Skip to content

GitLab

Commit 0c4f73d7 authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

Fixed memory bug in torque/force mapping; 

An exception is now thrown if the multipole axis type is not Bisector or Z-then-X
Redid velocity initialization in test code
parent 960c22af
Hide whitespace changes
Inline Side-by-side
Showing with 116 additions and 73 deletions
plugins/amoeba/openmmapi/include/AmoebaMultipoleForce.h
View file @ 0c4f73d7
......@@ -33,18 +33,21 @@
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include <vector>
#include "openmm/OpenMMException.h"
#include "openmm/internal/windowsExport.h"
#include <sstream>
#include <vector>
namespace OpenMM {
/**
* This class implements the Amoeba pi-torsion interaction
* To use it, create a MultipoleForce object then call addMultipole() once for each torsion. After
* a torsion has been added, you can modify its force field parameters by calling setMultipoleParameters().
* This class implements the Amoeba multipole interaction
* To use it, create a MultipoleForce object then call addMultipole() once for each atom. After
* a entry has been added, you can modify its force field parameters by calling setMultipoleParameters().
*/
class OPENMM_EXPORT AmoebaMultipoleForce : public Force {
class OPENMM_EXPORT AmoebaMultipoleForce : public Force {
public:
enum MultipoleAxisTypes { ZThenX, Bisector };
......@@ -281,6 +284,15 @@ public:
charge(charge), axisType(axisType), multipoleAtomId1(multipoleAtomId1), multipoleAtomId2(multipoleAtomId2),
thole(thole), dampingFactor(dampingFactor), polarity(polarity) {
// only 'Z-then-X' or 'Bisector' currently handled
if( axisType != ZThenX && axisType != Bisector ){
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: axis type=" << axisType;
buffer << " not currently handled - only axisTypes[ " << ZThenX << ", " << Bisector << "] (ZThenX, Bisector) currently handled .";
throw OpenMMException(buffer.str());
}
covalentInfo.resize( CovalentEnd );
molecularDipole.resize( 3 );
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 0c4f73d7
......@@ -40,6 +40,7 @@ const int AmoebaMultipoleForce::CovalentDegrees[8] = { 1, 2, 3, 4, 0, 1, 2, 3 };
AmoebaMultipoleForce::AmoebaMultipoleForce() {
mutualInducedIterationMethod = SOR;
mutualInducedMaxIterations = 60;
mutualInducedTargetEpsilon = 1.0e-06;
......
plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp
View file @ 0c4f73d7
......@@ -971,7 +971,8 @@ if( (index < DUMP_PARAMETERS || index > totalEntries - (DUMP_PARAMETERS + 1)) &&
}
#if 0
float* grids = (float*) malloc( totalGridEntries*sizeof( float ) );
std::vector<float> grids;
grids.resize( totalGridEntries );
int index = 0;
for (unsigned int ii = 0; ii < floatGrids.size(); ii++) {
for (unsigned int jj = 0; jj < floatGrids[ii].size(); jj++) {
......@@ -1022,7 +1023,6 @@ if( (index < DUMP_PARAMETERS || index > totalEntries - (DUMP_PARAMETERS + 1)) &&
if( !errors ){
(void) fprintf( amoebaGpu->log, "No errors in grid readback\n" );
}
free( grids );
exit(0);
#endif
......@@ -1458,13 +1458,19 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
#ifdef AMOEBA_DEBUG
static unsigned int targetAtoms[2] = { 0, 700000 };
float* pScaleCheckSum = (float*) malloc( sizeof( float )*charges.size() );
float* dScaleCheckSum = (float*) malloc( sizeof( float )*charges.size() );
float* mScaleCheckSum = (float*) malloc( sizeof( float )*charges.size() );
std::vector<float> pScaleCheckSum;
pScaleCheckSum.resize( charges.size() );
memset( pScaleCheckSum, 0, charges.size()*sizeof( float ) );
memset( dScaleCheckSum, 0, charges.size()*sizeof( float ) );
memset( mScaleCheckSum, 0, charges.size()*sizeof( float ) );
std::vector<float> dScaleCheckSum;
dScaleCheckSum.resize( charges.size() );
std::vector<float> mScaleCheckSum;
mScaleCheckSum.resize( charges.size() );
for( unsigned int ii = 0; ii < charges.size(); ii++ ){
pScaleCheckSum[ii] = 0.0;
dScaleCheckSum[ii] = 0.0;
mScaleCheckSum[ii] = 0.0;
}
amoebaGpu->pMapArray = (MapIntFloat**) malloc( sizeof( MapIntFloat* )*amoebaGpu->paddedNumberOfAtoms );
amoebaGpu->dMapArray = (MapIntFloat**) malloc( sizeof( MapIntFloat* )*amoebaGpu->paddedNumberOfAtoms );
......@@ -1502,9 +1508,9 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
unsigned int quadrupoleIndex = 0;
unsigned int maxPrint = 5;
int* maxIndices = (int*) malloc( charges.size()*sizeof(int) );
std::vector<int> maxIndices;
for( unsigned int ii = 0; ii < charges.size(); ii++ ){
maxIndices[ii] = ii;
maxIndices.push_back(ii);
amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][ii].z = ii;
}
......@@ -1788,9 +1794,6 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
(void) fprintf( filePtr, "%6u %14.6e %14.6e\n", kk, pScaleCheckSum[kk], dScaleCheckSum[kk] );
}
(void) fclose( filePtr );
free( pScaleCheckSum );
free( dScaleCheckSum );
free( mScaleCheckSum );
filePtr = fopen( "oldScaleMap.txt", "w" );
for( unsigned int kk = 0; kk < charges.size(); kk++ ){
MapIntFloat* pMap = amoebaGpu->pMapArray[kk];
......@@ -1813,24 +1816,24 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
for( unsigned int ii = 0; ii < charges.size(); ii++ ){
// axis type & multipole particles ids
int diff = maxIndices[ii] - amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][ii].z;
if( diff > amoebaGpu->maxMapTorqueDifference ){
amoebaGpu->maxMapTorqueDifference = diff;
}
}
amoebaGpu->maxMapTorqueDifference += 1;
// set maxMapTorqueDifferencePow2 to smallest power of 2 greater than maxMapTorqueDifference
float logDiff = logf( static_cast<float>(amoebaGpu->maxMapTorqueDifference) )/logf(2.0f);
int logDiffI = static_cast<int>(logDiff) + 1;
amoebaGpu->maxMapTorqueDifferencePow2 = static_cast<int>(powf( 2.0f, static_cast<float>(logDiffI) ));
amoebaGpu->torqueMapForce = new CUDAStream<float>(amoebaGpu->paddedNumberOfAtoms*3*amoebaGpu->maxMapTorqueDifference, 1, "torqueMapForce");
memset( amoebaGpu->torqueMapForce->_pSysStream[0], 0, amoebaGpu->paddedNumberOfAtoms*3*amoebaGpu->maxMapTorqueDifference*sizeof( float ) );
amoebaGpu->torqueMapForce->Upload();
free( maxIndices );
amoebaGpuBuildOutputBuffers( amoebaGpu );
amoebaGpuBuildThreadBlockWorkList( amoebaGpu );
amoebaGpuBuildScalingList( amoebaGpu );
......@@ -3196,14 +3199,20 @@ static unsigned int targetAtoms[2] = { 0, 1};
if( debugOn && amoebaGpu->log ){
float* pScaleCheckSum = (float*) malloc( sizeof( float )*paddedAtoms );
float* dScaleCheckSum = (float*) malloc( sizeof( float )*paddedAtoms );
float* mScaleCheckSum = (float*) malloc( sizeof( float )*paddedAtoms );
std::vector<float> pScaleCheckSum;
pScaleCheckSum.resize( paddedAtoms );
std::vector<float> dScaleCheckSum;
dScaleCheckSum.resize( paddedAtoms );
std::vector<float> mScaleCheckSum;
mScaleCheckSum.resize( paddedAtoms );
for( unsigned int ii = 0; ii < paddedAtoms; ii++ ){
pScaleCheckSum[ii] = 0.0;
dScaleCheckSum[ii] = 0.0;
mScaleCheckSum[ii] = 0.0;
}
memset( pScaleCheckSum, 0, paddedAtoms*sizeof( float ) );
memset( dScaleCheckSum, 0, paddedAtoms*sizeof( float ) );
memset( mScaleCheckSum, 0, paddedAtoms*sizeof( float ) );
MapIntFloat** pMapArray = (MapIntFloat**) malloc( sizeof( MapIntFloat* )*paddedAtoms );
MapIntFloat** dMapArray = (MapIntFloat**) malloc( sizeof( MapIntFloat* )*paddedAtoms );
for( unsigned int ii = 0; ii < paddedAtoms; ii++ ){
......@@ -3404,9 +3413,6 @@ tgx = 0;
(void) fprintf( filePtr, "%6u %14.6e %14.6e\n", kk, pScaleCheckSum[kk], dScaleCheckSum[kk] );
}
(void) fclose( filePtr );
free( pScaleCheckSum );
free( dScaleCheckSum );
free( mScaleCheckSum );
filePtr = fopen( "newScaleMap.txt", "w" );
//char buffer[1024];
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaElectrostatic.cu
View file @ 0c4f73d7
......@@ -963,4 +963,3 @@ void cudaComputeAmoebaElectrostatic( amoebaGpuContext amoebaGpu )
// ---------------------------------------------------------------------------------------
}
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaMapTorques.cu
View file @ 0c4f73d7
......@@ -125,9 +125,9 @@ void amoebaMapTorqueToForce_kernel(
norm = normVector3( vp );
float dphi[3];
dphi[0] = vector[0][0]*torque[threadId*3] + vector[0][1]*torque[threadId*3+1] + vector[0][2]*torque[threadId*3+2];
dphi[1] = vector[1][0]*torque[threadId*3] + vector[1][1]*torque[threadId*3+1] + vector[1][2]*torque[threadId*3+2];
dphi[2] = vector[2][0]*torque[threadId*3] + vector[2][1]*torque[threadId*3+1] + vector[2][2]*torque[threadId*3+2];
dphi[0] = vector[U][0]*torque[threadId*3] + vector[U][1]*torque[threadId*3+1] + vector[U][2]*torque[threadId*3+2];
dphi[1] = vector[V][0]*torque[threadId*3] + vector[V][1]*torque[threadId*3+1] + vector[V][2]*torque[threadId*3+2];
dphi[2] = vector[W][0]*torque[threadId*3] + vector[W][1]*torque[threadId*3+1] + vector[W][2]*torque[threadId*3+2];
// clamp c to interval [-1,1]
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaRotateFrame.cu
View file @ 0c4f73d7
......@@ -374,9 +374,7 @@ void kCalculateAmoebaMultipoleForces(amoebaGpuContext amoebaGpu, bool hasAmoebaG
// check if induce dipole calculation converged -- abort if it did not
if( amoebaGpu->mutualInducedDone ){
//cudaComputeAmoebaElectrostatic( amoebaGpuContextGlobal );
} else {
if( amoebaGpu->mutualInducedDone == 0 ){
(void) fprintf( amoebaGpu->log, "%s induced dipole calculation did not converge -- aborting!\n", methodName.c_str() );
(void) fflush( amoebaGpu->log );
exit(-1);
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp
View file @ 0c4f73d7
......@@ -30,6 +30,7 @@
#include "kernels/amoebaGpuTypes.h"
#include "AmoebaCudaData.h"
#include "openmm/LocalEnergyMinimizer.h"
#include "../../../../../platforms//reference/src//SimTKUtilities/SimTKOpenMMUtilities.h"
#include <exception>
......@@ -2769,7 +2770,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
(void) fprintf( log, "%8d %10.4f %10.4f", ii, radius, epsilon );
if( ii < maxDispersionEnergyVector.size() ){
wcaDispersionForce->getMaximumDispersionEnergy( ii, maxDispersionEnergy );
maxDispersionEnergy /= CalToJoule;
if( useOpenMMUnits )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",
......@@ -2791,7 +2792,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
for( unsigned int ii = 0; ii < arraySize && ii < maxDispersionEnergyVector.size(); ii++ ){
double maxDispersionEnergy;
wcaDispersionForce->getMaximumDispersionEnergy( ii, maxDispersionEnergy );
maxDispersionEnergy /= CalToJoule;
if( useOpenMMUnits )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] );
......@@ -3825,7 +3826,7 @@ void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVe
int useOpenMMUnits, FILE* log ) {
// ---------------------------------------------------------------------------------------
/*
static const std::string methodName = "checkIntermediateMultipoleQuantities";
// ---------------------------------------------------------------------------------------
......@@ -3951,7 +3952,7 @@ void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVe
unsigned int misses = 0;
double tolerance = 1.0e-03;
double dipoleConversion = useOpenMMUnits ? 1.0/AngstromToNm : 1.0;
numberOfEntries = expectedInducedDipoles.size() < numberOfEntries ? expectedInducedDipoles.size() : numberOfEntries;
numberOfEntries = expectedInducedDipoles.size() < numberOfEntries ? expectedInducedDipoles.size() : numberOfEntries;
for( unsigned int ii = 0; ii < numberOfEntries; ii++ ){
std::vector<double> expectedInducedDipole = expectedInducedDipoles[ii];
......@@ -3964,11 +3965,16 @@ void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVe
if( diff > 1.0e-04 ){
diff = 2.0*diff/(fabs( inducedDipoleValue ) + fabs( expectedInducedDipole[jj] ) );
}
int printDipole = 0;
if( diff > tolerance ){
misses++;
if( misses == 1 ){
(void) fprintf( log, "%s: induced dipole\n", methodName.c_str() );
}
printDipole = 1;
}
if( misses == 1 && printDipole ){
(void) fprintf( log, "%s: induced dipoles\n", methodName.c_str() );
}
if( printDipole ){
if( !rowHit ){
(void) fprintf( log, " Row %5u\n", ii );
rowHit = 1;
......@@ -3987,7 +3993,7 @@ void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVe
(void) fprintf( log, "Induced dipoles not available %s\n", e.what() );
(void) fflush( log );
}
*/
}
void calculateBorn1( System& amoebaSystem, std::vector<Vec3>& tinkerCoordinates, FILE* log ) {
......@@ -5235,20 +5241,45 @@ static void setVelocitiesBasedOnTemperature( const System& system, std::vector<V
// ---------------------------------------------------------------------------------------
// set velocities based on temperature
temperature *= BOLTZ;
double randMax = static_cast<double>(RAND_MAX);
randMax = 1.0/randMax;
for( unsigned int ii = 0; ii < velocities.size(); ii++ ){
double velocityScale = std::sqrt( temperature/system.getParticleMass(ii) );
randomValues[0] = randMax*( (double) rand() );
randomValues[1] = randMax*( (double) rand() );
randomValues[2] = randMax*( (double) rand() );
velocities[ii] = Vec3( randomValues[0]*velocityScale, randomValues[1]*velocityScale, randomValues[2]*velocityScale );
}
// set velocities based on temperature
return;
temperature *= BOLTZ;
double kineticEnergy = 0.0;
for( unsigned int ii = 0; ii < velocities.size(); ii++ ){
double mass = system.getParticleMass(ii);
double velocityScale = std::sqrt( temperature/mass );
randomValues[0] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
randomValues[1] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
randomValues[2] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
velocities[ii] = Vec3( randomValues[0]*velocityScale, randomValues[1]*velocityScale, randomValues[2]*velocityScale );
kineticEnergy += mass*(velocities[ii][0]*velocities[ii][0] + velocities[ii][1]*velocities[ii][1] + velocities[ii][2]*velocities[ii][2]);
}
double degreesOfFreedom = static_cast<double>(3*velocities.size() - system.getNumConstraints() - 3 );
double approximateT = (kineticEnergy)/(degreesOfFreedom*BOLTZ);
if( approximateT > 0.0 ){
double scale = sqrt(temperature/approximateT);
for( unsigned int ii = 0; ii < velocities.size(); ii++ ){
velocities[ii][0] *= scale;
velocities[ii][1] *= scale;
velocities[ii][2] *= scale;
}
}
if( log ){
double finalKineticEnergy = 0.0;
for( unsigned int ii = 0; ii < velocities.size(); ii++ ){
double mass = system.getParticleMass(ii);
finalKineticEnergy += mass*(velocities[ii][0]*velocities[ii][0] + velocities[ii][1]*velocities[ii][1] + velocities[ii][2]*velocities[ii][2]);
}
(void) fprintf( log, "%s KE=%15.7e approximateT=%15.7e desiredT=%15.7e dof=%12.3f final KE=%12.3e\n",
methodName.c_str(), kineticEnergy, approximateT, temperature/BOLTZ,
degreesOfFreedom, 0.5*finalKineticEnergy );
}
return;
}
/**
......@@ -5427,7 +5458,7 @@ double getEnergyDrift( std::vector<double>& totalEnergyArray, std::vector<double
std::vector<double> kineticEnergyStatistics;
getStatistics( kineticEnergyArray, kineticEnergyStatistics );
double temperature = kineticEnergyStatistics[0]/(degreesOfFreedom*BOLTZ);
double temperature = 2.0*kineticEnergyStatistics[0]/(degreesOfFreedom*BOLTZ);
double kT = temperature*BOLTZ;
// compute stddev in units of kT/dof/ns
......@@ -5503,6 +5534,15 @@ void testEnergyConservation( std::string parameterFileName, MapStringInt& forceM
writeIntermediateStateFile( *context, intermediateStateFile, log );
}
System& system = context->getSystem();
int numberOfAtoms = system.getNumParticles();
std::vector<Vec3> velocities;
velocities.resize( numberOfAtoms );
double initialT = 300.0;
setVelocitiesBasedOnTemperature( system, velocities, initialT, log );
context->setVelocities(velocities);
// energy minimize
setIntFromMap( inputArgumentMap, "energyMinimize", energyMinimize );
......@@ -5535,14 +5575,6 @@ void testEnergyConservation( std::string parameterFileName, MapStringInt& forceM
// set velocities based on temperature
System& system = context->getSystem();
int numberOfAtoms = system.getNumParticles();
std::vector<Vec3> velocities;
velocities.resize( numberOfAtoms );
double initialT = 300.0;
setVelocitiesBasedOnTemperature( system, velocities, initialT, log );
context->setVelocities(velocities);
// get integrator
Integrator& integrator = context->getIntegrator();
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.h
View file @ 0c4f73d7
......@@ -106,11 +106,6 @@ static std::string MUTUAL_INDUCED_TARGET_EPSILON = "mutualI
#define SumIndex 12
#define AmoebaLastIndex 13
#define BOLTZMANN (1.380658e-23) /* (J/K) */
#define AVOGADRO (6.0221367e23) /* () */
#define RGAS (BOLTZMANN*AVOGADRO) /* (J/(mol K)) */
#define BOLTZ (RGAS/1.0e+03) /* (kJ/(mol K)) */
#define AngstromToNm 0.1
#define CalToJoule 4.184
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment