CpuCustomManyParticleForce::ThreadData::ThreadData(const CustomManyParticleForce& force, Lepton::ParsedExpression& energyExpr,
map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
int numParticlesPerSet = force.getNumParticlesPerSet();
int numPerParticleParameters = force.getNumPerParticleParameters();
particleParamIndices.resize(numParticlesPerSet);
permutedParticles.resize(numParticlesPerSet);
f.resize(numParticlesPerSet);
energyExpression = energyExpr.createCompiledExpression();
expressionSet.registerExpression(energyExpression);
// Differentiate the energy to get expressions for the force.
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(CpuCustomManyParticleForce::ParticleTermInfo(xname.str(), i, 0, energyExpr.differentiate(xname.str()).optimize().createCompiledExpression(), *this));
particleTerms.push_back(CpuCustomManyParticleForce::ParticleTermInfo(yname.str(), i, 1, energyExpr.differentiate(yname.str()).optimize().createCompiledExpression(), *this));
particleTerms.push_back(CpuCustomManyParticleForce::ParticleTermInfo(zname.str(), i, 2, energyExpr.differentiate(zname.str()).optimize().createCompiledExpression(), *this));
for (int j = 0; j < numPerParticleParameters; j++) {
stringstream paramname;
paramname << force.getPerParticleParameterName(j) << (i+1);
particleParamIndices[i].push_back(expressionSet.getVariableIndex(paramname.str()));
}
}
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
dihedralTerms.push_back(CpuCustomManyParticleForce::DihedralTermInfo(iter->first, iter->second, energyExpr.differentiate(iter->first).optimize().createCompiledExpression(), *this));
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
distanceTerms.push_back(CpuCustomManyParticleForce::DistanceTermInfo(iter->first, iter->second, energyExpr.differentiate(iter->first).optimize().createCompiledExpression(), *this));
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
angleTerms.push_back(CpuCustomManyParticleForce::AngleTermInfo(iter->first, iter->second, energyExpr.differentiate(iter->first).optimize().createCompiledExpression(), *this));
for (int i = 0; i < particleTerms.size(); i++)
expressionSet.registerExpression(particleTerms[i].forceExpression);
for (int i = 0; i < distanceTerms.size(); i++)
expressionSet.registerExpression(distanceTerms[i].forceExpression);
for (int i = 0; i < angleTerms.size(); i++)
expressionSet.registerExpression(angleTerms[i].forceExpression);
for (int i = 0; i < dihedralTerms.size(); i++)
expressionSet.registerExpression(dihedralTerms[i].forceExpression);
int numDeltas = deltaPairs.size();
delta.resize(numDeltas);
normDelta.resize(numDeltas);
norm2Delta.resize(numDeltas);
cross1.resize(numDeltas);
cross2.resize(numDeltas);
}
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,
const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions) :
bondAtoms(bondAtoms), energyExpression(energyExpression.createCompiledExpression()), usePeriodic(false),
energyParamDerivExpressions(energyParamDerivExpressions) {
expressionSet.registerExpression(this->energyExpression);
for (int i = 0; i < this->energyParamDerivExpressions.size(); i++)
expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
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()).createCompiledExpression()));
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).createCompiledExpression()));
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).createCompiledExpression()));
}
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).createCompiledExpression()));
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).createCompiledExpression()));
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).createCompiledExpression()));
for (int i = 0; i < particleTerms.size(); i++) {
expressionSet.registerExpression(particleTerms[i].forceExpression);
particleTerms[i].index = expressionSet.getVariableIndex(particleTerms[i].name);
}
for (int i = 0; i < distanceTerms.size(); i++) {
expressionSet.registerExpression(distanceTerms[i].forceExpression);
distanceTerms[i].index = expressionSet.getVariableIndex(distanceTerms[i].name);
}
for (int i = 0; i < angleTerms.size(); i++) {
expressionSet.registerExpression(angleTerms[i].forceExpression);
angleTerms[i].index = expressionSet.getVariableIndex(angleTerms[i].name);
}
for (int i = 0; i < dihedralTerms.size(); i++) {
expressionSet.registerExpression(dihedralTerms[i].forceExpression);
dihedralTerms[i].index = expressionSet.getVariableIndex(dihedralTerms[i].name);
}
numParameters = bondParameterNames.size();
for (int i = 0; i < numParameters; i++)
bondParamIndex.push_back(expressionSet.getVariableIndex(bondParameterNames[i]));
}
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);
}
void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const CustomNonbondedForce& force) {
// Record the exclusions.
numParticles = force.getNumParticles();
exclusions.resize(numParticles);
for (int i = 0; i < force.getNumExclusions(); i++) {
int particle1, particle2;
force.getExclusionParticles(i, particle1, particle2);
exclusions[particle1].insert(particle2);
exclusions[particle2].insert(particle1);
}
// Build the arrays.
int numParameters = force.getNumPerParticleParameters();
particleParamArray = new double*[numParticles];
for (int i = 0; i < numParticles; i++)
particleParamArray[i] = new double[numParameters];
for (int i = 0; i < numParticles; ++i) {
vector<double> parameters;
force.getParticleParameters(i, parameters);
for (int j = 0; j < numParameters; j++)
particleParamArray[i][j] = parameters[j];
}
nonbondedMethod = CalcCustomNonbondedForceKernel::NonbondedMethod(force.getNonbondedMethod());
nonbondedCutoff = force.getCutoffDistance();
if (nonbondedMethod == NoCutoff)
useSwitchingFunction = false;
else {
neighborList = new CpuNeighborList(4);
useSwitchingFunction = force.getUseSwitchingFunction();
switchingDistance = force.getSwitchingDistance();
}
// Create custom functions for the tabulated functions.
map<string, Lepton::CustomFunction*> functions;
for (int i = 0; i < force.getNumFunctions(); i++)
functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
// Parse the various expressions used to calculate the force.
Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions).optimize();
Lepton::CompiledExpression energyExpression = expression.createCompiledExpression();
Lepton::CompiledExpression forceExpression = expression.differentiate("r").createCompiledExpression();
for (int i = 0; i < numParameters; i++)
parameterNames.push_back(force.getPerParticleParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParameterNames.push_back(force.getGlobalParameterName(i));
globalParamValues[force.getGlobalParameterName(i)] = force.getGlobalParameterDefaultValue(i);
}
// Delete the custom functions.
for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
delete iter->second;
// Record information for the long range correction.
if (force.getNonbondedMethod() == CustomNonbondedForce::CutoffPeriodic && force.getUseLongRangeCorrection()) {
forceCopy = new CustomNonbondedForce(force);
hasInitializedLongRangeCorrection = false;
}
else {
longRangeCoefficient = 0.0;
hasInitializedLongRangeCorrection = true;
}
// Record the interaction groups.
for (int i = 0; i < force.getNumInteractionGroups(); i++) {
set<int> set1, set2;
force.getInteractionGroupParameters(i, set1, set2);
interactionGroups.push_back(make_pair(set1, set2));
}
data.isPeriodic = (nonbondedMethod == CutoffPeriodic);
nonbonded = new CpuCustomNonbondedForce(energyExpression, forceExpression, parameterNames, exclusions, data.threads);
if (interactionGroups.size() > 0)
nonbonded->setInteractionGroups(interactionGroups);
}
bool CustomIntegratorUtilities::usesVariable(const Lepton::ParsedExpression& expression, const string& variable) {
return usesVariable(expression.getRootNode(), variable);
}
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()));
}