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Commit c2ea6c28 authored by Peter Eastman's avatar Peter Eastman
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Continuing CUDA implementation of extrapolated polarization

parent a4e2d9a6
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Showing with 770 additions and 131 deletions
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ c2ea6c28
......@@ -1019,10 +1019,10 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
int numOrders = force.getExtrapolationCoefficients().size();
extrapolatedDipole = new CudaArray(cu, 3*numMultipoles*numOrders, elementSize, "extrapolatedDipole");
extrapolatedDipolePolar = new CudaArray(cu, 3*numMultipoles*numOrders, elementSize, "extrapolatedDipolePolar");
inducedDipoleFieldGradient = new CudaArray(cu, 6*numMultipoles, elementSize, "inducedDipoleFieldGradient");
inducedDipoleFieldGradientPolar = new CudaArray(cu, 6*numMultipoles, elementSize, "inducedDipoleFieldGradientPolar");
extrapolatedDipoleFieldGradient = new CudaArray(cu, 6*numMultipoles*numOrders, elementSize, "extrapolatedDipoleFieldGradient");
extrapolatedDipoleFieldGradientPolar = new CudaArray(cu, 6*numMultipoles*numOrders, elementSize, "extrapolatedDipoleFieldGradientPolar");
inducedDipoleFieldGradient = new CudaArray(cu, 6*paddedNumAtoms, sizeof(long long), "inducedDipoleFieldGradient");
inducedDipoleFieldGradientPolar = new CudaArray(cu, 6*paddedNumAtoms, sizeof(long long), "inducedDipoleFieldGradientPolar");
extrapolatedDipoleFieldGradient = new CudaArray(cu, 6*numMultipoles*(numOrders-1), elementSize, "extrapolatedDipoleFieldGradient");
extrapolatedDipoleFieldGradientPolar = new CudaArray(cu, 6*numMultipoles*(numOrders-1), elementSize, "extrapolatedDipoleFieldGradientPolar");
}
cu.addAutoclearBuffer(*field);
cu.addAutoclearBuffer(*fieldPolar);
......@@ -1109,6 +1109,10 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
defines["ENERGY_SCALE_FACTOR"] = cu.doubleToString(138.9354558456/innerDielectric);
if (polarizationType == AmoebaMultipoleForce::Direct)
defines["DIRECT_POLARIZATION"] = "";
else if (polarizationType == AmoebaMultipoleForce::Mutual)
defines["MUTUAL_POLARIZATION"] = "";
else if (polarizationType == AmoebaMultipoleForce::Extrapolated)
defines["EXTRAPOLATED_POLARIZATION"] = "";
if (useShuffle)
defines["USE_SHUFFLE"] = "";
if (hasQuadrupoles)
......@@ -1129,7 +1133,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
coefficients << ",";
double sum = 0;
for (int j = i; j < maxExtrapolationOrder; j++)
sum = force.getExtrapolationCoefficients()[j];
sum += force.getExtrapolationCoefficients()[j];
coefficients << cu.doubleToString(sum);
}
defines["EXTRAPOLATION_COEFFICIENTS_SUM"] = coefficients.str();
......@@ -1176,8 +1180,8 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
extrapolatedDipoleGkPolar = new CudaArray(cu, 3*numMultipoles*numOrders, elementSize, "extrapolatedDipoleGkPolar");
inducedDipoleFieldGradientGk = new CudaArray(cu, 6*numMultipoles, elementSize, "inducedDipoleFieldGradientGk");
inducedDipoleFieldGradientGkPolar = new CudaArray(cu, 6*numMultipoles, elementSize, "inducedDipoleFieldGradientGkPolar");
extrapolatedDipoleFieldGradientGk = new CudaArray(cu, 6*numMultipoles*numOrders, elementSize, "extrapolatedDipoleFieldGradientGk");
extrapolatedDipoleFieldGradientGkPolar = new CudaArray(cu, 6*numMultipoles*numOrders, elementSize, "extrapolatedDipoleFieldGradientGkPolar");
extrapolatedDipoleFieldGradientGk = new CudaArray(cu, 6*numMultipoles*(numOrders-1), elementSize, "extrapolatedDipoleFieldGradientGk");
extrapolatedDipoleFieldGradientGkPolar = new CudaArray(cu, 6*numMultipoles*(numOrders-1), elementSize, "extrapolatedDipoleFieldGradientGkPolar");
}
}
int maxThreads = cu.getNonbondedUtilities().getForceThreadBlockSize();
......@@ -1203,6 +1207,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
initExtrapolatedKernel = cu.getKernel(module, "initExtrapolatedDipoles");
iterateExtrapolatedKernel = cu.getKernel(module, "iterateExtrapolatedDipoles");
computeExtrapolatedKernel = cu.getKernel(module, "computeExtrapolatedDipoles");
addExtrapolatedGradientKernel = cu.getKernel(module, "addExtrapolatedFieldGradientToForce");
}
stringstream electrostaticsSource;
electrostaticsSource << CudaKernelSources::vectorOps;
......@@ -1660,6 +1665,14 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
cu.executeKernel(pmeInducedForceKernel, pmeInducedForceArgs, cu.getNumAtoms());
}
// If using extrapolated polarization, add in force contributions from µ(m) T µ(n).
if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
void* extrapolatedArgs[] = {&cu.getForce().getDevicePointer(), &extrapolatedDipole->getDevicePointer(),
&extrapolatedDipolePolar->getDevicePointer(), &extrapolatedDipoleFieldGradient->getDevicePointer(), &extrapolatedDipoleFieldGradientPolar->getDevicePointer()};
cu.executeKernel(addExtrapolatedGradientKernel, extrapolatedArgs, numMultipoles);
}
// Map torques to force.
void* mapTorqueArgs[] = {&cu.getForce().getDevicePointer(), &torque->getDevicePointer(),
......@@ -1678,37 +1691,63 @@ void CudaCalcAmoebaMultipoleForceKernel::computeInducedField(void** recipBoxVect
int startTileIndex = nb.getStartTileIndex();
int numTileIndices = nb.getNumTiles();
int numForceThreadBlocks = nb.getNumForceThreadBlocks();
if (pmeGrid == NULL) {
unsigned int maxTiles = 0;
vector<void*> computeInducedFieldArgs;
computeInducedFieldArgs.push_back(&inducedField->getDevicePointer());
computeInducedFieldArgs.push_back(&inducedFieldPolar->getDevicePointer());
computeInducedFieldArgs.push_back(&cu.getPosq().getDevicePointer());
computeInducedFieldArgs.push_back(&nb.getExclusionTiles().getDevicePointer());
computeInducedFieldArgs.push_back(&inducedDipole->getDevicePointer());
computeInducedFieldArgs.push_back(&inducedDipolePolar->getDevicePointer());
computeInducedFieldArgs.push_back(&startTileIndex);
computeInducedFieldArgs.push_back(&numTileIndices);
if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
computeInducedFieldArgs.push_back(&inducedDipoleFieldGradient->getDevicePointer());
computeInducedFieldArgs.push_back(&inducedDipoleFieldGradientPolar->getDevicePointer());
}
if (pmeGrid != NULL) {
computeInducedFieldArgs.push_back(&nb.getInteractingTiles().getDevicePointer());
computeInducedFieldArgs.push_back(&nb.getInteractionCount().getDevicePointer());
computeInducedFieldArgs.push_back(cu.getPeriodicBoxSizePointer());
computeInducedFieldArgs.push_back(cu.getInvPeriodicBoxSizePointer());
computeInducedFieldArgs.push_back(cu.getPeriodicBoxVecXPointer());
computeInducedFieldArgs.push_back(cu.getPeriodicBoxVecYPointer());
computeInducedFieldArgs.push_back(cu.getPeriodicBoxVecZPointer());
computeInducedFieldArgs.push_back(&maxTiles);
computeInducedFieldArgs.push_back(&nb.getBlockCenters().getDevicePointer());
computeInducedFieldArgs.push_back(&nb.getInteractingAtoms().getDevicePointer());
}
if (gkKernel != NULL) {
computeInducedFieldArgs.push_back(&gkKernel->getInducedField()->getDevicePointer());
computeInducedFieldArgs.push_back(&gkKernel->getInducedFieldPolar()->getDevicePointer());
computeInducedFieldArgs.push_back(&gkKernel->getInducedDipoles()->getDevicePointer());
computeInducedFieldArgs.push_back(&gkKernel->getInducedDipolesPolar()->getDevicePointer());
computeInducedFieldArgs.push_back(&gkKernel->getBornRadii()->getDevicePointer());
if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
computeInducedFieldArgs.push_back(&inducedDipoleFieldGradientGk->getDevicePointer());
computeInducedFieldArgs.push_back(&inducedDipoleFieldGradientGkPolar->getDevicePointer());
}
}
computeInducedFieldArgs.push_back(&dampingAndThole->getDevicePointer());
cu.clearBuffer(*inducedField);
cu.clearBuffer(*inducedFieldPolar);
if (gkKernel == NULL) {
void* computeInducedFieldArgs[] = {&inducedField->getDevicePointer(), &inducedFieldPolar->getDevicePointer(), &cu.getPosq().getDevicePointer(),
&nb.getExclusionTiles().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), &startTileIndex, &numTileIndices,
&dampingAndThole->getDevicePointer()};
cu.executeKernel(computeInducedFieldKernel, computeInducedFieldArgs, numForceThreadBlocks*inducedFieldThreads, inducedFieldThreads);
if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
cu.clearBuffer(*inducedDipoleFieldGradient);
cu.clearBuffer(*inducedDipoleFieldGradientPolar);
}
else {
if (gkKernel != NULL) {
cu.clearBuffer(*gkKernel->getInducedField());
cu.clearBuffer(*gkKernel->getInducedFieldPolar());
void* computeInducedFieldArgs[] = {&inducedField->getDevicePointer(), &inducedFieldPolar->getDevicePointer(), &cu.getPosq().getDevicePointer(),
&nb.getExclusionTiles().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), &startTileIndex, &numTileIndices,
&gkKernel->getInducedField()->getDevicePointer(), &gkKernel->getInducedFieldPolar()->getDevicePointer(),
&gkKernel->getInducedDipoles()->getDevicePointer(), &gkKernel->getInducedDipolesPolar()->getDevicePointer(),
&gkKernel->getBornRadii()->getDevicePointer(), &dampingAndThole->getDevicePointer()};
cu.executeKernel(computeInducedFieldKernel, computeInducedFieldArgs, numForceThreadBlocks*inducedFieldThreads, inducedFieldThreads);
if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
cu.clearBuffer(*inducedDipoleFieldGradientGk);
cu.clearBuffer(*inducedDipoleFieldGradientGkPolar);
}
}
if (pmeGrid == NULL)
cu.executeKernel(computeInducedFieldKernel, &computeInducedFieldArgs[0], numForceThreadBlocks*inducedFieldThreads, inducedFieldThreads);
else {
cu.clearBuffer(*inducedField);
cu.clearBuffer(*inducedFieldPolar);
unsigned int maxTiles = nb.getInteractingTiles().getSize();
void* computeInducedFieldArgs[] = {&inducedField->getDevicePointer(), &inducedFieldPolar->getDevicePointer(), &cu.getPosq().getDevicePointer(),
&nb.getExclusionTiles().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), &startTileIndex, &numTileIndices,
&nb.getInteractingTiles().getDevicePointer(), &nb.getInteractionCount().getDevicePointer(), cu.getPeriodicBoxSizePointer(),
cu.getInvPeriodicBoxSizePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
&maxTiles, &nb.getBlockCenters().getDevicePointer(), &nb.getInteractingAtoms().getDevicePointer(),
&dampingAndThole->getDevicePointer()};
cu.executeKernel(computeInducedFieldKernel, computeInducedFieldArgs, numForceThreadBlocks*inducedFieldThreads, inducedFieldThreads);
maxTiles = nb.getInteractingTiles().getSize();
cu.executeKernel(computeInducedFieldKernel, &computeInducedFieldArgs[0], numForceThreadBlocks*inducedFieldThreads, inducedFieldThreads);
cu.clearBuffer(*pmeGrid);
void* pmeSpreadInducedDipolesArgs[] = {&cu.getPosq().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(),
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
......@@ -1859,17 +1898,6 @@ void CudaCalcAmoebaMultipoleForceKernel::computeExtrapolatedDipoles(void** recip
cu.executeKernel(iterateExtrapolatedKernel, iterateArgs, extrapolatedDipole->getSize());
}
cout << "CUDA"<< endl;
vector<float> d;
extrapolatedDipole->download(d);
for (int i = 0; i < maxExtrapolationOrder; i++) {
cout << "order "<<i<< endl;
for (int j = 0; j < numMultipoles; j++) {
int k = 3*(j+i*numMultipoles);
cout << d[k]<<" "<<d[k+1]<<" "<<d[k+2]<< endl;
}
}
// Take a linear combination of the µ_(n) components to form the total dipole
void* computeArgs[] = {&inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), &extrapolatedDipole->getDevicePointer(),
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ c2ea6c28
......@@ -459,7 +459,7 @@ private:
CUfunction pmeGridIndexKernel, pmeSpreadFixedMultipolesKernel, pmeSpreadInducedDipolesKernel, pmeFinishSpreadChargeKernel, pmeConvolutionKernel;
CUfunction pmeFixedPotentialKernel, pmeInducedPotentialKernel, pmeFixedForceKernel, pmeInducedForceKernel, pmeRecordInducedFieldDipolesKernel, computePotentialKernel;
CUfunction recordDIISDipolesKernel, buildMatrixKernel;
CUfunction initExtrapolatedKernel, iterateExtrapolatedKernel, computeExtrapolatedKernel;
CUfunction initExtrapolatedKernel, iterateExtrapolatedKernel, computeExtrapolatedKernel, addExtrapolatedGradientKernel;
CUfunction pmeTransformMultipolesKernel, pmeTransformPotentialKernel;
CudaCalcAmoebaGeneralizedKirkwoodForceKernel* gkKernel;
static const int PmeOrder = 5;
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ c2ea6c28
......@@ -25,6 +25,7 @@
#include "AmoebaReferenceMultipoleForce.h"
#include "jama_svd.h"
#include <algorithm>
// In case we're using some primitive version of Visual Studio this will
// make sure that erf() and erfc() are defined.
#include "openmm/internal/MSVC_erfc.h"
......@@ -1785,10 +1786,6 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostatic(const vector<Mu
vector<RealVec>& torques,
vector<RealVec>& forces)
{
const int deriv1[] = {1, 4, 7, 8, 10, 15, 17, 13, 14, 19};
const int deriv2[] = {2, 7, 5, 9, 13, 11, 18, 15, 19, 16};
const int deriv3[] = {3, 8, 9, 6, 14, 16, 12, 19, 17, 18};
RealOpenMM energy = 0.0;
vector<RealOpenMM> scaleFactors(LAST_SCALE_TYPE_INDEX);
for (unsigned int kk = 0; kk < scaleFactors.size(); kk++) {
......@@ -1796,6 +1793,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostatic(const vector<Mu
}
// main loop over particle pairs
for (unsigned int ii = 0; ii < particleData.size(); ii++) {
for (unsigned int jj = ii+1; jj < particleData.size(); jj++) {
......@@ -6072,7 +6070,6 @@ void AmoebaReferencePmeMultipoleForce::recordInducedDipoleField(vector<RealVec>&
fieldPolar[i][1] -= _phip[10*i+1]*fracToCart[1][0] + _phip[10*i+2]*fracToCart[1][1] + _phip[10*i+3]*fracToCart[1][2];
fieldPolar[i][2] -= _phip[10*i+1]*fracToCart[2][0] + _phip[10*i+2]*fracToCart[2][1] + _phip[10*i+3]*fracToCart[2][2];
}
}
void AmoebaReferencePmeMultipoleForce::calculateReciprocalSpaceInducedDipoleField(vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleFields)
......@@ -6238,7 +6235,6 @@ void AmoebaReferencePmeMultipoleForce::calculateDirectInducedDipolePairIxns(cons
alsq2n *= alsq2;
RealOpenMM bn3 = (5.0*bn2+alsq2n*exp2a)/r2;
// compute the error function scaled and unscaled terms
RealOpenMM scale3 = 1.0;
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ c2ea6c28
......@@ -673,8 +673,6 @@ protected:
std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientP;
std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientD;
int _mutualInducedDipoleConverged;
int _mutualInducedDipoleIterations;
int _maximumMutualInducedDipoleIterations;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaPTPolarization.cpp → plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaExtrapolatedPolarization.cpp
View file @ c2ea6c28
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
/**
* This tests the Reference implementation of the PT polarization algorithms in ReferenceAmoebaMultipoleForce.
* This tests the Reference implementation of the extrapolated polarization algorithms in AmoebaMultipoleForce.
*/
#include "openmm/internal/AssertionUtilities.h"
......@@ -307,9 +307,9 @@ static void check_finite_differences(vector<Vec3> analytic_forces, Context &cont
}
static void testWaterDimerExPTPolarizationTriclinicPME() {
static void testWaterDimerTriclinicPME() {
std::string testName = "testWaterDimerExPTPolarizationTriclinicPME";
std::string testName = "testWaterDimerTriclinicPME";
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
......@@ -356,9 +356,9 @@ static void testWaterDimerExPTPolarizationTriclinicPME() {
}
static void testWaterDimerExPTPolarizationTriclinicPMENoPolGroups() {
static void testWaterDimerTriclinicPMENoPolGroups() {
std::string testName = "testWaterDimerExPTPolarizationTriclinicPMENoPolGroups";
std::string testName = "testWaterDimerTriclinicPMENoPolGroups";
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
......@@ -406,9 +406,9 @@ static void testWaterDimerExPTPolarizationTriclinicPMENoPolGroups() {
}
static void testWaterDimerExPTPolarizationNoCutoff() {
static void testWaterDimerNoCutoff() {
std::string testName = "testWaterDimerExPTPolarizationNoCutoff";
std::string testName = "testWaterDimerNoCutoff";
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
......@@ -447,9 +447,9 @@ static void testWaterDimerExPTPolarizationNoCutoff() {
}
static void testWaterDimerExPTPolarizationNoCutoffNoPolGroups() {
static void testWaterDimerNoCutoffNoPolGroups() {
std::string testName = "testWaterDimerExPTPolarizationNoCutoffNoPolGroups";
std::string testName = "testWaterDimerNoCutoffNoPolGroups";
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
......@@ -499,16 +499,16 @@ int main(int numberOfArguments, char* argv[]) {
*/
// PME, triclinic
testWaterDimerExPTPolarizationTriclinicPME();
testWaterDimerTriclinicPME();
// PME, triclinic, no polarization groups
testWaterDimerExPTPolarizationTriclinicPMENoPolGroups();
testWaterDimerTriclinicPMENoPolGroups();
// No cutoff
testWaterDimerExPTPolarizationNoCutoff();
testWaterDimerNoCutoff();
// No cutoff, no polarization groups
testWaterDimerExPTPolarizationNoCutoffNoPolGroups();
testWaterDimerNoCutoffNoPolGroups();
}
catch(const std::exception& e) {
......
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