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Merge branch 'develop' of develop.openfoam.com:Development/OpenFOAM-plus into develop

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This commit is contained in:
sergio
2017-12-21 09:15:21 -08:00
parent 5a3dfc60b6 cc2e9cb404
commit 0b4a97bce5
36 changed files with 353 additions and 1693 deletions
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3
.gitmodules vendored
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@ -1,3 +1,6 @@
[submodule "cfmesh"]
path = modules/cfmesh
url = https://develop.openfoam.com/Community/integration-cfmesh.git
[submodule "avalanche"]
path = modules/avalanche
url = https://develop.openfoam.com/Community/avalanche.git

29
BuildIssues.txt
View File

@ -1,4 +1,4 @@
OpenFOAM-1706
OpenFOAM-1712
==================
Known Build Issues
==================
@ -75,6 +75,33 @@ If your system compiler is too old to build the minimum required gcc or
clang/llvm, it is just simply too old.
---------------------------------
ThirdParty clang without gmp/mpfr
---------------------------------
If using ThirdParty clang without gmp/mpfr, the ThirdParty makeCGAL
script will need to be run manually and specify that there is no
gmp/mpfr. Eg,
cd $WM_THIRD_PARTY_DIR
./makeCGAL gmp-none mpfr-none
Subequent compilation with Allwmake will now run largely without any
problems, except that the components linking against CGAL
(foamyMesh and surfaceBooleanFeatures) will also try to link against
a nonexistent mpfr library. As a workaround, the link-dependency can
be removed in wmake/rules/General/CGAL :
CGAL_LIBS = \
-L$(BOOST_ARCH_PATH)/lib \
-L$(BOOST_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-L$(CGAL_ARCH_PATH)/lib \
-L$(CGAL_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-lCGAL
This is a temporary inconvenience until a more robust solution is found.
-------------------------
Building with spack
-------------------------

2
applications/test/openmp/Make/options
View File

@ -1,4 +1,4 @@
EXE_INC = ${COMP_OPENMP}
EXE_INC = ${COMP_OPENMP} /* -UUSE_OMP */
/* Mostly do not need to explicitly link openmp libraries */
/* EXE_LIBS = ${LINK_OPENMP} */

16
applications/test/openmp/Test-openmp.C
View File

@ -30,7 +30,7 @@ Description
#include <cstdlib>
#include <iostream>
#ifdef USE_OMP
#if _OPENMP
#include <omp.h>
#endif
@ -39,11 +39,19 @@ Description
int main(int argc, char *argv[])
{
#if USE_OMP
std::cout << "USE_OMP defined (" << USE_OMP << ")\n";
#else
std::cout << "USE_OMP undefined\n";
#endif
#if _OPENMP
std::cout << "_OPENMP = " << _OPENMP << "\n\n";
// Fork threads with their own copies of variables
int nThreads, threadId;
// Fork threads with their own copies of variables
#ifdef USE_OMP
#pragma omp parallel private(nThreads, threadId)
#pragma omp parallel private(nThreads, threadId)
{
threadId = omp_get_thread_num();
nThreads = omp_get_num_threads();

17
bin/tools/CleanFunctions
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@ -6,20 +6,8 @@
# \\/ M anipulation | Copyright (C) 2015-2017 OpenCFD Ltd.
#------------------------------------------------------------------------------
# License
# This file is part of OpenFOAM.
#
# OpenFOAM is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# OpenFOAM 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 GNU General Public License
# for more details.
#
# You should have received a copy of the GNU General Public License
# along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
# This file is part of OpenFOAM, licensed under GNU General Public License
# <http://www.gnu.org/licenses/>.
#
# Script
# CleanFunctions
@ -158,6 +146,7 @@ cleanFaMesh ()
)
}
cleanApplication()
{
echo "Cleaning application $PWD"

120
bin/tools/LogFunctions Normal file
View File

@ -0,0 +1,120 @@
#!/bin/sh
#------------------------------------------------------------------------------
# ========= |
# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
# \\ / O peration |
# \\ / A nd | Copyright (C) 2017 OpenCFD Ltd.
# \\/ M anipulation |
#------------------------------------------------------------------------------
# License
# This file is part of OpenFOAM, licensed under GNU General Public License
# <http://www.gnu.org/licenses/>.
#
# Script
# LogFunctions
#
# Description
# Miscellaneous functions for running tutorials in a loop and for
# analyzing the output.
#
# Output is normally summarized as 'testLoopReport'
#
#------------------------------------------------------------------------------
# logReport <logfile>
# Extracts useful info from log file.
logReport()
{
local logfile=$1
# logfile is path/to/case/log.application
caseName=$(dirname $logfile | sed -e 's/\(.*\)\.\///g')
app=$(echo $logfile | sed -e 's/\(.*\)log\.//g')
appAndCase="Application $app - case $caseName"
if grep -q "FOAM FATAL" $logfile
then
echo "$appAndCase: ** FOAM FATAL ERROR **"
return 1
fi
# Check for solution singularity on U equation
for eqn in Ux Uy Uz
do
if grep -q -E "${eqn}[:| ]*solution singularity" $logfile
then
if [ "$eqn" = Uz ]
then
# Can only get here if Ux,Uy,Uz all failed
echo "$appAndCase: ** Solution singularity **"
return 1
fi
else
break
fi
done
if grep -q -E "^[\t ]*[Ee]nd" $logfile
then
# Extract time from this type of content
## ExecutionTime = 60.2 s ClockTime = 63 s --> "60.2 s"
completionTime=$(tail -10 $logfile | \
sed -n -e '/Execution/{s/^[^=]*=[ \t]*//; s/\( s\) .*$/\1/; p}')
echo "$appAndCase: completed${completionTime:+ in }$completionTime"
else
echo "$appAndCase: unconfirmed completion"
fi
}
# Collect and analyse all log files
collectLogs()
{
echo "Collecting log files..." 1>&2
rm -f logs testLoopReport > /dev/null 2>&1
touch logs testLoopReport
local appDir log logFiles
for appDir in *
do
[ -d $appDir ] || continue
echo -n " $appDir..." 1>&2
logFiles=$(find -L $appDir -name 'log.*' -type f)
if [ -n "$logFiles" ]
then
echo 1>&2
else
echo " (no logs)" 1>&2
continue
fi
# Sort logs by time-stamp
for log in $(echo $logFiles | xargs ls -rt)
do
# Concatenate and summarize logs
cat "$log" >> logs 2>/dev/null
logReport $log
done
echo
done > testLoopReport
}
removeLogs()
{
echo "Removing backup files"
find . \( \
-name '*~' -o -name '*.bak' \
-name core -o -name 'core.[1-9]*' \
-name '*.pvs' -o -name '*.foam' -o -name '*.OpenFOAM' \
\) -type f -delete
rm -f logs testLoopReport > /dev/null 2>&1
}
#------------------------------------------------------------------------------

17
bin/tools/RunFunctions
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@ -6,26 +6,15 @@
# \\/ M anipulation | Copyright (C) 2015-2017 OpenCFD Ltd.
#------------------------------------------------------------------------------
# License
# This file is part of OpenFOAM.
#
# OpenFOAM is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# OpenFOAM 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 GNU General Public License
# for more details.
#
# You should have received a copy of the GNU General Public License
# along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
# This file is part of OpenFOAM, licensed under GNU General Public License
# <http://www.gnu.org/licenses/>.
#
# Script
# RunFunctions
#
# Description
# Miscellaneous functions for running tutorial cases
#
#------------------------------------------------------------------------------
# The normal locations

57
etc/bashrc
View File

@ -36,7 +36,7 @@ export WM_PROJECT=OpenFOAM
export WM_PROJECT_VERSION=plus
# [FOAM_INST_DIR] - parent directory containing the OpenFOAM installation.
# * When this file is located as $WM_PROJECT_DIR/etc/bashrc, the next lines
# \- When this file is located as $WM_PROJECT_DIR/etc/bashrc, the next lines
# should work when sourced by BASH or ZSH shells. If this however fails,
# set one of the fallback values to an appropriate path.
# --
@ -104,23 +104,18 @@ export WM_MPLIB=SYSTEMOPENMPI
################################################################################
# The old dirs to be cleaned from the environment variables
# Old directories to be cleaned from PATH, LD_LIBRARY_PATH
foamOldDirs="$WM_PROJECT_DIR $WM_THIRD_PARTY_DIR \
$HOME/$WM_PROJECT/$USER $FOAM_USER_APPBIN $FOAM_USER_LIBBIN \
$WM_PROJECT_SITE $FOAM_SITE_APPBIN $FOAM_SITE_LIBBIN"
# Location of installation
# ~~~~~~~~~~~~~~~~~~~~~~~~
# Location of installation and third-party software
export WM_PROJECT_INST_DIR=$FOAM_INST_DIR
export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION
# Location of third-party software
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION
# Location of site-specific templates etc
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# unset is equivalent to $WM_PROJECT_INST_DIR/site
# [WM_PROJECT_SITE] - Location of site-specific (group) files
# default (unset) implies WM_PROJECT_INST_DIR/site
if [ -d "$WM_PROJECT_SITE" ]
then
export WM_PROJECT_SITE
@ -128,12 +123,10 @@ else
unset WM_PROJECT_SITE
fi
# Location of user files
# ~~~~~~~~~~~~~~~~~~~~~~
# [WM_PROJECT_USER_DIR] - Location of user files
export WM_PROJECT_USER_DIR=$HOME/$WM_PROJECT/$USER-$WM_PROJECT_VERSION
# Load shell functions
# ~~~~~~~~~~~~~~~~~~~~
. $WM_PROJECT_DIR/etc/config.sh/functions
# Override definitions via prefs, with 'other' first so the sys-admin
@ -163,35 +156,29 @@ cleaned=$($foamClean "$MANPATH" "$foamOldDirs") && MANPATH="$cleaned"
export PATH LD_LIBRARY_PATH MANPATH
# Source project setup files
# ~~~~~~~~~~~~~~~~~~~~~~~~~~
# Setup for OpenFOAM compilation etc
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_foamEtc config.sh/settings
if /usr/bin/tty -s 2>/dev/null # Interactive shell
then
_foamEtc config.sh/aliases
# Bash completions
if [ "${BASH_VERSINFO:-0}" -ge 4 ]
then
_foamEtc config.sh/bash_completion
fi
fi
# Source user setup files for optional packages
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Setup for third-party packages
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_foamEtc config.sh/mpi
_foamEtc config.sh/paraview
_foamEtc config.sh/vtk
_foamEtc config.sh/ensight
_foamEtc config.sh/gperftools
#_foamEtc config.sh/ADIOS
## _foamEtc config.csh/ADIOS
_foamEtc config.sh/CGAL
_foamEtc config.sh/scotch
_foamEtc config.sh/FFTW
# Interactive shell
if /usr/bin/tty -s 2>/dev/null
then
_foamEtc config.sh/aliases
[ "${BASH_VERSINFO:-0}" -ge 4 ] && _foamEtc config.sh/bash_completion
fi
# Clean environment paths again. Only remove duplicates
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@ -214,13 +201,13 @@ then
fi
# Cleanup environment
# ~~~~~~~~~~~~~~~~~~~
# Cleanup temporary information
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Functions
# Unload shell functions
. $WM_PROJECT_DIR/etc/config.sh/functions
# Variables (do as last for a clean exit code)
# Variables (done as the last statement for a clean exit code)
unset cleaned foamClean foamOldDirs
#------------------------------------------------------------------------------

10
etc/config.csh/settings
View File

@ -149,15 +149,14 @@ setenv FOAM_LIBBIN $WM_PROJECT_DIR/platforms/$WM_OPTIONS/lib
# External (ThirdParty) libraries
setenv FOAM_EXT_LIBBIN $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/lib
# Site-specific directory
# Site-specific (group) files
if ( $?WM_PROJECT_SITE ) then
set siteDir=$WM_PROJECT_SITE
else
set siteDir=$WM_PROJECT_INST_DIR/site
endif
# Shared site executables/libraries
# Similar naming convention as ~OpenFOAM expansion
# Shared site (group) executables/libraries
setenv FOAM_SITE_APPBIN $siteDir/$WM_PROJECT_VERSION/platforms/$WM_OPTIONS/bin
setenv FOAM_SITE_LIBBIN $siteDir/$WM_PROJECT_VERSION/platforms/$WM_OPTIONS/lib
@ -165,8 +164,8 @@ setenv FOAM_SITE_LIBBIN $siteDir/$WM_PROJECT_VERSION/platforms/$WM_OPTIONS/lib
setenv FOAM_USER_APPBIN $WM_PROJECT_USER_DIR/platforms/$WM_OPTIONS/bin
setenv FOAM_USER_LIBBIN $WM_PROJECT_USER_DIR/platforms/$WM_OPTIONS/lib
# DynamicCode templates
# - default location is the "~OpenFOAM/codeTemplates/dynamicCode" expansion
# [FOAM_CODE_TEMPLATES] - dynamicCode templates
# * fallback == "foamEtcFile -list codeTemplates/dynamicCode"
# setenv FOAM_CODE_TEMPLATES $WM_PROJECT_DIR/etc/codeTemplates/dynamicCode
# Convenience
@ -302,6 +301,7 @@ CLANG_NOT_FOUND
_foamAddMan $clangDir/man
_foamAddPath $clangDir/bin
_foamAddLib $clangDir/lib # For things like libomp (openmp) etc
if ($?FOAM_VERBOSE && $?prompt) then
echo "Using ThirdParty compiler"

10
etc/config.sh/settings
View File

@ -133,7 +133,7 @@ export FOAM_LIBBIN=$WM_PROJECT_DIR/platforms/$WM_OPTIONS/lib
# External (ThirdParty) libraries
export FOAM_EXT_LIBBIN=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/lib
# Site-specific directory
# Site-specific (group) files
if [ -n "$WM_PROJECT_SITE" ]
then
siteDir=$WM_PROJECT_SITE
@ -141,8 +141,7 @@ else
siteDir=$WM_PROJECT_INST_DIR/site
fi
# Shared site executables/libraries
# Similar naming convention as ~OpenFOAM expansion
# Shared site (group) executables/libraries
export FOAM_SITE_APPBIN=$siteDir/$WM_PROJECT_VERSION/platforms/$WM_OPTIONS/bin
export FOAM_SITE_LIBBIN=$siteDir/$WM_PROJECT_VERSION/platforms/$WM_OPTIONS/lib
@ -150,8 +149,8 @@ export FOAM_SITE_LIBBIN=$siteDir/$WM_PROJECT_VERSION/platforms/$WM_OPTIONS/lib
export FOAM_USER_APPBIN=$WM_PROJECT_USER_DIR/platforms/$WM_OPTIONS/bin
export FOAM_USER_LIBBIN=$WM_PROJECT_USER_DIR/platforms/$WM_OPTIONS/lib
# DynamicCode templates
# - default location is the "~OpenFOAM/codeTemplates/dynamicCode" expansion
# [FOAM_CODE_TEMPLATES] - dynamicCode templates
# * fallback == "foamEtcFile -list codeTemplates/dynamicCode"
# export FOAM_CODE_TEMPLATES=$WM_PROJECT_DIR/etc/codeTemplates/dynamicCode
# Convenience
@ -287,6 +286,7 @@ CLANG_NOT_FOUND
_foamAddMan $clangDir/share/man
_foamAddPath $clangDir/bin
_foamAddLib $clangDir/lib # For things like libomp (openmp) etc
if [ "$FOAM_VERBOSE" -a "$PS1" ]
then

54
etc/cshrc
View File

@ -36,7 +36,7 @@ setenv WM_PROJECT OpenFOAM
setenv WM_PROJECT_VERSION plus
# [FOAM_INST_DIR] - parent directory containing the OpenFOAM installation.
# * When this file is located as $WM_PROJECT_DIR/etc/cshrc, the next lines
# \- When this file is located as $WM_PROJECT_DIR/etc/cshrc, the next lines
# should work when sourced by CSH or TCSH shells. If this however fails,
# set one of the fallback values to an appropriate path.
# --
@ -101,7 +101,7 @@ setenv WM_MPLIB SYSTEMOPENMPI
################################################################################
# The old dirs to be cleaned from the environment variables
# Old directories to be cleaned from PATH, LD_LIBRARY_PATH
set foamOldDirs=
if ( $?WM_PROJECT_DIR ) then
set foamOldDirs="$foamOldDirs $WM_PROJECT_DIR"
@ -119,18 +119,13 @@ if ( $?FOAM_SITE_LIBBIN ) then
set foamOldDirs="$foamOldDirs $FOAM_SITE_LIBBIN"
endif
# Location of installation
# ~~~~~~~~~~~~~~~~~~~~~~~~
# Location of installation and third-party software
setenv WM_PROJECT_INST_DIR $FOAM_INST_DIR
setenv WM_PROJECT_DIR $WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION
setenv WM_PROJECT_DIR $WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION
setenv WM_THIRD_PARTY_DIR $WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION
# Location of third-party software
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
setenv WM_THIRD_PARTY_DIR $WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION
# Location of site-specific templates etc
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# unset is equivalent to $WM_PROJECT_INST_DIR/site
# [WM_PROJECT_SITE] - Location of site-specific (group) files
# default (unset) implies WM_PROJECT_INST_DIR/site
if ( $?WM_PROJECT_SITE ) then
set foamOldDirs="$WM_PROJECT_SITE $foamOldDirs"
if ( ! -d "$WM_PROJECT_SITE" ) unsetenv WM_PROJECT_SITE
@ -138,8 +133,7 @@ else
unsetenv WM_PROJECT_SITE
endif
# Location of user files
# ~~~~~~~~~~~~~~~~~~~~~~
# [WM_PROJECT_USER_DIR] - Location of user files
setenv WM_PROJECT_USER_DIR $HOME/$WM_PROJECT/$LOGNAME-$WM_PROJECT_VERSION
# Source an etc file, possibly with some verbosity
@ -210,27 +204,26 @@ set cleaned=`$foamClean "$MANPATH" "$foamOldDirs"`
if ( $status == 0 ) setenv MANPATH $cleaned
# Source project setup files
# ~~~~~~~~~~~~~~~~~~~~~~~~~~
# Setup for OpenFOAM compilation etc
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_foamEtc config.csh/settings
if ($?prompt) then # Interactive shell
_foamEtc config.csh/aliases
_foamEtc config.csh/tcsh_completion
endif
# Source user setup files for optional packages
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Setup for third-party packages
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_foamEtc config.csh/mpi
_foamEtc config.csh/paraview
_foamEtc config.csh/vtk
_foamEtc config.csh/ensight
#_foamEtc config.csh/ADIOS
## _foamEtc config.csh/ADIOS
_foamEtc config.csh/CGAL
_foamEtc config.csh/FFTW
# Interactive shell
if ($?prompt) then
_foamEtc config.csh/aliases
_foamEtc config.csh/tcsh_completion
endif
# Clean environment paths again. Only remove duplicates
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@ -253,12 +246,15 @@ if ( $?LD_PRELOAD ) then
endif
# Cleanup environment
# ~~~~~~~~~~~~~~~~~~~
unset cleaned foamClean foamOldDirs
# Cleanup temporary information
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Unload shell "functions"
unalias _foamEtc
unalias _foamAddPath
unalias _foamAddLib
unalias _foamAddMan
unset cleaned foamClean foamOldDirs
#------------------------------------------------------------------------------

59
modules/README.md
View File

@ -1,15 +1,64 @@
OpenFOAM Modules
================
This directory is a location to place additional OpenFOAM components
or tools and have them built as part of the normal OpenFOAM build
This directory is a location for additional OpenFOAM components or tools
to placed and have them built as part of the normal OpenFOAM build
process. It is assumed that each subdirectory contain an appropriate
Allwmake file, and that they should in all likelihood also build into
Allwmake file, and that they in all likelihood also build into
`$FOAM_APPBIN` and `$FOAM_LIBBIN` instead of
`$FOAM_USER_APPBIN` and `$FOAM_USER_LIBBIN`.
These additional components may be added as git submodules, by script
or by hand.
These additional components may be added as [git submodules][man git-submodule],
by script or by hand.
### git
On the first use, it will be necessary to register the submodules:
git submodule init
This will clone the relevant submodules from their respective
repositories.
The following will indicate the current state:
git submodule status
On the first use, or after merging upstream changes in the OpenFOAM
repository, it will be necessary to update the submodules:
git submodule update
A quick overview of `git submodule` can be in this
[*blog*][blog git-submodule] with full details in the
[*manpage*][man git-submodule].
An easy way to see which submodules are actually in use:
`cat .gitmodules`
Which will reveal content resembling the following:
[submodule "cfmesh"]
path = modules/cfmesh
url = https://develop.openfoam.com/Community/integration-cfmesh.git
### doxygen
To build the doxygen information for the components, it is also
necessary to link the directories to the doc/ subdirectory.
This is a purely manual operation.
<!-- General Information -->
[man git-submodule]: https://git-scm.com/docs/git-submodule
[blog git-submodule]: http://blog.joncairns.com/2011/10/how-to-use-git-submodules/
---

1
modules/avalanche Submodule

Submodule modules/avalanche added at 7859926d58

2
modules/cfmesh

Submodule modules/cfmesh updated: 7fb146a232...57b9896a21

42
src/randomProcesses/fft/fft.C
View File

@ -29,20 +29,20 @@ License
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Foam::tmp<Foam::complexField> fft::realTransform1D(const scalarField& field)
Foam::tmp<Foam::complexField>
Foam::fft::realTransform1D(const scalarField& field)
{
const label n = field.size();
const label nBy2 = n/2;
// Copy of input field for use by fftw
// - fftw requires non-const access to input and output...
scalar in[n], out[n];
forAll(field, i)
// - require non-const access to input and output
// - use double to avoid additional libfftwf for single-precision
List<double> in(n);
List<double> out(n);
for (label i=0; i < n; ++i)
{
in[i] = field[i];
}
@ -51,8 +51,8 @@ Foam::tmp<Foam::complexField> fft::realTransform1D(const scalarField& field)
fftw_plan plan = fftw_plan_r2r_1d
(
n,
in,
out,
in.data(),
out.data(),
FFTW_R2HC,
FFTW_ESTIMATE
);
@ -77,7 +77,7 @@ Foam::tmp<Foam::complexField> fft::realTransform1D(const scalarField& field)
}
Foam::tmp<Foam::complexField> fft::realTransform1D
Foam::tmp<Foam::complexField> Foam::fft::realTransform1D
(
const tmp<scalarField>& tfield
)
@ -88,7 +88,7 @@ Foam::tmp<Foam::complexField> fft::realTransform1D
}
void fft::transform
void Foam::fft::transform
(
complexField& field,
const UList<int>& nn,
@ -110,7 +110,7 @@ void fft::transform
}
// Copy field into fftw containers
label N = field.size();
const label N = field.size();
fftw_complex in[N], out[N];
forAll(field, i)
@ -128,7 +128,7 @@ void fft::transform
// fftw_plan_dft_1d(N, in, out, FFTW_FORWARD, FFTW_ESTIMATE);
// Generic 1..3-D plan
label rank = nn.size();
const label rank = nn.size();
fftw_plan plan =
fftw_plan_dft(rank, nn.begin(), in, out, dir, FFTW_ESTIMATE);
@ -163,7 +163,7 @@ void fft::transform
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
tmp<complexField> fft::forwardTransform
Foam::tmp<Foam::complexField> Foam::fft::forwardTransform
(
const tmp<complexField>& tfield,
const UList<int>& nn
@ -179,7 +179,7 @@ tmp<complexField> fft::forwardTransform
}
tmp<complexField> fft::reverseTransform
Foam::tmp<Foam::complexField> Foam::fft::reverseTransform
(
const tmp<complexField>& tfield,
const UList<int>& nn
@ -195,7 +195,7 @@ tmp<complexField> fft::reverseTransform
}
tmp<complexVectorField> fft::forwardTransform
Foam::tmp<Foam::complexVectorField> Foam::fft::forwardTransform
(
const tmp<complexVectorField>& tfield,
const UList<int>& nn
@ -224,7 +224,7 @@ tmp<complexVectorField> fft::forwardTransform
}
tmp<complexVectorField> fft::reverseTransform
Foam::tmp<Foam::complexVectorField> Foam::fft::reverseTransform
(
const tmp<complexVectorField>& tfield,
const UList<int>& nn
@ -253,8 +253,4 @@ tmp<complexVectorField> fft::reverseTransform
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
// ************************************************************************* //

10
src/randomProcesses/noise/noiseFFT/noiseFFT.C
View File

@ -285,8 +285,8 @@ Foam::tmp<Foam::scalarField> Foam::noiseFFT::Pf
<< abort(FatalError);
}
List<scalar>& in = planInfo_.in;
const List<scalar>& out = planInfo_.out;
List<double>& in = planInfo_.in;
const List<double>& out = planInfo_.out;
forAll(in, i)
{
in[i] = pn[i];
@ -305,8 +305,8 @@ Foam::tmp<Foam::scalarField> Foam::noiseFFT::Pf
result[0] = out[0];
for (label i = 1; i <= nBy2; ++i)
{
scalar re = out[i];
scalar im = out[n - i];
const auto re = out[i];
const auto im = out[n - i];
result[i] = sqrt(re*re + im*im);
}
@ -443,7 +443,7 @@ Foam::graph Foam::noiseFFT::PSD(const graph& gPSDf) const
Foam::graph Foam::noiseFFT::octaves
(
const graph& g,
const labelList& freqBandIDs,
const labelUList& freqBandIDs,
bool integrate
) const
{

9
src/randomProcesses/noise/noiseFFT/noiseFFT.H
View File

@ -68,13 +68,14 @@ class noiseFFT
:
public scalarField
{
//- FFTW planner information
//- FFTW planner information.
// Storage as double for use directly with FFTW.
struct planInfo
{
bool active;
label windowSize;
scalarList in;
scalarList out;
List<double> in;
List<double> out;
fftw_plan plan;
};
@ -174,7 +175,7 @@ public:
graph octaves
(
const graph& g,
const labelList& freqBandIDs,
const labelUList& freqBandIDs,
bool integrate
) const;

15
tutorials/Allclean
View File

@ -1,18 +1,11 @@
#!/bin/sh
cd ${0%/*} || exit 1 # Run from this directory
cd ${0%/*} || exit 1 # Run from this directory
. $WM_PROJECT_DIR/bin/tools/LogFunctions # Tutorial log-file functions
echo "--------"
removeLogs
echo "Cleaning tutorials ..."
echo "Removing backup files"
find . \( \
-name '*~' -o -name '*.bak' \
-name core -o -name 'core.[1-9]*' \
-name '*.pvs' -o -name '*.OpenFOAM' \
\) -type f -delete
rm -f logs testLoopReport > /dev/null 2>&1
foamCleanTutorials cases
echo "--------"

113
tutorials/Allrun
View File

@ -7,26 +7,14 @@
# \\/ M anipulation | Copyright (C) 2017 OpenCFD Ltd.
#------------------------------------------------------------------------------
# License
# This file is part of OpenFOAM.
#
# OpenFOAM is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# OpenFOAM 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 GNU General Public License
# for more details.
#
# You should have received a copy of the GNU General Public License
# along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
# This file is part of OpenFOAM, licensed under GNU General Public License
# <http://www.gnu.org/licenses/>.
#
# Script
# Allrun
#
# Description
# Runs tutorial cases and summarizes the outcome as 'testLoopReport'
# Run tutorial cases and summarize the outcome as 'testLoopReport'
#
#------------------------------------------------------------------------------
cd ${0%/*} || exit 1 # Run from this directory
@ -43,27 +31,26 @@ options:
-collect Collect logs only. Can be useful for aborted runs.
-help print the usage
* Runs tutorial cases and summarizes the outcome as 'testLoopReport'
Run tutorial cases and summarize the outcome as 'testLoopReport'
USAGE
exit 1
}
#------------------------------------------------------------------------------
unset optCollect
unset optCollectOnly
# parse options
# Parse options
while [ "$#" -gt 0 ]
do
case "$1" in
-h | -help)
-h | -help*)
usage
;;
-collect)
optCollectOnly=true
optCollect=true
;;
-test) # Known options that should be passed through
-test) # Known options to pass through
break
;;
-*)
@ -77,87 +64,13 @@ do
done
#------------------------------------------------------------------------------
. $WM_PROJECT_DIR/bin/tools/LogFunctions # Tutorial log-file functions
# logReport <logfile>
# Extracts useful info from log file.
logReport()
{
local logfile=$1
# logfile is path/to/case/log.application
caseName=$(dirname $logfile | sed -e 's/\(.*\)\.\///g')
app=$(echo $logfile | sed -e 's/\(.*\)log\.//g')
appAndCase="Application $app - case $caseName"
if grep -q "FOAM FATAL" $logfile
then
echo "$appAndCase: ** FOAM FATAL ERROR **"
return 1
fi
# Check for solution singularity on U equation
for eqn in Ux Uy Uz
do
if grep -q -E "${eqn}[:| ]*solution singularity" $logfile
then
if [ "$eqn" = Uz ]
then
# Can only get here if Ux,Uy,Uz all failed
echo "$appAndCase: ** Solution singularity **"
return 1
fi
else
break
fi
done
if grep -q -E "^[\t ]*[Ee]nd" $logfile
then
# Extract time from this type of content
## ExecutionTime = 60.2 s ClockTime = 63 s --> "60.2 s"
completionTime=$(tail -10 $logfile | \
sed -n -e '/Execution/{s/^[^=]*=[ \t]*//; s/\( s\) .*$/\1/; p}')
echo "$appAndCase: completed${completionTime:+ in }$completionTime"
else
echo "$appAndCase: unconfirmed completion"
fi
}
if [ -z "$optCollectOnly" ]
if [ -z "$optCollect" ]
then
# Recursively run all tutorials
foamRunTutorials -skipFirst $*
foamRunTutorials -skipFirst $* # Run tutorials recursively
fi
# Analyse all log files
echo "Collecting log files..." 1>&2
rm -f logs testLoopReport > /dev/null 2>&1
touch logs testLoopReport
for appDir in *
do
[ -d $appDir ] || continue
echo -n " $appDir..." 1>&2
logs=$(find -L $appDir -name 'log.*' -type f)
if [ -n "$logs" ]
then
echo 1>&2
else
echo " (no logs)" 1>&2
continue
fi
# Sort logs by time-stamp
for log in $(echo $logs | xargs ls -rt)
do
# Concatenate and summarize logs
cat "$log" >> logs 2>/dev/null
logReport $log
done
echo
done > testLoopReport
collectLogs
#------------------------------------------------------------------------------

212
tutorials/finiteArea/surfactantFoam/planeTransport/constant/faMesh/faBoundary
View File

@ -1,212 +0,0 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: plus |
| \\ / A nd | Web: www.OpenFOAM.com |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class faBoundaryMesh;
location "constant/faMesh";
object faBoundary;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
3
(
inlet
{
type patch;
edgeLabels List<label>
20
(
2321
2322
2323
2324
2325
2326
2327
2328
2329
2330
2331
2332
2333
2334
2335
2336
2337
2338
2339
2341
)
;
ngbPolyPatchIndex 0;
}
outlet
{
type patch;
edgeLabels List<label>
20
(
2459
2460
2461
2462
2463
2464
2465
2466
2467
2468
2469
2470
2471
2472
2473
2474
2475
2476
2477
2478
)
;
ngbPolyPatchIndex 2;
}
bound
{
type symmetry;
edgeLabels List<label>
120
(
2320
2340
2342
2343
2344
2345
2346
2347
2348
2349
2350
2351
2352
2353
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2400
2401
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2403
2404
2405
2406
2407
2408
2409
2410
2411
2412
2413
2414
2415
2416
2417
2418
2419
2420
2421
2422
2423
2424
2425
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2427
2428
2429
2430
2431
2432
2433
2434
2435
2436
2437
2438
2439
2440
2441
2442
2443
2444
2445
2446
2447
2448
2449
2450
2451
2452
2453
2454
2455
2456
2457
2458
2479
)
;
ngbPolyPatchIndex 1;
}
)
// ************************************************************************* //

1224
tutorials/finiteArea/surfactantFoam/planeTransport/constant/faMesh/faceLabels
View File

File diff suppressed because it is too large Load Diff

4
wmake/rules/linux64Clang/openmp
View File

@ -1,4 +1,8 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
# -
# Clang provides 'omp' and a link for 'gomp'.
# With 'gomp' we can use system libs.
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp

1
wmake/rules/linux64Cray/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp

1
wmake/rules/linux64Gcc/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp

1
wmake/rules/linux64GccKNL/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp

1
wmake/rules/linux64Icc/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -qopenmp
LINK_OPENMP = -liomp5

1
wmake/rules/linux64IccKNL/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -qopenmp
LINK_OPENMP = -liomp5

4
wmake/rules/linuxARM64Clang/openmp
View File

@ -1,4 +1,8 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
# -
# Clang provides 'omp' and a link for 'gomp'.
# With 'gomp' we can use system libs.
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp

1
wmake/rules/linuxARM64Gcc/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp

1
wmake/rules/linuxARM7Gcc/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp

4
wmake/rules/linuxClang/openmp
View File

@ -1,4 +1,8 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
# -
# Clang provides 'omp' and a link for 'gomp'.
# With 'gomp' we can use system libs.
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp

1
wmake/rules/linuxGcc/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp

1
wmake/rules/linuxIA64Gcc/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp

1
wmake/rules/linuxIA64Icc/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -qopenmp
LINK_OPENMP = -liomp5

1
wmake/rules/linuxPPC64Gcc/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp

1
wmake/rules/linuxPPC64leGcc/openmp
View File

@ -1,4 +1,5 @@
# Flags for compiling/linking openmp
# The USE_OMP is for OpenFOAM-specific use (general use is _OPENMP)
COMP_OPENMP = -DUSE_OMP -fopenmp
LINK_OPENMP = -lgomp