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Commit 74d273af authored by Spencer Sherwin's avatar Spencer Sherwin
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Merge branch 'fix/doc' into 'master' 

Fix/doc

This MR fixes a number of content and formatting issues with the user guide and developers guide. It adds some missing options and features in the earlier section of the user guide. The formatting and quality of the HTML output is improved with a number of fixes for tables, note/tip boxes and the CSS, although still not perfect.

See merge request !485
parents df13e623 a7c15680
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docs/developer-guide/CMakeLists.txt
+ 24
− 4
View file @ 74d273af
......@@ -5,19 +5,39 @@ FILE(MAKE_DIRECTORY ${DEVGUIDE}/html)
FIND_PROGRAM(HTLATEX htlatex)
ADD_CUSTOM_TARGET(developer-guide-html
export TEXINPUTS=${DEVGUIDESRC}//: && ${HTLATEX} ${DEVGUIDESRC}/developer-guide.tex
"${DEVGUIDESRC}/styling.cfg,html,2,next,NoFonts"
export TEXINPUTS=${CMAKE_SOURCE_DIR}//:${DEVGUIDESRC}//: &&
${HTLATEX} ${DEVGUIDESRC}/developer-guide.tex
"${DEVGUIDESRC}/styling.cfg,html,3,next,NoFonts"
WORKING_DIRECTORY ${DEVGUIDE}/html
)
# If tex4ht successful, create img dir and copy images across
FILE(GLOB_RECURSE imgfiles "*/img/*.png" "*/img/*.jpg")
ADD_CUSTOM_COMMAND(TARGET developer-guide-html
POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${DEVGUIDE}/html/img)
FOREACH(img ${imgfiles})
ADD_CUSTOM_COMMAND(TARGET developer-guide-html
POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy ${img} ${DEVGUIDE}/html/img)
ENDFOREACH()
FILE(GLOB_RECURSE pdffiles "*/img/*.pdf")
FIND_PROGRAM(CONVERT convert)
FOREACH(pdf ${pdffiles})
GET_FILENAME_COMPONENT(BASENAME ${pdf} NAME_WE)
ADD_CUSTOM_COMMAND(TARGET developer-guide-html
POST_BUILD COMMAND
${CONVERT} ${pdf} ${DEVGUIDE}/html/img/${BASENAME}.png)
ENDFOREACH()
FIND_PROGRAM(PDFLATEX pdflatex)
FIND_PROGRAM(BIBTEX bibtex)
FIND_PROGRAM(MAKEINDEX makeindex)
ADD_CUSTOM_TARGET(developer-guide-pdf
export TEXINPUTS=${CMAKE_SOURCE_DIR}//: &&
${PDFLATEX} --output-directory ${DEVGUIDE} ${DEVGUIDESRC}/developer-guide.tex
COMMAND TEXMFOUTPUT=${DEVGUIDE} ${BIBTEX} ${DEVGUIDE}/developer-guide.aux
COMMAND TEXMFOUTPUT=${DEVGUIDE} ${MAKEINDEX} ${DEVGUIDE}/developer-guide.idx
COMMAND ${PDFLATEX} --output-directory ${DEVGUIDE}
${DEVGUIDESRC}/developer-guide.tex
COMMAND export TEXINPUTS=${CMAKE_SOURCE_DIR}//: &&
${PDFLATEX} --output-directory ${DEVGUIDE} ${DEVGUIDESRC}/developer-guide.tex
WORKING_DIRECTORY ${DEVGUIDESRC}
)
docs/developer-guide/developer-guide.tex
+ 34
− 8
View file @ 74d273af
......@@ -25,8 +25,10 @@ openany, % A chapter may start on either a recto or verso page.
% \usepackage{kpfonts} %Font
\usepackage{amsmath,amssymb,mathtools} % Math
\usepackage{pifont}% http://ctan.org/pkg/pifont
\newcommand{\cmark}{\ding{51}}%
\newcommand{\xmark}{\ding{55}}%
% \usepackage{tikz} % Figures
\usepackage{graphicx} % Include figures
\usepackage{makeidx}
\usepackage{import}
......@@ -48,8 +50,8 @@ openany, % A chapter may start on either a recto or verso page.
%%% SECTIONAL DIVISIONS
%%%------------------------------------------------------------------------------
\maxsecnumdepth{subsection} % Subsections (and higher) are numbered
\setsecnumdepth{subsection}
\maxsecnumdepth{paragraph} % Subsections (and higher) are numbered
\setsecnumdepth{paragraph}
\makeatletter %
\makechapterstyle{standard}{
......@@ -92,6 +94,7 @@ openany, % A chapter may start on either a recto or verso page.
\changecaptionwidth % Change the width of the caption
\captionwidth{1\textwidth} %
\usepackage{tabularx}
%%% ABSTRACT
%%%------------------------------------------------------------------------------
......@@ -144,6 +147,9 @@ openany, % A chapter may start on either a recto or verso page.
%%% NEW COMMANDS
%%%-----------------------------------------------------------------------------
% Nektar++ version
\usepackage{xspace}
\newcommand{\nekver} {\input{VERSION}\unskip}
\newcommand{\p}{\partial} %Partial
% Or what ever you want
......@@ -154,7 +160,6 @@ openany, % A chapter may start on either a recto or verso page.
\usepackage{xcolor}
\usepackage{listings} % Display code / shell commands
\usepackage{lstautogobble}
\usepackage{xspace}
%\newcommand{\shellcommand}[1]{\begin{lstlisting} \#1 \end{lstlisting}
\lstdefinestyle{BashInputStyle}{
language=bash,
......@@ -214,16 +219,30 @@ openany, % A chapter may start on either a recto or verso page.
}
\usepackage{tikz}
\ifdefined\HCode
\newcommand{\inltt}[1]{\texttt{#1}}
\newcommand{\inlsh}[1]{\texttt{#1}}
\else
\newcommand{\inltt}[1]{\tikz[anchor=base,baseline]\node[inner sep=3pt,
rounded corners,outer sep=0,draw=black!30,fill=black!05]{\small\texttt{#1}};}
\newcommand{\inlsh}[1]{\tikz[anchor=base,baseline]\node[inner sep=2pt,
outer sep=0,fill=black!05]{\texttt{#1}};}
\fi
\newcommand{\nekpp}{{\em Nektar++}\xspace}
% Highlight box
\usepackage{environ}
\usepackage[tikz]{bclogo}
\usetikzlibrary{calc}
% Only use fancy boxes for PDF
\ifdefined\HCode
\NewEnviron{notebox}{\textbf{Note:} \BODY}
\NewEnviron{warningbox}{\textbf{Warning:} \BODY}
\NewEnviron{tipbox}{\textbf{Tip:} \BODY}
\NewEnviron{custombox}[3]{\textbf{#1} \BODY}
\else
\NewEnviron{notebox}
{\par\medskip\noindent
\begin{tikzpicture}
......@@ -284,6 +303,7 @@ outer sep=0,fill=black!05]{\texttt{#1}};}
};
\end{tikzpicture}\par\medskip%
}
\fi
%%% TABLE OF CONTENTS AND INDEX
%%%-----------------------------------------------------------------------------
......@@ -297,13 +317,13 @@ outer sep=0,fill=black!05]{\texttt{#1}};}
%%% INTERNAL HYPERLINKS
%%%-----------------------------------------------------------------------------
\usepackage[linktoc=all]{hyperref} % Internal hyperlinks
\usepackage[linktoc=all,hyperfootnotes=false]{hyperref} % Internal hyperlinks
\hypersetup{
colorlinks,
citecolor=darkblue,
filecolor=darkblue,
linkcolor=darkblue,
urlcolor=darkblue
urlcolor=darkblue,
pdfborder={0 0 0}, % No borders around internal hyperlinks
pdfauthor={I am the Author} % author
}
......@@ -330,7 +350,7 @@ pdfauthor={I am the Author} % author
\vspace{\drop}
{\Huge\bfseries\raggedright\@title\par}
\vskip2.37\baselineskip
{\huge\bfseries Version \input{../../VERSION}\par}
{\huge\bfseries Version \nekver\par}
\vskip4\baselineskip
{\huge\bfseries \textcolor{darkblue}{Developer Guide}\par}
\vskip1.0\baselineskip
......@@ -349,7 +369,7 @@ pdfauthor={I am the Author} % author
%%% Where all the important stuff is included!
%%%-------------------------------------------------------------------------------
\author{Department of Aeronautics, Imperial College London, UK\\
\author{Department of Aeronautics, Imperial College London, UK\newline
Scientific Computing and Imaging Institute, University of Utah, USA}
\title{Nektar++: Spectral/hp Element Framework}
\date{\today}
......@@ -361,6 +381,9 @@ Scientific Computing and Imaging Institute, University of Utah, USA}
% Render pretty title page if not building HTML
\ifdefined\HCode
\maketitle
\begin{center}
\huge{Developers Guide - Version \nekver}
\end{center}
\else
\titlepage
\fi
......@@ -411,6 +434,9 @@ information.
This document is still under development and may be incomplete in parts.
\end{warningbox}
For further information and to download the software, visit the Nektar++ website
at \url{http://www.nektar.info}.
\mainmatter
\import{core-concepts/}{core-concepts.tex}
......
docs/developer-guide/memoir.4ht 0 → 100644
+ 68
− 0
View file @ 74d273af
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% memoir.4ht 2009-05-21-09:32 %
% Copyright (C) 2003--2009 Eitan M. Gurari %
% %
% This work may be distributed and/or modified under the %
% conditions of the LaTeX Project Public License, either %
% version 1.3c of this license or (at your option) any %
% later version. The latest version of this license is %
% in %
% http://www.latex-project.org/lppl.txt %
% and version 1.3c or later is part of all distributions %
% of LaTeX version 2005/12/01 or later. %
% %
% This work has the LPPL maintenance status "maintained".%
% %
% This Current Maintainer of this work %
% is Eitan M. Gurari. %
% %
% If you modify this program your changing its signature %
% with a directive of the following form will be %
% appreciated. %
% \message{signature} %
% %
% gurari@cse.ohio-state.edu %
% http://www.cse.ohio-state.edu/~gurari %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\immediate\write-1{version 2009-05-21-09:32}
\input book.4ht
\input verse.4ht
% Tables Handling
\input array.4ht
\input dcolumn.4ht
\input tabularx.4ht
\input booktabs.4ht
\let\rm\empty
\let\sf\empty
\let\tt\empty
\let\bf\empty
\let\it\empty
\def\@chapter[#1]#2{%
\gHAdvance\:mpNum by 1
\HAssign\minipageNum=\:mpNum \relax
%
{\SkipRefstepAnchor \let\addcontentsline\:gobbleIII\no@chapter[#1]{}%
\global\let\f@rtoc\f@rtoc
\global\let\f@rhdr\f@rhdr }%
\HtmlEnv \Toc:Title{#1}\:chapter{#2}}
\NewConfigure{poemline}{2}
\ifx \memgobble\:UnDef
\pend:defI\getthelinenumber{%
\let\sv:thepoemline\thepoemline
\pend:def\thepoemline{\a:poemline}%
\append:def\thepoemline{\b:poemline}}
\append:defI\getthelinenumber{\let\thepoemline\sv:thepoemline}
\else
\pend:defII\getthelinenumber{%
\let\sv:thepoemline\thepoemline
\pend:def\thepoemline{\a:poemline}%
\append:def\thepoemline{\b:poemline}}
\append:defII\getthelinenumber{\let\thepoemline\sv:thepoemline}
\fi
\Hinput{memoir}
\endinput
docs/developer-guide/styling.cfg
+ 66
− 3
View file @ 74d273af
\Preamble{html}
\begin{document}
\Css{
h2 {color: \#000000; }
\Configure{graphics*}
{pdf}
{\Picture[pict]{\csname Gin@base\endcsname.png}}
%% Use HTML for italics and bold
\Configure{emph}{\ifvmode\ShowPar\fi\HCode{<em>}}{\HCode{</em>}}
\Configure{textbf}{\ifvmode\ShowPar\fi\HCode{<b>}}{\HCode{</b>}}
\Configure{texttt}{\ifvmode\ShowPar\fi\HCode{<code>}}{\HCode{</code>}}
\ConfigureEnv{notebox}{\ifvmode\ShowPar\fi\HCode{<div class="notebox">}}{\HCode{</div>}} {} {}
\ConfigureEnv{warningbox}{\ifvmode\ShowPar\fi\HCode{<div class="warningbox">}}{\HCode{</div>}} {} {}
\ConfigureEnv{tipbox}{\ifvmode\ShowPar\fi\HCode{<div class="tipbox">}}{\HCode{</div>}} {} {}
%% Remove div indents
\Configure{HtmlPar}
{\EndP\Tg<p>}
{\EndP\Tg<p>}
{\HCode{</p>\Hnewline}}
{\HCode{</p>\Hnewline}}
\begin{document}
\DeclareGraphicsExtensions{.pdf,.eps,.png,.jpg,.mp,.mps}
\Css{
body {
margin: 0 auto;
max-width: 800px;
background: \#ffffff;
font-family: "Helvetica Neue", Arial, Freesans, clean, sans-serif;
}
h2 {color: \#000000; text-align: right; font-size: 32pt;}
.chapterHead .titlemark {
font-size: 20pt;
}
a {
color: \#000066;
text-decoration: none;
......@@ -9,6 +39,18 @@
a:hover {
color: \#0000ff;
}
img {
max-width: 800px;
}
.figure {
text-align: center;
}
div .caption {
text-align: center;
}
.author {
font-size: 14pt;
}
.lstlisting {
background: \#eeeeee;
margin-left: 20px;
......@@ -20,6 +62,27 @@
padding: 2px;
font-family: "Lucida Console", Monaco, monospace;
}
.notebox {
border: 1px solid \#999999;
border-radius: 10px;
background: \#bbbbbb;
padding: 10px;
margin: 10px;
}
.warningbox {
border: 1px solid \#999999;
border-radius: 10px;
background: \#ffbbbb;
padding: 10px;
margin: 10px;
}
.tipbox {
border: 1px solid \#999999;
border-radius: 10px;
background: \#bbffbb;
padding: 10px;
margin: 10px;
}
}
\EndPreamble
docs/refs.bib
+ 2
− 0
View file @ 74d273af
......@@ -301,7 +301,9 @@ year={2011}
title={Nektar++: An open-source spectral/hp element framework},
author={Cantwell, CD and Moxey, D and Comerford, A and Bolis, A and Rocco, G and Mengaldo, G and De Grazia, D and Yakovlev, S and Lombard, J-E and Ekelschot, D and others},
journal={Computer Physics Communications},
volume={192},
year={2015},
pages={205-219},
publisher={Elsevier}
}
......
docs/user-guide/CMakeLists.txt
+ 26
− 4
View file @ 74d273af
......@@ -6,11 +6,32 @@ FILE(MAKE_DIRECTORY ${USERGUIDE}/html)
FIND_PROGRAM(HTLATEX htlatex)
MARK_AS_ADVANCED(HTLATEX)
ADD_CUSTOM_TARGET(user-guide-html
export TEXINPUTS=${USERGUIDESRC}//: && ${HTLATEX} ${USERGUIDESRC}/user-guide.tex
"${USERGUIDESRC}/styling.cfg,html,2,next,NoFonts"
export TEXINPUTS=${CMAKE_SOURCE_DIR}//:${USERGUIDESRC}//: &&
${HTLATEX} ${USERGUIDESRC}/user-guide.tex
"${USERGUIDESRC}/styling.cfg,html,3,next,NoFonts"
WORKING_DIRECTORY ${USERGUIDE}/html
)
# If tex4ht successful, create img dir and copy images across
FILE(GLOB_RECURSE imgfiles "*/img/*.png" "*/img/*.jpg")
ADD_CUSTOM_COMMAND(TARGET user-guide-html
POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${USERGUIDE}/html/img)
FOREACH(img ${imgfiles})
ADD_CUSTOM_COMMAND(TARGET user-guide-html
POST_BUILD COMMAND
${CMAKE_COMMAND} -E copy ${img} ${USERGUIDE}/html/img)
ENDFOREACH()
FILE(GLOB_RECURSE pdffiles "*/img/*.pdf")
FIND_PROGRAM(CONVERT convert)
FOREACH(pdf ${pdffiles})
GET_FILENAME_COMPONENT(BASENAME ${pdf} NAME_WE)
ADD_CUSTOM_COMMAND(TARGET user-guide-html
POST_BUILD COMMAND
${CONVERT} ${pdf} ${USERGUIDE}/html/img/${BASENAME}.png)
ENDFOREACH()
FIND_PROGRAM(PDFLATEX pdflatex)
MARK_AS_ADVANCED(PDFLATEX)
FIND_PROGRAM(BIBTEX bibtex)
......@@ -19,10 +40,11 @@ FIND_PROGRAM(MAKEINDEX makeindex)
MARK_AS_ADVANCED(MAKEINDEX)
ADD_CUSTOM_TARGET(user-guide-pdf
export TEXINPUTS=${CMAKE_SOURCE_DIR}//: &&
${PDFLATEX} --output-directory ${USERGUIDE} ${USERGUIDESRC}/user-guide.tex
COMMAND TEXMFOUTPUT=${USERGUIDE} ${BIBTEX} ${USERGUIDE}/user-guide.aux
COMMAND TEXMFOUTPUT=${USERGUIDE} ${MAKEINDEX} ${USERGUIDE}/user-guide.idx
COMMAND ${PDFLATEX} --output-directory ${USERGUIDE}
${USERGUIDESRC}/user-guide.tex
COMMAND export TEXINPUTS=${CMAKE_SOURCE_DIR}//: &&
${PDFLATEX} --output-directory ${USERGUIDE} ${USERGUIDESRC}/user-guide.tex
WORKING_DIRECTORY ${USERGUIDESRC}
)
docs/user-guide/faq/faq.tex
+ 13
− 1
View file @ 74d273af
......@@ -58,6 +58,18 @@ to the end, replacing
\end{itemize}
\textbf{Q. When compiling Nektar++ Thirdparty libraries I get an error ``CMake Error: Problem extracting tar''}
Nektar++ tries to download the appropriate ThirdParty
libraries. However if the download protocols are restricted on your
computer this may fail leading to the error ```CMake Error: Problem
extracting tar''. These libraries are available from
\hspace{1cm} \inlsh{http://www.nektar.info/thirdparty/}
and can be downloaded directly into the
\inlsh{\${NEKTAR\_HOME}/ThirdParty} directory
\section{Usage}
\textbf{Q. How do I run a solver in parallel?}
......@@ -82,4 +94,4 @@ formats include:
\item Polygon (.ply)
\item Nektar (.rea)
\item Semtex (.sem)
\end{itemize}
\ No newline at end of file
\end{itemize}
docs/user-guide/installation/installation.tex
+ 3
− 3
View file @ 74d273af
\chapter{Installation}
Nektar++ is available in both a source-code distribution and a number of
Nektar++ is available in both a source-code distribution and as
pre-compiled binary packages for a number of operating systems. We recommend
using the pre-compiled packages if you wish to use existing Nektar++ solvers for
simulation and do not need to perform additional code development.
using the pre-compiled packages if you wish to use the existing Nektar++
solvers for simulation and do not need to perform additional code development.
\input{precompiled}
......
docs/user-guide/installation/precompiled.tex
+ 5
− 3
View file @ 74d273af
......@@ -14,10 +14,12 @@ available.
\toprule
Distribution & Repository \\
\midrule
Debian 8.0 (jessie) &
\texttt{deb http://www.nektar.info/debian-jessie jessie contrib} \\
Debian 7.0 (wheezy) &
\texttt{deb http://www.nektar.info/debian wheezy contrib} \\
\texttt{deb http://www.nektar.info/debian-wheezy wheezy contrib} \\
Ubuntu 14.04 (trusty) &
\texttt{deb http://www.nektar.info/ubuntu trusty contrib}\\
\texttt{deb http://www.nektar.info/ubuntu-trusty trusty contrib}\\
\bottomrule
\end{tabular}
}
......@@ -25,7 +27,7 @@ available.
\begin{lstlisting}[style=BashInputStyle]
apt-get update
\end{lstlisting}
\item Install the required Nektar++ packages:
\item Install the required Nektar++ packages, or the complete suite with:
\begin{lstlisting}[style=BashInputStyle]
apt-get install nektar++
\end{lstlisting}
......
docs/user-guide/installation/source.tex
+ 20
− 1
View file @ 74d273af
......@@ -22,7 +22,7 @@ There are two ways to obtain the source code for \nekpp:
\item Using anonymous access. This does not require
credentials but any changes to the code cannot be pushed to the
public repository. Use this initially if you would like to try using
Nektar++.
Nektar++ or make local changes to the code.
\begin{lstlisting}[style=BashInputStyle]
git clone http://gitlab.nektar.info/clone/nektar/nektar.git nektar++
\end{lstlisting}
......@@ -521,6 +521,10 @@ A number of ThirdParty libraries are required by \nekpp. There are
also optional libraries which provide additional functionality. These
can be selected using the following options:
\begin{itemize}
\item \inlsh{NEKTAR\_USE\_ACML}
Use the optimised BLAS library for AMD processors.
\item \inlsh{NEKTAR\_USE\_ACCELERATE\_FRAMEWORK}
Use the Mac Osx accelerate framework for BLAS and LAPACK
......@@ -576,6 +580,21 @@ can be selected using the following options:
implementation and generally offers better performance than a non-optimised
system BLAS. However, the library must be installed on the system.
\item \inlsh{NEKTAR\_USE\_PETSC}
Build \nekpp with support for the PETSc package for solving linear systems.
\item \inlsh{NEKTAR\_USE\_SCOTCH}
Build \nekpp with support for the SCOTCH graph partitioning library. This
provides an alternative mesh partitioning algorithm to METIS. However, METIS
is still required as it is used by the multi-level static condensation
algorithm.
\item \inlsh{NEKTAR\_USE\_SMV}
Build \nekpp with support for optimised sparse matrix-vector operations.
\item \inlsh{NEKTAR\_USE\_VTK}
Build \nekpp with support for VTK libraries. This is only needed for
......
docs/user-guide/introduction/introduction.tex
+ 4
− 1
View file @ 74d273af
......@@ -26,4 +26,7 @@ Our current goals are to develop:
only $h$ and $p$ but also hardware considerations and mesh connectivity.
\item Temporal and spatial adaption.
\item Features enabling evaluation of high-order meshing techniques.
\end{itemize}
\ No newline at end of file
\end{itemize}
For further information and to download the software, visit the Nektar++ website
at \url{http://www.nektar.info}.
docs/user-guide/memoir.4ht 0 → 100644
+ 68
− 0
View file @ 74d273af
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% memoir.4ht 2009-05-21-09:32 %
% Copyright (C) 2003--2009 Eitan M. Gurari %
% %
% This work may be distributed and/or modified under the %
% conditions of the LaTeX Project Public License, either %
% version 1.3c of this license or (at your option) any %
% later version. The latest version of this license is %
% in %
% http://www.latex-project.org/lppl.txt %
% and version 1.3c or later is part of all distributions %
% of LaTeX version 2005/12/01 or later. %
% %
% This work has the LPPL maintenance status "maintained".%
% %
% This Current Maintainer of this work %
% is Eitan M. Gurari. %
% %
% If you modify this program your changing its signature %
% with a directive of the following form will be %
% appreciated. %
% \message{signature} %
% %
% gurari@cse.ohio-state.edu %
% http://www.cse.ohio-state.edu/~gurari %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\immediate\write-1{version 2009-05-21-09:32}
\input book.4ht
\input verse.4ht
% Tables Handling
\input array.4ht
\input dcolumn.4ht
\input tabularx.4ht
\input booktabs.4ht
\let\rm\empty
\let\sf\empty
\let\tt\empty
\let\bf\empty
\let\it\empty
\def\@chapter[#1]#2{%
\gHAdvance\:mpNum by 1
\HAssign\minipageNum=\:mpNum \relax
%
{\SkipRefstepAnchor \let\addcontentsline\:gobbleIII\no@chapter[#1]{}%
\global\let\f@rtoc\f@rtoc
\global\let\f@rhdr\f@rhdr }%
\HtmlEnv \Toc:Title{#1}\:chapter{#2}}
\NewConfigure{poemline}{2}
\ifx \memgobble\:UnDef
\pend:defI\getthelinenumber{%
\let\sv:thepoemline\thepoemline
\pend:def\thepoemline{\a:poemline}%
\append:def\thepoemline{\b:poemline}}
\append:defI\getthelinenumber{\let\thepoemline\sv:thepoemline}
\else
\pend:defII\getthelinenumber{%
\let\sv:thepoemline\thepoemline
\pend:def\thepoemline{\a:poemline}%
\append:def\thepoemline{\b:poemline}}
\append:defII\getthelinenumber{\let\thepoemline\sv:thepoemline}
\fi
\Hinput{memoir}
\endinput
docs/user-guide/solvers/adr.tex
+ 11
− 11
View file @ 74d273af
\chapter{ADRSolver}
\chapter{Advection-Diffusion-Reaction Solver}
%3.4/UserGuide/Tutorial/ADRSolver
%3.4/UserGuide/Examples/ADRSolver/1DAdvection
......@@ -78,10 +78,10 @@ The solver info are listed below:
\textbf{EqType} & \textbf{Explicit} & \textbf{Diagonally Implicit} &
\textbf{ IMEX} & \textbf{Implicit} \\
\midrule
\inltt{UnstedayAdvection} & \checkmark & & &\\
\inltt{UnstedayDifusion} & \checkmark & \checkmark & &\\
\inltt{UnstedayAdvectionDiffusion} & & & \checkmark &\\
\inltt{UnstedayInviscidBurger} & \checkmark & & &\\
\inltt{UnsteadyAdvection} & \checkmark & & &\\
\inltt{UnsteadyDiffusion} & \checkmark & \checkmark & &\\
\inltt{UnsteadyAdvectionDiffusion} & & & \checkmark &\\
\inltt{UnsteadyInviscidBurger} & \checkmark & & &\\
\bottomrule
\end{tabular}
\end{center}
......@@ -95,7 +95,7 @@ The solver info are listed below:
\begin{itemize}
\item \inltt{Explicit} Requires the use of an explicit time integration
scheme.
\item \inltt{Implcit} Requires the use of a diagonally implicit, IMEX or
\item \inltt{Implicit} Requires the use of a diagonally implicit, IMEX or
Implicit scheme.
\end{itemize}
\item \textbf{AdvectionAdvancement}: This specifies how to treat the advection term. This will be restricted by the choice of time integration scheme:
......@@ -242,8 +242,8 @@ ADRSolver Advection1D.xml
To visualise the output, we can convert it into either TecPlot or VTK formats
\begin{lstlisting}[style=BashInputStyle]
FldToTecplot Advection1D.xml Advection1D.fld
FldToVtk Advection1D.xml Advection1D.fld
FieldConvert Advection1D.xml Advection1D.fld Advection1D.dat
FieldConvert Advection1D.xml Advection1D.fld Advection1D.vtu
\end{lstlisting}
......@@ -370,7 +370,7 @@ Fig.~\ref{f:adrsolver:helmholtz2D}
\begin{figure}
\begin{center}
\includegraphics[width=6cm]{Figures/Helmholtz2D}
\includegraphics[width=6cm]{img/Helmholtz2D}
\caption{Solution of the 2D Helmholtz Problem.}
\label{f:adrsolver:helmholtz2D}
\end{center}
......@@ -429,7 +429,7 @@ The geometry under consideration is a pipe of radius, $R = 0.5$ and length $l =
\begin{figure}[h!]
\begin{center}
\includegraphics[width=6cm]{Figures/pipe}
\includegraphics[width=6cm]{img/pipe}
\caption{Pipe.}
\end{center}
\end{figure}
......@@ -544,7 +544,7 @@ streamwise direction, as shown in Fig.~\ref{f:adrsolver:masstransport}.
\begin{figure}[h!]
\begin{center}
\includegraphics[width=7cm]{Figures/graetz-nusselt}
\includegraphics[width=7cm]{img/graetz-nusselt}
\caption{Concentration gradient at the surface of the pipe.}
\label{f:adrsolver:masstransport}
\end{center}
......
docs/user-guide/solvers/ape.tex
+ 5
− 5
View file @ 74d273af
......@@ -65,7 +65,7 @@ of $64$ quadrilateral elements, as shown in Fig.~\ref{f:apesolver:geometry}.
\begin{figure}
\centering
\includegraphics[width=0.5\linewidth]{Figures/APE_Geometry.png}
\includegraphics[width=0.5\linewidth]{img/APE_Geometry.png}
\caption{Geometry used for the example case of modelling propagation of
acoustic waves where $\overline{u}_i = 0, \, \overline{p}=p_{\infty}=10^6, \, \overline{\rho} = \rho_0 = 1.204$}
\label{f:apesolver:geometry}
......@@ -131,9 +131,9 @@ time steps, showing the acoustic propagation.
\begin{figure}
\centering
\includegraphics[width=0.3\linewidth]{Figures/Prop_1.png}
\includegraphics[width=0.3\linewidth]{Figures/Prop_2.png}
\includegraphics[width=0.3\linewidth]{Figures/Prop_3.png}
\includegraphics[width=0.3\linewidth]{img/Prop_1.png}
\includegraphics[width=0.3\linewidth]{img/Prop_2.png}
\includegraphics[width=0.3\linewidth]{img/Prop_3.png}
\caption{}
\label{f:apesolver:results}
\end{figure}
......@@ -146,7 +146,7 @@ predicted by literature \cite{DoFf83}.
\begin{figure}
\centering
\includegraphics[width=0.7\linewidth]{Figures/prog_4.png}
\includegraphics[width=0.7\linewidth]{img/prog_4.png}
\caption{}
\end{figure}
docs/user-guide/solvers/cardiac-ep.tex
+ 1
− 1
View file @ 74d273af
......@@ -2,7 +2,7 @@
\section{Synopsis}
The CardiacEPSolver is intended to model the electrophysiology of cardiac
The CardiacEPSolver is used to model the electrophysiology of cardiac
tissue, specifically using the monodomain or bidomain model. These models are
continuum models and represent an average of the electrical activity over many
cells. The system is a reaction-diffusion system, with the reaction term
......
docs/user-guide/solvers/compressible-flow.tex
+ 2
− 2
View file @ 74d273af
......@@ -454,8 +454,8 @@ For the non-smooth artificial viscosity model the added artificial viscosity is
\end{equation}
\begin{figure}[!htbp]
\begin{center}
\includegraphics[width = 0.47 \textwidth]{Figures/Mach_P4.pdf}
\includegraphics[width = 0.47 \textwidth]{Figures/ArtVisc_P4.pdf}
\includegraphics[width = 0.47 \textwidth]{img/Mach_P4.pdf}
\includegraphics[width = 0.47 \textwidth]{img/ArtVisc_P4.pdf}
\caption{(a) Steady state solution for $M=0.8$ flow at $\alpha = 1.25^\circ$ past a NACA 0012 profile, (b) Artificial viscosity ($\epsilon$) distribution}
\label{fig:}
\end{center}
......
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