PATO v3.1 release

.gitignore

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+### Original OpenFOAM .gitignore with additions for PATO ###
+
+# Editor and misc backup files - anywhere
+*~
+.*~
+*.bak
+*.bak[0-9][0-9]
+*.orig
+*.orig[0-9][0-9]
+\#*\#
+
+# python
+*.pyc 
+src/thirdParty/patoPlot/patoPlot.pyc
+
+# File-browser settings - anywhere
+.directory
+
+# CVS recovered versions - anywhere
+.#*
+
+# Objects and archives - anywhere
+*.[oa]
+*.la
+*.so
+
+# Derived files
+lex.yy.c
+
+# Corefiles
+core
+
+# Dependency files - anywhere
+*.dep
+
+# lnInclude (symlink) directories - anywhere
+lnInclude
+
+# Build directories - anywhere
+linux*Clang*/
+linux*Gcc*/
+linux*Icc*/
+solaris*Gcc*/
+SunOS*Gcc*/
+platforms/
+
+# Reinstate wmake/rules that might look like build directories
+!wmake/rules/*/
+
+# doxygen generated documentation
+doc/Doxygen/html
+doc/Doxygen/latex
+doc/Doxygen/man
+doc/Doxygen/DTAGS
+
+# Generated files in the main directory (e.g. ReleaseNotes-?.?.html)
+# and in the doc directory
+/*.html
+/doc/*.html
+
+# Untracked configuration files
+/etc/prefs.csh
+/etc/prefs.sh
+/etc/config/prefs.csh
+/etc/config/prefs.sh
+
+# Source packages - anywhere
+*.tar.bz2
+*.tar.gz
+*.tar
+*.tgz
+*.gtgz
+
+# Ignore the persistent .build tag in the main directory
+/.build
+
+# Ignore .timeStamp in the main directory
+/.timeStamp
+
+# Ignore .tags in the main directory
+/.tags
+
+# Ignore eclipse project files in the main directory
+/.cproject
+/.project
+
+# Ignore the test directories
+/tutorialsTest
+tutorials/debug
+
+### Additional OpenFOAM files ###
+
+tutorials/*/*/[1-9]*
+tutorials/*/*/[0-9]*\.[0-9]*
+!tutorials/*/*/0/*
+!tutorials/**/[0-9]D*
+#tutorials/*/*/output/*
+tutorials/*/*/processor[0-9]*
+
+**/postProcessing/*
+**/plots/profiles/*
+**/plots/*.pdf
+*.OpenFOAM
+*.blockMesh
+
+# debug
+tutorials/debug/*
+
+### LaTeX ###
+
+*.acn
+*.acr
+*.alg
+*.aux
+*.bbl
+*.blg
+*.dvi
+*.fdb_latexmk
+*.fls
+*.glg
+*.glo
+*.gls
+*.idx
+*.ilg
+*.ind
+*.ist
+*.lof
+*.log
+*.lot
+*.maf
+*.mtc
+*.mtc0
+*.nav
+*.nlo
+*.out
+*.pdfsync
+*.ps
+*.snm
+*.synctex.gz
+*.toc
+*.vrb
+*.xdy
+*.tdo
+documentation/PATO_UserGuide/PATO_UserGuide.pdf
+
+### Sublime Text ###
+# Cache files
+*.tmlanguage.cache
+*.tmPreferences.cache
+*.stTheme.cache
+
+# Workspace files are user-specific
+*.sublime-workspace
+
+### IDE (Eclipse, netbeans, CLion, qtCreator, etc.) ###
+nbproject
+.idea
+.project
+.cproject
+*.creator.user
+*.creator
+*.config
+*.files
+*.includes
+*.cflags
+*.cxxflags
+*.dir-locals.el
+*.kdev4
+
+### Other protections ###
+.svn
+.~lock*
+log_log.dat
+*.aux
+*.log
+
+# PATO install system files
+install
+
+# Mutation build system files
+src/thirdParty/mutation++/mutation++/build
+src/thirdParty/mutation++/mutation++/install
+src/thirdParty/mutation++/run
+
+# Documentation
+documentation/Doxygen/DTAGS
+documentation/Doxygen/html
+
+# MACOS
+darwin64Clang*
+*.DS_Store
+
+# GNU tags files
+GPATH
+GRTAGS
+GTAGS
+TAGS

AllwcleanAllclean

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+#!/bin/bash
+cd ${0%/*} || exit 1 # Run from this directory
+
+ROOTDIR=`pwd`
+
+# remove executables
+cd src/applications/
+wclean all solvers
+wclean all utilities
+wclean all libraries
+cd $ROOTDIR
+rm  -rf install
+
+# clean tutorials
+cd tutorials
+./Allclean_tutorials
+cd $ROOTDIR
+
+# remove Mutation++ build directories
+cd $PATO_DIR/src/thirdParty
+./Allwclean
+cd $ROOTDIR
+
+# clean documentation
+documentation/Doxygen/Allclean
+
+# remove temporary files
+find . -name '*~' -ls -delete
+
+# ----------------------------------------------------------------- end-of-file

Allwmake

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+#!/bin/bash
+cd ${0%/*} || exit 1 # Run from this directory
+
+# Stop if error
+set -e
+
+ROOTDIR=`pwd`
+
+# compile Mutation++ and its thirdParty libraries
+if [ ! -d $MPP_DIRECTORY/install ]; then
+    cd $MPP_DIRECTORY
+    # python scripts/install_dependencies.py
+    mkdir build
+    cd build
+    cmake -DCMAKE_INSTALL_PREFIX:PATH=$(realpath ../install) -DCMAKE_INSTALL_LIBDIR=lib ..
+    make -j `nproc` install
+    loc_eigen=`find /usr/ -name signature_of_eigen3_matrix_library -print 2>/dev/null | sed 's|\(.*\)/.*|\1|'`
+    if [ -z "${loc_eigen}" ]; then
+        loc_eigen=`find $MPP_DIRECTORY -name signature_of_eigen3_matrix_library  -print 2>/dev/null | sed 's|\(.*\)/.*|\1|'`
+    fi
+    loc_eigen="$loc_eigen/Eigen"
+    ln -s ${loc_eigen} ../install/include/Eigen
+    if [ "$(uname)" = "Darwin" ]; then
+	lib_name=$PATO_DIR/src/thirdParty/mutation++/install/lib/libmutation++.dylib
+	install_name_tool -id $lib_name $lib_name
+    fi
+    cd $ROOTDIR
+fi
+
+# compile C++ coding style dependency
+wmake src/thirdParty/google-astyle
+
+# compile PATO library, solvers and utilities
+cd src/applications
+wmake libso libraries/samplingUser
+wmake libso libraries/libPATOx
+wmake all solvers
+wmake all utilities
+cd $ROOTDIR
+
+# compile the documentation
+if [ "$BUILD_DOCUMENTATION" = "yes" ]; then
+    if [ ! -d documentation/Doxygen/html ]; then
+	documentation/Doxygen/Allmake
+    fi
+fi
+
+# ----------------------------------------------------------------- end-of-file