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Commit f6aae604 authored by peastman's avatar peastman
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CPU PME works with triclinic boxes

parent 78e5f13a
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Showing with 147 additions and 61 deletions
olla/include/openmm/kernels.h
View file @ f6aae604
......@@ -1225,10 +1225,10 @@ public:
* Begin computing the force and energy.
*
* @param io an object that coordinates data transfer
* @param periodicBoxSize the size of the periodic box (measured in nm)
* @param periodicBoxVectors the vectors defining the periodic box (measured in nm)
* @param includeEnergy true if potential energy should be computed
*/
virtual void beginComputation(IO& io, Vec3 periodicBoxSize, bool includeEnergy) = 0;
virtual void beginComputation(IO& io, const Vec3* periodicBoxVectors, bool includeEnergy) = 0;
/**
* Finish computing the force and energy.
*
......
platforms/cpu/src/CpuKernels.cpp
View file @ f6aae604
......@@ -582,8 +582,8 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
if (includeReciprocal) {
if (useOptimizedPme) {
PmeIO io(&posq[0], &data.threadForce[0][0], numParticles);
Vec3 periodicBoxSize(boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]);
optimizedPme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, periodicBoxSize, includeEnergy);
Vec3 periodicBoxVectors[3] = {boxVectors[0], boxVectors[1], boxVectors[2]};
optimizedPme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, periodicBoxVectors, includeEnergy);
nonbondedEnergy += optimizedPme.getAs<CalcPmeReciprocalForceKernel>().finishComputation(io);
}
else
......
platforms/cpu/tests/TestCpuEwald.cpp
View file @ f6aae604
......@@ -201,6 +201,57 @@ void testEwald2Ions() {
ASSERT_EQUAL_TOL(-217.276, state.getPotentialEnergy(), 0.01/*10*TOL*/);
}
void testTriclinic() {
// Create a triclinic box containing eight particles.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(2.5, 0, 0), Vec3(0.5, 3.0, 0), Vec3(0.7, 0.9, 3.5));
for (int i = 0; i < 8; i++)
system.addParticle(1.0);
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
force->setNonbondedMethod(NonbondedForce::PME);
force->setCutoffDistance(1.0);
force->setPMEParameters(3.45891, 32, 40, 48);
for (int i = 0; i < 4; i++)
force->addParticle(-1, 0.440104, 0.4184); // Cl parameters
for (int i = 0; i < 4; i++)
force->addParticle(1, 0.332840, 0.0115897); // Na parameters
vector<Vec3> positions(8);
positions[0] = Vec3(1.744, 2.788, 3.162);
positions[1] = Vec3(1.048, 0.762, 2.340);
positions[2] = Vec3(2.489, 1.570, 2.817);
positions[3] = Vec3(1.027, 1.893, 3.271);
positions[4] = Vec3(0.937, 0.825, 0.009);
positions[5] = Vec3(2.290, 1.887, 3.352);
positions[6] = Vec3(1.266, 1.111, 2.894);
positions[7] = Vec3(0.933, 1.862, 3.490);
// Compute the forces and energy.
VerletIntegrator integ(0.001);
Context context(system, integ, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
// Compare them to values computed by Gromacs.
double expectedEnergy = -963.370;
vector<Vec3> expectedForce(8);
expectedForce[0] = Vec3(4.25253e+01, -1.23503e+02, 1.22139e+02);
expectedForce[1] = Vec3(9.74752e+01, 1.68213e+02, 1.93169e+02);
expectedForce[2] = Vec3(-1.50348e+02, 1.29165e+02, 3.70435e+02);
expectedForce[3] = Vec3(9.18644e+02, -3.52571e+00, -1.34772e+03);
expectedForce[4] = Vec3(-1.61193e+02, 9.01528e+01, -7.12904e+01);
expectedForce[5] = Vec3(2.82630e+02, 2.78029e+01, -3.72864e+02);
expectedForce[6] = Vec3(-1.47454e+02, -2.14448e+02, -3.55789e+02);
expectedForce[7] = Vec3(-8.82195e+02, -7.39132e+01, 1.46202e+03);
for (int i = 0; i < 8; i++) {
ASSERT_EQUAL_VEC(expectedForce[i], state.getForces()[i], 1e-4);
}
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-4);
}
void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
// Create a cloud of random point charges.
......@@ -261,6 +312,7 @@ int main(int argc, char* argv[]) {
testEwaldPME(false);
testEwaldPME(true);
// testEwald2Ions();
testTriclinic();
testErrorTolerance(NonbondedForce::Ewald);
testErrorTolerance(NonbondedForce::PME);
}
......
platforms/cuda/src/CudaKernels.cpp
View file @ f6aae604
......@@ -1377,8 +1377,8 @@ public:
PmePreComputation(CudaContext& cu, Kernel& pme, CalcPmeReciprocalForceKernel::IO& io) : cu(cu), pme(pme), io(io) {
}
void computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
Vec3 boxSize(cu.getPeriodicBoxSize().x, cu.getPeriodicBoxSize().y, cu.getPeriodicBoxSize().z);
pme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, boxSize, includeEnergy);
Vec3 boxVectors[3] = {Vec3(cu.getPeriodicBoxSize().x, 0, 0), Vec3(0, cu.getPeriodicBoxSize().y, 0), Vec3(0, 0, cu.getPeriodicBoxSize().z)};
pme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, boxVectors, includeEnergy);
}
private:
CudaContext& cu;
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ f6aae604
......@@ -1363,8 +1363,8 @@ public:
PmePreComputation(OpenCLContext& cl, Kernel& pme, CalcPmeReciprocalForceKernel::IO& io) : cl(cl), pme(pme), io(io) {
}
void computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
Vec3 boxSize(cl.getPeriodicBoxSize().x, cl.getPeriodicBoxSize().y, cl.getPeriodicBoxSize().z);
pme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, boxSize, includeEnergy);
Vec3 boxVectors[3] = {Vec3(cl.getPeriodicBoxSize().x, 0, 0), Vec3(0, cl.getPeriodicBoxSize().y, 0), Vec3(0, 0, cl.getPeriodicBoxSize().z)};
pme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, boxVectors, includeEnergy);
}
private:
OpenCLContext& cl;
......
platforms/reference/src/SimTKReference/ReferencePME.cpp
View file @ f6aae604
......@@ -256,7 +256,8 @@ pme_update_grid_index_and_fraction(pme_t pme,
coord[d] -= floor(coord[d]*recipBoxVectors[d][d])*periodicBoxVectors[d][d];
for(d=0;d<3;d++)
{
t = (coord[0]*recipBoxVectors[0][d]+coord[1]*recipBoxVectors[1][d]+coord[2]*recipBoxVectors[2][d])*pme->ngrid[d];
t = coord[0]*recipBoxVectors[0][d]+coord[1]*recipBoxVectors[1][d]+coord[2]*recipBoxVectors[2][d];
t = (t-floor(t))*pme->ngrid[d];
ti = (int) t;
pme->particlefraction[i][d] = t - ti;
......
plugins/cpupme/src/CpuPmeKernels.cpp
View file @ f6aae604
......@@ -47,10 +47,13 @@ static const int PME_ORDER = 5;
bool CpuCalcPmeReciprocalForceKernel::hasInitializedThreads = false;
int CpuCalcPmeReciprocalForceKernel::numThreads = 0;
static void spreadCharge(int start, int end, float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3 periodicBoxSize) {
static void spreadCharge(int start, int end, float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors) {
float temp[4];
fvec4 boxSize((float) periodicBoxSize[0], (float) periodicBoxSize[1], (float) periodicBoxSize[2], 0);
fvec4 invBoxSize((float) (1/periodicBoxSize[0]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[2]), 0);
fvec4 boxSize((float) periodicBoxVectors[0][0], (float) periodicBoxVectors[1][1], (float) periodicBoxVectors[2][2], 0);
fvec4 invBoxSize((float) recipBoxVectors[0][0], (float) recipBoxVectors[1][1], (float) recipBoxVectors[2][2], 0);
fvec4 recipBoxVec0((float) recipBoxVectors[0][0], (float) recipBoxVectors[0][1], (float) recipBoxVectors[0][2], 0);
fvec4 recipBoxVec1((float) recipBoxVectors[1][0], (float) recipBoxVectors[1][1], (float) recipBoxVectors[1][2], 0);
fvec4 recipBoxVec2((float) recipBoxVectors[2][0], (float) recipBoxVectors[2][1], (float) recipBoxVectors[2][2], 0);
fvec4 gridSize(gridx, gridy, gridz, 0);
ivec4 gridSizeInt(gridx, gridy, gridz, 0);
fvec4 one(1);
......@@ -61,9 +64,10 @@ static void spreadCharge(int start, int end, float* posq, float* grid, int gridx
// Find the position relative to the nearest grid point.
fvec4 pos(&posq[4*i]);
fvec4 posFloor = floor(pos*invBoxSize);
fvec4 posInBox = pos-boxSize*posFloor;
fvec4 t = posInBox*invBoxSize*gridSize;
float posInBox[4];
(pos-boxSize*floor(pos*invBoxSize)).store(posInBox);
fvec4 t = posInBox[0]*recipBoxVec0 + posInBox[1]*recipBoxVec1 + posInBox[2]*recipBoxVec2;
t = (t-floor(t))*gridSize;
ivec4 ti = t;
fvec4 dr = t-ti;
ivec4 gridIndex = ti-(gridSizeInt&ti==gridSizeInt);
......@@ -142,29 +146,26 @@ static void spreadCharge(int start, int end, float* posq, float* grid, int gridx
}
}
static void computeReciprocalEterm(int start, int end, int gridx, int gridy, int gridz, vector<float>& recipEterm, double alpha, vector<float>* bsplineModuli, Vec3 periodicBoxSize) {
static void computeReciprocalEterm(int start, int end, int gridx, int gridy, int gridz, vector<float>& recipEterm, double alpha, vector<float>* bsplineModuli, Vec3* periodicBoxVectors, Vec3* recipBoxVectors) {
const unsigned int zsize = gridz/2+1;
const unsigned int yzsize = gridy*zsize;
const float scaleFactor = (float) (M_PI*periodicBoxSize[0]*periodicBoxSize[1]*periodicBoxSize[2]);
const float scaleFactor = (float) (M_PI*periodicBoxVectors[0][0]*periodicBoxVectors[1][1]*periodicBoxVectors[2][2]);
const float recipExpFactor = (float) (M_PI*M_PI/(alpha*alpha));
const float invPeriodicBoxSizeX = (float) (1.0/periodicBoxSize[0]);
const float invPeriodicBoxSizeY = (float) (1.0/periodicBoxSize[1]);
const float invPeriodicBoxSizeZ = (float) (1.0/periodicBoxSize[2]);
int firstz = (start == 0 ? 1 : 0);
for (int kx = start; kx < end; kx++) {
int mx = (kx < (gridx+1)/2) ? kx : kx-gridx;
float mhx = mx*invPeriodicBoxSizeX;
float mhx = mx*(float)recipBoxVectors[0][0];
float bx = scaleFactor*bsplineModuli[0][kx];
for (int ky = 0; ky < gridy; ky++) {
int my = (ky < (gridy+1)/2) ? ky : ky-gridy;
float mhy = my*invPeriodicBoxSizeY;
float mhy = mx*(float)recipBoxVectors[1][0] + my*(float)recipBoxVectors[1][1];
float mhx2y2 = mhx*mhx + mhy*mhy;
float bxby = bx*bsplineModuli[1][ky];
for (int kz = firstz; kz < zsize; kz++) {
int index = kx*yzsize + ky*zsize + kz;
int mz = (kz < (gridz+1)/2) ? kz : kz-gridz;
float mhz = mz*invPeriodicBoxSizeZ;
float mhz = mx*(float)recipBoxVectors[2][0] + my*(float)recipBoxVectors[2][1] + mz*(float)recipBoxVectors[2][2];
float bz = bsplineModuli[2][kz];
float m2 = mhx2y2 + mhz*mhz;
float denom = m2*bxby*bz;
......@@ -175,29 +176,26 @@ static void computeReciprocalEterm(int start, int end, int gridx, int gridy, int
}
}
static float reciprocalEnergy(int start, int end, fftwf_complex* grid, int gridx, int gridy, int gridz, double alpha, vector<float>* bsplineModuli, Vec3 periodicBoxSize) {
static float reciprocalEnergy(int start, int end, fftwf_complex* grid, int gridx, int gridy, int gridz, double alpha, vector<float>* bsplineModuli, Vec3* periodicBoxVectors, Vec3* recipBoxVectors) {
const unsigned int zsizeHalf = gridz/2+1;
const unsigned int yzsizeHalf = gridy*zsizeHalf;
const float scaleFactor = (float) (M_PI*periodicBoxSize[0]*periodicBoxSize[1]*periodicBoxSize[2]);
const float scaleFactor = (float) (M_PI*periodicBoxVectors[0][0]*periodicBoxVectors[1][1]*periodicBoxVectors[2][2]);
const float recipExpFactor = (float) (M_PI*M_PI/(alpha*alpha));
const float invPeriodicBoxSizeX = (float) (1.0/periodicBoxSize[0]);
const float invPeriodicBoxSizeY = (float) (1.0/periodicBoxSize[1]);
const float invPeriodicBoxSizeZ = (float) (1.0/periodicBoxSize[2]);
float energy = 0.0f;
int firstz = (start == 0 ? 1 : 0);
for (int kx = start; kx < end; kx++) {
int mx = (kx < (gridx+1)/2) ? kx : kx-gridx;
float mhx = mx*invPeriodicBoxSizeX;
float mhx = mx*(float)recipBoxVectors[0][0];
float bx = scaleFactor*bsplineModuli[0][kx];
for (int ky = 0; ky < gridy; ky++) {
int my = (ky < (gridy+1)/2) ? ky : ky-gridy;
float mhy = my*invPeriodicBoxSizeY;
float mhy = mx*(float)recipBoxVectors[1][0] + my*(float)recipBoxVectors[1][1];
float mhx2y2 = mhx*mhx + mhy*mhy;
float bxby = bx*bsplineModuli[1][ky];
for (int kz = firstz; kz < gridz; kz++) {
int mz = (kz < (gridz+1)/2) ? kz : kz-gridz;
float mhz = mz*invPeriodicBoxSizeZ;
float mhz = mx*(float)recipBoxVectors[2][0] + my*(float)recipBoxVectors[2][1] + mz*(float)recipBoxVectors[2][2];
float bz = bsplineModuli[2][kz];
float m2 = mhx2y2 + mhz*mhz;
float denom = m2*bxby*bz;
......@@ -242,9 +240,12 @@ static void reciprocalConvolution(int start, int end, fftwf_complex* grid, int g
}
}
static void interpolateForces(int start, int end, float* posq, float* force, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3 periodicBoxSize) {
fvec4 boxSize((float) periodicBoxSize[0], (float) periodicBoxSize[1], (float) periodicBoxSize[2], 0);
fvec4 invBoxSize((float) (1/periodicBoxSize[0]), (float) (1/periodicBoxSize[1]), (float) (1/periodicBoxSize[2]), 0);
static void interpolateForces(int start, int end, float* posq, float* force, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors) {
fvec4 boxSize((float) periodicBoxVectors[0][0], (float) periodicBoxVectors[1][1], (float) periodicBoxVectors[2][2], 0);
fvec4 invBoxSize((float) recipBoxVectors[0][0], (float) recipBoxVectors[1][1], (float) recipBoxVectors[2][2], 0);
fvec4 recipBoxVec0((float) recipBoxVectors[0][0], (float) recipBoxVectors[0][1], (float) recipBoxVectors[0][2], 0);
fvec4 recipBoxVec1((float) recipBoxVectors[1][0], (float) recipBoxVectors[1][1], (float) recipBoxVectors[1][2], 0);
fvec4 recipBoxVec2((float) recipBoxVectors[2][0], (float) recipBoxVectors[2][1], (float) recipBoxVectors[2][2], 0);
fvec4 gridSize(gridx, gridy, gridz, 0);
ivec4 gridSizeInt(gridx, gridy, gridz, 0);
fvec4 one(1);
......@@ -254,9 +255,10 @@ static void interpolateForces(int start, int end, float* posq, float* force, flo
// Find the position relative to the nearest grid point.
fvec4 pos(&posq[4*i]);
fvec4 posFloor = floor(pos*invBoxSize);
fvec4 posInBox = pos-boxSize*posFloor;
fvec4 t = posInBox*invBoxSize*gridSize;
float posInBox[4];
(pos-boxSize*floor(pos*invBoxSize)).store(posInBox);
fvec4 t = posInBox[0]*recipBoxVec0 + posInBox[1]*recipBoxVec1 + posInBox[2]*recipBoxVec2;
t = (t-floor(t))*gridSize;
ivec4 ti = t;
fvec4 dr = t-ti;
ivec4 gridIndex = ti-(gridSizeInt&ti==gridSizeInt);
......@@ -321,8 +323,12 @@ static void interpolateForces(int start, int end, float* posq, float* force, flo
}
}
}
f = invBoxSize*gridSize*f*(-epsilonFactor*posq[4*i+3]);
f.store(&force[4*i]);
f *= -epsilonFactor*posq[4*i+3];
float fc[4];
f.store(fc);
force[4*i+0] = fc[0]*gridx*(float)recipBoxVectors[0][0];
force[4*i+1] = fc[0]*gridx*(float)recipBoxVectors[1][0]+fc[1]*gridy*(float)recipBoxVectors[1][1];
force[4*i+2] = fc[0]*gridx*(float)recipBoxVectors[2][0]+fc[1]*gridy*(float)recipBoxVectors[2][1]+fc[2]*gridz*(float)recipBoxVectors[2][2];
}
}
......@@ -476,7 +482,7 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) {
advanceThreads(); // Signal threads to perform charge spreading.
advanceThreads(); // Signal threads to sum the charge grids.
fftwf_execute_dft_r2c(forwardFFT, realGrid, complexGrid);
if (lastBoxSize != periodicBoxSize)
if (lastBoxVectors[0] != periodicBoxVectors[0] || lastBoxVectors[1] != periodicBoxVectors[1] || lastBoxVectors[2] != periodicBoxVectors[2])
advanceThreads(); // Signal threads to compute the reciprocal scale factors.
if (includeEnergy)
advanceThreads(); // Signal threads to compute energy.
......@@ -484,7 +490,9 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) {
fftwf_execute_dft_c2r(backwardFFT, complexGrid, realGrid);
advanceThreads(); // Signal threads to interpolate forces.
isFinished = true;
lastBoxSize = periodicBoxSize;
lastBoxVectors[0] = periodicBoxVectors[0];
lastBoxVectors[1] = periodicBoxVectors[1];
lastBoxVectors[2] = periodicBoxVectors[2];
pthread_cond_signal(&mainThreadEndCondition);
}
pthread_mutex_unlock(&lock);
......@@ -503,7 +511,7 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) {
threadWait();
if (isDeleted)
break;
spreadCharge(particleStart, particleEnd, posq, threadData[index]->tempGrid, gridx, gridy, gridz, numParticles, periodicBoxSize);
spreadCharge(particleStart, particleEnd, posq, threadData[index]->tempGrid, gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors);
threadWait();
int numGrids = threadData.size();
for (int i = gridStart; i < gridEnd; i += 4) {
......@@ -513,12 +521,12 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) {
sum.store(&realGrid[i]);
}
threadWait();
if (lastBoxSize != periodicBoxSize) {
computeReciprocalEterm(gridxStart, gridxEnd, gridx, gridy, gridz, recipEterm, alpha, bsplineModuli, periodicBoxSize);
if (lastBoxVectors[0] != periodicBoxVectors[0] || lastBoxVectors[1] != periodicBoxVectors[1] || lastBoxVectors[2] != periodicBoxVectors[2]) {
computeReciprocalEterm(gridxStart, gridxEnd, gridx, gridy, gridz, recipEterm, alpha, bsplineModuli, periodicBoxVectors, recipBoxVectors);
threadWait();
}
if (includeEnergy) {
double threadEnergy = reciprocalEnergy(gridxStart, gridxEnd, complexGrid, gridx, gridy, gridz, alpha, bsplineModuli, periodicBoxSize);
double threadEnergy = reciprocalEnergy(gridxStart, gridxEnd, complexGrid, gridx, gridy, gridz, alpha, bsplineModuli, periodicBoxVectors, recipBoxVectors);
pthread_mutex_lock(&lock);
energy += threadEnergy;
pthread_mutex_unlock(&lock);
......@@ -526,7 +534,7 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) {
}
reciprocalConvolution(gridxStart, gridxEnd, complexGrid, gridx, gridy, gridz, recipEterm);
threadWait();
interpolateForces(particleStart, particleEnd, posq, &force[0], realGrid, gridx, gridy, gridz, numParticles, periodicBoxSize);
interpolateForces(particleStart, particleEnd, posq, &force[0], realGrid, gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors);
}
}
}
......@@ -547,11 +555,24 @@ void CpuCalcPmeReciprocalForceKernel::advanceThreads() {
}
}
void CpuCalcPmeReciprocalForceKernel::beginComputation(IO& io, Vec3 periodicBoxSize, bool includeEnergy) {
void CpuCalcPmeReciprocalForceKernel::beginComputation(IO& io, const Vec3* periodicBoxVectors, bool includeEnergy) {
this->io = &io;
this->periodicBoxSize = periodicBoxSize;
this->periodicBoxVectors[0] = periodicBoxVectors[0];
this->periodicBoxVectors[1] = periodicBoxVectors[1];
this->periodicBoxVectors[2] = periodicBoxVectors[2];
this->includeEnergy = includeEnergy;
energy = 0.0;
// Invert the box vectors.
double determinant = periodicBoxVectors[0][0]*periodicBoxVectors[1][1]*periodicBoxVectors[2][2];
double scale = 1.0/determinant;
recipBoxVectors[0] = Vec3(periodicBoxVectors[1][1]*periodicBoxVectors[2][2], 0, 0)*scale;
recipBoxVectors[1] = Vec3(-periodicBoxVectors[1][0]*periodicBoxVectors[2][2], periodicBoxVectors[0][0]*periodicBoxVectors[2][2], 0)*scale;
recipBoxVectors[2] = Vec3(periodicBoxVectors[1][0]*periodicBoxVectors[2][1]-periodicBoxVectors[1][1]*periodicBoxVectors[2][0], -periodicBoxVectors[0][0]*periodicBoxVectors[2][1], periodicBoxVectors[0][0]*periodicBoxVectors[1][1])*scale;
// Do the calculation.
pthread_mutex_lock(&lock);
isFinished = false;
pthread_cond_signal(&mainThreadStartCondition);
......
plugins/cpupme/src/CpuPmeKernels.h
View file @ f6aae604
......@@ -67,10 +67,10 @@ public:
* Begin computing the force and energy.
*
* @param io an object that coordinates data transfer
* @param periodicBoxSize the size of the periodic box (measured in nm)
* @param periodicBoxVectors the vectors defining the periodic box (measured in nm)
* @param includeEnergy true if potential energy should be computed
*/
void beginComputation(IO& io, Vec3 periodicBoxSize, bool includeEnergy);
void beginComputation(IO& io, const Vec3* periodicBoxVectors, bool includeEnergy);
/**
* Finish computing the force and energy.
*
......@@ -107,7 +107,7 @@ private:
std::vector<float> force;
std::vector<float> bsplineModuli[3];
std::vector<float> recipEterm;
Vec3 lastBoxSize;
Vec3 lastBoxVectors[3];
float* realGrid;
fftwf_complex* complexGrid;
fftwf_plan forwardFFT, backwardFFT;
......@@ -122,7 +122,7 @@ private:
IO* io;
float energy;
float* posq;
Vec3 periodicBoxSize;
Vec3 periodicBoxVectors[3], recipBoxVectors[3];
bool includeEnergy;
};
......
plugins/cpupme/tests/TestCpuPme.cpp
View file @ f6aae604
......@@ -61,14 +61,25 @@ public:
}
};
void testPME() {
void testPME(bool triclinic) {
// Create a cloud of random point charges.
const int numParticles = 51;
const double boxWidth = 5.0;
const double cutoff = 1.0;
Vec3 boxVectors[3];
if (triclinic) {
boxVectors[0] = Vec3(boxWidth, 0, 0);
boxVectors[1] = Vec3(0.2*boxWidth, boxWidth, 0);
boxVectors[2] = Vec3(-0.3*boxWidth, -0.1*boxWidth, boxWidth);
}
else {
boxVectors[0] = Vec3(boxWidth, 0, 0);
boxVectors[1] = Vec3(0, boxWidth, 0);
boxVectors[2] = Vec3(0, 0, boxWidth);
}
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
system.setDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
vector<Vec3> positions(numParticles);
......@@ -112,7 +123,7 @@ void testPME() {
}
double ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
pme.initialize(gridx, gridy, gridz, numParticles, alpha);
pme.beginComputation(io, Vec3(boxWidth, boxWidth, boxWidth), true);
pme.beginComputation(io, boxVectors, true);
double energy = pme.finishComputation(io);
// See if they match.
......@@ -128,7 +139,8 @@ int main(int argc, char* argv[]) {
cout << "CPU is not supported. Exiting." << endl;
return 0;
}
testPME();
testPME(false);
testPME(true);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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