/**
* Check which context parameters have changed and register them with the context.
*/
void ReferenceCustomDynamics::recordChangedParameters(OpenMM::ContextImpl& context, std::map<std::string, RealOpenMM>& globals) {
for (map<string, double>::const_iterator iter = context.getParameters().begin(); iter != context.getParameters().end(); ++iter) {
string name = iter->first;
double value = globals[name];
if (value != iter->second)
context.setParameter(name, globals[name]);
}
}
double ReferenceCustomDynamics::computeKineticEnergy(OpenMM::ContextImpl& context, int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses,
std::map<std::string, RealOpenMM>& globals, std::vector<std::vector<OpenMM::RealVec> >& perDof, bool& forcesAreValid) {
globals.insert(context.getParameters().begin(), context.getParameters().end());
if (kineticEnergyNeedsForce) {
energy = context.calcForcesAndEnergy(true, true, -1);
forcesAreValid = true;
}
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, globals, perDof, kineticEnergyExpression, "f");
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];
return sum;
}
double ReferenceCustomDynamics::computeKineticEnergy(OpenMM::ContextImpl& context, int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses,
std::map<std::string, RealOpenMM>& globals, std::vector<std::vector<OpenMM::RealVec> >& perDof, bool& forcesAreValid) {
if (invalidatesForces.size() == 0)
initialize(context, masses, globals);
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);
if (kineticEnergyNeedsForce) {
energy = context.calcForcesAndEnergy(true, true, -1);
forcesAreValid = true;
}
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, kineticEnergyExpression);
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];
return sum;
}
void StepKernel::Integrate( OpenMM::ContextImpl &context, const Integrator &integrator ) {
ProjectionVectors( integrator );
#ifdef FAST_NOISE
// Add noise for step
kFastNoise( &fastmodule, data.contexts[0], integrator.getNumProjectionVectors(), ( float )( BOLTZ * integrator.getTemperature() ), iterations, *modes, *modeWeights, integrator.getMaxEigenvalue(), *NoiseValues, *pPosqP, integrator.getStepSize() );
#endif
// Calculate Constants
const double friction = integrator.getFriction();
context.updateContextState();
// Do Step
kNMLUpdate( &updatemodule,
data.contexts[0],
integrator.getStepSize(),
friction == 0.0f ? 0.0f : 1.0f / friction,
( float )( BOLTZ * integrator.getTemperature() ),
integrator.getNumProjectionVectors(), kIterations, *modes, *modeWeights, *NoiseValues ); // TMC setting parameters for this
}