void RMSDForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcRMSDForceKernel::Name(), context);
// Check for errors in the specification of particles.
const System& system = context.getSystem();
int numParticles = system.getNumParticles();
if (owner.getReferencePositions().size() != numParticles)
throw OpenMMException("RMSDForce: Number of reference positions does not equal number of particles in the System");
set<int> particles;
for (int i : owner.getParticles()) {
if (i < 0 || i >= numParticles) {
stringstream msg;
msg << "RMSDForce: Illegal particle index for RMSD: ";
msg << i;
throw OpenMMException(msg.str());
}
if (particles.find(i) != particles.end()) {
stringstream msg;
msg << "RMSDForce: Duplicated particle index for RMSD: ";
msg << i;
throw OpenMMException(msg.str());
}
particles.insert(i);
}
kernel.getAs<CalcRMSDForceKernel>().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.");
}
kernel.getAs<CalcCustomNonbondedForceKernel>().initialize(context.getSystem(), owner);
}
void AmoebaWcaDispersionForceImpl::initialize(ContextImpl& context) {
const System& system = context.getSystem();
if (owner.getNumParticles() != system.getNumParticles())
throw OpenMMException("AmoebaWcaDispersionForce must have exactly as many particles as the System it belongs to.");
kernel = context.getPlatform().createKernel(CalcAmoebaWcaDispersionForceKernel::Name(), context);
kernel.getAs<CalcAmoebaWcaDispersionForceKernel>().initialize(context.getSystem(), owner);
}
void RPMDIntegrator::initialize(ContextImpl& contextRef) {
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
if (contextRef.getSystem().getNumConstraints() > 0)
throw OpenMMException("RPMDIntegrator cannot be used with Systems that include constraints");
context = &contextRef;
owner = &contextRef.getOwner();
kernel = context->getPlatform().createKernel(IntegrateRPMDStepKernel::Name(), contextRef);
kernel.getAs<IntegrateRPMDStepKernel>().initialize(contextRef.getSystem(), *this);
}
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::CutoffPeriodic ||
owner.getNonbondedMethod() == NonbondedForce::Ewald ||
owner.getNonbondedMethod() == NonbondedForce::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("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 GBSAOBCForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcGBSAOBCForceKernel::Name(), context);
if (owner.getNumParticles() != context.getSystem().getNumParticles())
throw OpenMMException("GBSAOBCForce must have exactly as many particles as the System it belongs to.");
if (owner.getNonbondedMethod() == GBSAOBCForce::CutoffPeriodic) {
Vec3 boxVectors[3];
context.getSystem().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("GBSAOBCForce: The cutoff distance cannot be greater than half the periodic box size.");
}
kernel.getAs<CalcGBSAOBCForceKernel>().initialize(context.getSystem(), owner);
}
static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>& inverseMasses, double timeShift, ReferenceConstraintAlgorithm* constraints) {
const System& system = context.getSystem();
int numParticles = system.getNumParticles();
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& velData = extractVelocities(context);
vector<RealVec>& forceData = extractForces(context);
// Compute the shifted velocities.
vector<RealVec> shiftedVel(numParticles);
for (int i = 0; i < numParticles; ++i) {
if (inverseMasses[i] > 0)
shiftedVel[i] = velData[i]+forceData[i]*(timeShift*inverseMasses[i]);
else
shiftedVel[i] = velData[i];
}
// Apply constraints to them.
if (constraints != NULL) {
constraints->setTolerance(1e-4);
constraints->applyToVelocities(numParticles, posData, shiftedVel, inverseMasses);
}
// Compute the kinetic energy.
double energy = 0.0;
for (int i = 0; i < numParticles; ++i)
if (inverseMasses[i] > 0)
energy += (shiftedVel[i].dot(shiftedVel[i]))/inverseMasses[i];
return 0.5*energy;
}
/**
* Compute the kinetic energy of the system, possibly shifting the velocities in time to account
* for a leapfrog integrator.
*/
static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>& masses, double timeShift) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& velData = extractVelocities(context);
vector<RealVec>& forceData = extractForces(context);
int numParticles = context.getSystem().getNumParticles();
// Compute the shifted velocities.
vector<RealVec> shiftedVel(numParticles);
for (int i = 0; i < numParticles; ++i) {
if (masses[i] > 0)
shiftedVel[i] = velData[i]+forceData[i]*(timeShift/masses[i]);
else
shiftedVel[i] = velData[i];
}
// Apply constraints to them.
vector<double> inverseMasses(numParticles);
for (int i = 0; i < numParticles; i++)
inverseMasses[i] = (masses[i] == 0 ? 0 : 1/masses[i]);
extractConstraints(context).applyToVelocities(posData, shiftedVel, inverseMasses, 1e-4);
// Compute the kinetic energy.
double energy = 0.0;
for (int i = 0; i < numParticles; ++i)
if (masses[i] > 0)
energy += masses[i]*(shiftedVel[i].dot(shiftedVel[i]));
return 0.5*energy;
}
void CustomIntegrator::initialize(ContextImpl& contextRef) {
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
vector<std::string> variableList;
set<std::string> variableSet;
variableList.insert(variableList.end(), globalNames.begin(), globalNames.end());
variableList.insert(variableList.end(), perDofNames.begin(), perDofNames.end());
for (int i = 0; i < (int) variableList.size(); i++) {
string& name = variableList[i];
if (variableSet.find(name) != variableSet.end())
throw OpenMMException("The Integrator defines two variables with the same name: "+name);
variableSet.insert(name);
if (contextRef.getParameters().find(name) != contextRef.getParameters().end())
throw OpenMMException("The Integrator defines a variable with the same name as a Context parameter: "+name);
}
set<std::string> globalTargets;
globalTargets.insert(globalNames.begin(), globalNames.end());
globalTargets.insert("dt");
for (map<string, double>::const_iterator iter = contextRef.getParameters().begin(); iter != contextRef.getParameters().end(); ++iter)
globalTargets.insert(iter->first);
for (int i = 0; i < computations.size(); i++) {
if (computations[i].type == ComputeGlobal && globalTargets.find(computations[i].variable) == globalTargets.end())
throw OpenMMException("Unknown global variable: "+computations[i].variable);
}
context = &contextRef;
owner = &contextRef.getOwner();
kernel = context->getPlatform().createKernel(IntegrateCustomStepKernel::Name(), contextRef);
kernel.getAs<IntegrateCustomStepKernel>().initialize(contextRef.getSystem(), *this);
kernel.getAs<IntegrateCustomStepKernel>().setGlobalVariables(contextRef, globalValues);
for (int i = 0; i < (int) perDofValues.size(); i++) {
if (perDofValues[i].size() == 1)
perDofValues[i].resize(context->getSystem().getNumParticles(), perDofValues[i][0]);
kernel.getAs<IntegrateCustomStepKernel>().setPerDofVariable(contextRef, i, perDofValues[i]);
}
}
double CpuCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) {
// Sum the forces from all the threads.
SumForceTask task(context.getSystem().getNumParticles(), extractForces(context), data);
data.threads.execute(task);
data.threads.waitForThreads();
return referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().finishComputation(context, includeForce, includeEnergy, groups);
}
void VariableLangevinIntegrator::initialize(ContextImpl& contextRef) {
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
context = &contextRef;
owner = &contextRef.getOwner();
kernel = context->getPlatform().createKernel(IntegrateVariableLangevinStepKernel::Name(), contextRef);
kernel.getAs<IntegrateVariableLangevinStepKernel>().initialize(contextRef.getSystem(), *this);
}
void Integrator::initialize( ContextImpl &contextRef ) {
context = &contextRef;
if( context->getSystem().getNumConstraints() > 0 ) {
throw OpenMMException( "LTMD Integrator does not support constraints" );
}
kernel = context->getPlatform().createKernel( StepKernel::Name(), contextRef );
( ( StepKernel & )( kernel.getImpl() ) ).initialize( contextRef.getSystem(), *this );
//(dynamic_cast<StepKernel &>( kernel.getImpl() )).initialize( contextRef.getSystem(), *this );
}
void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) {
referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().beginComputation(context, includeForce, includeEnergy, groups);
// Convert positions to single precision and clear the forces.
InitForceTask task(context.getSystem().getNumParticles(), context, data);
data.threads.execute(task);
data.threads.waitForThreads();
}
void DrudeLangevinIntegrator::initialize(ContextImpl& contextRef) {
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
const DrudeForce* force = NULL;
const System& system = contextRef.getSystem();
for (int i = 0; i < system.getNumForces(); i++)
if (dynamic_cast<const DrudeForce*>(&system.getForce(i)) != NULL) {
if (force == NULL)
force = dynamic_cast<const DrudeForce*>(&system.getForce(i));
else
throw OpenMMException("The System contains multiple DrudeForces");
}
if (force == NULL)
throw OpenMMException("The System does not contain a DrudeForce");
context = &contextRef;
owner = &contextRef.getOwner();
kernel = context->getPlatform().createKernel(IntegrateDrudeLangevinStepKernel::Name(), contextRef);
kernel.getAs<IntegrateDrudeLangevinStepKernel>().initialize(contextRef.getSystem(), *this, *force);
}
void MonteCarloAnisotropicBarostatImpl::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];
for (int i=0; i<3; i++) {
volumeScale[i] = 0.01*volume;
numAttempted[i] = 0;
numAccepted[i] = 0;
}
init_gen_rand(owner.getRandomNumberSeed(), random);
}
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);
}
double ReferenceIntegrateRPMDStepKernel::computeKineticEnergy(ContextImpl& context, const RPMDIntegrator& integrator) {
const System& system = context.getSystem();
int numParticles = system.getNumParticles();
vector<RealVec>& velData = extractVelocities(context);
double energy = 0.0;
for (int i = 0; i < numParticles; ++i) {
double mass = system.getParticleMass(i);
if (mass > 0) {
RealVec v = velData[i];
energy += mass*(v.dot(v));
}
}
return 0.5*energy;
}
void CpuIntegrateLangevinStepKernel::execute(ContextImpl& context, const LangevinIntegrator& integrator) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& velData = extractVelocities(context);
vector<RealVec>& forceData = extractForces(context);
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters.
if (dynamics)
delete dynamics;
RealOpenMM tau = (friction == 0.0 ? 0.0 : 1.0/friction);
dynamics = new CpuLangevinDynamics(context.getSystem().getNumParticles(), stepSize, tau, temperature, data.threads, data.random);
dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
prevTemp = temperature;
prevFriction = friction;
prevStepSize = stepSize;
}
dynamics->update(context.getSystem(), posData, velData, forceData, masses, integrator.getConstraintTolerance());
ReferencePlatform::PlatformData* refData = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
refData->time += stepSize;
refData->stepCount++;
}
void CpuCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const NonbondedForce& force) {
if (force.getNumParticles() != numParticles)
throw OpenMMException("updateParametersInContext: The number of particles has changed");
vector<int> nb14s;
for (int i = 0; i < force.getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
if (chargeProd != 0.0 || epsilon != 0.0)
nb14s.push_back(i);
}
if (nb14s.size() != num14)
throw OpenMMException("updateParametersInContext: The number of non-excluded exceptions has changed");
// Record the values.
double sumSquaredCharges = 0.0;
for (int i = 0; i < numParticles; ++i) {
double charge, radius, depth;
force.getParticleParameters(i, charge, radius, depth);
data.posq[4*i+3] = (float) charge;
particleParams[i] = make_pair((float) (0.5*radius), (float) (2.0*sqrt(depth)));
sumSquaredCharges += charge*charge;
}
if (nonbondedMethod == Ewald || nonbondedMethod == PME)
ewaldSelfEnergy = -ONE_4PI_EPS0*ewaldAlpha*sumSquaredCharges/sqrt(M_PI);
else
ewaldSelfEnergy = 0.0;
for (int i = 0; i < num14; ++i) {
int particle1, particle2;
double charge, radius, depth;
force.getExceptionParameters(nb14s[i], particle1, particle2, charge, radius, depth);
bonded14IndexArray[i][0] = particle1;
bonded14IndexArray[i][1] = particle2;
bonded14ParamArray[i][0] = static_cast<RealOpenMM>(radius);
bonded14ParamArray[i][1] = static_cast<RealOpenMM>(4.0*depth);
bonded14ParamArray[i][2] = static_cast<RealOpenMM>(charge);
}
// Recompute the coefficient for the dispersion correction.
NonbondedForce::NonbondedMethod method = force.getNonbondedMethod();
if (force.getUseDispersionCorrection() && (method == NonbondedForce::CutoffPeriodic || method == NonbondedForce::Ewald || method == NonbondedForce::PME))
dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(context.getSystem(), force);
}
void ReferenceCalcMBPolElectrostaticsForceKernel::getSystemElectrostaticsMoments(ContextImpl& context, std::vector< double >& outputElectrostaticsMoments){
// retrieve masses
const OpenMM::System& system = context.getSystem();
vector<RealOpenMM> masses;
for (int i = 0; i < system.getNumParticles(); ++i) {
masses.push_back( static_cast<RealOpenMM>(system.getParticleMass(i)) );
}
MBPolReferenceElectrostaticsForce* mbpolReferenceElectrostaticsForce = setupMBPolReferenceElectrostaticsForce( context );
vector<RealVec>& posData = extractPositions(context);
mbpolReferenceElectrostaticsForce->calculateMBPolSystemElectrostaticsMoments( masses, posData, charges, tholes,
dampingFactors, polarity, axisTypes,
multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, outputElectrostaticsMoments );
delete mbpolReferenceElectrostaticsForce;
return;
}
void ReferenceIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const DrudeSCFIntegrator& integrator) {
vector<RealVec>& pos = extractPositions(context);
vector<RealVec>& vel = extractVelocities(context);
vector<RealVec>& force = extractForces(context);
// Update the positions and velocities.
int numParticles = particleInvMass.size();
vector<RealVec> xPrime(numParticles);
RealOpenMM dt = integrator.getStepSize();
for (int i = 0; i < numParticles; i++) {
if (particleInvMass[i] != 0.0) {
vel[i] += force[i]*particleInvMass[i]*dt;
xPrime[i] = pos[i]+vel[i]*dt;
}
}
// Apply constraints.
if (constraints != NULL)
constraints->apply(numParticles, pos, xPrime, particleInvMass);
// Record the constrained positions and velocities.
RealOpenMM dtInv = 1.0/dt;
for (int i = 0; i < numParticles; i++) {
if (particleInvMass[i] != 0.0) {
vel[i] = (xPrime[i]-pos[i])*dtInv;
pos[i] = xPrime[i];
}
}
// Update the positions of virtual sites and Drude particles.
ReferenceVirtualSites::computePositions(context.getSystem(), pos);
minimize(context, integrator.getMinimizationErrorTolerance());
data.time += integrator.getStepSize();
data.stepCount++;
}
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);
}
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 ReferencePlatform::contextCreated(ContextImpl& context, const map<string, string>& properties) const {
context.setPlatformData(new PlatformData(context.getSystem()));
}
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses,
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance) {
if (invalidatesForces.size() == 0)
initialize(context, masses, globals);
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
oldPos = atomCoordinates;
// Loop over steps and execute them.
for (int step = 0; step < numSteps; ) {
if ((needsForces[step] || needsEnergy[step]) && (!forcesAreValid || context.getLastForceGroups() != forceGroupFlags[step])) {
// Recompute forces and/or energy.
bool computeForce = needsForces[step] || computeBothForceAndEnergy[step];
bool computeEnergy = needsEnergy[step] || computeBothForceAndEnergy[step];
recordChangedParameters(context, globals);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
if (computeEnergy) {
energy = e;
context.getEnergyParameterDerivatives(energyParamDerivs);
}
forcesAreValid = true;
}
// Execute the step.
int nextStep = step+1;
switch (stepType[step]) {
case CustomIntegrator::ComputeGlobal: {
uniform = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
gaussian = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
RealOpenMM result = stepExpressions[step][0].evaluate();
globals[stepVariable[step]] = result;
expressionSet.setVariable(stepVariableIndex[step], result);
break;
}
case CustomIntegrator::ComputePerDof: {
vector<RealVec>* results = NULL;
if (stepVariableIndex[step] == xIndex)
results = &atomCoordinates;
else if (stepVariableIndex[step] == vIndex)
results = &velocities;
else {
for (int j = 0; j < integrator.getNumPerDofVariables(); j++)
if (stepVariableIndex[step] == perDofVariableIndex[j])
results = &perDof[j];
}
if (results == NULL)
throw OpenMMException("Illegal per-DOF output variable: "+stepVariable[step]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0]);
break;
}
case CustomIntegrator::ComputeSum: {
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0]);
RealOpenMM sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
sum += sumBuffer[j][0]+sumBuffer[j][1]+sumBuffer[j][2];
globals[stepVariable[step]] = sum;
expressionSet.setVariable(stepVariableIndex[step], sum);
break;
}
case CustomIntegrator::ConstrainPositions: {
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses, tolerance);
oldPos = atomCoordinates;
break;
}
case CustomIntegrator::ConstrainVelocities: {
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses, tolerance);
break;
}
case CustomIntegrator::UpdateContextState: {
recordChangedParameters(context, globals);
context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
break;
}
case CustomIntegrator::IfBlockStart: {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::WhileBlockStart: {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::BlockEnd: {
if (blockEnd[step] != -1)
nextStep = blockEnd[step]; // Return to the start of a while block.
break;
}
}
if (invalidatesForces[step])
forcesAreValid = false;
step = nextStep;
}
ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
incrementTimeStep();
recordChangedParameters(context, globals);
}
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 RBTorsionForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcRBTorsionForceKernel::Name(), context);
kernel.getAs<CalcRBTorsionForceKernel>().initialize(context.getSystem(), owner);
}
void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
vector<RealVec>& pos = extractPositions(context);
vector<RealVec>& vel = extractVelocities(context);
vector<RealVec>& force = extractForces(context);
// Update velocities of ordinary particles.
const RealOpenMM vscale = exp(-integrator.getStepSize()*integrator.getFriction());
const RealOpenMM fscale = (1-vscale)/integrator.getFriction();
const RealOpenMM kT = BOLTZ*integrator.getTemperature();
const RealOpenMM noisescale = sqrt(2*kT*integrator.getFriction())*sqrt(0.5*(1-vscale*vscale)/integrator.getFriction());
for (int i = 0; i < (int) normalParticles.size(); i++) {
int index = normalParticles[i];
RealOpenMM invMass = particleInvMass[index];
if (invMass != 0.0) {
RealOpenMM sqrtInvMass = sqrt(invMass);
for (int j = 0; j < 3; j++)
vel[index][j] = vscale*vel[index][j] + fscale*invMass*force[index][j] + noisescale*sqrtInvMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
}
// Update velocities of Drude particle pairs.
const RealOpenMM vscaleDrude = exp(-integrator.getStepSize()*integrator.getDrudeFriction());
const RealOpenMM fscaleDrude = (1-vscaleDrude)/integrator.getDrudeFriction();
const RealOpenMM kTDrude = BOLTZ*integrator.getDrudeTemperature();
const RealOpenMM noisescaleDrude = sqrt(2*kTDrude*integrator.getDrudeFriction())*sqrt(0.5*(1-vscaleDrude*vscaleDrude)/integrator.getDrudeFriction());
for (int i = 0; i < (int) pairParticles.size(); i++) {
int p1 = pairParticles[i].first;
int p2 = pairParticles[i].second;
RealOpenMM mass1fract = pairInvTotalMass[i]/particleInvMass[p1];
RealOpenMM mass2fract = pairInvTotalMass[i]/particleInvMass[p2];
RealOpenMM sqrtInvTotalMass = sqrt(pairInvTotalMass[i]);
RealOpenMM sqrtInvReducedMass = sqrt(pairInvReducedMass[i]);
RealVec cmVel = vel[p1]*mass1fract+vel[p2]*mass2fract;
RealVec relVel = vel[p2]-vel[p1];
RealVec cmForce = force[p1]+force[p2];
RealVec relForce = force[p2]*mass1fract - force[p1]*mass2fract;
for (int j = 0; j < 3; j++) {
cmVel[j] = vscale*cmVel[j] + fscale*pairInvTotalMass[i]*cmForce[j] + noisescale*sqrtInvTotalMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
relVel[j] = vscaleDrude*relVel[j] + fscaleDrude*pairInvReducedMass[i]*relForce[j] + noisescaleDrude*sqrtInvReducedMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
vel[p1] = cmVel-relVel*mass2fract;
vel[p2] = cmVel+relVel*mass1fract;
}
// Update the particle positions.
int numParticles = particleInvMass.size();
vector<RealVec> xPrime(numParticles);
RealOpenMM dt = integrator.getStepSize();
for (int i = 0; i < numParticles; i++)
if (particleInvMass[i] != 0.0)
xPrime[i] = pos[i]+vel[i]*dt;
// Apply constraints.
extractConstraints(context).apply(pos, xPrime, particleInvMass, integrator.getConstraintTolerance());
// Record the constrained positions and velocities.
RealOpenMM dtInv = 1.0/dt;
for (int i = 0; i < numParticles; i++) {
if (particleInvMass[i] != 0.0) {
vel[i] = (xPrime[i]-pos[i])*dtInv;
pos[i] = xPrime[i];
}
}
// Apply hard wall constraints.
const RealOpenMM maxDrudeDistance = integrator.getMaxDrudeDistance();
if (maxDrudeDistance > 0) {
const RealOpenMM hardwallscaleDrude = sqrt(kTDrude);
for (int i = 0; i < (int) pairParticles.size(); i++) {
int p1 = pairParticles[i].first;
int p2 = pairParticles[i].second;
RealVec delta = pos[p1]-pos[p2];
RealOpenMM r = sqrt(delta.dot(delta));
RealOpenMM rInv = 1/r;
if (rInv*maxDrudeDistance < 1.0) {
// The constraint has been violated, so make the inter-particle distance "bounce"
// off the hard wall.
if (rInv*maxDrudeDistance < 0.5)
throw OpenMMException("Drude particle moved too far beyond hard wall constraint");
RealVec bondDir = delta*rInv;
RealVec vel1 = vel[p1];
RealVec vel2 = vel[p2];
RealOpenMM mass1 = particleMass[p1];
RealOpenMM mass2 = particleMass[p2];
RealOpenMM deltaR = r-maxDrudeDistance;
RealOpenMM deltaT = dt;
RealOpenMM dotvr1 = vel1.dot(bondDir);
RealVec vb1 = bondDir*dotvr1;
RealVec vp1 = vel1-vb1;
if (mass2 == 0) {
// The parent particle is massless, so move only the Drude particle.
if (dotvr1 != 0.0)
deltaT = deltaR/abs(dotvr1);
if (deltaT > dt)
deltaT = dt;
dotvr1 = -dotvr1*hardwallscaleDrude/(abs(dotvr1)*sqrt(mass1));
RealOpenMM dr = -deltaR + deltaT*dotvr1;
pos[p1] += bondDir*dr;
vel[p1] = vp1 + bondDir*dotvr1;
}
else {
// Move both particles.
RealOpenMM invTotalMass = pairInvTotalMass[i];
RealOpenMM dotvr2 = vel2.dot(bondDir);
RealVec vb2 = bondDir*dotvr2;
RealVec vp2 = vel2-vb2;
RealOpenMM vbCMass = (mass1*dotvr1 + mass2*dotvr2)*invTotalMass;
dotvr1 -= vbCMass;
dotvr2 -= vbCMass;
if (dotvr1 != dotvr2)
deltaT = deltaR/abs(dotvr1-dotvr2);
if (deltaT > dt)
deltaT = dt;
RealOpenMM vBond = hardwallscaleDrude/sqrt(mass1);
dotvr1 = -dotvr1*vBond*mass2*invTotalMass/abs(dotvr1);
dotvr2 = -dotvr2*vBond*mass1*invTotalMass/abs(dotvr2);
RealOpenMM dr1 = -deltaR*mass2*invTotalMass + deltaT*dotvr1;
RealOpenMM dr2 = deltaR*mass1*invTotalMass + deltaT*dotvr2;
dotvr1 += vbCMass;
dotvr2 += vbCMass;
pos[p1] += bondDir*dr1;
pos[p2] += bondDir*dr2;
vel[p1] = vp1 + bondDir*dotvr1;
vel[p2] = vp2 + bondDir*dotvr2;
}
}
}
}
ReferenceVirtualSites::computePositions(context.getSystem(), pos);
data.time += integrator.getStepSize();
data.stepCount++;
}
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses,
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance) {
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
oldPos = atomCoordinates;
if (invalidatesForces.size() == 0) {
// Some initialization can't be done in the constructor, since we need a ContextImpl from which to get the list of
// Context parameters. Instead, we do it the first time this method is called.
vector<int> forceGroup;
vector<vector<Lepton::ParsedExpression> > expressions;
CustomIntegratorUtilities::analyzeComputations(context, integrator, expressions, comparisons, blockEnd, invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy, forceGroup);
stepExpressions.resize(expressions.size());
for (int i = 0; i < numSteps; i++) {
for (int j = 0; j < (int) expressions[i].size(); j++)
stepExpressions[i].push_back(expressions[i][j].createProgram());
if (stepType[i] == CustomIntegrator::BeginWhileBlock)
blockEnd[blockEnd[i]] = i; // Record where to branch back to.
}
// Record the variable names and flags for the force and energy in each step.
forceGroupFlags.resize(numSteps, -1);
forceName.resize(numSteps, "f");
energyName.resize(numSteps, "energy");
vector<string> forceGroupName;
vector<string> energyGroupName;
for (int i = 0; i < 32; i++) {
stringstream fname;
fname << "f" << i;
forceGroupName.push_back(fname.str());
stringstream ename;
ename << "energy" << i;
energyGroupName.push_back(ename.str());
}
for (int i = 0; i < numSteps; i++) {
if (needsForces[i] && forceGroup[i] > -1)
forceName[i] = forceGroupName[forceGroup[i]];
if (needsEnergy[i] && forceGroup[i] > -1)
energyName[i] = energyGroupName[forceGroup[i]];
if (forceGroup[i] > -1)
forceGroupFlags[i] = 1<<forceGroup[i];
}
// Build the list of inverse masses.
inverseMasses.resize(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; i++) {
if (masses[i] == 0.0)
inverseMasses[i] = 0.0;
else
inverseMasses[i] = 1.0/masses[i];
}
}
// Loop over steps and execute them.
for (int step = 0; step < numSteps; ) {
if ((needsForces[step] || needsEnergy[step]) && (!forcesAreValid || context.getLastForceGroups() != forceGroupFlags[step])) {
// Recompute forces and/or energy.
bool computeForce = needsForces[step] || computeBothForceAndEnergy[step];
bool computeEnergy = needsEnergy[step] || computeBothForceAndEnergy[step];
recordChangedParameters(context, globals);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
if (computeEnergy)
energy = e;
forcesAreValid = true;
}
globals[energyName[step]] = energy;
// Execute the step.
int nextStep = step+1;
switch (stepType[step]) {
case CustomIntegrator::ComputeGlobal: {
map<string, RealOpenMM> variables = globals;
variables["uniform"] = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
variables["gaussian"] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
globals[stepVariable[step]] = stepExpressions[step][0].evaluate(variables);
break;
}
case CustomIntegrator::ComputePerDof: {
vector<RealVec>* results = NULL;
if (stepVariable[step] == "x")
results = &atomCoordinates;
else if (stepVariable[step] == "v")
results = &velocities;
else {
for (int j = 0; j < integrator.getNumPerDofVariables(); j++)
if (stepVariable[step] == integrator.getPerDofVariableName(j))
results = &perDof[j];
}
if (results == NULL)
throw OpenMMException("Illegal per-DOF output variable: "+stepVariable[step]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpressions[step][0], forceName[step]);
break;
}
case CustomIntegrator::ComputeSum: {
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpressions[step][0], forceName[step]);
RealOpenMM sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
sum += sumBuffer[j][0]+sumBuffer[j][1]+sumBuffer[j][2];
globals[stepVariable[step]] = sum;
break;
}
case CustomIntegrator::ConstrainPositions: {
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses, tolerance);
oldPos = atomCoordinates;
break;
}
case CustomIntegrator::ConstrainVelocities: {
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses, tolerance);
break;
}
case CustomIntegrator::UpdateContextState: {
recordChangedParameters(context, globals);
context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
break;
}
case CustomIntegrator::BeginIfBlock: {
if (!evaluateCondition(step, globals))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::BeginWhileBlock: {
if (!evaluateCondition(step, globals))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::EndBlock: {
if (blockEnd[step] != -1)
nextStep = blockEnd[step]; // Return to the start of a while block.
break;
}
}
if (invalidatesForces[step])
forcesAreValid = false;
step = nextStep;
}
ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
incrementTimeStep();
recordChangedParameters(context, globals);
}
void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
vector<RealVec>& pos = extractPositions(context);
vector<RealVec>& vel = extractVelocities(context);
vector<RealVec>& force = extractForces(context);
// Update velocities of ordinary particles.
const RealOpenMM vscale = exp(-integrator.getStepSize()*integrator.getFriction());
const RealOpenMM fscale = (1-vscale)/integrator.getFriction();
const RealOpenMM kT = BOLTZ*integrator.getTemperature();
const RealOpenMM noisescale = sqrt(2*kT*integrator.getFriction())*sqrt(0.5*(1-vscale*vscale)/integrator.getFriction());
for (int i = 0; i < (int) normalParticles.size(); i++) {
int index = normalParticles[i];
RealOpenMM invMass = particleInvMass[index];
if (invMass != 0.0) {
RealOpenMM sqrtInvMass = sqrt(invMass);
for (int j = 0; j < 3; j++)
vel[index][j] = vscale*vel[index][j] + fscale*invMass*force[index][j] + noisescale*sqrtInvMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
}
// Update velocities of Drude particle pairs.
const RealOpenMM vscaleDrude = exp(-integrator.getStepSize()*integrator.getDrudeFriction());
const RealOpenMM fscaleDrude = (1-vscaleDrude)/integrator.getDrudeFriction();
const RealOpenMM kTDrude = BOLTZ*integrator.getDrudeTemperature();
const RealOpenMM noisescaleDrude = sqrt(2*kTDrude*integrator.getDrudeFriction())*sqrt(0.5*(1-vscaleDrude*vscaleDrude)/integrator.getDrudeFriction());
for (int i = 0; i < (int) pairParticles.size(); i++) {
int p1 = pairParticles[i].first;
int p2 = pairParticles[i].second;
RealOpenMM mass1fract = pairInvTotalMass[i]/particleInvMass[p1];
RealOpenMM mass2fract = pairInvTotalMass[i]/particleInvMass[p2];
RealOpenMM sqrtInvTotalMass = sqrt(pairInvTotalMass[i]);
RealOpenMM sqrtInvReducedMass = sqrt(pairInvReducedMass[i]);
RealVec cmVel = vel[p1]*mass1fract+vel[p2]*mass2fract;
RealVec relVel = vel[p2]-vel[p1];
RealVec cmForce = force[p1]+force[p2];
RealVec relForce = force[p2]*mass1fract - force[p1]*mass2fract;
for (int j = 0; j < 3; j++) {
cmVel[j] = vscale*cmVel[j] + fscale*pairInvTotalMass[i]*cmForce[j] + noisescale*sqrtInvTotalMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
relVel[j] = vscaleDrude*relVel[j] + fscaleDrude*pairInvReducedMass[i]*relForce[j] + noisescaleDrude*sqrtInvReducedMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
vel[p1] = cmVel-relVel*mass2fract;
vel[p2] = cmVel+relVel*mass1fract;
}
// Update the particle positions.
int numParticles = particleInvMass.size();
vector<RealVec> xPrime(numParticles);
RealOpenMM dt = integrator.getStepSize();
for (int i = 0; i < numParticles; i++)
if (particleInvMass[i] != 0.0)
xPrime[i] = pos[i]+vel[i]*dt;
// Apply constraints.
if (constraints != NULL)
constraints->apply(numParticles, pos, xPrime, particleInvMass);
// Record the constrained positions and velocities.
RealOpenMM dtInv = 1.0/dt;
for (int i = 0; i < numParticles; i++) {
if (particleInvMass[i] != 0.0) {
vel[i] = (xPrime[i]-pos[i])*dtInv;
pos[i] = xPrime[i];
}
}
ReferenceVirtualSites::computePositions(context.getSystem(), pos);
data.time += integrator.getStepSize();
data.stepCount++;
}