Merge pull request #26 from ParticulateFlow/feature/environment_setup

Feature/environment setup

applications/solvers/cfdemSolverIB/Make/options

@@ -1,6 +1,7 @@
 include $(CFDEM_ADD_LIBS_DIR)/additionalLibs
 
 EXE_INC = \
+    -I$(CFDEM_OFVERSION_DIR) \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \

applications/solvers/cfdemSolverPiso/Make/options

@@ -1,6 +1,7 @@
 include $(CFDEM_ADD_LIBS_DIR)/additionalLibs
 
 EXE_INC = \
+    -I$(CFDEM_OFVERSION_DIR) \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \

applications/solvers/cfdemSolverPisoMS/Make/options

@@ -1,6 +1,7 @@
 include $(CFDEM_ADD_LIBS_DIR)/additionalLibs
 
 EXE_INC = \
+    -I$(CFDEM_OFVERSION_DIR) \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(CFDEM_SRC_DIR)/lagrangian/cfdemParticle/lnInclude \

applications/solvers/cfdemSolverPisoScalar/Make/options

@@ -1,6 +1,7 @@
 include $(CFDEM_ADD_LIBS_DIR)/additionalLibs
 
 EXE_INC = \
+    -I$(CFDEM_OFVERSION_DIR) \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \

applications/solvers/cfdemSolverRhoPimple/Make/options

@@ -4,6 +4,7 @@ PFLAGS+= -Dcompre
 
 EXE_INC = \
      $(PFLAGS) \
+    -I$(CFDEM_OFVERSION_DIR) \
     -I$(LIB_SRC)/transportModels/compressible/lnInclude \
     -I$(LIB_SRC)/thermophysicalModels/basic/lnInclude \
     -I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \

applications/utilities/cfdemPostproc/Make/options

@@ -1,6 +1,7 @@
 include $(CFDEM_ADD_LIBS_DIR)/additionalLibs
 
 EXE_INC = \
+    -I$(CFDEM_OFVERSION_DIR) \
     -I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \
     -I$(LIB_SRC)/TurbulenceModels/incompressible/lnInclude \
     -I$(LIB_SRC)/transportModels \

etc/bashrc

@@ -0,0 +1,259 @@
+#----------------------------------*-sh-*--------------------------------------
+# CFDEMcoupling
+#
+# Copyright 2009-2012 JKU Linz
+# Copyright 2012-2015 DCS Computing GmbH, Linz
+# Copyright 2015-     JKU Linz
+#------------------------------------------------------------------------------
+#
+# File
+#     etc/bashrc
+#
+# Description
+#     Startup file for CFDEMcoupling
+#     Sourced from ~/.profile or ~/.bashrc
+#
+# you can test the correctness using cfdemSystemTest.sh
+#------------------------------------------------------------------------------
+
+export CFDEM_PROJECT=CFDEM
+export CFDEM_VERSION=17.02
+
+################################################################################
+# USER EDITABLE PART: Changes made here may be lost with the next upgrade
+#
+# Please set to the appropriate path if the default is not correct.
+#
+# activate compatible OpenFOAM version
+. $HOME/OpenFOAM/OpenFOAM-4.x/etc/bashrc
+#
+# CFDEMcoupling
+export CFDEM_INST_DIR=$HOME/$CFDEM_PROJECT
+export CFDEM_PROJECT_DIR=$CFDEM_INST_DIR/CFDEMcoupling
+export CFDEM_PROJECT_USER_DIR=$CFDEM_INST_DIR/$USER-$WM_PROJECT_VERSION
+#
+# LIGGGHTS
+export CFDEM_LIGGGHTS_INST_DIR=$CFDEM_INST_DIR/LIGGGHTS
+#
+# LPP installation path
+export CFDEM_LPP_INST_DIR=$CFDEM_INST_DIR/LPP
+#
+# Path to additional libraries
+export CFDEM_ADD_LIBS_DIR=
+#
+# END OF (NORMAL) USER EDITABLE PART
+################################################################################
+
+#- The old dirs to be cleaned from the environment variables
+cfdemOldDirs="$CFDEM_LIGGGHTS_BIN_DIR $CFDEM_APP_DIR $CFDEM_LIB_DIR"
+
+export CFDEM_LIGGGHTS_SRC_DIR=$CFDEM_LIGGGHTS_INST_DIR/src
+export CFDEM_LIGGGHTS_BIN_DIR=$CFDEM_LIGGGHTS_INST_DIR/src-build
+
+#------------------------------------------------------------------------------
+# Source initialization functions
+#------------------------------------------------------------------------------
+. $WM_PROJECT_DIR/etc/config.sh/functions
+
+#------------------------------------------------------------------------------
+# Evaluate command-line parameters
+# these can be used to set/unset values
+#------------------------------------------------------------------------------
+_foamEval $@
+
+#------------------------------------------------------------------------------
+
+export CFDEM_SRC_DIR=$CFDEM_PROJECT_DIR/src
+export CFDEM_SOLVER_DIR=$CFDEM_PROJECT_DIR/applications/solvers
+export CFDEM_UT_DIR=$CFDEM_PROJECT_DIR/applications/utilities
+export CFDEM_DOC_DIR=$CFDEM_PROJECT_DIR/doc
+export CFDEM_TUT_DIR=$CFDEM_PROJECT_DIR/tutorials
+export CFDEM_LPP_DIR=$CFDEM_LPP_INST_DIR/src
+
+#------------------------------------------------------------------------------
+
+#- CFDEM lib name
+export CFDEM_LIB_NAME=lagrangianCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
+
+#- CFDEM compressible lib name
+export CFDEM_LIB_COMP_NAME=lagrangianCFDEMcomp-$CFDEM_VERSION-$WM_PROJECT_VERSION
+
+#- Check if additional libraries should be compiled together with solvers
+if [[ $CFDEM_ADD_LIBS_DIR == "" ]]; then
+    export CFDEM_ADD_LIBS_DIR=$CFDEM_PROJECT_DIR/etc
+else
+    echo "using CFDEM_ADD_LIBS_DIR=$CFDEM_ADD_LIBS_DIR defined by user."
+fi
+
+#------------------------------------------------------------------------------
+
+#- LMP Many2Many lib path and makefile
+export CFDEM_Many2ManyLIB_PATH=$CFDEM_SRC_DIR/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library
+export CFDEM_Many2ManyLIB_MAKEFILENAME=fedora_fpic
+
+#------------------------------------------------------------------------------
+
+#- path to test harness
+export CFDEM_TEST_HARNESS_PATH=$CFDEM_PROJECT_USER_DIR/log/logFilesCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
+
+#- path to libraries
+export CFDEM_LIB_DIR=$CFDEM_PROJECT_DIR/platforms/$WM_OPTIONS/lib
+
+#- path to apps
+export CFDEM_APP_DIR=$CFDEM_PROJECT_DIR/platforms/$WM_OPTIONS/bin
+
+#- create directories
+mkdir -p $CFDEM_LIB_DIR
+mkdir -p $CFDEM_APP_DIR
+
+#- path to OF version flag file
+export CFDEM_OFVERSION_DIR=$CFDEM_PROJECT_DIR/etc/OFversion
+
+#------------------------------------------------------------------------------
+# Clean standard environment variables (PATH, LD_LIBRARY_PATH)
+#------------------------------------------------------------------------------
+foamClean=$WM_PROJECT_DIR/bin/foamCleanPath
+
+#- Clean PATH
+cleaned=`$foamClean "$PATH" "$cfdemOldDirs"` && PATH="$cleaned"
+
+#- Clean LD_LIBRARY_PATH
+cleaned=`$foamClean "$LD_LIBRARY_PATH" "$cfdemOldDirs"` \
+    && LD_LIBRARY_PATH="$cleaned"
+
+export PATH LD_LIBRARY_PATH
+
+#- add binary directories to $PATH
+_foamAddPath $CFDEM_APP_DIR:$CFDEM_LIGGGHTS_BIN_DIR
+_foamAddLib $CFDEM_LIB_DIR
+
+#------------------------------------------------------------------------------
+# Cleanup environment:
+#------------------------------------------------------------------------------
+unset cleaned foamClean cfdemOldDirs
+
+#------------------------------------------------------------------------------
+# Unload initialization functions:
+#------------------------------------------------------------------------------
+. $WM_PROJECT_DIR/etc/config.sh/functions
+
+#------------------------------------------------------------------------------
+# Settings for lpp postproc tool
+#------------------------------------------------------------------------------
+
+#- nr of procs for lpp tool
+export CFDEM_LPP_NPROCS=4
+
+#- nr of procs for lpp tool
+export CFDEM_LPP_CHUNKSIZE=1
+
+#- shortcut to run lpp
+alias lpp='python -i $CFDEM_LPP_DIR/lpp.py --cpunum $CFDEM_LPP_NPROCS --chunksize $CFDEM_LPP_CHUNKSIZE'
+
+#------------------------------------------------------------------------------
+# aliases for easy navigation (no changes necessary)
+#------------------------------------------------------------------------------
+
+#- shortcut to cfdem path
+alias cfdem='cd $CFDEM_PROJECT_DIR'
+
+#- shortcut to src path
+alias cfdemSrc='cd $CFDEM_SRC_DIR'
+
+#- shortcut to tutorial path
+alias cfdemTut='cd $CFDEM_TUT_DIR'
+
+#- shortcut to solver path
+alias cfdemSol='cd $CFDEM_SOLVER_DIR'
+
+#- shortcut to utilities path
+alias cfdemUt='cd $CFDEM_UT_DIR'
+
+#- shortcut to run path
+alias cfdemRun='cd $CFDEM_PROJECT_USER_DIR/run'
+
+#- shortcut to user solver path
+alias cfdemUsrSol='cd $CFDEM_PROJECT_USER_DIR/applications/solvers'
+
+#- shortcut to documentation path
+alias cfdemDoc='cd $CFDEM_DOC_DIR'
+
+#- shortcut to open the doxygen with firefox
+alias cfdemDox='firefox $CFDEM_DOC_DIR/doxygen/html/index.html'
+
+#- shortcut to LIGGGHTS path
+alias cfdemLIG='cd $CFDEM_LIGGGHTS_SRC_DIR'
+
+#- shortcut to system test
+alias cfdemSysTest='bash $CFDEM_PROJECT_DIR/etc/cfdemSystemTest.sh'
+
+#- shortcut to pull LIGGGHTS
+alias cfdemPullLIG='bash $CFDEM_PROJECT_DIR/etc/pullLIGGGHTS.sh'
+
+#- shortcut to pull CFDEMcoupling
+alias cfdemPullCFDEMcoupling='bash $CFDEM_PROJECT_DIR/etc/pullCFDEMcoupling.sh'
+
+#- shortcut to clean CFDEM
+alias cfdemCleanCFDEM='bash $CFDEM_PROJECT_DIR/etc/cleanCFDEMcoupling.sh'
+
+#- shortcut to compile LIGGGHTS + sublibraries
+alias cfdemCompLIG='bash $CFDEM_PROJECT_DIR/etc/compileLIGGGHTS.sh'
+
+#- shortcut to compile CFDEMcoupling +LIGGGHTS
+alias cfdemCompCFDEMall='bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling_all.sh'
+
+#- shortcut to compile CFDEMcoupling (src+solvers)
+alias cfdemCompCFDEM='bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling.sh'
+
+#- shortcut to compile CFDEMcoupling src
+alias cfdemCompCFDEMsrc='bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling_src.sh'
+
+#- shortcut to compile CFDEMcoupling solvers
+alias cfdemCompCFDEMsol='bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling_sol.sh'
+
+#- shortcut to compile CFDEMcoupling utilities
+alias cfdemCompCFDEMuti='bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling_uti.sh'
+
+#- shortcut to test basic tutorials
+alias cfdemTestTUT='bash $CFDEM_PROJECT_DIR/etc/testTutorials.sh'
+
+#- shortcut to visualize the clock model data
+alias vizClock='python $CFDEM_UT_DIR/vizClock/matPlot.py'
+
+#- recursive touch of current directory
+alias touchRec='find ./* -exec touch {} \;'
+
+#- shortcut to run liggghts in serial
+cfdemLiggghts() { $CFDEM_LIGGGHTS_BIN_DIR/liggghts < $1; }
+export -f cfdemLiggghts
+
+#- shortcut to run liggghts in parallel
+cfdemLiggghtsPar() { mpirun -np $2 $CFDEM_LIGGGHTS_BIN_DIR/liggghts < $1; }
+export -f cfdemLiggghtsPar
+
+#- shortcut to open files including a pattern
+cfdemGrep() { grep -rl "$1" ./* | xargs gedit; }
+export -f cfdemGrep
+
+#- shortcut lo list files in a directory
+#cfdemListFiles() { find $1 | sed s:""$1"":: > listOfFiles.txt; }   #leave out the dir iteslf in list
+cfdemListFiles() { find $1 > listOfFiles.txt; }                     #keep the dir in list
+export -f cfdemListFiles
+
+#- check if the user directory exists
+if [ -d "$CFDEM_PROJECT_USER_DIR" ]; then
+    :
+else
+        echo "make new dirs $CFDEM_PROJECT_USER_DIR ? (y/n)"
+        read YN
+        if [ $YN == "y" ]; then
+            mkdir -p $CFDEM_PROJECT_USER_DIR
+            cd $CFDEM_PROJECT_USER_DIR
+            mkdir run
+            mkdir -p log/logFilesCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
+            mkdir -p applications/solvers
+        else
+            echo "aborted by user."
+            #exit
+        fi
+fi

etc/cfdemSystemTest.sh

@@ -1,12 +1,12 @@
 #!/bin/bash
 
 #===================================================================#
-# sytsem settings test routine for cfdem project 
+# sytsem settings test routine for cfdem project
 # Christoph Goniva - May. 2011, DCS Computing GmbH
 #===================================================================#
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #- show gcc settings
 checkGPP="true"
@@ -36,16 +36,14 @@ checkDirComment "$CFDEM_LIGGGHTS_SRC_DIR" '$CFDEM_LIGGGHTS_SRC_DIR' "yes"
 checkEnvComment "$CFDEM_LIGGGHTS_BIN_DIR" '$CFDEM_LIGGGHTS_BIN_DIR' "yes"
 checkDirComment "$CFDEM_LPP_DIR" '$CFDEM_LPP_DIR' "yes"
 checkDirComment "$CFDEM_ADD_LIBS_DIR" '$CFDEM_ADD_LIBS_DIR' "yes"
-checkDirComment "$CFDEM_PIZZA_DIR" '$CFDEM_PIZZA_DIR' "no"
 checkDirComment "$CFDEM_TEST_HARNESS_PATH" '$CFDEM_TEST_HARNESS_PATH' "no"
-#checkDirComment "$C3PO_SRC_DIR" '$C3PO_SRC_DIR' "no"
 echo ""
 
 echo "library names"
-echo '$CFDEM_LIGGGHTS_LIB_NAME = '"$CFDEM_LIGGGHTS_LIB_NAME"
 echo '$CFDEM_LIB_NAME = '"$CFDEM_LIB_NAME"
-echo '$LD_LIBRARY_PATH  = '"$LD_LIBRARY_PATH"
-echo '$WM_NCOMPPROCS  = '"$WM_NCOMPPROCS"
+echo '$PATH = '"$PATH"
+echo '$LD_LIBRARY_PATH = '"$LD_LIBRARY_PATH"
+echo '$WM_NCOMPPROCS = '"$WM_NCOMPPROCS"
 
 echo "*******************"
 
@@ -79,6 +77,6 @@ if [ $checkAddOn == "true" ]
     if [ $(checkDir $filePath) == "true" ]; then
         source $filePath/etc/$packageName"SystemTest.sh"
     else
-        echo "$packageName does not exist." 
+        echo "$packageName does not exist."
     fi
 fi

etc/cleanCFDEMcoupling.sh

@@ -6,7 +6,7 @@
 #===================================================================#
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #================================================================================#
 # clean src remove object files

etc/compileCFDEMcoupling.sh

@@ -6,26 +6,26 @@
 #===================================================================#
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 NOW="$(date +"%Y-%m-%d-%H:%M")"
 logDir="log"
 
 
-cd $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc
+cd $CFDEM_PROJECT_DIR/etc
 mkdir -p $logDir
 
 #================================================================================#
 # compile src
 #================================================================================#
-bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling_src.sh
+bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling_src.sh
 
 #================================================================================#
 # compile solvers
 #================================================================================#
-bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling_sol.sh
+bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling_sol.sh
 
 #================================================================================#
 # compile utilities
 #================================================================================#
-bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling_uti.sh
+bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling_uti.sh

etc/compileCFDEMcoupling_all.sh

@@ -7,26 +7,26 @@
 #===================================================================#
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 NOW="$(date +"%Y-%m-%d-%H:%M")"
 logDir="log"
 
 
-cd $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc
+cd $CFDEM_PROJECT_DIR/etc
 mkdir -p $logDir
 
 #================================================================================#
 # compile LIGGGHTS src
 #================================================================================#
-bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileLIGGGHTS.sh
+bash $CFDEM_PROJECT_DIR/etc/compileLIGGGHTS.sh
 
 #================================================================================#
 # compile LIGGGHTS libraries
 #================================================================================#
-bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileLIGGGHTS_lib.sh
+bash $CFDEM_PROJECT_DIR/etc/compileLIGGGHTS_lib.sh
 
 #================================================================================#
 # compile CFDEMcoupling
 #================================================================================#
-bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling.sh
+bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling.sh

etc/compileCFDEMcoupling_sol.sh

@@ -8,9 +8,9 @@
 whitelist="solver-list.txt"
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 logDir="log"
-cd $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc
+cd $CFDEM_PROJECT_DIR/etc
 mkdir -p $logDir
 
 #- remove old success/fail logs

etc/compileCFDEMcoupling_src.sh

@@ -7,20 +7,20 @@
 #===================================================================#
  
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 NOW="$(date +"%Y-%m-%d-%H:%M")"
 logDir="log"
 
 
-cd $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc
+cd $CFDEM_PROJECT_DIR/etc
 mkdir -p $logDir
 
 
 #================================================================================#
 # compile src
 #================================================================================#
-whitelist="$CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/library-list.txt"
+whitelist="$CFDEM_PROJECT_DIR/etc/library-list.txt"
 echo ""
 echo "Please provide the libraries to be compiled in the $CWD/$whitelist file."
 

etc/compileCFDEMcoupling_uti.sh

@@ -8,9 +8,9 @@
 whitelist="utilities-list.txt"
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 logDir="log"
-cd $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc
+cd $CFDEM_PROJECT_DIR/etc
 mkdir -p $logDir
 
 CWD="$(dirname "$(readlink -f ${BASH_SOURCE[0]})")"

etc/compileLIGGGHTS.sh

@@ -6,12 +6,12 @@
 #===================================================================
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 NOW="$(date +"%Y-%m-%d-%H:%M")"
 logDir="log"
 
-cd $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc
+cd $CFDEM_PROJECT_DIR/etc
 mkdir -p $logDir
 
 #================================================================================#
@@ -38,4 +38,4 @@ compileLIGGGHTS $logpath $logfileName $headerText
 #================================================================================#
 # compile LIGGGHTS libraries
 #================================================================================#
-bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileLIGGGHTS_lib.sh
+bash $CFDEM_PROJECT_DIR/etc/compileLIGGGHTS_lib.sh

etc/compileLIGGGHTS_lib.sh

@@ -6,19 +6,19 @@
 #===================================================================#
  
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 NOW="$(date +"%Y-%m-%d-%H:%M")"
 logDir="log"
 
 
-cd $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc
+cd $CFDEM_PROJECT_DIR/etc
 mkdir -p $logDir
 
 #================================================================================#
 # compile src
 #================================================================================#
-    whitelist="$CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/library-liggghts-list.txt"
+    whitelist="$CFDEM_PROJECT_DIR/etc/library-liggghts-list.txt"
     echo ""
     echo "Compiling sub-libraries of LIGGGHTS now..."
     echo "Please provide the libraries to be compiled in the $CWD/$whitelist file."

etc/cshrc

@@ -0,0 +1,289 @@
+#----------------------------------*-sh-*--------------------------------------
+# CFDEMcoupling
+#
+# Copyright 2009-2012 JKU Linz
+# Copyright 2012-2015 DCS Computing GmbH, Linz
+# Copyright 2015-     JKU Linz
+#------------------------------------------------------------------------------
+#
+# File
+#     etc/cshrc
+#
+# Description
+#     Startup file for CFDEMcoupling
+#     Sourced from ~/.cshrc
+#------------------------------------------------------------------------------
+
+setenv CFDEM_PROJECT CFDEM
+setenv CFDEM_VERSION 17.02
+
+################################################################################
+# USER EDITABLE PART: Changes made here may be lost with the next upgrade
+#
+# Please set to the appropriate path if the default is not correct.
+#
+# activate compatible OpenFOAM version
+. $HOME/OpenFOAM/OpenFOAM-4.x/etc/cshrc
+#
+# CFDEMcoupling
+setenv CFDEM_INST_DIR $HOME/$CFDEM_PROJECT
+setenv CFDEM_PROJECT_DIR $CFDEM_INST_DIR/CFDEMcoupling
+setenv CFDEM_PROJECT_USER_DIR $CFDEM_INST_DIR/$USER-$WM_PROJECT_VERSION
+#
+# LIGGGHTS
+setenv CFDEM_LIGGGHTS_INST_DIR $CFDEM_INST_DIR/LIGGGHTS
+#
+# LPP installation path
+setenv CFDEM_LPP_INST_DIR $CFDEM_INST_DIR/LPP
+#
+# Path to additional libraries
+setenv CFDEM_ADD_LIBS_DIR
+#
+# END OF (NORMAL) USER EDITABLE PART
+################################################################################
+
+#- The old dirs to be cleaned from the environment variables
+set cfdemOldDirs=
+if ( $?CFDEM_LIGGGHTS_BIN_DIR ) then
+   set cfdemOldDirs="$cfdemOldDirs $CFDEM_LIGGGHTS_BIN_DIR"
+endif
+if ( $?CFDEM_APP_DIR ) then
+   set cfdemOldDirs="$cfdemOldDirs $CFDEM_APP_DIR"
+endif
+if ( $?CFDEM_LIB_DIR ) then
+   set cfdemOldDirs="$cfdemOldDirs $CFDEM_LIB_DIR"
+endif
+
+setenv CFDEM_LIGGGHTS_SRC_DIR $CFDEM_LIGGGHTS_INST_DIR/src
+setenv CFDEM_LIGGGHTS_BIN_DIR $CFDEM_LIGGGHTS_INST_DIR/src-build
+
+#------------------------------------------------------------------------------
+# Source files, possibly with some verbosity
+#------------------------------------------------------------------------------
+alias _foamSource 'if ($?FOAM_VERBOSE && $?prompt) echo "Sourcing: \!*"; if (\!* != "") source \!*'
+
+#------------------------------------------------------------------------------
+# Evaluate command-line parameters
+# these can be used to set/unset values
+#------------------------------------------------------------------------------
+while ( $#argv > 0 )
+    switch ($argv[1])
+    case -*:
+        # stray option (not meant for us here) -> get out
+        break
+        breaksw
+    case *=:
+        # name=       -> unsetenv name
+        if ($?FOAM_VERBOSE && $?prompt) echo "unsetenv $argv[1]:s/=//"
+        eval "unsetenv $argv[1]:s/=//"
+        breaksw
+    case *=*:
+        # name=value  -> setenv name value
+        if ($?FOAM_VERBOSE && $?prompt) echo "setenv $argv[1]:s/=/ /"
+        eval "setenv $argv[1]:s/=/ /"
+        breaksw
+    default:
+        # filename: source it
+        if ( -f "$1" ) then
+            _foamSource "$1"
+        else
+            _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -silent "$1"`
+        endif
+        breaksw
+    endsw
+    shift
+end
+
+#------------------------------------------------------------------------------
+
+setenv CFDEM_SRC_DIR $CFDEM_PROJECT_DIR/src
+setenv CFDEM_SOLVER_DIR $CFDEM_PROJECT_DIR/applications/solvers
+setenv CFDEM_UT_DIR $CFDEM_PROJECT_DIR/applications/utilities
+setenv CFDEM_DOC_DIR $CFDEM_PROJECT_DIR/doc
+setenv CFDEM_TUT_DIR $CFDEM_PROJECT_DIR/tutorials
+setenv CFDEM_LPP_DIR $CFDEM_LPP_INST_DIR/src
+
+#------------------------------------------------------------------------------
+
+#- CFDEM lib name
+setenv CFDEM_LIB_NAME lagrangianCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
+
+#- CFDEM compressible lib name
+setenv CFDEM_LIB_COMP_NAME lagrangianCFDEMcomp-$CFDEM_VERSION-$WM_PROJECT_VERSION
+
+#- Check if additional libraries should be compiled together with solvers
+if ( ! ($?CFDEM_ADD_LIBS_DIR) ) then
+    setenv CFDEM_ADD_LIBS_DIR $CFDEM_PROJECT_DIR/etc
+else
+    echo "using CFDEM_ADD_LIBS_DIR=$CFDEM_ADD_LIBS_DIR defined by user."
+endif
+
+#------------------------------------------------------------------------------
+
+#- LMP Many2Many lib path and makefile
+setenv CFDEM_Many2ManyLIB_PATH $CFDEM_SRC_DIR/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library
+setenv CFDEM_Many2ManyLIB_MAKEFILENAME fedora_fpic
+
+#------------------------------------------------------------------------------
+
+#- path to test harness
+setenv CFDEM_TEST_HARNESS_PATH $CFDEM_PROJECT_USER_DIR/log/logFilesCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
+
+#- path to libraries
+setenv CFDEM_LIB_DIR $CFDEM_PROJECT_DIR/platforms/$WM_OPTIONS/lib
+
+#- path to apps
+setenv CFDEM_APP_DIR $CFDEM_PROJECT_DIR/platforms/$WM_OPTIONS/bin
+
+#- create directories
+mkdir -p $CFDEM_LIB_DIR
+mkdir -p $CFDEM_APP_DIR
+
+#- path to OF version flag file
+setenv CFDEM_OFVERSION_DIR $CFDEM_PROJECT_DIR/etc/OFversion
+
+#------------------------------------------------------------------------------
+# Clean standard environment variables (PATH, LD_LIBRARY_PATH)
+#------------------------------------------------------------------------------
+set foamClean=$WM_PROJECT_DIR/bin/foamCleanPath
+
+#- prevent local variables from shadowing setenv variables
+unset PATH LD_LIBRARY_PATH
+
+if (! $?LD_LIBRARY_PATH ) setenv LD_LIBRARY_PATH ''
+
+#- Clean PATH
+set cleaned=`$foamClean "$PATH" "$cfdemOldDirs"`
+if ( $status == 0 ) setenv PATH $cleaned
+
+#- Clean LD_LIBRARY_PATH
+set cleaned=`$foamClean "$LD_LIBRARY_PATH" "$cfdemOldDirs"`
+if ( $status == 0 ) setenv LD_LIBRARY_PATH $cleaned
+
+#- add binary directories to $PATH
+_foamAddPath $CFDEM_APP_DIR:$CFDEM_LIGGGHTS_BIN_DIR
+_foamAddLib $CFDEM_LIB_DIR
+
+#------------------------------------------------------------------------------
+# Cleanup environment:
+#------------------------------------------------------------------------------
+unset cleaned foamClean cfdemOldDirs
+unalias _foamSource
+
+#------------------------------------------------------------------------------
+#- settings for lpp postproc tool
+#------------------------------------------------------------------------------
+
+#- nr of procs for lpp tool
+setenv CFDEM_LPP_NPROCS 4
+
+#- nr of procs for lpp tool
+setenv CFDEM_LPP_CHUNKSIZE 1
+
+#- shortcut to run lpp
+alias lpp 'python -i $CFDEM_LPP_DIR/lpp.py --cpunum $CFDEM_LPP_NPROCS --chunksize $CFDEM_LPP_CHUNKSIZE \!:1'
+
+#------------------------------------------------------------------------------
+# aliases for easy navigation (no changes necessary)
+#------------------------------------------------------------------------------
+
+#- shortcut to cfdem path
+alias cfdem 'cd $CFDEM_PROJECT_DIR'
+
+#- shortcut to src path
+alias cfdemSrc 'cd $CFDEM_SRC_DIR'
+
+#- shortcut to tutorial path
+alias cfdemTut 'cd $CFDEM_TUT_DIR'
+
+#- shortcut to solver path
+alias cfdemSol 'cd $CFDEM_SOLVER_DIR'
+
+#- shortcut to utilities path
+alias cfdemUt 'cd $CFDEM_UT_DIR'
+
+#- shortcut to run path
+alias cfdemRun 'cd $CFDEM_PROJECT_USER_DIR/run'
+
+#- shortcut to user solver path
+alias cfdemUsrSol 'cd $CFDEM_PROJECT_USER_DIR/applications/solvers'
+
+#- shortcut to documentation path
+alias cfdemDoc 'cd $CFDEM_DOC_DIR'
+
+#- shortcut to open the doxygen with firefox
+alias cfdemDox 'firefox $CFDEM_DOC_DIR/doxygen/html/index.html'
+
+#- shortcut to LIGGGHTS path
+alias cfdemLIG 'cd $CFDEM_LIGGGHTS_SRC_DIR'
+
+#- shortcut to system test
+alias cfdemSysTest 'bash $CFDEM_PROJECT_DIR/etc/cfdemSystemTest.sh'
+
+#- shortcut to pull LIGGGHTS
+alias cfdemPullLIG 'bash $CFDEM_PROJECT_DIR/etc/pullLIGGGHTS.sh'
+
+#- shortcut to pull CFDEMcoupling
+alias cfdemPullCFDEMcoupling 'bash $CFDEM_PROJECT_DIR/etc/pullCFDEMcoupling.sh'
+
+#- shortcut to clean CFDEM
+alias cfdemCleanCFDEM 'bash $CFDEM_PROJECT_DIR/etc/cleanCFDEMcoupling.sh'
+
+#- shortcut to compile LIGGGHTS + sublibraries
+alias cfdemCompLIG 'bash $CFDEM_PROJECT_DIR/etc/compileLIGGGHTS.sh'
+
+#- shortcut to compile CFDEMcoupling +LIGGGHTS
+alias cfdemCompCFDEMall 'bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling_all.sh'
+
+#- shortcut to compile CFDEMcoupling (src+solvers)
+alias cfdemCompCFDEM 'bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling.sh'
+
+#- shortcut to compile CFDEMcoupling src
+alias cfdemCompCFDEMsrc 'bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling_src.sh'
+
+#- shortcut to compile CFDEMcoupling solvers
+alias cfdemCompCFDEMsol 'bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling_sol.sh'
+
+#- shortcut to compile CFDEMcoupling utilities
+alias cfdemCompCFDEMuti 'bash $CFDEM_PROJECT_DIR/etc/compileCFDEMcoupling_uti.sh'
+
+#- shortcut to test basic tutorials
+alias cfdemTestTUT 'bash $CFDEM_PROJECT_DIR/etc/testTutorials.sh'
+
+#- shortcut to visualize the clock model data
+alias vizClock 'python $CFDEM_UT_DIR/vizClock/matPlot.py'
+
+#- shortcut to run liggghts in serial
+alias cfdemLiggghts '$CFDEM_LIGGGHTS_BIN_DIR/liggghts'
+
+#- shortcut to run liggghts in parallel (no fcts in csh...)
+alias cfdemLiggghtsPar 'echo "mpirun -np xx -machinefile mynodes $CFDEM_LIGGGHTS_BIN_DIR/liggghts < in.liggghts_init"'
+
+#- shortcut to run liggghts in parallel
+# unfortunately no functions available in csh
+
+#- shortcut to run lpp
+alias lpp 'python -i $CFDEM_LPP_DIR/lpp.py \!:1'
+
+#- check if the user directory exists
+if ( -d "$CFDEM_PROJECT_USER_DIR" ) then
+    :
+else
+    if ( -d "$CFDEM_PROJECT_DIR" ) then
+        echo "make new dirs $CFDEM_PROJECT_USER_DIR ? (y/n)"
+        set YN=$<
+        if ( $YN == "y" ) then
+            mkdir -p $CFDEM_PROJECT_USER_DIR
+            cd $CFDEM_PROJECT_USER_DIR
+            mkdir run
+            mkdir -p log/logFilesCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
+            mkdir -p applications/solvers
+        else
+            echo "aborted by user."
+            exit
+        endif
+    else
+        echo "error in CFDEMcoupling's cshrc."
+        exit
+    endif
+endif

etc/functions.sh

@@ -249,7 +249,7 @@ cleanCFDEM()
 
     #**********************************************
     #cleaning libraries
-    whitelist="$CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/library-list.txt"
+    whitelist="$CFDEM_PROJECT_DIR/etc/library-list.txt"
     echo ""
     echo "Please provide the libraries to be cleaned in the $CWD/$whitelist file."
 
@@ -303,7 +303,7 @@ cleanCFDEM()
 
     #**********************************************
     #cleaning solvers
-    whitelist="$CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/solver-list.txt"
+    whitelist="$CFDEM_PROJECT_DIR/etc/solver-list.txt"
     echo ""
     echo "Please provide the solvers to be cleaned in the $CWD/$whitelist file."
 

etc/pullLIGGGHTS.sh

@@ -6,12 +6,12 @@
 #===================================================================
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 NOW="$(date +"%Y-%m-%d-%H:%M")"
 logDir="log"
 
-cd $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc
+cd $CFDEM_PROJECT_DIR/etc
 mkdir -p $logDir
 
 #--------------------------------------------------------------------------------#

src/lagrangian/cfdemParticle/Make/options

@@ -9,6 +9,7 @@ include $(CFDEM_ADD_LIBS_DIR)/additionalLibs
 EXE_INC = \
      $(PFLAGS) \
      $(PINC) \
+    -I$(CFDEM_OFVERSION_DIR) \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/transportModels \
     -I$(LIB_SRC)/TurbulenceModels/turbulenceModels/lnInclude \

src/lagrangian/cfdemParticle/etc/bashrc

@@ -1,216 +0,0 @@
-#----------------------------------*-sh-*--------------------------------------
-# CFDEMcoupling
-# Christoph Goniva
-# June 2012
-#------------------------------------------------------------------------------
-#
-# Script
-#     etc/bashrc
-#
-# Description
-#     Startup file for cfdem exporting environment variables
-#     Sourced  ~/.bashrc
-#
-#- adapt this and add to ./bashrc 
-#- you can test the correctness using cfdemSystemTest.sh
-
-##================================================#
-##- source cfdem env vars
-#export CFDEM_VERSION=PUBLIC
-#export CFDEM_PROJECT_DIR=$HOME/CFDEM/CFDEMcoupling-$CFDEM_VERSION-$WM_PROJECT_VERSION
-#export CFDEM_SRC_DIR=$CFDEM_PROJECT_DIR/src
-#export CFDEM_SOLVER_DIR=$CFDEM_PROJECT_DIR/applications/solvers
-#export CFDEM_DOC_DIR=$CFDEM_PROJECT_DIR/doc
-#export CFDEM_UT_DIR=$CFDEM_PROJECT_DIR/applications/utilities
-#export CFDEM_TUT_DIR=$CFDEM_PROJECT_DIR/tutorials
-#export CFDEM_PROJECT_USER_DIR=$HOME/CFDEM/$LOGNAME-$CFDEM_VERSION-$WM_PROJECT_VERSION
-#export CFDEM_bashrc=$CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/bashrc
-#export CFDEM_LIGGGHTS_SRC_DIR=$HOME/LIGGGHTS/LIGGGHTS-PUBLIC/src
-#export CFDEM_LIGGGHTS_BIN_DIR=$HOME/LIGGGHTS/LIGGGHTS-PUBLIC/src-build
-#export CFDEM_LIGGGHTS_MAKEFILE_NAME=fedora_fpic # obsolete with CMake
-#export CFDEM_LPP_DIR=$HOME/LIGGGHTS/mylpp/src
-#export CFDEM_PIZZA_DIR=$HOME/LIGGGHTS/PIZZA/gran_pizza_17Aug10/src
-#. $CFDEM_bashrc
-#================================================#
-#------------------------------------------------------------------------------
-
-#------------------------------------------------------------------------------
-#- export environment variables (adapt to your paths)
-#------------------------------------------------------------------------------
-
-#check if default lammps lib path should be used
-if [[ $CFDEM_LAMMPS_LIB_DIR == "" ]]; then
-    export CFDEM_LAMMPS_LIB_DIR=$CFDEM_LIGGGHTS_SRC_DIR/../lib/
-else
-    echo "using CFDEM_LAMMPS_LIB_DIR=$CFDEM_LAMMPS_LIB_DIR defined by user."
-fi
-
-#- LIGGGHTS lib name
-export CFDEM_LIGGGHTS_LIB_NAME=lmp_$CFDEM_LIGGGHTS_MAKEFILE_NAME
-
-#- CFDEM lib name
-export CFDEM_LIB_NAME=lagrangianCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
-
-#- CFDEM compressible lib name
-export CFDEM_LIB_COMP_NAME=lagrangianCFDEMcomp-$CFDEM_VERSION-$WM_PROJECT_VERSION
-
-#check if additional libraries should be compiled together with solvers
-if [[ $CFDEM_ADD_LIBS_DIR == "" ]]; then
-    export CFDEM_ADD_LIBS_DIR=$CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc
-else
-    echo "using CFDEM_ADD_LIBS_DIR=$CFDEM_ADD_LIBS_DIR defined by user."
-fi
-
-#-----------------------------------------------------
-# additional libraries
-
-#- LMP Many2Many lib path and makefile
-export CFDEM_Many2ManyLIB_PATH=$CFDEM_SRC_DIR/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library
-export CFDEM_Many2ManyLIB_MAKEFILENAME=$CFDEM_LIGGGHTS_MAKEFILE_NAME
-
-#- LMP M2M lib path and makefile
-export CFDEM_M2MLIB_PATH=$CFDEM_SRC_DIR/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayM2M/library
-export CFDEM_M2MLIB_MAKEFILENAME=$CFDEM_LIGGGHTS_MAKEFILE_NAME
-
-#- LMP POEMS lib path and makefile
-export CFDEM_POEMSLIB_PATH=$CFDEM_LAMMPS_LIB_DIR/poems
-export CFDEM_POEMSLIB_MAKEFILENAME=g++
-
-#- LMP ASPHERE lib path and makefile
-export CFDEM_ASPHERELIB_PATH=$CFDEM_LAMMPS_LIB_DIR/poems
-export CFDEM_ASPHERELIB_MAKEFILENAME=g++
-
-#-C3PO library
-export C3PO_SRC_DIR=$CFDEM_SRC_DIR/c3po
-#-----------------------------------------------------
-
-#- path to test harness
-export CFDEM_TEST_HARNESS_PATH=$CFDEM_PROJECT_USER_DIR/log/logFilesCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
-
-#- path to libraries
-export CFDEM_LIB_DIR=$FOAM_USER_LIBBIN
-
-#- path to apps
-export CFDEM_APP_DIR=$FOAM_USER_APPBIN
-
-#- path to OF version flag file
-export CFDEM_OFVERSION_DIR=$CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/OFversion
-#------------------------------------------------------------------------------
-#- settings for lpp postproc tool
-#------------------------------------------------------------------------------
-
-#- nr of procs for lpp tool
-export CFDEM_LPP_NPROCS=4
-
-#- nr of procs for lpp tool
-export CFDEM_LPP_CHUNKSIZE=1
-
-#- shortcut to run lpp
-alias lpp='python -i $CFDEM_LPP_DIR/lpp.py --cpunum $CFDEM_LPP_NPROCS --chunksize $CFDEM_LPP_CHUNKSIZE'
-
-#------------------------------------------------------------------------------
-#- aliases for easy navigation (no changes necessary)
-#------------------------------------------------------------------------------
-#- shortcut to cfdem path
-alias cfdem='cd $CFDEM_PROJECT_DIR'
-
-#- shortcut to src path
-alias cfdemSrc='cd $CFDEM_SRC_DIR'
-
-#- shortcut to tutorial path
-alias cfdemTut='cd $CFDEM_TUT_DIR'
-
-#- shortcut to solver path
-alias cfdemSol='cd $CFDEM_SOLVER_DIR'
-
-#- shortcut to utilities path
-alias cfdemUt='cd $CFDEM_UT_DIR'
-
-#- shortcut to run path
-alias cfdemRun='cd $CFDEM_PROJECT_USER_DIR/run'
-
-#- shortcut to user solver path
-alias cfdemUsrSol='cd $CFDEM_PROJECT_USER_DIR/applications/solvers'
-
-#- shortcut to documentation path
-alias cfdemDoc='cd $CFDEM_DOC_DIR'
-
-#- shortcut to open the doxygen with firefox
-alias cfdemDox='firefox $CFDEM_DOC_DIR/doxygen/html/index.html'
-
-#- shortcut to LIGGGHTS path
-alias cfdemLIG='cd $CFDEM_LIGGGHTS_SRC_DIR'
-
-#- shortcut to system test
-alias cfdemSysTest='bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/cfdemSystemTest.sh'
-
-#- shortcut to pull LIGGGHTS
-alias cfdemPullLIG='bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/pullLIGGGHTS.sh'
-
-#- shortcut to pull CFDEMcoupling
-alias cfdemPullCFDEMcoupling='bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/pullCFDEMcoupling.sh'
-
-#- shortcut to clean CFDEM
-alias cfdemCleanCFDEM='bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/cleanCFDEMcoupling.sh'
-
-#- shortcut to compile LIGGGHTS + sublibraries
-alias cfdemCompLIG='bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileLIGGGHTS.sh'
-
-#- shortcut to compile CFDEMcoupling +LIGGGHTS
-alias cfdemCompCFDEMall='bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling_all.sh'
-
-#- shortcut to compile CFDEMcoupling (src+solvers)
-alias cfdemCompCFDEM='bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling.sh'
-
-#- shortcut to compile CFDEMcoupling src
-alias cfdemCompCFDEMsrc='bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling_src.sh'
-
-#- shortcut to compile CFDEMcoupling solvers
-alias cfdemCompCFDEMsol='bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling_sol.sh'
-
-#- shortcut to compile CFDEMcoupling utilities
-alias cfdemCompCFDEMuti='bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling_uti.sh'
-
-#- shortcut to test basic tutorials
-alias cfdemTestTUT='bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/testTutorials.sh'
-
-#- shortcut to visualize the clock model data
-alias vizClock='python $CFDEM_UT_DIR/vizClock/matPlot.py'
-
-#- recursive touch of current directory
-alias touchRec='find ./* -exec touch {} \;'
-
-#- shortcut to run liggghts in serial
-cfdemLiggghts() { $CFDEM_LIGGGHTS_SRC_DIR/lmp_$CFDEM_LIGGGHTS_MAKEFILE_NAME < $1; }
-export -f cfdemLiggghts
-
-#- shortcut to run liggghts in parallel
-cfdemLiggghtsPar() { mpirun -np $2 $CFDEM_LIGGGHTS_SRC_DIR/lmp_$CFDEM_LIGGGHTS_MAKEFILE_NAME < $1; }
-export -f cfdemLiggghtsPar
-
-#- shortcut to open files including a pattern
-cfdemGrep() { grep -rl "$1" ./* | xargs gedit; }
-export -f cfdemGrep
-
-#- shortcut lo list files in a directory
-#cfdemListFiles() { find $1 | sed s:""$1"":: > listOfFiles.txt; }   #leave out the dir iteslf in list
-cfdemListFiles() { find $1 > listOfFiles.txt; }                     #keep the dir in list
-export -f cfdemListFiles
-
-# check if the run directory exists
-if [ -d "$CFDEM_PROJECT_USER_DIR" ]; then
-    :
-else
-        echo "make new dirs $CFDEM_PROJECT_USER_DIR ? (y/n)"
-        read YN
-        if [ $YN == "y" ]; then
-            mkdir -p $CFDEM_PROJECT_USER_DIR
-            cd $CFDEM_PROJECT_USER_DIR
-            mkdir run
-            mkdir -p log/logFilesCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
-            mkdir -p applications/solvers
-        else
-            echo "aborted by user."
-            #exit
-        fi
-fi

src/lagrangian/cfdemParticle/etc/cshrc

@@ -1,202 +0,0 @@
-#----------------------------------*-sh-*--------------------------------------
-# CFDEMcoupling
-# Christoph Goniva
-# June 2012
-#------------------------------------------------------------------------------
-#
-# Script
-#     etc/cshrc
-#
-# Description
-#     Startup file for cfdem exporting environment variables
-#     Sourced  ~/.cshrc
-#
-#- adapt this and add to ./cshrc 
-#- you can test the correctness using cfdemSystemTest.sh
-
-##================================================#
-##- source cfdem env vars
-#setenv CFDEM_VERSION PUBLIC
-#setenv CFDEM_PROJECT_DIR $HOME/CFDEM/CFDEMcoupling-$CFDEM_VERSION-$WM_PROJECT_VERSION
-#setenv CFDEM_SRC_DIR $CFDEM_PROJECT_DIR/src/lagrangian/cfdemParticle
-#setenv CFDEM_SOLVER_DIR $CFDEM_PROJECT_DIR/applications/solvers
-#setenv CFDEM_DOC_DIR $CFDEM_PROJECT_DIR/doc
-#setenv CFDEM_UT_DIR $CFDEM_PROJECT_DIR/applications/utilities
-#setenv CFDEM_TUT_DIR $CFDEM_PROJECT_DIR/tutorials
-#setenv CFDEM_PROJECT_USER_DIR $HOME/CFDEM/$LOGNAME-$CFDEM_VERSION-$WM_PROJECT_VERSION
-#setenv CFDEM_bashrc $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/cshrc
-#setenv CFDEM_LIGGGHTS_SRC_DIR $HOME/LIGGGHTS/LIGGGHTS-PUBLIC/src
-#setenv CFDEM_LIGGGHTS_MAKEFILE_NAME fedora_fpic
-#setenv CFDEM_LPP_DIR $HOME/LIGGGHTS/mylpp/src
-#setenv CFDEM_PIZZA_DIR $HOME/LIGGGHTS/PIZZA/gran_pizza_17Aug10/src
-#source $CFDEM_bashrc
-#================================================#
-#------------------------------------------------------------------------------
-
-#------------------------------------------------------------------------------
-#- export environment variables (adapt to your paths)
-#------------------------------------------------------------------------------
-
-#check if default lammps lib path should be used
-if ( ! ($?CFDEM_LAMMPS_LIB_DIR) ) then
-    setenv CFDEM_LAMMPS_LIB_DIR $CFDEM_LIGGGHTS_SRC_DIR"/../lib/"
-else
-    echo "using CFDEM_LAMMPS_LIB_DIR=$CFDEM_LAMMPS_LIB_DIR defined by user."
-endif
-
-#- LIGGGHTS lib name
-setenv CFDEM_LIGGGHTS_LIB_NAME lmp_$CFDEM_LIGGGHTS_MAKEFILE_NAME
-
-#- CFDEM lib name
-setenv CFDEM_LIB_NAME lagrangianCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
-
-#- CFDEM compressible lib name
-setenv CFDEM_LIB_COMP_NAME lagrangianCFDEMcomp-$CFDEM_VERSION-$WM_PROJECT_VERSION
-
-#check if additional libraries should be compiled together with solvers
-if ( ! ($?CFDEM_ADD_LIBS_DIR) ) then
-    setenv CFDEM_ADD_LIBS_DIR $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc
-else
-    echo "using CFDEM_ADD_LIBS_DIR=$CFDEM_ADD_LIBS_DIR defined by user."
-endif
-
-#-----------------------------------------------------
-# additional libraries
-
-#- LMP Many2Many lib path and makefile
-setenv CFDEM_Many2ManyLIB_PATH $CFDEM_SRC_DIR/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library
-setenv CFDEM_Many2ManyLIB_MAKEFILENAME $CFDEM_LIGGGHTS_MAKEFILE_NAME
-
-#- LMP M2M lib path
-setenv CFDEM_M2MLIB_PATH $CFDEM_SRC_DIR/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayM2M/library
-setenv CFDEM_M2MLIB_MAKEFILENAME $CFDEM_LIGGGHTS_MAKEFILE_NAME
-
-#- LMP POEMS lib path
-setenv CFDEM_POEMSLIB_PATH $CFDEM_LIGGGHTS_SRC_DIR/../lib/poems
-setenv CFDEM_POEMSLIB_MAKEFILENAME g++
-
-#- path to test harness
-setenv CFDEM_TEST_HARNESS_PATH $CFDEM_PROJECT_USER_DIR/log/logFilesCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
-
-#- path to libraries
-setenv CFDEM_LIB_DIR $FOAM_USER_LIBBIN
-
-#- path to apps
-setenv CFDEM_APP_DIR $FOAM_USER_APPBIN
-
-#------------------------------------------------------------------------------
-#- settings for lpp postproc tool
-#------------------------------------------------------------------------------
-
-#- nr of procs for lpp tool
-setenv CFDEM_LPP_NPROCS 4
-
-#- nr of procs for lpp tool
-setenv CFDEM_LPP_CHUNKSIZE 1
-
-#- shortcut to run lpp
-alias lpp 'python -i $CFDEM_LPP_DIR/lpp.py --cpunum $CFDEM_LPP_NPROCS --chunksize $CFDEM_LPP_CHUNKSIZE \!:1'
-
-#------------------------------------------------------------------------------
-#- aliases for easy navigation (no changes necessary)
-#------------------------------------------------------------------------------
-#- shortcut to cfdem path
-alias cfdem 'cd $CFDEM_PROJECT_DIR'
-
-#- shortcut to src path
-alias cfdemSrc 'cd $CFDEM_SRC_DIR'
-
-#- shortcut to tutorial path
-alias cfdemTut 'cd $CFDEM_TUT_DIR'
-
-#- shortcut to solver path
-alias cfdemSol 'cd $CFDEM_SOLVER_DIR'
-
-#- shortcut to utilities path
-alias cfdemUt 'cd $CFDEM_UT_DIR'
-
-#- shortcut to run path
-alias cfdemRun 'cd $CFDEM_PROJECT_USER_DIR/run'
-
-#- shortcut to user solver path
-alias cfdemUsrSol 'cd $CFDEM_PROJECT_USER_DIR/applications/solvers'
-
-#- shortcut to documentation path
-alias cfdemDoc 'cd $CFDEM_DOC_DIR'
-
-#- shortcut to open the doxygen with firefox
-alias cfdemDox 'firefox $CFDEM_DOC_DIR/doxygen/html/index.html'
-
-#- shortcut to LIGGGHTS path
-alias cfdemLIG 'cd $CFDEM_LIGGGHTS_SRC_DIR'
-
-#- shortcut to system test
-alias cfdemSysTest 'bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/cfdemSystemTest.sh'
-
-#- shortcut to pull LIGGGHTS
-alias cfdemPullLIG 'bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/pullLIGGGHTS.sh'
-
-#- shortcut to pull CFDEMcoupling
-alias cfdemPullCFDEMcoupling 'bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/pullCFDEMcoupling.sh'
-
-#- shortcut to clean CFDEM
-alias cfdemCleanCFDEM 'bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/cleanCFDEMcoupling.sh'
-
-#- shortcut to compile LIGGGHTS + sublibraries
-alias cfdemCompLIG 'bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileLIGGGHTS.sh'
-
-#- shortcut to compile CFDEMcoupling +LIGGGHTS
-alias cfdemCompCFDEMall 'bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling_all.sh'
-
-#- shortcut to compile CFDEMcoupling (src+solvers)
-alias cfdemCompCFDEM 'bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling.sh'
-
-#- shortcut to compile CFDEMcoupling src
-alias cfdemCompCFDEMsrc 'bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling_src.sh'
-
-#- shortcut to compile CFDEMcoupling solvers
-alias cfdemCompCFDEMsol 'bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling_sol.sh'
-
-#- shortcut to compile CFDEMcoupling utilities
-alias cfdemCompCFDEMuti 'bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/compileCFDEMcoupling_uti.sh'
-
-#- shortcut to test basic tutorials
-alias cfdemTestTUT 'bash $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/testTutorials.sh'
-
-#- shortcut to visualize the clock model data
-alias vizClock 'python $CFDEM_UT_DIR/vizClock/matPlot.py'
-
-#- shortcut to run liggghts in serial
-alias cfdemLiggghts '$CFDEM_LIGGGHTS_SRC_DIR/lmp_$CFDEM_LIGGGHTS_MAKEFILE_NAME'
-
-#- shortcut to run liggghts in parallel (no fcts in csh...)
-alias cfdemLiggghtsPar 'echo "mpirun -np xx -machinefile mynodes $CFDEM_LIGGGHTS_SRC_DIR/lmp_$CFDEM_LIGGGHTS_MAKEFILE_NAME < in.liggghts_init"'
-
-#- shortcut to run liggghts in parallel
-# unfortunately no functions available in csh
-
-#- shortcut to run lpp
-alias lpp 'python -i $CFDEM_LPP_DIR/lpp.py \!:1'
-
-# check if the directory exists
-if ( -d "$CFDEM_PROJECT_USER_DIR" ) then
-    :
-else
-    if ( -d "$CFDEM_PROJECT_DIR" ) then
-        echo "make new dirs $CFDEM_PROJECT_USER_DIR ? (y/n)"
-	set YN=$<
-        if ( $YN == "y" ) then
-            mkdir -p $CFDEM_PROJECT_USER_DIR
-            cd $CFDEM_PROJECT_USER_DIR
-            mkdir run
-            mkdir -p log/logFilesCFDEM-$CFDEM_VERSION-$WM_PROJECT_VERSION
-            mkdir -p applications/solvers
-        else
-            echo "aborted by user."
-            exit
-        endif
-    else
-        echo "error in CFDEMcoupling's cshrc."
-        exit
-    endif
-endif

src/lagrangian/cfdemParticleComp/Make/options

@@ -4,7 +4,7 @@
 sinclude $(GENERAL_RULES)/mplib$(WM_MPLIB)
 sinclude $(RULES)/mplib$(WM_MPLIB)
 
-GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always --tags)
+GIT_VERSION := $(shell git describe --dirty --always --tags)
 PFLAGS+= -DGITVERSION=\"$(GIT_VERSION)\"
 PFLAGS+= -Dcompre
 
@@ -12,6 +12,7 @@ PFLAGS+= -Dcompre
 EXE_INC = \
      $(PFLAGS) \
      $(PINC) \
+    -I$(CFDEM_OFVERSION_DIR) \
     -I../cfdemParticle/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/transportModels \
@@ -23,6 +24,9 @@ EXE_INC = \
     -I$(CFDEM_LIGGGHTS_SRC_DIR) \
     -I$(CFDEM_M2MLIB_PATH) \
     -I$(CFDEM_SRC_DIR)/cfdTools \
+    -Wno-old-style-cast \
+    -Wno-unused-result \
+    -Wno-literal-suffix
 
 LIB_LIBS = \
      $(PLIBS) \

tutorials/cfdemPostproc/fillCylinder/Allrun.sh

@@ -9,7 +9,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #- define variables
 casePath="$(dirname "$(readlink -f ${BASH_SOURCE[0]})")"
@@ -73,7 +73,7 @@ if [ $postproc == "true" ]
 
     #- get VTK data from CFD sim
     #foamToVTK
-    
+
     #- start paraview
     echo ""
     echo "trying to start paraview..."

tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/Allrun.sh

@@ -1,12 +1,12 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
+# allrun script for testcase as part of test routine
 # run settlingTest
 # Christoph Goniva - July. 2011, mod by Alice Hager - July 2011
 #===================================================================#
 
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #- define variables
 casePath="$(dirname "$(readlink -f ${BASH_SOURCE[0]})")"

tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/parCFDDEMrun.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
+# allrun script for testcase as part of test routine
 # run settlingTest CFD part
 # Christoph Goniva - Feb. 2011
 #===================================================================#
@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables
@@ -32,11 +32,11 @@ parCFDDEMrun $logpath $logfileName $casePath $headerText $solverName $nrProcs $m
 
 if [ $runOctave == "true" ]
   then
-    
+
     cd $casePath/CFD/octave
     octave postproc.m
-    evince pos_z_two_part_rec_glow.eps 
-    evince vel_z_two_part_rec_glow.eps 
+    evince pos_z_two_part_rec_glow.eps
+    evince vel_z_two_part_rec_glow.eps
     #display pos_y_two_part_rec_glow.png &
     #display vel_y_two_part_rec_glow.png &
 fi

tutorials/cfdemSolverPiso/ErgunTestCG/Allrun.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
+# allrun script for testcase as part of test routine
 # run ErgunTestCG
 # Christoph Goniva - Sept. 2010
 #===================================================================#
@@ -10,7 +10,7 @@
 casePath="$(dirname "$(readlink -f ${BASH_SOURCE[0]})")"
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 # check if mesh was built
 if [ -f "$casePath/CFD/constant/polyMesh/points" ]; then
@@ -29,4 +29,4 @@ else
 fi
 
 #- run parallel CFD-DEM in new terminal
-gnome-terminal --title='cfdemSolverPiso ErgunTestCG CFD'  -e "bash $casePath/parCFDDEMrun.sh" 
+gnome-terminal --title='cfdemSolverPiso ErgunTestCG CFD'  -e "bash $casePath/parCFDDEMrun.sh"

tutorials/cfdemSolverPiso/ErgunTestCG/parCFDDEMrun.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
+# allrun script for testcase as part of test routine
 # run settlingTest CFD part
 # Christoph Goniva - Feb. 2011
 #===================================================================#
@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables
@@ -45,7 +45,7 @@ if [ $runOctave == "true" ]
         #- run octave
         octave totalPressureDrop.m
 
-        #- show plot 
+        #- show plot
         evince cfdemSolverPiso_ErgunTestCG.eps
 
         #- copy log file to test harness
@@ -67,8 +67,6 @@ if [ $postproc == "true" ]
     #- get VTK data from CFD sim
     cd $casePath/CFD
     foamToVTK                                                   #- serial run of foamToVTK
-    #source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh                       #- include functions
-    #pseudoParallelRun "foamToVTK" $nrPostProcProcessors          #- pseudo parallel run of foamToVTK
 
     #- start paraview
     paraview

tutorials/cfdemSolverPiso/ErgunTestCG/parDEMrun.sh

@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables

tutorials/cfdemSolverPiso/ErgunTestMPI/parCFDDEMrun.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
+# allrun script for testcase as part of test routine
 # run settlingTest CFD part
 # Christoph Goniva - Feb. 2011
 #===================================================================#
@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables
@@ -45,7 +45,7 @@ if [ $runOctave == "true" ]
         #- run octave
         octave totalPressureDrop.m
 
-        #- show plot 
+        #- show plot
         evince cfdemSolverPiso_ErgunTestMPI.eps
 
         #- copy log file to test harness
@@ -67,8 +67,6 @@ if [ $postproc == "true" ]
     #- get VTK data from CFD sim
     cd $casePath/CFD
     foamToVTK                                                   #- serial run of foamToVTK
-    #source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh                       #- include functions
-    #pseudoParallelRun "foamToVTK" $nrPostProcProcessors          #- pseudo parallel run of foamToVTK
 
     #- start paraview
     paraview

tutorials/cfdemSolverPiso/ErgunTestMPI/parDEMrun.sh

@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 echo "starting DEM run in parallel..."
 #--------------------------------------------------------------------------------#

tutorials/cfdemSolverPiso/ErgunTestMPI_cgs/parCFDDEMrun.sh

@@ -1,8 +1,8 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
-# run ErgunTestMPI_cgs 
+# allrun script for testcase as part of test routine
+# run ErgunTestMPI_cgs
 # Christoph Goniva - March 2013
 #===================================================================#
 
@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables
@@ -45,7 +45,7 @@ if [ $runOctave == "true" ]
         #- run octave
         octave totalPressureDrop.m
 
-        #- show plot 
+        #- show plot
         evince cfdemSolverPiso_ErgunTestMPI.eps
 
         #- copy log file to test harness
@@ -67,8 +67,6 @@ if [ $postproc == "true" ]
     #- get VTK data from CFD sim
     cd $casePath/CFD
     foamToVTK                                                   #- serial run of foamToVTK
-    #source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh                       #- include functions
-    #pseudoParallelRun "foamToVTK" $nrPostProcProcessors          #- pseudo parallel run of foamToVTK
 
     #- start paraview
     paraview

tutorials/cfdemSolverPiso/ErgunTestMPI_cgs/parDEMrun.sh

@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables

tutorials/cfdemSolverPiso/ErgunTestMPI_restart/Allrun.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
+# allrun script for testcase as part of test routine
 # run settlingTest
 # Christoph Goniva - Sept. 2010
 #===================================================================#
@@ -35,7 +35,7 @@ cp $casePath/CFD/system/controlDict_run $casePath/CFD/system/controlDict
 #-------------------------------------------------------#
 
 #- run parallel CFD-DEM in new terminal
-gnome-terminal --title='cfdemSolverPiso ErgunTestMPI_restart CFD'  -e "bash $casePath/parCFDDEMrun.sh" 
+gnome-terminal --title='cfdemSolverPiso ErgunTestMPI_restart CFD'  -e "bash $casePath/parCFDDEMrun.sh"
 
 #- wait until sim has finished then run octave
 echo "simulation finished? ...press enter to proceed"
@@ -49,7 +49,7 @@ cp $casePath/CFD/constant/couplingProperties_restart $casePath/CFD/constant/coup
 cp $casePath/CFD/system/controlDict_restart $casePath/CFD/system/controlDict
 
 #- run parallel CFD-DEM in new terminal
-#gnome-terminal --title='cfdemSolverPiso ErgunTestMPI_restart CFD'  -e "bash $casePath/parCFDDEMrun.sh" 
+#gnome-terminal --title='cfdemSolverPiso ErgunTestMPI_restart CFD'  -e "bash $casePath/parCFDDEMrun.sh"
 bash $casePath/parCFDDEMrun.sh
 
 
@@ -70,7 +70,7 @@ if [ $runOctave == "true" ]
     #- run octave
     octave totalPressureDrop.m
 
-    #- show plot 
+    #- show plot
     evince cfdemSolverPiso_ErgunTestMPI.eps
 
     #- copy log file to test harness
@@ -92,8 +92,6 @@ if [ $postproc == "true" ]
     #- get VTK data from CFD sim
     cd $casePath/CFD
     foamToVTK                                                   #- serial run of foamToVTK
-    #source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh                       #- include functions
-    #pseudoParallelRun "foamToVTK" $nrPostProcProcessors          #- pseudo parallel run of foamToVTK
 
     #- start paraview
     paraview

tutorials/cfdemSolverPiso/ErgunTestMPI_restart/parCFDDEMrun.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
+# allrun script for testcase as part of test routine
 # run settlingTest CFD part
 # Christoph Goniva - Feb. 2011
 #===================================================================#
@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables

tutorials/cfdemSolverPiso/ErgunTestMPI_restart/parDEMrun.sh

@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables

tutorials/cfdemSolverPiso/settlingTestMPI/parCFDDEMrun.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
+# allrun script for testcase as part of test routine
 # run settlingTest CFD part
 # Christoph Goniva - Feb. 2011
 #===================================================================#
@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables
@@ -42,7 +42,7 @@ if [ $runOctave == "true" ]
         #- run octave
         octave settlingVelocity.m
 
-        #- show plot 
+        #- show plot
         evince cfdemSolverPiso_settlingTestMPI.eps
 
         #- copy log file to test harness
@@ -64,8 +64,6 @@ if [ $postproc == "true" ]
     #- get VTK data from CFD sim
     cd $casePath/CFD
     foamToVTK                                                   #- serial run of foamToVTK
-    #source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh                       #- include functions
-    #pseudoParallelRun "foamToVTK" $nrPostProcProcessors          #- pseudo parallel run of foamToVTK
 
     #- start paraview
     paraview

tutorials/cfdemSolverPisoMS/ErgunTestMPI/Allrun.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
+# allrun script for testcase as part of test routine
 # run settlingTest
 # Christoph Goniva - Sept. 2010
 #===================================================================#
@@ -22,7 +22,7 @@ else
 fi
 
 #- run parallel CFD-DEM in new terminal
-gnome-terminal --title='cfdemSolverPisoMS ErgunTestMPI CFD'  -e "bash $casePath/parCFDDEMrun.sh" 
+gnome-terminal --title='cfdemSolverPisoMS ErgunTestMPI CFD'  -e "bash $casePath/parCFDDEMrun.sh"
 
 if [ $postproc == "true" ]
   then
@@ -38,7 +38,7 @@ if [ $postproc == "true" ]
     #- get VTK data from CFD sim
     cd $casePath/CFD
     #foamToVTK                                                   #- serial run of foamToVTK
-    source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh                       #- include functions
+    source $CFDEM_PROJECT_DIR/etc/functions.sh                   #- include functions
     pseudoParallelRun "foamToVTK" $nrPostProcProcessors          #- pseudo parallel run of foamToVTK
 
     #- start paraview

tutorials/cfdemSolverPisoMS/ErgunTestMPI/parCFDDEMrun.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
+# allrun script for testcase as part of test routine
 # run settlingTest CFD part
 # Christoph Goniva - Feb. 2011
 #===================================================================#
@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables
@@ -42,7 +42,7 @@ rm cfdemSolverPisoMS_ErgunTestMPI.eps
 #- run octave
 octave totalPressureDrop.m
 
-#- show plot 
+#- show plot
 evince cfdemSolverPisoMS_ErgunTestMPI.eps
 #------------------------------#
 

tutorials/cfdemSolverPisoScalar/packedBedTemp/parCFDDEMrun.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 #===================================================================#
-# allrun script for testcase as part of test routine 
+# allrun script for testcase as part of test routine
 # run settlingTest CFD part
 # Christoph Goniva - May. 2011
 #===================================================================#
@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables
@@ -43,7 +43,7 @@ if [ $runOctave == "true" ]
     #- run octave
     octave totalPressureDropAndNusselt.m
 
-    #- show plots 
+    #- show plots
     evince cfdemSolverPisoScalar_Nusselt.eps &
     evince cfdemSolverPisoScalar_pressureDrop.eps
     #------------------------------#
@@ -70,8 +70,6 @@ if [ $postproc == "true" ]
     #- get VTK data from CFD sim
     cd $casePath/CFD
     foamToVTK                                                   #- serial run of foamToVTK
-    #source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh                       #- include functions
-    #pseudoParallelRun "foamToVTK" $nrPostProcProcessors          #- pseudo parallel run of foamToVTK
 
     #- start paraview
     paraview

tutorials/cfdemSolverPisoScalar/packedBedTemp/parDEMrun.sh

@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables

tutorials/cfdemSolverRhoPimple/ErgunTestMPI/parDEMrun.sh

@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 echo "starting DEM run in parallel..."
 #--------------------------------------------------------------------------------#

tutorials/cfdemSolverRhoPimple/FinesColumn/parCFDDEMrun.sh

@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 #--------------------------------------------------------------------------------#
 #- define variables

tutorials/cfdemSolverRhoPimple/FinesColumn/parDEMrun.sh

@@ -10,7 +10,7 @@
 . ~/.bashrc
 
 #- include functions
-source $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/functions.sh
+source $CFDEM_PROJECT_DIR/etc/functions.sh
 
 echo "starting DEM run in parallel..."
 #--------------------------------------------------------------------------------#