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Commit 47fe6d40 authored by Peter Eastman's avatar Peter Eastman
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Optimizations to AMOEBA PME

parent e38c6907
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Showing with 121 additions and 182 deletions
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 47fe6d40
......@@ -822,7 +822,7 @@ CudaCalcAmoebaMultipoleForceKernel::CudaCalcAmoebaMultipoleForceKernel(std::stri
inducedDipoleFieldGradientGk(NULL), inducedDipoleFieldGradientGkPolar(NULL), extrapolatedDipoleFieldGradient(NULL), extrapolatedDipoleFieldGradientPolar(NULL),
extrapolatedDipoleFieldGradientGk(NULL), extrapolatedDipoleFieldGradientGkPolar(NULL), covalentFlags(NULL), polarizationGroupFlags(NULL),
pmeGrid(NULL), pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeIgrid(NULL), pmePhi(NULL),
pmePhid(NULL), pmePhip(NULL), pmePhidp(NULL), pmeCphi(NULL), pmeAtomGridIndex(NULL), lastPositions(NULL), sort(NULL), gkKernel(NULL) {
pmePhid(NULL), pmePhip(NULL), pmePhidp(NULL), pmeCphi(NULL), lastPositions(NULL), sort(NULL), gkKernel(NULL) {
}
CudaCalcAmoebaMultipoleForceKernel::~CudaCalcAmoebaMultipoleForceKernel() {
......@@ -927,8 +927,6 @@ CudaCalcAmoebaMultipoleForceKernel::~CudaCalcAmoebaMultipoleForceKernel() {
delete pmePhidp;
if (pmeCphi != NULL)
delete pmeCphi;
if (pmeAtomGridIndex != NULL)
delete pmeAtomGridIndex;
if (lastPositions != NULL)
delete lastPositions;
if (sort != NULL)
......@@ -1253,7 +1251,6 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
else if (polarizationType == AmoebaMultipoleForce::Extrapolated)
pmeDefines["EXTRAPOLATED_POLARIZATION"] = "";
CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaAmoebaKernelSources::multipolePme, pmeDefines);
pmeGridIndexKernel = cu.getKernel(module, "findAtomGridIndex");
pmeTransformMultipolesKernel = cu.getKernel(module, "transformMultipolesToFractionalCoordinates");
pmeTransformPotentialKernel = cu.getKernel(module, "transformPotentialToCartesianCoordinates");
pmeSpreadFixedMultipolesKernel = cu.getKernel(module, "gridSpreadFixedMultipoles");
......@@ -1285,7 +1282,6 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
pmePhidp = new CudaArray(cu, 20*numMultipoles, elementSize, "pmePhidp");
pmeCphi = new CudaArray(cu, 10*numMultipoles, elementSize, "pmeCphi");
pmeAtomRange = CudaArray::create<int>(cu, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
pmeAtomGridIndex = CudaArray::create<int2>(cu, numMultipoles, "pmeAtomGridIndex");
sort = new CudaSort(cu, new SortTrait(), cu.getNumAtoms());
cufftResult result = cufftPlan3d(&fft, gridSizeX, gridSizeY, gridSizeZ, cu.getUseDoublePrecision() ? CUFFT_Z2Z : CUFFT_C2C);
if (result != CUFFT_SUCCESS)
......@@ -1569,16 +1565,11 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
// Reciprocal space calculation.
unsigned int maxTiles = nb.getInteractingTiles().getSize();
void* gridIndexArgs[] = {&cu.getPosq().getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(),
cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeGridIndexKernel, gridIndexArgs, cu.getNumAtoms(), cu.ThreadBlockSize, cu.ThreadBlockSize*PmeOrder*PmeOrder*elementSize);
sort->sort(*pmeAtomGridIndex);
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.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
&pmeGrid->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeSpreadFixedMultipolesKernel, pmeSpreadFixedMultipolesArgs, cu.getNumAtoms());
void* finishSpreadArgs[] = {&pmeGrid->getDevicePointer()};
......@@ -1590,7 +1581,7 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_FORWARD);
void* pmeConvolutionArgs[] = {&pmeGrid->getDevicePointer(), &pmeBsplineModuliX->getDevicePointer(), &pmeBsplineModuliY->getDevicePointer(),
&pmeBsplineModuliZ->getDevicePointer(), cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, cu.getNumAtoms());
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, gridSizeX*gridSizeY*gridSizeZ, 256);
if (cu.getUseDoublePrecision())
cufftExecZ2Z(fft, (double2*) pmeGrid->getDevicePointer(), (double2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
else
......@@ -1598,7 +1589,7 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
void* pmeFixedPotentialArgs[] = {&pmeGrid->getDevicePointer(), &pmePhi->getDevicePointer(), &field->getDevicePointer(),
&fieldPolar ->getDevicePointer(), &cu.getPosq().getDevicePointer(), &labFrameDipoles->getDevicePointer(),
cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2], &pmeAtomGridIndex->getDevicePointer()};
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeFixedPotentialKernel, pmeFixedPotentialArgs, cu.getNumAtoms());
void* pmeTransformFixedPotentialArgs[] = {&pmePhi->getDevicePointer(), &pmeCphi->getDevicePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeTransformPotentialKernel, pmeTransformFixedPotentialArgs, cu.getNumAtoms());
......@@ -1625,7 +1616,7 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
cu.clearBuffer(*pmeGrid);
void* pmeSpreadInducedDipolesArgs[] = {&cu.getPosq().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(),
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
&pmeGrid->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeSpreadInducedDipolesKernel, pmeSpreadInducedDipolesArgs, cu.getNumAtoms());
if (cu.getUseDoublePrecision())
......@@ -1634,15 +1625,14 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
cufftExecZ2Z(fft, (double2*) pmeGrid->getDevicePointer(), (double2*) pmeGrid->getDevicePointer(), CUFFT_FORWARD);
else
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_FORWARD);
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, cu.getNumAtoms());
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, gridSizeX*gridSizeY*gridSizeZ, 256);
if (cu.getUseDoublePrecision())
cufftExecZ2Z(fft, (double2*) pmeGrid->getDevicePointer(), (double2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
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.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(),
cu.getPeriodicBoxVecZPointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2],
&pmeAtomGridIndex->getDevicePointer()};
cu.getPeriodicBoxVecZPointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeInducedPotentialKernel, pmeInducedPotentialArgs, cu.getNumAtoms());
// Iterate until the dipoles converge.
......@@ -1771,7 +1761,7 @@ void CudaCalcAmoebaMultipoleForceKernel::computeInducedField(void** recipBoxVect
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(),
&pmeGrid->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeSpreadInducedDipolesKernel, pmeSpreadInducedDipolesArgs, cu.getNumAtoms());
if (cu.getUseDoublePrecision()) {
......@@ -1784,15 +1774,14 @@ void CudaCalcAmoebaMultipoleForceKernel::computeInducedField(void** recipBoxVect
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_FORWARD);
void* pmeConvolutionArgs[] = {&pmeGrid->getDevicePointer(), &pmeBsplineModuliX->getDevicePointer(), &pmeBsplineModuliY->getDevicePointer(),
&pmeBsplineModuliZ->getDevicePointer(), cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, cu.getNumAtoms());
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, gridSizeX*gridSizeY*gridSizeZ, 256);
if (cu.getUseDoublePrecision())
cufftExecZ2Z(fft, (double2*) pmeGrid->getDevicePointer(), (double2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
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.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(),
cu.getPeriodicBoxVecZPointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2],
&pmeAtomGridIndex->getDevicePointer()};
cu.getPeriodicBoxVecZPointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeInducedPotentialKernel, pmeInducedPotentialArgs, cu.getNumAtoms());
if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
void* pmeRecordInducedFieldDipolesArgs[] = {&pmePhid->getDevicePointer(), &pmePhip->getDevicePointer(),
......@@ -1896,11 +1885,11 @@ bool CudaCalcAmoebaMultipoleForceKernel::iterateDipolesByDIIS(int iteration) {
void* updateInducedFieldArgs[] = {&inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(),
&prevDipoles->getDevicePointer(), &prevDipolesPolar->getDevicePointer(), &diisCoefficients->getDevicePointer(), &numPrev};
cu.executeKernel(updateInducedFieldKernel, updateInducedFieldArgs, cu.getNumThreadBlocks()*cu.ThreadBlockSize);
cu.executeKernel(updateInducedFieldKernel, updateInducedFieldArgs, 3*cu.getNumAtoms(), 256);
if (gkKernel != NULL) {
void* updateInducedFieldGkArgs[] = {&gkKernel->getInducedDipoles()->getDevicePointer(), &gkKernel->getInducedDipolesPolar()->getDevicePointer(),
&prevDipolesGk->getDevicePointer(), &prevDipolesGkPolar->getDevicePointer(), &diisCoefficients->getDevicePointer(), &numPrev};
cu.executeKernel(updateInducedFieldKernel, updateInducedFieldGkArgs, cu.getNumThreadBlocks()*cu.ThreadBlockSize);
cu.executeKernel(updateInducedFieldKernel, updateInducedFieldGkArgs, 3*cu.getNumAtoms(), 256);
}
return false;
}
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ 47fe6d40
......@@ -465,12 +465,11 @@ private:
CudaArray* pmePhidp;
CudaArray* pmeCphi;
CudaArray* pmeAtomRange;
CudaArray* pmeAtomGridIndex;
CudaArray* lastPositions;
CudaSort* sort;
cufftHandle fft;
CUfunction computeMomentsKernel, recordInducedDipolesKernel, computeFixedFieldKernel, computeInducedFieldKernel, updateInducedFieldKernel, electrostaticsKernel, mapTorqueKernel;
CUfunction pmeGridIndexKernel, pmeSpreadFixedMultipolesKernel, pmeSpreadInducedDipolesKernel, pmeFinishSpreadChargeKernel, pmeConvolutionKernel;
CUfunction pmeSpreadFixedMultipolesKernel, pmeSpreadInducedDipolesKernel, pmeFinishSpreadChargeKernel, pmeConvolutionKernel;
CUfunction pmeFixedPotentialKernel, pmeInducedPotentialKernel, pmeFixedForceKernel, pmeInducedForceKernel, pmeRecordInducedFieldDipolesKernel, computePotentialKernel;
CUfunction recordDIISDipolesKernel, buildMatrixKernel;
CUfunction initExtrapolatedKernel, iterateExtrapolatedKernel, computeExtrapolatedKernel, addExtrapolatedGradientKernel;
......
plugins/amoeba/platforms/cuda/src/kernels/multipolePme.cu
View file @ 47fe6d40
......@@ -69,47 +69,6 @@ __device__ void computeBSplinePoint(real4* thetai, real w, real* array) {
thetai[i-1] = make_real4(ARRAY(PME_ORDER,i), ARRAY(PME_ORDER-1,i), ARRAY(PME_ORDER-2,i), ARRAY(PME_ORDER-3,i));
}
/**
* Compute the index of the grid point each atom is associated with.
*/
extern "C" __global__ void findAtomGridIndex(const real4* __restrict__ posq, int2* __restrict__ pmeAtomGridIndex,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_ATOMS; i += blockDim.x*gridDim.x) {
real4 pos = posq[i];
pos -= periodicBoxVecZ*floor(pos.z*recipBoxVecZ.z+0.5f);
pos -= periodicBoxVecY*floor(pos.y*recipBoxVecY.z+0.5f);
pos -= periodicBoxVecX*floor(pos.x*recipBoxVecX.z+0.5f);
// First axis.
real w = pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x;
real fr = GRID_SIZE_X*(w-(int)(w+0.5f)+0.5f);
int ifr = (int) fr;
int igrid1 = ifr-PME_ORDER+1;
// Second axis.
w = pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y;
fr = GRID_SIZE_Y*(w-(int)(w+0.5f)+0.5f);
ifr = (int) fr;
int igrid2 = ifr-PME_ORDER+1;
// Third axis.
w = pos.z*recipBoxVecZ.z;
fr = GRID_SIZE_Z*(w-(int)(w+0.5f)+0.5f);
ifr = (int) fr;
int igrid3 = ifr-PME_ORDER+1;
// Record the grid point.
igrid1 += (igrid1 < 0 ? GRID_SIZE_X : 0);
igrid2 += (igrid2 < 0 ? GRID_SIZE_Y : 0);
igrid3 += (igrid3 < 0 ? GRID_SIZE_Z : 0);
pmeAtomGridIndex[i] = make_int2(i, igrid1*GRID_SIZE_Y*GRID_SIZE_Z+igrid2*GRID_SIZE_Z+igrid3);
}
}
/**
* Convert the fixed multipoles from Cartesian to fractional coordinates.
*/
......@@ -209,7 +168,7 @@ extern "C" __global__ void transformPotentialToCartesianCoordinates(const real*
}
extern "C" __global__ void gridSpreadFixedMultipoles(const real4* __restrict__ posq, const real* __restrict__ fracDipole,
const real* __restrict__ fracQuadrupole, real2* __restrict__ pmeGrid, int2* __restrict__ pmeAtomGridIndex,
const real* __restrict__ fracQuadrupole, real2* __restrict__ pmeGrid,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
#if __CUDA_ARCH__ < 500
real array[PME_ORDER*PME_ORDER];
......@@ -300,7 +259,7 @@ extern "C" __global__ void gridSpreadFixedMultipoles(const real4* __restrict__ p
}
extern "C" __global__ void gridSpreadInducedDipoles(const real4* __restrict__ posq, const real* __restrict__ inducedDipole,
const real* __restrict__ inducedDipolePolar, real2* __restrict__ pmeGrid, int2* __restrict__ pmeAtomGridIndex,
const real* __restrict__ inducedDipolePolar, real2* __restrict__ pmeGrid,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
#if __CUDA_ARCH__ < 500
real array[PME_ORDER*PME_ORDER];
......@@ -451,7 +410,7 @@ extern "C" __global__ void reciprocalConvolution(real2* __restrict__ pmeGrid, co
extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict__ pmeGrid, real* __restrict__ phi,
long long* __restrict__ fieldBuffers, long long* __restrict__ fieldPolarBuffers, const real4* __restrict__ posq,
const real* __restrict__ labFrameDipole, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ, int2* __restrict__ pmeAtomGridIndex) {
real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
#if __CUDA_ARCH__ < 500
real array[PME_ORDER*PME_ORDER];
#else
......@@ -476,11 +435,7 @@ extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict
}
__syncthreads();
// Process the atoms in spatially sorted order. This improves cache performance when loading
// the grid values.
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_ATOMS; i += blockDim.x*gridDim.x) {
int m = pmeAtomGridIndex[i].x;
for (int m = blockIdx.x*blockDim.x+threadIdx.x; m < NUM_ATOMS; m += blockDim.x*gridDim.x) {
real4 pos = posq[m];
pos -= periodicBoxVecZ*floor(pos.z*recipBoxVecZ.z+0.5f);
pos -= periodicBoxVecY*floor(pos.y*recipBoxVecY.z+0.5f);
......@@ -533,9 +488,9 @@ extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict
real tuv102 = 0;
real tuv012 = 0;
real tuv111 = 0;
for (int iz = 0; iz < PME_ORDER; iz++) {
int k = igrid3+iz-(igrid3+iz >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
real4 v = theta3[iz];
for (int ix = 0; ix < PME_ORDER; ix++) {
int i = igrid1+ix-(igrid1+ix >= GRID_SIZE_X ? GRID_SIZE_X : 0);
real4 v = theta1[ix];
real tu00 = 0;
real tu10 = 0;
real tu01 = 0;
......@@ -550,47 +505,47 @@ extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict
int j = igrid2+iy-(igrid2+iy >= GRID_SIZE_Y ? GRID_SIZE_Y : 0);
real4 u = theta2[iy];
real4 t = make_real4(0, 0, 0, 0);
for (int ix = 0; ix < PME_ORDER; ix++) {
int i = igrid1+ix-(igrid1+ix >= GRID_SIZE_X ? GRID_SIZE_X : 0);
for (int iz = 0; iz < PME_ORDER; iz++) {
int k = igrid3+iz-(igrid3+iz >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
int gridIndex = i*GRID_SIZE_Y*GRID_SIZE_Z + j*GRID_SIZE_Z + k;
real tq = pmeGrid[gridIndex].x;
real4 tadd = theta1[ix];
real4 tadd = theta3[iz];
t.x += tq*tadd.x;
t.y += tq*tadd.y;
t.z += tq*tadd.z;
t.w += tq*tadd.w;
}
tu00 += t.x*u.x;
tu10 += t.y*u.x;
tu01 += t.x*u.y;
tu20 += t.z*u.x;
tu11 += t.y*u.y;
tu02 += t.x*u.z;
tu30 += t.w*u.x;
tu21 += t.z*u.y;
tu12 += t.y*u.z;
tu03 += t.x*u.w;
tu00 += u.x*t.x;
tu10 += u.y*t.x;
tu01 += u.x*t.y;
tu20 += u.z*t.x;
tu11 += u.y*t.y;
tu02 += u.x*t.z;
tu30 += u.w*t.x;
tu21 += u.z*t.y;
tu12 += u.y*t.z;
tu03 += u.x*t.w;
}
tuv000 += tu00*v.x;
tuv100 += tu10*v.x;
tuv010 += tu01*v.x;
tuv001 += tu00*v.y;
tuv200 += tu20*v.x;
tuv020 += tu02*v.x;
tuv002 += tu00*v.z;
tuv110 += tu11*v.x;
tuv101 += tu10*v.y;
tuv011 += tu01*v.y;
tuv300 += tu30*v.x;
tuv030 += tu03*v.x;
tuv003 += tu00*v.w;
tuv210 += tu21*v.x;
tuv201 += tu20*v.y;
tuv120 += tu12*v.x;
tuv021 += tu02*v.y;
tuv102 += tu10*v.z;
tuv012 += tu01*v.z;
tuv111 += tu11*v.y;
tuv000 += v.x*tu00;
tuv100 += v.y*tu00;
tuv010 += v.x*tu10;
tuv001 += v.x*tu01;
tuv200 += v.z*tu00;
tuv020 += v.x*tu20;
tuv002 += v.x*tu02;
tuv110 += v.y*tu10;
tuv101 += v.y*tu01;
tuv011 += v.x*tu11;
tuv300 += v.w*tu00;
tuv030 += v.x*tu30;
tuv003 += v.x*tu03;
tuv210 += v.z*tu10;
tuv201 += v.z*tu01;
tuv120 += v.y*tu20;
tuv021 += v.x*tu21;
tuv102 += v.y*tu02;
tuv012 += v.x*tu12;
tuv111 += v.y*tu11;
}
phi[m] = tuv000;
phi[m+NUM_ATOMS] = tuv100;
......@@ -628,7 +583,7 @@ extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict
extern "C" __global__ void computeInducedPotentialFromGrid(const real2* __restrict__ pmeGrid, real* __restrict__ phid,
real* __restrict__ phip, real* __restrict__ phidp, const real4* __restrict__ posq,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real3 recipBoxVecX,
real3 recipBoxVecY, real3 recipBoxVecZ, int2* __restrict__ pmeAtomGridIndex) {
real3 recipBoxVecY, real3 recipBoxVecZ) {
#if __CUDA_ARCH__ < 500
real array[PME_ORDER*PME_ORDER];
#else
......@@ -640,11 +595,7 @@ extern "C" __global__ void computeInducedPotentialFromGrid(const real2* __restri
real4 theta2[PME_ORDER];
real4 theta3[PME_ORDER];
// Process the atoms in spatially sorted order. This improves cache performance when loading
// the grid values.
for (int atom = blockIdx.x*blockDim.x+threadIdx.x; atom < NUM_ATOMS; atom += blockDim.x*gridDim.x) {
int m = pmeAtomGridIndex[atom].x;
for (int m = blockIdx.x*blockDim.x+threadIdx.x; m < NUM_ATOMS; m += blockDim.x*gridDim.x) {
real4 pos = posq[m];
pos -= periodicBoxVecZ*floor(pos.z*recipBoxVecZ.z+0.5f);
pos -= periodicBoxVecY*floor(pos.y*recipBoxVecY.z+0.5f);
......@@ -715,9 +666,9 @@ extern "C" __global__ void computeInducedPotentialFromGrid(const real2* __restri
real tuv102 = 0;
real tuv012 = 0;
real tuv111 = 0;
for (int iz = 0; iz < PME_ORDER; iz++) {
int k = igrid3+iz-(igrid3+iz >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
real4 v = theta3[iz];
for (int ix = 0; ix < PME_ORDER; ix++) {
int i = igrid1+ix-(igrid1+ix >= GRID_SIZE_X ? GRID_SIZE_X : 0);
real4 v = theta1[ix];
real tu00_1 = 0;
real tu01_1 = 0;
real tu10_1 = 0;
......@@ -750,11 +701,11 @@ extern "C" __global__ void computeInducedPotentialFromGrid(const real2* __restri
real t1_2 = 0;
real t2_2 = 0;
real t3 = 0;
for (int ix = 0; ix < PME_ORDER; ix++) {
int i = igrid1+ix-(igrid1+ix >= GRID_SIZE_X ? GRID_SIZE_X : 0);
for (int iz = 0; iz < PME_ORDER; iz++) {
int k = igrid3+iz-(igrid3+iz >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
int gridIndex = i*GRID_SIZE_Y*GRID_SIZE_Z + j*GRID_SIZE_Z + k;
real2 tq = pmeGrid[gridIndex];
real4 tadd = theta1[ix];
real4 tadd = theta3[iz];
t0_1 += tq.x*tadd.x;
t1_1 += tq.x*tadd.y;
t2_1 += tq.x*tadd.z;
......@@ -763,70 +714,70 @@ extern "C" __global__ void computeInducedPotentialFromGrid(const real2* __restri
t2_2 += tq.y*tadd.z;
t3 += (tq.x+tq.y)*tadd.w;
}
tu00_1 += t0_1*u.x;
tu10_1 += t1_1*u.x;
tu01_1 += t0_1*u.y;
tu20_1 += t2_1*u.x;
tu11_1 += t1_1*u.y;
tu02_1 += t0_1*u.z;
tu00_2 += t0_2*u.x;
tu10_2 += t1_2*u.x;
tu01_2 += t0_2*u.y;
tu20_2 += t2_2*u.x;
tu11_2 += t1_2*u.y;
tu02_2 += t0_2*u.z;
tu00_1 += u.x*t0_1;
tu10_1 += u.y*t0_1;
tu01_1 += u.x*t1_1;
tu20_1 += u.z*t0_1;
tu11_1 += u.y*t1_1;
tu02_1 += u.x*t2_1;
tu00_2 += u.x*t0_2;
tu10_2 += u.y*t0_2;
tu01_2 += u.x*t1_2;
tu20_2 += u.z*t0_2;
tu11_2 += u.y*t1_2;
tu02_2 += u.x*t2_2;
real t0 = t0_1 + t0_2;
real t1 = t1_1 + t1_2;
real t2 = t2_1 + t2_2;
tu00 += t0*u.x;
tu10 += t1*u.x;
tu01 += t0*u.y;
tu20 += t2*u.x;
tu11 += t1*u.y;
tu02 += t0*u.z;
tu30 += t3*u.x;
tu21 += t2*u.y;
tu12 += t1*u.z;
tu03 += t0*u.w;
tu00 += u.x*t0;
tu10 += u.y*t0;
tu01 += u.x*t1;
tu20 += u.z*t0;
tu11 += u.y*t1;
tu02 += u.x*t2;
tu30 += u.w*t0;
tu21 += u.z*t1;
tu12 += u.y*t2;
tu03 += u.x*t3;
}
tuv100_1 += tu10_1*v.x;
tuv010_1 += tu01_1*v.x;
tuv001_1 += tu00_1*v.y;
tuv200_1 += tu20_1*v.x;
tuv020_1 += tu02_1*v.x;
tuv002_1 += tu00_1*v.z;
tuv110_1 += tu11_1*v.x;
tuv101_1 += tu10_1*v.y;
tuv011_1 += tu01_1*v.y;
tuv100_2 += tu10_2*v.x;
tuv010_2 += tu01_2*v.x;
tuv001_2 += tu00_2*v.y;
tuv200_2 += tu20_2*v.x;
tuv020_2 += tu02_2*v.x;
tuv002_2 += tu00_2*v.z;
tuv110_2 += tu11_2*v.x;
tuv101_2 += tu10_2*v.y;
tuv011_2 += tu01_2*v.y;
tuv000 += tu00*v.x;
tuv100 += tu10*v.x;
tuv010 += tu01*v.x;
tuv001 += tu00*v.y;
tuv200 += tu20*v.x;
tuv020 += tu02*v.x;
tuv002 += tu00*v.z;
tuv110 += tu11*v.x;
tuv101 += tu10*v.y;
tuv011 += tu01*v.y;
tuv300 += tu30*v.x;
tuv030 += tu03*v.x;
tuv003 += tu00*v.w;
tuv210 += tu21*v.x;
tuv201 += tu20*v.y;
tuv120 += tu12*v.x;
tuv021 += tu02*v.y;
tuv102 += tu10*v.z;
tuv012 += tu01*v.z;
tuv111 += tu11*v.y;
tuv100_1 += v.y*tu00_1;
tuv010_1 += v.x*tu10_1;
tuv001_1 += v.x*tu01_1;
tuv200_1 += v.z*tu00_1;
tuv020_1 += v.x*tu20_1;
tuv002_1 += v.x*tu02_1;
tuv110_1 += v.y*tu10_1;
tuv101_1 += v.y*tu01_1;
tuv011_1 += v.x*tu11_1;
tuv100_2 += v.y*tu00_2;
tuv010_2 += v.x*tu10_2;
tuv001_2 += v.x*tu01_2;
tuv200_2 += v.z*tu00_2;
tuv020_2 += v.x*tu20_2;
tuv002_2 += v.x*tu02_2;
tuv110_2 += v.y*tu10_2;
tuv101_2 += v.y*tu01_2;
tuv011_2 += v.x*tu11_2;
tuv000 += v.x*tu00;
tuv100 += v.y*tu00;
tuv010 += v.x*tu10;
tuv001 += v.x*tu01;
tuv200 += v.z*tu00;
tuv020 += v.x*tu20;
tuv002 += v.x*tu02;
tuv110 += v.y*tu10;
tuv101 += v.y*tu01;
tuv011 += v.x*tu11;
tuv300 += v.w*tu00;
tuv030 += v.x*tu30;
tuv003 += v.x*tu03;
tuv210 += v.z*tu10;
tuv201 += v.z*tu01;
tuv120 += v.y*tu20;
tuv021 += v.x*tu21;
tuv102 += v.y*tu02;
tuv012 += v.x*tu12;
tuv111 += v.y*tu11;
}
phid[m] = 0;
phid[m+NUM_ATOMS] = tuv100_1;
......
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