void ReferenceIntegrateRPMDStepKernel::initialize(const System& system, const RPMDIntegrator& integrator) {
int numCopies = integrator.getNumCopies();
int numParticles = system.getNumParticles();
positions.resize(numCopies);
velocities.resize(numCopies);
forces.resize(numCopies);
for (int i = 0; i < numCopies; i++) {
positions[i].resize(numParticles);
velocities[i].resize(numParticles);
forces[i].resize(numParticles);
}
fftpack_init_1d(&fft, numCopies);
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
// Build a list of contractions.
groupsNotContracted = -1;
const map<int, int>& contractions = integrator.getContractions();
int maxContractedCopies = 0;
for (map<int, int>::const_iterator iter = contractions.begin(); iter != contractions.end(); ++iter) {
int group = iter->first;
int copies = iter->second;
if (group < 0 || group > 31)
throw OpenMMException("RPMDIntegrator: Force group must be between 0 and 31");
if (copies < 0 || copies > numCopies)
throw OpenMMException("RPMDIntegrator: Number of copies for contraction cannot be greater than the total number of copies being simulated");
if (copies != numCopies) {
if (groupsByCopies.find(copies) == groupsByCopies.end()) {
groupsByCopies[copies] = 1<<group;
contractionFFT[copies] = NULL;
fftpack_init_1d(&contractionFFT[copies], copies);
if (copies > maxContractedCopies)
maxContractedCopies = copies;
}
else
groupsByCopies[copies] |= 1<<group;
groupsNotContracted -= 1<<group;
}
}
// Create workspace for doing contractions.
contractedPositions.resize(maxContractedCopies);
contractedForces.resize(maxContractedCopies);
for (int i = 0; i < maxContractedCopies; i++) {
contractedPositions[i].resize(numParticles);
contractedForces[i].resize(numParticles);
}
}
void CudaIntegrateRPMDStepKernel::initialize(const System& system, const RPMDIntegrator& integrator) {
cu.getPlatformData().initializeContexts(system);
numCopies = integrator.getNumCopies();
numParticles = system.getNumParticles();
workgroupSize = numCopies;
if (numCopies != findFFTDimension(numCopies))
throw OpenMMException("RPMDIntegrator: the number of copies must be a multiple of powers of 2, 3, and 5.");
int paddedParticles = cu.getPaddedNumAtoms();
bool useDoublePrecision = (cu.getUseDoublePrecision() || cu.getUseMixedPrecision());
int elementSize = (useDoublePrecision ? sizeof(double4) : sizeof(float4));
forces = CudaArray::create<long long>(cu, numCopies*paddedParticles*3, "rpmdForces");
positions = new CudaArray(cu, numCopies*paddedParticles, elementSize, "rpmdPositions");
velocities = new CudaArray(cu, numCopies*paddedParticles, elementSize, "rpmdVelocities");
cu.getIntegrationUtilities().initRandomNumberGenerator((unsigned int) integrator.getRandomNumberSeed());
// Fill in the posq and velm arrays with safe values to avoid a risk of nans.
if (useDoublePrecision) {
vector<double4> temp(positions->getSize());
for (int i = 0; i < positions->getSize(); i++)
temp[i] = make_double4(0, 0, 0, 0);
positions->upload(temp);
for (int i = 0; i < velocities->getSize(); i++)
temp[i] = make_double4(0, 0, 0, 1);
velocities->upload(temp);
}
else {
vector<float4> temp(positions->getSize());
for (int i = 0; i < positions->getSize(); i++)
temp[i] = make_float4(0, 0, 0, 0);
positions->upload(temp);
for (int i = 0; i < velocities->getSize(); i++)
temp[i] = make_float4(0, 0, 0, 1);
velocities->upload(temp);
}
// Build a list of contractions.
groupsNotContracted = -1;
const map<int, int>& contractions = integrator.getContractions();
int maxContractedCopies = 0;
for (map<int, int>::const_iterator iter = contractions.begin(); iter != contractions.end(); ++iter) {
int group = iter->first;
int copies = iter->second;
if (group < 0 || group > 31)
throw OpenMMException("RPMDIntegrator: Force group must be between 0 and 31");
if (copies < 0 || copies > numCopies)
throw OpenMMException("RPMDIntegrator: Number of copies for contraction cannot be greater than the total number of copies being simulated");
if (copies != findFFTDimension(copies))
throw OpenMMException("RPMDIntegrator: Number of copies for contraction must be a multiple of powers of 2, 3, and 5.");
if (copies != numCopies) {
if (groupsByCopies.find(copies) == groupsByCopies.end()) {
groupsByCopies[copies] = 1<<group;
if (copies > maxContractedCopies)
maxContractedCopies = copies;
}
else
groupsByCopies[copies] |= 1<<group;
groupsNotContracted -= 1<<group;
}
}
if (maxContractedCopies > 0) {
contractedForces = CudaArray::create<long long>(cu, maxContractedCopies*paddedParticles*3, "rpmdContractedForces");
contractedPositions = new CudaArray(cu, maxContractedCopies*paddedParticles, elementSize, "rpmdContractedPositions");
}
// Create kernels.
map<string, string> defines;
defines["NUM_ATOMS"] = cu.intToString(cu.getNumAtoms());
defines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
defines["NUM_COPIES"] = cu.intToString(numCopies);
defines["THREAD_BLOCK_SIZE"] = cu.intToString(workgroupSize);
defines["HBAR"] = cu.doubleToString(1.054571628e-34*AVOGADRO/(1000*1e-12));
defines["SCALE"] = cu.doubleToString(1.0/sqrt((double) numCopies));
defines["M_PI"] = cu.doubleToString(M_PI);
map<string, string> replacements;
replacements["FFT_Q_FORWARD"] = createFFT(numCopies, "q", true);
replacements["FFT_Q_BACKWARD"] = createFFT(numCopies, "q", false);
replacements["FFT_V_FORWARD"] = createFFT(numCopies, "v", true);
replacements["FFT_V_BACKWARD"] = createFFT(numCopies, "v", false);
CUmodule module = cu.createModule(cu.replaceStrings(CudaKernelSources::vectorOps+CudaRpmdKernelSources::rpmd, replacements), defines, "");
pileKernel = cu.getKernel(module, "applyPileThermostat");
stepKernel = cu.getKernel(module, "integrateStep");
velocitiesKernel = cu.getKernel(module, "advanceVelocities");
copyToContextKernel = cu.getKernel(module, "copyDataToContext");
copyFromContextKernel = cu.getKernel(module, "copyDataFromContext");
translateKernel = cu.getKernel(module, "applyCellTranslations");
// Create kernels for doing contractions.
for (map<int, int>::const_iterator iter = groupsByCopies.begin(); iter != groupsByCopies.end(); ++iter) {
int copies = iter->first;
replacements.clear();
replacements["NUM_CONTRACTED_COPIES"] = cu.intToString(copies);
replacements["POS_SCALE"] = cu.doubleToString(1.0/numCopies);
replacements["FORCE_SCALE"] = cu.doubleToString(0x100000000/(double) copies);
replacements["FFT_Q_FORWARD"] = createFFT(numCopies, "q", true);
replacements["FFT_Q_BACKWARD"] = createFFT(copies, "q", false);
replacements["FFT_F_FORWARD"] = createFFT(copies, "f", true);
replacements["FFT_F_BACKWARD"] = createFFT(numCopies, "f", false);
module = cu.createModule(cu.replaceStrings(CudaKernelSources::vectorOps+CudaRpmdKernelSources::rpmdContraction, replacements), defines, "");
positionContractionKernels[copies] = cu.getKernel(module, "contractPositions");
forceContractionKernels[copies] = cu.getKernel(module, "contractForces");
}
}