ReferenceCustomCompoundBondIxn::ReferenceCustomCompoundBondIxn(int numParticlesPerBond, const vector<vector<int> >& bondAtoms,
const Lepton::ParsedExpression& energyExpression, const vector<string>& bondParameterNames,
const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals) :
bondAtoms(bondAtoms), energyExpression(energyExpression.createProgram()), bondParamNames(bondParameterNames) {
for (int i = 0; i < numParticlesPerBond; i++) {
stringstream xname, yname, zname;
xname << 'x' << (i+1);
yname << 'y' << (i+1);
zname << 'z' << (i+1);
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(xname.str(), i, 0, energyExpression.differentiate(xname.str()).optimize().createProgram()));
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).optimize().createProgram()));
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).optimize().createProgram()));
}
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
distanceTerms.push_back(ReferenceCustomCompoundBondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
angleTerms.push_back(ReferenceCustomCompoundBondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
dihedralTerms.push_back(ReferenceCustomCompoundBondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
}
ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(const CustomManyParticleForce& force) : useCutoff(false), usePeriodic(false) {
numParticlesPerSet = force.getNumParticlesPerSet();
numPerParticleParameters = force.getNumPerParticleParameters();
centralParticleMode = (force.getPermutationMode() == CustomManyParticleForce::UniqueCentralParticle);
// Create custom functions for the tabulated functions.
map<string, Lepton::CustomFunction*> functions;
for (int i = 0; i < (int) force.getNumTabulatedFunctions(); i++)
functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
// Parse the expression and create the object used to calculate the interaction.
map<string, vector<int> > distances;
map<string, vector<int> > angles;
map<string, vector<int> > dihedrals;
Lepton::ParsedExpression energyExpr = CustomManyParticleForceImpl::prepareExpression(force, functions, distances, angles, dihedrals);
energyExpression = energyExpr.createProgram();
vector<string> particleParameterNames;
if (force.getNonbondedMethod() != CustomManyParticleForce::NoCutoff)
setUseCutoff(force.getCutoffDistance());
// Delete the custom functions.
for (auto& function : functions)
delete function.second;
// Differentiate the energy to get expressions for the force.
particleParamNames.resize(numParticlesPerSet);
for (int i = 0; i < numParticlesPerSet; i++) {
stringstream xname, yname, zname;
xname << 'x' << (i+1);
yname << 'y' << (i+1);
zname << 'z' << (i+1);
particleTerms.push_back(ReferenceCustomManyParticleIxn::ParticleTermInfo(xname.str(), i, 0, energyExpr.differentiate(xname.str()).optimize().createProgram()));
particleTerms.push_back(ReferenceCustomManyParticleIxn::ParticleTermInfo(yname.str(), i, 1, energyExpr.differentiate(yname.str()).optimize().createProgram()));
particleTerms.push_back(ReferenceCustomManyParticleIxn::ParticleTermInfo(zname.str(), i, 2, energyExpr.differentiate(zname.str()).optimize().createProgram()));
for (int j = 0; j < numPerParticleParameters; j++) {
stringstream paramname;
paramname << force.getPerParticleParameterName(j) << (i+1);
particleParamNames[i].push_back(paramname.str());
}
}
for (auto& term : distances)
distanceTerms.push_back(ReferenceCustomManyParticleIxn::DistanceTermInfo(term.first, term.second, energyExpr.differentiate(term.first).optimize().createProgram()));
for (auto& term : angles)
angleTerms.push_back(ReferenceCustomManyParticleIxn::AngleTermInfo(term.first, term.second, energyExpr.differentiate(term.first).optimize().createProgram()));
for (auto& term : dihedrals)
dihedralTerms.push_back(ReferenceCustomManyParticleIxn::DihedralTermInfo(term.first, term.second, energyExpr.differentiate(term.first).optimize().createProgram()));
// Record exclusions.
exclusions.resize(force.getNumParticles());
for (int i = 0; i < (int) force.getNumExclusions(); i++) {
int p1, p2;
force.getExclusionParticles(i, p1, p2);
exclusions[p1].insert(p2);
exclusions[p2].insert(p1);
}
// Record information about type filters.
CustomManyParticleForceImpl::buildFilterArrays(force, numTypes, particleTypes, orderIndex, particleOrder);
}
ReferenceCustomHbondIxn::ReferenceCustomHbondIxn(const vector<vector<int> >& donorAtoms, const vector<vector<int> >& acceptorAtoms,
const Lepton::ParsedExpression& energyExpression, const vector<string>& donorParameterNames, const vector<string>& acceptorParameterNames,
const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals) :
cutoff(false), periodic(false), donorAtoms(donorAtoms), acceptorAtoms(acceptorAtoms), energyExpression(energyExpression.createProgram()),
donorParamNames(donorParameterNames), acceptorParamNames(acceptorParameterNames) {
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
distanceTerms.push_back(ReferenceCustomHbondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
angleTerms.push_back(ReferenceCustomHbondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
dihedralTerms.push_back(ReferenceCustomHbondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
}