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Merge remote-tracking branch 'origin/cmake_support' into bugfixing

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This commit is contained in:
dqueteschiner
2015-03-23 12:08:25 +01:00
parent ee44d40c0e ea0d7b0351
commit 3d1bd01bc4
44 changed files with 67 additions and 65 deletions
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1
src/lagrangian/cfdemParticle/.gitignore vendored Normal file
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@ -0,0 +1 @@
lnInclude

5
src/lagrangian/cfdemParticle/Make/options
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@ -28,7 +28,8 @@ LIB_LIBS = \
-lmeshTools \
-llagrangian \
-lmpi_cxx \
-L$(CFDEM_LIGGGHTS_SRC_DIR) \
-Wl,--whole-archive -l$(CFDEM_LIGGGHTS_LIB_NAME) -Wl,--no-whole-archive \
-Wl,-rpath,$(CFDEM_LIGGGHTS_BIN_DIR) \
-L$(CFDEM_LIGGGHTS_BIN_DIR) \
-lliggghts \
-L$(CFDEM_Many2ManyLIB_PATH) \
-lcoupleMany2Many

8
src/lagrangian/cfdemParticle/cfdTools/mathExtra.H
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@ -37,10 +37,10 @@ Description
#include <vector>
//#include "math.h"
#include "stdio.h"
#include "string.h"
#include "error.h"
#include "ctype.h"
#include <stdio.h>
#include <string.h>
#include <error.h>
#include <ctype.h>
#define TOLERANCE_ORTHO 1e-10

4
src/lagrangian/cfdemParticle/cfdemCloud/cfdemCloud.H
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@ -50,9 +50,9 @@ SourceFiles
#include "IFstream.H"
#if defined(version21) || defined(version16ext)
#include "turbulenceModel.H"
#include <turbulenceModel.H>
#elif defined(version15)
#include "RASModel.H"
#include <RASModel.H>
#endif
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/derived/cfdemCloudIB/cfdemCloudIB.C
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@ -36,7 +36,7 @@ Description
#include "locateModel.H"
#include "dataExchangeModel.H"
#include "IOModel.H"
#include "mpi.h"
#include <mpi.h>
#include "IOmanip.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/derived/cfdemCloudMS/cfdemCloudMS.C
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@ -35,7 +35,7 @@ Description
#include "locateModel.H"
#include "dataExchangeModel.H"
//#include "mpi.h" // only for debug reason
//#include <mpi.h> // only for debug reason
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam

3
src/lagrangian/cfdemParticle/etc/bashrc
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@ -26,7 +26,8 @@
#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_MAKEFILE_NAME=fedora_fpic
#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

21
src/lagrangian/cfdemParticle/etc/functions.sh
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@ -161,7 +161,8 @@ compileLIGGGHTS()
rm $logpath/$logfileName
#- change path
cd $CFDEM_LIGGGHTS_SRC_DIR
mkdir -p $CFDEM_LIGGGHTS_BIN_DIR
cd $CFDEM_LIGGGHTS_BIN_DIR
#- header
echo 2>&1 | tee -a $logpath/$logfileName
@ -176,20 +177,18 @@ compileLIGGGHTS()
if [[ $clean == "false" ]]; then
echo "not cleaning LIGGGHTS"
else
rm $CFDEM_LIGGGHTS_SRC_DIR/"lmp_"$CFDEM_LIGGGHTS_MAKEFILE_NAME
rm $CFDEM_LIGGGHTS_SRC_DIR/"lib"$CFDEM_LIGGGHTS_LIB_NAME".a"
make clean-all 2>&1 | tee -a $logpath/$logfileName
make clean 2>&1 | tee -a $logpath/$logfileName
rm CMakeCache.txt 2>&1 | tee -a $logpath/$logfileName
echo "cleaning LIGGGHTS"
fi
cmake $CFDEM_LIGGGHTS_SRC_DIR
if [[ $WM_NCOMPPROCS == "" ]]; then
echo "compiling LIGGGHTS on one CPU"
make $CFDEM_LIGGGHTS_MAKEFILE_NAME 2>&1 | tee -a $logpath/$logfileName
make 2>&1 | tee -a $logpath/$logfileName
else
echo "compiling LIGGGHTS on $WM_NCOMPPROCS CPUs"
make $CFDEM_LIGGGHTS_MAKEFILE_NAME -j $WM_NCOMPPROCS 2>&1 | tee -a $logpath/$logfileName
make -j $WM_NCOMPPROCS 2>&1 | tee -a $logpath/$logfileName
fi
make makelib 2>&1 | tee -a $logpath/$logfileName
make -f Makefile.lib $CFDEM_LIGGGHTS_MAKEFILE_NAME 2>&1 | tee -a $logpath/$logfileName
}
#==================================#
@ -405,7 +404,7 @@ DEMrun()
echo 2>&1 | tee -a $logpath/$logfileName
#- run applictaion
$debugMode $CFDEM_LIGGGHTS_SRC_DIR/$CFDEM_LIGGGHTS_LIB_NAME < $solverName 2>&1 | tee -a $logpath/$logfileName
$debugMode $CFDEM_LIGGGHTS_BIN_DIR/liggghts -in $solverName 2>&1 | tee -a $logpath/$logfileName
#- keep terminal open (if started in new terminal)
#read
@ -455,9 +454,9 @@ parDEMrun()
#- run applictaion
if [ $machineFileName == "none" ]; then
mpirun -np $nrProcs $debugMode $CFDEM_LIGGGHTS_SRC_DIR/$CFDEM_LIGGGHTS_LIB_NAME < $solverName 2>&1 | tee -a $logpath/$logfileName
mpirun -np $nrProcs $debugMode $CFDEM_LIGGGHTS_BIN_DIR/liggghts -in $solverName 2>&1 | tee -a $logpath/$logfileName
else
mpirun -machinefile $machineFileName -np $nrProcs $debugMode $CFDEM_LIGGGHTS_SRC_DIR/$CFDEM_LIGGGHTS_LIB_NAME < $solverName 2>&1 | tee -a $logpath/$logfileName
mpirun -machinefile $machineFileName -np $nrProcs $debugMode $CFDEM_LIGGGHTS_BIN_DIR/liggghts -in $solverName 2>&1 | tee -a $logpath/$logfileName
fi
#- keep terminal open (if started in new terminal)

2
src/lagrangian/cfdemParticle/subModels/averagingModel/dense/dense.C
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@ -35,7 +35,7 @@ Description
#include "addToRunTimeSelectionTable.H"
#include "voidFractionModel.H"
//#include "mpi.h"
//#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam

2
src/lagrangian/cfdemParticle/subModels/clockModel/clockModel/clockModel.C
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@ -30,7 +30,7 @@ Description
\*---------------------------------------------------------------------------*/
#include "error.H"
#include "mpi.h"
#include <mpi.h>
#include "clockModel.H"
#include <unistd.h>

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayFiles/twoWayFiles.H
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@ -43,7 +43,7 @@ SourceFiles
#include "dataExchangeModel.H"
#include "OFstream.H"
#include "sys/stat.h"
#include <sys/stat.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

4
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMPI/twoWayMPI.H
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@ -44,7 +44,7 @@ SourceFiles
#include "dataExchangeModel.H"
#include "liggghtsCommandModel.H"
#include "OFstream.H"
#include "sys/stat.h"
#include <sys/stat.h>
#include "pair.h"
#include "force.h"
#include "forceModel.H"
@ -54,7 +54,7 @@ SourceFiles
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "mpi.h"
#include <mpi.h>
#include <lammps.h> // these are LAMMPS include files
#include <input.h>
#include <atom.h>

4
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/error.cpp
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@ -1,6 +1,6 @@
#include "mpi.h"
#include <mpi.h>
#include "stdlib.h"
#include "stdio.h"
#include <stdio.h>
#include "error.h"
/* ---------------------------------------------------------------------- */

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/error.h
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@ -1,7 +1,7 @@
#ifndef ERROR_H
#define ERROR_H
#include "mpi.h"
#include <mpi.h>
class Error {
public:

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/files.cpp
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@ -1,4 +1,4 @@
#include "stdio.h"
#include <stdio.h>
#include "string.h"
#include "files.h"

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/irregular.cpp
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@ -1,4 +1,4 @@
#include "stdio.h"
#include <stdio.h>
#include "stdlib.h"
#include "string.h"
#include "irregular.h"

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/irregular.h
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@ -1,7 +1,7 @@
#ifndef IRREGULAR_H
#define IRREGULAR_H
#include "mpi.h"
#include <mpi.h>
class Irregular {
public:

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/lammps_data_write.h
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@ -2,7 +2,7 @@
#define LAMMPS_DATA_WRITE_H
#include "send2one.h"
#include "stdio.h"
#include <stdio.h>
class LAMMPSDataWrite : public Send2One {
public:

4
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/many2many.cpp
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@ -1,5 +1,5 @@
#include "mpi.h"
#include "stdio.h"
#include <mpi.h>
#include <stdio.h>
#include "many2many.h"
#include "irregular.h"
#include "memory.h"

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/many2many.h
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@ -1,7 +1,7 @@
#ifndef MANY2MANY_H
#define MANY2MANY_H
#include "mpi.h"
#include <mpi.h>
class Many2Many {
public:

4
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/many2one.cpp
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@ -1,5 +1,5 @@
#include "mpi.h"
#include "stdio.h"
#include <mpi.h>
#include <stdio.h>
#include "stdlib.h"
#include "many2one.h"
#include "memory.h"

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/many2one.h
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@ -1,7 +1,7 @@
#ifndef MANY2ONE_H
#define MANY2ONE_H
#include "mpi.h"
#include <mpi.h>
class Many2One {
public:

4
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/memory.cpp
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@ -1,6 +1,6 @@
#include "mpi.h"
#include <mpi.h>
#include "stdlib.h"
#include "stdio.h"
#include <stdio.h>
#include "memory.h"
#include "error.h"

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/memory.h
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@ -1,7 +1,7 @@
#ifndef MEMORY_H
#define MEMORY_H
#include "mpi.h"
#include <mpi.h>
class Memory {
public:

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/one2many.cpp
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@ -1,4 +1,4 @@
#include "mpi.h"
#include <mpi.h>
#include "one2many.h"
#include "memory.h"

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/one2many.h
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@ -1,7 +1,7 @@
#ifndef ONE2MANY_H
#define ONE2MANY_H
#include "mpi.h"
#include <mpi.h>
#include <map>

4
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/send2one.cpp
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@ -1,6 +1,6 @@
#include "mpi.h"
#include <mpi.h>
#include "stdlib.h"
#include "stdio.h"
#include <stdio.h>
#include "send2one.h"
#include "memory.h"
#include "error.h"

2
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/library/send2one.h
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@ -1,7 +1,7 @@
#ifndef SEND2ONE_H
#define SEND2ONE_H
#include "mpi.h"
#include <mpi.h>
class Send2One {
public:

4
src/lagrangian/cfdemParticle/subModels/dataExchangeModel/twoWayMany2Many/twoWayMany2Many.H
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@ -44,7 +44,7 @@ SourceFiles
#include "dataExchangeModel.H"
#include "liggghtsCommandModel.H"
#include "OFstream.H"
#include "sys/stat.h"
#include <sys/stat.h>
#include "pair.h"
#include "force.h"
#include "forceModel.H"
@ -52,7 +52,7 @@ SourceFiles
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "mpi.h"
#include <mpi.h>
#include <lammps.h>
#include <input.h>
#include <atom.h>

2
src/lagrangian/cfdemParticle/subModels/forceModel/DiFeliceDrag/DiFeliceDrag.C
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@ -34,7 +34,7 @@ Description
#include "DiFeliceDrag.H"
#include "addToRunTimeSelectionTable.H"
//#include "mpi.h"
//#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/subModels/forceModel/KochHillDrag/KochHillDrag.C
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@ -35,7 +35,7 @@ Description
#include "addToRunTimeSelectionTable.H"
#include "dataExchangeModel.H"
//#include "mpi.h"
//#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam

2
src/lagrangian/cfdemParticle/subModels/forceModel/KochHillRWDrag/KochHillRWDrag.C
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@ -35,7 +35,7 @@ Description
#include "addToRunTimeSelectionTable.H"
#include "dataExchangeModel.H"
//#include "mpi.h"
//#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam

2
src/lagrangian/cfdemParticle/subModels/forceModel/MeiLift/MeiLift.C
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@ -34,7 +34,7 @@ Description
#include "MeiLift.H"
#include "addToRunTimeSelectionTable.H"
//#include "mpi.h"
//#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/subModels/forceModel/SchillerNaumannDrag/SchillerNaumannDrag.C
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@ -34,7 +34,7 @@ Description
#include "SchillerNaumannDrag.H"
#include "addToRunTimeSelectionTable.H"
//#include "mpi.h"
//#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/subModels/forceModel/checkCouplingInterval/checkCouplingInterval.C
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@ -34,7 +34,7 @@ Description
#include "checkCouplingInterval.H"
#include "addToRunTimeSelectionTable.H"
//#include "mpi.h"
//#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/subModels/forceModel/checkCouplingInterval/checkCouplingInterval.H
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@ -44,7 +44,7 @@ SourceFiles
#include "forceModel.H"
#include "dataExchangeModel.H"
#include "mpi.h"
#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/subModels/forceModel/particleCellVolume/particleCellVolume.C
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@ -34,7 +34,7 @@ Description
#include "particleCellVolume.H"
#include "addToRunTimeSelectionTable.H"
#include "dataExchangeModel.H"
#include "mpi.h"
#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam

2
src/lagrangian/cfdemParticle/subModels/forceModel/volWeightedAverage/volWeightedAverage.C
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@ -34,7 +34,7 @@ Description
#include "volWeightedAverage.H"
#include "addToRunTimeSelectionTable.H"
#include "dataExchangeModel.H"
#include "mpi.h"
#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam

2
src/lagrangian/cfdemParticle/subModels/forceModelMS/DiFeliceDragMS/DiFeliceDragMS.C
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@ -34,7 +34,7 @@ Description
#include "DiFeliceDragMS.H"
#include "addToRunTimeSelectionTable.H"
//#include "mpi.h"
//#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/subModels/locateModel/engineSearchIB/engineSearchIB.C
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@ -36,7 +36,7 @@ Description
#include "addToRunTimeSelectionTable.H"
#include "mathematicalConstants.H"
#include "mpi.h"
#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/subModels/probeModel/noProbe/noProbe.C
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@ -33,7 +33,7 @@ Description
#include "noProbe.H"
#include "addToRunTimeSelectionTable.H"
#include "mpi.h"
#include <mpi.h>
#include "IOmanip.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/subModels/probeModel/particleProbe/particleProbe.C
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@ -33,7 +33,7 @@ Description
#include "particleProbe.H"
#include "addToRunTimeSelectionTable.H"
#include "mpi.h"
#include <mpi.h>
#include "IOmanip.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/subModels/voidFractionModel/IBVoidFraction/IBVoidFraction.C
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@ -36,7 +36,7 @@ Description
#include "locateModel.H"
#include "dataExchangeModel.H"
#include "mpi.h"
#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

2
src/lagrangian/cfdemParticle/subModels/voidFractionModel/dividedVoidFraction/dividedVoidFraction.C
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@ -36,7 +36,7 @@ Description
#include "locateModel.H"
#include "dataExchangeModel.H"
//#include "mpi.h"
//#include <mpi.h>
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam