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Commit ac8cb97f authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

Cleanup of AmoebaTinkerParameterFile

parent 9a1ddaff
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Showing with 598 additions and 585 deletions
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ ac8cb97f
...@@ -657,10 +657,13 @@ CudaCalcAmoebaGeneralizedKirkwoodForceKernel::~CudaCalcAmoebaGeneralizedKirkwood ...@@ -657,10 +657,13 @@ CudaCalcAmoebaGeneralizedKirkwoodForceKernel::~CudaCalcAmoebaGeneralizedKirkwood
void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::initialize(const System& system, const AmoebaGeneralizedKirkwoodForce& force) { void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::initialize(const System& system, const AmoebaGeneralizedKirkwoodForce& force) {
data.setHasAmoebaGeneralizedKirkwood( true ); data.setHasAmoebaGeneralizedKirkwood( true );
int numParticles = system.getNumParticles(); int numParticles = system.getNumParticles();
std::vector<float> radius(numParticles); std::vector<float> radius(numParticles);
std::vector<float> scale(numParticles); std::vector<float> scale(numParticles);
std::vector<float> charge(numParticles); std::vector<float> charge(numParticles);
for( int ii = 0; ii < numParticles; ii++ ){ for( int ii = 0; ii < numParticles; ii++ ){
double particleCharge, particleRadius, scalingFactor; double particleCharge, particleRadius, scalingFactor;
force.getParticleParameters(ii, particleCharge, particleRadius, scalingFactor); force.getParticleParameters(ii, particleCharge, particleRadius, scalingFactor);
......
plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp
View file @ ac8cb97f
...@@ -2925,6 +2925,10 @@ void amoebaGpuBuildScalingList( amoebaGpuContext amoebaGpu ) ...@@ -2925,6 +2925,10 @@ void amoebaGpuBuildScalingList( amoebaGpuContext amoebaGpu )
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
if( amoebaGpu->psCovalentDegree == NULL ){
return;
}
const unsigned int paddedAtoms = amoebaGpu->paddedNumberOfAtoms; const unsigned int paddedAtoms = amoebaGpu->paddedNumberOfAtoms;
const unsigned int actualAtoms = amoebaGpu->gpuContext->natoms; const unsigned int actualAtoms = amoebaGpu->gpuContext->natoms;
const unsigned int grid = amoebaGpu->gpuContext->grid; const unsigned int grid = amoebaGpu->gpuContext->grid;
...@@ -4050,4 +4054,99 @@ void readFile( std::string fileName, StringVectorVector& fileContents ){ ...@@ -4050,4 +4054,99 @@ void readFile( std::string fileName, StringVectorVector& fileContents ){
return; return;
} }
/**---------------------------------------------------------------------------------------
Report whether a number is a nan or infinity
@param number number to test
@return 1 if number is nan or infinity; else return 0
--------------------------------------------------------------------------------------- */
int isNanOrInfinity( double number ){
return (number != number || number == std::numeric_limits<double>::infinity() || number == -std::numeric_limits<double>::infinity()) ? 1 : 0;
}
/**---------------------------------------------------------------------------------------
Track iterations for MI dipoles
@param amoebaGpu amoebaGpuContext reference
@param iteration MI iteration
--------------------------------------------------------------------------------------- */
void trackMutualInducedIterations( amoebaGpuContext amoebaGpu, int iteration){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "trackMutualInducedIterations";
static int currentStep = 0;
static double iterationStat[6] = { 0.0, 0.0, 1000.0, 0.0, 0.0, 0.0 };
// ---------------------------------------------------------------------------------------
if( amoebaGpu->log == NULL || currentStep > 20000 )return;
gpuContext gpu = amoebaGpu->gpuContext;
currentStep++;
double interationD = static_cast<double>(iteration);
iterationStat[0] += interationD;
iterationStat[1] += interationD*interationD;
iterationStat[2] = interationD < iterationStat[2] ? interationD : iterationStat[2];
iterationStat[3] = interationD > iterationStat[3] ? interationD : iterationStat[3];
iterationStat[4] += 1.0;
if( iterationStat[4] >= 1000.0 ){
double average = iterationStat[0]/iterationStat[4];
double stddev = iterationStat[1] - average*average*iterationStat[4];
stddev = sqrt( stddev )/(iterationStat[4]-1.0);
(void) fprintf( amoebaGpu->log, "%s %8d iteration=%10.3f stddev=%10.3f min/max[%10.3f %10.3f] %10.1f eps=%14.7e\n",
methodName.c_str(), currentStep, average, stddev, iterationStat[2], iterationStat[3], iterationStat[4], amoebaGpu->mutualInducedCurrentEpsilon );
(void) fflush( amoebaGpu->log );
iterationStat[0] = iterationStat[1] = iterationStat[4] = 0.0;
}
if( 0 ){
std::vector<int> fileId;
if( interationD < (amoebaGpu->mutualInducedMaxIterations-10) ) {
int id = (currentStep % 20);
fileId.push_back( id );
} else {
fileId.push_back( currentStep );
}
if( (currentStep % 20) == 0 || fileId[0] > 20 ){
(void) fprintf( amoebaGpu->log, "step=%d fileId=%d\n", currentStep, fileId[0] );
}
(void) fflush( amoebaGpu->log );
VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psVelm4, outputVector );
/*
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipoleS, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolarS,outputVector );
*/
cudaWriteVectorOfDoubleVectorsToFile( "CudaMIT", fileId, outputVector );
int nansPresent = isNanOrInfinity( amoebaGpu->mutualInducedCurrentEpsilon );
if( nansPresent == 0 ){
for( int ii = 0; ii < gpu->natoms && nansPresent == 0; ii++ ){
if( isNanOrInfinity( gpu->psPosq4->_pSysStream[0][ii].x ) ||
isNanOrInfinity( gpu->psPosq4->_pSysStream[0][ii].y ) ||
isNanOrInfinity( gpu->psPosq4->_pSysStream[0][ii].z ) ||
isNanOrInfinity( gpu->psVelm4->_pSysStream[0][ii].x ) ||
isNanOrInfinity( gpu->psVelm4->_pSysStream[0][ii].y ) ||
isNanOrInfinity( gpu->psVelm4->_pSysStream[0][ii].z ) ){
nansPresent = 1;
}
}
}
if( nansPresent ){
(void) fprintf( amoebaGpu->log, "epsilon nan - exiting\n" );
(void) fflush( amoebaGpu->log );
exit(-1);
}
}
}
#undef AMOEBA_DEBUG #undef AMOEBA_DEBUG
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaKernels.h
View file @ ac8cb97f
...@@ -149,5 +149,8 @@ extern void kClearFields_1( amoebaGpuContext amoebaGpu ); ...@@ -149,5 +149,8 @@ extern void kClearFields_1( amoebaGpuContext amoebaGpu );
extern void kClearFields_3( amoebaGpuContext amoebaGpu, unsigned int numberToClear ); extern void kClearFields_3( amoebaGpuContext amoebaGpu, unsigned int numberToClear );
extern unsigned int getThreadsPerBlock( amoebaGpuContext amoebaGpu, unsigned int sharedMemoryPerThread ); extern unsigned int getThreadsPerBlock( amoebaGpuContext amoebaGpu, unsigned int sharedMemoryPerThread );
extern int isNanOrInfinity( double number );
extern void trackMutualInducedIterations( amoebaGpuContext amoebaGpu, int iteration);
#endif //__AMOEBA_GPU_TYPES_H__ #endif //__AMOEBA_GPU_TYPES_H__
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMutualInducedAndGkFields.cu
View file @ ac8cb97f
...@@ -767,9 +767,8 @@ static void cudaComputeAmoebaMutualInducedAndGkFieldBySOR( amoebaGpuContext amoe ...@@ -767,9 +767,8 @@ static void cudaComputeAmoebaMutualInducedAndGkFieldBySOR( amoebaGpuContext amoe
static int timestep = 0; static int timestep = 0;
timestep++; timestep++;
static const char* methodName = "cudaComputeAmoebaMutualInducedAndGkFieldBySOR";
static double iterationStat[6] = { 0.0, 0.0, 1000.0, 0.0, 0.0, 0.0 };
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
static const char* methodName = "cudaComputeAmoebaMutualInducedAndGkFieldBySOR";
std::vector<int> fileId; std::vector<int> fileId;
fileId.resize( 2 ); fileId.resize( 2 );
fileId[0] = timestep; fileId[0] = timestep;
...@@ -781,7 +780,7 @@ static void cudaComputeAmoebaMutualInducedAndGkFieldBySOR( amoebaGpuContext amoe ...@@ -781,7 +780,7 @@ static void cudaComputeAmoebaMutualInducedAndGkFieldBySOR( amoebaGpuContext amoe
int done; int done;
int iteration; int iteration;
gpuContext gpu = amoebaGpu->gpuContext; gpuContext gpu = amoebaGpu->gpuContext;
int numOfElems = gpu->natoms*3; int numOfElems = gpu->natoms*3;
int numThreads = min( THREADS_PER_BLOCK, numOfElems ); int numThreads = min( THREADS_PER_BLOCK, numOfElems );
int numBlocks = numOfElems/numThreads; int numBlocks = numOfElems/numThreads;
...@@ -859,7 +858,6 @@ static void cudaComputeAmoebaMutualInducedAndGkFieldBySOR( amoebaGpuContext amoe ...@@ -859,7 +858,6 @@ static void cudaComputeAmoebaMutualInducedAndGkFieldBySOR( amoebaGpuContext amoe
done = 0; done = 0;
iteration = 1; iteration = 1;
time_t start = clock();
while( !done ){ while( !done ){
// matrix multiply // matrix multiply
...@@ -919,6 +917,7 @@ time_t start = clock(); ...@@ -919,6 +917,7 @@ time_t start = clock();
#endif #endif
// Debye=4.8033324f // Debye=4.8033324f
amoebaGpu->psCurrentEpsilon->Download(); amoebaGpu->psCurrentEpsilon->Download();
float currentEpsilon = amoebaGpu->psCurrentEpsilon->_pSysStream[0][0]; float currentEpsilon = amoebaGpu->psCurrentEpsilon->_pSysStream[0][0];
amoebaGpu->mutualInducedCurrentEpsilon = currentEpsilon; amoebaGpu->mutualInducedCurrentEpsilon = currentEpsilon;
...@@ -983,43 +982,24 @@ time_t start = clock(); ...@@ -983,43 +982,24 @@ time_t start = clock();
} }
#endif #endif
iteration++; iteration++;
//done = 1;
//if( iteration > 1 )exit(0);
} }
amoebaGpu->mutualInducedDone = done; amoebaGpu->mutualInducedDone = done;
amoebaGpu->mutualInducedConverged = ( !done || iteration > amoebaGpu->mutualInducedMaxIterations ) ? 0 : 1; amoebaGpu->mutualInducedConverged = ( !done || iteration > amoebaGpu->mutualInducedMaxIterations ) ? 0 : 1;
if( amoebaGpu->log ){ if( amoebaGpu->log ){
static int count = 0; trackMutualInducedIterations( amoebaGpu, iteration );
count++;
double interationD = static_cast<double>(iteration);
iterationStat[0] += interationD;
iterationStat[1] += interationD*interationD;
iterationStat[2] = interationD < iterationStat[2] ? interationD : iterationStat[2];
iterationStat[3] = interationD > iterationStat[3] ? interationD : iterationStat[3];
iterationStat[4] += 1.0;
if( count == 100 ){
double average = iterationStat[0]/iterationStat[4];
double stddev = iterationStat[1] - average*average*iterationStat[4];
stddev = sqrt( stddev )/(iterationStat[4]-1.0);
(void) fprintf( amoebaGpu->log, "%s iteration=%10.3f stddev=%10.3f min/max[%10.3f %10.3f] %10.1f eps=%14.7e\n",
methodName, average, stddev, iterationStat[2], iterationStat[3], iterationStat[4], amoebaGpu->mutualInducedCurrentEpsilon );
(void) fflush( amoebaGpu->log );
iterationStat[0] = iterationStat[1] = iterationStat[4] = 0.0;
count = 0;
}
} }
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( 1 ){ if( 0 ){
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector ); cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipole, outputVector );
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector );
cudaWriteVectorOfDoubleVectorsToFile( "CudaMI", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaMI_GK", fileId, outputVector );
} }
#endif #endif
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMutualInducedField.cu
View file @ ac8cb97f
...@@ -34,6 +34,7 @@ void GetCalculateAmoebaCudaMutualInducedFieldSim(amoebaGpuContext amoebaGpu) ...@@ -34,6 +34,7 @@ void GetCalculateAmoebaCudaMutualInducedFieldSim(amoebaGpuContext amoebaGpu)
} }
//#define AMOEBA_DEBUG //#define AMOEBA_DEBUG
#undef AMOEBA_DEBUG
__device__ void calculateMutualInducedFieldPairIxn_kernel( float4 atomCoordinatesI, float4 atomCoordinatesJ, __device__ void calculateMutualInducedFieldPairIxn_kernel( float4 atomCoordinatesI, float4 atomCoordinatesJ,
float dampingFactorI, float dampingFactorJ, float dampingFactorI, float dampingFactorJ,
...@@ -602,9 +603,8 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu ...@@ -602,9 +603,8 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
static const char* methodName = "cudaComputeAmoebaMutualInducedFieldBySOR";
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
static const char* methodName = "cudaComputeAmoebaMutualInducedFieldBySOR";
static int timestep = 0; static int timestep = 0;
std::vector<int> fileId; std::vector<int> fileId;
timestep++; timestep++;
...@@ -739,29 +739,16 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu ...@@ -739,29 +739,16 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu
amoebaGpu->psWorkVector[0]->_pDevStream[0], amoebaGpu->psWorkVector[1]->_pDevStream[0] ); amoebaGpu->psWorkVector[0]->_pDevStream[0], amoebaGpu->psWorkVector[1]->_pDevStream[0] );
LAUNCHERROR("kSorUpdateMutualInducedField"); LAUNCHERROR("kSorUpdateMutualInducedField");
// // get total epsilon -- performing sums on gpu // get total epsilon -- performing sums on gpu
kReduceMutualInducedFieldDelta_kernel<<<1, amoebaGpu->epsilonThreadsPerBlock, 2*sizeof(float)*amoebaGpu->epsilonThreadsPerBlock>>>( kReduceMutualInducedFieldDelta_kernel<<<1, amoebaGpu->epsilonThreadsPerBlock, 2*sizeof(float)*amoebaGpu->epsilonThreadsPerBlock>>>(
3*gpu->natoms, amoebaGpu->psWorkVector[0]->_pDevStream[0], amoebaGpu->psWorkVector[1]->_pDevStream[0], 3*gpu->natoms, amoebaGpu->psWorkVector[0]->_pDevStream[0], amoebaGpu->psWorkVector[1]->_pDevStream[0],
amoebaGpu->psCurrentEpsilon->_pDevStream[0] ); amoebaGpu->psCurrentEpsilon->_pDevStream[0] );
LAUNCHERROR("kReduceMutualInducedFieldDelta"); LAUNCHERROR("kReduceMutualInducedFieldDelta");
#if 1 if( amoebaGpu->log ){
// get total epsilon -- performing sums on cpu trackMutualInducedIterations( amoebaGpu, iteration);
{ }
float sum1 = cudaGetSum( 3*gpu->natoms, amoebaGpu->psWorkVector[0] );
float sum2 = cudaGetSum( 3*gpu->natoms, amoebaGpu->psWorkVector[1] );
sum1 = 4.8033324f*sqrtf( sum1/( (float) gpu->natoms) );
sum2 = 4.8033324f*sqrtf( sum2/( (float) gpu->natoms) );
float currentEpsilon = sum1 > sum2 ? sum1 : sum2;
amoebaGpu->mutualInducedCurrentEpsilon = currentEpsilon;
(void) fprintf( amoebaGpu->log, "%s iteration=%3d eps %14.6e [%14.6e %14.6e] done=%d sums=%14.6e %14.6e\n",
methodName, iteration, amoebaGpu->mutualInducedCurrentEpsilon,
amoebaGpu->psCurrentEpsilon->_pSysStream[0][1],
amoebaGpu->psCurrentEpsilon->_pSysStream[0][2], done, sum1, sum2 );
}
#endif
// Debye=4.8033324f // Debye=4.8033324f
amoebaGpu->psCurrentEpsilon->Download(); amoebaGpu->psCurrentEpsilon->Download();
...@@ -810,14 +797,14 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu ...@@ -810,14 +797,14 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu
} }
#endif #endif
iteration++; iteration++;
//if( iteration > 1 )exit(0);
} }
amoebaGpu->mutualInducedDone = done; amoebaGpu->mutualInducedDone = done;
amoebaGpu->mutualInducedConverged = ( !done || iteration > amoebaGpu->mutualInducedMaxIterations ) ? 0 : 1; amoebaGpu->mutualInducedConverged = ( !done || iteration > amoebaGpu->mutualInducedMaxIterations ) ? 0 : 1;
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( 1 ){ /*
if( 0 ){
std::vector<int> fileId; std::vector<int> fileId;
//fileId.push_back( 0 ); //fileId.push_back( 0 );
VectorOfDoubleVectors outputVector; VectorOfDoubleVectors outputVector;
...@@ -826,6 +813,7 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu ...@@ -826,6 +813,7 @@ static void cudaComputeAmoebaMutualInducedFieldBySOR( amoebaGpuContext amoebaGpu
cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector ); cudaLoadCudaFloatArray( gpu->natoms, 3, amoebaGpu->psInducedDipolePolar, outputVector );
cudaWriteVectorOfDoubleVectorsToFile( "CudaMI", fileId, outputVector ); cudaWriteVectorOfDoubleVectorsToFile( "CudaMI", fileId, outputVector );
} }
*/
#endif #endif
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp
View file @ ac8cb97f
...@@ -817,8 +817,8 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM ...@@ -817,8 +817,8 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
if( log ){ if( log ){
static const unsigned int maxPrint = MAX_PRINT; static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(bondForce->getNumBonds()); unsigned int arraySize = static_cast<unsigned int>(bondForce->getNumBonds());
(void) fprintf( log, "%s: %u sample of %sAmoebaHarmonicBondForce parameters; cubic=%15.7e quartic=%15.7e\n", (void) fprintf( log, "%s: %u sample of AmoebaHarmonicBondForce parameters in %s units; cubic=%15.7e quartic=%15.7e\n",
methodName.c_str(), arraySize, (useOpenMMUnits ? "CONVERTED " : ""), methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba"),
bondForce->getAmoebaGlobalHarmonicBondCubic(), bondForce->getAmoebaGlobalHarmonicBondQuartic() ); bondForce->getAmoebaGlobalHarmonicBondCubic(), bondForce->getAmoebaGlobalHarmonicBondQuartic() );
for( unsigned int ii = 0; ii < arraySize; ii++ ){ for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2; int particle1, particle2;
...@@ -937,13 +937,26 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force ...@@ -937,13 +937,26 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force
} }
} }
// convert units to kJ-nm from kCal-Angstrom?
if( useOpenMMUnits ){
for( int ii = 0; ii < angleForce->getNumAngles(); ii++ ){
int particle1, particle2, particle3;
double length, k;
angleForce->getAngleParameters( ii, particle1, particle2, particle3, length, k );
k *= CalToJoule;
angleForce->setAngleParameters( ii, particle1, particle2, particle3, length, k );
}
}
// diagnostics // diagnostics
if( log ){ if( log ){
static const unsigned int maxPrint = MAX_PRINT; static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(angleForce->getNumAngles()); unsigned int arraySize = static_cast<unsigned int>(angleForce->getNumAngles());
(void) fprintf( log, "%s: %u sample of AmoebaHarmonicAngleForce parameters; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n", (void) fprintf( log, "%s: %u sample of AmoebaHarmonicAngleForce parameters in %s units; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n",
methodName.c_str(), arraySize, angleForce->getAmoebaGlobalHarmonicAngleCubic(), methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba"),
angleForce->getAmoebaGlobalHarmonicAngleCubic(),
angleForce->getAmoebaGlobalHarmonicAngleQuartic(), angleForce->getAmoebaGlobalHarmonicAnglePentic(), angleForce->getAmoebaGlobalHarmonicAngleQuartic(), angleForce->getAmoebaGlobalHarmonicAnglePentic(),
angleForce->getAmoebaGlobalHarmonicAngleSextic() ); angleForce->getAmoebaGlobalHarmonicAngleSextic() );
...@@ -961,40 +974,6 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force ...@@ -961,40 +974,6 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force
} }
} }
} }
// convert units to kJ-nm from kCal-Angstrom?
if( useOpenMMUnits ){
for( int ii = 0; ii < angleForce->getNumAngles(); ii++ ){
int particle1, particle2, particle3;
double length, k;
angleForce->getAngleParameters( ii, particle1, particle2, particle3, length, k );
k *= CalToJoule;
angleForce->setAngleParameters( ii, particle1, particle2, particle3, length, k );
}
if( log ){
static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(angleForce->getNumAngles());
(void) fprintf( log, "%s: %u sample of CONVERTED AmoebaHarmonicAngleForce parameters; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n",
methodName.c_str(), arraySize, angleForce->getAmoebaGlobalHarmonicAngleCubic(),
angleForce->getAmoebaGlobalHarmonicAngleQuartic(), angleForce->getAmoebaGlobalHarmonicAnglePentic(),
angleForce->getAmoebaGlobalHarmonicAngleSextic() );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3;
double length, k;
angleForce->getAngleParameters( ii, particle1, particle2, particle3, length, k );
(void) fprintf( log, "%8d %8d %8d %8d %15.7e %15.7e\n",
ii, particle1, particle2, particle3, length, k );
// skip to end
if( ii == maxPrint && (arraySize - maxPrint) > ii ){
ii = arraySize - maxPrint - 1;
}
}
}
}
return angleForce->getNumAngles(); return angleForce->getNumAngles();
} }
...@@ -1098,14 +1077,28 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt ...@@ -1098,14 +1077,28 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt
} }
} }
// convert units to kJ-nm from kCal-Angstrom?
if( useOpenMMUnits ){
for( int ii = 0; ii < angleForce->getNumAngles(); ii++ ){
int particle1, particle2, particle3, particle4;
double length, k;
angleForce->getAngleParameters( ii, particle1, particle2, particle3, particle4, length, k );
k *= CalToJoule;
angleForce->setAngleParameters( ii, particle1, particle2, particle3, particle4, length, k );
}
}
// diagnostics // diagnostics
if( log ){ if( log ){
static const unsigned int maxPrint = MAX_PRINT; static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(angleForce->getNumAngles()); unsigned int arraySize = static_cast<unsigned int>(angleForce->getNumAngles());
(void) fprintf( log, "%s: %u sample of AmoebaHarmonicInPlaneAngleForce parameters; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n", (void) fprintf( log, "%s: %u sample of AmoebaHarmonicInPlaneAngleForce parameters in %s units; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n",
methodName.c_str(), arraySize, angleForce->getAmoebaGlobalHarmonicInPlaneAngleCubic(), methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba"),
angleForce->getAmoebaGlobalHarmonicInPlaneAngleQuartic(), angleForce->getAmoebaGlobalHarmonicInPlaneAnglePentic(), angleForce->getAmoebaGlobalHarmonicInPlaneAngleCubic(),
angleForce->getAmoebaGlobalHarmonicInPlaneAngleQuartic(),
angleForce->getAmoebaGlobalHarmonicInPlaneAnglePentic(),
angleForce->getAmoebaGlobalHarmonicInPlaneAngleSextic() ); angleForce->getAmoebaGlobalHarmonicInPlaneAngleSextic() );
for( unsigned int ii = 0; ii < arraySize; ii++ ){ for( unsigned int ii = 0; ii < arraySize; ii++ ){
...@@ -1123,39 +1116,6 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt ...@@ -1123,39 +1116,6 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt
} }
} }
// convert units to kJ-nm from kCal-Angstrom?
if( useOpenMMUnits ){
for( int ii = 0; ii < angleForce->getNumAngles(); ii++ ){
int particle1, particle2, particle3, particle4;
double length, k;
angleForce->getAngleParameters( ii, particle1, particle2, particle3, particle4, length, k );
k *= CalToJoule;
angleForce->setAngleParameters( ii, particle1, particle2, particle3, particle4, length, k );
}
if( log ){
static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(angleForce->getNumAngles());
(void) fprintf( log, "%s: %u sample of AmoebaHarmonicInPlaneAngleForce CONVERTED parameters; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n",
methodName.c_str(), arraySize, angleForce->getAmoebaGlobalHarmonicInPlaneAngleCubic(),
angleForce->getAmoebaGlobalHarmonicInPlaneAngleQuartic(), angleForce->getAmoebaGlobalHarmonicInPlaneAnglePentic(),
angleForce->getAmoebaGlobalHarmonicInPlaneAngleSextic() );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3, particle4;
double length, k;
angleForce->getAngleParameters( ii, particle1, particle2, particle3, particle4, length, k );
(void) fprintf( log, "%8d %8d %8d %8d %8d %15.7e %15.7e\n",
ii, particle1, particle2, particle3, particle4, length, k );
// skip to end
if( ii == maxPrint && (arraySize - maxPrint) > ii ){
ii = arraySize - maxPrint - 1;
}
}
}
}
return angleForce->getNumAngles(); return angleForce->getNumAngles();
} }
...@@ -1245,13 +1205,29 @@ static int readAmoebaTorsionParameters( FILE* filePtr, MapStringInt& forceMap, c ...@@ -1245,13 +1205,29 @@ static int readAmoebaTorsionParameters( FILE* filePtr, MapStringInt& forceMap, c
} }
} }
// convert units to kJ-nm from kCal-Angstrom?
if( useOpenMMUnits ){
for( int ii = 0; ii < torsionForce->getNumTorsions(); ii++ ){
int particle1, particle2, particle3, particle4;
std::vector<double> torsion1;
std::vector<double> torsion2;
std::vector<double> torsion3;
torsionForce->getTorsionParameters( ii, particle1, particle2, particle3, particle4, torsion1, torsion2, torsion3 );
torsion1[0] *= CalToJoule;
torsion2[0] *= CalToJoule;
torsion3[0] *= CalToJoule;
torsionForce->setTorsionParameters( ii, particle1, particle2, particle3, particle4, torsion1, torsion2, torsion3 );
}
}
// diagnostics // diagnostics
if( log ){ if( log ){
static const unsigned int maxPrint = MAX_PRINT; static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(torsionForce->getNumTorsions()); unsigned int arraySize = static_cast<unsigned int>(torsionForce->getNumTorsions());
(void) fprintf( log, "%s: %u sample of AmoebaTorsionForce parameters\n", (void) fprintf( log, "%s: %u sample of AmoebaTorsionForce parameters in %s units.\n",
methodName.c_str(), arraySize ); methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba") );
for( unsigned int ii = 0; ii < arraySize; ii++ ){ for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3, particle4; int particle1, particle2, particle3, particle4;
...@@ -1271,46 +1247,6 @@ static int readAmoebaTorsionParameters( FILE* filePtr, MapStringInt& forceMap, c ...@@ -1271,46 +1247,6 @@ static int readAmoebaTorsionParameters( FILE* filePtr, MapStringInt& forceMap, c
} }
} }
// convert units to kJ-nm from kCal-Angstrom?
if( useOpenMMUnits ){
for( int ii = 0; ii < torsionForce->getNumTorsions(); ii++ ){
int particle1, particle2, particle3, particle4;
std::vector<double> torsion1;
std::vector<double> torsion2;
std::vector<double> torsion3;
torsionForce->getTorsionParameters( ii, particle1, particle2, particle3, particle4, torsion1, torsion2, torsion3 );
torsion1[0] *= CalToJoule;
torsion2[0] *= CalToJoule;
torsion3[0] *= CalToJoule;
torsionForce->setTorsionParameters( ii, particle1, particle2, particle3, particle4, torsion1, torsion2, torsion3 );
}
if( log ){
static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(torsionForce->getNumTorsions());
(void) fprintf( log, "%s: %u sample of CONVERTED AmoebaTorsionForce parameters\n",
methodName.c_str(), arraySize );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3, particle4;
std::vector<double> torsion1;
std::vector<double> torsion2;
std::vector<double> torsion3;
torsionForce->getTorsionParameters( ii, particle1, particle2, particle3, particle4, torsion1, torsion2, torsion3 );
(void) fprintf( log, "%8d %8d %8d %8d %8d [%15.7e %15.7e] [%15.7e %15.7e] [%15.7e %15.7e]\n",
ii, particle1, particle2, particle3, particle4,
torsion1[0], torsion1[1]/DegreesToRadians, torsion2[0], torsion2[1]/DegreesToRadians, torsion3[0], torsion3[1]/DegreesToRadians );
// skip to end
if( ii == maxPrint && (arraySize - maxPrint) > ii ){
ii = arraySize - maxPrint - 1;
}
}
}
}
return torsionForce->getNumTorsions(); return torsionForce->getNumTorsions();
} }
...@@ -1386,13 +1322,25 @@ static int readAmoebaPiTorsionParameters( FILE* filePtr, MapStringInt& forceMap, ...@@ -1386,13 +1322,25 @@ static int readAmoebaPiTorsionParameters( FILE* filePtr, MapStringInt& forceMap,
} }
} }
// convert to OpenMM units
if( useOpenMMUnits ){
for( int ii = 0; ii < piTorsionForce->getNumPiTorsions(); ii++ ){
int particle1, particle2, particle3, particle4, particle5, particle6;
double torsionK;
piTorsionForce->getPiTorsionParameters( ii, particle1, particle2, particle3, particle4, particle5, particle6, torsionK );
torsionK *= CalToJoule;
piTorsionForce->setPiTorsionParameters( ii, particle1, particle2, particle3, particle4, particle5, particle6, torsionK );
}
}
// diagnostics // diagnostics
if( log ){ if( log ){
static const unsigned int maxPrint = MAX_PRINT; static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(piTorsionForce->getNumPiTorsions()); unsigned int arraySize = static_cast<unsigned int>(piTorsionForce->getNumPiTorsions());
(void) fprintf( log, "%s: %u sample of AmoebaPiTorsionForce parameters\n", (void) fprintf( log, "%s: %u sample of AmoebaPiTorsionForce parameters in %s units.\n",
methodName.c_str(), arraySize ); methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba") );
for( unsigned int ii = 0; ii < arraySize; ii++ ){ for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3, particle4, particle5, particle6; int particle1, particle2, particle3, particle4, particle5, particle6;
...@@ -1409,36 +1357,6 @@ static int readAmoebaPiTorsionParameters( FILE* filePtr, MapStringInt& forceMap, ...@@ -1409,36 +1357,6 @@ static int readAmoebaPiTorsionParameters( FILE* filePtr, MapStringInt& forceMap,
} }
} }
if( useOpenMMUnits ){
for( int ii = 0; ii < piTorsionForce->getNumPiTorsions(); ii++ ){
int particle1, particle2, particle3, particle4, particle5, particle6;
double torsionK;
piTorsionForce->getPiTorsionParameters( ii, particle1, particle2, particle3, particle4, particle5, particle6, torsionK );
torsionK *= CalToJoule;
piTorsionForce->setPiTorsionParameters( ii, particle1, particle2, particle3, particle4, particle5, particle6, torsionK );
}
if( log ){
static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(piTorsionForce->getNumPiTorsions());
(void) fprintf( log, "%s: %u sample of CONVERTED AmoebaPiTorsionForce parameters\n",
methodName.c_str(), arraySize );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3, particle4, particle5, particle6;
double torsionK;
piTorsionForce->getPiTorsionParameters( ii, particle1, particle2, particle3, particle4, particle5, particle6, torsionK );
(void) fprintf( log, "%8d %8d %8d %8d %8d %8d %8d k=%15.7e\n",
ii, particle1, particle2, particle3, particle4, particle5, particle6, torsionK );
// skip to end
if( ii == maxPrint && (arraySize - maxPrint) > ii ){
ii = arraySize - maxPrint - 1;
}
}
}
}
return piTorsionForce->getNumPiTorsions(); return piTorsionForce->getNumPiTorsions();
} }
...@@ -1517,13 +1435,27 @@ static int readAmoebaStretchBendParameters( FILE* filePtr, MapStringInt& forceMa ...@@ -1517,13 +1435,27 @@ static int readAmoebaStretchBendParameters( FILE* filePtr, MapStringInt& forceMa
} }
} }
// convert to OpenMM units
if( useOpenMMUnits ){
for( int ii = 0; ii < stretchBendForce->getNumStretchBends(); ii++ ){
int particle1, particle2, particle3;
double lengthAB, lengthCB, angle, k;
stretchBendForce->getStretchBendParameters( ii, particle1, particle2, particle3, lengthAB, lengthCB, angle, k );
lengthAB *= AngstromToNm;
lengthCB *= AngstromToNm;
k *= CalToJoule/AngstromToNm;
stretchBendForce->setStretchBendParameters( ii, particle1, particle2, particle3, lengthAB, lengthCB, angle, k );
}
}
// diagnostics // diagnostics
if( log ){ if( log ){
static const unsigned int maxPrint = MAX_PRINT; static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(stretchBendForce->getNumStretchBends()); unsigned int arraySize = static_cast<unsigned int>(stretchBendForce->getNumStretchBends());
(void) fprintf( log, "%s: %u sample of AmoebaStretchBendForce parameters\n", (void) fprintf( log, "%s: %u sample of AmoebaStretchBendForce parameters in %s units.\n",
methodName.c_str(), arraySize ); methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba") );
for( unsigned int ii = 0; ii < arraySize; ii++ ){ for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3; int particle1, particle2, particle3;
double lengthAB, lengthCB, angle, k; double lengthAB, lengthCB, angle, k;
...@@ -1539,37 +1471,6 @@ static int readAmoebaStretchBendParameters( FILE* filePtr, MapStringInt& forceMa ...@@ -1539,37 +1471,6 @@ static int readAmoebaStretchBendParameters( FILE* filePtr, MapStringInt& forceMa
} }
} }
if( useOpenMMUnits ){
for( int ii = 0; ii < stretchBendForce->getNumStretchBends(); ii++ ){
int particle1, particle2, particle3;
double lengthAB, lengthCB, angle, k;
stretchBendForce->getStretchBendParameters( ii, particle1, particle2, particle3, lengthAB, lengthCB, angle, k );
lengthAB *= AngstromToNm;
lengthCB *= AngstromToNm;
k *= CalToJoule/AngstromToNm;
stretchBendForce->setStretchBendParameters( ii, particle1, particle2, particle3, lengthAB, lengthCB, angle, k );
}
if( log ){
static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(stretchBendForce->getNumStretchBends());
(void) fprintf( log, "%s: %u sample of AmoebaStretchBendForce parameters\n",
methodName.c_str(), arraySize );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3;
double lengthAB, lengthCB, angle, k;
stretchBendForce->getStretchBendParameters( ii, particle1, particle2, particle3, lengthAB, lengthCB, angle, k );
(void) fprintf( log, "%8d %8d %8d %8d %15.7e %15.7e %15.7e %15.7e\n",
ii, particle1, particle2, particle3, lengthAB, lengthCB, angle/DegreesToRadians, k );
// skip to end
if( ii == maxPrint && (arraySize - maxPrint) > ii ){
ii = arraySize - maxPrint - 1;
}
}
}
}
return stretchBendForce->getNumStretchBends(); return stretchBendForce->getNumStretchBends();
} }
...@@ -1679,13 +1580,26 @@ static int readAmoebaOutOfPlaneBendParameters( FILE* filePtr, MapStringInt& forc ...@@ -1679,13 +1580,26 @@ static int readAmoebaOutOfPlaneBendParameters( FILE* filePtr, MapStringInt& forc
} }
} }
// convert to OpenMM units
if( useOpenMMUnits ){
for( int ii = 0; ii < outOfPlaneBendForce->getNumOutOfPlaneBends(); ii++ ){
int particle1, particle2, particle3, particle4;
double k;
outOfPlaneBendForce->getOutOfPlaneBendParameters( ii, particle1, particle2, particle3, particle4, k );
//k *= CalToJoule/(AngstromToNm*AngstromToNm);
k *= CalToJoule;
outOfPlaneBendForce->setOutOfPlaneBendParameters( ii, particle1, particle2, particle3, particle4, k );
}
}
// diagnostics // diagnostics
if( log ){ if( log ){
static const unsigned int maxPrint = MAX_PRINT; static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(outOfPlaneBendForce->getNumOutOfPlaneBends()); unsigned int arraySize = static_cast<unsigned int>(outOfPlaneBendForce->getNumOutOfPlaneBends());
(void) fprintf( log, "%s: %u sample of AmoebaOutOfPlaneBendForce parameters\n", (void) fprintf( log, "%s: %u sample of AmoebaOutOfPlaneBendForce parameters in %s units.\n",
methodName.c_str(), arraySize ); methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba") );
(void) fprintf( log, "%s: %u sample of AmoebaOutOfPlaneBendForce parameters; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n", (void) fprintf( log, "%s: %u sample of AmoebaOutOfPlaneBendForce parameters; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n",
methodName.c_str(), arraySize, methodName.c_str(), arraySize,
outOfPlaneBendForce->getAmoebaGlobalOutOfPlaneBendCubic(), outOfPlaneBendForce->getAmoebaGlobalOutOfPlaneBendCubic(),
...@@ -1708,43 +1622,6 @@ static int readAmoebaOutOfPlaneBendParameters( FILE* filePtr, MapStringInt& forc ...@@ -1708,43 +1622,6 @@ static int readAmoebaOutOfPlaneBendParameters( FILE* filePtr, MapStringInt& forc
} }
} }
if( useOpenMMUnits ){
for( int ii = 0; ii < outOfPlaneBendForce->getNumOutOfPlaneBends(); ii++ ){
int particle1, particle2, particle3, particle4;
double k;
outOfPlaneBendForce->getOutOfPlaneBendParameters( ii, particle1, particle2, particle3, particle4, k );
//k *= CalToJoule/(AngstromToNm*AngstromToNm);
k *= CalToJoule;
outOfPlaneBendForce->setOutOfPlaneBendParameters( ii, particle1, particle2, particle3, particle4, k );
}
if( log ){
static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(outOfPlaneBendForce->getNumOutOfPlaneBends());
(void) fprintf( log, "%s: %u sample of AmoebaOutOfPlaneBendForce parameters\n",
methodName.c_str(), arraySize );
(void) fprintf( log, "%s: %u sample of AmoebaOutOfPlaneBendForce parameters; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n",
methodName.c_str(), arraySize,
outOfPlaneBendForce->getAmoebaGlobalOutOfPlaneBendCubic(),
outOfPlaneBendForce->getAmoebaGlobalOutOfPlaneBendQuartic(),
outOfPlaneBendForce->getAmoebaGlobalOutOfPlaneBendPentic(),
outOfPlaneBendForce->getAmoebaGlobalOutOfPlaneBendSextic() );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3, particle4;
double k;
outOfPlaneBendForce->getOutOfPlaneBendParameters( ii, particle1, particle2, particle3, particle4, k );
(void) fprintf( log, "%8d %8d %8d %8d %8d %15.7e\n",
ii, particle1, particle2, particle3, particle4, k );
// skip to end
if( ii == maxPrint && (arraySize - maxPrint) > ii ){
ii = arraySize - maxPrint - 1;
}
}
}
}
return outOfPlaneBendForce->getNumOutOfPlaneBends(); return outOfPlaneBendForce->getNumOutOfPlaneBends();
} }
...@@ -1819,7 +1696,8 @@ static int readAmoebaTorsionTorsionGrid( FILE* filePtr, int numX, int numY, Tors ...@@ -1819,7 +1696,8 @@ static int readAmoebaTorsionTorsionGrid( FILE* filePtr, int numX, int numY, Tors
if( log ){ if( log ){
static const unsigned int maxPrint = 20; static const unsigned int maxPrint = 20;
(void) fprintf( log, "%s: %dx%d sample of grid values\n", methodName.c_str(), numX, numY ); (void) fprintf( log, "%s: %dx%d sample of grid values; using %s units\n", methodName.c_str(), numX, numY,
(useOpenMMUnits ? "OpenMM" : "Amoeba") );
int xI = 0; int xI = 0;
int yI = 0; int yI = 0;
...@@ -2197,11 +2075,54 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap, ...@@ -2197,11 +2075,54 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap,
multipoleForce->setMutualInducedTargetEpsilon( atof( isPresent->second.c_str() ) ); multipoleForce->setMutualInducedTargetEpsilon( atof( isPresent->second.c_str() ) );
} }
// convert to OpenMM units
if( useOpenMMUnits ){
double dipoleConversion = AngstromToNm;
double quadrupoleConversion = AngstromToNm*AngstromToNm;
double polarityConversion = AngstromToNm*AngstromToNm*AngstromToNm;
double dampingFactorConversion = sqrt( AngstromToNm );
float scalingDistanceCutoff = static_cast<float>(multipoleForce->getScalingDistanceCutoff());
scalingDistanceCutoff *= static_cast<float>(AngstromToNm);
multipoleForce->setScalingDistanceCutoff( scalingDistanceCutoff );
for( int ii = 0; ii < multipoleForce->getNumMultipoles(); ii++ ){
int axisType, zAxis, xAxis;
std::vector<double> dipole;
std::vector<double> quadrupole;
double charge, thole, dampingFactor, polarity;
multipoleForce->getMultipoleParameters( ii, charge, dipole, quadrupole, axisType, zAxis, xAxis, thole, dampingFactor, polarity );
for( unsigned int jj = 0; jj < dipole.size(); jj++ ){
dipole[jj] *= dipoleConversion;
}
for( unsigned int jj = 0; jj < quadrupole.size(); jj++ ){
quadrupole[jj] *= quadrupoleConversion;
}
polarity *= polarityConversion;
dampingFactor *= dampingFactorConversion;
multipoleForce->setMultipoleParameters( ii, charge, dipole, quadrupole, axisType, zAxis, xAxis, thole, dampingFactor, polarity );
}
} else {
float electricConstant = static_cast<float>(multipoleForce->getElectricConstant());
electricConstant /= static_cast<float>(AngstromToNm*CalToJoule);
multipoleForce->setElectricConstant( electricConstant );
}
// diagnostics // diagnostics
if( log ){ if( log ){
(void) fprintf( log, "%s Supplementary fields %u: ", methodName.c_str(), static_cast<unsigned int>(supplementary.size()) ); (void) fprintf( log, "%s Sample of parameters using %s units.\n", methodName.c_str(),
(useOpenMMUnits ? "OpenMM" : "Amoeba") );
(void) fprintf( log, "Supplementary fields %u: ", static_cast<unsigned int>(supplementary.size()) );
for( MapStringVectorOfVectorsCI ii = supplementary.begin(); ii != supplementary.end(); ii++ ){ for( MapStringVectorOfVectorsCI ii = supplementary.begin(); ii != supplementary.end(); ii++ ){
(void) fprintf( log, "%s ", (*ii).first.c_str() ); (void) fprintf( log, "%s ", (*ii).first.c_str() );
} }
...@@ -2220,8 +2141,8 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap, ...@@ -2220,8 +2141,8 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap,
//static const unsigned int maxPrint = MAX_PRINT; //static const unsigned int maxPrint = MAX_PRINT;
static const unsigned int maxPrint = 15; static const unsigned int maxPrint = 15;
unsigned int arraySize = static_cast<unsigned int>(multipoleForce->getNumMultipoles()); unsigned int arraySize = static_cast<unsigned int>(multipoleForce->getNumMultipoles());
(void) fprintf( log, "%s: %u maxIter=%d targetEps=%15.7e\n", (void) fprintf( log, "%u maxIter=%d targetEps=%15.7e\n",
methodName.c_str(), arraySize, arraySize,
multipoleForce->getMutualInducedMaxIterations(), multipoleForce->getMutualInducedMaxIterations(),
multipoleForce->getMutualInducedTargetEpsilon() ); multipoleForce->getMutualInducedTargetEpsilon() );
(void) fprintf( log, "Sample of AmoebaMultipoleForce parameters\n" ); (void) fprintf( log, "Sample of AmoebaMultipoleForce parameters\n" );
...@@ -2260,54 +2181,6 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap, ...@@ -2260,54 +2181,6 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap,
(void) fflush( log ); (void) fflush( log );
} }
if( useOpenMMUnits ){
/*
scalingDistanceCutoff, thole, dampingFactor, pGamma,
gkc = cAmoebaSim.gkc;
fc = cAmoebaSim.fc;
fd = cAmoebaSim.fd;
fq = cAmoebaSim.fq;
*/
double dipoleConversion = AngstromToNm;
double quadrupoleConversion = AngstromToNm*AngstromToNm;
double polarityConversion = AngstromToNm*AngstromToNm*AngstromToNm;
double dampingFactorConversion = sqrt( AngstromToNm );
float scalingDistanceCutoff = static_cast<float>(multipoleForce->getScalingDistanceCutoff());
scalingDistanceCutoff *= static_cast<float>(AngstromToNm);
multipoleForce->setScalingDistanceCutoff( scalingDistanceCutoff );
for( int ii = 0; ii < multipoleForce->getNumMultipoles(); ii++ ){
int axisType, zAxis, xAxis;
std::vector<double> dipole;
std::vector<double> quadrupole;
double charge, thole, dampingFactor, polarity;
multipoleForce->getMultipoleParameters( ii, charge, dipole, quadrupole, axisType, zAxis, xAxis, thole, dampingFactor, polarity );
for( unsigned int jj = 0; jj < dipole.size(); jj++ ){
dipole[jj] *= dipoleConversion;
}
for( unsigned int jj = 0; jj < quadrupole.size(); jj++ ){
quadrupole[jj] *= quadrupoleConversion;
}
polarity *= polarityConversion;
dampingFactor *= dampingFactorConversion;
multipoleForce->setMultipoleParameters( ii, charge, dipole, quadrupole, axisType, zAxis, xAxis, thole, dampingFactor, polarity );
}
} else {
float electricConstant = static_cast<float>(multipoleForce->getElectricConstant());
electricConstant /= static_cast<float>(AngstromToNm*CalToJoule);
multipoleForce->setElectricConstant( electricConstant );
}
return multipoleForce->getNumMultipoles(); return multipoleForce->getNumMultipoles();
} }
...@@ -2448,8 +2321,16 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt& ...@@ -2448,8 +2321,16 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
gbsaObcForce->setIncludeCavityTerm( atoi( isPresent->second.c_str() ) ); gbsaObcForce->setIncludeCavityTerm( atoi( isPresent->second.c_str() ) );
} }
// convert to OpenMM units
if( useOpenMMUnits ){ if( useOpenMMUnits ){
gbsaObcForce->setDielectricOffset( 0.009 ); gbsaObcForce->setDielectricOffset( 0.009 );
for( int ii = 0; ii < gbsaObcForce->getNumParticles(); ii++ ){
double charge, radius, scalingFactor;
gbsaObcForce->getParticleParameters( ii, charge, radius, scalingFactor );
radius *= AngstromToNm;
gbsaObcForce->setParticleParameters( ii, charge, radius, scalingFactor );
}
} else { } else {
gbsaObcForce->setDielectricOffset( 0.09 ); gbsaObcForce->setDielectricOffset( 0.09 );
gbsaObcForce->setProbeRadius( 1.4 ); gbsaObcForce->setProbeRadius( 1.4 );
...@@ -2458,11 +2339,14 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt& ...@@ -2458,11 +2339,14 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
gbsaObcForce->setSurfaceAreaFactor( surfaceAreaFactor ); gbsaObcForce->setSurfaceAreaFactor( surfaceAreaFactor );
} }
// diagnostics
if( log ){ if( log ){
static const unsigned int maxPrint = MAX_PRINT; static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(gbsaObcForce->getNumParticles()); unsigned int arraySize = static_cast<unsigned int>(gbsaObcForce->getNumParticles());
(void) fprintf( log, "%s: sample of GK force parameters; no. of particles=%d useOpenMMUnits=%d\n", (void) fprintf( log, "%s: sample of GK force parameters; no. of particles=%d using %s units.\n",
methodName.c_str(), gbsaObcForce->getNumParticles(), useOpenMMUnits ); methodName.c_str(), gbsaObcForce->getNumParticles(),
(useOpenMMUnits ? "OpenMM" : "Amoeba") );
(void) fprintf( log, "solute/solvent dielectrics: [%10.4f %10.4f] includeCavityTerm=%1d probeRadius=%15.7e SA prefactor=%15.7e\n", (void) fprintf( log, "solute/solvent dielectrics: [%10.4f %10.4f] includeCavityTerm=%1d probeRadius=%15.7e SA prefactor=%15.7e\n",
gbsaObcForce->getSoluteDielectric(), gbsaObcForce->getSolventDielectric(), gbsaObcForce->getSoluteDielectric(), gbsaObcForce->getSolventDielectric(),
gbsaObcForce->getIncludeCavityTerm(), gbsaObcForce->getProbeRadius( ), gbsaObcForce->getSurfaceAreaFactor( ) ); gbsaObcForce->getIncludeCavityTerm(), gbsaObcForce->getProbeRadius( ), gbsaObcForce->getSurfaceAreaFactor( ) );
...@@ -2478,15 +2362,6 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt& ...@@ -2478,15 +2362,6 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
} }
} }
if( useOpenMMUnits ){
for( int ii = 0; ii < gbsaObcForce->getNumParticles(); ii++ ){
double charge, radius, scalingFactor;
gbsaObcForce->getParticleParameters( ii, charge, radius, scalingFactor );
radius *= AngstromToNm;
gbsaObcForce->setParticleParameters( ii, charge, radius, scalingFactor );
}
}
return gbsaObcForce->getNumParticles(); return gbsaObcForce->getNumParticles();
} }
...@@ -2626,7 +2501,6 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const ...@@ -2626,7 +2501,6 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
} }
} }
(void) fprintf( log, "%s AmoebaVdwForce scales read\n", methodName.c_str() ); fflush( log );
lineTokensT.resize(0); lineTokensT.resize(0);
isNotEof = readLine( filePtr, lineTokensT, lineCount, log ); isNotEof = readLine( filePtr, lineTokensT, lineCount, log );
if( lineTokensT[0] == "AmoebaVdw14_7Exclusion" ){ if( lineTokensT[0] == "AmoebaVdw14_7Exclusion" ){
...@@ -2668,18 +2542,58 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const ...@@ -2668,18 +2542,58 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
throwException(__FILE__, __LINE__, buffer ); throwException(__FILE__, __LINE__, buffer );
exit(-1); exit(-1);
} }
} }
// get combining rule
lineTokensT.resize(0);
isNotEof = readLine( filePtr, lineTokensT, lineCount, log );
if( lineTokensT[0] == "AmoebaVdw14_CombiningRule" ){
int tokenIndex = 1;
std::string sigmaCombiningRule = lineTokensT[tokenIndex++].c_str();
std::string epsilonCombiningRule = lineTokensT[tokenIndex++].c_str();
vdwForce->setSigmaCombiningRule( sigmaCombiningRule );
vdwForce->setEpsilonCombiningRule( epsilonCombiningRule );
}
// convert units to kJ-nm from kCal-Angstrom?
if( useOpenMMUnits ){
unsigned int tableSize = static_cast<unsigned int>(vdwForce->getSigEpsTableSize());
if( tableLoaded ){
/*
for( unsigned int ii = 0; ii < tableSize; ii++ ){
for( unsigned int jj = 0; jj < tableSize; jj++ ){
double sig, eps, sig4, eps4;
vdwForce->getSigEpsTableEntry( ii, jj, sig, eps, sig4, eps4);
(void) fprintf( log, "%8d %8d %10.4f %10.4f %10.4f %10.4f\n", ii, jj, sig, eps, sig4, eps4 );
// skip to end
if( jj == maxPrint && (tableSize - maxPrint) > jj ){
jj = tableSize - maxPrint - 1;
}
}
// skip to end
if( ii == maxPrint && (tableSize - maxPrint) > ii ){
ii = tableSize - maxPrint - 1;
}
}
*/
}
// get combining rule for( int ii = 0; ii < vdwForce->getNumParticles(); ii++ ){
int indexIV, indexClass;
lineTokensT.resize(0); double sigma, sigma4, epsilon, epsilon4, reduction;
isNotEof = readLine( filePtr, lineTokensT, lineCount, log ); vdwForce->getParticleParameters( ii, indexIV, indexClass, sigma, sigma4, epsilon, epsilon4, reduction );
if( lineTokensT[0] == "AmoebaVdw14_CombiningRule" ){ sigma *= AngstromToNm;
int tokenIndex = 1; sigma4 *= AngstromToNm;
std::string sigmaCombiningRule = lineTokensT[tokenIndex++].c_str(); epsilon *= CalToJoule;
std::string epsilonCombiningRule = lineTokensT[tokenIndex++].c_str(); vdwForce->setParticleParameters( ii, indexIV, indexClass, sigma, sigma4, epsilon, epsilon4, reduction );
vdwForce->setSigmaCombiningRule( sigmaCombiningRule ); }
vdwForce->setEpsilonCombiningRule( epsilonCombiningRule );
} }
// diagnostics // diagnostics
...@@ -2690,8 +2604,9 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const ...@@ -2690,8 +2604,9 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
static const int maxPrint = 15; static const int maxPrint = 15;
unsigned int arraySize = static_cast<unsigned int>(vdwForce->getNumParticles()); unsigned int arraySize = static_cast<unsigned int>(vdwForce->getNumParticles());
unsigned int tableSize = static_cast<unsigned int>(vdwForce->getSigEpsTableSize()); unsigned int tableSize = static_cast<unsigned int>(vdwForce->getSigEpsTableSize());
(void) fprintf( log, "%s: %u sample of AmoebaVdwForce parameters; SigEpsTableSize=%d combining rules=[sig=%s eps=%s]\n", (void) fprintf( log, "%s: %u sample of AmoebaVdwForce parameters using %s units; SigEpsTableSize=%d combining rules=[sig=%s eps=%s]\n",
methodName.c_str(), arraySize, vdwForce->getSigEpsTableSize(), methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba"),
vdwForce->getSigEpsTableSize(),
vdwForce->getSigmaCombiningRule().c_str(), vdwForce->getEpsilonCombiningRule().c_str() ); vdwForce->getSigmaCombiningRule().c_str(), vdwForce->getEpsilonCombiningRule().c_str() );
if( tableLoaded ){ if( tableLoaded ){
...@@ -2765,47 +2680,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const ...@@ -2765,47 +2680,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
(void) fflush( log ); (void) fflush( log );
} }
// convert units to kJ-nm from kCal-Angstrom?
if( useOpenMMUnits ){
unsigned int tableSize = static_cast<unsigned int>(vdwForce->getSigEpsTableSize());
if( tableLoaded ){
/*
for( unsigned int ii = 0; ii < tableSize; ii++ ){
for( unsigned int jj = 0; jj < tableSize; jj++ ){
double sig, eps, sig4, eps4;
vdwForce->getSigEpsTableEntry( ii, jj, sig, eps, sig4, eps4);
(void) fprintf( log, "%8d %8d %10.4f %10.4f %10.4f %10.4f\n", ii, jj, sig, eps, sig4, eps4 );
// skip to end
if( jj == maxPrint && (tableSize - maxPrint) > jj ){
jj = tableSize - maxPrint - 1;
}
}
// skip to end
if( ii == maxPrint && (tableSize - maxPrint) > ii ){
ii = tableSize - maxPrint - 1;
}
}
*/
}
for( int ii = 0; ii < vdwForce->getNumParticles(); ii++ ){
int indexIV, indexClass;
double sigma, sigma4, epsilon, epsilon4, reduction;
vdwForce->getParticleParameters( ii, indexIV, indexClass, sigma, sigma4, epsilon, epsilon4, reduction );
sigma *= AngstromToNm;
sigma4 *= AngstromToNm;
epsilon *= CalToJoule;
vdwForce->setParticleParameters( ii, indexIV, indexClass, sigma, sigma4, epsilon, epsilon4, reduction );
}
}
return vdwForce->getNumParticles(); return vdwForce->getNumParticles();
} }
...@@ -2929,61 +2804,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force ...@@ -2929,61 +2804,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
} }
} }
// diagnostics // convert to OpenMM units
if( log ){
//static const unsigned int maxPrint = MAX_PRINT;
static const unsigned int maxPrint = 15;
unsigned int arraySize = static_cast<unsigned int>(wcaDispersionForce->getNumParticles());
(void) fprintf( log, "%s: %u sample of AmoebaVdwForce parameters\n",
methodName.c_str(), arraySize );
(void) fprintf( log, "Eps[%14.7f %14.7f] Rmin[%14.7f %14.7f]\nAwater %14.7f Shctd %14.7f Dispoff %14.7f Slevy %14.7f\n",
wcaDispersionForce->getEpso( ), wcaDispersionForce->getEpsh( ),
wcaDispersionForce->getRmino( ), wcaDispersionForce->getRminh( ),
wcaDispersionForce->getAwater( ), wcaDispersionForce->getShctd( ), wcaDispersionForce->getDispoff( ), wcaDispersionForce->getSlevy( ) );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
double radius, epsilon, maxDispersionEnergy;
wcaDispersionForce->getParticleParameters( ii, radius, epsilon );
(void) fprintf( log, "%8d %10.4f %10.4f", ii, radius, epsilon );
if( ii < maxDispersionEnergyVector.size() ){
wcaDispersionForce->getMaximumDispersionEnergy( ii, maxDispersionEnergy );
double delta = fabs( maxDispersionEnergy - maxDispersionEnergyVector[ii] );
const char* error = (delta > 1.0e-05) ? "XXX" : "";
(void) fprintf( log, " maxDispEDiff=%12.5e %14.7f %14.7f %s",
delta, maxDispersionEnergy, maxDispersionEnergyVector[ii], error );
}
(void) fprintf( log, "\n" );
// skip to end
if( ii == maxPrint && (arraySize - maxPrint) > ii ){
ii = arraySize - maxPrint - 1;
}
}
(void) fflush( log );
// check max dispersion energy for all particles
int errors = 0;
for( unsigned int ii = 0; ii < arraySize && ii < maxDispersionEnergyVector.size(); ii++ ){
double maxDispersionEnergy;
wcaDispersionForce->getMaximumDispersionEnergy( ii, maxDispersionEnergy );
double delta = fabs( maxDispersionEnergy - maxDispersionEnergyVector[ii] );
if( delta > 1.0e-05 ){
(void) fprintf( log, " maxDispEDiff=%12.5e %14.7f %14.7f XXX\n", delta, maxDispersionEnergy, maxDispersionEnergyVector[ii] );
errors++;
}
}
if( errors ){
exit(-1);
} else {
(void) fprintf( log, "No errors detected in maxDispEnergy!\n" );
}
(void) fflush( log );
}
if( useOpenMMUnits ){ if( useOpenMMUnits ){
...@@ -3041,6 +2862,64 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force ...@@ -3041,6 +2862,64 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
} }
} }
// diagnostics
if( log ){
//static const unsigned int maxPrint = MAX_PRINT;
static const unsigned int maxPrint = 15;
unsigned int arraySize = static_cast<unsigned int>(wcaDispersionForce->getNumParticles());
(void) fprintf( log, "%s: %u sample of AmoebaVdwForce parameters in %s units.\n",
methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba") );
(void) fprintf( log, "Eps[%14.7f %14.7f] Rmin[%14.7f %14.7f]\nAwater %14.7f Shctd %14.7f Dispoff %14.7f Slevy %14.7f\n",
wcaDispersionForce->getEpso( ), wcaDispersionForce->getEpsh( ),
wcaDispersionForce->getRmino( ), wcaDispersionForce->getRminh( ),
wcaDispersionForce->getAwater( ), wcaDispersionForce->getShctd( ), wcaDispersionForce->getDispoff( ), wcaDispersionForce->getSlevy( ) );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
double radius, epsilon, maxDispersionEnergy;
wcaDispersionForce->getParticleParameters( ii, radius, epsilon );
(void) fprintf( log, "%8d %10.4f %10.4f", ii, radius, epsilon );
if( ii < maxDispersionEnergyVector.size() ){
wcaDispersionForce->getMaximumDispersionEnergy( ii, maxDispersionEnergy );
maxDispersionEnergy /= CalToJoule;
double delta = fabs( maxDispersionEnergy - maxDispersionEnergyVector[ii] );
const char* error = (delta > 1.0e-05) ? "XXX" : "";
(void) fprintf( log, " maxDispEDiff=%12.5e %14.7f %14.7f %s",
delta, maxDispersionEnergy, maxDispersionEnergyVector[ii], error );
}
(void) fprintf( log, "\n" );
// skip to end
if( ii == maxPrint && (arraySize - maxPrint) > ii ){
ii = arraySize - maxPrint - 1;
}
}
(void) fflush( log );
// check max dispersion energy for all particles
int errors = 0;
for( unsigned int ii = 0; ii < arraySize && ii < maxDispersionEnergyVector.size(); ii++ ){
double maxDispersionEnergy;
wcaDispersionForce->getMaximumDispersionEnergy( ii, maxDispersionEnergy );
maxDispersionEnergy /= CalToJoule;
double delta = fabs( maxDispersionEnergy - maxDispersionEnergyVector[ii] );
if( delta > 1.0e-05 ){
(void) fprintf( log, " maxDispEDiff=%12.5e %14.7f %14.7f XXX\n", delta, maxDispersionEnergy, maxDispersionEnergyVector[ii] );
errors++;
}
}
if( errors ){
exit(-1);
} else {
(void) fprintf( log, "No errors detected in maxDispEnergy!\n" );
}
(void) fflush( log );
}
return wcaDispersionForce->getNumParticles(); return wcaDispersionForce->getNumParticles();
} }
...@@ -3148,8 +3027,10 @@ static int readAmoebaSurfaceParameters( FILE* filePtr, MapStringInt& forceMap, c ...@@ -3148,8 +3027,10 @@ static int readAmoebaSurfaceParameters( FILE* filePtr, MapStringInt& forceMap, c
//static const unsigned int maxPrint = MAX_PRINT; //static const unsigned int maxPrint = MAX_PRINT;
static const unsigned int maxPrint = 15; static const unsigned int maxPrint = 15;
unsigned int arraySize = static_cast<unsigned int>(sasaForce->getNumParticles()); unsigned int arraySize = static_cast<unsigned int>(sasaForce->getNumParticles());
(void) fprintf( log, "%s: %u sample of AmoebaSASAForce parameters; probe radius=%10.4f\n", (void) fprintf( log, "%s: %u sample of AmoebaSASAForce parameters in %s units; probe radius=%10.4f\n",
methodName.c_str(), arraySize, sasaForce->getProbeRadius() ); methodName.c_str(), arraySize,
//methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba"),
sasaForce->getProbeRadius() );
for( unsigned int ii = 0; ii < arraySize; ii++ ){ for( unsigned int ii = 0; ii < arraySize; ii++ ){
double radius, weight; double radius, weight;
...@@ -3221,6 +3102,7 @@ static int readConstraints( FILE* filePtr, const StringVector& tokens, System& s ...@@ -3221,6 +3102,7 @@ static int readConstraints( FILE* filePtr, const StringVector& tokens, System& s
} }
} }
// convert to OpenMM units
// scale constraint distances // scale constraint distances
if( useOpenMMUnits ){ if( useOpenMMUnits ){
...@@ -3233,9 +3115,12 @@ static int readConstraints( FILE* filePtr, const StringVector& tokens, System& s ...@@ -3233,9 +3115,12 @@ static int readConstraints( FILE* filePtr, const StringVector& tokens, System& s
} }
} }
// diagnostics
if( log ){ if( log ){
int maxPrint = 10; int maxPrint = 10;
(void) fprintf( log, "%s: sample constraints %susing OpenMM units.\n", methodName.c_str(), (useOpenMMUnits ? "" : "not ") ); (void) fprintf( log, "%s: sample of %d constraints using %s units.\n", methodName.c_str(),
system.getNumConstraints(), (useOpenMMUnits ? "OpenMM" : "Amoeba") );
for( int ii = 0; ii < system.getNumConstraints(); ii++ ){ for( int ii = 0; ii < system.getNumConstraints(); ii++ ){
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -3347,35 +3232,39 @@ static Integrator* readIntegrator( FILE* filePtr, const StringVector& tokens, Sy ...@@ -3347,35 +3232,39 @@ static Integrator* readIntegrator( FILE* filePtr, const StringVector& tokens, Sy
Integrator* returnIntegrator = NULL; Integrator* returnIntegrator = NULL;
if( integratorName == "LangevinIntegrator" ){ if( integratorName == "LangevinIntegrator" ){
returnIntegrator = new LangevinIntegrator( temperature, friction, stepSize );
// returnIntegrator->setRandomNumberSeed( randomNumberSeed ); LangevinIntegrator* langevinIntegrator = new LangevinIntegrator( temperature, friction, stepSize );
langevinIntegrator->setRandomNumberSeed( randomNumberSeed );
returnIntegrator = langevinIntegrator;
} else if( integratorName == "VariableLangevinIntegrator" ){ } else if( integratorName == "VariableLangevinIntegrator" ){
returnIntegrator = new VariableLangevinIntegrator( temperature, friction, errorTolerance );
returnIntegrator->setStepSize( stepSize ); VariableLangevinIntegrator* variableLangevinIntegrator = new VariableLangevinIntegrator( temperature, friction, errorTolerance );
// returnIntegrator->setRandomNumberSeed( randomNumberSeed ); variableLangevinIntegrator->setStepSize( stepSize );
variableLangevinIntegrator->setRandomNumberSeed( randomNumberSeed );
returnIntegrator = variableLangevinIntegrator;
} else if( integratorName == "VerletIntegrator" ){ } else if( integratorName == "VerletIntegrator" ){
returnIntegrator = new VerletIntegrator( stepSize ); returnIntegrator = new VerletIntegrator( stepSize );
} else if( integratorName == "VariableVerletIntegrator" ){ } else if( integratorName == "VariableVerletIntegrator" ){
returnIntegrator = new VariableVerletIntegrator( errorTolerance ); returnIntegrator = new VariableVerletIntegrator( errorTolerance );
returnIntegrator->setStepSize( stepSize ); returnIntegrator->setStepSize( stepSize );
} else if( integratorName == "BrownianIntegrator" ){ } else if( integratorName == "BrownianIntegrator" ){
returnIntegrator = new BrownianIntegrator( temperature, friction, stepSize ); BrownianIntegrator* brownianIntegrator = new BrownianIntegrator( temperature, friction, stepSize );
// returnIntegrator->setRandomNumberSeed( randomNumberSeed ); brownianIntegrator->setRandomNumberSeed( randomNumberSeed );
returnIntegrator = brownianIntegrator;
} }
returnIntegrator->setConstraintTolerance( constraintTolerance ); returnIntegrator->setConstraintTolerance( constraintTolerance );
if( log ){ if( log ){
static const unsigned int maxPrint = MAX_PRINT; static const unsigned int maxPrint = MAX_PRINT;
(void) fprintf( log, "%s: parameters\n", methodName.c_str() ); (void) fprintf( log, "%s: ", methodName.c_str() );
(void) fprintf( log, "StepSize=%15.7e constraint tolerance=%15.7e ", stepSize, constraintTolerance ); (void) fprintf( log, "stepSize=%12.3f constraint tolerance=%12.3e ", stepSize, constraintTolerance );
if( integratorName == "LangevinIntegrator" || if( integratorName == "LangevinIntegrator" || integratorName == "BrownianIntegrator" || integratorName == "VariableLangevinIntegrator" ){
integratorName == "BrownianIntegrator" || (void) fprintf( log, "temperature=%12.3f friction=%12.3f seed=%d ", temperature, friction, randomNumberSeed );
integratorName == "VariableLangevinIntegrator" ){
(void) fprintf( log, "Temperature=%15.7e friction=%15.7e seed=%d (seed may not be set!) ", temperature, friction, randomNumberSeed );
} }
if( integratorName == "VariableLangevinIntegrator" || if( integratorName == "VariableLangevinIntegrator" || integratorName == "VariableVerletIntegrator" ){
integratorName == "VariableVerletIntegrator" ){ (void) fprintf( log, "error tolerance=%12.3e", errorTolerance);
(void) fprintf( log, "Error tolerance=%15.7e", errorTolerance);
} }
(void) fprintf( log, "\n" ); (void) fprintf( log, "\n" );
} }
...@@ -3408,7 +3297,7 @@ static int readVec3( FILE* filePtr, const StringVector& tokens, std::vector<Vec3 ...@@ -3408,7 +3297,7 @@ static int readVec3( FILE* filePtr, const StringVector& tokens, std::vector<Vec3
if( tokens.size() < 1 ){ if( tokens.size() < 1 ){
char buffer[1024]; char buffer[1024];
(void) sprintf( buffer, "%s no Coordinates terms entry???\n", methodName.c_str() ); (void) sprintf( buffer, "%s no entries?\n", methodName.c_str() );
throwException(__FILE__, __LINE__, buffer ); throwException(__FILE__, __LINE__, buffer );
exit(-1); exit(-1);
} }
...@@ -3440,7 +3329,7 @@ static int readVec3( FILE* filePtr, const StringVector& tokens, std::vector<Vec3 ...@@ -3440,7 +3329,7 @@ static int readVec3( FILE* filePtr, const StringVector& tokens, std::vector<Vec3
if( log ){ if( log ){
static const unsigned int maxPrint = MAX_PRINT; static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = coordinates.size(); unsigned int arraySize = coordinates.size();
(void) fprintf( log, "%s: sample of vec3: %u\n", methodName.c_str(), arraySize ); (void) fprintf( log, "%s: sample of vec3 (raw values): %u\n", methodName.c_str(), arraySize );
for( unsigned int ii = 0; ii < arraySize; ii++ ){ for( unsigned int ii = 0; ii < arraySize; ii++ ){
(void) fprintf( log, "%6u [%15.7e %15.7e %15.7e]\n", ii, (void) fprintf( log, "%6u [%15.7e %15.7e %15.7e]\n", ii,
coordinates[ii][0], coordinates[ii][1], coordinates[ii][2] ); coordinates[ii][0], coordinates[ii][1], coordinates[ii][2] );
...@@ -3514,7 +3403,7 @@ static void getStringForceMap( System& system, MapStringForce& forceMap, FILE* l ...@@ -3514,7 +3403,7 @@ static void getStringForceMap( System& system, MapStringForce& forceMap, FILE* l
if( !hit ){ if( !hit ){
try { try {
AmoebaMultipoleForce& multipoleForce = dynamic_cast<AmoebaMultipoleForce &>(force); AmoebaMultipoleForce& multipoleForce = dynamic_cast<AmoebaMultipoleForce&>(force);
forceMap[AMOEBA_MULTIPOLE_FORCE] = &force; forceMap[AMOEBA_MULTIPOLE_FORCE] = &force;
hit++; hit++;
} catch( std::bad_cast ){ } catch( std::bad_cast ){
...@@ -3664,7 +3553,7 @@ static void getStringForceMap( System& system, MapStringForce& forceMap, FILE* l ...@@ -3664,7 +3553,7 @@ static void getStringForceMap( System& system, MapStringForce& forceMap, FILE* l
} }
if( !hit && log ){ if( !hit && log ){
(void) fprintf( log, " entry=%2d force not recognized XXXX\n", ii ); (void) fprintf( log, " entry=%2d force not recognized.\n", ii );
} }
} }
...@@ -3726,10 +3615,10 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS ...@@ -3726,10 +3615,10 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
FILE* filePtr = openFile( inputParameterFile, "r", log ); FILE* filePtr = openFile( inputParameterFile, "r", log );
if( filePtr == NULL ){ if( filePtr == NULL ){
char buffer[1024]; char buffer[1024];
(void) sprintf( buffer, "Input parameter file=<%s> could not be opened -- aborting.\n", methodName.c_str(), inputParameterFile.c_str() ); (void) sprintf( buffer, "Input parameter file=<%s> could not be opened -- aborting.\n", inputParameterFile.c_str() );
throwException(__FILE__, __LINE__, buffer ); throwException(__FILE__, __LINE__, buffer );
} else if( log ){ } else if( log ){
(void) fprintf( log, "Input parameter file=<%s> opened.\n", methodName.c_str(), inputParameterFile.c_str() ); (void) fprintf( log, "Input parameter file=<%s> opened.\n", inputParameterFile.c_str() );
(void) fflush( log ); (void) fflush( log );
} }
...@@ -3763,10 +3652,8 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS ...@@ -3763,10 +3652,8 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
(void) fprintf( log, "Version=<%s> at line=%d\n", version.c_str(), lineCount ); (void) fprintf( log, "Version=<%s> at line=%d\n", version.c_str(), lineCount );
} }
} }
} else if( field == "Particles" || field == "Masses" ){ } else if( field == "Masses" ){
readMasses( filePtr, tokens, system, &lineCount, log ); readMasses( filePtr, tokens, system, &lineCount, log );
} else if( field == "NumberOfForces" ){
// skip
} else if( field == "CMMotionRemover" ){ } else if( field == "CMMotionRemover" ){
int frequency = atoi( tokens[1].c_str() ); int frequency = atoi( tokens[1].c_str() );
system.addForce( new CMMotionRemover( frequency ) ); system.addForce( new CMMotionRemover( frequency ) );
...@@ -3774,7 +3661,7 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS ...@@ -3774,7 +3661,7 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
(void) fprintf( log, "CMMotionRemover added w/ frequency=%d at line=%d\n", frequency, lineCount ); (void) fprintf( log, "CMMotionRemover added w/ frequency=%d at line=%d\n", frequency, lineCount );
} }
// All forces // All forces/energy
} else if( field == ALL_FORCES ){ } else if( field == ALL_FORCES ){
readVec3( filePtr, tokens, forces[ALL_FORCES], &lineCount, field, log ); readVec3( filePtr, tokens, forces[ALL_FORCES], &lineCount, field, log );
...@@ -3881,11 +3768,14 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS ...@@ -3881,11 +3768,14 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
if( tokens.size() > 1 ){ if( tokens.size() > 1 ){
potentialEnergy[AMOEBA_MULTIPOLE_FORCE] = atof( tokens[1].c_str() ); potentialEnergy[AMOEBA_MULTIPOLE_FORCE] = atof( tokens[1].c_str() );
} }
} else if( field == "AmoebaGeneralizedKirkwoodParameters" ){
readAmoebaGeneralizedKirkwoodParameters( filePtr, forceMap, tokens, system, useOpenMMUnits, supplementary, inputArgumentMap, &lineCount, log ); // Amoeba GK
} else if( field == "AmoebaGkForce" ){
readVec3( filePtr, tokens, forces[AMOEBA_GK_FORCE], &lineCount, field, log ); } else if( field == "AmoebaGeneralizedKirkwoodParameters" ){
} else if( field == "AmoebaGk_A_ForceAndTorque" || 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" ||
field == "AmoebaGk_A_Force" || field == "AmoebaGk_A_Force" ||
field == "AmoebaGk_A_DrB" || field == "AmoebaGk_A_DrB" ||
field == "AmoebaDBorn" || field == "AmoebaDBorn" ||
...@@ -3893,76 +3783,86 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS ...@@ -3893,76 +3783,86 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
field == "AmoebaBornForce" || field == "AmoebaBornForce" ||
field == "AmoebaGkEdiffForceAndTorque" || field == "AmoebaGkEdiffForceAndTorque" ||
field == "AmoebaGkEdiffForce" ){ field == "AmoebaGkEdiffForce" ){
std::vector< std::vector<double> > vectorOfDoubleVectors; std::vector< std::vector<double> > vectorOfDoubleVectors;
readVectorOfDoubleVectors( filePtr, tokens, vectorOfDoubleVectors, &lineCount, field, log ); readVectorOfDoubleVectors( filePtr, tokens, vectorOfDoubleVectors, &lineCount, field, log );
supplementary[field] = vectorOfDoubleVectors; supplementary[field] = vectorOfDoubleVectors;
} else if( field == "AmoebaGkEnergy" || } else if( field == "AmoebaGkEnergy" ||
field == "AmoebaGkEdiffEnergy" || field == "AmoebaGkEdiffEnergy" ||
field == "AmoebaGk_A_Energy" || field == "AmoebaGk_A_Energy" ||
field == "AmoebaBorn1Energy" || field == "AmoebaBorn1Energy" ||
field == "AmoebaBornEnergy" ){ field == "AmoebaBornEnergy" ){
double value = atof( tokens[1].c_str() ); double value = atof( tokens[1].c_str() );
std::vector< std::vector<double> > vectorOfDoubleVectors; std::vector< std::vector<double> > vectorOfDoubleVectors;
std::vector<double> doubleVectors; std::vector<double> doubleVectors;
doubleVectors.push_back( value ); doubleVectors.push_back( value );
vectorOfDoubleVectors.push_back( doubleVectors ); vectorOfDoubleVectors.push_back( doubleVectors );
supplementary[field] = vectorOfDoubleVectors; supplementary[field] = vectorOfDoubleVectors;
if( field == "AmoebaGkEnergy" ){ if( field == "AmoebaGkEnergy" ){
potentialEnergy[AMOEBA_GK_FORCE] = value; potentialEnergy[AMOEBA_GK_FORCE] = value;
} }
} else if( field == "AmoebaSurfaceParameters" ){
readAmoebaSurfaceParameters( filePtr, forceMap, tokens, system, &lineCount, supplementary, log ); // Amoeba SASA
} else if( field == "AmoebaVdw14_7SigEpsTable" || field == "AmoebaVdw14_7Reduction" ){
readAmoebaVdwParameters( filePtr, forceMap, tokens, system, useOpenMMUnits, supplementary, inputArgumentMap, &lineCount, log ); } else if( field == "AmoebaSurfaceParameters" ){
} else if( field == "AmoebaVdwForce" ){ readAmoebaSurfaceParameters( filePtr, forceMap, tokens, system, &lineCount, supplementary, log );
readVec3( filePtr, tokens, forces[AMOEBA_VDW_FORCE], &lineCount, field, log );
} else if( field == "AmoebaVdwEnergy" ){ // Amoeba Vdw
if( tokens.size() > 1 ){
potentialEnergy[AMOEBA_VDW_FORCE] = atof( tokens[1].c_str() ); } else if( field == "AmoebaVdw14_7SigEpsTable" || field == "AmoebaVdw14_7Reduction" ){
} readAmoebaVdwParameters( filePtr, forceMap, tokens, system, useOpenMMUnits, supplementary, inputArgumentMap, &lineCount, log );
} else if( field == "AmoebaWcaDispersionParameters" ){ } else if( field == "AmoebaVdwForce" ){
readAmoebaWcaDispersionParameters( filePtr, forceMap, tokens, system, useOpenMMUnits, supplementary, inputArgumentMap, &lineCount, log ); readVec3( filePtr, tokens, forces[AMOEBA_VDW_FORCE], &lineCount, field, log );
} else if( field == "AmoebaWcaDispersionForce" ){ } else if( field == "AmoebaVdwEnergy" ){
readVec3( filePtr, tokens, forces[AMOEBA_WCA_DISPERSION_FORCE], &lineCount, field, log ); if( tokens.size() > 1 ){
} else if( field == "AmoebaWcaDispersionEnergy" ){ potentialEnergy[AMOEBA_VDW_FORCE] = atof( tokens[1].c_str() );
if( tokens.size() > 1 ){ }
potentialEnergy[AMOEBA_WCA_DISPERSION_FORCE] = atof( tokens[1].c_str() ); } else if( field == "AmoebaWcaDispersionParameters" ){
} readAmoebaWcaDispersionParameters( filePtr, forceMap, tokens, system, useOpenMMUnits, supplementary, inputArgumentMap, &lineCount, log );
} else if( field == "Constraints" ){ } else if( field == "AmoebaWcaDispersionForce" ){
readConstraints( filePtr, tokens, system, useOpenMMUnits, supplementary, inputArgumentMap, &lineCount, log ); readVec3( filePtr, tokens, forces[AMOEBA_WCA_DISPERSION_FORCE], &lineCount, field, log );
} else if( field == "Integrator" ){ } else if( field == "AmoebaWcaDispersionEnergy" ){
returnIntegrator = readIntegrator( filePtr, tokens, system, &lineCount, log ); if( tokens.size() > 1 ){
} else if( field == "Positions" || field == "Coordinates" ){ potentialEnergy[AMOEBA_WCA_DISPERSION_FORCE] = atof( tokens[1].c_str() );
readVec3( filePtr, tokens, coordinates, &lineCount, field, log ); }
if( useOpenMMUnits ){ } else if( field == "Constraints" ){
for( unsigned int ii = 0; ii < coordinates.size(); ii++ ){ readConstraints( filePtr, tokens, system, useOpenMMUnits, supplementary, inputArgumentMap, &lineCount, log );
coordinates[ii][0] *= AngstromToNm; } else if( field == "Integrator" ){
coordinates[ii][1] *= AngstromToNm; returnIntegrator = readIntegrator( filePtr, tokens, system, &lineCount, log );
coordinates[ii][2] *= AngstromToNm; } else if( field == "Positions" || field == "Coordinates" ){
} readVec3( filePtr, tokens, coordinates, &lineCount, field, log );
} if( useOpenMMUnits ){
} else if( field == "Velocities" ){ for( unsigned int ii = 0; ii < coordinates.size(); ii++ ){
readVec3( filePtr, tokens, velocities, &lineCount, field, log ); coordinates[ii][0] *= AngstromToNm;
if( useOpenMMUnits ){ coordinates[ii][1] *= AngstromToNm;
for( unsigned int ii = 0; ii < velocities.size(); ii++ ){ coordinates[ii][2] *= AngstromToNm;
velocities[ii][0] *= AngstromToNm; }
velocities[ii][1] *= AngstromToNm; }
velocities[ii][2] *= AngstromToNm; } else if( field == "Velocities" ){
} readVec3( filePtr, tokens, velocities, &lineCount, field, log );
} if( useOpenMMUnits ){
} else { for( unsigned int ii = 0; ii < velocities.size(); ii++ ){
char buffer[1024]; velocities[ii][0] *= AngstromToNm;
(void) sprintf( buffer, "Field=<%s> not recognized at line=%d\n", field.c_str(), lineCount ); velocities[ii][1] *= AngstromToNm;
throwException(__FILE__, __LINE__, buffer ); velocities[ii][2] *= AngstromToNm;
exit(-1); }
} }
} else {
char buffer[1024];
(void) sprintf( buffer, "Field=<%s> not recognized at line=%d.\n", field.c_str(), lineCount );
throwException(__FILE__, __LINE__, buffer );
exit(-1);
}
} }
} }
// if integrator not set, default to Verlet integrator
if( returnIntegrator == NULL ){ if( returnIntegrator == NULL ){
returnIntegrator = new VerletIntegrator(0.001); returnIntegrator = new VerletIntegrator(0.001);
} }
// sum energies
double totalPotentialEnergy = 0.0; double totalPotentialEnergy = 0.0;
if( log )(void) fprintf( log, "Potential energies\n" ); if( log )(void) fprintf( log, "Potential energies\n" );
...@@ -4186,7 +4086,7 @@ void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVe ...@@ -4186,7 +4086,7 @@ void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVe
} }
void calculateBorn1( System& amoebaSystem, std::vector<Vec3>& tinkerCoordinates, FILE* log ) { void calculateBorn1( System& amoebaSystem, std::vector<Vec3>& tinkerCoordinates, FILE* log ) {
/*
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
static const std::string methodName = "calculateBorn1"; static const std::string methodName = "calculateBorn1";
...@@ -4239,20 +4139,16 @@ void calculateBorn1( System& amoebaSystem, std::vector<Vec3>& tinkerCoordinates, ...@@ -4239,20 +4139,16 @@ void calculateBorn1( System& amoebaSystem, std::vector<Vec3>& tinkerCoordinates,
} }
(void) fflush( log ); (void) fflush( log );
} }
*/
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
* Get integrator * Get integrator
* *
* @param integratorName integratorName (VerletIntegrator, BrownianIntegrator, LangevinIntegrator, ...) * @param inputArgumentMap StringString Map w/ argumement values
* @param timeStep time step * @param log optional logging reference
* @param friction (ps) friction
* @param temperature temperature
* @param shakeTolerance Shake tolerance
* @param errorTolerance Error tolerance
* @param randomNumberSeed seed
* *
* @return DefaultReturnValue or ErrorReturnValue * @return OpenMM integrator
* *
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
...@@ -4279,7 +4175,8 @@ Integrator* getIntegrator( MapStringString& inputArgumentMap, FILE* log ){ ...@@ -4279,7 +4175,8 @@ Integrator* getIntegrator( MapStringString& inputArgumentMap, FILE* log ){
setDoubleFromMap( inputArgumentMap, "shakeTolerance", shakeTolerance ); setDoubleFromMap( inputArgumentMap, "shakeTolerance", shakeTolerance );
setDoubleFromMap( inputArgumentMap, "errorTolerance", errorTolerance ); setDoubleFromMap( inputArgumentMap, "errorTolerance", errorTolerance );
setIntFromMap( inputArgumentMap, "randomNumberSeed", randomNumberSeed ); setIntFromMap( inputArgumentMap, "randomNumberSeed", randomNumberSeed );
// Create an integrator
// create integrator
Integrator* integrator; Integrator* integrator;
...@@ -4456,7 +4353,7 @@ static void printIntegratorInfo( Integrator& integrator, FILE* log ){ ...@@ -4456,7 +4353,7 @@ static void printIntegratorInfo( Integrator& integrator, FILE* log ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static int _synchContexts( const Context& context1, Context& context2 ){ static int synchContexts( const Context& context1, Context& context2 ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -4474,7 +4371,6 @@ static int _synchContexts( const Context& context1, Context& context2 ){ ...@@ -4474,7 +4371,6 @@ static int _synchContexts( const Context& context1, Context& context2 ){
return DefaultReturnValue; return DefaultReturnValue;
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Get statistics of elements in array Get statistics of elements in array
...@@ -4556,6 +4452,23 @@ static void getStatistics( const std::vector<double> & array, std::vector<doubl ...@@ -4556,6 +4452,23 @@ static void getStatistics( const std::vector<double> & array, std::vector<doubl
return; return;
} }
/**---------------------------------------------------------------------------------------
Cret a OpenMM context
@param amoebaTinkerParameterFileName parameter file name
@param forceMap StringInt map[Force] = 1 or 0 (include/not include)
@param useOpenMMUnits if set, convert to OpenMM units (kJ/nm)
@param inputArgumentMap StringString map w/ command-line arguments/values
@param supplementary output of supplementary info (rotation matrices, ...)
@param tinkerForces Tinker calculated forces
@param tinkerEnergies Tinker calculated energies
@param log optional file logging reference
@return OpenMM context
--------------------------------------------------------------------------------------- */
Context* createContext( const std::string& amoebaTinkerParameterFileName, MapStringInt& forceMap, Context* createContext( const std::string& amoebaTinkerParameterFileName, MapStringInt& forceMap,
int useOpenMMUnits, MapStringString& inputArgumentMap, MapStringVectorOfVectors& supplementary, int useOpenMMUnits, MapStringString& inputArgumentMap, MapStringVectorOfVectors& supplementary,
MapStringVec3& tinkerForces, MapStringDouble& tinkerEnergies, FILE* log ) { MapStringVec3& tinkerForces, MapStringDouble& tinkerEnergies, FILE* log ) {
...@@ -4589,21 +4502,23 @@ Context* createContext( const std::string& amoebaTinkerParameterFileName, MapStr ...@@ -4589,21 +4502,23 @@ Context* createContext( const std::string& amoebaTinkerParameterFileName, MapStr
Integrator* integrator = getIntegrator( inputArgumentMap, log ); Integrator* integrator = getIntegrator( inputArgumentMap, log );
Context* context; Platform& platform = Platform::getPlatformByName("Cuda");
map<string, string> properties;
if( getenv("CudaDevice") || cudaDevice > -1 ){ if( getenv("CudaDevice") || cudaDevice > -1 ){
Platform& platform = Platform::getPlatformByName("Cuda"); std::string cudaDevice;
map<string, string> properties;
if( getenv("CudaDevice") ){ if( getenv("CudaDevice") ){
properties["CudaDevice"] = getenv("CudaDevice"); cudaDevice = getenv("CudaDevice");
} else { } else {
std::stringstream cudaDeviceStrStr; std::stringstream cudaDeviceStrStr;
cudaDeviceStrStr << cudaDevice; cudaDeviceStrStr << cudaDevice;
properties["CudaDevice"] = cudaDeviceStrStr.str(); cudaDevice = cudaDeviceStrStr.str();
}
properties["CudaDevice"] = cudaDevice;
if( log ){
(void) fprintf( log, "Setting Cuda device to %s.\n", cudaDevice.c_str() );
} }
context = new Context(*system, *integrator, platform, properties);
} else {
context = new Context(*system, *integrator, Platform::getPlatformByName( "Cuda"));
} }
Context* context = new Context(*system, *integrator, platform, properties);
context->setPositions(coordinates); context->setPositions(coordinates);
return context; return context;
...@@ -4664,14 +4579,7 @@ void checkIntermediateStatesUsingAmoebaTinkerParameterFile( const std::string& a ...@@ -4664,14 +4579,7 @@ void checkIntermediateStatesUsingAmoebaTinkerParameterFile( const std::string& a
unsigned int stateIndex = 0; unsigned int stateIndex = 0;
//fprintf( log, "%8u total lines\n", fileContents.size() );
while( lineIndex < (fileContents.size()-1) ){ while( lineIndex < (fileContents.size()-1) ){
/*
fprintf( log, "%8u Line %u state=%u ", lineIndex, fileContents[lineIndex].size(), stateIndex );
for( int ii = 0; ii < fileContents[lineIndex].size(); ii++ ){
fprintf( log, "%s ", fileContents[lineIndex][ii].c_str() );
}
fprintf( log, "\n" ); fflush( log ); */
int numberOfAtoms = atoi( fileContents[lineIndex++][0].c_str() ); int numberOfAtoms = atoi( fileContents[lineIndex++][0].c_str() );
...@@ -4681,13 +4589,6 @@ fprintf( log, "\n" ); fflush( log ); */ ...@@ -4681,13 +4589,6 @@ fprintf( log, "\n" ); fflush( log ); */
int skip = 0; int skip = 0;
for( int ii = 0; ii < numberOfAtoms; ii++ ){ for( int ii = 0; ii < numberOfAtoms; ii++ ){
StringVector& stateTokenArray = fileContents[lineIndex++]; StringVector& stateTokenArray = fileContents[lineIndex++];
/*
fprintf( log, "%8u xLine %u state=%u ", lineIndex, fileContents[lineIndex-1].size(), stateIndex );
for( int ii = 0; ii < fileContents[lineIndex-1].size(); ii++ ){
fprintf( log, "%s ", fileContents[lineIndex-1][ii].c_str() );
}
fprintf( log, "\n" ); fflush( log ); */
if( stateTokenArray[1] == "nan" || stateTokenArray[2] == "nan" || stateTokenArray[3] == "nan" ){ if( stateTokenArray[1] == "nan" || stateTokenArray[2] == "nan" || stateTokenArray[3] == "nan" ){
skip = 1; skip = 1;
} else { } else {
...@@ -4696,14 +4597,15 @@ fprintf( log, "\n" ); fflush( log ); */ ...@@ -4696,14 +4597,15 @@ fprintf( log, "\n" ); fflush( log ); */
atof( stateTokenArray[3].c_str() ) ); atof( stateTokenArray[3].c_str() ) );
} }
} }
if( skip ){ if( skip && log ){
(void) fprintf( log, "Skipping state=%u line=%u\n", stateIndex, lineIndex ); (void) fprintf( log, "Skipping state=%u line=%u\n", stateIndex, lineIndex );
} else { } else if( !skip ){
(void) fprintf( log, "State=%u coordinates=%u\n", stateIndex, static_cast<unsigned int>(coordinates.size()) ); if( log ){
(void) fprintf( log, "State=%u coordinates=%u\n", stateIndex, static_cast<unsigned int>(coordinates.size()) );
}
context->setPositions( coordinates ); context->setPositions( coordinates );
State state = context->getState(State::Forces | State::Energy); State state = context->getState(State::Forces | State::Energy);
System& system = context->getSystem(); System& system = context->getSystem();
//double kineticEnergy = state.getPotentialEnergy();
double potentialEnergy = state.getPotentialEnergy(); double potentialEnergy = state.getPotentialEnergy();
if( summaryFile ){ if( summaryFile ){
...@@ -4970,10 +4872,6 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete ...@@ -4970,10 +4872,6 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
} }
} }
static int isNanOrInfinity( double number ){
return (number != number || number == std::numeric_limits<double>::infinity() || number == -std::numeric_limits<double>::infinity()) ? 1 : 0;
}
/** /**
* Check that energy and force are consistent * Check that energy and force are consistent
* *
...@@ -5002,7 +4900,7 @@ void testEnergyForcesConsistent( std::string parameterFileName, MapStringInt& fo ...@@ -5002,7 +4900,7 @@ void testEnergyForcesConsistent( std::string parameterFileName, MapStringInt& fo
Context* context = createContext( parameterFileName, forceMap, useOpenMMUnits, inputArgumentMap, supplementary, Context* context = createContext( parameterFileName, forceMap, useOpenMMUnits, inputArgumentMap, supplementary,
tinkerForces, tinkerEnergies, log ); tinkerForces, tinkerEnergies, log );
setIntFromMap( inputArgumentMap, "applyAssertion", applyAssertion ); setIntFromMap( inputArgumentMap, "applyAssert", applyAssertion );
setDoubleFromMap( inputArgumentMap, "energyForceDelta", delta ); setDoubleFromMap( inputArgumentMap, "energyForceDelta", delta );
setDoubleFromMap( inputArgumentMap, "energyForceTolerance", tolerance ); setDoubleFromMap( inputArgumentMap, "energyForceTolerance", tolerance );
...@@ -5416,7 +5314,7 @@ void testEnergyConservation( std::string parameterFileName, MapStringInt& forceM ...@@ -5416,7 +5314,7 @@ void testEnergyConservation( std::string parameterFileName, MapStringInt& forceM
Context* context = createContext( parameterFileName, forceMap, useOpenMMUnits, inputArgumentMap, supplementary, Context* context = createContext( parameterFileName, forceMap, useOpenMMUnits, inputArgumentMap, supplementary,
tinkerForces, tinkerEnergies, log ); tinkerForces, tinkerEnergies, log );
setIntFromMap( inputArgumentMap, "applyAssertion", applyAssertion ); setIntFromMap( inputArgumentMap, "applyAsser", applyAssertion );
// energy minimize // energy minimize
...@@ -5728,6 +5626,44 @@ int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ){ ...@@ -5728,6 +5626,44 @@ int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
/* command-line args
Int "cudaDevice" cudaDevice
Int "applyAssert" apply assertions
// integrator args
String "integrator" integratorName
Double "timeStep" timeStep
Double "friction" friction
Double "temperature" temperature
Double "shakeTolerance" shakeTolerance
Double "errorTolerance" errorTolerance
Int "randomNumberSeed" randomNumberSeed
// save states or read
String "states" statesFileName
Double "tolerance" general tolerance
Double "energyForceDelta" delta energy/force consistency check
Double "energyForceTolerance" tolerance nergy/force consistency check
Int "energyMinimize" energyMinimize -- minimize structures before runs
Double "equilibrationTime" equilibrationTime
Double "simulationTime" simulationTime
String "intermediateStateFileName" intermediateStateFileName -- name of file to write intermediate structures
Double "equilibrationTimeBetweenReportsRatio" equilibrationTimeBetweenReportsRatio -- if for example set to 0.1, then output at t=0.1*equilibrationTime
0.2*equilibrationTime
...
0.9*equilibrationTime
1.0*equilibrationTime
Double "simulationTimeBetweenReportsRatio" simulationTimeBetweenReportsRatio (see equilibrationTimeBetweenReportsRatio)
*/
// ---------------------------------------------------------------------------------------
std::string parameterFileName = "1UBQ.prm"; std::string parameterFileName = "1UBQ.prm";
MapStringInt forceMap; MapStringInt forceMap;
initializeForceMap( forceMap, 0 ); initializeForceMap( forceMap, 0 );
...@@ -5739,7 +5675,7 @@ int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ){ ...@@ -5739,7 +5675,7 @@ int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ){
std::string summaryFileName; std::string summaryFileName;
int specifiedOpenmmPluginDirectory = 0; int specifiedOpenmmPluginDirectory = 0;
int useOpenMMUnits = 0; int useOpenMMUnits = 1;
int logControl = 0; int logControl = 0;
int checkForces = 1; int checkForces = 1;
...@@ -5821,11 +5757,15 @@ int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ){ ...@@ -5821,11 +5757,15 @@ int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ){
std::string value = ii->second; std::string value = ii->second;
(void) fprintf( log, " %30s %40s\n", key.c_str(), value.c_str() ); (void) fprintf( log, " %30s %40s\n", key.c_str(), value.c_str() );
} }
(void) fprintf( log, "parameter file=<%s>\n", parameterFileName.c_str() ); (void) fprintf( log, "\nParameter file=<%s>\n", parameterFileName.c_str() );
(void) fprintf( log, "Argument map: %u\n", static_cast<unsigned int>(inputArgumentMap.size()) ); (void) fprintf( log, "\nArgument map: %u\n", static_cast<unsigned int>(inputArgumentMap.size()) );
for( MapStringStringCI ii = inputArgumentMap.begin(); ii != inputArgumentMap.end(); ii++ ){ for( MapStringStringCI ii = inputArgumentMap.begin(); ii != inputArgumentMap.end(); ii++ ){
(void) fprintf( log, "Map %s %s\n", (*ii).first.c_str(), (*ii).second.c_str() ); (void) fprintf( log, " %s=%s\n", (*ii).first.c_str(), (*ii).second.c_str() );
}
(void) fprintf( log, "\nForce map: %u\n", static_cast<unsigned int>(forceMap.size()) );
for( MapStringIntCI ii = forceMap.begin(); ii != forceMap.end(); ii++ ){
(void) fprintf( log, " %s=%d\n", (*ii).first.c_str(), (*ii).second );
} }
(void) fflush( log ); (void) fflush( log );
} }
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaForceFromParameterFile.cpp
View file @ ac8cb97f
...@@ -48,8 +48,8 @@ int main( int numberOfArguments, char* argv[] ) { ...@@ -48,8 +48,8 @@ int main( int numberOfArguments, char* argv[] ) {
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() ); Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
if( numberOfArguments > 1 ){ if( numberOfArguments > 1 ){
MapStringString argumentMap; MapStringString argumentMap;
appendInputArgumentsToArgumentMap( numberOfArguments, argv, argumentMap );
argumentMap[INCLUDE_OBC_CAVITY_TERM] = "0"; argumentMap[INCLUDE_OBC_CAVITY_TERM] = "0";
appendInputArgumentsToArgumentMap( numberOfArguments, argv, argumentMap );
runTestsUsingAmoebaTinkerParameterFile( argumentMap ); runTestsUsingAmoebaTinkerParameterFile( argumentMap );
} }
} }
......
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