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Merge pull request #420 in SUNDIALS/sunrepo from release/5.6.1 to dev…
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commit 99ee1ac
Author: David J. Gardner <gardner48@llnl.gov>
Date:   Tue Dec 15 12:14:50 2020 -0800

    regen ARKODE examples tex

commit 21932f2
Author: Balos, Cody Joe <balos1@llnl.gov>
Date:   Tue Dec 15 12:11:07 2020 -0800

    update recent changes

commit 48df03b
Author: Balos, Cody Joe <balos1@llnl.gov>
Date:   Tue Dec 15 11:30:37 2020 -0800

    bump version
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24 changes: 12 additions & 12 deletions CMakeLists.txt
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Expand Up @@ -28,14 +28,14 @@ project(SUNDIALS C)
# Set some variables with info on the SUNDIALS project
set(PACKAGE_BUGREPORT "sundials-users@llnl.gov")
set(PACKAGE_NAME "SUNDIALS")
set(PACKAGE_STRING "SUNDIALS 5.6.0")
set(PACKAGE_STRING "SUNDIALS 5.6.1")
set(PACKAGE_TARNAME "sundials")

# set SUNDIALS version numbers
# (use "" for the version label if none is needed)
set(PACKAGE_VERSION_MAJOR "5")
set(PACKAGE_VERSION_MINOR "6")
set(PACKAGE_VERSION_PATCH "0")
set(PACKAGE_VERSION_PATCH "1")
set(PACKAGE_VERSION_LABEL "")

if(PACKAGE_VERSION_LABEL)
Expand All @@ -50,37 +50,37 @@ endif()

# Specify the VERSION and SOVERSION for shared libraries

set(arkodelib_VERSION "4.6.0")
set(arkodelib_VERSION "4.6.1")
set(arkodelib_SOVERSION "4")

set(cvodelib_VERSION "5.6.0")
set(cvodelib_VERSION "5.6.1")
set(cvodelib_SOVERSION "5")

set(cvodeslib_VERSION "5.6.0")
set(cvodeslib_VERSION "5.6.1")
set(cvodeslib_SOVERSION "5")

set(idalib_VERSION "5.6.0")
set(idalib_VERSION "5.6.1")
set(idalib_SOVERSION "5")

set(idaslib_VERSION "4.6.0")
set(idaslib_VERSION "4.6.1")
set(idaslib_SOVERSION "4")

set(kinsollib_VERSION "5.6.0")
set(kinsollib_VERSION "5.6.1")
set(kinsollib_SOVERSION "5")

set(cpodeslib_VERSION "0.0.0")
set(cpodeslib_SOVERSION "0")

set(nveclib_VERSION "5.6.0")
set(nveclib_VERSION "5.6.1")
set(nveclib_SOVERSION "5")

set(sunmatrixlib_VERSION "3.6.0")
set(sunmatrixlib_VERSION "3.6.1")
set(sunmatrixlib_SOVERSION "3")

set(sunlinsollib_VERSION "3.6.0")
set(sunlinsollib_VERSION "3.6.1")
set(sunlinsollib_SOVERSION "3")

set(sunnonlinsollib_VERSION "2.6.0")
set(sunnonlinsollib_VERSION "2.6.1")
set(sunnonlinsollib_SOVERSION "2")

set(sundialslib_VERSION
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2 changes: 1 addition & 1 deletion README.md
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@@ -1,5 +1,5 @@
# SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic equation Solvers #
### Version 5.6.0 (Dec 2020) ###
### Version 5.6.1 (Dec 2020) ###

**Center for Applied Scientific Computing, Lawrence Livermore National Laboratory**

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54 changes: 27 additions & 27 deletions doc/arkode/examples/build/latex/ark_examples.tex
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Expand Up @@ -67,23 +67,23 @@
\usepackage{footnotebackref}

% Add new command for SUNDIALS version
\newcommand{\sunreleasename}{v5.6.0}
\newcommand{\sunreleasename}{v5.6.1}

% ===================================================
% End custom preamble (see latex_elements in conf.py)
% ===================================================


\title{Example Programs for ARKode}
\date{December 11, 2020}
\date{December 15, 2020}
\release{}
\author{
Daniel R. Reynolds\\
{\em Department of Mathematics} \\
{\em Southern Methodist University}
}
\newcommand{\sphinxlogo}{\sphinxincludegraphics{doc_logo_blue.pdf}\par}
\renewcommand{\releasename}{v4.6.0}
\renewcommand{\releasename}{v4.6.1}
\makeindex

\begin{document}
Expand Down Expand Up @@ -650,7 +650,7 @@


\chapter{Serial C example problems}
\label{\detokenize{c_serial:arkode-example-documentation}}\label{\detokenize{c_serial:serial-c-example-problems}}\label{\detokenize{c_serial::doc}}\label{\detokenize{c_serial:serial-c}}
\label{\detokenize{c_serial:arkode-example-documentation}}\label{\detokenize{c_serial:serial-c-example-problems}}\label{\detokenize{c_serial:serial-c}}\label{\detokenize{c_serial::doc}}

\section{ark\_analytic}
\label{\detokenize{c_serial:id1}}\label{\detokenize{c_serial:ark-analytic}}
Expand Down Expand Up @@ -740,7 +740,7 @@ \subsection{Solutions}


\section{ark\_brusselator}
\label{\detokenize{c_serial:ark-brusselator}}\label{\detokenize{c_serial:id5}}
\label{\detokenize{c_serial:id5}}\label{\detokenize{c_serial:ark-brusselator}}
We now wish to exercise the ARKode solvers on more challenging
nonlinear ODE systems. The following test simulates a brusselator
problem from chemical kinetics, and is widely used as a standard
Expand Down Expand Up @@ -822,7 +822,7 @@ \subsection{Solutions}


\section{ark\_brusselator\_fp}
\label{\detokenize{c_serial:id8}}\label{\detokenize{c_serial:ark-brusselator-fp}}
\label{\detokenize{c_serial:ark-brusselator-fp}}\label{\detokenize{c_serial:id8}}
This test problem is a duplicate of the \sphinxcode{ark\_brusselator} problem
above, but with a few key changes in the methods used for time
integration and nonlinear solver. As with the previous test, this
Expand Down Expand Up @@ -962,7 +962,7 @@ \subsection{Solutions}


\section{ark\_robertson\_root}
\label{\detokenize{c_serial:id15}}\label{\detokenize{c_serial:ark-robertson-root}}
\label{\detokenize{c_serial:ark-robertson-root}}\label{\detokenize{c_serial:id15}}
We again test the Robertson problem, but in this example we will
utilize both a logarithmically-spaced set of output times (to properly
show the solution behavior), as well as ARKode’s root-finding
Expand Down Expand Up @@ -1258,7 +1258,7 @@ \subsection{Numerical method}


\section{ark\_KrylovDemo\_prec}
\label{\detokenize{c_serial:ark-krylovdemo-prec}}\label{\detokenize{c_serial:id30}}
\label{\detokenize{c_serial:id30}}\label{\detokenize{c_serial:ark-krylovdemo-prec}}
This problem is an ARKode clone of the CVODE problem,
\sphinxcode{cv\_KrylovDemo\_prec}. This is a demonstration program using the
SUNLINSOL\_SPGMR linear solver module. As explained more thoroughly in
Expand Down Expand Up @@ -1346,7 +1346,7 @@ \subsection{Numerical method}


\section{ark\_onewaycouple\_mri}
\label{\detokenize{c_serial:ark-onewaycouple-mri}}\label{\detokenize{c_serial:id33}}
\label{\detokenize{c_serial:id33}}\label{\detokenize{c_serial:ark-onewaycouple-mri}}
This example simulates a linear system of 3 dependent variables \(u\),
\(v\) and \(w\), that depend on the independent variable \(t\) via
the IVP system
Expand Down Expand Up @@ -1381,7 +1381,7 @@ \subsection{Solutions}
\end{equation*}

\section{ark\_twowaycouple\_mri}
\label{\detokenize{c_serial:id36}}\label{\detokenize{c_serial:ark-twowaycouple-mri}}
\label{\detokenize{c_serial:ark-twowaycouple-mri}}\label{\detokenize{c_serial:id36}}
This example simulates a linear system of 3 dependent variables \(u\),
\(v\) and \(w\), that depend on the independent variable \(t\) via
the IVP system
Expand All @@ -1408,7 +1408,7 @@ \subsection{Numerical method}


\chapter{OpenMP C example problems}
\label{\detokenize{c_openmp:openmp-c-example-problems}}\label{\detokenize{c_openmp::doc}}\label{\detokenize{c_openmp:openmp-c}}
\label{\detokenize{c_openmp::doc}}\label{\detokenize{c_openmp:openmp-c}}\label{\detokenize{c_openmp:openmp-c-example-problems}}

\section{ark\_brusselator1D\_omp}
\label{\detokenize{c_openmp:id1}}\label{\detokenize{c_openmp:ark-brusselator1d-omp}}
Expand Down Expand Up @@ -1448,10 +1448,10 @@ \subsection{Numerical method}


\chapter{Parallel C example problems}
\label{\detokenize{c_parallel:parallel-c}}\label{\detokenize{c_parallel::doc}}\label{\detokenize{c_parallel:parallel-c-example-problems}}
\label{\detokenize{c_parallel::doc}}\label{\detokenize{c_parallel:parallel-c-example-problems}}\label{\detokenize{c_parallel:parallel-c}}

\section{ark\_diurnal\_kry\_bbd\_p}
\label{\detokenize{c_parallel:id1}}\label{\detokenize{c_parallel:ark-diurnal-kry-bbd-p}}
\label{\detokenize{c_parallel:ark-diurnal-kry-bbd-p}}\label{\detokenize{c_parallel:id1}}
This problem is an ARKode clone of the CVODE problem,
\sphinxcode{cv\_diurnal\_kry\_bbd\_p}. As described in \phantomsection\label{\detokenize{c_parallel:id2}}{\hyperref[\detokenize{References:hsr2017}]{\sphinxcrossref{{[}HSR2017{]}}}}, this problem
models a two-species diurnal kinetics advection-diffusion PDE system
Expand Down Expand Up @@ -1518,7 +1518,7 @@ \subsection{Numerical method}


\section{ark\_diurnal\_kry\_p}
\label{\detokenize{c_parallel:id3}}\label{\detokenize{c_parallel:ark-diurnal-kry-p}}
\label{\detokenize{c_parallel:ark-diurnal-kry-p}}\label{\detokenize{c_parallel:id3}}
This problem is an ARKode clone of the CVODE problem,
\sphinxcode{cv\_diurnal\_kry\_p}. As described in \phantomsection\label{\detokenize{c_parallel:id4}}{\hyperref[\detokenize{References:hsr2017}]{\sphinxcrossref{{[}HSR2017{]}}}}, this test problem
models a two-species diurnal kinetics advection-diffusion PDE system
Expand Down Expand Up @@ -1580,7 +1580,7 @@ \subsection{Numerical method}


\chapter{Parallel Hypre example problems}
\label{\detokenize{c_parhyp:parallel-hypre-example-problems}}\label{\detokenize{c_parhyp::doc}}\label{\detokenize{c_parhyp:parhyp-c}}
\label{\detokenize{c_parhyp::doc}}\label{\detokenize{c_parhyp:parallel-hypre-example-problems}}\label{\detokenize{c_parhyp:parhyp-c}}

\section{ark\_diurnal\_kry\_ph}
\label{\detokenize{c_parhyp:ark-diurnal-kry-ph}}\label{\detokenize{c_parhyp:id1}}
Expand Down Expand Up @@ -1679,7 +1679,7 @@ \subsection{Numerical method}


\chapter{Serial C++ example problems}
\label{\detokenize{cpp_serial:serial-c-example-problems}}\label{\detokenize{cpp_serial::doc}}\label{\detokenize{cpp_serial:serial-cpp}}
\label{\detokenize{cpp_serial::doc}}\label{\detokenize{cpp_serial:serial-c-example-problems}}\label{\detokenize{cpp_serial:serial-cpp}}

\section{ark\_analytic\_sys}
\label{\detokenize{cpp_serial:id1}}\label{\detokenize{cpp_serial:ark-analytic-sys}}
Expand Down Expand Up @@ -1745,7 +1745,7 @@ \chapter{Parallel C++ example problems}
\label{\detokenize{cpp_parallel::doc}}\label{\detokenize{cpp_parallel:parallel-c-example-problems}}\label{\detokenize{cpp_parallel:parallel-cpp}}

\section{ark\_heat2D}
\label{\detokenize{cpp_parallel:id1}}\label{\detokenize{cpp_parallel:ark-heat2d}}
\label{\detokenize{cpp_parallel:ark-heat2d}}\label{\detokenize{cpp_parallel:id1}}
ARKode provides one parallel C++ example problem, that extends our
previous {\hyperref[\detokenize{c_serial:ark-heat1d}]{\sphinxcrossref{\DUrole{std,std-ref}{ark\_heat1D}}}} test to now simulate a two-dimensional heat
equation,
Expand Down Expand Up @@ -1814,10 +1814,10 @@ \subsection{Solutions}


\chapter{Serial Fortran 77 example problems}
\label{\detokenize{f77_serial::doc}}\label{\detokenize{f77_serial:serial-fortran-77-example-problems}}\label{\detokenize{f77_serial:serial-f77}}
\label{\detokenize{f77_serial::doc}}\label{\detokenize{f77_serial:serial-f77}}\label{\detokenize{f77_serial:serial-fortran-77-example-problems}}

\section{fark\_diurnal\_kry\_bp}
\label{\detokenize{f77_serial:id1}}\label{\detokenize{f77_serial:fark-diurnal-kry-bp}}
\label{\detokenize{f77_serial:fark-diurnal-kry-bp}}\label{\detokenize{f77_serial:id1}}
This problem is an ARKode clone of the CVODE problem,
\sphinxcode{fcv\_diurnal\_kry\_bp}. As described in \phantomsection\label{\detokenize{f77_serial:id2}}{\hyperref[\detokenize{References:hsr2017}]{\sphinxcrossref{{[}HSR2017{]}}}}, this problem
models a two-species diurnal kinetics advection-diffusion PDE system
Expand Down Expand Up @@ -1876,7 +1876,7 @@ \subsection{Numerical method}


\section{fark\_roberts\_dnsL}
\label{\detokenize{f77_serial:id3}}\label{\detokenize{f77_serial:fark-roberts-dnsl}}
\label{\detokenize{f77_serial:fark-roberts-dnsl}}\label{\detokenize{f77_serial:id3}}
This problem is an ARKode clone of the CVODE problem,
\sphinxcode{fcv\_roberts\_dnsL}. As described in \phantomsection\label{\detokenize{f77_serial:id4}}{\hyperref[\detokenize{References:hsr2017}]{\sphinxcrossref{{[}HSR2017{]}}}}, this problem models
the kinetics of a three-species autocatalytic reaction. This is an
Expand Down Expand Up @@ -1916,10 +1916,10 @@ \subsection{Numerical method}


\chapter{Parallel Fortran 77 example problems}
\label{\detokenize{f77_parallel:parallel-fortran-77-example-problems}}\label{\detokenize{f77_parallel:parallel-f77}}\label{\detokenize{f77_parallel::doc}}
\label{\detokenize{f77_parallel::doc}}\label{\detokenize{f77_parallel:parallel-f77}}\label{\detokenize{f77_parallel:parallel-fortran-77-example-problems}}

\section{fark\_diag\_kry\_bbd\_p}
\label{\detokenize{f77_parallel:id1}}\label{\detokenize{f77_parallel:fark-diag-kry-bbd-p}}
\label{\detokenize{f77_parallel:fark-diag-kry-bbd-p}}\label{\detokenize{f77_parallel:id1}}
This problem is an ARKode clone of the CVODE problem,
\sphinxcode{fcv\_diag\_kry\_bbd\_p}. As described in \phantomsection\label{\detokenize{f77_parallel:id2}}{\hyperref[\detokenize{References:hsr2017}]{\sphinxcrossref{{[}HSR2017{]}}}}, this problem
models a stiff, linear, diagonal ODE system,
Expand Down Expand Up @@ -1974,10 +1974,10 @@ \subsection{Numerical method}


\chapter{Serial Fortran 90 example problems}
\label{\detokenize{f90_serial:serial-fortran-90-example-problems}}\label{\detokenize{f90_serial::doc}}\label{\detokenize{f90_serial:serial-f90}}
\label{\detokenize{f90_serial::doc}}\label{\detokenize{f90_serial:serial-fortran-90-example-problems}}\label{\detokenize{f90_serial:serial-f90}}

\section{ark\_bruss}
\label{\detokenize{f90_serial:id1}}\label{\detokenize{f90_serial:ark-bruss}}
\label{\detokenize{f90_serial:ark-bruss}}\label{\detokenize{f90_serial:id1}}
This test problem is a Fortran-90 version of the same brusselator
problem as before, {\hyperref[\detokenize{c_serial:ark-brusselator}]{\sphinxcrossref{\DUrole{std,std-ref}{ark\_brusselator}}}}, in which the “test 1”
parameters are hard-coded into the solver. As with the previous test,
Expand Down Expand Up @@ -2046,7 +2046,7 @@ \section{ark\_bruss1D\_FEM\_klu}


\chapter{Parallel Fortran 90 example problems}
\label{\detokenize{f90_parallel:parallel-f90}}\label{\detokenize{f90_parallel::doc}}\label{\detokenize{f90_parallel:parallel-fortran-90-example-problems}}
\label{\detokenize{f90_parallel::doc}}\label{\detokenize{f90_parallel:parallel-f90}}\label{\detokenize{f90_parallel:parallel-fortran-90-example-problems}}

\section{fark\_heat2D}
\label{\detokenize{f90_parallel:id1}}\label{\detokenize{f90_parallel:fark-heat2d}}
Expand Down Expand Up @@ -2094,12 +2094,12 @@ \subsection{Numerical method}
\begin{sphinxthebibliography}{HSR2017}
\bibitem[HSR2017]{\detokenize{HSR2017}}{\phantomsection\label{\detokenize{References:hsr2017}}
A.C. Hindmarsh, R. Serban and D.R. Reynolds. Example
Programs for CVODE v5.6.0. Technical Report
Programs for CVODE v5.6.1. Technical Report
UCRL-SM-208110, LLNL, 2020.
}
\bibitem[R2018]{\detokenize{R2018}}{\phantomsection\label{\detokenize{References:r2018}}
D.R. Reynolds. User Documentation for ARKode
v4.6.0. Technical Report LLNL-CODE-667205, LLNL, 2020.
v4.6.1. Technical Report LLNL-CODE-667205, LLNL, 2020.
}
\end{sphinxthebibliography}

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4 changes: 2 additions & 2 deletions doc/arkode/examples/source/References.rst
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Expand Up @@ -23,8 +23,8 @@
==========

.. [HSR2017] A.C. Hindmarsh, R. Serban and D.R. Reynolds. Example
Programs for CVODE v5.6.0. Technical Report
Programs for CVODE v5.6.1. Technical Report
UCRL-SM-208110, LLNL, 2020.
.. [R2018] D.R. Reynolds. User Documentation for ARKode
v4.6.0. Technical Report LLNL-CODE-667205, LLNL, 2020.
v4.6.1. Technical Report LLNL-CODE-667205, LLNL, 2020.
4 changes: 2 additions & 2 deletions doc/arkode/examples/source/conf.py
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Expand Up @@ -49,8 +49,8 @@
# built documents.
#
# The short X.Y version.
version = 'v4.6.0'
sun_version = 'v5.6.0'
version = 'v4.6.1'
sun_version = 'v5.6.1'

# Set the date format (full-month-name day, full-year)
today_fmt = '%B %d, %Y'
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