コード例 #1
0
/**
 * 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]);
    }
}
コード例 #2
0
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;
}
コード例 #3
0
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;
}
コード例 #4
0
ファイル: StepKernel.cpp プロジェクト: LCLS/LTMDOpenMM
			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
			}