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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 ...@@ -1019,10 +1019,10 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
int numOrders = force.getExtrapolationCoefficients().size(); int numOrders = force.getExtrapolationCoefficients().size();
extrapolatedDipole = new CudaArray(cu, 3*numMultipoles*numOrders, elementSize, "extrapolatedDipole"); extrapolatedDipole = new CudaArray(cu, 3*numMultipoles*numOrders, elementSize, "extrapolatedDipole");
extrapolatedDipolePolar = new CudaArray(cu, 3*numMultipoles*numOrders, elementSize, "extrapolatedDipolePolar"); extrapolatedDipolePolar = new CudaArray(cu, 3*numMultipoles*numOrders, elementSize, "extrapolatedDipolePolar");
inducedDipoleFieldGradient = new CudaArray(cu, 6*numMultipoles, elementSize, "inducedDipoleFieldGradient"); inducedDipoleFieldGradient = new CudaArray(cu, 6*paddedNumAtoms, sizeof(long long), "inducedDipoleFieldGradient");
inducedDipoleFieldGradientPolar = new CudaArray(cu, 6*numMultipoles, elementSize, "inducedDipoleFieldGradientPolar"); inducedDipoleFieldGradientPolar = new CudaArray(cu, 6*paddedNumAtoms, sizeof(long long), "inducedDipoleFieldGradientPolar");
extrapolatedDipoleFieldGradient = new CudaArray(cu, 6*numMultipoles*numOrders, elementSize, "extrapolatedDipoleFieldGradient"); extrapolatedDipoleFieldGradient = new CudaArray(cu, 6*numMultipoles*(numOrders-1), elementSize, "extrapolatedDipoleFieldGradient");
extrapolatedDipoleFieldGradientPolar = new CudaArray(cu, 6*numMultipoles*numOrders, elementSize, "extrapolatedDipoleFieldGradientPolar"); extrapolatedDipoleFieldGradientPolar = new CudaArray(cu, 6*numMultipoles*(numOrders-1), elementSize, "extrapolatedDipoleFieldGradientPolar");
} }
cu.addAutoclearBuffer(*field); cu.addAutoclearBuffer(*field);
cu.addAutoclearBuffer(*fieldPolar); cu.addAutoclearBuffer(*fieldPolar);
...@@ -1109,6 +1109,10 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const ...@@ -1109,6 +1109,10 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
defines["ENERGY_SCALE_FACTOR"] = cu.doubleToString(138.9354558456/innerDielectric); defines["ENERGY_SCALE_FACTOR"] = cu.doubleToString(138.9354558456/innerDielectric);
if (polarizationType == AmoebaMultipoleForce::Direct) if (polarizationType == AmoebaMultipoleForce::Direct)
defines["DIRECT_POLARIZATION"] = ""; defines["DIRECT_POLARIZATION"] = "";
else if (polarizationType == AmoebaMultipoleForce::Mutual)
defines["MUTUAL_POLARIZATION"] = "";
else if (polarizationType == AmoebaMultipoleForce::Extrapolated)
defines["EXTRAPOLATED_POLARIZATION"] = "";
if (useShuffle) if (useShuffle)
defines["USE_SHUFFLE"] = ""; defines["USE_SHUFFLE"] = "";
if (hasQuadrupoles) if (hasQuadrupoles)
...@@ -1129,7 +1133,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const ...@@ -1129,7 +1133,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
coefficients << ","; coefficients << ",";
double sum = 0; double sum = 0;
for (int j = i; j < maxExtrapolationOrder; j++) for (int j = i; j < maxExtrapolationOrder; j++)
sum = force.getExtrapolationCoefficients()[j]; sum += force.getExtrapolationCoefficients()[j];
coefficients << cu.doubleToString(sum); coefficients << cu.doubleToString(sum);
} }
defines["EXTRAPOLATION_COEFFICIENTS_SUM"] = coefficients.str(); defines["EXTRAPOLATION_COEFFICIENTS_SUM"] = coefficients.str();
...@@ -1176,8 +1180,8 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const ...@@ -1176,8 +1180,8 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
extrapolatedDipoleGkPolar = new CudaArray(cu, 3*numMultipoles*numOrders, elementSize, "extrapolatedDipoleGkPolar"); extrapolatedDipoleGkPolar = new CudaArray(cu, 3*numMultipoles*numOrders, elementSize, "extrapolatedDipoleGkPolar");
inducedDipoleFieldGradientGk = new CudaArray(cu, 6*numMultipoles, elementSize, "inducedDipoleFieldGradientGk"); inducedDipoleFieldGradientGk = new CudaArray(cu, 6*numMultipoles, elementSize, "inducedDipoleFieldGradientGk");
inducedDipoleFieldGradientGkPolar = new CudaArray(cu, 6*numMultipoles, elementSize, "inducedDipoleFieldGradientGkPolar"); inducedDipoleFieldGradientGkPolar = new CudaArray(cu, 6*numMultipoles, elementSize, "inducedDipoleFieldGradientGkPolar");
extrapolatedDipoleFieldGradientGk = new CudaArray(cu, 6*numMultipoles*numOrders, elementSize, "extrapolatedDipoleFieldGradientGk"); extrapolatedDipoleFieldGradientGk = new CudaArray(cu, 6*numMultipoles*(numOrders-1), elementSize, "extrapolatedDipoleFieldGradientGk");
extrapolatedDipoleFieldGradientGkPolar = new CudaArray(cu, 6*numMultipoles*numOrders, elementSize, "extrapolatedDipoleFieldGradientGkPolar"); extrapolatedDipoleFieldGradientGkPolar = new CudaArray(cu, 6*numMultipoles*(numOrders-1), elementSize, "extrapolatedDipoleFieldGradientGkPolar");
} }
} }
int maxThreads = cu.getNonbondedUtilities().getForceThreadBlockSize(); int maxThreads = cu.getNonbondedUtilities().getForceThreadBlockSize();
...@@ -1203,6 +1207,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const ...@@ -1203,6 +1207,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
initExtrapolatedKernel = cu.getKernel(module, "initExtrapolatedDipoles"); initExtrapolatedKernel = cu.getKernel(module, "initExtrapolatedDipoles");
iterateExtrapolatedKernel = cu.getKernel(module, "iterateExtrapolatedDipoles"); iterateExtrapolatedKernel = cu.getKernel(module, "iterateExtrapolatedDipoles");
computeExtrapolatedKernel = cu.getKernel(module, "computeExtrapolatedDipoles"); computeExtrapolatedKernel = cu.getKernel(module, "computeExtrapolatedDipoles");
addExtrapolatedGradientKernel = cu.getKernel(module, "addExtrapolatedFieldGradientToForce");
} }
stringstream electrostaticsSource; stringstream electrostaticsSource;
electrostaticsSource << CudaKernelSources::vectorOps; electrostaticsSource << CudaKernelSources::vectorOps;
...@@ -1659,6 +1664,14 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in ...@@ -1659,6 +1664,14 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
&pmePhip->getDevicePointer(), &pmePhidp->getDevicePointer(), &pmeCphi->getDevicePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]}; &pmePhip->getDevicePointer(), &pmePhidp->getDevicePointer(), &pmeCphi->getDevicePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeInducedForceKernel, pmeInducedForceArgs, cu.getNumAtoms()); 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. // Map torques to force.
...@@ -1678,37 +1691,63 @@ void CudaCalcAmoebaMultipoleForceKernel::computeInducedField(void** recipBoxVect ...@@ -1678,37 +1691,63 @@ void CudaCalcAmoebaMultipoleForceKernel::computeInducedField(void** recipBoxVect
int startTileIndex = nb.getStartTileIndex(); int startTileIndex = nb.getStartTileIndex();
int numTileIndices = nb.getNumTiles(); int numTileIndices = nb.getNumTiles();
int numForceThreadBlocks = nb.getNumForceThreadBlocks(); int numForceThreadBlocks = nb.getNumForceThreadBlocks();
if (pmeGrid == NULL) { unsigned int maxTiles = 0;
cu.clearBuffer(*inducedField); vector<void*> computeInducedFieldArgs;
cu.clearBuffer(*inducedFieldPolar); computeInducedFieldArgs.push_back(&inducedField->getDevicePointer());
if (gkKernel == NULL) { computeInducedFieldArgs.push_back(&inducedFieldPolar->getDevicePointer());
void* computeInducedFieldArgs[] = {&inducedField->getDevicePointer(), &inducedFieldPolar->getDevicePointer(), &cu.getPosq().getDevicePointer(), computeInducedFieldArgs.push_back(&cu.getPosq().getDevicePointer());
&nb.getExclusionTiles().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), &startTileIndex, &numTileIndices, computeInducedFieldArgs.push_back(&nb.getExclusionTiles().getDevicePointer());
&dampingAndThole->getDevicePointer()}; computeInducedFieldArgs.push_back(&inducedDipole->getDevicePointer());
cu.executeKernel(computeInducedFieldKernel, computeInducedFieldArgs, numForceThreadBlocks*inducedFieldThreads, inducedFieldThreads); 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());
} }
else { }
cu.clearBuffer(*gkKernel->getInducedField()); computeInducedFieldArgs.push_back(&dampingAndThole->getDevicePointer());
cu.clearBuffer(*gkKernel->getInducedFieldPolar()); cu.clearBuffer(*inducedField);
void* computeInducedFieldArgs[] = {&inducedField->getDevicePointer(), &inducedFieldPolar->getDevicePointer(), &cu.getPosq().getDevicePointer(), cu.clearBuffer(*inducedFieldPolar);
&nb.getExclusionTiles().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), &startTileIndex, &numTileIndices, if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
&gkKernel->getInducedField()->getDevicePointer(), &gkKernel->getInducedFieldPolar()->getDevicePointer(), cu.clearBuffer(*inducedDipoleFieldGradient);
&gkKernel->getInducedDipoles()->getDevicePointer(), &gkKernel->getInducedDipolesPolar()->getDevicePointer(), cu.clearBuffer(*inducedDipoleFieldGradientPolar);
&gkKernel->getBornRadii()->getDevicePointer(), &dampingAndThole->getDevicePointer()}; }
cu.executeKernel(computeInducedFieldKernel, computeInducedFieldArgs, numForceThreadBlocks*inducedFieldThreads, inducedFieldThreads); if (gkKernel != NULL) {
cu.clearBuffer(*gkKernel->getInducedField());
cu.clearBuffer(*gkKernel->getInducedFieldPolar());
if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
cu.clearBuffer(*inducedDipoleFieldGradientGk);
cu.clearBuffer(*inducedDipoleFieldGradientGkPolar);
} }
} }
if (pmeGrid == NULL)
cu.executeKernel(computeInducedFieldKernel, &computeInducedFieldArgs[0], numForceThreadBlocks*inducedFieldThreads, inducedFieldThreads);
else { else {
cu.clearBuffer(*inducedField); maxTiles = nb.getInteractingTiles().getSize();
cu.clearBuffer(*inducedFieldPolar); cu.executeKernel(computeInducedFieldKernel, &computeInducedFieldArgs[0], numForceThreadBlocks*inducedFieldThreads, inducedFieldThreads);
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);
cu.clearBuffer(*pmeGrid); cu.clearBuffer(*pmeGrid);
void* pmeSpreadInducedDipolesArgs[] = {&cu.getPosq().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), void* pmeSpreadInducedDipolesArgs[] = {&cu.getPosq().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(),
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(), &pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
...@@ -1859,17 +1898,6 @@ void CudaCalcAmoebaMultipoleForceKernel::computeExtrapolatedDipoles(void** recip ...@@ -1859,17 +1898,6 @@ void CudaCalcAmoebaMultipoleForceKernel::computeExtrapolatedDipoles(void** recip
cu.executeKernel(iterateExtrapolatedKernel, iterateArgs, extrapolatedDipole->getSize()); 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 // Take a linear combination of the µ_(n) components to form the total dipole
void* computeArgs[] = {&inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), &extrapolatedDipole->getDevicePointer(), void* computeArgs[] = {&inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), &extrapolatedDipole->getDevicePointer(),
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ c2ea6c28
...@@ -459,7 +459,7 @@ private: ...@@ -459,7 +459,7 @@ private:
CUfunction pmeGridIndexKernel, pmeSpreadFixedMultipolesKernel, pmeSpreadInducedDipolesKernel, pmeFinishSpreadChargeKernel, pmeConvolutionKernel; CUfunction pmeGridIndexKernel, pmeSpreadFixedMultipolesKernel, pmeSpreadInducedDipolesKernel, pmeFinishSpreadChargeKernel, pmeConvolutionKernel;
CUfunction pmeFixedPotentialKernel, pmeInducedPotentialKernel, pmeFixedForceKernel, pmeInducedForceKernel, pmeRecordInducedFieldDipolesKernel, computePotentialKernel; CUfunction pmeFixedPotentialKernel, pmeInducedPotentialKernel, pmeFixedForceKernel, pmeInducedForceKernel, pmeRecordInducedFieldDipolesKernel, computePotentialKernel;
CUfunction recordDIISDipolesKernel, buildMatrixKernel; CUfunction recordDIISDipolesKernel, buildMatrixKernel;
CUfunction initExtrapolatedKernel, iterateExtrapolatedKernel, computeExtrapolatedKernel; CUfunction initExtrapolatedKernel, iterateExtrapolatedKernel, computeExtrapolatedKernel, addExtrapolatedGradientKernel;
CUfunction pmeTransformMultipolesKernel, pmeTransformPotentialKernel; CUfunction pmeTransformMultipolesKernel, pmeTransformPotentialKernel;
CudaCalcAmoebaGeneralizedKirkwoodForceKernel* gkKernel; CudaCalcAmoebaGeneralizedKirkwoodForceKernel* gkKernel;
static const int PmeOrder = 5; static const int PmeOrder = 5;
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ c2ea6c28
...@@ -25,6 +25,7 @@ ...@@ -25,6 +25,7 @@
#include "AmoebaReferenceMultipoleForce.h" #include "AmoebaReferenceMultipoleForce.h"
#include "jama_svd.h" #include "jama_svd.h"
#include <algorithm> #include <algorithm>
// In case we're using some primitive version of Visual Studio this will // In case we're using some primitive version of Visual Studio this will
// make sure that erf() and erfc() are defined. // make sure that erf() and erfc() are defined.
#include "openmm/internal/MSVC_erfc.h" #include "openmm/internal/MSVC_erfc.h"
...@@ -1785,10 +1786,6 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostatic(const vector<Mu ...@@ -1785,10 +1786,6 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostatic(const vector<Mu
vector<RealVec>& torques, vector<RealVec>& torques,
vector<RealVec>& forces) 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; RealOpenMM energy = 0.0;
vector<RealOpenMM> scaleFactors(LAST_SCALE_TYPE_INDEX); vector<RealOpenMM> scaleFactors(LAST_SCALE_TYPE_INDEX);
for (unsigned int kk = 0; kk < scaleFactors.size(); kk++) { for (unsigned int kk = 0; kk < scaleFactors.size(); kk++) {
...@@ -1796,6 +1793,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostatic(const vector<Mu ...@@ -1796,6 +1793,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateElectrostatic(const vector<Mu
} }
// main loop over particle pairs // main loop over particle pairs
for (unsigned int ii = 0; ii < particleData.size(); ii++) { for (unsigned int ii = 0; ii < particleData.size(); ii++) {
for (unsigned int jj = ii+1; jj < particleData.size(); jj++) { for (unsigned int jj = ii+1; jj < particleData.size(); jj++) {
...@@ -6072,7 +6070,6 @@ void AmoebaReferencePmeMultipoleForce::recordInducedDipoleField(vector<RealVec>& ...@@ -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][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]; 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) void AmoebaReferencePmeMultipoleForce::calculateReciprocalSpaceInducedDipoleField(vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleFields)
...@@ -6238,7 +6235,6 @@ void AmoebaReferencePmeMultipoleForce::calculateDirectInducedDipolePairIxns(cons ...@@ -6238,7 +6235,6 @@ void AmoebaReferencePmeMultipoleForce::calculateDirectInducedDipolePairIxns(cons
alsq2n *= alsq2; alsq2n *= alsq2;
RealOpenMM bn3 = (5.0*bn2+alsq2n*exp2a)/r2; RealOpenMM bn3 = (5.0*bn2+alsq2n*exp2a)/r2;
// compute the error function scaled and unscaled terms // compute the error function scaled and unscaled terms
RealOpenMM scale3 = 1.0; RealOpenMM scale3 = 1.0;
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ c2ea6c28
...@@ -673,8 +673,6 @@ protected: ...@@ -673,8 +673,6 @@ protected:
std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientP; std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientP;
std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientD; std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientD;
int _mutualInducedDipoleConverged; int _mutualInducedDipoleConverged;
int _mutualInducedDipoleIterations; int _mutualInducedDipoleIterations;
int _maximumMutualInducedDipoleIterations; int _maximumMutualInducedDipoleIterations;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaPTPolarization.cpp → plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaExtrapolatedPolarization.cpp
View file @ c2ea6c28
...@@ -30,7 +30,7 @@ ...@@ -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" #include "openmm/internal/AssertionUtilities.h"
...@@ -307,9 +307,9 @@ static void check_finite_differences(vector<Vec3> analytic_forces, Context &cont ...@@ -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; System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();; AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
...@@ -356,9 +356,9 @@ static void testWaterDimerExPTPolarizationTriclinicPME() { ...@@ -356,9 +356,9 @@ static void testWaterDimerExPTPolarizationTriclinicPME() {
} }
static void testWaterDimerExPTPolarizationTriclinicPMENoPolGroups() { static void testWaterDimerTriclinicPMENoPolGroups() {
std::string testName = "testWaterDimerExPTPolarizationTriclinicPMENoPolGroups"; std::string testName = "testWaterDimerTriclinicPMENoPolGroups";
System system; System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();; AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
...@@ -406,9 +406,9 @@ static void testWaterDimerExPTPolarizationTriclinicPMENoPolGroups() { ...@@ -406,9 +406,9 @@ static void testWaterDimerExPTPolarizationTriclinicPMENoPolGroups() {
} }
static void testWaterDimerExPTPolarizationNoCutoff() { static void testWaterDimerNoCutoff() {
std::string testName = "testWaterDimerExPTPolarizationNoCutoff"; std::string testName = "testWaterDimerNoCutoff";
System system; System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();; AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
...@@ -447,9 +447,9 @@ static void testWaterDimerExPTPolarizationNoCutoff() { ...@@ -447,9 +447,9 @@ static void testWaterDimerExPTPolarizationNoCutoff() {
} }
static void testWaterDimerExPTPolarizationNoCutoffNoPolGroups() { static void testWaterDimerNoCutoffNoPolGroups() {
std::string testName = "testWaterDimerExPTPolarizationNoCutoffNoPolGroups"; std::string testName = "testWaterDimerNoCutoffNoPolGroups";
System system; System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();; AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
...@@ -499,16 +499,16 @@ int main(int numberOfArguments, char* argv[]) { ...@@ -499,16 +499,16 @@ int main(int numberOfArguments, char* argv[]) {
*/ */
// PME, triclinic // PME, triclinic
testWaterDimerExPTPolarizationTriclinicPME(); testWaterDimerTriclinicPME();
// PME, triclinic, no polarization groups // PME, triclinic, no polarization groups
testWaterDimerExPTPolarizationTriclinicPMENoPolGroups(); testWaterDimerTriclinicPMENoPolGroups();
// No cutoff // No cutoff
testWaterDimerExPTPolarizationNoCutoff(); testWaterDimerNoCutoff();
// No cutoff, no polarization groups // No cutoff, no polarization groups
testWaterDimerExPTPolarizationNoCutoffNoPolGroups(); testWaterDimerNoCutoffNoPolGroups();
} }
catch(const std::exception& e) { catch(const std::exception& e) {
......
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