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Commit 43c792f4 authored by Mark Friedrichs's avatar Mark Friedrichs
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Added tests for Gk + cavity term

parent a80b8a02
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Showing with 36 additions and 15 deletions
plugins/amoeba/platforms/cuda/src/AmoebaCudaData.cpp
View file @ 43c792f4
......@@ -113,6 +113,7 @@ void AmoebaCudaData::initializeGpu( void ) {
}
amoebaGpuBuildOutputBuffers( amoebaGpu );
amoebaGpuBuildThreadBlockWorkList( amoebaGpu );
amoebaGpuBuildScalingList( amoebaGpu );
amoebaGpuSetConstants( amoebaGpu );
gpuInitialized = true;
if( log ){
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernelFactory.cpp
View file @ 43c792f4
......@@ -90,7 +90,6 @@ KernelImpl* AmoebaCudaKernelFactory::createKernelImpl(std::string name, const Pl
contextToAmoebaDataMap[&context] = amoebaCudaData;
amoebaCudaData->setLog( stderr );
amoebaCudaData->setContextImpl( static_cast<void*>(&context) );
//(void) fprintf( stderr, "AmoebaCudaKernelFactory::createKernelImpl amoebaCudaDataV=%p\n", static_cast<void*>(amoebaCudaData) );
} else {
amoebaCudaData = mapIterator->second;
}
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp
View file @ 43c792f4
......@@ -3776,22 +3776,25 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
readAmoebaGeneralizedKirkwoodParameters( filePtr, forceMap, tokens, system, useOpenMMUnits, supplementary, inputArgumentMap, &lineCount, log );
} else if( field == "AmoebaGkForce" ){
readVec3( filePtr, tokens, forces[AMOEBA_GK_FORCE], &lineCount, field, log );
} else if( field == "AmoebaGk_A_ForceAndTorque" ||
} else if( field == "AmoebaGkAndCavityForce" ){
readVec3( filePtr, tokens, forces[AMOEBA_GK_CAVITY_FORCE], &lineCount, field, log );
} else if( field == "AmoebaGk_A_ForceAndTorque" ||
field == "AmoebaGk_A_Force" ||
field == "AmoebaGk_A_DrB" ||
field == "AmoebaDBorn" ||
field == "AmoebaBorn1Force" ||
field == "AmoebaBornForce" ||
field == "AmoebaGkEdiffForceAndTorque" ||
field == "AmoebaGkEdiffForce" ){
field == "AmoebaGkEdiffForce" ){
std::vector< std::vector<double> > vectorOfDoubleVectors;
readVectorOfDoubleVectors( filePtr, tokens, vectorOfDoubleVectors, &lineCount, field, log );
supplementary[field] = vectorOfDoubleVectors;
} else if( field == "AmoebaGkEnergy" ||
field == "AmoebaGkEdiffEnergy" ||
field == "AmoebaGk_A_Energy" ||
field == "AmoebaBorn1Energy" ||
field == "AmoebaBornEnergy" ){
} else if( field == "AmoebaGkEnergy" ||
field == "AmoebaGkEdiffEnergy" ||
field == "AmoebaGk_A_Energy" ||
field == "AmoebaBorn1Energy" ||
field == "AmoebaBornEnergy" ||
field == "AmoebaGkAndCavityEnergy" ){
double value = atof( tokens[1].c_str() );
std::vector< std::vector<double> > vectorOfDoubleVectors;
std::vector<double> doubleVectors;
......@@ -3800,6 +3803,8 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
supplementary[field] = vectorOfDoubleVectors;
if( field == "AmoebaGkEnergy" ){
potentialEnergy[AMOEBA_GK_FORCE] = value;
} else if( field == "AmoebaGkAndCavityEnergy" ){
potentialEnergy[AMOEBA_GK_CAVITY_FORCE] = value;
}
// Amoeba SASA
......@@ -3871,7 +3876,7 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
for( MapStringDoubleI ii = potentialEnergy.begin(); ii != potentialEnergy.end(); ii++ ){
if( ii->first == ALL_FORCES ){
allEnergy = ii->second;
} else {
} else if( ii->first != AMOEBA_GK_CAVITY_FORCE ){
totalPotentialEnergy += ii->second;
}
if( log )(void) fprintf( log, "%30s %15.7e\n", ii->first.c_str(), ii->second );
......@@ -3879,6 +3884,11 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
potentialEnergy["SumOfInputEnergies"] = totalPotentialEnergy;
if( log ){
MapStringDoubleI isPresent = potentialEnergy.find( AMOEBA_GK_CAVITY_FORCE );
if( isPresent != potentialEnergy.end() ){
double cavityEnergy = potentialEnergy[AMOEBA_GK_CAVITY_FORCE] - potentialEnergy[AMOEBA_GK_FORCE];
(void) fprintf( log, "Cavity energy %15.7e\n", cavityEnergy );
}
(void) fprintf( log, "Total PE %15.7e %15.7e\n", totalPotentialEnergy, allEnergy );
(void) fprintf( log, "Read %d lines from file=<%s>\n", lineCount, inputParameterFile.c_str() );
(void) fflush( log );
......@@ -4646,18 +4656,21 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
// ---------------------------------------------------------------------------------------
int applyAssert = 0;
int includeCavityTerm = 0;
double tolerance = 1.0e-02;
static const std::string methodName = "testUsingAmoebaTinkerParameterFile";
// ---------------------------------------------------------------------------------------
setIntFromMap( inputArgumentMap, "applyAssert", applyAssert);
setDoubleFromMap( inputArgumentMap, "tolerance", tolerance );
setIntFromMap( inputArgumentMap, "applyAssert", applyAssert);
setDoubleFromMap( inputArgumentMap, "tolerance", tolerance );
setIntFromMap( inputArgumentMap, INCLUDE_OBC_CAVITY_TERM, includeCavityTerm );
MapStringVec3 tinkerForces;
MapStringDouble tinkerEnergies;
MapStringVectorOfVectors supplementary;
MapStringIntI isPresent = forceMap.find( AMOEBA_GK_FORCE );
bool gkIsActive;
if( isPresent != forceMap.end() && isPresent->second != 0 ){
......@@ -4684,12 +4697,17 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
std::string activeForceNames;
for( MapStringInt::const_iterator ii = forceMap.begin(); ii != forceMap.end(); ii++ ){
if( ii->second ){
forceList.push_back( ii->first );
activeForceNames += ii->first + ":";
if( includeCavityTerm && ii->first == AMOEBA_GK_FORCE ){
forceList.push_back( AMOEBA_GK_CAVITY_FORCE );
activeForceNames += AMOEBA_GK_CAVITY_FORCE + ":";
} else {
forceList.push_back( ii->first );
activeForceNames += ii->first + ":";
}
}
}
if( forceList.size() >= 11 ){
activeForceNames =ALL_FORCES;
activeForceNames = ALL_FORCES;
}
std::vector<Vec3> expectedForces;
......@@ -4805,6 +4823,7 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
coordinateConversion*(box[1][2] - box[0][2]) );
unsigned int maxPrint = 5;
/*
(void) fprintf( filePtr, "Sample raw coordinates (w/o conversion) %8u\n", static_cast<unsigned int>(coordinates.size()) );
for( unsigned int ii = 0; ii < coordinates.size(); ii++ ){
(void) fprintf( filePtr, "%8u [%16.7f %16.7f %16.7f]\n", ii,
......@@ -4813,6 +4832,7 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
ii = coordinates.size() - maxPrint - 1;
}
}
*/
(void) fflush( filePtr );
}
}
......@@ -4844,7 +4864,7 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
}
}
}
(void) fprintf( filePtr, "%30s maxRelF/E %10.3e %10.3e E[%15.7e %15.7e] %20s %d\n", activeForceNames.c_str(), maxRelativeDelta,
(void) fprintf( filePtr, "%40s maxRelF/E %10.3e %10.3e E[%15.7e %15.7e] %20s %d\n", activeForceNames.c_str(), maxRelativeDelta,
deltaE, expectedEnergy, energyConversion*state.getPotentialEnergy(), amoebaTinkerParameterFileName.c_str(), useOpenMMUnits );
(void) fflush( filePtr );
}
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.h
View file @ 43c792f4
......@@ -74,6 +74,7 @@ static std::string AMOEBA_OUT_OF_PLANE_BEND_FORCE = "AmoebaO
static std::string AMOEBA_TORSION_TORSION_FORCE = "AmoebaTorsionTorsion";
static std::string AMOEBA_MULTIPOLE_FORCE = "AmoebaMultipole";
static std::string AMOEBA_GK_FORCE = "AmoebaGk";
static std::string AMOEBA_GK_CAVITY_FORCE = "AmoebaGkAndCavity";
static std::string AMOEBA_VDW_FORCE = "AmoebaVdw";
static std::string AMOEBA_WCA_DISPERSION_FORCE = "AmoebaWcaDispersion";
static std::string AMOEBA_SASA_FORCE = "AmoebaSASA";
......
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