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Updated with MPI FFTW. 

- Added initialization with Voronoi tesselations.
- Added MPI/FFTW
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FrankieLi
FrankieLi committed Apr 24, 2014
1 parent fc7b10d commit 66ae50feeceeb63b69076fc787dd3ca959350906
Unified Split
Showing with 1,186 additions and 165 deletions.
  1. +8 −4 Makefile
  2. +304 −0 Src/Config.cpp
  3. +88 −0 Src/Config.h
  4. +403 −137 Src/MaterialGrid.cpp
  5. +58 −11 Src/MaterialGrid.h
  6. +64 −0 Src/Parser.cpp
  7. +37 −0 Src/Parser.h
  8. +8 −0 Src/Solvers.cpp
  9. 0 Src/Test_FFTW_Mpi.h
  10. +10 −1 Src/Types.h
  11. +192 −9 Src/UnitTester.cpp
  12. +11 −0 Src/UnitTester.h
  13. +3 −3 Src/main.cpp
View
12 Makefile
@@ -23,7 +23,11 @@ EXEC = VPFFT++
#----------------------------------------------------
PROJ_PATH = ./Src
PROJ_CPPS = main.cpp LinearAlgebra.cpp Solvers.cpp MaterialGrid.cpp UnitTester.cpp Debug.cpp
PROJ_CPPS = main.cpp LinearAlgebra.cpp Solvers.cpp MaterialGrid.cpp UnitTester.cpp Debug.cpp Config.cpp Parser.cpp
#main.cpp LinearAlgebra.cpp Solvers.cpp MaterialGrid.cpp UnitTester.cpp Debug.cpp
CPPS = $(patsubst %.cpp, $(PROJ_PATH)/%.cpp, $(PROJ_CPPS) )
@@ -40,7 +44,7 @@ OBJS_DEBUG = $(patsubst %.cpp, %.do, $(CPPS))
# Specifying precomile external library locations
#
#----------------------------------------------------
INCL = -I. -I${EIGEN_PATH}
INCL = -I. -I${EIGEN_PATH} -I/opt/local/include/
#----------------------------------------------------
#
@@ -61,8 +65,8 @@ DEBUG_FLAGS = -fopenmp -ggdb -DDEBUG_LEVEL_MAX \
RELEASE_FLAGS += ${LIB_ROOT}
DEBUG_FLAGS += ${LIB_ROOT}
LIBS = -lm -lfftw3_threads -lfftw3 -lpthread
CC = /opt/local/bin/g++-mp-4.5 # g++ #icpc
LIBS = -lm -lfftw3_threads -lfftw3 -lfftw3_mpi -lpthread
CC = mpic++ # /opt/local/bin/g++-mp-4.5 # g++ #icpc
View
304 Src/Config.cpp
@@ -0,0 +1,304 @@
#include "Config.h"
namespace Utilities
{
//-----------------------------------
// Read
//-----------------------------------
bool ConfigFile::Read( const std::string & ConfigFilename )
{
Size_Type nBufferSize = 0;
char *pBuffer = ReadFileToBuf( nBufferSize, ConfigFilename);
if( nBufferSize<= 0 || !pBuffer )
{
std::cerr << "ERROR: Unable to read config file" << endl;
return false;
}
if( !Parse( std::string( pBuffer, nBufferSize ) ) )
{
std::cerr << "ERROR: Unable to parse config file" << endl;
return false;
}
if( pBuffer )
delete[] pBuffer;
return true;
}
//-----------------------------------
// Parser
//-----------------------------------
bool ConfigFile::Parse( const string & sBuf )
{
const char* KeywordStrings[] =
{
"#", // comment
"GridDimension",
"InputStrainRate",
"MaxNRIter",
"TimeStep",
"NumTimeIter",
"NRTolerence",
"TwoGrainInit",
"FileInit",
"CRSS",
"GammaDotBase",
"RateSensitivity"
};
enum EKeyword
{
// comment
eComment,
eGridDimension,
eInputStrainRate,
eMaxNRIter,
eTimeStep,
eNumTimeIter,
eNRTolerence,
eTwoGrainInit,
eFileInit,
eCRSS,
eGammaDotBase,
eRateSensitivity,
// error check on number of keywords
eNumKeywords
};
vector< vector<string> > vsTokens;
Tokenize( vsTokens, sBuf, " \t\n");
bool *vInitializationCheck;
bool *vRequirementCheck;
vInitializationCheck = new bool[eNumKeywords]; // a check list to see which variable is not initialized
vRequirementCheck = new bool[eNumKeywords]; // a check list to see which variable is not initialized
for( int i = 0; i < eNumKeywords; i ++ )
{
vInitializationCheck[i] = false;
vRequirementCheck[i] = true;
}
vRequirementCheck[eFileInit] = false;
vRequirementCheck[eTwoGrainInit] = false;
for(Size_Type i = 0; i < vsTokens.size(); i ++)
{
Size_Type iFirstToken;
if ( vsTokens[i].size() == 0)
{
iFirstToken = eComment;
}
else if ( vsTokens[i][0].find_first_of( KeywordStrings[ eComment ] ) == 0) // if first token is comment
{
iFirstToken = eComment;
}
else
{
// Identify the keyword in the beginning of the line
for( iFirstToken = 0; iFirstToken < eNumKeywords; iFirstToken ++ )
{
if(strcmp(KeywordStrings[iFirstToken], vsTokens[i][0].c_str()) == 0)
break;
}
std::cout << i + 1 << " " << KeywordStrings[iFirstToken] << " "
<< vsTokens[i][0].c_str() << " Token " << iFirstToken << endl;
}
vInitializationCheck[ iFirstToken ] = true;
switch( iFirstToken ) // look at first token of each line
{
case eComment: // Comment
break;
case eGridDimension:
RUNTIME_ASSERT( vsTokens[i].size() >= 4,
"GridDimension: Expect 3 parameters [NumX NumY NumZ]");
NumX = atoi( vsTokens[i][1].c_str() );
NumY = atoi( vsTokens[i][2].c_str() );
NumZ = atoi( vsTokens[i][3].c_str() );
break;
case eInputStrainRate:
{
bool bSuccess = HasLineContinuation( i, 3, vsTokens, KeywordStrings, eNumKeywords );
RUNTIME_ASSERT( bSuccess, "InputStrainRate: Expect s00 s11 s22 \n <empty space> s10 s11 s12 \n <empty space> s20 s21 s22 " );
for(int di = 0; di < 3; di ++ )
{
++i;
InputStrainRate.m[di][0] = atof( vsTokens[i][0].c_str() );
InputStrainRate.m[di][1] = atof( vsTokens[i][1].c_str() );
InputStrainRate.m[di][2] = atof( vsTokens[i][2].c_str() );
}
std::cout << "Parsed input strain rate " << std::endl;
std::cout << InputStrainRate << std::endl;
}
break;
case eMaxNRIter:
MaxNRIter = atoi( vsTokens[i][1].c_str() );
break;
case eTimeStep:
TimeStep = atof( vsTokens[i][1].c_str() );
break;
case eNumTimeIter:
NumTimeIter = atoi( vsTokens[i][1].c_str() );
break;
case eNRTolerence:
NRTolerence = atof( vsTokens[i][1].c_str() );
break;
case eTwoGrainInit:
InitMethod = eInitTwoGrain;
break;
case eFileInit:
{
RUNTIME_ASSERT( vsTokens[i].size() >= 2,
"FileInit: Expect Filename for initialization" );
InputMicrostructureFilename = vsTokens[i][1];
std::ifstream fd;
fd.open( InputMicrostructureFilename.c_str() );
if( !fd )
{
std::cout << "FileInit " << InputMicrostructureFilename << " Not found " << std::endl;
exit(0);
}
fd.close();
InitMethod = eInitFile;
break;
}
case eCRSS:
RUNTIME_ASSERT( vsTokens[i].size() >= VPFFT::FCC_CrystalTest::NumSystems,
"GridDimension: Expect the same number of parameters as number slip systems in the symmetry\n");
CRSS.resize( VPFFT::FCC_CrystalTest::NumSystems );
for( int n = 1; n <= VPFFT::FCC_CrystalTest::NumSystems; n ++ )
CRSS[n] = atof( vsTokens[i][n].c_str() );
break;
case eGammaDotBase:
RUNTIME_ASSERT( vsTokens[i].size() >= VPFFT::FCC_CrystalTest::NumSystems,
"GridDimension: Expect the same number of parameters as number slip systems in the symmetry\n");
GammaDotBase.resize( VPFFT::FCC_CrystalTest::NumSystems );
for( int n = 1; n <= VPFFT::FCC_CrystalTest::NumSystems; n ++ )
GammaDotBase[n] = atof( vsTokens[i][n].c_str() );
break;
case eRateSensitivity:
RUNTIME_ASSERT( vsTokens[i].size() >= VPFFT::FCC_CrystalTest::NumSystems,
"GridDimension: Expect the same number of parameters as number slip systems in the symmetry\n");
RateSensitivity.resize( VPFFT::FCC_CrystalTest::NumSystems );
for( int n = 1; n <= VPFFT::FCC_CrystalTest::NumSystems; n ++ )
RateSensitivity[n] = atoi( vsTokens[i][n].c_str() );
break;
default:
{
std::cerr << "[ConfigFile] Error: syntax not recognized: Line " << i
<< " Keyword: " << vsTokens[i][0] << endl;
return false;
}
}
} // end loop over tokens
bool Success = true;
for( int i = 0; i < eNumKeywords; i ++ )
{
if( !vInitializationCheck[i] && vRequirementCheck[i] )
{
std::cerr << "[ConfigFile] Initialization Error: Missing parameter: "
<< KeywordStrings[i] << " not optional." << std::endl;
Success = false;
}
}
if( ! vInitializationCheck[eFileInit] &&
! vInitializationCheck[eTwoGrainInit] )
{
std::cerr << "Initialization scheme (either FileInit or TwoGrain init) needs to be specified." << std::endl;
Success = false;
}
if( !Success )
{
std::cerr << "[ConfigFile] Initialization Failed" << std::endl;
exit(0);
}
delete [] vInitializationCheck;
delete [] vRequirementCheck;
std::cout << "GridDimension "
<< NumX << " "
<< NumY << " "
<< NumZ << std::endl;
std::cout << "InputStrainRate " << std::endl
<< InputStrainRate << std::endl;
std::cout << "MaxNRIter " << MaxNRIter << std::endl;
std::cout << "TimeStep " << TimeStep << std::endl;
std::cout << "InitMethod " << InitMethod << std::endl;
}
//--------------------------------------------
// Returns a Null terminated C-string
//--------------------------------------------
char* ConfigFile::ReadFileToBuf( Size_Type & nBufferSize, std::string filename)
{
std::ifstream infile;
infile.open(filename.c_str());
FILE *pFile;
char *pBuffer;
if ( (pFile = fopen(filename.c_str(), "r" )) == NULL ){
cerr << "[ReadFileToBuf]Cannot Open File: " << filename.c_str() << endl;
return NULL;
}
// Get the size of the file
fseek( pFile, 0L, SEEK_END ); // Position to end of file
nBufferSize = ftell( pFile ); // Get file length
rewind( pFile ); // Back to start of file
if( nBufferSize <= 0 )
return NULL;
// Read in the entire file and close the file handle
pBuffer = new char[nBufferSize + 1];
if ( fread( pBuffer, nBufferSize, 1, pFile ) <= 0 ){
fclose( pFile );
cerr << "[ReadFileToBuf]:File read error" << endl;
return NULL;
}
fclose( pFile );
pBuffer[ nBufferSize ] = '\0'; // NULL termination of string
return pBuffer;
}
}
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