Пример #1
0
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);
}
Пример #3
0
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);
}
Пример #4
0
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;
        }
    }
}
Пример #5
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);
}
Пример #6
0
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;
    }
}
Пример #7
0
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;
        }
    }
}