void CudaCalcDrudeForceKernel::copyParametersToContext(ContextImpl& context, const DrudeForce& force) {
int numContexts = cu.getPlatformData().contexts.size();
// Set the particle parameters.
int startParticleIndex = cu.getContextIndex()*force.getNumParticles()/numContexts;
int endParticleIndex = (cu.getContextIndex()+1)*force.getNumParticles()/numContexts;
int numParticles = endParticleIndex-startParticleIndex;
if (numParticles > 0) {
if (particleParams == NULL || numParticles != particleParams->getSize())
throw OpenMMException("updateParametersInContext: The number of Drude particles has changed");
vector<float4> paramVector(numParticles);
for (int i = 0; i < numParticles; i++) {
int p, p1, p2, p3, p4;
double charge, polarizability, aniso12, aniso34;
force.getParticleParameters(startParticleIndex+i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
double a1 = (p2 == -1 ? 1 : aniso12);
double a2 = (p3 == -1 || p4 == -1 ? 1 : aniso34);
double a3 = 3-a1-a2;
double k3 = ONE_4PI_EPS0*charge*charge/(polarizability*a3);
double k1 = ONE_4PI_EPS0*charge*charge/(polarizability*a1) - k3;
double k2 = ONE_4PI_EPS0*charge*charge/(polarizability*a2) - k3;
if (p2 == -1)
k1 = 0;
if (p3 == -1 || p4 == -1)
k2 = 0;
paramVector[i] = make_float4((float) k1, (float) k2, (float) k3, 0.0f);
}
particleParams->upload(paramVector);
}
// Set the pair parameters.
int startPairIndex = cu.getContextIndex()*force.getNumScreenedPairs()/numContexts;
int endPairIndex = (cu.getContextIndex()+1)*force.getNumScreenedPairs()/numContexts;
int numPairs = endPairIndex-startPairIndex;
if (numPairs > 0) {
if (pairParams == NULL || numPairs != pairParams->getSize())
throw OpenMMException("updateParametersInContext: The number of screened pairs has changed");
vector<float2> paramVector(numPairs);
for (int i = 0; i < numPairs; i++) {
int drude1, drude2;
double thole;
force.getScreenedPairParameters(startPairIndex+i, drude1, drude2, thole);
int p, p1, p2, p3, p4;
double charge1, charge2, polarizability1, polarizability2, aniso12, aniso34;
force.getParticleParameters(drude1, p, p1, p2, p3, p4, charge1, polarizability1, aniso12, aniso34);
force.getParticleParameters(drude2, p, p1, p2, p3, p4, charge2, polarizability2, aniso12, aniso34);
double screeningScale = thole/pow(polarizability1*polarizability2, 1.0/6.0);
double energyScale = ONE_4PI_EPS0*charge1*charge2;
paramVector[i] = make_float2((float) screeningScale, (float) energyScale);
}
pairParams->upload(paramVector);
}
}
void ReferenceCalcDrudeForceKernel::initialize(const System& system, const DrudeForce& force) {
// Initialize particle parameters.
int numParticles = force.getNumParticles();
particle.resize(numParticles);
particle1.resize(numParticles);
particle2.resize(numParticles);
particle3.resize(numParticles);
particle4.resize(numParticles);
charge.resize(numParticles);
polarizability.resize(numParticles);
aniso12.resize(numParticles);
aniso34.resize(numParticles);
for (int i = 0; i < numParticles; i++)
force.getParticleParameters(i, particle[i], particle1[i], particle2[i], particle3[i], particle4[i], charge[i], polarizability[i], aniso12[i], aniso34[i]);
// Initialize screened pair parameters.
int numPairs = force.getNumScreenedPairs();
pair1.resize(numPairs);
pair2.resize(numPairs);
pairThole.resize(numPairs);
for (int i = 0; i < numPairs; i++)
force.getScreenedPairParameters(i, pair1[i], pair2[i], pairThole[i]);
}
void ReferenceCalcDrudeForceKernel::copyParametersToContext(ContextImpl& context, const DrudeForce& force) {
if (force.getNumParticles() != particle.size())
throw OpenMMException("updateParametersInContext: The number of Drude particles has changed");
if (force.getNumScreenedPairs() != pair1.size())
throw OpenMMException("updateParametersInContext: The number of screened pairs has changed");
for (int i = 0; i < force.getNumParticles(); i++) {
int p, p1, p2, p3, p4;
force.getParticleParameters(i, p, p1, p2, p3, p4, charge[i], polarizability[i], aniso12[i], aniso34[i]);
if (p != particle[i] || p1 != particle1[i] || p2 != particle2[i] || p3 != particle3[i] || p4 != particle4[i])
throw OpenMMException("updateParametersInContext: A particle index has changed");
}
for (int i = 0; i < force.getNumScreenedPairs(); i++) {
int p1, p2;
force.getScreenedPairParameters(i, p1, p2, pairThole[i]);
if (p1 != pair1[i] || p2 != pair2[i])
throw OpenMMException("updateParametersInContext: A particle index for a screened pair has changed");
}
}
void CudaCalcDrudeForceKernel::initialize(const System& system, const DrudeForce& force) {
cu.setAsCurrent();
int numContexts = cu.getPlatformData().contexts.size();
int startParticleIndex = cu.getContextIndex()*force.getNumParticles()/numContexts;
int endParticleIndex = (cu.getContextIndex()+1)*force.getNumParticles()/numContexts;
int numParticles = endParticleIndex-startParticleIndex;
if (numParticles > 0) {
// Create the harmonic interaction .
vector<vector<int> > atoms(numParticles, vector<int>(5));
particleParams = CudaArray::create<float4>(cu, numParticles, "drudeParticleParams");
vector<float4> paramVector(numParticles);
for (int i = 0; i < numParticles; i++) {
double charge, polarizability, aniso12, aniso34;
force.getParticleParameters(startParticleIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], atoms[i][4], charge, polarizability, aniso12, aniso34);
double a1 = (atoms[i][2] == -1 ? 1 : aniso12);
double a2 = (atoms[i][3] == -1 || atoms[i][4] == -1 ? 1 : aniso34);
double a3 = 3-a1-a2;
double k3 = ONE_4PI_EPS0*charge*charge/(polarizability*a3);
double k1 = ONE_4PI_EPS0*charge*charge/(polarizability*a1) - k3;
double k2 = ONE_4PI_EPS0*charge*charge/(polarizability*a2) - k3;
if (atoms[i][2] == -1) {
atoms[i][2] = 0;
k1 = 0;
}
if (atoms[i][3] == -1 || atoms[i][4] == -1) {
atoms[i][3] = 0;
atoms[i][4] = 0;
k2 = 0;
}
paramVector[i] = make_float4((float) k1, (float) k2, (float) k3, 0.0f);
}
particleParams->upload(paramVector);
map<string, string> replacements;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(particleParams->getDevicePointer(), "float4");
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaDrudeKernelSources::drudeParticleForce, replacements), force.getForceGroup());
}
int startPairIndex = cu.getContextIndex()*force.getNumScreenedPairs()/numContexts;
int endPairIndex = (cu.getContextIndex()+1)*force.getNumScreenedPairs()/numContexts;
int numPairs = endPairIndex-startPairIndex;
if (numPairs > 0) {
// Create the screened interaction between dipole pairs.
vector<vector<int> > atoms(numPairs, vector<int>(4));
pairParams = CudaArray::create<float2>(cu, numPairs, "drudePairParams");
vector<float2> paramVector(numPairs);
for (int i = 0; i < numPairs; i++) {
int drude1, drude2;
double thole;
force.getScreenedPairParameters(startPairIndex+i, drude1, drude2, thole);
int p2, p3, p4;
double charge1, charge2, polarizability1, polarizability2, aniso12, aniso34;
force.getParticleParameters(drude1, atoms[i][0], atoms[i][1], p2, p3, p4, charge1, polarizability1, aniso12, aniso34);
force.getParticleParameters(drude2, atoms[i][2], atoms[i][3], p2, p3, p4, charge2, polarizability2, aniso12, aniso34);
double screeningScale = thole/pow(polarizability1*polarizability2, 1.0/6.0);
double energyScale = ONE_4PI_EPS0*charge1*charge2;
paramVector[i] = make_float2((float) screeningScale, (float) energyScale);
}
pairParams->upload(paramVector);
map<string, string> replacements;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(pairParams->getDevicePointer(), "float2");
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaDrudeKernelSources::drudePairForce, replacements), force.getForceGroup());
}
cu.addForce(new CudaDrudeForceInfo(force));
}
