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]);
}
}
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 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 MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
if (++step < owner.getFrequency() || owner.getFrequency() == 0)
return;
step = 0;
// Compute the current potential energy.
double initialEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
// Modify the periodic box size.
Vec3 box[3];
context.getPeriodicBoxVectors(box[0], box[1], box[2]);
double volume = box[0][0]*box[1][1]*box[2][2];
double deltaVolume = volumeScale*2*(genrand_real2(random)-0.5);
double newVolume = volume+deltaVolume;
double lengthScale = std::pow(newVolume/volume, 1.0/3.0);
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale, lengthScale, lengthScale);
context.getOwner().setPeriodicBoxVectors(box[0]*lengthScale, box[1]*lengthScale, box[2]*lengthScale);
// Compute the energy of the modified system.
double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
double pressure = context.getParameter(MonteCarloBarostat::Pressure())*(AVOGADRO*1e-25);
double kT = BOLTZ*context.getParameter(MonteCarloBarostat::Temperature());
double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
// Reject the step.
kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
volume = newVolume;
}
else
numAccepted++;
numAttempted++;
if (numAttempted >= 10) {
if (numAccepted < 0.25*numAttempted) {
volumeScale /= 1.1;
numAttempted = 0;
numAccepted = 0;
}
else if (numAccepted > 0.75*numAttempted) {
volumeScale = std::min(volumeScale*1.1, volume*0.3);
numAttempted = 0;
numAccepted = 0;
}
}
}
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 CpuCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force) {
if (numParticles != force.getNumParticles())
throw OpenMMException("updateParametersInContext: The number of particles has changed");
// Record the values.
int numParameters = force.getNumPerParticleParameters();
vector<double> params;
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];
}
// If necessary, recompute the long range correction.
if (forceCopy != NULL) {
longRangeCoefficient = CustomNonbondedForceImpl::calcLongRangeCorrection(force, context.getOwner());
hasInitializedLongRangeCorrection = true;
*forceCopy = force;
}
}
double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
RealVec& box = extractBoxSize(context);
float floatBoxSize[3] = {(float) box[0], (float) box[1], (float) box[2]};
double energy = 0;
bool periodic = (nonbondedMethod == CutoffPeriodic);
if (nonbondedMethod != NoCutoff) {
neighborList->computeNeighborList(numParticles, data.posq, exclusions, floatBoxSize, data.isPeriodic, nonbondedCutoff, data.threads);
nonbonded->setUseCutoff(nonbondedCutoff, *neighborList);
}
if (periodic) {
double minAllowedSize = 2*nonbondedCutoff;
if (box[0] < minAllowedSize || box[1] < minAllowedSize || box[2] < minAllowedSize)
throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
nonbonded->setPeriodic(box);
}
bool globalParamsChanged = false;
for (int i = 0; i < (int) globalParameterNames.size(); i++) {
double value = context.getParameter(globalParameterNames[i]);
if (globalParamValues[globalParameterNames[i]] != value)
globalParamsChanged = true;
globalParamValues[globalParameterNames[i]] = value;
}
if (useSwitchingFunction)
nonbonded->setUseSwitchingFunction(switchingDistance);
nonbonded->calculatePairIxn(numParticles, &data.posq[0], posData, particleParamArray, 0, globalParamValues, data.threadForce, includeForces, includeEnergy, energy);
// Add in the long range correction.
if (!hasInitializedLongRangeCorrection || (globalParamsChanged && forceCopy != NULL)) {
longRangeCoefficient = CustomNonbondedForceImpl::calcLongRangeCorrection(*forceCopy, context.getOwner());
hasInitializedLongRangeCorrection = true;
}
energy += longRangeCoefficient/(box[0]*box[1]*box[2]);
return energy;
}
void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context) {
if (++step < owner.getFrequency() || owner.getFrequency() == 0)
return;
if (!owner.getScaleX() && !owner.getScaleY() && !owner.getScaleZ())
return;
step = 0;
// Compute the current potential energy.
double initialEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
double pressure;
// Choose which axis to modify at random.
int axis;
while (true) {
double rnd = genrand_real2(random)*3.0;
if (rnd < 1.0) {
if (owner.getScaleX()) {
axis = 0;
pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureX())*(AVOGADRO*1e-25);
break;
}
} else if (rnd < 2.0) {
if (owner.getScaleY()) {
axis = 1;
pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureY())*(AVOGADRO*1e-25);
break;
}
} else if (owner.getScaleZ()) {
axis = 2;
pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureZ())*(AVOGADRO*1e-25);
break;
}
}
// Modify the periodic box size.
Vec3 box[3];
context.getPeriodicBoxVectors(box[0], box[1], box[2]);
double volume = box[0][0]*box[1][1]*box[2][2];
double deltaVolume = volumeScale[axis]*2*(genrand_real2(random)-0.5);
double newVolume = volume+deltaVolume;
Vec3 lengthScale(1.0, 1.0, 1.0);
lengthScale[axis] = newVolume/volume;
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale[0], lengthScale[1], lengthScale[2]);
context.getOwner().setPeriodicBoxVectors(box[0]*lengthScale[0], box[1]*lengthScale[1], box[2]*lengthScale[2]);
// Compute the energy of the modified system.
double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
double kT = BOLTZ*owner.getTemperature();
double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
// Reject the step.
kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
volume = newVolume;
}
else
numAccepted[axis]++;
numAttempted[axis]++;
if (numAttempted[axis] >= 10) {
if (numAccepted[axis] < 0.25*numAttempted[axis]) {
volumeScale[axis] /= 1.1;
numAttempted[axis] = 0;
numAccepted[axis] = 0;
}
else if (numAccepted[axis] > 0.75*numAttempted[axis]) {
volumeScale[axis] = std::min(volumeScale[axis]*1.1, volume*0.3);
numAttempted[axis] = 0;
numAccepted[axis] = 0;
}
}
}