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EXTRA_DIST = cantera.dox cantera.page txt_common fig_common
EXTRA_DIST += install.page tutorial.page
dist-hook:
rm -rf `find $(distdir)/ -name .svn`
rm -rf `find $(distdir)/ -name .deps`

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#-----------------------------------
# PECOS - add any additional doxygen
# dependencies here.
#-----------------------------------
PECOS_extra_dependencies = doxygen/cantera.page \
doxygen/txt_common/about.page \
doxygen/txt_common/gpl.page \
doxygen/txt_common/acknowledgment.page
## --------------------------------- ##
## Format-independent Doxygen rules. ##
## --------------------------------- ##
if DX_COND_doc
## ------------------------------- ##
## Rules specific for HTML output. ##
## ------------------------------- ##
if DX_COND_html
DX_CLEAN_HTML = @DX_DOCDIR@/html
endif DX_COND_html
## ------------------------------ ##
## Rules specific for CHM output. ##
## ------------------------------ ##
if DX_COND_chm
DX_CLEAN_CHM = @DX_DOCDIR@/chm
if DX_COND_chi
DX_CLEAN_CHI = @DX_DOCDIR@/@PACKAGE@.chi
endif DX_COND_chi
endif DX_COND_chm
## ------------------------------ ##
## Rules specific for MAN output. ##
## ------------------------------ ##
if DX_COND_man
DX_CLEAN_MAN = @DX_DOCDIR@/man
endif DX_COND_man
## ------------------------------ ##
## Rules specific for RTF output. ##
## ------------------------------ ##
if DX_COND_rtf
DX_CLEAN_RTF = @DX_DOCDIR@/rtf
endif DX_COND_rtf
## ------------------------------ ##
## Rules specific for XML output. ##
## ------------------------------ ##
if DX_COND_xml
DX_CLEAN_XML = @DX_DOCDIR@/xml
endif DX_COND_xml
## ----------------------------- ##
## Rules specific for PS output. ##
## ----------------------------- ##
if DX_COND_ps
DX_CLEAN_PS = @DX_DOCDIR@/@PACKAGE@.ps
DX_PS_GOAL = doxygen-ps
doxygen-ps: @DX_DOCDIR@/@PACKAGE@.ps
@DX_DOCDIR@/@PACKAGE@.ps: @DX_DOCDIR@/@PACKAGE@.tag
cd @DX_DOCDIR@/latex; \
rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
$(DX_LATEX) refman.tex; \
$(MAKEINDEX_PATH) refman.idx; \
$(DX_LATEX) refman.tex; \
countdown=5; \
while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
refman.log > /dev/null 2>&1 \
&& test $$countdown -gt 0; do \
$(DX_LATEX) refman.tex; \
countdown=`expr $$countdown - 1`; \
done; \
$(DX_DVIPS) -o ../@PACKAGE@.ps refman.dvi
endif DX_COND_ps
## ------------------------------ ##
## Rules specific for PDF output. ##
## ------------------------------ ##
if DX_COND_pdf
DX_CLEAN_PDF = @DX_DOCDIR@/@PACKAGE@.pdf
DX_PDF_GOAL = doxygen-pdf
doxygen-pdf: @DX_DOCDIR@/@PACKAGE@.pdf
@DX_DOCDIR@/@PACKAGE@.pdf: @DX_DOCDIR@/@PACKAGE@.tag
cd @DX_DOCDIR@/latex; \
rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
$(DX_PDFLATEX) refman.tex; \
$(DX_MAKEINDEX) refman.idx; \
$(DX_PDFLATEX) refman.tex; \
countdown=5; \
while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
refman.log > /dev/null 2>&1 \
&& test $$countdown -gt 0; do \
$(DX_PDFLATEX) refman.tex; \
countdown=`expr $$countdown - 1`; \
done; \
mv refman.pdf ../@PACKAGE@.pdf
endif DX_COND_pdf
## ------------------------------------------------- ##
## Rules specific for LaTeX (shared for PS and PDF). ##
## ------------------------------------------------- ##
if DX_COND_latex
DX_CLEAN_LATEX = @DX_DOCDIR@/latex
endif DX_COND_latex
.PHONY: doxygen-run doxygen-doc $(DX_PS_GOAL) $(DX_PDF_GOAL)
.INTERMEDIATE: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
doxygen-run: @DX_DOCDIR@/@PACKAGE@.tag
doxygen-doc: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
doc: doxygen-doc
docs: doxygen-doc
@DX_DOCDIR@/@PACKAGE@.tag: $(DX_CONFIG) $(pkginclude_HEADERS) $(PECOS_extra_dependencies)
rm -rf @DX_DOCDIR@
$(DX_ENV) $(DX_DOXYGEN) $(srcdir)/$(DX_CONFIG)
DX_CLEANFILES = \
@DX_DOCDIR@/@PACKAGE@.tag \
-r \
$(DX_CLEAN_HTML) \
$(DX_CLEAN_CHM) \
$(DX_CLEAN_CHI) \
$(DX_CLEAN_MAN) \
$(DX_CLEAN_RTF) \
$(DX_CLEAN_XML) \
$(DX_CLEAN_PS) \
$(DX_CLEAN_PDF) \
$(DX_CLEAN_LATEX)
# Additional PECOS dependencies
endif DX_COND_doc

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/*! \mainpage The MASA Library
<b>Version \version</b>, Build Date: \builddate
Built by: \builduser on \buildhost
<hr>
\section overview Overview
The MASA (Manufactured Analytical Solutions Abstraction) library is
a software interface that provides access to all manufactured solutions to
be used by various models throughout the PECOS center.
The library is written in
C++, but provides an API for development in C and Fortran.
Thanks for your interest in MASA. To aid in usage, this manual is
further divided into the following subsections:
<ul>
<li> \subpage model "Library Overview" </li>
<li> \subpage install "Installation/Linkage" </li>
<li> \link masa.h C/C++ Interface \endlink </li>
<li> \subpage apif "Fortran Interface" </li>
<li> \link tut "Tutorial" </li>
<li> \subpage mms_avail "Available Manufactured Solutions"</li>
<li> \subpage add_sol "Adding Additional Manufactured Solutions to MASA" </li>
<li> <a href="http://buildbot.ices.utexas.edu/docs/buildbot/masa/docs/html/lcov/build/src/index.html">Buildbot Coverage</a> </li>
</ul>
<!-- \subpage apiF Fortran API -->
<!-- \subpage examples Examples -->
\section bugs Reporting Bugs
Bugs in the code and errors or omissions in the documentation can be
reported to masa-dev@ices.utexas.edu. Requests and contributions are
welcome at the same e-mail address. All bug reports should include:
<ul>
<li>the version number of the MASA library,
<li>the hardware and operating system,
<li>the compiler used, including version number and compilation options,
<li>a description of the bug behavior, and ideally,
<li>a short program which reproduces the bug.
</ul>
\section licence License
Copyright (C) 2010 The PECOS Development Team
\copydoc LicenseLGPL
\section acknowledgements Acknowledgments
\copydoc Acknowledgments
\section pecos-center More Information About PECOS
\copydoc About2
*/
/*! \page model Library Overview
\copydoc LicenseLGPL
The MASA (Manufactured Analytical Solutions Abstraction) library is a software interface that provides access
to various manufactured solutions for a wide variety of differential equations. The library is written in C++,
and provides an API for development in C and Fortran.
<h2>Software Verification</h2>
Verification of numerical computations, in which one asks if numerical results are an accurate representation of the solution
to the mathematical model that is being solved, is relatively well understood. It requires
careful attention to good software engineering practices, continuous software testing, and control of numerical
discretization errors, through error estimation and adaptivity. While verification processes are well understood,
they require substantial effort. As verification of numerical results is a prerequisite for reliable computational
predictions, verification processes are integral to all activities in scientific computation.
MASA is designed to simplify the verification process by providing a common repository of manufactured solutions
for common problems in scientific computation.
<h2>Manufactured Solution Generation</h2>
The analytical solutions used in this library were generated using symbolic manipulation software, such as Maple.
<h2>PECOS Center Background</h2>
The Center for Predictive Engineering and COmputational Sciences (PECOS) is a DOE-funded Center
of Excellence within the Institute for Computational Engineering and Sciences (ICES)
at The University of Texas at Austin. PECOS is one of five such centers sponsored under
the Predictive Science Academic Alliance Program (PSAAP) of the National Nuclear Security
Administration’s Advanced Simulation and Computing Program.
PECOS brings together an interdisciplinary, multi-university team with partners at the
DOE National Labs and NASA. The goal of the PECOS Center is to develop the next generation
of advanced computational methods for predictive simulation of multiscale, multiphysics phenomena,
and to apply these methods to the analysis of vehicles reentering the atmosphere. In pursuing
this research, PECOS is advancing the science and modeling of atmospheric reentry, and
the science of predictive simulation.
<h2> Developers </h2>
Developers of the MASA library include:
Paul Bauman
Kemelli Estacio-Hiroms
<a href="mailto:nick@ices.utexas.edu">Nicholas Malaya</a>
Todd Oliver
Onkar Sahni
Karl W. Schulz
Chris Simmons
Roy Stogner
<h2> Citing MASA </h2>
A paper detailing the MASA library has been submitted for publication.
Upon acceptance, this section will be updated.
Please check back for details on how to cite MASA.
*/
/*! \page mms_avail Available Manufactured Solutions
The following sections detail all available manufactured solutions in MASA.
<ul>
<li> \subpage heat </li>
<li> \subpage laplace </li>
<li> \subpage euler </li>
<li> \subpage cns </li>
<li> \subpage sod </li>
<li> \subpage rans </li>
</ul>
*/
/*! \page tut Tutorial
The following sections detail all available manufactured solutions in MASA.
*/

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\typeout{Document Style `masa'. Released 04 March 2011}
\usepackage{pdflscape}
\usepackage[authoryear]{natbib}
%\usepackage[utf8x]{inputenc}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{geometry}
\newcommand{\D}{\partial}
\newcommand{\Diff}[2] {\dfrac{\partial( #1)}{\partial #2}}
\newcommand{\diff}[2] {\dfrac{\partial #1}{\partial #2}}
\newcommand{\bv}[1]{\ensuremath{\mbox{\boldmath$ #1 $}}}
\newcommand{\gv}[1]{\ensuremath{\mbox{\boldmath$ #1 $}}}
\newcommand{\grad}[1]{\gv{\nabla} #1}
\newcommand{\Rho}{\,\mathtt{Rho}}
\newcommand{\PP}{\,\mathtt{P}}
%\newcommand{\U}{\,\mathtt{U}}
\newcommand{\V}{\,\mathtt{V}}
\newcommand{\W}{\,\mathtt{W}}
\newcommand{\Lo}{\,\mathcal{L}}

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/*! \page install Installation/Linkage
libMASA uses the GNU autotools suite (autoconf, automake, and libtool)
for its development build system. This system is popular among the
Linux development community and provides a familiar build environment
for end users.
To build libMASA starting from a release distribution, untar the distribution and
enter the top-level directory.
<div class="fragment"><pre class="fragment">
> tar xvfz masa-$(VERSION).tar.gz
> cd masa-$(VERSION)/
</pre></div>
<h2>Configuration Requirements</h2>
Since libMASA provides a Fortran interface, a valid Fortran90 compiler is
also required. To date, libMASA has been successfully tested with \e
gfortran and the Intel \e ifort compilers. The configuration step
will look for available compilers in the user environment but as with
any \e autoconf based configuration, these can be overridden with
command line arguments (by setting \c CXX, \c FC, and \c F77
appropriately).
<b>Installation Directory</b>: Use the <tt>--prefix</tt> option to
specify your desired top-level installation directory for MASA. The
examples below all configure libMASA to be installed in the user's ~/bin/masa
directory.
Once configured, issue a <tt>make</tt> to build the software. If successful, this
will build the libMASA library (static and dynamic versions) and several
examples.
\code > make \endcode
<b> Verifying the build:</b> To verify that the software is working
properly, a test option is provided to run a short suite of
functionality tests against the local build. To run, issue a <tt>make
check</tt> to run the tests. If successful, output similar to the
following will be generated.
\code
> make check
-------------------------------------------------------
Initializing MASA Tests
-------------------------------------------------------
PASS: init.sh
PASS: misc
PASS: fail_cond
PASS: catch_exception
PASS: register
PASS: poly
PASS: uninit
PASS: pass_func
PASS: purge
PASS: heat_const_steady
PASS: heat_var_steady
PASS: heat_const_unsteady
PASS: heat_var_unsteady
PASS: euler1d
PASS: euler2d
PASS: euler3d
PASS: euler_transient_1d
PASS: euler_chem_1d
PASS: ns2d
PASS: ns3d
PASS: ns3d_phys
PASS: n2d3d
PASS: axi_euler
PASS: axi_cns
PASS: rans_sa
PASS: sod
-------------------------------------------------------
Initializing CMASA Tests
-------------------------------------------------------
PASS: c_init.sh
PASS: c_misc
PASS: c_purge
PASS: c_heat1dsc
PASS: c_heat2dsc
PASS: c_heat3dsc
PASS: c_euler1d
PASS: c_euler2d
PASS: c_euler3d
PASS: c_euler_chem_1d
PASS: c_navierstokes2d
PASS: c_navierstokes3d
-------------------------------------------------------
Initializing FortMASA Tests
-------------------------------------------------------
PASS: f_init.sh
MASA :: selected mytest
PASS: f_misc
PASS: f_purge
PASS: f_heat
PASS: f_euler1d
PASS: f_euler2d
PASS: f_euler3d
PASS: f_euler_chem_1d
PASS: f_cns2d
PASS: f_cns3d
-------------------------------------------------------
Initializing MASA Examples Tests
-------------------------------------------------------
PASS: example_test.sh
-------------------------------------------------------
Finalizing MASA Tests, have a well verified day
-------------------------------------------------------
PASS: finalize.sh
===================
All 50 tests passed
===================
\endcode
<h2> Installation </h2>
After the build is complete, issue a <tt>make install</tt> to install
the library. The installation will consist of three top-level
directories housing the library, include files, and
example files. An example of the top-level directories after
installation is shown below:
\code > make install \endcode
Top-level libMASA installation directory:
\code
> ls $HOME/bin/masa/
examples/ include/ lib/
\endcode
<h2>Library Linkage</h2>
To link an external C/C++ or Fortran application with the library, the
\c include directory must be added to the compilers include search
path in order to access the masa.h header file (or for Fortran, the \c
lib directory should be added to access the pre-compiled
masa F90 module). The \c lib directory should also be added
to the linker search path along with a request to link against the
libMASA library. Several example link steps are provided below. These
examples assume that the libMASA library has been successfully built and
installed previously in the users's ~/bin/masa directory:
<h3>C/C++ Example</h3>
\code > $(CC) -I$HOME/bin/masa/include app.c -L$HOME/bin/masa/lib -lmasa \endcode
If you set your <tt>PKG_CONFIG_PATH</tt> environment variable to contain
<tt>$HOME/lib/pkgconfig</tt> you can use <ahref="http://pkg-config.freedesktop.org/wiki/"><tt>pkg-config</tt></a> to
lookup the relevant linking information automatically:
\code > $(CC) `pkg-config --cflags masa` app.c `pkg-config --libs masa` \endcode
<h3>Fortran Example</h3>
Fortran applications also require linking against the fmasa library:
\code > $(FC) -I$HOME/bin/masa/lib app.f90 -L$HOME/bin/masa/lib -lfmasa -lmasa \endcode
As with C/C++, users can use make use of pkg-config:
\code > $(FC) `pkg-config --variable=fflags masa` app.f90 `pkg-config --variable=flibs masa` \endcode
To embed the dynamic library search path for the libMASA library
directly into the application executable, use an additional linker
option as follows:
<h3>C/C++ Example</h3>
\code > $(CC) -I$HOME/bin/masa/include app.c -L$HOME/bin/masa/lib \
-Wl,-rpath,$HOME/bin/masa/lib -lmasa \endcode
<b>Important Note:</b> F90 module file formats are not consistent
across multiple compilers. Therefore, a Fortran application and the libMASA
F90 interface \em must be built with the same Fortran compiler family to ensure
compatibility.
*/

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/*! \page tut Tutorial
This chapter will introduce the user to the basics of the MASA library.
This chapter assumes the user has already built and linked the MASA library
into their codebase. Now, you desire to access the magic of MASA
and begin the process of verification of your codebase.
This tutorial will detail the essential subroutines for any MASA program.
The c++ MASA bindings are used throughout, but a tutorial using the Fotran90
or C-code would be essentially unchanged.
<h1> Initalizing </h1>
To begin, any MASA program will call \c masa_init. This routine initalizes
a manufactured solution class of some particular type. It requires two inputs:
the manufactured solution class name as well as a unique name for this solution.
Thus, to initalize a one dimensional euler equation manufactured solution with
the unique name of 'nick', the function call would look something like:
\code
masa_init("nick","euler_1d");
\endcode
The unique name allows you to initalize several manufactured solutions of the same
problem type, should you so desire. This can be useful if you want to access several
manufactured solutions of the same type with different parameter sets.
You cannot, of course, specify several manufactured solutions with the same unique name!
Please be careful when specifying the second string: this \em must match the unique
identifier for that masa solution. Failing to match here will likely result in MASA aborting.
A logical question to ask at this juncture is where can you find a list of the
available manufactured solutions? The available solutions can be found several ways:
<ul>
<li> Browsing the available manufactured solutions page of this documentation
<li> Running the display_solutions executable in your examples directory
<li> Browsing through the solutions interactively using MASAshell (also in the examples dir)
<li> Calling the function: \c masa_printid()
</ul>
<h2> Setting up the Solution </h2>
Having initalized the solution, you need to set the variables to some reasonable value.
This will depend on your particular problem, but let's continue with the 1d euler example.
Firstly, let's determine \em what variables need to be set. A list of variables for
your solution can be found by:
<ul>
<li> Browsing the particular manufactured solution's page in this documentation
<li> Selecting the solution and then displaying the variables interactively using MASAshell
<li> Calling the function: \c masa_display_param()
</ul>
The output from masa_display_param() for our euler1d example will look something like:
\code
MASA :: Solution has 14 variables.
*-------------------------------------*
Gamma is set to: Uninitialized
L is set to: Uninitialized
R is set to: Uninitialized
a_px is set to: Uninitialized
a_rhox is set to: Uninitialized
a_ux is set to: Uninitialized
k is set to: Uninitialized
mu is set to: Uninitialized
p_0 is set to: Uninitialized
p_x is set to: Uninitialized
rho_0 is set to: Uninitialized
rho_x is set to: Uninitialized
u_0 is set to: Uninitialized
u_x is set to: Uninitialized
*-------------------------------------*
\endcode
Thus, euler_1d has 14 variables, all of which should be set to something.
We can set a value of a parameter in MASA using the function, \c masa_set_param.
\c masa_set_param takes as input a string and a double. The string specifies the
parameter we are setting and the double will become the parameter's new value.
This overwrites the any previous value the paramter may have had.
Continuing our example, let's set a_rhox to 33.33 (repeating, of course).
In our code, this would look like:
\code
masa_set_param("a_rhox",33.3333333333333)
\endcode
Now, checking \c masa_display_param, we can see we have set the value of a_rhox:
\code
MASA :: Solution has 14 variables.
*-------------------------------------*
Gamma is set to: Uninitialized
L is set to: Uninitialized
R is set to: Uninitialized
a_px is set to: Uninitialized
a_rhox is set to: 33.3333333333333
a_ux is set to: Uninitialized
k is set to: Uninitialized
mu is set to: Uninitialized
p_0 is set to: Uninitialized
p_x is set to: Uninitialized
rho_0 is set to: Uninitialized
rho_x is set to: Uninitialized
u_0 is set to: Uninitialized
u_x is set to: Uninitialized
*-------------------------------------*
\endcode
At this point, we could continue the same process for
each remaining variable.
To save you the tedium of doing this, MASA has graciously provided
default values for all manufactured solution classes.
In general, the default values have been selected to provide reasonable
test conditions for verification and whenever possible, defauls
correspond to some simple physical constraints
(such as not producing negative energy, or density, etc.).
A user can invoke these defaults using the routine: \c masa_init_param().
For our euler1d problem, the defaults look like:
\code
MASA :: Solution has 14 variables.
*-------------------------------------*
Gamma is set to: 16.1
L is set to: 3.02
R is set to: 1.01
a_px is set to: 6.151
a_rhox is set to: 1.2
a_ux is set to: 0.03
k is set to: 1.38
mu is set to: 0.091
p_0 is set to: 0.1984
p_x is set to: 3.151
rho_0 is set to: 91.5
rho_x is set to: 5.13
u_0 is set to: 0.191
u_x is set to: 1.63
*-------------------------------------*
\endcode
Note that setting the defaults \em will \em overwrite \em all \em previously
\em initalized \em values for the masa parameters! So if you desire to
alter the default values, call \c masa_set_param \em after \c masa_init_param.
Finally, you have initalized all the parameters and you are ready to move on
... Or are you? Are you certain you initalized every parameter? Do you really
want to verify this by checking \c masa_display_param()? Luckily, MASA provides
an alternative. The subroutine \c masa_sanity_check() will check that every
parameter has been set to \em something.
<h2> Accessing the Source Terms </h2>
\code
> ls $HOME/bin/masa/
examples/ include/ lib/
\endcode
For further examples (including c-code and fortran), the user is directed
to the examples directory included in the MASA distribution.
*/

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/*! \page About
\htmlonly
<table border="0" width="660" >
<tr><td width=95> <img src="circle-logo-small.png" /> </td>
<td>
The <a href="http://pecos.ices.utexas.edu">Center for
Predictive Engineering and Computational Sciences</a> (PECOS)
is one of five US centers sponsored under the Predictive
Science Academic Alliance Program (PSAAP) of the National
Nuclear Security Administration's Advanced Simulation and
Computing Program. The PECOS center is housed within
the <a href="http://www.ices.utexas.edu">Institute for
Computational Engineering and Sciences (ICES) </a> at the
<a href="http://www.utexas.edu">University of Texas at
Austin</a>. For additional information or questions regarding
the PECOS center, please contact <a href="mailto:info@pecos.ices.utexas.edu">info@pecos.ices.utexas.edu</a>.
</td>
</tr>
</table>
\endhtmlonly
\latexonly
\begin{tabular}{m{2.2cm} m{0.80\textwidth} }
\includegraphics[width=2cm]{../../doxygen/fig_common/circle-logo.pdf} &
The \href{http://pecos.ices.utexas.edu}{Center for Predictive
Engineering and Computational Sciences} (PECOS) is one of five US
centers sponsored under the Predictive Science Academic Alliance
Program (PSAAP) of the National Nuclear Security Administration's
Advanced Simulation and Computing Program. The PECOS center is housed
within the \href{http://www.ices.utexas.edu}{Institute for
Computational Engineering and Sciences} (ICES) at the
\href{http://www.utexas.edu"}{University of Texas at Austin}. For
additional information or questions regarding the PECOS center, please
contact info@pecos.ices.utexas.edu.
\end{tabular}
\endlatexonly
*/

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/*! \page Acknowledgments
This material is based in part upon work supported by the Department
of Energy National Nuclear Security Administration under Award
Number \e DE-FC52-08NA28615.
*/

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<hr size="1"/><address style="text-align: right;"><small>
Generated on $datetime for $projectname
by&nbsp;<a href="http://www.doxygen.org/index.html">
<em>doxygen</em></a>
$doxygenversion</small></address>
</body>
</html>

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/*! \page License
<br>
This program is free software; you can redistribute it and/or modify
it under the terms of the Version 2 GNU General Public License as published by
the Free Software Foundation.<br>
<br>
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
<a href="http://www.gnu.org/licenses/gpl-2.0.html">GNU General Public License</a>
for more details.
*/