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Commit 3b91c945 authored by Peter Eastman's avatar Peter Eastman
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Continuing CUDA implementation of triclinic boxes for AmoebaMultipoleForce

parent c83f2a12
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plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 3b91c945
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs *
* Contributors: *
* *
......@@ -801,7 +801,7 @@ CudaCalcAmoebaMultipoleForceKernel::CudaCalcAmoebaMultipoleForceKernel(std::stri
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),
pmePhid(NULL), pmePhip(NULL), pmePhidp(NULL), pmeAtomGridIndex(NULL), lastPositions(NULL), sort(NULL), gkKernel(NULL) {
pmePhid(NULL), pmePhip(NULL), pmePhidp(NULL), pmeCphi(NULL), pmeAtomGridIndex(NULL), lastPositions(NULL), sort(NULL), gkKernel(NULL) {
}
CudaCalcAmoebaMultipoleForceKernel::~CudaCalcAmoebaMultipoleForceKernel() {
......@@ -876,6 +876,8 @@ CudaCalcAmoebaMultipoleForceKernel::~CudaCalcAmoebaMultipoleForceKernel() {
delete pmePhip;
if (pmePhidp != NULL)
delete pmePhidp;
if (pmeCphi != NULL)
delete pmeCphi;
if (pmeAtomGridIndex != NULL)
delete pmeAtomGridIndex;
if (lastPositions != NULL)
......@@ -1192,6 +1194,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
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");
pmeSpreadInducedDipolesKernel = cu.getKernel(module, "gridSpreadInducedDipoles");
pmeFinishSpreadChargeKernel = cu.getKernel(module, "finishSpreadCharge");
......@@ -1219,6 +1222,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
pmePhid = new CudaArray(cu, 10*numMultipoles, elementSize, "pmePhid");
pmePhip = new CudaArray(cu, 10*numMultipoles, elementSize, "pmePhip");
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());
......@@ -1520,14 +1524,16 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
unsigned int maxTiles = nb.getInteractingTiles().getSize();
void* gridIndexArgs[] = {&cu.getPosq().getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(),
cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
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.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeSpreadFixedMultipolesKernel, pmeSpreadFixedMultipolesArgs, cu.getNumAtoms());
void* finishSpreadArgs[] = {&pmeGrid->getDevicePointer()};
if (cu.getUseDoublePrecision())
......@@ -1547,9 +1553,11 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
&fieldPolar ->getDevicePointer(), &cu.getPosq().getDevicePointer(), &labFrameDipoles->getDevicePointer(),
cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2], &pmeAtomGridIndex->getDevicePointer()};
cu.executeKernel(pmeFixedPotentialKernel, pmeFixedPotentialArgs, cu.getNumAtoms());
void* pmeTransformFixedPotentialArgs[] = {&pmePhi->getDevicePointer(), &pmeCphi->getDevicePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeTransformPotentialKernel, pmeTransformFixedPotentialArgs, cu.getNumAtoms());
void* pmeFixedForceArgs[] = {&cu.getPosq().getDevicePointer(), &cu.getForce().getDevicePointer(), &torque->getDevicePointer(),
&cu.getEnergyBuffer().getDevicePointer(), &labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(),
&fracDipoles->getDevicePointer(), &fracQuadrupoles->getDevicePointer(), &pmePhi->getDevicePointer(),
&fracDipoles->getDevicePointer(), &fracQuadrupoles->getDevicePointer(), &pmePhi->getDevicePointer(), &pmeCphi->getDevicePointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeFixedForceKernel, pmeFixedForceArgs, cu.getNumAtoms());
......@@ -1570,7 +1578,8 @@ 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(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeSpreadInducedDipolesKernel, pmeSpreadInducedDipolesArgs, cu.getNumAtoms());
if (cu.getUseDoublePrecision())
cu.executeKernel(pmeFinishSpreadChargeKernel, finishSpreadArgs, pmeGrid->getSize());
......@@ -1634,11 +1643,13 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
&labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(), &inducedDipole->getDevicePointer(),
&inducedDipolePolar->getDevicePointer(), &dampingAndThole->getDevicePointer()};
cu.executeKernel(electrostaticsKernel, electrostaticsArgs, numForceThreadBlocks*electrostaticsThreads, electrostaticsThreads);
void* pmeTransformInducedPotentialArgs[] = {&pmePhidp->getDevicePointer(), &pmeCphi->getDevicePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeTransformPotentialKernel, pmeTransformInducedPotentialArgs, cu.getNumAtoms());
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(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
&pmePhip->getDevicePointer(), &pmePhidp->getDevicePointer(), &pmeCphi->getDevicePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeInducedForceKernel, pmeInducedForceArgs, cu.getNumAtoms());
}
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ 3b91c945
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -421,6 +421,7 @@ private:
CudaArray* pmePhid;
CudaArray* pmePhip;
CudaArray* pmePhidp;
CudaArray* pmeCphi;
CudaArray* pmeAtomRange;
CudaArray* pmeAtomGridIndex;
CudaArray* lastPositions;
......@@ -430,7 +431,7 @@ private:
CUfunction pmeGridIndexKernel, pmeSpreadFixedMultipolesKernel, pmeSpreadInducedDipolesKernel, pmeFinishSpreadChargeKernel, pmeConvolutionKernel;
CUfunction pmeFixedPotentialKernel, pmeInducedPotentialKernel, pmeFixedForceKernel, pmeInducedForceKernel, pmeRecordInducedFieldDipolesKernel, computePotentialKernel;
CUfunction recordDIISDipolesKernel, buildMatrixKernel;
CUfunction pmeTransformMultipolesKernel;
CUfunction pmeTransformMultipolesKernel, pmeTransformPotentialKernel;
CudaCalcAmoebaGeneralizedKirkwoodForceKernel* gkKernel;
static const int PmeOrder = 5;
static const int MaxPrevDIISDipoles = 20;
......
plugins/amoeba/platforms/cuda/src/kernels/multipolePme.cu
View file @ 3b91c945
......@@ -73,12 +73,12 @@ __device__ void computeBSplinePoint(real4* thetai, real w, real* array) {
* 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 periodicBoxSize, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
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.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
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.
......@@ -109,6 +109,7 @@ extern "C" __global__ void findAtomGridIndex(const real4* __restrict__ posq, int
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.
*/
......@@ -161,9 +162,55 @@ extern "C" __global__ void transformMultipolesToFractionalCoordinates(const real
}
}
/**
* Convert the potential from fractional to Cartesian coordinates.
*/
extern "C" __global__ void transformPotentialToCartesianCoordinates(const real* __restrict__ fphi, real* __restrict__ cphi, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
// Build matrices for transforming the potential.
__shared__ real a[3][3];
if (threadIdx.x == 0) {
a[0][0] = GRID_SIZE_X*recipBoxVecX.x;
a[1][0] = GRID_SIZE_X*recipBoxVecY.x;
a[2][0] = GRID_SIZE_X*recipBoxVecZ.x;
a[0][1] = GRID_SIZE_Y*recipBoxVecX.y;
a[1][1] = GRID_SIZE_Y*recipBoxVecY.y;
a[2][1] = GRID_SIZE_Y*recipBoxVecZ.y;
a[0][2] = GRID_SIZE_Z*recipBoxVecX.z;
a[1][2] = GRID_SIZE_Z*recipBoxVecY.z;
a[2][2] = GRID_SIZE_Z*recipBoxVecZ.z;
}
__syncthreads();
int index1[] = {0, 1, 2, 0, 0, 1};
int index2[] = {0, 1, 2, 1, 2, 2};
__shared__ real b[6][6];
if (threadIdx.x < 36) {
int i = threadIdx.x/6;
int j = threadIdx.x-6*i;
b[i][j] = a[index1[i]][index1[j]]*a[index2[i]][index2[j]];
if (index1[i] != index2[i])
b[i][j] += (i < 3 ? b[i][j] : a[index1[i]][index2[j]]*a[index2[i]][index1[j]]);
}
__syncthreads();
// Transform the potential.
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_ATOMS; i += blockDim.x*gridDim.x) {
cphi[10*i] = fphi[20*i];
cphi[10*i+1] = a[0][0]*fphi[20*i+1] + a[0][1]*fphi[20*i+2] + a[0][2]*fphi[20*i+3];
cphi[10*i+2] = a[1][0]*fphi[20*i+1] + a[1][1]*fphi[20*i+2] + a[1][2]*fphi[20*i+3];
cphi[10*i+3] = a[2][0]*fphi[20*i+1] + a[2][1]*fphi[20*i+2] + a[2][2]*fphi[20*i+3];
for (int j = 0; j < 6; j++) {
cphi[10*i+4+j] = 0;
for (int k = 0; k < 6; k++)
cphi[10*i+4+j] += b[j][k]*fphi[20*i+4+k];
}
}
}
extern "C" __global__ void gridSpreadFixedMultipoles(const real4* __restrict__ posq, const real* __restrict__ fracDipole,
const real* __restrict__ fracQuadrupole, real2* __restrict__ pmeGrid, int2* __restrict__ pmeAtomGridIndex,
real4 periodicBoxSize, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
real array[PME_ORDER*PME_ORDER];
real4 theta1[PME_ORDER];
real4 theta2[PME_ORDER];
......@@ -175,28 +222,28 @@ extern "C" __global__ void gridSpreadFixedMultipoles(const real4* __restrict__ p
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_ATOMS; i += blockDim.x*gridDim.x) {
int m = pmeAtomGridIndex[i].x;
real4 pos = posq[m];
pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
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);
// Since we need the full set of thetas, it's faster to compute them here than load them
// from global memory.
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 ifr = (int) floor(fr);
w = fr - ifr;
int igrid1 = ifr-PME_ORDER+1;
computeBSplinePoint(theta1, w, array);
w = pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y;
fr = GRID_SIZE_Y*(w-(int)(w+0.5f)+0.5f);
ifr = (int) fr;
ifr = (int) floor(fr);
w = fr - ifr;
int igrid2 = ifr-PME_ORDER+1;
computeBSplinePoint(theta2, w, array);
w = pos.z*recipBoxVecZ.z;
fr = GRID_SIZE_Z*(w-(int)(w+0.5f)+0.5f);
ifr = (int) fr;
ifr = (int) floor(fr);
w = fr - ifr;
int igrid3 = ifr-PME_ORDER+1;
computeBSplinePoint(theta3, w, array);
......@@ -252,14 +299,24 @@ 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,
real4 periodicBoxSize, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
const real xscale = GRID_SIZE_X*recipBoxVecX.x;
const real yscale = GRID_SIZE_Y*recipBoxVecY.y;
const real zscale = GRID_SIZE_Z*recipBoxVecZ.z;
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
real array[PME_ORDER*PME_ORDER];
real4 theta1[PME_ORDER];
real4 theta2[PME_ORDER];
real4 theta3[PME_ORDER];
__shared__ real cartToFrac[3][3];
if (threadIdx.x == 0) {
cartToFrac[0][0] = GRID_SIZE_X*recipBoxVecX.x;
cartToFrac[0][1] = GRID_SIZE_X*recipBoxVecY.x;
cartToFrac[0][2] = GRID_SIZE_X*recipBoxVecZ.x;
cartToFrac[1][0] = GRID_SIZE_Y*recipBoxVecX.y;
cartToFrac[1][1] = GRID_SIZE_Y*recipBoxVecY.y;
cartToFrac[1][2] = GRID_SIZE_Y*recipBoxVecZ.y;
cartToFrac[2][0] = GRID_SIZE_Z*recipBoxVecX.z;
cartToFrac[2][1] = GRID_SIZE_Z*recipBoxVecY.z;
cartToFrac[2][2] = GRID_SIZE_Z*recipBoxVecZ.z;
}
__syncthreads();
// Process the atoms in spatially sorted order. This improves cache performance when loading
// the grid values.
......@@ -267,28 +324,28 @@ extern "C" __global__ void gridSpreadInducedDipoles(const real4* __restrict__ po
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_ATOMS; i += blockDim.x*gridDim.x) {
int m = pmeAtomGridIndex[i].x;
real4 pos = posq[m];
pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
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);
// Since we need the full set of thetas, it's faster to compute them here than load them
// from global memory.
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 ifr = (int) floor(fr);
w = fr - ifr;
int igrid1 = ifr-PME_ORDER+1;
computeBSplinePoint(theta1, w, array);
w = pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y;
fr = GRID_SIZE_Y*(w-(int)(w+0.5f)+0.5f);
ifr = (int) fr;
ifr = (int) floor(fr);
w = fr - ifr;
int igrid2 = ifr-PME_ORDER+1;
computeBSplinePoint(theta2, w, array);
w = pos.z*recipBoxVecZ.z;
fr = GRID_SIZE_Z*(w-(int)(w+0.5f)+0.5f);
ifr = (int) fr;
ifr = (int) floor(fr);
w = fr - ifr;
int igrid3 = ifr-PME_ORDER+1;
computeBSplinePoint(theta3, w, array);
......@@ -316,16 +373,18 @@ extern "C" __global__ void gridSpreadInducedDipoles(const real4* __restrict__ po
int index = ybase + zindex;
real4 v = theta3[iz];
real inducedDipoleX = xscale*inducedDipole[m*3];
real inducedDipoleY = yscale*inducedDipole[m*3+1];
real inducedDipoleZ = zscale*inducedDipole[m*3+2];
real inducedDipolePolarX = xscale*inducedDipolePolar[m*3];
real inducedDipolePolarY = yscale*inducedDipolePolar[m*3+1];
real inducedDipolePolarZ = zscale*inducedDipolePolar[m*3+2];
real term01 = inducedDipoleY*u.y*v.x + inducedDipoleZ*u.x*v.y;
real term11 = inducedDipoleX*u.x*v.x;
real term02 = inducedDipolePolarY*u.y*v.x + inducedDipolePolarZ*u.x*v.y;
real term12 = inducedDipolePolarX*u.x*v.x;
real3 cinducedDipole = make_real3(inducedDipole[m*3], inducedDipole[m*3+1], inducedDipole[m*3+2]);
real3 cinducedDipolePolar = make_real3(inducedDipolePolar[m*3], inducedDipolePolar[m*3+1], inducedDipolePolar[m*3+2]);
real3 finducedDipole = make_real3(cinducedDipole.x*cartToFrac[0][0] + cinducedDipole.y*cartToFrac[0][1] + cinducedDipole.z*cartToFrac[0][2],
cinducedDipole.x*cartToFrac[1][0] + cinducedDipole.y*cartToFrac[1][1] + cinducedDipole.z*cartToFrac[1][2],
cinducedDipole.x*cartToFrac[2][0] + cinducedDipole.y*cartToFrac[2][1] + cinducedDipole.z*cartToFrac[2][2]);
real3 finducedDipolePolar = make_real3(cinducedDipolePolar.x*cartToFrac[0][0] + cinducedDipolePolar.y*cartToFrac[0][1] + cinducedDipolePolar.z*cartToFrac[0][2],
cinducedDipolePolar.x*cartToFrac[1][0] + cinducedDipolePolar.y*cartToFrac[1][1] + cinducedDipolePolar.z*cartToFrac[1][2],
cinducedDipolePolar.x*cartToFrac[2][0] + cinducedDipolePolar.y*cartToFrac[2][1] + cinducedDipolePolar.z*cartToFrac[2][2]);
real term01 = finducedDipole.y*u.y*v.x + finducedDipole.z*u.x*v.y;
real term11 = finducedDipole.x*u.x*v.x;
real term02 = finducedDipolePolar.y*u.y*v.x + finducedDipolePolar.z*u.x*v.y;
real term12 = finducedDipolePolar.x*u.x*v.x;
real add1 = term01*t.x + term11*t.y;
real add2 = term02*t.x + term12*t.y;
#ifdef USE_DOUBLE_PRECISION
......@@ -392,6 +451,19 @@ extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict
real4 theta1[PME_ORDER];
real4 theta2[PME_ORDER];
real4 theta3[PME_ORDER];
__shared__ real fracToCart[3][3];
if (threadIdx.x == 0) {
fracToCart[0][0] = GRID_SIZE_X*recipBoxVecX.x;
fracToCart[1][0] = GRID_SIZE_X*recipBoxVecY.x;
fracToCart[2][0] = GRID_SIZE_X*recipBoxVecZ.x;
fracToCart[0][1] = GRID_SIZE_Y*recipBoxVecX.y;
fracToCart[1][1] = GRID_SIZE_Y*recipBoxVecY.y;
fracToCart[2][1] = GRID_SIZE_Y*recipBoxVecZ.y;
fracToCart[0][2] = GRID_SIZE_Z*recipBoxVecX.z;
fracToCart[1][2] = GRID_SIZE_Z*recipBoxVecY.z;
fracToCart[2][2] = GRID_SIZE_Z*recipBoxVecZ.z;
}
__syncthreads();
// Process the atoms in spatially sorted order. This improves cache performance when loading
// the grid values.
......@@ -530,13 +602,13 @@ extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict
phi[20*m+18] = tuv012;
phi[20*m+19] = tuv111;
real dipoleScale = (4/(real) 3)*(EWALD_ALPHA*EWALD_ALPHA*EWALD_ALPHA)/SQRT_PI;
long long fieldx = (long long) ((dipoleScale*labFrameDipole[m*3]-GRID_SIZE_X*recipBoxVecX.x*tuv100)*0x100000000);
long long fieldx = (long long) ((dipoleScale*labFrameDipole[m*3]-tuv100*fracToCart[0][0]-tuv010*fracToCart[0][1]-tuv001*fracToCart[0][2])*0x100000000);
fieldBuffers[m] = fieldx;
fieldPolarBuffers[m] = fieldx;
long long fieldy = (long long) ((dipoleScale*labFrameDipole[m*3+1]-GRID_SIZE_Y*recipBoxVecY.y*tuv010)*0x100000000);
long long fieldy = (long long) ((dipoleScale*labFrameDipole[m*3+1]-tuv100*fracToCart[1][0]-tuv010*fracToCart[1][1]-tuv001*fracToCart[1][2])*0x100000000);
fieldBuffers[m+PADDED_NUM_ATOMS] = fieldy;
fieldPolarBuffers[m+PADDED_NUM_ATOMS] = fieldy;
long long fieldz = (long long) ((dipoleScale*labFrameDipole[m*3+2]-GRID_SIZE_Z*recipBoxVecZ.z*tuv001)*0x100000000);
long long fieldz = (long long) ((dipoleScale*labFrameDipole[m*3+2]-tuv100*fracToCart[2][0]-tuv010*fracToCart[2][1]-tuv001*fracToCart[2][2])*0x100000000);
fieldBuffers[m+2*PADDED_NUM_ATOMS] = fieldz;
fieldPolarBuffers[m+2*PADDED_NUM_ATOMS] = fieldz;
}
......@@ -786,14 +858,11 @@ extern "C" __global__ void computeInducedPotentialFromGrid(const real2* __restri
extern "C" __global__ void computeFixedMultipoleForceAndEnergy(real4* __restrict__ posq, unsigned long long* __restrict__ forceBuffers,
long long* __restrict__ torqueBuffers, real* __restrict__ energyBuffer, const real* __restrict__ labFrameDipole,
const real* __restrict__ labFrameQuadrupole, const real* __restrict__ fracDipole, const real* __restrict__ fracQuadrupole,
const real* __restrict__ phi_global, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
const real* __restrict__ phi_global, const real* __restrict__ cphi_global, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
real multipole[10];
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};
const real xscale = GRID_SIZE_X*recipBoxVecX.x;
const real yscale = GRID_SIZE_Y*recipBoxVecY.y;
const real zscale = GRID_SIZE_Z*recipBoxVecZ.z;
real energy = 0;
__shared__ real fracToCart[3][3];
if (threadIdx.x == 0) {
......@@ -822,22 +891,22 @@ extern "C" __global__ void computeFixedMultipoleForceAndEnergy(real4* __restrict
multipole[8] = 2*labFrameQuadrupole[i*5+2];
multipole[9] = 2*labFrameQuadrupole[i*5+4];
const real* phi = &phi_global[20*i];
const real* cphi = &cphi_global[10*i];
torqueBuffers[i] = (long long) (EPSILON_FACTOR*(multipole[3]*yscale*phi[2] - multipole[2]*zscale*phi[3]
+ 2*(multipole[6]-multipole[5])*yscale*zscale*phi[9]
+ multipole[8]*xscale*yscale*phi[7] + multipole[9]*yscale*yscale*phi[5]
- multipole[7]*xscale*zscale*phi[8] - multipole[9]*zscale*zscale*phi[6])*0x100000000);
torqueBuffers[i] = (long long) (EPSILON_FACTOR*(multipole[3]*cphi[2] - multipole[2]*cphi[3]
+ 2*(multipole[6]-multipole[5])*cphi[9]
+ multipole[8]*cphi[7] + multipole[9]*cphi[5]
- multipole[7]*cphi[8] - multipole[9]*cphi[6])*0x100000000);
torqueBuffers[i+PADDED_NUM_ATOMS] = (long long) (EPSILON_FACTOR*(multipole[1]*zscale*phi[3] - multipole[3]*xscale*phi[1]
+ 2*(multipole[4]-multipole[6])*xscale*zscale*phi[8]
+ multipole[7]*yscale*zscale*phi[9] + multipole[8]*zscale*zscale*phi[6]
- multipole[8]*xscale*xscale*phi[4] - multipole[9]*xscale*yscale*phi[7])*0x100000000);
torqueBuffers[i+PADDED_NUM_ATOMS] = (long long) (EPSILON_FACTOR*(multipole[1]*cphi[3] - multipole[3]*cphi[1]
+ 2*(multipole[4]-multipole[6])*cphi[8]
+ multipole[7]*cphi[9] + multipole[8]*cphi[6]
- multipole[8]*cphi[4] - multipole[9]*cphi[7])*0x100000000);
torqueBuffers[i+PADDED_NUM_ATOMS*2] = (long long) (EPSILON_FACTOR*(multipole[2]*xscale*phi[1] - multipole[1]*yscale*phi[2]
+ 2*(multipole[5]-multipole[4])*xscale*yscale*phi[7]
+ multipole[7]*xscale*xscale*phi[4] + multipole[9]*xscale*zscale*phi[8]
- multipole[7]*yscale*yscale*phi[5] - multipole[8]*yscale*zscale*phi[9])*0x100000000);
torqueBuffers[i+PADDED_NUM_ATOMS*2] = (long long) (EPSILON_FACTOR*(multipole[2]*cphi[1] - multipole[1]*cphi[2]
+ 2*(multipole[5]-multipole[4])*cphi[7]
+ multipole[7]*cphi[4] + multipole[9]*cphi[8]
- multipole[7]*cphi[5] - multipole[8]*cphi[9])*0x100000000);
// Compute the force and energy.
......@@ -851,6 +920,7 @@ extern "C" __global__ void computeFixedMultipoleForceAndEnergy(real4* __restrict
multipole[8] = fracQuadrupole[i*6+2];
multipole[9] = fracQuadrupole[i*6+4];
const real* phi = &phi_global[20*i];
real4 f = make_real4(0, 0, 0, 0);
for (int k = 0; k < 10; k++) {
energy += multipole[k]*phi[k];
......@@ -873,20 +943,13 @@ extern "C" __global__ void computeInducedDipoleForceAndEnergy(real4* __restrict_
const real* __restrict__ labFrameQuadrupole, const real* __restrict__ fracDipole, const real* __restrict__ fracQuadrupole,
const real* __restrict__ inducedDipole_global, const real* __restrict__ inducedDipolePolar_global,
const real* __restrict__ phi_global, const real* __restrict__ phid_global, const real* __restrict__ phip_global,
const real* __restrict__ phidp_global, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
const real* __restrict__ phidp_global, const real* __restrict__ cphi_global, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
real multipole[10];
real cinducedDipole[3], inducedDipole[3];
real cinducedDipolePolar[3], inducedDipolePolar[3];
real scales[3];
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};
const real xscale = GRID_SIZE_X*recipBoxVecX.x;
const real yscale = GRID_SIZE_Y*recipBoxVecY.y;
const real zscale = GRID_SIZE_Z*recipBoxVecZ.z;
scales[0] = xscale;
scales[1] = yscale;
scales[2] = zscale;
real energy = 0;
__shared__ real fracToCart[3][3];
if (threadIdx.x == 0) {
......@@ -914,22 +977,22 @@ extern "C" __global__ void computeInducedDipoleForceAndEnergy(real4* __restrict_
multipole[7] = 2*labFrameQuadrupole[i*5+1];
multipole[8] = 2*labFrameQuadrupole[i*5+2];
multipole[9] = 2*labFrameQuadrupole[i*5+4];
const real* phidp = &phidp_global[20*i];
const real* cphi = &cphi_global[10*i];
torqueBuffers[i] += (long long) (0.5f*EPSILON_FACTOR*(multipole[3]*yscale*phidp[2] - multipole[2]*zscale*phidp[3]
+ 2*(multipole[6]-multipole[5])*yscale*zscale*phidp[9]
+ multipole[8]*xscale*yscale*phidp[7] + multipole[9]*yscale*yscale*phidp[5]
- multipole[7]*xscale*zscale*phidp[8] - multipole[9]*zscale*zscale*phidp[6])*0x100000000);
torqueBuffers[i] += (long long) (0.5f*EPSILON_FACTOR*(multipole[3]*cphi[2] - multipole[2]*cphi[3]
+ 2*(multipole[6]-multipole[5])*cphi[9]
+ multipole[8]*cphi[7] + multipole[9]*cphi[5]
- multipole[7]*cphi[8] - multipole[9]*cphi[6])*0x100000000);
torqueBuffers[i+PADDED_NUM_ATOMS] += (long long) (0.5f*EPSILON_FACTOR*(multipole[1]*zscale*phidp[3] - multipole[3]*xscale*phidp[1]
+ 2*(multipole[4]-multipole[6])*xscale*zscale*phidp[8]
+ multipole[7]*yscale*zscale*phidp[9] + multipole[8]*zscale*zscale*phidp[6]
- multipole[8]*xscale*xscale*phidp[4] - multipole[9]*xscale*yscale*phidp[7])*0x100000000);
torqueBuffers[i+PADDED_NUM_ATOMS] += (long long) (0.5f*EPSILON_FACTOR*(multipole[1]*cphi[3] - multipole[3]*cphi[1]
+ 2*(multipole[4]-multipole[6])*cphi[8]
+ multipole[7]*cphi[9] + multipole[8]*cphi[6]
- multipole[8]*cphi[4] - multipole[9]*cphi[7])*0x100000000);
torqueBuffers[i+PADDED_NUM_ATOMS*2] += (long long) (0.5f*EPSILON_FACTOR*(multipole[2]*xscale*phidp[1] - multipole[1]*yscale*phidp[2]
+ 2*(multipole[5]-multipole[4])*xscale*yscale*phidp[7]
+ multipole[7]*xscale*xscale*phidp[4] + multipole[9]*xscale*zscale*phidp[8]
- multipole[7]*yscale*yscale*phidp[5] - multipole[8]*yscale*zscale*phidp[9])*0x100000000);
torqueBuffers[i+PADDED_NUM_ATOMS*2] += (long long) (0.5f*EPSILON_FACTOR*(multipole[2]*cphi[1] - multipole[1]*cphi[2]
+ 2*(multipole[5]-multipole[4])*cphi[7]
+ multipole[7]*cphi[4] + multipole[9]*cphi[8]
- multipole[7]*cphi[5] - multipole[8]*cphi[9])*0x100000000);
// Compute the force and energy.
......@@ -981,6 +1044,7 @@ extern "C" __global__ void computeInducedDipoleForceAndEnergy(real4* __restrict_
#endif
}
const real* phidp = &phidp_global[20*i];
for (int k = 0; k < 10; k++) {
f.x += multipole[k]*phidp[deriv1[k]];
f.y += multipole[k]*phidp[deriv2[k]];
......@@ -998,15 +1062,25 @@ extern "C" __global__ void computeInducedDipoleForceAndEnergy(real4* __restrict_
extern "C" __global__ void recordInducedFieldDipoles(const real* __restrict__ phid, real* const __restrict__ phip,
long long* __restrict__ inducedField, long long* __restrict__ inducedFieldPolar, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
real xscale = GRID_SIZE_X*recipBoxVecX.x*0x100000000;
real yscale = GRID_SIZE_Y*recipBoxVecY.y*0x100000000;
real zscale = GRID_SIZE_Z*recipBoxVecZ.z*0x100000000;
__shared__ real fracToCart[3][3];
if (threadIdx.x == 0) {
fracToCart[0][0] = GRID_SIZE_X*recipBoxVecX.x;
fracToCart[1][0] = GRID_SIZE_X*recipBoxVecY.x;
fracToCart[2][0] = GRID_SIZE_X*recipBoxVecZ.x;
fracToCart[0][1] = GRID_SIZE_Y*recipBoxVecX.y;
fracToCart[1][1] = GRID_SIZE_Y*recipBoxVecY.y;
fracToCart[2][1] = GRID_SIZE_Y*recipBoxVecZ.y;
fracToCart[0][2] = GRID_SIZE_Z*recipBoxVecX.z;
fracToCart[1][2] = GRID_SIZE_Z*recipBoxVecY.z;
fracToCart[2][2] = GRID_SIZE_Z*recipBoxVecZ.z;
}
__syncthreads();
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_ATOMS; i += blockDim.x*gridDim.x) {
inducedField[i] -= (long long) (xscale*phid[10*i+1]);
inducedField[i+PADDED_NUM_ATOMS] -= (long long) (yscale*phid[10*i+2]);
inducedField[i+PADDED_NUM_ATOMS*2] -= (long long) (zscale*phid[10*i+3]);
inducedFieldPolar[i] -= (long long) (xscale*phip[10*i+1]);
inducedFieldPolar[i+PADDED_NUM_ATOMS] -= (long long) (yscale*phip[10*i+2]);
inducedFieldPolar[i+PADDED_NUM_ATOMS*2] -= (long long) (zscale*phip[10*i+3]);
inducedField[i] -= (long long) (0x100000000*(phid[10*i+1]*fracToCart[0][0] + phid[10*i+2]*fracToCart[0][1] + phid[10*i+3]*fracToCart[0][2]));
inducedField[i+PADDED_NUM_ATOMS] -= (long long) (0x100000000*(phid[10*i+1]*fracToCart[1][0] + phid[10*i+2]*fracToCart[1][1] + phid[10*i+3]*fracToCart[1][2]));
inducedField[i+PADDED_NUM_ATOMS*2] -= (long long) (0x100000000*(phid[10*i+1]*fracToCart[2][0] + phid[10*i+2]*fracToCart[2][1] + phid[10*i+3]*fracToCart[2][2]));
inducedFieldPolar[i] -= (long long) (0x100000000*(phip[10*i+1]*fracToCart[0][0] + phip[10*i+2]*fracToCart[0][1] + phip[10*i+3]*fracToCart[0][2]));
inducedFieldPolar[i+PADDED_NUM_ATOMS] -= (long long) (0x100000000*(phip[10*i+1]*fracToCart[1][0] + phip[10*i+2]*fracToCart[1][1] + phip[10*i+3]*fracToCart[1][2]));
inducedFieldPolar[i+PADDED_NUM_ATOMS*2] -= (long long) (0x100000000*(phip[10*i+1]*fracToCart[2][0] + phip[10*i+2]*fracToCart[2][1] + phip[10*i+3]*fracToCart[2][2]));
}
}
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