex.pd f> <./chapters/lopes/pdf/depth.pdf>] [499 <./chapters/lopes/pdf/sponge_tex.pdf> <./chapters/lopes/pdf/eta.pdf> <./chapters/lopes/pdf/pvel2.pdf>] [500 <./chapt ers/lopes/pdf/etaprofile.pdf> <./chapters/lopes/pdf/velprofile.pdf>] pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/depth0.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/depth6.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed [501 <./chapters/lopes/pdf/depth0.pdf> <./c hapters/lopes/pdf/depth6.pdf>] pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/eta3.pdf): PDF inclusion: f ound PDF version <1.5>, but at most version <1.4> allowed [502 <./chapters/lopes/pdf/eta1.pdf> <./chap ters/lopes/pdf/eta3.pdf> <./chapters/lopes/pdf/eta45.pdf>] pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/eta6.pdf): PDF inclusion: f ound PDF version <1.5>, but at most version <1.4> allowed [503 <./chapters/lopes/pdf/eta6.pdf>]) (./tex/26.tex [504] Chapter 26. [505] Underfull \vbox (badness 10000) has occurred while \output is active [506] Underfull \vbox (badness 1917) has occurred while \output is active [507] [508] Underfull \vbox (badness 10000) has occurred while \output is active [509] Underfull \vbox (badness 10000) has occurred while \output is active [510] [511] Underfull \vbox (badness 10000) has occurred while \output is active [512] [513] [514] [515] [516] [517] Underfull \vbox (badness 3291) has occurred while \output is active [518] Underfull \vbox (badness 2181) has occurred while \output is active [519] [520] [521] Underfull \hbox (badness 1178) in paragraph at lines 1410--1410 []\T1/pplx/m/n/9 (+20) Figure 26.6: |Com-plete DOLFIN Underfull \hbox (badness 1102) in paragraph at lines 1410--1410 \T1/pplx/m/n/9 (+20) solver for the com-press-ible neo- LaTeX Warning: Float too large for page by 23.41197pt on input line 1532. [522] [523] [524] [525]) (./tex/27.tex [526] Chapter 27. [527] [528] Underfull \hbox (badness 4316) in paragraph at lines 296--296 []\T1/pplx/m/n/9 (+20) Figure 27.2: |Sam-ples of how Overfull \hbox (1.10251pt too wide) in paragraph at lines 300--306 []\T1/pplx/m/n/10 (-20) In CBC.Twist, each of the forms listed in Ta-ble [][]27 .1[][] have been im-ple-mented in the file \T1/fvm/m/n/10 kinematics.py [529 <./chapters/narayanan/images/pdf/continuumpotato.pdf>] [530] [531] Underfull \hbox (badness 1019) in paragraph at lines 449--449 \T1/pplx/m/n/9 (+20) en-ergy func-tion for a two term [532] Underfull \hbox (badness 10000) in paragraph at lines 597--597 []\T1/pplx/m/n/9 (+20) Figure 27.6: |The rel-e- Underfull \hbox (badness 10000) in paragraph at lines 597--597 \T1/pplx/m/n/9 (+20) vant sec-tion of the class Underfull \hbox (badness 10000) in paragraph at lines 597--597 \T1/fvm/m/n/9 StaticMomentumBalanceSolver\T1/pplx/m/n/9 (+20) , [533] [534] [535] [536] [537 <./chapters/nara yanan/images/png/twistedcube.png (PNG copy)>] [538] [539] [540] [541 <./chapters/n arayanan/images/png/release_000.png (PNG copy)> <./chapters/narayanan/images/pn g/release_100.png (PNG copy)> <./chapters/narayanan/images/png/release_200.png (PNG copy)> <./chapters/narayanan/images/png/release_300.png (PNG copy)> <./cha pters/narayanan/images/png/release_400.png (PNG copy)> <./chapters/narayanan/im ages/png/release_500.png (PNG copy)>] [542 <./chapters/narayanan/images/pdf/ene rgies.pdf>] ) (./tex/28.tex [543] [544 <./chapters/narayanan/images/png/dolphin_000.png (PNG copy)> <./chapters/n arayanan/images/png/dolphin_001.png (PNG copy)> <./chapters/narayanan/images/pn g/dolphin_002.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_003.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_004.png (PNG copy)> <./cha pters/narayanan/images/png/dolphin_005.png (PNG copy)> <./chapters/narayanan/im ages/png/dolphin_006.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_0 07.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_008.png (PNG copy)> ] Chapter 28. [545] [546] Underfull \vbox (badness 4899) has occurred while \output is active [547] [548 <./chapters/hoffman-1/png/fig1a.png (PNG copy)> <./chapters/hoffman-1/png/fig1b.png (PNG copy)>] [549 <./chapters/ hoffman-1/png/fig3a.png (PNG copy)> <./chapters/hoffman-1/png/fig3b.png (PNG co py)>] Underfull \vbox (badness 1024) has occurred while \output is active [550 <./cha pters/hoffman-1/png/Hoffman_fig2a.png (PNG copy)> <./chapters/hoffman-1/png/Hof fman_fig2b.png (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig2c.png (PNG cop y)> <./chapters/hoffman-1/png/Hoffman_fig2d.png (PNG copy)> <./chapters/hoffman -1/png/Hoffman_fig3a.png (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig3b.pn g (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig3c.png (PNG copy)> <./chapte rs/hoffman-1/png/Hoffman_fig3d.png (PNG copy)>] Underfull \vbox (badness 7047) has occurred while \output is active [551 <./cha pters/hoffman-1/png/Hoffman_fig5a.png (PNG copy)> <./chapters/hoffman-1/png/Hof fman_fig5b.png (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig5c.png (PNG cop y)> <./chapters/hoffman-1/png/Hoffman_fig5d.png (PNG copy)> <./chapters/hoffman -1/png/rlg_vorticity.png (PNG copy)> <./chapters/hoffman-1/png/oilfilm_back_sim .png (PNG copy)>] Underfull \hbox (badness 1584) in paragraph at lines 431--431 \T1/pplx/m/n/9 (+20) benchmark prob-lem FLUSTRUK- Underfull \hbox (badness 1783) in paragraph at lines 431--431 \T1/pplx/m/n/9 (+20) uni-formly re-fined meshes us-ing [552 <./chapters/hoffman-1/png/fsi_bench3D_displacement_aligned.pdf>] [553 <./chapters/hoffman-1/png/cube000 .png (PNG copy)> <./chapters/hoffman-1/png/cube115.png (PNG copy)> <./chapters/ hoffman-1/png/cube125.png (PNG copy)> <./chapters/hoffman-1/png/cube168.png (PN G copy)> <./chapters/hoffman-1/png/cube187.png (PNG copy)> <./chapters/hoffman- 1/png/cube405.png (PNG copy)> <./chapters/hoffman-1/png/cube550.png (PNG copy)> <./chapters/hoffman-1/png/cube649.png (PNG copy)>]) (./tex/29.tex [554] Chapter 29. [555] [556] pdfTeX warning: pdflatex (file ./chapters/selim/pdf/mapping.pdf): PDF inclusion : found PDF version <1.5>, but at most version <1.4> allowed [557 <./chapters/selim/pdf/mapping.pdf>] Underfull \vbox (badness 2512) has occurred while \output is active [558] [559 <./chapters/selim/pdf/primal.pdf>] [560] [561] Underfull \vbox (badness 10000) has occurred while \output is active [562] Underfull \vbox (badness 10000) has occurred while \output is active [563] Underfull \vbox (badness 10000) has occurred while \output is active [564] [565] Underfull \hbox (badness 3579) in paragraph at lines 929--929 []\T1/pplx/m/n/9 (+20) Figure 29.7: |A schematic pic- Underfull \hbox (badness 3354) in paragraph at lines 929--929 \T1/pplx/m/n/9 (+20) ture of the adap-tive FSI al-go- [566 <./chapters/selim/pdf/adaptive.pdf> ] [567] [568]) (./tex/30.tex [569 <./chapters/selim/p ng/new_channel.png (PNG copy)> <./chapters/selim/png/channel_test_zoom.png (PNG copy)>] [570 <./chapters/selim/png/channelZF.png (PNG copy)> <./chapters/selim /png/channelZS.png (PNG copy)> <./chapters/selim/png/channelZM.png (PNG copy)>] [571 <./chapters/selim/png/new_cavity.png> <./chapters/selim/png/zoom_cavity.pn g (PNG copy)> <./chapters/selim/pdf/plot.pdf>] [572] Chapter 30. [573] (./chapters/nikbakht/pdf/domain.pdf_tex ) [574 <./chapters/nikbakht/pdf/domain.pd f>] [575] [576] [577] [578] [579] [580] [581] [582 <./chapters/nikba kht/png/mesh.png> <./chapters/nikbakht/png/result.png>] [583]) (./tex/31.tex [584] [585] [586] Chapter 31. [587] [588 <./chapters/vynnytska/png/la yout.png>] Underfull \vbox (badness 10000) has occurred while \output is active [589] [590] [591] Underfull \vbox (badness 10000) has occurred while \output is active [592] Underfull \vbox (badness 6157) has occurred while \output is active [593] [594] Underfull \hbox (badness 2027) in paragraph at lines 766--766 \T1/pplx/m/n/8.5 main predictor--corrector al-go-rithm, Underfull \hbox (badness 1253) in paragraph at lines 766--766 \T1/pplx/m/n/8.5 ini-tial-iza-tion is not in-cluded here). LaTeX Warning: Float too large for page by 15.77048pt on input line 768. [595] [596] [597] [598] Underfull \hbox (badness 1038) in paragraph at lines 975--975 []\T1/pplx/m/n/9 (+20) Figure 31.7: |Di-men-sion-less root Overfull \hbox (1.66838pt too wide) in paragraph at lines 981--1019 [][] Overfull \hbox (1.66838pt too wide) in paragraph at lines 1025--1053 [][] [599] [600 <./chapters/vynnytska/png/u_rms.png>] [601 <./chapters/vynnytska/png /tmB.png (PNG copy)> <./chapters/vynnytska/png/visB.png (PNG copy)> <./chapters /vynnytska/png/tmC.png (PNG copy)> <./chapters/vynnytska/png/visC.png (PNG copy )> <./chapters/vynnytska/png/tmD.png (PNG copy)> <./chapters/vynnytska/png/visD .png (PNG copy)> <./chapters/vynnytska/png/tmE.png (PNG copy)> <./chapters/vynn ytska/png/visE.png (PNG copy)> <./chapters/vynnytska/png/tmF.png (PNG copy)> <. /chapters/vynnytska/png/visF.png (PNG copy)> <./chapters/vynnytska/png/tmG.png (PNG copy)> <./chapters/vynnytska/png/visG.png (PNG copy)> <./chapters/vynnytsk a/png/tmleg.png (PNG copy)> <./chapters/vynnytska/png/visleg.png (PNG copy)>] [602 <./chapters/vynnytska/png/tmH.png (PNG copy)> <./chapters/vynnytska/png/vi sH.png (PNG copy)> <./chapters/vynnytska/png/tmI.png (PNG copy)> <./chapters/vy nnytska/png/visI.png (PNG copy)> <./chapters/vynnytska/png/tmJ.png (PNG copy)> <./chapters/vynnytska/png/visJ.png (PNG copy)> <./chapters/vynnytska/png/tmK.pn g (PNG copy)> <./chapters/vynnytska/png/visK.png (PNG copy)> <./chapters/vynnyt ska/png/tmL.png (PNG copy)> <./chapters/vynnytska/png/visL.png (PNG copy)> <./c hapters/vynnytska/png/tmM.png (PNG copy)> <./chapters/vynnytska/png/visM.png (P NG copy)>]) (./tex/32.tex Chapter 32. [603] [604] Underfull \vbox (badness 1496) has occurred while \output is active [605] Underfull \vbox (badness 10000) has occurred while \output is active [606] [607] [608] [609 <./chapters/schroll/pdf/h0_typica l.pdf> <./chapters/schroll/pdf/h_typical.pdf>] [610 <./chapters/schroll/pdf/a1a 2scan4.pdf> <./chapters/schroll/pdf/a1a2scan4-5.pdf> <./chapters/schroll/pdf/b1 b2scan4.pdf> <./chapters/schroll/pdf/b1b2scan4-5.pdf> <./chapters/schroll/pdf/4 Dscan3.pdf> <./chapters/schroll/pdf/4Dscan3-5.pdf>] [611 <./chapters/schroll/pdf/4Dscan 3b.pdf> <./chapters/schroll/pdf/4Dscan3b-5.pdf> <./chapters/schroll/pdf/4Dsampl e3-5.pdf> <./chapters/schroll/pdf/4Dsample3b-5.pdf> <./chapters/schroll/pdf/4D- 1scan4b.pdf> <./chapters/schroll/pdf/4D-1scan4b-5.pdf>]) (./tex/33.tex [612] Chapter 33. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 23. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 23. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 23. [613] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [614 <./chapters/hake/pdf/morphology.pdf>] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [615] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [616 <./chapters/hake/pdf/markov_models.pdf>] Underfull \vbox (badness 1231) has occurred while \output is active Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [617] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [618] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [619] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [620] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [621 <./chapters/hake/pdf/error_plot.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [622 <./chapters/hake/pdf/traces_mesh_1.pdf>] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [623 <./chapters/hake/pdf/traces_mesh_2.pdf>] Underfull \hbox (badness 3965) in paragraph at lines 844--844 []\T1/pplx/m/n/9 (+20) Figure 33.7: |Di-a-gram for the Underfull \hbox (badness 6316) in paragraph at lines 844--844 \T1/pplx/m/n/9 (+20) time step-ping al-go-rithm us-ing Underfull \hbox (badness 3769) in paragraph at lines 844--844 \T1/pplx/m/n/9 (+20) 3 dis-crete ob-jects: \T1/fvm/m/n/9 DtExpander\T1/pplx/m/n /9 (+20) , Underfull \vbox (badness 10000) has occurred while \output is active Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [624 <./chapters/hake/pdf/traces_mesh_3.pdf> <./chapters/hake/pdf/timeline.pdf> ] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [625] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [626]) (./tex/34.tex Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [627] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [628] Chapter 34. Underfull \vbox (badness 10000) has occurred while \output is active [629] [630] (./chapters/lezar/svg/arbitrary_waveguide_cross_section.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/arbitrary_waveguide_cross_s ection.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [631 <./chapter s/lezar/svg/arbitrary_waveguide_cross_section.pdf>] [632] [633] (./chapters/lezar/svg/rectangular_fenics_mesh.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/rectangular_fenics_mesh.pdf ): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [634 <./chapters/le zar/svg/rectangular_fenics_mesh.pdf>] [635] [636] (./chapters/lezar/svg/hollow_rectangular_waveguide.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_rectangular_waveguid e.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allow ed ) Underfull \vbox (badness 4024) has occurred while \output is active [637 <./cha pters/lezar/svg/hollow_rectangular_waveguide.pdf>] (./chapters/lezar/svg/hollow_cutoff_TE.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_cutoff_TE.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) (./chapters/lezar/svg/hollow_cutoff_TM.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_cutoff_TM.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) (./chapters/lezar/svg/hollow_rectangular_waveguide_dispersion_curve.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_rectangular_waveguid e_dispersion_curve.pdf): PDF inclusion: found PDF version <1.5>, but at most ve rsion <1.4> allowed ) [638 <./chapters/lezar/svg/hollow_cutoff_TE.pdf> <./chapters/lezar/svg/hollow_c utoff_TM.pdf>] (./chapters/lezar/svg/half_filled_rectangular_waveguide.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_rectangular_wav eguide.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) (./chapters/lezar/svg/half_filled_cutoff_TE.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_cutoff_TE.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [639 <./chapters/lezar /svg/hollow_rectangular_waveguide_dispersion_curve.pdf> <./chapters/lezar/svg/h alf_filled_rectangular_waveguide.pdf>] (./chapters/lezar/svg/half_filled_cutoff_TM.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_cutoff_TM.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \hbox (badness 2698) in paragraph at lines 848--848 []\T1/pplx/m/n/9 (+20) Figure 34.9: |The fourth cal-cu- [640 <./chapters/lezar/svg/half_filled_cutoff_TE.pdf> <./chapters/lezar/svg/hal f_filled_cutoff_TM.pdf>] (./chapters/lezar/svg/half_filled_rectangular_waveguide_dispersion_curve.pdf_te x pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_rectangular_wav eguide_dispersion_curve.pdf): PDF inclusion: found PDF version <1.5>, but at mo st version <1.4> allowed ) (./chapters/lezar/svg/shielded_microstrip_waveguide.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/shielded_microstrip_wavegui de.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allo wed ) [641 <./chapters/lezar/svg/half_filled_rectangular_waveguide_dispersion_curve.p df> <./chapters/lezar/svg/shielded_microstrip_waveguide.pdf>] (./chapters/lezar/svg/boxed_microstrip_dispersion_curves.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/boxed_microstrip_dispersion _curves.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed )) (./tex/35.tex [642 <./chapters/lezar/svg/boxed_microstrip_dispersion_curves.pdf>] Chapter 35. Underfull \vbox (badness 3281) has occurred while \output is active [643] (./chapters/mardal-4/pdf/block.pdf_tex pdfTeX warning: pdflatex (file ./chapters/mardal-4/pdf/block.pdf): PDF inclusio n: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \vbox (badness 2443) has occurred while \output is active [644 <./cha pters/mardal-4/pdf/block.pdf>] [645] [646] [647] [648] [649] Underfull \vbox (badness 2512) has occurred while \output is active [650] [651] [652] [653]) (./tex/36.tex [654] Chapter 36. [655] [656] [657 <./chapters/rognes/pdf/CG.pdf> <./c hapters/rognes/pdf/RT.pdf>] [658] Underfull \vbox (badness 6188) has occurred while \output is active [659] [660] [661] [662] [663] [664] [665] [666] [667] [668]) [669] [670] (./tex/BM1.tex Underfull \vbox (badness 10000) has occurred while \output is active [671] Underfull \vbox (badness 10000) has occurred while \output is active [672] Underfull \vbox (badness 10000) has occurred while \output is active [673] Underfull \vbox (badness 10000) has occurred while \output is active [674] Underfull \vbox (badness 10000) has occurred while \output is active [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] (./book.ind [713] [714] [715] [716] [717] Overfull \hbox (7.21391pt too wide) in paragraph at lines 435--437 []\T1/pplx/m/n/10 (-20) LBB con-di-tions, \T1/pplx/m/it/10 see \T1/pplx/m/n/10 (-20) Ladyzhenskaya--BabuČka--Brezzi [718] [719] [720])) Package caption Warning: Unused \captionsetup[subalgorithm] on input line 14. (./book.aux) LaTeX Font Warning: Size substitutions with differences (Font) up to 0.43996pt have occurred. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Hfootnote.38} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.37} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.36} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.35} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.34} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.33} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.32} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.31} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.30} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.29} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.28} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.27} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.26} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.25} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.24} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.23} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.22} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.21} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.20} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.19} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.18} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.17} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.16} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.15} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.14} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.13} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.12} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.11} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.10} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.9} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.8} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.7} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.6} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.5} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.4} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.3} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.2} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.1} has been referenced but does not exist , replaced by a fixed one {/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc} Output written on book.pdf (732 pages, 66380029 bytes). Transcript written on book.log. This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. entering extended mode (./book.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded. (./fenicsbook.cls Document Class: fenicsbook (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/geometry.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/etc/texmf/tex/xelatex/xetexconfig/geometry.cfg)) (/usr/share/texmf-texlive/tex/latex/oberdiek/bookmark.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdfescape.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty) (/etc/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty)) (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) (/usr/share/texmf-texlive/tex/latex/oberdiek/auxhook.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/bkm-pdftex.def)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/emptypage.sty) (/usr/share/texmf-texlive/tex/latex/psnfss/mathpazo.sty) (/usr/share/texmf-texlive/tex/latex/psnfss/helvet.sty) (/usr/share/texmf-texlive/tex/latex/bera/beramono.sty) (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def)) (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def)) (/usr/share/texmf-texlive/tex/latex/textcase/textcase.sty) (/usr/share/texmf-texlive/tex/latex/titlesec/titlesec.sty) (/usr/share/texmf-texlive/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texmf-texlive/tex/latex/tools/multicol.sty) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/natbib/natbib.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty (/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf-texlive/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf-texlive/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texmf-texlive/tex/latex/amsmath/amscd.sty) (/usr/share/texmf-texlive/tex/latex/stmaryrd/stmaryrd.sty) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/codehighlight.sty (/usr/src/RPM/BUILD/fenics-book-20130430/packages/mylistings.sty (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) (/usr/share/texmf-texlive/tex/latex/listings/listings.cfg)) (/usr/share/texmf/tex/latex/xcolor/xcolor.sty (/etc/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))) (/usr/share/texmf-texlive/tex/latex/ltxmisc/import.sty) (/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty (/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty (/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) (/etc/texmf/tex/latex/config/graphics.cfg))) (/usr/share/texmf-texlive/tex/latex/subfig/subfig.sty (/usr/share/texmf-texlive/tex/latex/caption/caption3.sty)) (/usr/share/texmf-texlive/tex/latex/booktabs/booktabs.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty) (/usr/share/texmf-texlive/tex/latex/tools/array.sty) (/usr/share/texmf-texlive/tex/latex/microtype/microtype.sty (/usr/share/texmf-texlive/tex/latex/microtype/microtype.cfg)) (/usr/share/texmf-texlive/tex/latex/tools/xspace.sty) (/usr/share/texmf-texlive/tex/latex/setspace/setspace.sty Package: `setspace' 6.7 <2000/12/01> ) (/usr/share/texmf-texlive/tex/latex/floatrow/floatrow.sty) (/usr/share/texmf-texlive/tex/latex/caption/caption.sty (/usr/share/texmf-texlive/tex/latex/caption/ltcaption.sty)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithm.sty Document Style `algorithm' - floating environment (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algorithmicx.sty Document Style algorithmicx 1.2 - a greatly improved `algorithmic' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/algpseudocode.sty Document Style - pseudocode environments for use with the `algorithmicx' style ) (/usr/src/RPM/BUILD/fenics-book-20130430/packages/todonotes.sty (/usr/share/texmf-texlive/tex/latex/xkeyval/xkeyval.sty (/usr/share/texmf-texlive/tex/generic/xkeyval/xkeyval.tex)) (/usr/share/texmf/tex/latex/pgf/frontendlayer/tikz.sty (/usr/share/texmf/tex/latex/pgf/basiclayer/pgf.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfrcs.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-common-lists.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgfutil-latex.def (/usr/share/texmf-texlive/tex/latex/ms/everyshi.sty)) (/usr/share/texmf/tex/generic/pgf/utilities/pgfrcs.code.tex)) (/usr/share/texmf/tex/latex/pgf/basiclayer/pgfcore.sty (/usr/share/texmf/tex/latex/pgf/systemlayer/pgfsys.sty (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys.code.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeysfiltered.code.tex)) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgf.cfg) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-pdftex.def (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsys-common-pdf.def))) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsyssoftpath.code.tex) (/usr/share/texmf/tex/generic/pgf/systemlayer/pgfsysprotocol.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcore.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathcalc.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathutil.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathparser.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.basic.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.trigonometric.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.random.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.comparison.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.base.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.round.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.misc.code.tex) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfunctions.integerarithmetics.code .tex))) (/usr/share/texmf/tex/generic/pgf/math/pgfmathfloat.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepoints.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathconstruct.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathusage.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorescopes.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoregraphicstate.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransformations.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorequick.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreobjects.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepathprocessing.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorearrows.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreshade.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreimage.code.tex (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoreexternal.code.tex)) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorelayers.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcoretransparency.code.tex) (/usr/share/texmf/tex/generic/pgf/basiclayer/pgfcorepatterns.code.tex))) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleshapes.code.tex) (/usr/share/texmf/tex/generic/pgf/modules/pgfmoduleplot.code.tex) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-0-65.sty) (/usr/share/texmf/tex/latex/pgf/compatibility/pgfcomp-version-1-18.sty)) (/usr/share/texmf/tex/latex/pgf/utilities/pgffor.sty (/usr/share/texmf/tex/latex/pgf/utilities/pgfkeys.sty (/usr/share/texmf/tex/generic/pgf/utilities/pgfkeys.code.tex)) (/usr/share/texmf/tex/latex/pgf/math/pgfmath.sty (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex)) (/usr/share/texmf/tex/generic/pgf/utilities/pgffor.code.tex (/usr/share/texmf/tex/generic/pgf/math/pgfmath.code.tex))) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/tikz.code.tex (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryplothandlers.code.tex) (/usr/share/texmf/tex/generic/pgf/modules/pgfmodulematrix.code.tex) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibrarytopat hs.code.tex))) (/usr/share/texmf-texlive/tex/latex/tools/calc.sty) (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryshado ws.code.tex (/usr/share/texmf/tex/generic/pgf/frontendlayer/tikz/libraries/tikzlibraryfadin gs.code.tex (/usr/share/texmf/tex/generic/pgf/libraries/pgflibraryfadings.code.tex))))) Writing index file book.idx (./book.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/t1pplx.fd) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (/usr/share/texmf-texlive/tex/latex/microtype/mt-ppl.cfg) (/usr/share/texmf-texlive/tex/latex/floatrow/fr-subfig.sty) (/usr/share/texmf-texlive/tex/latex/floatrow/fr-longtable.sty) ABD: EveryShipout initializing macros (./tex/FM1.tex (/usr/share/texmf-texlive/tex/latex/psnfss/ot1pplx.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omlzplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omszplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/omxzplm.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/ot1zplm.fd) (/usr/share/texmf-texlive/tex/latex/microtype/mt-msa.cfg) (/usr/share/texmf-texlive/tex/latex/microtype/mt-msb.cfg) (/usr/share/texmf-texlive/tex/latex/stmaryrd/Ustmry.fd) (/usr/share/texmf-texlive/tex/latex/bera/t1fvm.fd) [1{/var/cache/texmf/fonts/ma p/pdftex/updmap/pdftex.map}] Underfull \hbox (badness 10000) in paragraph at lines 59--67 Overfull \hbox (2.20999pt too wide) in paragraph at lines 46--68 $[]$ $[]$ (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pplx.fd) [2] (./book.toc [3] [4] [5] [6] [7] [8]) [9] [10]) [11] [12] (./tex/1.tex Chapter 1. [1] [2] [3] [4] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) [5] [6] [7] [8] [9 <./chapters/langtangen/pdf/ex1_u. pdf>] [10 <./chapters/langtangen/png/ex1_mesh.png (PNG copy)>] [11] [12] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) [13] [14] [15] [16] Underfull \vbox (badness 1033) has occurred while \output is active [17] [18] Underfull \vbox (badness 10000) has occurred while \output is active [19 <./cha pters/langtangen/pdf/membrane_waxis.pdf>] [20 <./chapters/langtangen/pdf/ex1_ gradu.pdf>] [21] [22] [23] [24] [25] [26] [27] Underfull \vbox (badness 3536) has occurred while \output is active [28] [29] Underfull \vbox (badness 10000) has occurred while \output is active [30 <./cha pters/langtangen/pdf/Poisson2D_Dvc_contour1.pdf> <./chapters/langtangen/pdf/Poi sson2D_Dvc_flux_x.pdf> <./chapters/langtangen/pdf/Poisson2D_Dvc_surf1.pdf> <./c hapters/langtangen/pdf/Poisson2D_Dvc_mesh1.pdf>] [31] [32] Underfull \vbox (badness 1122) has occurred while \output is active [33] [34] [35] [36] Underfull \vbox (badness 3646) has occurred while \output is active [37] [38] [39] Underfull \vbox (badness 1412) has occurred while \output is active [40] [41] [42] [43] Underfull \hbox (badness 1331) in paragraph at lines 3053--3059 []\T1/pplx/m/n/10 (+20) The im-ple-men-ta-tion is iden-ti-cal to the one in Sec -tion [][]1.2.2[][] and is found in the file [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] Underfull \vbox (badness 2088) has occurred while \output is active [53 <./chap ters/langtangen/pdf/daynight.pdfError: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap Error: Illegal entry in bfrange block in ToUnicode CMap >] [54] Underfull \vbox (badness 3977) has occurred while \output is active [55] [56] [57] [58] [59 <./chapters/langtangen/pd f/hollow_cylinder.pdf>] [60] Underfull \hbox (badness 1215) in paragraph at lines 4284--4288 []\T1/pplx/m/n/10 (+20) Calling \T1/fvm/m/n/10 subdomains.array() \T1/pplx/m/n/ 10 (+20) re-turns a \T1/fvm/m/n/10 numpy \T1/pplx/m/n/10 (+20) ar-ray of the su b-do-main val-ues. That is, [61] [62] Underfull \vbox (badness 10000) has occurred while \output is active [63] [64] [65] [66] Overfull \hbox (2.004pt too wide) in paragraph at lines 4672--4674 []\T1/pplx/m/n/10 (-20) generate mesh over [67] [68] [69]) (./tex/Part1.tex [70] [71] [72]) (./tex/2.tex Chapter 2. (/usr/share/texmf-texlive/tex/latex/psnfss/ufplmbb.fd) Underfull \vbox (badness 2951) has occurred while \output is active [73] (./chapters/kirby-7/pdf/heat_equation_model_domain.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/heat_equation_model_domai n.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allow ed ) [74 <./ch apters/kirby-7/pdf/heat_equation_model_domain.pdf>] [75] [76] Underfull \vbox (badness 7451) has occurred while \output is active [77] [78] [79 <./chapters/kirby-7/pdf/cells.pdf>] [80 <./chapters/kirby-7/pdf/P1.pdf>] pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/dofmap.pdf): PDF inclusio n: found PDF version <1.5>, but at most version <1.4> allowed Underfull \vbox (badness 4060) has occurred while \output is active [81] Underfull \hbox (badness 1107) in paragraph at lines 694--694 []\T1/pplx/m/n/9 (+20) Figure 2.5: |Patch-ing to-gether a Underfull \hbox (badness 1755) in paragraph at lines 694--694 \T1/pplx/m/n/9 (+20) pair of quadratic lo-cal func-tion [82 <./chapters/kirby-7/pdf/dofmap.pdf> <./chapters/kirby-7/pdf/femspace.pdf>] (./chapters/kirby-7/pdf/affine_map.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/affine_map.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) [83 <./chapters/kirby-7/pdf/affine_m ap.pdf>] [84] [85] (./chapters/kirby-7/pdf/projection.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-7/pdf/projection.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \vbox (badness 10000) has occurred while \output is active [86 <./cha pters/kirby-7/pdf/projection.pdf>] [87] [88] [89 <./chapters/kirby-7/png/refinemen t.png (PNG copy)>]) (./tex/3.tex [90] Chapter 3. [91] [92] (./chapters/kirby-6/pdf/notation_new.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-6/pdf/notation_new.pdf): PDF in clusion: found PDF version <1.5>, but at most version <1.4> allowed ) [93] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 238. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 238. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 238. [94 <./chapters/kirby-6/pdf/notation_new.pdf>] pdfTeX warning: pdflatex (file ./chapters/kirby-6/pdf/P1_1d2d3d.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed [95 <./chapters/kirby-6/pdf/P1_1d2d3d.pdf >] [96 <./chapters/kirby-6/png/CG1_2d.png (PNG copy)> <./chapters/kirby-6/png/C G2_2d.png (PNG copy)> <./chapters/kirby-6/png/CG3_2d.png (PNG copy)> <./chapter s/kirby-6/png/CG4_2d.png (PNG copy)> <./chapters/kirby-6/png/CG5_2d.png (PNG co py)> <./chapters/kirby-6/png/CG6_2d.png (PNG copy)> <./chapters/kirby-6/png/CG1 _3d.png (PNG copy)> <./chapters/kirby-6/png/CG2_3d.png (PNG copy)> <./chapters/ kirby-6/png/CG3_3d.png (PNG copy)> <./chapters/kirby-6/png/CG4_3d.png (PNG copy )> <./chapters/kirby-6/png/CG5_3d.png (PNG copy)> <./chapters/kirby-6/png/CG6_3 d.png (PNG copy)>] Underfull \hbox (badness 3503) in paragraph at lines 394--394 []\T1/pplx/m/n/9 (+20) Figure 3.5: |Il-lus-tra-tion of the Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 430. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 430. [97 <./chapters/kirby-6/png/CR1_2d.png (PNG copy)> <./chapters/kirby-6/png/CR1_ 3d.png (PNG copy)>] Underfull \hbox (badness 1354) in paragraph at lines 510--510 \T1/pplx/m/n/9 (+20) mo-ments of the nor-mal com-po- Underfull \hbox (badness 1968) in paragraph at lines 510--510 \T1/pplx/m/n/9 (+20) ter-na-tively, as in-di-cated in this [98 <./chapters/kirby-6/png/RT1_2d.png (PNG copy)> <./chapters/kirby-6/png/RT2_ 2d.png (PNG copy)> <./chapters/kirby-6/png/RT3_2d.png (PNG copy)> <./chapters/k irby-6/png/RT1_3d.png (PNG copy)> <./chapters/kirby-6/png/RT2_3d.png (PNG copy) > <./chapters/kirby-6/png/RT3_3d.png (PNG copy)>] Underfull \hbox (badness 4995) in paragraph at lines 585--587 []\T1/pplx/m/it/10 The Brezzi--Douglas--Marini el-e-ment ($[][]$) is [99 <./chapters/kirby-6/png/BDM1_2d.png (PNG copy)> <./chapters/kirby-6/png/BDM 2_2d.png (PNG copy)> <./chapters/kirby-6/png/BDM3_2d.png (PNG copy)> <./chapter s/kirby-6/png/BDM1_3d.png (PNG copy)> <./chapters/kirby-6/png/BDM2_3d.png (PNG copy)> <./chapters/kirby-6/png/BDM3_3d.png (PNG copy)>] Underfull \hbox (badness 3503) in paragraph at lines 677--677 []\T1/pplx/m/n/9 (+20) Figure 3.8: |Il-lus-tra-tion of the [100] Overfull \hbox (1.29993pt too wide) in paragraph at lines 737--737 []\T1/pplx/m/n/9 (-20) Figure 3.9: |Illustration of the Arnold-- [101 <./chapters/kirby-6/png/MTW_2d.png (PNG copy)> <./chapters/kirby-6/png/AW_ 2d.png (PNG copy)>] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 748. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 748. Underfull \vbox (badness 10000) has occurred while \output is active [102] Underfull \vbox (badness 10000) has occurred while \output is active [103 <./ch apters/kirby-6/png/NED1_1_2d.png (PNG copy)> <./chapters/kirby-6/png/NED1_2_2d. png (PNG copy)> <./chapters/kirby-6/png/NED1_3_2d.png (PNG copy)> <./chapters/k irby-6/png/NED1_1_3d.png (PNG copy)> <./chapters/kirby-6/png/NED1_2_3d.png (PNG copy)> <./chapters/kirby-6/png/NED1_3_3d.png (PNG copy)>] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 963. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 963. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 963. [104 <./chapters/kirby-6/png/NED2_1_2d.png (PNG copy)> <./chapters/kirby-6/png/ NED2_2_2d.png (PNG copy)> <./chapters/kirby-6/png/NED2_3_2d.png (PNG copy)> <./ chapters/kirby-6/png/NED2_1_3d.png (PNG copy)>] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 1026. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 1026. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 1026. [105] [106 <./chapters/kirby-6/png/DG0_2 d.png (PNG copy)> <./chapters/kirby-6/png/DG1_2d.png (PNG copy)> <./chapters/ki rby-6/png/DG2_2d.png (PNG copy)> <./chapters/kirby-6/png/DG3_2d.png (PNG copy)> <./chapters/kirby-6/png/DG0_3d.png (PNG copy)> <./chapters/kirby-6/png/DG1_3d. png (PNG copy)> <./chapters/kirby-6/png/DG2_3d.png (PNG copy)> <./chapters/kirb y-6/png/DG3_3d.png (PNG copy)> <./chapters/kirby-6/pdf/dgspace.pdf>] [107 <./chapters/kirby-6/png/ARG5_2d.png (PNG copy)>] Underfull \vbox (badness 1092) has occurred while \output is active [108 <./cha pters/kirby-6/png/HER_2d.png (PNG copy)> <./chapters/kirby-6/png/HER_3d.png (PN G copy)>] [109 <./chapters/kirby-6/png/MOR_2d.png ( PNG copy)>] [110] Overfull \hbox (2.96089pt too wide) in paragraph at lines 1410--1410 []|\T1/pplx/m/n/9 (-20) Dimension| Underfull \hbox (badness 1484) in paragraph at lines 1425--1425 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 12$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 1484) in paragraph at lines 1428--1428 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 12$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 1484) in paragraph at lines 1431--1431 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 24$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 1484) in paragraph at lines 1434--1434 []$\OT1/zplm/m/n/9 [\OMS/zplm/m/n/9 P[]\OT1/zplm/m/n/9 ][]$ \T1/pplx/m/n/9 (+20 ) (vec-tor); $\OT1/pplx/m/n/9 (+20) 40$ \T1/pplx/m/n/9 (+20) nor-mal Underfull \hbox (badness 10000) in alignment at lines 1408--1468 [] [] [] [] [] Underfull \vbox (badness 10000) detected at line 1468 Underfull \hbox (badness 10000) in alignment at lines 1468--1528 [] [] [] [] [] [111] [112] Underfull \hbox (badness 10000) in alignment at lines 1528--1544 [] [] [] [] [] [113] [114] [115]) (./tex/4.tex [116] Chapter 4. [117] [118] [119] [120] [121] [122 <./chapters/kirby-1/pdf/tricoord.p df>] [123 <./chapters/kirby-6/pdf/P1.pdf> <./chapters/kirby-6/pdf/P2.pdf>] Underfull \hbox (badness 2744) in paragraph at lines 495--495 []\T1/pplx/m/n/9 (+20) Figure 4.4: |Tri-an-gu-lar Raviart-- [124 <./chapters/kirby-6/pdf/RT0.pdf>] [125] [126] [127] ) (./tex/5.tex [128 <./chapters/kirby-1/pdf /patch.pdf>] Chapter 5. Underfull \vbox (badness 10000) has occurred while \output is active [129] Underfull \vbox (badness 3219) has occurred while \output is active [130] (./chapters/kirby-5/pdf/lift_drag.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-5/pdf/lift_drag.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) [131] [132 <./chapters/kirby-5/pdf/li ft_drag.pdf>] (./chapters/kirby-5/pdf/element_tensors.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-5/pdf/element_tensors.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [133 <./chapters/kirby-5/pdf/el ement_tensors.pdf>] [134] [135]) (./tex/6.tex [136] Chapter 6. [137] (./chapters/logg-3/pdf/insertion.pdf_tex pdfTeX warning: pdflatex (file ./chapters/logg-3/pdf/insertion.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \vbox (badness 10000) has occurred while \output is active [138] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) [139 <./chapters/logg -3/pdf/insertion.pdf>] [140]) (./tex/7.tex [141] [142] Chapter 7. [143] [144] [145] Underfull \hbox (badness 1430) in paragraph at lines 293--293 \T1/pplx/m/n/9 (+20) from Fig-ure [][]7.1[][] with one ta-ble [146] [147] Underfull \vbox (badness 4805) has occurred while \output is active [148] [149] [150] [151 <./chapters/oelgaa rd-2/pdf/runtime_laplace.pdf>] [152] [153 <./chapter s/oelgaard-2/pdf/runtime_hyperelasticity.pdf>] [154]) (./tex/8.tex [155] [156] Chapter 8. [157] (./chapters/kirby-8/pdf/affinemap.pdf_tex pdfTeX warning: pdflatex (file ./chapters/kirby-8/pdf/affinemap.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \vbox (badness 10000) has occurred while \output is active [158 <./ch apters/kirby-8/pdf/affinemap.pdf>] [159]) (./tex/9.tex [160] Chapter 9. [161] Underfull \vbox (badness 1389) has occurred while \output is active [162] Underfull \vbox (badness 4981) has occurred while \output is active [163] (./chapters/kirby-4/pdf/small_mst.pdf_tex ) [164 <./chapters/kirby-4/pdf/small_ms t.pdf>] (./chapters/kirby-4/pdf/gg2.pdf_tex ) [165 <./chapters/kirby-4/pdf/gg2.pdf>] Underfull \vbox (badness 1215) has occurred while \output is active [166]) (./tex/Part2.tex [167] [168] [169] [170]) (./tex/10.tex Chapter 10. pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/fenics-map.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed Underfull \hbox (badness 1215) in paragraph at lines 61--61 \T1/pplx/m/n/9 (+20) the main user in-ter-face of FEn- [171] [172 <./chapters/logg-2/pdf/fenics-map .pdf>] [173 <./chapters/logg-2/pdf/dolfin-uml.pdf>] [174] [175] [176] [177] [178] Underfull \hbox (badness 1412) in paragraph at lines 563--570 \T1/pplx/m/n/10 (+20) abled when DOLFIN is con-fig-ured. The back-end can be se t via the global pa-ram-e-ter [179] [180] [181] (/usr/share/texmf-texlive/tex/latex/listings/lstlang1.sty) (/usr/share/texmf-texlive/tex/latex/listings/lstmisc.sty) [182] [183 <./chapters/logg-2/pdf/mesh -p1-entities.pdf>] [184] [185] [186] [187] [188 <./chapters/logg-2/png/refined_ cube.png (PNG copy)>] [189] [190] (./chapters/logg-2/pdf/femsolution.pdf_tex pdfTeX warning: pdflatex (file ./chapters/logg-2/pdf/femsolution.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) [191] [192 <./chapters/logg-2/pdf/fe msolution.pdf>] [193] [194] [195] [196] [197] [198] [199] [200] [201] Underfull \vbox (badness 1448) has occurred while \output is active [202] [203] [204] [205 <./chapters/logg-2/png/plot_mesh .png (PNG copy)> <./chapters/logg-2/png/plots.png (PNG copy)>] [206] Underfull \hbox (badness 1184) in paragraph at lines 2529--2532 \T1/pplx/m/n/10 (+20) One can-not read-/write \T1/fvm/m/n/10 Function \T1/pplx/ m/n/10 (+20) and \T1/fvm/m/n/10 FunctionSpace \T1/pplx/m/n/10 (+20) ob-jects si nce the rep-re-sen-ta-tion of a [207] [208] [209] [210] [211] [212] [213] Overfull \hbox (1.6556pt too wide) in paragraph at lines 3058--3067 [][] [214 <./chapters/logg-2/png/coloured.png (PNG copy)> <./chapters/logg-2/png/par tition.png (PNG copy)>] [215] [216] Underfull \hbox (badness 1533) in paragraph at lines 3274--3279 [] []\T1/pplx/m/it/10 Con-struct-ing ar-gu-ments (trial and test func-tions).[] \T1/pplx/m/n/10 (+20) The \T1/fvm/m/n/10 ufl.Argument \T1/pplx/m/n/10 (+20) cl ass (the base class of [217] [218] [219] Underfull \vbox (badness 1067) has occurred while \output is active [220] [221]) (./tex/11.tex [222] Chapter 11. [223 <./chapters/logg-1/pdf/ufl_ffc_u fc.pdf>] [224] [225] [226] [227] Underfull \hbox (badness 1975) in paragraph at lines 428--428 \T1/pplx/m/n/9 (+20) guage, Anal-y-sis, Rep-re-sen-ta-tion, [228] [229 <./chapters/logg-1/pdf/compilerdesign.pdf>] [230] [231] Underfull \hbox (badness 2961) in paragraph at lines 626--647 \T1/pplx/m/n/10 (+20) interface by giv-ing the ad-di-tional op-tions \T1/fvm/m/ n/10 -f eliminate_zeros\T1/pplx/m/n/10 (+20) , \T1/fvm/m/n/10 -f simplify_expre ssions\T1/pplx/m/n/10 (+20) , Underfull \hbox (badness 1308) in paragraph at lines 701--701 []\T1/pplx/m/n/9 (+20) Figure 11.7: |JIT com-pi-la-tion of [232]) (./tex/12.tex [233 <./chapters/logg-1/pdf/jit.pdf>] [234] Chapter 12. [235] [236] [237] Underfull \vbox (badness 1946) has occurred while \output is active [238 <./cha pters/kirby-3/pdf/MassH1.pdf>] [239 <./chapters/kirby-3/pdf/Poisson.pdf> <./cha pters/kirby-3/pdf/WeightedPoisson.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active [240 <./ch apters/kirby-3/pdf/NavierStokes.pdf>] [241 <./chapters/kirby-3/pdf/MassHdiv.pdf > <./chapters/kirby-3/pdf/MassHcurl.pdf>]) (./tex/13.tex [242] Chapter 13. Underfull \vbox (badness 10000) has occurred while \output is active [243] [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] [247] Underfull \hbox (badness 1371) in paragraph at lines 428--435 \T1/pplx/m/n/10 (+20) Then, a ba-sis for the null space of this ma-trix is con- structed us-ing the sin-gu-lar value [248] [249 <./chapters/kirby-2/pdf/reftri.pdf>] [250 <./chapters/kirby-2/pdf/P3.pdf>] ) (./tex/14.tex [251 <./chapters/kirby-2/p df/struct.pdf>] [252] Chapter 14. [253] [254] [255] [256 <./chapters/wilbers/pdf /pressure_plot.pdf>] [257] [258] Underfull \hbox (badness 10000) in paragraph at lines 350--357 \T1/fvm/m/n/10 /tmp/tmpZ4M_ZO2010-11-9-08-24_instant/instant_module_dff94651124 1aab327593a2d71105c5fc/\T1/pplx/m/n/10 (+20) . [259] [260] [261] [262] [263] [264] [265] [266] [267]) (./tex/15.tex [268] Chapter 15. [269] [270] [271] [272] [273] Underfull \vbox (badness 10000) has occurred while \output is active [274] [275]) (./tex/16.tex [276] [277] [278] Chapter 16. pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ufc_flowdiagram.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed Underfull \vbox (badness 10000) has occurred while \output is active [279] Underfull \vbox (badness 2181) has occurred while \output is active [280 <./cha pters/alnes-2/pdf/ufc_flowdiagram.pdf>] pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ufc_classes.pdf): PDF inc lusion: found PDF version <1.5>, but at most version <1.4> allowed [281 <./chapters/alnes-2/pdf/ufc_cla sses.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active [282] [283] [284] Underfull \vbox (badness 10000) has occurred while \output is active [285] [286] Underfull \vbox (badness 10000) has occurred while \output is active [287] [288] [289] (./chapters/alnes-2/pdf/interval.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/interval.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 51--730 []|[]| (./chapters/alnes-2/pdf/triangle.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/triangle.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 50--753 []|[]| (./chapters/alnes-2/pdf/quadrilateral.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/quadrilateral.pdf): PDF i nclusion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 51--777 []|[]| [290 <./chapters/alnes-2/pdf/interval.pdf> <./chapters/alnes-2/pdf/triangle.pdf >] (./chapters/alnes-2/pdf/tetrahedron.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/tetrahedron.pdf): PDF inc lusion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 51--802 []|[]| (./chapters/alnes-2/pdf/hexahedron.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/hexahedron.pdf): PDF incl usion: found PDF version <1.5>, but at most version <1.4> allowed ) Overfull \hbox (7.96405pt too wide) in paragraph at lines 53--827 []|[]| Underfull \vbox (badness 7740) has occurred while \output is active [291 <./cha pters/alnes-2/pdf/quadrilateral.pdf> <./chapters/alnes-2/pdf/tetrahedron.pdf>] (./chapters/alnes-2/pdf/numbering_example_triangles.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/numbering_example_triangl es.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allo wed ) (./chapters/alnes-2/pdf/numbering_example_quadrilaterals.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/numbering_example_quadril aterals.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [292 <./chapte rs/alnes-2/pdf/hexahedron.pdf>] [293 <./chapters/alnes-2/pdf/numbering_example_ triangles.pdf> <./chapters/alnes-2/pdf/numbering_example_quadrilaterals.pdf>] (./chapters/alnes-2/pdf/ordering_example_triangle.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ordering_example_triangle .pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowe d ) (./chapters/alnes-2/pdf/ordering_example_tetrahedron.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/ordering_example_tetrahed ron.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> all owed ) [294 <./chapters/alnes-2/pdf/ordering_example_triangle.pdf> <./chapters/alnes-2 /pdf/ordering_example_tetrahedron.pdf>] (./chapters/alnes-2/pdf/orientation_example_triangles.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-2/pdf/orientation_example_trian gles.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> al lowed ) [295 <./chapters/alnes-2/pdf/orientation_example_triangles.pdf>] [296] [297]) (./tex/17.tex [298] Chapter 17. Underfull \vbox (badness 1092) has occurred while \output is active [299] [300] Underfull \vbox (badness 10000) has occurred while \output is active [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] (/usr/share/texmf-texlive/tex/latex/microtype/mt-euf.cfg) [315] (./chapters/alnes-1/pdf/expr.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/expr.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [316 <./chapters/alnes-1/pdf/expr.pdf>] (./chapters/alnes-1/pdf/stiffness.pdf_tex pdfTeX warning: pdflatex (file ./chapters/alnes-1/pdf/stiffness.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) [317] [318 <./chapters/alnes-1/pdf/st iffness.pdf>] [319] Underfull \vbox (badness 10000) has occurred while \output is active [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] Underfull \vbox (badness 1681) has occurred while \output is active [330] [331] [332] [333]) (./tex/18.tex [334] Chapter 18. Underfull \hbox (badness 1442) in paragraph at lines 89--89 \T1/pplx/m/n/9 (+20) around a cylin-der with par-al-lel [335] [336 <./chapters/hoffman-2/pdf/cube556.pdf> <./chapters/hoffman-2/pdf/com pressible3D.pdf> <./chapters/hoffman-2/pdf/Hoffman_fig3d.pdf>] [337] [338] [339] LaTeX Warning: Float too large for page by 32.91196pt on input line 472. [340] [341] [342 <./chapters/hoffman-2/pdf/speedup_solve.pdf> <./chapters/hoffm an-2/pdf/speedup_unrivara.pdf>] [343] [344] [345] [346] [347] Overfull \hbox (1.6596pt too wide) in paragraph at lines 807--818 [][] [348] [349 <./chapters/hoffman-2/pdf/force_smooth01.pdf> <./chapters/hoffman-2/ pdf/force_hybrid01.pdf> <./chapters/hoffman-2/pdf/force_smooth02.pdf> <./chapte rs/hoffman-2/pdf/force_hybrid02.pdf> <./chapters/hoffman-2/pdf/force_smooth03.p df> <./chapters/hoffman-2/pdf/force_hybrid03.pdf>] [350] [351 <./chapters/hoffman-2/pdf/ swap.pdf> <./chapters/hoffman-2/pdf/swap_config1.pdf>] [352] [353 <./chapters/hoffman-2/png/fsi 3_vel_050.png (PNG copy)> <./chapters/hoffman-2/png/fsi3_theta_050.png (PNG cop y)> <./chapters/hoffman-2/png/fsi3_vel_250.png (PNG copy)> <./chapters/hoffman- 2/png/fsi3_theta_250.png (PNG copy)>] [354 <./chapters/hoffman-1/png/fig2b.png (PNG copy)> <./chapters/hoffman-1/png/fig2c.png (PNG copy)>] LaTeX Warning: Float too large for page by 4.412pt on input line 1281. ) (./tex/19.tex [355] [356] [357] [358] [359] [360] Chapter 19. Overfull \hbox (1.19252pt too wide) in paragraph at lines 5--5 |[]\T1/pplx/m/it/20.74 Lessons learned in mixed lan-guage pro-gram-ming| [361] (./chapters/mardal-2/code/Array.h) (./chapters/mardal-2/code/Array_1.i) (./chapters/mardal-2/code/setup.py [362]) [363] (./chapters/mardal-2/code/segfault_test.py) [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] [376] [377]) (./tex/Part3.tex [378] [379] [380]) (./tex/20.tex Chapter 20. [381] [382] [383 <./chapters/kirby-6/pdf/P3.pdf>] pdfTeX warning: pdflatex (file ./chapters/terrel/pdf/MINI.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed [384 <./chapters/kirby-6/pdf/CR1.pdf> <./cha pters/terrel/pdf/MINI.pdf>] [385] Underfull \vbox (badness 10000) has occurred while \output is active [386] LaTeX Warning: Float too large for page by 3.70213pt on input line 417. [387] [388 <./chapters/terrel/pdf/mesh.pdf> <./chapters/terrel/pdf/vel_test.pdf > <./chapters/terrel/pdf/vel_lid.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active [389] [390] [391] [392 <./chapters/terrel/pdf/vel_ 4.pdf> <./chapters/terrel/pdf/press_4.pdf>] [393 <./chapters/terrel/pdf/div_4.p df> <./chapters/terrel/pdf/run_4.pdf>] ) (./tex/21.tex [394 <./chapters/ter rel/pdf/div_4_test.pdf> <./chapters/terrel/png/lid_div_error.png (PNG copy)>] Chapter 21. [395] [396] [397] [398] Underfull \vbox (badness 10000) has occurred while \output is active [399] Overfull \hbox (25.00003pt too wide) detected at line 474 [] Overfull \hbox (25.00003pt too wide) detected at line 474 [] [400] [401] Underfull \vbox (badness 10000) has occurred while \output is active [402] [403] Underfull \vbox (badness 10000) has occurred while \output is active [404] [405] Underfull \vbox (badness 2126) has occurred while \output is active [406] Underfull \vbox (badness 1515) has occurred while \output is active [407] [408 <./chapters/kvs-1/pdf/new_drivencavity_res.pdf> <./chapters/kvs-1/pdf/new_ channel_res.pdf>] Underfull \vbox (badness 3396) has occurred while \output is active [409] [410 <./chapters/kvs-1/pdf/periodic_v.pdf> <./chapters/kvs-1/pdf/periodic_p.pdf > <./chapters/kvs-1/pdf/new_periodic_res.pdf>] Underfull \vbox (badness 6428) has occurred while \output is active [411 <./cha pters/kvs-1/pdf/cylinderandgeoattime5nr2.pdf> <./chapters/kvs-1/pdf/new_cylinde r_res.pdf>] [412 <./chapters/kvs-1/pdf/new_be ltrami_illustration.pdf>] [413 <./chapters/kvs-1/pdf/new_beltram i_res.pdf>] [414 <./chapters/kvs-1/pdf/aneurysm_at_end_css1.pdf> <./chapters/kv s-1/pdf/new_aneurysm_res.pdf>] [415 <./chapters/kvs-1/pdf/new_scatter.pdf>] ) (./tex/22.tex Underfull \vbox (badness 4108) has occurred while \output is active [416 <./cha pters/kvs-1/pdf/drivencavity-plots.pdf>] [417 <./chapters/kvs-1/pdf/drivencavit y-scatter.pdf>] [418] Chapter 22. [419] Underfull \vbox (badness 1515) has occurred while \output is active [420] Underfull \vbox (badness 1038) has occurred while \output is active [421] Underfull \vbox (badness 2662) has occurred while \output is active [422] [423] [424] Underfull \vbox (badness 2351) has occurred while \output is active [425] [426] [427] [428] [429] [430] [431 <./chapters/mortensen/pd f/Burgers_KE_IM1.pdf> <./chapters/mortensen/pdf/Burgers_KE_IM2.pdf>] [432] Underfull \hbox (badness 1331) in paragraph at lines 1115--1115 []\T1/pplx/m/n/9 (+20) Figure 22.3: |Ac-cu-mu-lated er-ror Underfull \hbox (badness 1331) in paragraph at lines 1132--1132 []\T1/pplx/m/n/9 (+20) Figure 22.4: |Ac-cu-mu-lated er-ror [433 <./chapters/mortensen/pdf/OS_init.pdf> <./chapters/mortensen/pdf/OrrS_eigv als.pdf>] [434 <./chapters/mortensen/pdf/OS_init_cfl_1.pdf> <./chapters/mortens en/pdf/OS_init_cfl_0.pdf> <./chapters/mortensen/pdf/OS_init_dx_1.pdf> <./chapte rs/mortensen/pdf/OS_init_dx_0.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active [435] [436 <./chapters/mortensen/pdf/OS_energy_cfl_0_1_model_1.pdf> <./chapters/morte nsen/pdf/OS_energy_cfl_0_1_model_0.pdf> <./chapters/mortensen/pdf/OS_energy_cfl _0_05_model_1.pdf> <./chapters/mortensen/pdf/OS_energy_cfl_0_05_model_0.pdf>] [437 <./chapters/mortensen/pdf/TG_disserror_model_0_cfl_0_05_Re_100_dofs.pdf> < ./chapters/mortensen/pdf/TG_energyerror_model_0_cfl_0_05_Re_100_dofs.pdf>]) (./tex/23.tex [438] Chapter 23. [439] [440 <./chapters/kvs-2/png/cow_gray_1 .png (PNG copy)> <./chapters/kvs-2/pdf/kentus.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active [441] [442 <./cha pters/kvs-2/pdf/systolic.pdf>] [443 <./chapters/kvs-2/png/zero_dp_vs_res.png>] [444 <./chapters/kvs-2/pdf/stacks.pdf> <./chapters/kvs-2/pdf/3d.pdf> <./chapter s/kvs-2/pdf/viper3.pdf>] [445 <./chapters/kvs-2/pdf/bifurcation_cl ean.pdf>] [446 <./chapters/kvs-2/pdf/mcas_wss_II4.pdf> <./chapters/kvs-2/pdf/ic as_wss.pdf>] [447 <./chapters/kvs-2/pdf/mass_do g.pdf>] [448 <./chapters/kvs-2/pdf/dog_data_mr_cfd.pdf>] [449] [450 <./chapters/kvs-2/pdf/ica.pdf> <./ chapters/kvs-2/pdf/cok_inflow.pdf>] ) (./tex/24.tex [451] [452 <./chapters/kvs-2/pdf/cok_top_steam_white.pdf>] [453 <./chapters/kvs -2/pdf/cok_slice.pdf> <./chapters/kvs-2/pdf/cok_ica_vel_peak_syst.pdf>] [454] Chapter 24. [455] Underfull \vbox (badness 4391) has occurred while \output is active [456 <./cha pters/hentschel/pdf/ChiariImage2.pdf>] [457] [458] [459 <./chapters/hentschel/pdf/sin_p ulse.pdf>] [460] [461] [462] [463] [464 <./chapters/hentschel/pdf/gmsh.pdf>] [465 <./chapters/hen tschel/pdf/pulse_f1_08_sysmax_nmb7.pdf> <./chapters/hentschel/pdf/pulse_f1_08_s ysdia_nmb18.pdf> <./chapters/hentschel/pdf/pulse_f1_08_diamin1_nmb25.pdf>] [466] [467 <./chapters/hentschel/pdf/sin_sysmax_nmb2.pdf> <./chapters/hentschel/pdf/s in_sysdia_nmb4.pdf> <./chapters/hentschel/pdf/sin_diamin_nmb6.pdf>] [468 <./cha pters/hentschel/pdf/pulse_f1_08_elliptic_sysmax_nmb7.pdf> <./chapters/hentschel /pdf/pulse_f1_08_elliptic_sysdia_nmb18.pdf> <./chapters/hentschel/pdf/pulse_f1_ 08_elliptic_diamin1_nmb25.pdf> <./chapters/hentschel/pdf/pulse_f1_08_elliptic_e ccentric_sysmax_nmb7.pdf> <./chapters/hentschel/pdf/pulse_f1_08_elliptic_eccent ric_sysdia_nmb18.pdf> <./chapters/hentschel/pdf/pulse_f1_08_elliptic_eccentric_ diamin1_nmb25.pdf>]) (./tex/25.tex [469 <./chapters/hentschel/pdf/pulse_syrinx_ f1_08_syrinx05_sysmax_nmb7.pdf> <./chapters/hentschel/pdf/pulse_syrinx_f1_08_sy rinx05_sysdia_nmb18.pdf> <./chapters/hentschel/pdf/pulse_syrinx_f1_08_syrinx05_ diamin1_nmb25.pdf>] [470] Chapter 25. [471] [472 <./chapters/lopes/pdf/nazare1.p df>] [473] (./chapters/lopes/pdf/graph.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/graph.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [474pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.1}) has been already used, duplicate i gnored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.290 \end{figure} ]pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.2}) has been already used, duplicate ignored \relax l.295 \begin{equation} pdfTeX warning (ext4): destination with the same identifi er (name{equation.25.3.3}) has been already used, duplicate ignored \relax l.307 \begin{equation} [475 <./chapters/lopes/pdf/graph.pdf>]pdfTeX warning (ex t4): destination with the same identifier (name{equation.25.3.1}) has been alre ady used, duplicate ignored \relax l.461 \end{align} pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.2}) has been already used, duplicate ignored \relax l.461 \end{align} Underfull \vbox (badness 2744) has occurred while \output is active [476]pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.1}) h as been already used, duplicate ignored \relax l.512 \end{align} pdfTeX warning (ext4): destination with the same identifier (n ame{equation.25.3.2}) has been already used, duplicate ignored \relax l.512 \end{align} pdfTeX warning (ext4): destination with the same identifier (n ame{equation.25.3.1}) has been already used, duplicate ignored \relax l.545 \end{align} pdfTeX warning (ext4): destination with the same identifier (n ame{equation.25.3.2}) has been already used, duplicate ignored \relax l.545 \end{align} [477]pdfTeX warning (ext4): destination with the same identif ier (name{equation.25.3.1}) has been already used, duplicate ignored \relax l.571 \end{align} pdfTeX warning (ext4): destination with the same identifier (name{equation.25.3.2}) has been already used, duplicate ignored \relax l.571 \end{align} [478] Underfull \hbox (badness 5681) in paragraph at lines 667--667 []\T1/pplx/m/n/9 (+20) Figure 25.3: |Pos-i-tive part of [479 <./chapters/lopes/pdf/phase_velocity_simple.pdf>] Overfull \hbox (0.95473pt too wide) in paragraph at lines 771--777 \T1/pplx/m/n/10 (-20) Corr and RungeKutta classes (see \T1/fvm/m/n/10 dolfwave/ src/predictorcorrector \T1/pplx/m/n/10 (-20) and \T1/fvm/m/n/10 dolfwave/src/ru ngekutta\T1/pplx/m/n/10 (-20) ). [480pdfTeX warning (ext4): destination with the same identifier (name{equation. 25.5.1}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.820 pdfTeX warning (ext4): destination with the same identifier (name{equatio n.25.5.2}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.820 ] Underfull \vbox (badness 10000) has occurred while \output is active [481] [482] [483] Underfull \vbox (badness 10000) has occurred while \output is active [484] (./chapters/lopes/pdf/spike_shelf.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/spike_shelf.pdf): PDF inclu sion: found PDF version <1.5>, but at most version <1.4> allowed ) [485] Underfull \hbox (badness 1377) in paragraph at lines 1290--1290 \T1/pplx/m/n/9 (+20) pan-els) and ZTC (lower pan-els) Underfull \hbox (badness 1377) in paragraph at lines 1305--1305 \T1/pplx/m/n/9 (+20) pan-els) and ZTC (lower pan-els) Underfull \hbox (badness 1377) in paragraph at lines 1319--1319 \T1/pplx/m/n/9 (+20) pan-els) and ZTC (lower pan-els) [486 <./chapters/lopes/pdf/spike_shelf.pdf> <./chapters/lopes/png/L2_spike_stab ility.png> <./chapters/lopes/png/L2_shelf_stability.png> <./chapters/lopes/png/ L1_spike_stability.png> <./chapters/lopes/png/L1_shelf_stability.png>] [487 <./ chapters/lopes/png/L0_5_spike_stability.png> <./chapters/lopes/png/L0_5_shelf_s tability.png> <./chapters/lopes/png/L2_dx_0_02_hm_spike_spectrum_StdPot.png> <. /chapters/lopes/png/L2_dx_0_02_hm_shelf_spectrum_StdPot.png> <./chapters/lopes/ png/L2_dx_0_02_hm_spike_spectrum_Zhao.png> <./chapters/lopes/png/L2_dx_0_02_hm_ shelf_spectrum_Zhao.png> <./chapters/lopes/png/L1_dx_0_1_hm_spike_spectrum_StdP ot.png> <./chapters/lopes/png/L1_dx_0_1_hm_shelf_spectrum_StdPot.png> <./chapte rs/lopes/png/L1_dx_0_1_hm_spike_spectrum_Zhao.png> <./chapters/lopes/png/L1_dx_ 0_1_hm_shelf_spectrum_Zhao.png>] [488 <./chapters/lopes/png/L0_5_dx_0_25_hm_spi ke_spectrum_StdPot.png> <./chapters/lopes/png/L0_5_dx_0_25_hm_shelf_spectrum_St dPot.png> <./chapters/lopes/png/L0_5_dx_0_25_hm_spike_spectrum_Zhao.png> <./cha pters/lopes/png/L0_5_dx_0_25_hm_shelf_spectrum_Zhao.png>] [489] [490] LaTeX Warning: `!h' float specifier changed to `!ht'. LaTeX Warning: `!h' float specifier changed to `!ht'. [491 <./chapters/lopes/pdf/submergedbar.pdf>] [492 <./chapters/lopes/pdf/ZhaoNw ogu.pdf> <./chapters/lopes/pdf/deptheps.pdf>] [493 <./chapters/lopes/pdf/epsilo n0_1.pdf> <./chapters/lopes/pdf/epsilon0_25.pdf>] [494 <./chapters/lopes/pdf/epsilon0_5. pdf>] [495 <./chapters/lopes/pdf/eta000000.pdf> <./chapters/lopes/pdf/eta002000 .pdf> <./chapters/lopes/pdf/eta004000.pdf> <./chapters/lopes/pdf/eta006000.pdf> <./chapters/lopes/pdf/eta007972.pdf> <./chapters/lopes/pdf/eta009946.pdf>] [496 <./chapters/lopes/pdf/unstr.pdf> <./chapters/lopes/pdf/unstrcorner.pdf>] Underfull \vbox (badness 4048) has occurred while \output is active [497 <./cha pters/lopes/pdf/detail_unstr.pdf>] (./chapters/lopes/pdf/scale_tex.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/scale_tex.pdf): PDF inclusi on: found PDF version <1.5>, but at most version <1.4> allowed ) (./chapters/lopes/pdf/sponge_tex.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/sponge_tex.pdf): PDF inclus ion: found PDF version <1.5>, but at most version <1.4> allowed ) [498 <./chapters/lopes/pdf/scale_tex.pd f> <./chapters/lopes/pdf/depth.pdf>] [499 <./chapters/lopes/pdf/sponge_tex.pdf> <./chapters/lopes/pdf/eta.pdf> <./chapters/lopes/pdf/pvel2.pdf>] [500 <./chapt ers/lopes/pdf/etaprofile.pdf> <./chapters/lopes/pdf/velprofile.pdf>] pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/depth0.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/depth6.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed [501 <./chapters/lopes/pdf/depth0.pdf> <./c hapters/lopes/pdf/depth6.pdf>] pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/eta3.pdf): PDF inclusion: f ound PDF version <1.5>, but at most version <1.4> allowed [502 <./chapters/lopes/pdf/eta1.pdf> <./chap ters/lopes/pdf/eta3.pdf> <./chapters/lopes/pdf/eta45.pdf>] pdfTeX warning: pdflatex (file ./chapters/lopes/pdf/eta6.pdf): PDF inclusion: f ound PDF version <1.5>, but at most version <1.4> allowed [503 <./chapters/lopes/pdf/eta6.pdf>]) (./tex/26.tex [504] Chapter 26. [505] Underfull \vbox (badness 10000) has occurred while \output is active [506] Underfull \vbox (badness 1917) has occurred while \output is active [507] [508] Underfull \vbox (badness 10000) has occurred while \output is active [509] Underfull \vbox (badness 10000) has occurred while \output is active [510] [511] Underfull \vbox (badness 10000) has occurred while \output is active [512] [513] [514] [515] [516] [517] Underfull \vbox (badness 3291) has occurred while \output is active [518] Underfull \vbox (badness 2181) has occurred while \output is active [519] [520] [521] Underfull \hbox (badness 1178) in paragraph at lines 1410--1410 []\T1/pplx/m/n/9 (+20) Figure 26.6: |Com-plete DOLFIN Underfull \hbox (badness 1102) in paragraph at lines 1410--1410 \T1/pplx/m/n/9 (+20) solver for the com-press-ible neo- LaTeX Warning: Float too large for page by 23.41197pt on input line 1532. [522] [523] [524] [525]) (./tex/27.tex [526] Chapter 27. [527] [528] Underfull \hbox (badness 4316) in paragraph at lines 296--296 []\T1/pplx/m/n/9 (+20) Figure 27.2: |Sam-ples of how Overfull \hbox (1.10251pt too wide) in paragraph at lines 300--306 []\T1/pplx/m/n/10 (-20) In CBC.Twist, each of the forms listed in Ta-ble [][]27 .1[][] have been im-ple-mented in the file \T1/fvm/m/n/10 kinematics.py [529 <./chapters/narayanan/images/pdf/continuumpotato.pdf>] [530] [531] Underfull \hbox (badness 1019) in paragraph at lines 449--449 \T1/pplx/m/n/9 (+20) en-ergy func-tion for a two term [532] Underfull \hbox (badness 10000) in paragraph at lines 597--597 []\T1/pplx/m/n/9 (+20) Figure 27.6: |The rel-e- Underfull \hbox (badness 10000) in paragraph at lines 597--597 \T1/pplx/m/n/9 (+20) vant sec-tion of the class Underfull \hbox (badness 10000) in paragraph at lines 597--597 \T1/fvm/m/n/9 StaticMomentumBalanceSolver\T1/pplx/m/n/9 (+20) , [533] [534] [535] [536] [537 <./chapters/nara yanan/images/png/twistedcube.png (PNG copy)>] [538] [539] [540] [541 <./chapters/n arayanan/images/png/release_000.png (PNG copy)> <./chapters/narayanan/images/pn g/release_100.png (PNG copy)> <./chapters/narayanan/images/png/release_200.png (PNG copy)> <./chapters/narayanan/images/png/release_300.png (PNG copy)> <./cha pters/narayanan/images/png/release_400.png (PNG copy)> <./chapters/narayanan/im ages/png/release_500.png (PNG copy)>] [542 <./chapters/narayanan/images/pdf/ene rgies.pdf>] ) (./tex/28.tex [543] [544 <./chapters/narayanan/images/png/dolphin_000.png (PNG copy)> <./chapters/n arayanan/images/png/dolphin_001.png (PNG copy)> <./chapters/narayanan/images/pn g/dolphin_002.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_003.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_004.png (PNG copy)> <./cha pters/narayanan/images/png/dolphin_005.png (PNG copy)> <./chapters/narayanan/im ages/png/dolphin_006.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_0 07.png (PNG copy)> <./chapters/narayanan/images/png/dolphin_008.png (PNG copy)> ] Chapter 28. [545] [546] Underfull \vbox (badness 4899) has occurred while \output is active [547] [548 <./chapters/hoffman-1/png/fig1a.png (PNG copy)> <./chapters/hoffman-1/png/fig1b.png (PNG copy)>] [549 <./chapters/ hoffman-1/png/fig3a.png (PNG copy)> <./chapters/hoffman-1/png/fig3b.png (PNG co py)>] Underfull \vbox (badness 1024) has occurred while \output is active [550 <./cha pters/hoffman-1/png/Hoffman_fig2a.png (PNG copy)> <./chapters/hoffman-1/png/Hof fman_fig2b.png (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig2c.png (PNG cop y)> <./chapters/hoffman-1/png/Hoffman_fig2d.png (PNG copy)> <./chapters/hoffman -1/png/Hoffman_fig3a.png (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig3b.pn g (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig3c.png (PNG copy)> <./chapte rs/hoffman-1/png/Hoffman_fig3d.png (PNG copy)>] Underfull \vbox (badness 7047) has occurred while \output is active [551 <./cha pters/hoffman-1/png/Hoffman_fig5a.png (PNG copy)> <./chapters/hoffman-1/png/Hof fman_fig5b.png (PNG copy)> <./chapters/hoffman-1/png/Hoffman_fig5c.png (PNG cop y)> <./chapters/hoffman-1/png/Hoffman_fig5d.png (PNG copy)> <./chapters/hoffman -1/png/rlg_vorticity.png (PNG copy)> <./chapters/hoffman-1/png/oilfilm_back_sim .png (PNG copy)>] Underfull \hbox (badness 1584) in paragraph at lines 431--431 \T1/pplx/m/n/9 (+20) benchmark prob-lem FLUSTRUK- Underfull \hbox (badness 1783) in paragraph at lines 431--431 \T1/pplx/m/n/9 (+20) uni-formly re-fined meshes us-ing [552 <./chapters/hoffman-1/png/fsi_bench3D_displacement_aligned.pdf>] [553 <./chapters/hoffman-1/png/cube000 .png (PNG copy)> <./chapters/hoffman-1/png/cube115.png (PNG copy)> <./chapters/ hoffman-1/png/cube125.png (PNG copy)> <./chapters/hoffman-1/png/cube168.png (PN G copy)> <./chapters/hoffman-1/png/cube187.png (PNG copy)> <./chapters/hoffman- 1/png/cube405.png (PNG copy)> <./chapters/hoffman-1/png/cube550.png (PNG copy)> <./chapters/hoffman-1/png/cube649.png (PNG copy)>]) (./tex/29.tex [554] Chapter 29. [555] [556] pdfTeX warning: pdflatex (file ./chapters/selim/pdf/mapping.pdf): PDF inclusion : found PDF version <1.5>, but at most version <1.4> allowed [557 <./chapters/selim/pdf/mapping.pdf>] Underfull \vbox (badness 2512) has occurred while \output is active [558] [559 <./chapters/selim/pdf/primal.pdf>] [560] [561] Underfull \vbox (badness 10000) has occurred while \output is active [562] Underfull \vbox (badness 10000) has occurred while \output is active [563] Underfull \vbox (badness 10000) has occurred while \output is active [564] [565] Underfull \hbox (badness 3579) in paragraph at lines 929--929 []\T1/pplx/m/n/9 (+20) Figure 29.7: |A schematic pic- Underfull \hbox (badness 3354) in paragraph at lines 929--929 \T1/pplx/m/n/9 (+20) ture of the adap-tive FSI al-go- [566 <./chapters/selim/pdf/adaptive.pdf> ] [567] [568]) (./tex/30.tex [569 <./chapters/selim/p ng/new_channel.png (PNG copy)> <./chapters/selim/png/channel_test_zoom.png (PNG copy)>] [570 <./chapters/selim/png/channelZF.png (PNG copy)> <./chapters/selim /png/channelZS.png (PNG copy)> <./chapters/selim/png/channelZM.png (PNG copy)>] [571 <./chapters/selim/png/new_cavity.png> <./chapters/selim/png/zoom_cavity.pn g (PNG copy)> <./chapters/selim/pdf/plot.pdf>] [572] Chapter 30. [573] (./chapters/nikbakht/pdf/domain.pdf_tex ) [574 <./chapters/nikbakht/pdf/domain.pd f>] [575] [576] [577] [578] [579] [580] [581] [582 <./chapters/nikba kht/png/mesh.png> <./chapters/nikbakht/png/result.png>] [583]) (./tex/31.tex [584] [585] [586] Chapter 31. [587] [588 <./chapters/vynnytska/png/la yout.png>] Underfull \vbox (badness 10000) has occurred while \output is active [589] [590] [591] Underfull \vbox (badness 10000) has occurred while \output is active [592] Underfull \vbox (badness 6157) has occurred while \output is active [593] [594] Underfull \hbox (badness 2027) in paragraph at lines 766--766 \T1/pplx/m/n/8.5 main predictor--corrector al-go-rithm, Underfull \hbox (badness 1253) in paragraph at lines 766--766 \T1/pplx/m/n/8.5 ini-tial-iza-tion is not in-cluded here). LaTeX Warning: Float too large for page by 15.77048pt on input line 768. [595] [596] [597] [598] Underfull \hbox (badness 1038) in paragraph at lines 975--975 []\T1/pplx/m/n/9 (+20) Figure 31.7: |Di-men-sion-less root Overfull \hbox (1.66838pt too wide) in paragraph at lines 981--1019 [][] Overfull \hbox (1.66838pt too wide) in paragraph at lines 1025--1053 [][] [599] [600 <./chapters/vynnytska/png/u_rms.png>] [601 <./chapters/vynnytska/png /tmB.png (PNG copy)> <./chapters/vynnytska/png/visB.png (PNG copy)> <./chapters /vynnytska/png/tmC.png (PNG copy)> <./chapters/vynnytska/png/visC.png (PNG copy )> <./chapters/vynnytska/png/tmD.png (PNG copy)> <./chapters/vynnytska/png/visD .png (PNG copy)> <./chapters/vynnytska/png/tmE.png (PNG copy)> <./chapters/vynn ytska/png/visE.png (PNG copy)> <./chapters/vynnytska/png/tmF.png (PNG copy)> <. /chapters/vynnytska/png/visF.png (PNG copy)> <./chapters/vynnytska/png/tmG.png (PNG copy)> <./chapters/vynnytska/png/visG.png (PNG copy)> <./chapters/vynnytsk a/png/tmleg.png (PNG copy)> <./chapters/vynnytska/png/visleg.png (PNG copy)>] [602 <./chapters/vynnytska/png/tmH.png (PNG copy)> <./chapters/vynnytska/png/vi sH.png (PNG copy)> <./chapters/vynnytska/png/tmI.png (PNG copy)> <./chapters/vy nnytska/png/visI.png (PNG copy)> <./chapters/vynnytska/png/tmJ.png (PNG copy)> <./chapters/vynnytska/png/visJ.png (PNG copy)> <./chapters/vynnytska/png/tmK.pn g (PNG copy)> <./chapters/vynnytska/png/visK.png (PNG copy)> <./chapters/vynnyt ska/png/tmL.png (PNG copy)> <./chapters/vynnytska/png/visL.png (PNG copy)> <./c hapters/vynnytska/png/tmM.png (PNG copy)> <./chapters/vynnytska/png/visM.png (P NG copy)>]) (./tex/32.tex Chapter 32. [603] [604] Underfull \vbox (badness 1496) has occurred while \output is active [605] Underfull \vbox (badness 10000) has occurred while \output is active [606] [607] [608] [609 <./chapters/schroll/pdf/h0_typica l.pdf> <./chapters/schroll/pdf/h_typical.pdf>] [610 <./chapters/schroll/pdf/a1a 2scan4.pdf> <./chapters/schroll/pdf/a1a2scan4-5.pdf> <./chapters/schroll/pdf/b1 b2scan4.pdf> <./chapters/schroll/pdf/b1b2scan4-5.pdf> <./chapters/schroll/pdf/4 Dscan3.pdf> <./chapters/schroll/pdf/4Dscan3-5.pdf>] [611 <./chapters/schroll/pdf/4Dscan 3b.pdf> <./chapters/schroll/pdf/4Dscan3b-5.pdf> <./chapters/schroll/pdf/4Dsampl e3-5.pdf> <./chapters/schroll/pdf/4Dsample3b-5.pdf> <./chapters/schroll/pdf/4D- 1scan4b.pdf> <./chapters/schroll/pdf/4D-1scan4b-5.pdf>]) (./tex/33.tex [612] Chapter 33. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 23. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `superscript' on input line 23. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding), (hyperref) removing `math shift' on input line 23. [613] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [614 <./chapters/hake/pdf/morphology.pdf>] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [615] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [616 <./chapters/hake/pdf/markov_models.pdf>] Underfull \vbox (badness 1231) has occurred while \output is active Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [617] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [618] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [619] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [620] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [621 <./chapters/hake/pdf/error_plot.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [622 <./chapters/hake/pdf/traces_mesh_1.pdf>] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [623 <./chapters/hake/pdf/traces_mesh_2.pdf>] Underfull \hbox (badness 3965) in paragraph at lines 844--844 []\T1/pplx/m/n/9 (+20) Figure 33.7: |Di-a-gram for the Underfull \hbox (badness 6316) in paragraph at lines 844--844 \T1/pplx/m/n/9 (+20) time step-ping al-go-rithm us-ing Underfull \hbox (badness 3769) in paragraph at lines 844--844 \T1/pplx/m/n/9 (+20) 3 dis-crete ob-jects: \T1/fvm/m/n/9 DtExpander\T1/pplx/m/n /9 (+20) , Underfull \vbox (badness 10000) has occurred while \output is active Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [624 <./chapters/hake/pdf/traces_mesh_3.pdf> <./chapters/hake/pdf/timeline.pdf> ] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [625] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [626]) (./tex/34.tex Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [627] Package Fancyhdr Warning: \headheight is too small (12.0pt): Make it at least 12.79222pt. We now make it that large for the rest of the document. This may cause the page layout to be inconsistent, however. [628] Chapter 34. Underfull \vbox (badness 10000) has occurred while \output is active [629] [630] (./chapters/lezar/svg/arbitrary_waveguide_cross_section.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/arbitrary_waveguide_cross_s ection.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [631 <./chapter s/lezar/svg/arbitrary_waveguide_cross_section.pdf>] [632] [633] (./chapters/lezar/svg/rectangular_fenics_mesh.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/rectangular_fenics_mesh.pdf ): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [634 <./chapters/le zar/svg/rectangular_fenics_mesh.pdf>] [635] [636] (./chapters/lezar/svg/hollow_rectangular_waveguide.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_rectangular_waveguid e.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allow ed ) Underfull \vbox (badness 4024) has occurred while \output is active [637 <./cha pters/lezar/svg/hollow_rectangular_waveguide.pdf>] (./chapters/lezar/svg/hollow_cutoff_TE.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_cutoff_TE.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) (./chapters/lezar/svg/hollow_cutoff_TM.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_cutoff_TM.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) (./chapters/lezar/svg/hollow_rectangular_waveguide_dispersion_curve.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/hollow_rectangular_waveguid e_dispersion_curve.pdf): PDF inclusion: found PDF version <1.5>, but at most ve rsion <1.4> allowed ) [638 <./chapters/lezar/svg/hollow_cutoff_TE.pdf> <./chapters/lezar/svg/hollow_c utoff_TM.pdf>] (./chapters/lezar/svg/half_filled_rectangular_waveguide.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_rectangular_wav eguide.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) (./chapters/lezar/svg/half_filled_cutoff_TE.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_cutoff_TE.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) [639 <./chapters/lezar /svg/hollow_rectangular_waveguide_dispersion_curve.pdf> <./chapters/lezar/svg/h alf_filled_rectangular_waveguide.pdf>] (./chapters/lezar/svg/half_filled_cutoff_TM.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_cutoff_TM.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \hbox (badness 2698) in paragraph at lines 848--848 []\T1/pplx/m/n/9 (+20) Figure 34.9: |The fourth cal-cu- [640 <./chapters/lezar/svg/half_filled_cutoff_TE.pdf> <./chapters/lezar/svg/hal f_filled_cutoff_TM.pdf>] (./chapters/lezar/svg/half_filled_rectangular_waveguide_dispersion_curve.pdf_te x pdfTeX warning: pdflatex (file ./chapters/lezar/svg/half_filled_rectangular_wav eguide_dispersion_curve.pdf): PDF inclusion: found PDF version <1.5>, but at mo st version <1.4> allowed ) (./chapters/lezar/svg/shielded_microstrip_waveguide.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/shielded_microstrip_wavegui de.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allo wed ) [641 <./chapters/lezar/svg/half_filled_rectangular_waveguide_dispersion_curve.p df> <./chapters/lezar/svg/shielded_microstrip_waveguide.pdf>] (./chapters/lezar/svg/boxed_microstrip_dispersion_curves.pdf_tex pdfTeX warning: pdflatex (file ./chapters/lezar/svg/boxed_microstrip_dispersion _curves.pdf): PDF inclusion: found PDF version <1.5>, but at most version <1.4> allowed )) (./tex/35.tex [642 <./chapters/lezar/svg/boxed_microstrip_dispersion_curves.pdf>] Chapter 35. Underfull \vbox (badness 3281) has occurred while \output is active [643] (./chapters/mardal-4/pdf/block.pdf_tex pdfTeX warning: pdflatex (file ./chapters/mardal-4/pdf/block.pdf): PDF inclusio n: found PDF version <1.5>, but at most version <1.4> allowed ) Underfull \vbox (badness 2443) has occurred while \output is active [644 <./cha pters/mardal-4/pdf/block.pdf>] [645] [646] [647] [648] [649] Underfull \vbox (badness 2512) has occurred while \output is active [650] [651] [652] [653]) (./tex/36.tex [654] Chapter 36. [655] [656] [657 <./chapters/rognes/pdf/CG.pdf> <./c hapters/rognes/pdf/RT.pdf>] [658] Underfull \vbox (badness 6188) has occurred while \output is active [659] [660] [661] [662] [663] [664] [665] [666] [667] [668]) [669] [670] (./tex/BM1.tex Underfull \vbox (badness 10000) has occurred while \output is active [671] Underfull \vbox (badness 10000) has occurred while \output is active [672] Underfull \vbox (badness 10000) has occurred while \output is active [673] Underfull \vbox (badness 10000) has occurred while \output is active [674] Underfull \vbox (badness 10000) has occurred while \output is active [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] (./book.ind [713] [714] [715] [716] [717] Overfull \hbox (7.21391pt too wide) in paragraph at lines 435--437 []\T1/pplx/m/n/10 (-20) LBB con-di-tions, \T1/pplx/m/it/10 see \T1/pplx/m/n/10 (-20) Ladyzhenskaya--BabuČka--Brezzi [718] [719] [720])) Package caption Warning: Unused \captionsetup[subalgorithm] on input line 14. (./book.aux) LaTeX Font Warning: Size substitutions with differences (Font) up to 0.43996pt have occurred. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Hfootnote.38} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.37} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.36} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.35} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.34} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.33} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.32} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.31} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.30} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.29} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.28} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.27} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.26} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.25} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.24} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.23} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.22} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.21} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.20} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.19} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.18} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.17} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.16} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.15} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.14} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.13} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.12} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.11} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.10} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.9} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.8} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.7} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.6} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.5} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.4} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.3} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.2} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Hfootnote.1} has been referenced but does not exist , replaced by a fixed one {/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc} Output written on book.pdf (732 pages, 66379724 bytes). Transcript written on book.log. make: Leaving directory `/usr/src/RPM/BUILD/fenics-book-20130430' + exit 0 Processing files: fenics-book-20130430-alt1 Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.10998 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd fenics-book-20130430 + DOCDIR=/usr/src/tmp/fenics-book-buildroot/usr/share/doc/fenics-book-20130430 + export DOCDIR + rm -rf /usr/src/tmp/fenics-book-buildroot/usr/share/doc/fenics-book-20130430 + /bin/mkdir -p /usr/src/tmp/fenics-book-buildroot/usr/share/doc/fenics-book-20130430 + cp -prL book.pdf /usr/src/tmp/fenics-book-buildroot/usr/share/doc/fenics-book-20130430 + chmod -R go-w /usr/src/tmp/fenics-book-buildroot/usr/share/doc/fenics-book-20130430 + chmod -R a+rX /usr/src/tmp/fenics-book-buildroot/usr/share/doc/fenics-book-20130430 + exit 0 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.Rw6i1j find-provides: running scripts (alternatives,debuginfo,lib,pam,perl,pkgconfig,python,shell) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.f1a0lm find-requires: running scripts (cpp,debuginfo,files,lib,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks) Wrote: /usr/src/RPM/RPMS/noarch/fenics-book-20130430-alt1.noarch.rpm 132.05user 1.53system 2:55.66elapsed 76%CPU (0avgtext+0avgdata 85368maxresident)k 0inputs+0outputs (0major+78173minor)pagefaults 0swaps 201.89user 7.98system 4:50.47elapsed 72%CPU (0avgtext+0avgdata 142084maxresident)k 0inputs+0outputs (0major+1140208minor)pagefaults 0swaps