void NonbondedForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcNonbondedForceKernel::Name(), context);
// Check for errors in the specification of exceptions.
const System& system = context.getSystem();
if (owner.getNumParticles() != system.getNumParticles())
throw OpenMMException("NonbondedForce must have exactly as many particles as the System it belongs to.");
if (owner.getUseSwitchingFunction()) {
if (owner.getSwitchingDistance() < 0 || owner.getSwitchingDistance() >= owner.getCutoffDistance())
throw OpenMMException("NonbondedForce: Switching distance must satisfy 0 <= r_switch < r_cutoff");
}
vector<set<int> > exceptions(owner.getNumParticles());
for (int i = 0; i < owner.getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
owner.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
stringstream msg;
msg << "NonbondedForce: Illegal particle index for an exception: ";
msg << particle1;
throw OpenMMException(msg.str());
}
if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
stringstream msg;
msg << "NonbondedForce: Illegal particle index for an exception: ";
msg << particle2;
throw OpenMMException(msg.str());
}
if (exceptions[particle1].count(particle2) > 0 || exceptions[particle2].count(particle1) > 0) {
stringstream msg;
msg << "NonbondedForce: Multiple exceptions are specified for particles ";
msg << particle1;
msg << " and ";
msg << particle2;
throw OpenMMException(msg.str());
}
exceptions[particle1].insert(particle2);
exceptions[particle2].insert(particle1);
}
if (owner.getNonbondedMethod() != NonbondedForce::NoCutoff && owner.getNonbondedMethod() != NonbondedForce::CutoffNonPeriodic) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double cutoff = owner.getCutoffDistance();
if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
throw OpenMMException("NonbondedForce: The cutoff distance cannot be greater than half the periodic box size.");
if (owner.getNonbondedMethod() == NonbondedForce::Ewald && (boxVectors[1][0] != 0.0 || boxVectors[2][0] != 0.0 || boxVectors[2][1] != 0))
throw OpenMMException("NonbondedForce: Ewald is not supported with non-rectangular boxes. Use PME instead.");
}
kernel.getAs<CalcNonbondedForceKernel>().initialize(context.getSystem(), owner);
}
void MonteCarloBarostatImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(ApplyMonteCarloBarostatKernel::Name(), context);
kernel.getAs<ApplyMonteCarloBarostatKernel>().initialize(context.getSystem(), owner);
Vec3 box[3];
context.getPeriodicBoxVectors(box[0], box[1], box[2]);
double volume = box[0][0]*box[1][1]*box[2][2];
volumeScale = 0.01*volume;
numAttempted = 0;
numAccepted = 0;
int randSeed = owner.getRandomNumberSeed();
// A random seed of 0 means use a unique one
if (randSeed == 0) randSeed = osrngseed();
init_gen_rand(randSeed, random);
}
void CustomHbondForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcCustomHbondForceKernel::Name(), context);
// Check for errors in the specification of parameters and exclusions.
const System& system = context.getSystem();
vector<set<int> > exclusions(owner.getNumDonors());
vector<double> parameters;
int numDonorParameters = owner.getNumPerDonorParameters();
for (int i = 0; i < owner.getNumDonors(); i++) {
int d1, d2, d3;
owner.getDonorParameters(i, d1, d2, d3, parameters);
if (d1 < 0 || d1 >= system.getNumParticles()) {
stringstream msg;
msg << "CustomHbondForce: Illegal particle index for a donor: ";
msg << d1;
throw OpenMMException(msg.str());
}
if (d2 < -1 || d2 >= system.getNumParticles()) {
stringstream msg;
msg << "CustomHbondForce: Illegal particle index for a donor: ";
msg << d2;
throw OpenMMException(msg.str());
}
if (d3 < -1 || d3 >= system.getNumParticles()) {
stringstream msg;
msg << "CustomHbondForce: Illegal particle index for a donor: ";
msg << d3;
throw OpenMMException(msg.str());
}
if (parameters.size() != numDonorParameters) {
stringstream msg;
msg << "CustomHbondForce: Wrong number of parameters for donor ";
msg << i;
throw OpenMMException(msg.str());
}
}
int numAcceptorParameters = owner.getNumPerAcceptorParameters();
for (int i = 0; i < owner.getNumAcceptors(); i++) {
int a1, a2, a3;
owner.getAcceptorParameters(i, a1, a2, a3, parameters);
if (a1 < 0 || a1 >= system.getNumParticles()) {
stringstream msg;
msg << "CustomHbondForce: Illegal particle index for an acceptor: ";
msg << a1;
throw OpenMMException(msg.str());
}
if (a2 < -1 || a2 >= system.getNumParticles()) {
stringstream msg;
msg << "CustomHbondForce: Illegal particle index for an acceptor: ";
msg << a2;
throw OpenMMException(msg.str());
}
if (a3 < -1 || a3 >= system.getNumParticles()) {
stringstream msg;
msg << "CustomHbondForce: Illegal particle index for an acceptor: ";
msg << a3;
throw OpenMMException(msg.str());
}
if (parameters.size() != numAcceptorParameters) {
stringstream msg;
msg << "CustomHbondForce: Wrong number of parameters for acceptor ";
msg << i;
throw OpenMMException(msg.str());
}
}
for (int i = 0; i < owner.getNumExclusions(); i++) {
int donor, acceptor;
owner.getExclusionParticles(i, donor, acceptor);
if (donor < 0 || donor >= owner.getNumDonors()) {
stringstream msg;
msg << "CustomHbondForce: Illegal donor index for an exclusion: ";
msg << donor;
throw OpenMMException(msg.str());
}
if (acceptor < 0 || acceptor >= owner.getNumAcceptors()) {
stringstream msg;
msg << "CustomHbondForce: Illegal acceptor index for an exclusion: ";
msg << acceptor;
throw OpenMMException(msg.str());
}
if (exclusions[donor].count(acceptor) > 0) {
stringstream msg;
msg << "CustomHbondForce: Multiple exclusions are specified for donor ";
msg << donor;
msg << " and acceptor ";
msg << acceptor;
throw OpenMMException(msg.str());
}
exclusions[donor].insert(acceptor);
}
if (owner.getNonbondedMethod() == CustomHbondForce::CutoffPeriodic) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double cutoff = owner.getCutoffDistance();
if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
throw OpenMMException("CustomHbondForce: The cutoff distance cannot be greater than half the periodic box size.");
}
kernel.getAs<CalcCustomHbondForceKernel>().initialize(context.getSystem(), owner);
}
void CustomNonbondedForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcCustomNonbondedForceKernel::Name(), context);
// Check for errors in the specification of parameters and exclusions.
const System& system = context.getSystem();
if (owner.getNumParticles() != system.getNumParticles())
throw OpenMMException("CustomNonbondedForce must have exactly as many particles as the System it belongs to.");
if (owner.getUseSwitchingFunction()) {
if (owner.getSwitchingDistance() < 0 || owner.getSwitchingDistance() >= owner.getCutoffDistance())
throw OpenMMException("CustomNonbondedForce: Switching distance must satisfy 0 <= r_switch < r_cutoff");
}
vector<set<int> > exclusions(owner.getNumParticles());
vector<double> parameters;
int numParameters = owner.getNumPerParticleParameters();
for (int i = 0; i < owner.getNumParticles(); i++) {
owner.getParticleParameters(i, parameters);
if (parameters.size() != numParameters) {
stringstream msg;
msg << "CustomNonbondedForce: Wrong number of parameters for particle ";
msg << i;
throw OpenMMException(msg.str());
}
}
for (int i = 0; i < owner.getNumExclusions(); i++) {
int particle1, particle2;
owner.getExclusionParticles(i, particle1, particle2);
if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
stringstream msg;
msg << "CustomNonbondedForce: Illegal particle index for an exclusion: ";
msg << particle1;
throw OpenMMException(msg.str());
}
if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
stringstream msg;
msg << "CustomNonbondedForce: Illegal particle index for an exclusion: ";
msg << particle2;
throw OpenMMException(msg.str());
}
if (exclusions[particle1].count(particle2) > 0 || exclusions[particle2].count(particle1) > 0) {
stringstream msg;
msg << "CustomNonbondedForce: Multiple exclusions are specified for particles ";
msg << particle1;
msg << " and ";
msg << particle2;
throw OpenMMException(msg.str());
}
exclusions[particle1].insert(particle2);
exclusions[particle2].insert(particle1);
}
if (owner.getNonbondedMethod() == CustomNonbondedForce::CutoffPeriodic) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double cutoff = owner.getCutoffDistance();
if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
throw OpenMMException("CustomNonbondedForce: The cutoff distance cannot be greater than half the periodic box size.");
}
// Check that all interaction groups only specify particles that have been defined.
for (int group = 0; group < owner.getNumInteractionGroups(); group++) {
set<int> set1, set2;
owner.getInteractionGroupParameters(group, set1, set2);
for (set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
if ((*it < 0) || (*it >= owner.getNumParticles())) {
stringstream msg;
msg << "CustomNonbondedForce: Interaction group " << group << " set1 contains a particle index (" << *it << ") "
<< "not present in system (" << owner.getNumParticles() << " particles).";
throw OpenMMException(msg.str());
}
for (set<int>::iterator it = set2.begin(); it != set2.end(); ++it)
if ((*it < 0) || (*it >= owner.getNumParticles())) {
stringstream msg;
msg << "CustomNonbondedForce: Interaction group " << group << " set2 contains a particle index (" << *it << ") "
<< "not present in system (" << owner.getNumParticles() << " particles).";
throw OpenMMException(msg.str());
}
}
kernel.getAs<CalcCustomNonbondedForceKernel>().initialize(context.getSystem(), owner);
}
void RBTorsionForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcRBTorsionForceKernel::Name(), context);
kernel.getAs<CalcRBTorsionForceKernel>().initialize(context.getSystem(), owner);
}
void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
const System& system = context.getSystem();
if (owner.getNumMultipoles() != system.getNumParticles())
throw OpenMMException("AmoebaMultipoleForce must have exactly as many particles as the System it belongs to.");
// check cutoff < 0.5*boxSize
if (owner.getNonbondedMethod() == AmoebaMultipoleForce::PME) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double cutoff = owner.getCutoffDistance();
if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
throw OpenMMException("AmoebaMultipoleForce: The cutoff distance cannot be greater than half the periodic box size.");
}
double quadrupoleValidationTolerance = 1.0e-05;
for( int ii = 0; ii < system.getNumParticles(); ii++ ){
int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
double charge, thole, dampingFactor, polarity ;
std::vector<double> molecularDipole;
std::vector<double> molecularQuadrupole;
owner.getMultipoleParameters( ii, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
thole, dampingFactor, polarity );
// check quadrupole is traceless and symmetric
double trace = fabs( molecularQuadrupole[0] + molecularQuadrupole[4] + molecularQuadrupole[8] );
if( trace > quadrupoleValidationTolerance ){
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: qudarupole for particle=" << ii;
buffer << " has nonzero trace: " << trace << "; AMOEBA plugin assumes traceless quadrupole.";
throw OpenMMException(buffer.str());
}
if( fabs( molecularQuadrupole[1] - molecularQuadrupole[3] ) > quadrupoleValidationTolerance ){
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: XY and YX components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[1] << " " << molecularQuadrupole[3] << "];";
buffer << " AMOEBA plugin assumes symmetric quadrupole tensor.";
throw OpenMMException(buffer.str());
}
if( fabs( molecularQuadrupole[2] - molecularQuadrupole[6] ) > quadrupoleValidationTolerance ){
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: XZ and ZX components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[2] << " " << molecularQuadrupole[6] << "];";
buffer << " AMOEBA plugin assumes symmetric quadrupole tensor.";
throw OpenMMException(buffer.str());
}
if( fabs( molecularQuadrupole[5] - molecularQuadrupole[7] ) > quadrupoleValidationTolerance ){
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: YZ and ZY components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[5] << " " << molecularQuadrupole[7] << "];";
buffer << " AMOEBA plugin assumes symmetric quadrupole tensor.";
throw OpenMMException(buffer.str());
}
// only 'Z-then-X', 'Bisector', Z-Bisect, ThreeFold currently handled
if( axisType != AmoebaMultipoleForce::ZThenX && axisType != AmoebaMultipoleForce::Bisector &&
axisType != AmoebaMultipoleForce::ZBisect && axisType != AmoebaMultipoleForce::ThreeFold &&
axisType != AmoebaMultipoleForce::ZOnly && axisType != AmoebaMultipoleForce::NoAxisType ) {
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: axis type=" << axisType;
buffer << " not currently handled - only axisTypes[ ";
buffer << AmoebaMultipoleForce::ZThenX << ", " << AmoebaMultipoleForce::Bisector << ", ";
buffer << AmoebaMultipoleForce::ZBisect << ", " << AmoebaMultipoleForce::ThreeFold << ", ";
buffer << AmoebaMultipoleForce::NoAxisType;
buffer << "] (ZThenX, Bisector, Z-Bisect, ThreeFold, NoAxisType) currently handled .";
throw OpenMMException(buffer.str());
}
}
kernel = context.getPlatform().createKernel(CalcAmoebaMultipoleForceKernel::Name(), context);
kernel.getAs<CalcAmoebaMultipoleForceKernel>().initialize(context.getSystem(), owner);
}
void DrudeForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcDrudeForceKernel::Name(), context);
const System& system = context.getSystem();
// Check for errors in the specification of particles.
set<int> usedParticles;
for (int i = 0; i < owner.getNumParticles(); i++) {
int particle, particle1, particle2, particle3, particle4;
double charge, k, k2, k3;
owner.getParticleParameters(i, particle, particle1, particle2, particle3, particle4, charge, k, k2, k3);
if (particle < 0 || particle >= system.getNumParticles()) {
stringstream msg;
msg << "DrudeForce: Illegal particle index: ";
msg << particle;
throw OpenMMException(msg.str());
}
if (particle1 < 0 || particle1 >= system.getNumParticles()) {
stringstream msg;
msg << "DrudeForce: Illegal particle index: ";
msg << particle1;
throw OpenMMException(msg.str());
}
if (particle2 < -1 || particle2 >= system.getNumParticles()) {
stringstream msg;
msg << "DrudeForce: Illegal particle index: ";
msg << particle2;
throw OpenMMException(msg.str());
}
if (particle3 < -1 || particle3 >= system.getNumParticles()) {
stringstream msg;
msg << "DrudeForce: Illegal particle index: ";
msg << particle3;
throw OpenMMException(msg.str());
}
if (particle4 < -1 || particle4 >= system.getNumParticles()) {
stringstream msg;
msg << "DrudeForce: Illegal particle index: ";
msg << particle4;
throw OpenMMException(msg.str());
}
if (usedParticles.find(particle) != usedParticles.end()) {
stringstream msg;
msg << "DrudeForce: Particle index is used by two different Drude particles: ";
msg << particle;
throw OpenMMException(msg.str());
}
usedParticles.insert(particle);
if (usedParticles.find(particle1) != usedParticles.end()) {
stringstream msg;
msg << "DrudeForce: Particle index is used by two different Drude particles: ";
msg << particle1;
throw OpenMMException(msg.str());
}
usedParticles.insert(particle1);
}
// Check for errors in the specification of screened pairs.
vector<set<int> > screenedPairs(owner.getNumParticles());
for (int i = 0; i < owner.getNumScreenedPairs(); i++) {
int particle1, particle2;
double thole;
owner.getScreenedPairParameters(i, particle1, particle2, thole);
if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
stringstream msg;
msg << "DrudeForce: Illegal particle index for a screened pair: ";
msg << particle1;
throw OpenMMException(msg.str());
}
if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
stringstream msg;
msg << "DrudeForce: Illegal particle index for a screened pair: ";
msg << particle2;
throw OpenMMException(msg.str());
}
if (screenedPairs[particle1].count(particle2) > 0 || screenedPairs[particle2].count(particle1) > 0) {
stringstream msg;
msg << "DrudeForce: Multiple screened pairs are specified for particles ";
msg << particle1;
msg << " and ";
msg << particle2;
throw OpenMMException(msg.str());
}
screenedPairs[particle1].insert(particle2);
screenedPairs[particle2].insert(particle1);
}
kernel.getAs<CalcDrudeForceKernel>().initialize(context.getSystem(), owner);
}