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Commit fa21870f authored by peastman's avatar peastman
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Began CUDA implementation of spherical harmonics for multipoles

parent 3b4dca22
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Showing with 100 additions and 16 deletions
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ fa21870f
......@@ -806,8 +806,8 @@ 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), fracDipoles(NULL),
fracQuadrupoles(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), sphericalDipoles(NULL), sphericalQuadrupoles(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),
......@@ -826,6 +826,10 @@ CudaCalcAmoebaMultipoleForceKernel::~CudaCalcAmoebaMultipoleForceKernel() {
delete labFrameDipoles;
if (labFrameQuadrupoles != NULL)
delete labFrameQuadrupoles;
if (sphericalDipoles != NULL)
delete sphericalDipoles;
if (sphericalQuadrupoles != NULL)
delete sphericalQuadrupoles;
if (fracDipoles != NULL)
delete fracDipoles;
if (fracQuadrupoles != NULL)
......@@ -985,6 +989,8 @@ 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, 5*paddedNumAtoms, elementSize, "labFrameQuadrupoles");
sphericalDipoles = new CudaArray(cu, 3*paddedNumAtoms, elementSize, "sphericalDipoles");
sphericalQuadrupoles = new CudaArray(cu, 5*paddedNumAtoms, elementSize, "sphericalQuadrupoles");
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");
......@@ -1433,7 +1439,8 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
void* computeMomentsArgs[] = {&cu.getPosq().getDevicePointer(), &multipoleParticles->getDevicePointer(),
&molecularDipoles->getDevicePointer(), &molecularQuadrupoles->getDevicePointer(),
&labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer()};
&labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(),
&sphericalDipoles->getDevicePointer(), &sphericalQuadrupoles->getDevicePointer()};
cu.executeKernel(computeMomentsKernel, computeMomentsArgs, cu.getNumAtoms());
int startTileIndex = nb.getStartTileIndex();
int numTileIndices = nb.getNumTiles();
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ fa21870f
......@@ -392,6 +392,8 @@ private:
CudaArray* molecularQuadrupoles;
CudaArray* labFrameDipoles;
CudaArray* labFrameQuadrupoles;
CudaArray* sphericalDipoles;
CudaArray* sphericalQuadrupoles;
CudaArray* fracDipoles;
CudaArray* fracQuadrupoles;
CudaArray* field;
......
plugins/amoeba/platforms/cuda/src/kernels/multipoles.cu
View file @ fa21870f
extern "C" __global__ void computeLabFrameMoments(real4* __restrict__ posq, int4* __restrict__ multipoleParticles, float* __restrict__ molecularDipoles,
float* __restrict__ molecularQuadrupoles, real* __restrict__ labFrameDipoles, real* __restrict__ labFrameQuadrupoles) {
// get coordinates of this atom and the z & x axis atoms
// compute the vector between the atoms and 1/sqrt(d2), d2 is distance between
// this atom and the axis atom
// this atom is referred to as the k-atom in notes below
// code common to ZThenX and Bisector
float* __restrict__ molecularQuadrupoles, real* __restrict__ labFrameDipoles, real* __restrict__ labFrameQuadrupoles,
real* __restrict__ sphericalDipoles, real* __restrict__ sphericalQuadrupoles) {
for (int atom = blockIdx.x*blockDim.x+threadIdx.x; atom < NUM_ATOMS; atom += gridDim.x*blockDim.x) {
// Load the spherical multipoles.
int offset = 3*atom;
sphericalDipoles[offset+0] = molecularDipoles[offset+2]; // z -> Q_10
sphericalDipoles[offset+1] = molecularDipoles[offset+0]; // x -> Q_11c
sphericalDipoles[offset+2] = molecularDipoles[offset+1]; // y -> Q_11s
offset = 5*atom;
sphericalQuadrupoles[offset+0] = -3.0f*(molecularQuadrupoles[offset+0]+molecularQuadrupoles[offset+3]); // zz -> Q_20
sphericalQuadrupoles[offset+1] = (2*SQRT(3))*molecularQuadrupoles[offset+2]; // xz -> Q_21c
sphericalQuadrupoles[offset+2] = (2*SQRT(3))*molecularQuadrupoles[offset+4]; // yz -> Q_21s
sphericalQuadrupoles[offset+3] = SQRT(3)*(molecularQuadrupoles[offset+0]-molecularQuadrupoles[offset+3]); // xx-yy -> Q_22c
sphericalQuadrupoles[offset+4] = (2*SQRT(3))*molecularQuadrupoles[offset+1]; // xy -> Q_22s
// get coordinates of this atom and the z & x axis atoms
// compute the vector between the atoms and 1/sqrt(d2), d2 is distance between
// this atom and the axis atom
// this atom is referred to as the k-atom in notes below
// code common to ZThenX and Bisector
int4 particles = multipoleParticles[atom];
if (particles.x >= 0 && particles.z >= 0) {
real4 thisParticlePos = posq[atom];
......@@ -149,7 +163,7 @@ extern "C" __global__ void computeLabFrameMoments(real4* __restrict__ posq, int4
// Transform the dipole
unsigned int offset = 3*atom;
offset = 3*atom;
real molDipole[3];
molDipole[0] = molecularDipoles[offset];
molDipole[1] = molecularDipoles[offset+1];
......@@ -192,6 +206,67 @@ extern "C" __global__ void computeLabFrameMoments(real4* __restrict__ posq, int4
labFrameQuadrupoles[offset+4] = vectorX.y*(vectorX.z*mPoleXX + vectorY.z*mPoleXY + vectorZ.z*mPoleXZ)
+ vectorY.y*(vectorX.z*mPoleXY + vectorY.z*mPoleYY + vectorZ.z*mPoleYZ)
+ vectorZ.y*(vectorX.z*mPoleXZ + vectorY.z*mPoleYZ + vectorZ.z*mPoleZZ);
// ---------------------------------------------------------------------------------------
// Now transform the spherical multipoles. First do the dipoles.
offset = 3*atom;
real sphericalDipole[3];
sphericalDipole[0] = sphericalDipoles[offset];
sphericalDipole[1] = sphericalDipoles[offset+1];
sphericalDipole[2] = sphericalDipoles[offset+2];
if (reverse)
sphericalDipole[2] *= -1;
sphericalDipoles[offset] = sphericalDipole[0]*vectorZ.z + sphericalDipole[1]*vectorX.z + sphericalDipole[2]*vectorY.z;
sphericalDipoles[offset+1] = sphericalDipole[0]*vectorZ.x + sphericalDipole[1]*vectorX.x + sphericalDipole[2]*vectorY.x;
sphericalDipoles[offset+2] = sphericalDipole[0]*vectorZ.y + sphericalDipole[1]*vectorX.y + sphericalDipole[2]*vectorY.y;
// Now the quadrupoles.
offset = 5*atom;
real sphericalQuadrupole[5];
sphericalQuadrupole[0] = sphericalQuadrupoles[offset];
sphericalQuadrupole[1] = sphericalQuadrupoles[offset+1];
sphericalQuadrupole[2] = sphericalQuadrupoles[offset+2];
sphericalQuadrupole[3] = sphericalQuadrupoles[offset+3];
sphericalQuadrupole[4] = sphericalQuadrupoles[offset+4];
if (reverse) {
sphericalQuadrupole[2] *= -1;
sphericalQuadrupole[4] *= -1;
}
real rotatedQuadrupole[5] = {0, 0, 0, 0, 0};
real sqrtThree = SQRT(3);
rotatedQuadrupole[0] += sphericalQuadrupole[0]*0.5f*(3.0f*vectorZ.z*vectorZ.z - 1.0f);
rotatedQuadrupole[1] += sphericalQuadrupole[0]*sqrtThree*vectorZ.z*vectorZ.x;
rotatedQuadrupole[2] += sphericalQuadrupole[0]*sqrtThree*vectorZ.z*vectorZ.y;
rotatedQuadrupole[3] += sphericalQuadrupole[0]*0.5f*sqrtThree*(vectorZ.x*vectorZ.x - vectorZ.y*vectorZ.y);
rotatedQuadrupole[4] += sphericalQuadrupole[0]*sqrtThree*vectorZ.x*vectorZ.y;
rotatedQuadrupole[0] += sphericalQuadrupole[1]*sqrtThree*vectorZ.z*vectorX.z;
rotatedQuadrupole[1] += sphericalQuadrupole[1]*(vectorZ.x*vectorX.z + vectorZ.z*vectorX.x);
rotatedQuadrupole[2] += sphericalQuadrupole[1]*(vectorZ.y*vectorX.z + vectorZ.z*vectorX.y);
rotatedQuadrupole[3] += sphericalQuadrupole[1]*(vectorZ.x*vectorX.x - vectorZ.y*vectorX.y);
rotatedQuadrupole[4] += sphericalQuadrupole[1]*(vectorZ.y*vectorX.x + vectorZ.x*vectorX.y);
rotatedQuadrupole[0] += sphericalQuadrupole[2]*sqrtThree*vectorZ.z*vectorY.z;
rotatedQuadrupole[1] += sphericalQuadrupole[2]*(vectorZ.x*vectorY.z + vectorZ.z*vectorY.x);
rotatedQuadrupole[2] += sphericalQuadrupole[2]*(vectorZ.y*vectorY.z + vectorZ.z*vectorY.y);
rotatedQuadrupole[3] += sphericalQuadrupole[2]*(vectorZ.x*vectorY.x - vectorZ.y*vectorY.y);
rotatedQuadrupole[4] += sphericalQuadrupole[2]*(vectorZ.y*vectorY.x + vectorZ.x*vectorY.y);
rotatedQuadrupole[0] += sphericalQuadrupole[3]*0.5f*sqrtThree*(vectorX.z*vectorX.z - vectorY.z*vectorY.z);
rotatedQuadrupole[1] += sphericalQuadrupole[3]*(vectorX.z*vectorX.x - vectorY.z*vectorY.x);
rotatedQuadrupole[2] += sphericalQuadrupole[3]*(vectorX.z*vectorX.y - vectorY.z*vectorY.y);
rotatedQuadrupole[3] += sphericalQuadrupole[3]*0.5f*(vectorX.x*vectorX.x - vectorX.y*vectorX.y - vectorY.x*vectorY.x + vectorY.y*vectorY.y);
rotatedQuadrupole[4] += sphericalQuadrupole[3]*(vectorX.x*vectorX.y - vectorY.x*vectorY.y);
rotatedQuadrupole[0] += sphericalQuadrupole[4]*sqrtThree*vectorX.z*vectorY.z;
rotatedQuadrupole[1] += sphericalQuadrupole[4]*(vectorX.x*vectorY.z + vectorX.z*vectorY.x);
rotatedQuadrupole[2] += sphericalQuadrupole[4]*(vectorX.y*vectorY.z + vectorX.z*vectorY.y);
rotatedQuadrupole[3] += sphericalQuadrupole[4]*(vectorX.x*vectorY.x - vectorX.y*vectorY.y);
rotatedQuadrupole[4] += sphericalQuadrupole[4]*(vectorX.y*vectorY.x + vectorX.x*vectorY.y);
sphericalQuadrupoles[offset] = rotatedQuadrupole[0];
sphericalQuadrupoles[offset+1] = rotatedQuadrupole[1];
sphericalQuadrupoles[offset+2] = rotatedQuadrupole[2];
sphericalQuadrupoles[offset+3] = rotatedQuadrupole[3];
sphericalQuadrupoles[offset+4] = rotatedQuadrupole[4];
}
else {
labFrameDipoles[3*atom] = molecularDipoles[3*atom];
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ fa21870f
......@@ -25,9 +25,6 @@
#include "AmoebaReferenceMultipoleForce.h"
#include "jama_svd.h"
#include <algorithm>
#include <iostream>
#include <iomanip>
#define FMT(x) std::setw(16) << std::setprecision(10) << (x)
// In case we're using some primitive version of Visual Studio this will
// make sure that erf() and erfc() are defined.
......@@ -362,6 +359,9 @@ void AmoebaReferenceMultipoleForce::checkChiralCenterAtParticle(MultipoleParticl
RealOpenMM volume = deltaC.dot(deltaAD);
if (volume < 0.0) {
particleI.dipole[1] *= -1.0; // pole(3,i)
particleI.quadrupole[QXY] *= -1.0; // pole(6,i) && pole(8,i)
particleI.quadrupole[QYZ] *= -1.0; // pole(10,i) && pole(12,i)
particleI.sphericalDipole[2] *= -1.0; // y
particleI.sphericalQuadrupole[2] *= -1.0; // yz
particleI.sphericalQuadrupole[4] *= -1.0; // xy
......
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