AmoebaVdwForce.cpp

/* -------------------------------------------------------------------------- *
 *                                OpenMMAmoeba                                *
 * -------------------------------------------------------------------------- *
 * This is part of the OpenMM molecular simulation toolkit originating from   *
 * Simbios, the NIH National Center for Physics-Based Simulation of           *
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
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#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "openmm/AmoebaVdwForce.h"
#include "openmm/internal/AmoebaVdwForceImpl.h"

using namespace OpenMM;
using std::string;
using std::vector;

AmoebaVdwForce::AmoebaVdwForce() : nonbondedMethod(NoCutoff), sigmaCombiningRule("CUBIC-MEAN"), epsilonCombiningRule("HHG"), cutoff(1.0e+10), useDispersionCorrection(true), alchemicalMethod(None), n(5), alpha(0.7) {
}

int AmoebaVdwForce::addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor, bool isAlchemical) {
    parameters.push_back(VdwInfo(parentIndex, sigma, epsilon, reductionFactor, isAlchemical));
    return parameters.size()-1;
}

void AmoebaVdwForce::getParticleParameters(int particleIndex, int& parentIndex,
                                           double& sigma, double& epsilon, double& reductionFactor, bool& isAlchemical) const {
    parentIndex     = parameters[particleIndex].parentIndex;
    sigma           = parameters[particleIndex].sigma;
    epsilon         = parameters[particleIndex].epsilon;
    reductionFactor = parameters[particleIndex].reductionFactor;
    isAlchemical    = parameters[particleIndex].isAlchemical;
}

void AmoebaVdwForce::setParticleParameters(int particleIndex, int parentIndex,
                                           double sigma, double epsilon, double reductionFactor, bool isAlchemical) {
    parameters[particleIndex].parentIndex     = parentIndex;
    parameters[particleIndex].sigma           = sigma;
    parameters[particleIndex].epsilon         = epsilon;
    parameters[particleIndex].reductionFactor = reductionFactor;
    parameters[particleIndex].isAlchemical    = isAlchemical;
}

void AmoebaVdwForce::setSigmaCombiningRule(const std::string& inputSigmaCombiningRule) {
    sigmaCombiningRule = inputSigmaCombiningRule;
}

const std::string& AmoebaVdwForce::getSigmaCombiningRule() const {
    return sigmaCombiningRule;
}

void AmoebaVdwForce::setEpsilonCombiningRule(const std::string& inputEpsilonCombiningRule) {
    epsilonCombiningRule = inputEpsilonCombiningRule;
}

const std::string& AmoebaVdwForce::getEpsilonCombiningRule() const {
    return epsilonCombiningRule;
}

void AmoebaVdwForce::setParticleExclusions(int particleIndex, const std::vector< int >& inputExclusions) {

   if (exclusions.size() < parameters.size()) {
       exclusions.resize(parameters.size());
   }
   if (static_cast<int>(exclusions.size()) < particleIndex) {
       exclusions.resize(particleIndex + 10);
   }
   for (unsigned int ii = 0; ii < inputExclusions.size(); ii++) {
       exclusions[particleIndex].push_back(inputExclusions[ii]);
   }
}

void AmoebaVdwForce::getParticleExclusions(int particleIndex, std::vector< int >& outputExclusions) const {

   if (particleIndex < static_cast<int>(exclusions.size())) {
       outputExclusions.resize(exclusions[particleIndex].size());
       for (unsigned int ii = 0; ii < exclusions[particleIndex].size(); ii++) {
           outputExclusions[ii] = exclusions[particleIndex][ii];
       }
   }

}

double AmoebaVdwForce::getCutoffDistance() const {
    return cutoff;
}

void AmoebaVdwForce::setCutoffDistance(double inputCutoff) {
    cutoff = inputCutoff;
}

void AmoebaVdwForce::setCutoff(double inputCutoff) {
    setCutoffDistance(inputCutoff);
}

double AmoebaVdwForce::getCutoff() const {
    return getCutoffDistance();
}

AmoebaVdwForce::NonbondedMethod AmoebaVdwForce::getNonbondedMethod() const {
    return nonbondedMethod;
}

void AmoebaVdwForce::setNonbondedMethod(NonbondedMethod method) {
    if (method < 0 || method > 1)
        throw OpenMMException("AmoebaVdwForce: Illegal value for nonbonded method");
    nonbondedMethod = method;
}

AmoebaVdwForce::AlchemicalMethod AmoebaVdwForce::getAlchemicalMethod() const {
    return alchemicalMethod;
}

void AmoebaVdwForce::setAlchemicalMethod(AlchemicalMethod method) {
    if (method < 0 || method > 2)
        throw OpenMMException("AmoebaVdwForce: Illegal value for alchemical method");
    alchemicalMethod = method;
}

void AmoebaVdwForce::setSoftcorePower(int power) {
    n = power;
}

int AmoebaVdwForce::getSoftcorePower() const {
    return n;
}

void AmoebaVdwForce::setSoftcoreAlpha(double a) {
    alpha = a;
}

double AmoebaVdwForce::getSoftcoreAlpha() const {
    return alpha;
}


ForceImpl* AmoebaVdwForce::createImpl() const {
    return new AmoebaVdwForceImpl(*this);
}

void AmoebaVdwForce::updateParametersInContext(Context& context) {
    dynamic_cast<AmoebaVdwForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}