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Commit 747dd2bc authored by Mark Friedrichs's avatar Mark Friedrichs
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Modified calculateElectrostaticPotentialForAtomGridPoint_kernel to apply... 

Modified calculateElectrostaticPotentialForAtomGridPoint_kernel to apply periodic boundary conditions
Unit test for multipole grid potential changed to system comprised of 216 water molecules; 
Tinker potential values now based on PBC
parent 97f5ce05
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Showing with 121 additions and 116 deletions
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaElectrostaticPotential.cu
View file @ 747dd2bc
...@@ -143,7 +143,11 @@ __device__ void calculateElectrostaticPotentialForAtomGridPoint_kernel( volatile ...@@ -143,7 +143,11 @@ __device__ void calculateElectrostaticPotentialForAtomGridPoint_kernel( volatile
float xr = atomI.x - gridPoint.x; float xr = atomI.x - gridPoint.x;
float yr = atomI.y - gridPoint.y; float yr = atomI.y - gridPoint.y;
float zr = atomI.z - gridPoint.z; float zr = atomI.z - gridPoint.z;
xr -= floorf(xr*cSim.invPeriodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
yr -= floorf(yr*cSim.invPeriodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
zr -= floorf(zr*cSim.invPeriodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
float r2 = xr*xr + yr*yr + zr*zr; float r2 = xr*xr + yr*yr + zr*zr;
float r = sqrtf( r2 ); float r = sqrtf( r2 );
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaMultipoleForce.cpp
View file @ 747dd2bc
...@@ -941,8 +941,7 @@ static void testQuadrupoleValidation( FILE* log ){ ...@@ -941,8 +941,7 @@ static void testQuadrupoleValidation( FILE* log ){
static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::AmoebaNonbondedMethod nonbondedMethod, static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::AmoebaNonbondedMethod nonbondedMethod,
AmoebaMultipoleForce::AmoebaPolarizationType polarizationType, AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
double cutoff, int inputPmeGridDimension, std::string testName, double cutoff, int inputPmeGridDimension, std::string testName,
std::vector<Vec3>& forces, double& energy, std::vector<Vec3>& forces, double& energy, FILE* log ){
std::vector<Vec3>& inputGrid, std::vector< double >& outputGridPotential, FILE* log ){
// beginning of Multipole setup // beginning of Multipole setup
...@@ -1123,13 +1122,9 @@ static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce:: ...@@ -1123,13 +1122,9 @@ static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::
context.setPositions(positions); context.setPositions(positions);
if( testName == "testMultipoleGridPotential" ){ State state = context.getState(State::Forces | State::Energy);
amoebaMultipoleForce->getElectrostaticPotential( inputGrid, context, outputGridPotential ); forces = state.getForces();
} else { energy = state.getPotentialEnergy();
State state = context.getState(State::Forces | State::Energy);
forces = state.getForces();
energy = state.getPotentialEnergy();
}
return; return;
...@@ -1148,12 +1143,8 @@ static void testMultipoleIonsAndWaterPMEDirectPolarization( FILE* log ) { ...@@ -1148,12 +1143,8 @@ static void testMultipoleIonsAndWaterPMEDirectPolarization( FILE* log ) {
std::vector<Vec3> forces; std::vector<Vec3> forces;
double energy; double energy;
std::vector<Vec3> inputGrid;
std::vector<double> outputGridPotential;
setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::PME, AmoebaMultipoleForce::Direct, setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::PME, AmoebaMultipoleForce::Direct,
cutoff, inputPmeGridDimension, testName, forces, energy, cutoff, inputPmeGridDimension, testName, forces, energy, log );
inputGrid, outputGridPotential, log );
std::vector<Vec3> expectedForces(numberOfParticles); std::vector<Vec3> expectedForces(numberOfParticles);
...@@ -1187,11 +1178,9 @@ static void testMultipoleIonsAndWaterPMEMutualPolarization( FILE* log ) { ...@@ -1187,11 +1178,9 @@ static void testMultipoleIonsAndWaterPMEMutualPolarization( FILE* log ) {
double energy; double energy;
std::vector<Vec3> inputGrid; std::vector<Vec3> inputGrid;
std::vector<double> outputGridPotential;
setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::PME, AmoebaMultipoleForce::Mutual, setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::PME, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension, testName, forces, energy, cutoff, inputPmeGridDimension, testName, forces, energy, log );
inputGrid, outputGridPotential, log );
std::vector<Vec3> expectedForces(numberOfParticles); std::vector<Vec3> expectedForces(numberOfParticles);
...@@ -1211,101 +1200,6 @@ static void testMultipoleIonsAndWaterPMEMutualPolarization( FILE* log ) { ...@@ -1211,101 +1200,6 @@ static void testMultipoleIonsAndWaterPMEMutualPolarization( FILE* log ) {
double tolerance = 5.0e-04; double tolerance = 5.0e-04;
compareForceNormsEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log ); compareForceNormsEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
}
// test computation of multipole potential on a grid
static void testMultipoleGridPotential( FILE* log ) {
std::string testName = "testMultipoleGridPotential";
int numberOfParticles = 8;
int inputPmeGridDimension = 64;
double cutoff = 0.70;
std::vector<Vec3> forces;
double energy;
// initialize grid
int gridSize = 27;
std::vector<Vec3> inputGrid(gridSize);
inputGrid[0] = Vec3( -3.2894000e+00, -1.3098000e+00, -1.7064092e+00);
inputGrid[1] = Vec3( -3.2894000e+00, -1.3098000e+00, 6.3928525e-01);
inputGrid[2] = Vec3( -3.2894000e+00, -1.3098000e+00, 2.9849797e+00);
inputGrid[3] = Vec3( -3.2894000e+00, 5.1360000e-01, -1.7064092e+00);
inputGrid[4] = Vec3( -3.2894000e+00, 5.1360000e-01, 6.3928525e-01);
inputGrid[5] = Vec3( -3.2894000e+00, 5.1360000e-01, 2.9849797e+00);
inputGrid[6] = Vec3( -3.2894000e+00, 2.3370000e+00, -1.7064092e+00);
inputGrid[7] = Vec3( -3.2894000e+00, 2.3370000e+00, 6.3928525e-01);
inputGrid[8] = Vec3( -3.2894000e+00, 2.3370000e+00, 2.9849797e+00);
inputGrid[9] = Vec3( -2.3754000e+00, -1.3098000e+00, -1.7064092e+00);
inputGrid[10] = Vec3( -2.3754000e+00, -1.3098000e+00, 6.3928525e-01);
inputGrid[11] = Vec3( -2.3754000e+00, -1.3098000e+00, 2.9849797e+00);
inputGrid[12] = Vec3( -2.3754000e+00, 5.1360000e-01, -1.7064092e+00);
inputGrid[13] = Vec3( -2.3754000e+00, 5.1360000e-01, 6.3928525e-01);
inputGrid[14] = Vec3( -2.3754000e+00, 5.1360000e-01, 2.9849797e+00);
inputGrid[15] = Vec3( -2.3754000e+00, 2.3370000e+00, -1.7064092e+00);
inputGrid[16] = Vec3( -2.3754000e+00, 2.3370000e+00, 6.3928525e-01);
inputGrid[17] = Vec3( -2.3754000e+00, 2.3370000e+00, 2.9849797e+00);
inputGrid[18] = Vec3( -1.4614000e+00, -1.3098000e+00, -1.7064092e+00);
inputGrid[19] = Vec3( -1.4614000e+00, -1.3098000e+00, 6.3928525e-01);
inputGrid[20] = Vec3( -1.4614000e+00, -1.3098000e+00, 2.9849797e+00);
inputGrid[21] = Vec3( -1.4614000e+00, 5.1360000e-01, -1.7064092e+00);
inputGrid[22] = Vec3( -1.4614000e+00, 5.1360000e-01, 6.3928525e-01);
inputGrid[23] = Vec3( -1.4614000e+00, 5.1360000e-01, 2.9849797e+00);
inputGrid[24] = Vec3( -1.4614000e+00, 2.3370000e+00, -1.7064092e+00);
inputGrid[25] = Vec3( -1.4614000e+00, 2.3370000e+00, 6.3928525e-01);
inputGrid[26] = Vec3( -1.4614000e+00, 2.3370000e+00, 2.9849797e+00);
std::vector<double> outputGridPotential;
setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::PME, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension, testName, forces, energy,
inputGrid, outputGridPotential, log );
// TINKER computed grid values
std::vector<double> tinkerGridPotential(gridSize);
tinkerGridPotential[0] = -1.8587681e+01;
tinkerGridPotential[1] = -3.7731481e+01;
tinkerGridPotential[2] = -1.4093518e+01;
tinkerGridPotential[3] = -8.6733284e-01;
tinkerGridPotential[4] = 1.6378362e+01;
tinkerGridPotential[5] = 1.7545816e+01;
tinkerGridPotential[6] = 1.2115085e+01;
tinkerGridPotential[7] = 1.5693689e+02;
tinkerGridPotential[8] = 5.6517394e+01;
tinkerGridPotential[9] = -2.8489173e+01;
tinkerGridPotential[10] = -1.1037348e+02;
tinkerGridPotential[11] = -7.1050586e+01;
tinkerGridPotential[12] = -5.9901289e+00;
tinkerGridPotential[13] = -4.0533846e+00;
tinkerGridPotential[14] = 1.0506199e+01;
tinkerGridPotential[15] = -8.6421838e+00;
tinkerGridPotential[16] = 8.3729402e+01;
tinkerGridPotential[17] = 4.4286652e+01;
tinkerGridPotential[18] = -3.4746066e+01;
tinkerGridPotential[19] = -1.0763056e+03;
tinkerGridPotential[20] = -2.0034673e+01;
tinkerGridPotential[21] = -1.2131063e+01;
tinkerGridPotential[22] = -2.4662346e+01;
tinkerGridPotential[23] = 1.4630799e+00;
tinkerGridPotential[24] = 5.1623298e+00;
tinkerGridPotential[25] = 3.3114482e+01;
tinkerGridPotential[26] = 2.5828622e+01;
double tolerance = 1.0e-04;
for( unsigned int ii = 0; ii < gridSize; ii++ ){
double difference = fabs( outputGridPotential[ii] - tinkerGridPotential[ii] );
//fprintf( stderr, "%2d %15.7e %15.7e %15.7e %15.7e\n", ii, difference, difference/fabs(tinkerGridPotential[ii]), outputGridPotential[ii], tinkerGridPotential[ii] );
if( difference > tolerance ){
std::stringstream details;
details << testName << "Multipole moment " << ii << " does not agree w/ TINKER computed moments: OpenMM=" << outputGridPotential[ii];
details << " TINKER=" << tinkerGridPotential[ii] << " difference=" << difference;
throwException(__FILE__, __LINE__, details.str());
}
}
} }
// setup for box of 216 water molecules -- used to test PME // setup for box of 216 water molecules -- used to test PME
...@@ -1314,7 +1208,9 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::Am ...@@ -1314,7 +1208,9 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::Am
AmoebaMultipoleForce::AmoebaPolarizationType polarizationType, AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
double cutoff, int inputPmeGridDimension, std::string& testName, double cutoff, int inputPmeGridDimension, std::string& testName,
std::vector<Vec3>& forces, double& energy, std::vector<Vec3>& forces, double& energy,
std::vector< double >& outputMultipoleMoments, FILE* log ){ std::vector< double >& outputMultipoleMoments,
std::vector< Vec3 >& inputGrid,
std::vector< double >& outputGridPotential, FILE* log ){
// beginning of Multipole setup // beginning of Multipole setup
...@@ -2099,6 +1995,8 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::Am ...@@ -2099,6 +1995,8 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::Am
if( testName == "testSystemMultipoleMoments" ){ if( testName == "testSystemMultipoleMoments" ){
Vec3 origin( 0.0, 0.0, 0.0 ); Vec3 origin( 0.0, 0.0, 0.0 );
amoebaMultipoleForce->getSystemMultipoleMoments( origin, context, outputMultipoleMoments ); amoebaMultipoleForce->getSystemMultipoleMoments( origin, context, outputMultipoleMoments );
} else if( testName == "testMultipoleGridPotential" ){
amoebaMultipoleForce->getElectrostaticPotential( inputGrid, context, outputGridPotential );
} else { } else {
State state = context.getState(State::Forces | State::Energy); State state = context.getState(State::Forces | State::Energy);
forces = state.getForces(); forces = state.getForces();
...@@ -2120,10 +2018,12 @@ static void testPMEMutualPolarizationLargeWater( FILE* log ) { ...@@ -2120,10 +2018,12 @@ static void testPMEMutualPolarizationLargeWater( FILE* log ) {
std::vector<Vec3> forces; std::vector<Vec3> forces;
double energy; double energy;
std::vector< double > outputMultipoleMoments; std::vector< double > outputMultipoleMoments;
std::vector< Vec3 > inputGrid;
std::vector< double > outputGridPotential;
setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::PME, AmoebaMultipoleForce::Mutual, setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::PME, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension, testName, cutoff, inputPmeGridDimension, testName,
forces, energy, outputMultipoleMoments, log ); forces, energy, outputMultipoleMoments, inputGrid, outputGridPotential, log );
std::vector<Vec3> expectedForces(numberOfParticles); std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = -1.3268930e+04; double expectedEnergy = -1.3268930e+04;
...@@ -2795,10 +2695,12 @@ static void testSystemMultipoleMoments( FILE* log ) { ...@@ -2795,10 +2695,12 @@ static void testSystemMultipoleMoments( FILE* log ) {
std::vector<Vec3> forces; std::vector<Vec3> forces;
double energy; double energy;
std::vector<double> outputMultipoleMoments; std::vector<double> outputMultipoleMoments;
std::vector< Vec3 > inputGrid;
std::vector< double > outputGridPotential;
setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::PME, AmoebaMultipoleForce::Mutual, setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::PME, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension, testName, cutoff, inputPmeGridDimension, testName,
forces, energy, outputMultipoleMoments, log ); forces, energy, outputMultipoleMoments, inputGrid, outputGridPotential, log );
std::vector<double> tinkerMoments(13); std::vector<double> tinkerMoments(13);
...@@ -2842,6 +2744,105 @@ static void testSystemMultipoleMoments( FILE* log ) { ...@@ -2842,6 +2744,105 @@ static void testSystemMultipoleMoments( FILE* log ) {
} }
// test computation of multipole potential on a grid
static void testMultipoleGridPotential( FILE* log ) {
std::string testName = "testMultipoleGridPotential";
int numberOfParticles = 648;
int inputPmeGridDimension = 24;
double cutoff = 0.70;
std::vector<Vec3> forces;
double energy;
// initialize grid
int gridSize = 27;
std::vector<Vec3> inputGrid(gridSize);
inputGrid[0] = Vec3( -1.0318535e+00, -1.0224502e+00, -1.0202836e+00);
inputGrid[1] = Vec3( -1.0318535e+00, -1.0224502e+00, -3.4032700e-02);
inputGrid[2] = Vec3( -1.0318535e+00, -1.0224502e+00, 9.5221820e-01);
inputGrid[3] = Vec3( -1.0318535e+00, -3.0961200e-02, -1.0202836e+00);
inputGrid[4] = Vec3( -1.0318535e+00, -3.0961200e-02, -3.4032700e-02);
inputGrid[5] = Vec3( -1.0318535e+00, -3.0961200e-02, 9.5221820e-01);
inputGrid[6] = Vec3( -1.0318535e+00, 9.6052780e-01, -1.0202836e+00);
inputGrid[7] = Vec3( -1.0318535e+00, 9.6052780e-01, -3.4032700e-02);
inputGrid[8] = Vec3( -1.0318535e+00, 9.6052780e-01, 9.5221820e-01);
inputGrid[9] = Vec3( -3.3969000e-02, -1.0224502e+00, -1.0202836e+00);
inputGrid[10] = Vec3( -3.3969000e-02, -1.0224502e+00, -3.4032700e-02);
inputGrid[11] = Vec3( -3.3969000e-02, -1.0224502e+00, 9.5221820e-01);
inputGrid[12] = Vec3( -3.3969000e-02, -3.0961200e-02, -1.0202836e+00);
inputGrid[13] = Vec3( -3.3969000e-02, -3.0961200e-02, -3.4032700e-02);
inputGrid[14] = Vec3( -3.3969000e-02, -3.0961200e-02, 9.5221820e-01);
inputGrid[15] = Vec3( -3.3969000e-02, 9.6052780e-01, -1.0202836e+00);
inputGrid[16] = Vec3( -3.3969000e-02, 9.6052780e-01, -3.4032700e-02);
inputGrid[17] = Vec3( -3.3969000e-02, 9.6052780e-01, 9.5221820e-01);
inputGrid[18] = Vec3( 9.6391550e-01, -1.0224502e+00, -1.0202836e+00);
inputGrid[19] = Vec3( 9.6391550e-01, -1.0224502e+00, -3.4032700e-02);
inputGrid[20] = Vec3( 9.6391550e-01, -1.0224502e+00, 9.5221820e-01);
inputGrid[21] = Vec3( 9.6391550e-01, -3.0961200e-02, -1.0202836e+00);
inputGrid[22] = Vec3( 9.6391550e-01, -3.0961200e-02, -3.4032700e-02);
inputGrid[23] = Vec3( 9.6391550e-01, -3.0961200e-02, 9.5221820e-01);
inputGrid[24] = Vec3( 9.6391550e-01, 9.6052780e-01, -1.0202836e+00);
inputGrid[25] = Vec3( 9.6391550e-01, 9.6052780e-01, -3.4032700e-02);
inputGrid[26] = Vec3( 9.6391550e-01, 9.6052780e-01, 9.5221820e-01);
std::vector<double> outputGridPotential;
std::vector< double > outputMultipoleMoments;
setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::PME, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension, testName, forces, energy,
outputMultipoleMoments, inputGrid, outputGridPotential, log );
// TINKER computed grid values
std::vector<double> tinkerGridPotential(gridSize);
tinkerGridPotential[0] = 7.5696473e+01;
tinkerGridPotential[1] = -1.5382673e+01;
tinkerGridPotential[2] = 6.9487135e+01;
tinkerGridPotential[3] = 1.5459661e+03;
tinkerGridPotential[4] = -4.5138366e+02;
tinkerGridPotential[5] = 4.6553857e+01;
tinkerGridPotential[6] = 1.8486978e+01;
tinkerGridPotential[7] = -5.9235079e+01;
tinkerGridPotential[8] = 1.0448125e+01;
tinkerGridPotential[9] = 1.9529845e+00;
tinkerGridPotential[10] = 5.3587575e+00;
tinkerGridPotential[11] = -3.3794408e+01;
tinkerGridPotential[12] = 1.5197977e+01;
tinkerGridPotential[13] = 4.3613381e+02;
tinkerGridPotential[14] = 1.6620315e+01;
tinkerGridPotential[15] = 5.3724507e+01;
tinkerGridPotential[16] = 6.9026934e+02;
tinkerGridPotential[17] = -1.2708548e+01;
tinkerGridPotential[18] = -9.8826500e+02;
tinkerGridPotential[19] = 3.2952143e+01;
tinkerGridPotential[20] = 9.1165100e+02;
tinkerGridPotential[21] = 4.0844598e+01;
tinkerGridPotential[22] = -1.3509483e+01;
tinkerGridPotential[23] = 1.4499749e+00;
tinkerGridPotential[24] = 1.5011664e+02;
tinkerGridPotential[25] = -2.8581208e+02;
tinkerGridPotential[26] = 1.3960144e+02;
double tolerance = 3.0e-04;
for( unsigned int ii = 0; ii < gridSize; ii++ ){
double difference = fabs( (outputGridPotential[ii] - tinkerGridPotential[ii] )/tinkerGridPotential[ii] );
//(void) fprintf( stderr, "Grid: %2d %15.7e %15.7e %15.7e\n", ii, difference, outputGridPotential[ii], tinkerGridPotential[ii] );
if( difference > tolerance ){
std::stringstream details;
details << testName << " potential for grid point " << ii << " does not agree w/ TINKER computed value: OpenMM=" << outputGridPotential[ii];
details << " TINKER=" << tinkerGridPotential[ii] << " difference=" << difference;
throwException(__FILE__, __LINE__, details.str());
}
}
}
int main( int numberOfArguments, char* argv[] ) { int main( int numberOfArguments, char* argv[] ) {
try { try {
......
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