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Commit c83f2a12 authored by Peter Eastman's avatar Peter Eastman
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Began CUDA implementation of triclinic boxes for AmoebaMultipoleForce

parent 82e118fb
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Showing with 286 additions and 168 deletions
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ c83f2a12
......@@ -796,8 +796,8 @@ private:
CudaCalcAmoebaMultipoleForceKernel::CudaCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) :
CalcAmoebaMultipoleForceKernel(name, platform), cu(cu), system(system), hasInitializedScaleFactors(false), hasInitializedFFT(false), multipolesAreValid(false),
multipoleParticles(NULL), molecularDipoles(NULL), molecularQuadrupoles(NULL), labFrameDipoles(NULL), labFrameQuadrupoles(NULL),
field(NULL), fieldPolar(NULL), inducedField(NULL), inducedFieldPolar(NULL), torque(NULL), dampingAndThole(NULL), inducedDipole(NULL),
multipoleParticles(NULL), molecularDipoles(NULL), molecularQuadrupoles(NULL), labFrameDipoles(NULL), labFrameQuadrupoles(NULL), fracDipoles(NULL),
fracQuadrupoles(NULL), field(NULL), fieldPolar(NULL), inducedField(NULL), inducedFieldPolar(NULL), torque(NULL), dampingAndThole(NULL), inducedDipole(NULL),
diisCoefficients(NULL), inducedDipolePolar(NULL), inducedDipoleErrors(NULL), prevDipoles(NULL), prevDipolesPolar(NULL), prevDipolesGk(NULL),
prevDipolesGkPolar(NULL), prevErrors(NULL), diisMatrix(NULL), polarizability(NULL), covalentFlags(NULL), polarizationGroupFlags(NULL),
pmeGrid(NULL), pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeIgrid(NULL), pmePhi(NULL),
......@@ -816,6 +816,10 @@ CudaCalcAmoebaMultipoleForceKernel::~CudaCalcAmoebaMultipoleForceKernel() {
delete labFrameDipoles;
if (labFrameQuadrupoles != NULL)
delete labFrameQuadrupoles;
if (fracDipoles != NULL)
delete fracDipoles;
if (fracQuadrupoles != NULL)
delete fracQuadrupoles;
if (field != NULL)
delete field;
if (fieldPolar != NULL)
......@@ -968,7 +972,9 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
int elementSize = (cu.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
labFrameDipoles = new CudaArray(cu, 3*paddedNumAtoms, elementSize, "labFrameDipoles");
labFrameQuadrupoles = new CudaArray(cu, 9*paddedNumAtoms, elementSize, "labFrameQuadrupoles");
labFrameQuadrupoles = new CudaArray(cu, 5*paddedNumAtoms, elementSize, "labFrameQuadrupoles");
fracDipoles = new CudaArray(cu, 3*paddedNumAtoms, elementSize, "fracDipoles");
fracQuadrupoles = new CudaArray(cu, 6*paddedNumAtoms, elementSize, "fracQuadrupoles");
field = new CudaArray(cu, 3*paddedNumAtoms, sizeof(long long), "field");
fieldPolar = new CudaArray(cu, 3*paddedNumAtoms, sizeof(long long), "fieldPolar");
torque = new CudaArray(cu, 3*paddedNumAtoms, sizeof(long long), "torque");
......@@ -1185,6 +1191,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
pmeDefines["DIRECT_POLARIZATION"] = "";
CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaAmoebaKernelSources::multipolePme, pmeDefines);
pmeGridIndexKernel = cu.getKernel(module, "findAtomGridIndex");
pmeTransformMultipolesKernel = cu.getKernel(module, "transformMultipolesToFractionalCoordinates");
pmeSpreadFixedMultipolesKernel = cu.getKernel(module, "gridSpreadFixedMultipoles");
pmeSpreadInducedDipolesKernel = cu.getKernel(module, "gridSpreadInducedDipoles");
pmeFinishSpreadChargeKernel = cu.getKernel(module, "finishSpreadCharge");
......@@ -1483,15 +1490,44 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
gkKernel->finishComputation(*torque, *labFrameDipoles, *labFrameQuadrupoles, *inducedDipole, *inducedDipolePolar, *dampingAndThole, *covalentFlags, *polarizationGroupFlags);
}
else {
// Compute reciprocal box vectors.
Vec3 boxVectors[3];
cu.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double determinant = boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2];
double scale = 1.0/determinant;
double3 recipBoxVectors[3];
recipBoxVectors[0] = make_double3(boxVectors[1][1]*boxVectors[2][2]*scale, 0, 0);
recipBoxVectors[1] = make_double3(-boxVectors[1][0]*boxVectors[2][2]*scale, boxVectors[0][0]*boxVectors[2][2]*scale, 0);
recipBoxVectors[2] = make_double3((boxVectors[1][0]*boxVectors[2][1]-boxVectors[1][1]*boxVectors[2][0])*scale, -boxVectors[0][0]*boxVectors[2][1]*scale, boxVectors[0][0]*boxVectors[1][1]*scale);
float3 recipBoxVectorsFloat[3];
void* recipBoxVectorPointer[3];
if (cu.getUseDoublePrecision()) {
recipBoxVectorPointer[0] = &recipBoxVectors[0];
recipBoxVectorPointer[1] = &recipBoxVectors[1];
recipBoxVectorPointer[2] = &recipBoxVectors[2];
}
else {
recipBoxVectorsFloat[0] = make_float3((float) recipBoxVectors[0].x, 0, 0);
recipBoxVectorsFloat[1] = make_float3((float) recipBoxVectors[1].x, (float) recipBoxVectors[1].y, 0);
recipBoxVectorsFloat[2] = make_float3((float) recipBoxVectors[2].x, (float) recipBoxVectors[2].y, (float) recipBoxVectors[2].z);
recipBoxVectorPointer[0] = &recipBoxVectorsFloat[0];
recipBoxVectorPointer[1] = &recipBoxVectorsFloat[1];
recipBoxVectorPointer[2] = &recipBoxVectorsFloat[2];
}
// Reciprocal space calculation.
unsigned int maxTiles = nb.getInteractingTiles().getSize();
void* gridIndexArgs[] = {&cu.getPosq().getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(),
cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeGridIndexKernel, gridIndexArgs, cu.getNumAtoms(), cu.ThreadBlockSize, cu.ThreadBlockSize*PmeOrder*PmeOrder*elementSize);
sort->sort(*pmeAtomGridIndex);
void* pmeSpreadFixedMultipolesArgs[] = {&cu.getPosq().getDevicePointer(), &labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(),
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
void* pmeTransformMultipolesArgs[] = {&labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(),
&fracDipoles->getDevicePointer(), &fracQuadrupoles->getDevicePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeTransformMultipolesKernel, pmeTransformMultipolesArgs, cu.getNumAtoms());
void* pmeSpreadFixedMultipolesArgs[] = {&cu.getPosq().getDevicePointer(), &fracDipoles->getDevicePointer(), &fracQuadrupoles->getDevicePointer(),
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeSpreadFixedMultipolesKernel, pmeSpreadFixedMultipolesArgs, cu.getNumAtoms());
void* finishSpreadArgs[] = {&pmeGrid->getDevicePointer()};
if (cu.getUseDoublePrecision())
......@@ -1501,7 +1537,7 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
else
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_FORWARD);
void* pmeConvolutionArgs[] = {&pmeGrid->getDevicePointer(), &pmeBsplineModuliX->getDevicePointer(), &pmeBsplineModuliY->getDevicePointer(),
&pmeBsplineModuliZ->getDevicePointer(), cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
&pmeBsplineModuliZ->getDevicePointer(), cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, cu.getNumAtoms());
if (cu.getUseDoublePrecision())
cufftExecZ2Z(fft, (double2*) pmeGrid->getDevicePointer(), (double2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
......@@ -1509,11 +1545,12 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
void* pmeFixedPotentialArgs[] = {&pmeGrid->getDevicePointer(), &pmePhi->getDevicePointer(), &field->getDevicePointer(),
&fieldPolar ->getDevicePointer(), &cu.getPosq().getDevicePointer(), &labFrameDipoles->getDevicePointer(),
cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer(), &pmeAtomGridIndex->getDevicePointer()};
cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2], &pmeAtomGridIndex->getDevicePointer()};
cu.executeKernel(pmeFixedPotentialKernel, pmeFixedPotentialArgs, cu.getNumAtoms());
void* pmeFixedForceArgs[] = {&cu.getPosq().getDevicePointer(), &cu.getForce().getDevicePointer(), &torque->getDevicePointer(),
&cu.getEnergyBuffer().getDevicePointer(), &labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(),
&pmePhi->getDevicePointer(), cu.getInvPeriodicBoxSizePointer()};
&fracDipoles->getDevicePointer(), &fracQuadrupoles->getDevicePointer(), &pmePhi->getDevicePointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeFixedForceKernel, pmeFixedForceArgs, cu.getNumAtoms());
// Direct space calculation.
......@@ -1521,7 +1558,8 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
void* computeFixedFieldArgs[] = {&field->getDevicePointer(), &fieldPolar->getDevicePointer(), &cu.getPosq().getDevicePointer(),
&covalentFlags->getDevicePointer(), &polarizationGroupFlags->getDevicePointer(), &nb.getExclusionTiles().getDevicePointer(), &startTileIndex, &numTileIndices,
&nb.getInteractingTiles().getDevicePointer(), &nb.getInteractionCount().getDevicePointer(), cu.getPeriodicBoxSizePointer(),
cu.getInvPeriodicBoxSizePointer(), &maxTiles, &nb.getBlockCenters().getDevicePointer(), &nb.getInteractingAtoms().getDevicePointer(),
cu.getInvPeriodicBoxSizePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
&maxTiles, &nb.getBlockCenters().getDevicePointer(), &nb.getInteractingAtoms().getDevicePointer(),
&labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(), &dampingAndThole->getDevicePointer()};
cu.executeKernel(computeFixedFieldKernel, computeFixedFieldArgs, numForceThreadBlocks*fixedFieldThreads, fixedFieldThreads);
void* recordInducedDipolesArgs[] = {&field->getDevicePointer(), &fieldPolar->getDevicePointer(),
......@@ -1532,7 +1570,7 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
cu.clearBuffer(*pmeGrid);
void* pmeSpreadInducedDipolesArgs[] = {&cu.getPosq().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(),
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeSpreadInducedDipolesKernel, pmeSpreadInducedDipolesArgs, cu.getNumAtoms());
if (cu.getUseDoublePrecision())
cu.executeKernel(pmeFinishSpreadChargeKernel, finishSpreadArgs, pmeGrid->getSize());
......@@ -1546,7 +1584,7 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
else
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
void* pmeInducedPotentialArgs[] = {&pmeGrid->getDevicePointer(), &pmePhid->getDevicePointer(), &pmePhip->getDevicePointer(),
&pmePhidp->getDevicePointer(), &cu.getPosq().getDevicePointer(), cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer(),
&pmePhidp->getDevicePointer(), &cu.getPosq().getDevicePointer(), cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2],
&pmeAtomGridIndex->getDevicePointer()};
cu.executeKernel(pmeInducedPotentialKernel, pmeInducedPotentialArgs, cu.getNumAtoms());
......@@ -1559,7 +1597,8 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
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(), &maxTiles, &nb.getBlockCenters().getDevicePointer(), &nb.getInteractingAtoms().getDevicePointer(),
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);
......@@ -1577,7 +1616,7 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
cu.executeKernel(pmeInducedPotentialKernel, pmeInducedPotentialArgs, cu.getNumAtoms());
void* pmeRecordInducedFieldDipolesArgs[] = {&pmePhid->getDevicePointer(), &pmePhip->getDevicePointer(),
&inducedField->getDevicePointer(), &inducedFieldPolar->getDevicePointer(), cu.getInvPeriodicBoxSizePointer()};
&inducedField->getDevicePointer(), &inducedFieldPolar->getDevicePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeRecordInducedFieldDipolesKernel, pmeRecordInducedFieldDipolesArgs, cu.getNumAtoms());
bool converged = iterateDipolesByDIIS(i);
if (converged)
......@@ -1590,14 +1629,16 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
&cu.getPosq().getDevicePointer(), &covalentFlags->getDevicePointer(), &polarizationGroupFlags->getDevicePointer(),
&nb.getExclusionTiles().getDevicePointer(), &startTileIndex, &numTileIndices,
&nb.getInteractingTiles().getDevicePointer(), &nb.getInteractionCount().getDevicePointer(),
cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer(), &maxTiles, &nb.getBlockCenters().getDevicePointer(), &nb.getInteractingAtoms().getDevicePointer(),
cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
&maxTiles, &nb.getBlockCenters().getDevicePointer(), &nb.getInteractingAtoms().getDevicePointer(),
&labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(), &inducedDipole->getDevicePointer(),
&inducedDipolePolar->getDevicePointer(), &dampingAndThole->getDevicePointer()};
cu.executeKernel(electrostaticsKernel, electrostaticsArgs, numForceThreadBlocks*electrostaticsThreads, electrostaticsThreads);
void* pmeInducedForceArgs[] = {&cu.getPosq().getDevicePointer(), &cu.getForce().getDevicePointer(), &torque->getDevicePointer(),
&cu.getEnergyBuffer().getDevicePointer(), &labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(),
&fracDipoles->getDevicePointer(), &fracQuadrupoles->getDevicePointer(),
&inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), &pmePhi->getDevicePointer(), &pmePhid->getDevicePointer(),
&pmePhip->getDevicePointer(), &pmePhidp->getDevicePointer(), cu.getInvPeriodicBoxSizePointer()};
&pmePhip->getDevicePointer(), &pmePhidp->getDevicePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeInducedForceKernel, pmeInducedForceArgs, cu.getNumAtoms());
}
......@@ -1785,7 +1826,8 @@ void CudaCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextImpl&
void* computePotentialArgs[] = {&cu.getPosq().getDevicePointer(), &labFrameDipoles->getDevicePointer(),
&labFrameQuadrupoles->getDevicePointer(), &inducedDipole->getDevicePointer(), &points.getDevicePointer(),
&potential.getDevicePointer(), &numPoints, cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
&potential.getDevicePointer(), &numPoints, cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer(),
cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer()};
int blockSize = 128;
cu.executeKernel(computePotentialKernel, computePotentialArgs, numPoints, blockSize, blockSize*15*elementSize);
outputElectrostaticPotential.resize(numPoints);
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ c83f2a12
......@@ -391,6 +391,8 @@ private:
CudaArray* molecularQuadrupoles;
CudaArray* labFrameDipoles;
CudaArray* labFrameQuadrupoles;
CudaArray* fracDipoles;
CudaArray* fracQuadrupoles;
CudaArray* field;
CudaArray* fieldPolar;
CudaArray* inducedField;
......@@ -428,6 +430,7 @@ private:
CUfunction pmeGridIndexKernel, pmeSpreadFixedMultipolesKernel, pmeSpreadInducedDipolesKernel, pmeFinishSpreadChargeKernel, pmeConvolutionKernel;
CUfunction pmeFixedPotentialKernel, pmeInducedPotentialKernel, pmeFixedForceKernel, pmeInducedForceKernel, pmeRecordInducedFieldDipolesKernel, computePotentialKernel;
CUfunction recordDIISDipolesKernel, buildMatrixKernel;
CUfunction pmeTransformMultipolesKernel;
CudaCalcAmoebaGeneralizedKirkwoodForceKernel* gkKernel;
static const int PmeOrder = 5;
static const int MaxPrevDIISDipoles = 20;
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleElectrostatics.cu
View file @ c83f2a12
......@@ -65,7 +65,9 @@ extern "C" __global__ void computeElectrostatics(
const real4* __restrict__ posq, const uint2* __restrict__ covalentFlags, const unsigned int* __restrict__ polarizationGroupFlags,
const ushort2* __restrict__ exclusionTiles, unsigned int startTileIndex, unsigned int numTileIndices,
#ifdef USE_CUTOFF
const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, const real4* __restrict__ blockCenter,
const unsigned int* __restrict__ interactingAtoms,
#endif
const real* __restrict__ labFrameDipole, const real* __restrict__ labFrameQuadrupole, const real* __restrict__ inducedDipole,
const real* __restrict__ inducedDipolePolar, const float2* __restrict__ dampingAndThole) {
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleFixedField.cu
View file @ c83f2a12
......@@ -440,7 +440,9 @@ extern "C" __global__ void computeFixedField(
const uint2* __restrict__ covalentFlags, const unsigned int* __restrict__ polarizationGroupFlags, const ushort2* __restrict__ exclusionTiles,
unsigned int startTileIndex, unsigned int numTileIndices,
#ifdef USE_CUTOFF
const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, const real4* __restrict__ blockCenter,
const unsigned int* __restrict__ interactingAtoms,
#elif defined USE_GK
const real* __restrict__ bornRadii, unsigned long long* __restrict__ gkFieldBuffers,
#endif
......@@ -494,9 +496,7 @@ extern "C" __global__ void computeFixedField(
for (unsigned int j = 0; j < TILE_SIZE; j++) {
real3 delta = trimTo3(localData[tbx+j].posq-data.posq);
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
int atom2 = y*TILE_SIZE+j;
if (atom1 != atom2 && atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
......@@ -532,9 +532,7 @@ extern "C" __global__ void computeFixedField(
for (j = 0; j < TILE_SIZE; j++) {
real3 delta = trimTo3(localData[tbx+tj].posq-data.posq);
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
int atom2 = y*TILE_SIZE+tj;
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
......@@ -675,9 +673,7 @@ extern "C" __global__ void computeFixedField(
for (j = 0; j < TILE_SIZE; j++) {
real3 delta = trimTo3(localData[tbx+tj].posq-data.posq);
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
int atom2 = atomIndices[tbx+tj];
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleInducedField.cu
View file @ c83f2a12
......@@ -207,7 +207,8 @@ extern "C" __global__ void computeInducedField(
unsigned long long* __restrict__ field, unsigned long long* __restrict__ fieldPolar, const real4* __restrict__ posq, const ushort2* __restrict__ exclusionTiles,
const real* __restrict__ inducedDipole, const real* __restrict__ inducedDipolePolar, unsigned int startTileIndex, unsigned int numTileIndices,
#ifdef USE_CUTOFF
const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
#elif defined USE_GK
unsigned long long* __restrict__ fieldS, unsigned long long* __restrict__ fieldPolarS, const real* __restrict__ inducedDipoleS,
const real* __restrict__ inducedDipolePolarS, const real* __restrict__ bornRadii,
......@@ -251,9 +252,7 @@ extern "C" __global__ void computeInducedField(
for (unsigned int j = 0; j < TILE_SIZE; j++) {
real3 delta = localData[tbx+j].pos-data.pos;
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
int atom2 = y*TILE_SIZE+j;
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS)
......@@ -273,9 +272,7 @@ extern "C" __global__ void computeInducedField(
for (unsigned int j = 0; j < TILE_SIZE; j++) {
real3 delta = localData[tbx+tj].pos-data.pos;
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
int atom2 = y*TILE_SIZE+j;
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS)
......@@ -404,9 +401,7 @@ extern "C" __global__ void computeInducedField(
for (j = 0; j < TILE_SIZE; j++) {
real3 delta = localData[tbx+tj].pos-data.pos;
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
int atom2 = atomIndices[tbx+tj];
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS)
......
plugins/amoeba/platforms/cuda/src/kernels/multipoles.cu
View file @ c83f2a12
......@@ -448,7 +448,7 @@ extern "C" __global__ void mapTorqueToForce(unsigned long long* __restrict__ for
*/
extern "C" __global__ void computePotentialAtPoints(const real4* __restrict__ posq, const real* __restrict__ labFrameDipole,
const real* __restrict__ labFrameQuadrupole, const real* __restrict__ inducedDipole, const real4* __restrict__ points,
real* __restrict__ potential, int numPoints, real4 periodicBoxSize, real4 invPeriodicBoxSize) {
real* __restrict__ potential, int numPoints, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ) {
extern __shared__ real4 localPosq[];
real3* localDipole = (real3*) &localPosq[blockDim.x];
real3* localInducedDipole = (real3*) &localDipole[blockDim.x];
......@@ -481,9 +481,7 @@ extern "C" __global__ void computePotentialAtPoints(const real4* __restrict__ po
for (int i = 0; i < end; i++) {
real3 delta = trimTo3(localPosq[i]-pointPos);
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = dot(delta, delta);
real rInv = RSQRT(r2);
......
plugins/amoeba/platforms/cuda/src/kernels/pmeMultipoleElectrostatics.cu
View file @ c83f2a12
......@@ -65,7 +65,7 @@ __device__ float computePScaleFactor(uint2 covalent, unsigned int polarizationGr
}
__device__ void computeOneInteraction(AtomData& atom1, AtomData& atom2, bool hasExclusions, float dScale, float pScale, float mScale, float forceFactor,
real& energy, real4 periodicBoxSize, real4 invPeriodicBoxSize) {
real& energy, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ) {
real4 delta;
delta.x = atom2.pos.x - atom1.pos.x;
delta.y = atom2.pos.y - atom1.pos.y;
......@@ -73,10 +73,7 @@ __device__ void computeOneInteraction(AtomData& atom1, AtomData& atom2, bool has
// periodic box
delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_DELTA(delta)
delta.w = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
if (delta.w > CUTOFF_SQUARED)
return;
......@@ -203,7 +200,9 @@ extern "C" __global__ void computeElectrostatics(
const real4* __restrict__ posq, const uint2* __restrict__ covalentFlags, const unsigned int* __restrict__ polarizationGroupFlags,
const ushort2* __restrict__ exclusionTiles, unsigned int startTileIndex, unsigned int numTileIndices,
#ifdef USE_CUTOFF
const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const real4* __restrict__ blockCenter, const unsigned int* __restrict__ interactingAtoms,
const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, const real4* __restrict__ blockCenter,
const unsigned int* __restrict__ interactingAtoms,
#endif
const real* __restrict__ labFrameDipole, const real* __restrict__ labFrameQuadrupole, const real* __restrict__ inducedDipole,
const real* __restrict__ inducedDipolePolar, const float2* __restrict__ dampingAndThole) {
......@@ -255,7 +254,7 @@ extern "C" __global__ void computeElectrostatics(
float d = computeDScaleFactor(polarizationGroup, j);
float p = computePScaleFactor(covalent, polarizationGroup, j);
float m = computeMScaleFactor(covalent, j);
computeOneInteraction(data, localData[tbx+j], true, d, p, m, 0.5f, energy, periodicBoxSize, invPeriodicBoxSize);
computeOneInteraction(data, localData[tbx+j], true, d, p, m, 0.5f, energy, periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);
}
}
if (atom1 < NUM_ATOMS)
......@@ -283,7 +282,7 @@ extern "C" __global__ void computeElectrostatics(
float d = computeDScaleFactor(polarizationGroup, tj);
float p = computePScaleFactor(covalent, polarizationGroup, tj);
float m = computeMScaleFactor(covalent, tj);
computeOneInteraction(data, localData[tbx+tj], true, d, p, m, 1, energy, periodicBoxSize, invPeriodicBoxSize);
computeOneInteraction(data, localData[tbx+tj], true, d, p, m, 1, energy, periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);
}
tj = (tj + 1) & (TILE_SIZE - 1);
}
......@@ -386,7 +385,7 @@ extern "C" __global__ void computeElectrostatics(
for (j = 0; j < TILE_SIZE; j++) {
int atom2 = atomIndices[tbx+tj];
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
computeOneInteraction(data, localData[tbx+tj], false, 1, 1, 1, 1, energy, periodicBoxSize, invPeriodicBoxSize);
computeOneInteraction(data, localData[tbx+tj], false, 1, 1, 1, 1, energy, periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);
}
tj = (tj + 1) & (TILE_SIZE - 1);
}
......
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