ReferenceCustomCentroidBondIxn.cpp

/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
 * Contributors: Peter Eastman
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#include <string.h>
#include <sstream>
#include <utility>

#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "ReferenceCustomCentroidBondIxn.h"

using std::map;
using std::pair;
using std::string;
using std::stringstream;
using std::vector;
using namespace OpenMM;

ReferenceCustomCentroidBondIxn::ReferenceCustomCentroidBondIxn(int numGroupsPerBond, const vector<vector<int> >& groupAtoms,
            const vector<vector<double> >& normalizedWeights, const vector<vector<int> >& bondGroups,
            const Lepton::ParsedExpression& energyExpression, const vector<string>& bondParameterNames,
            const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals) :
            groupAtoms(groupAtoms), normalizedWeights(normalizedWeights), bondGroups(bondGroups), energyExpression(energyExpression.createProgram()), bondParamNames(bondParameterNames), usePeriodic(false) {
    for (int i = 0; i < numGroupsPerBond; i++) {
        stringstream xname, yname, zname;
        xname << 'x' << (i+1);
        yname << 'y' << (i+1);
        zname << 'z' << (i+1);
        positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(xname.str(), i, 0, energyExpression.differentiate(xname.str()).optimize().createProgram()));
        positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).optimize().createProgram()));
        positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).optimize().createProgram()));
    }
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
        distanceTerms.push_back(ReferenceCustomCentroidBondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
        angleTerms.push_back(ReferenceCustomCentroidBondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
        dihedralTerms.push_back(ReferenceCustomCentroidBondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
}

ReferenceCustomCentroidBondIxn::~ReferenceCustomCentroidBondIxn() {
}

void ReferenceCustomCentroidBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
    usePeriodic = true;
    boxVectors[0] = vectors[0];
    boxVectors[1] = vectors[1];
    boxVectors[2] = vectors[2];
}

void ReferenceCustomCentroidBondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates, RealOpenMM** bondParameters,
                                             const map<string, double>& globalParameters, vector<RealVec>& forces,
                                             RealOpenMM* totalEnergy) const {

    // First compute the center of each group.

    int numGroups = groupAtoms.size();
    vector<RealVec> groupCenters(numGroups);
    for (int group = 0; group < numGroups; group++) {
        for (int i = 0; i < groupAtoms[group].size(); i++)
            groupCenters[group] += atomCoordinates[groupAtoms[group][i]]*normalizedWeights[group][i];
    }

    // Compute the forces on groups.

    map<string, double> variables = globalParameters;
    vector<RealVec> groupForces(numGroups);
    int numBonds = bondGroups.size();
    for (int bond = 0; bond < numBonds; bond++) {
        for (int j = 0; j < (int) bondParamNames.size(); j++)
            variables[bondParamNames[j]] = bondParameters[bond][j];
        calculateOneIxn(bond, groupCenters, variables, groupForces, totalEnergy);
    }

    // Apply the forces to the individual atoms.

    for (int group = 0; group < numGroups; group++) {
        for (int i = 0; i < groupAtoms[group].size(); i++)
            forces[groupAtoms[group][i]] += groupForces[group]*normalizedWeights[group][i];
    }
}

void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>& groupCenters,
                        map<string, double>& variables, vector<RealVec>& forces, RealOpenMM* totalEnergy) const {

    // ---------------------------------------------------------------------------------------

    static const std::string methodName = "\nReferenceCustomCentroidBondIxn::calculateOneIxn";

    // ---------------------------------------------------------------------------------------

    // Compute all of the variables the energy can depend on.

    const vector<int>& groups = bondGroups[bond];
    for (int i = 0; i < (int) positionTerms.size(); i++) {
        const PositionTermInfo& term = positionTerms[i];
        variables[term.name] = groupCenters[groups[term.group]][term.component];
    }
    for (int i = 0; i < (int) distanceTerms.size(); i++) {
        const DistanceTermInfo& term = distanceTerms[i];
        computeDelta(groups[term.g1], groups[term.g2], term.delta, groupCenters);
        variables[term.name] = term.delta[ReferenceForce::RIndex];
    }
    for (int i = 0; i < (int) angleTerms.size(); i++) {
        const AngleTermInfo& term = angleTerms[i];
        computeDelta(groups[term.g1], groups[term.g2], term.delta1, groupCenters);
        computeDelta(groups[term.g3], groups[term.g2], term.delta2, groupCenters);
        variables[term.name] = computeAngle(term.delta1, term.delta2);
    }
    for (int i = 0; i < (int) dihedralTerms.size(); i++) {
        const DihedralTermInfo& term = dihedralTerms[i];
        computeDelta(groups[term.g2], groups[term.g1], term.delta1, groupCenters);
        computeDelta(groups[term.g2], groups[term.g3], term.delta2, groupCenters);
        computeDelta(groups[term.g4], groups[term.g3], term.delta3, groupCenters);
        RealOpenMM dotDihedral, signOfDihedral;
        RealOpenMM* crossProduct[] = {term.cross1, term.cross2};
        variables[term.name] = getDihedralAngleBetweenThreeVectors(term.delta1, term.delta2, term.delta3, crossProduct, &dotDihedral, term.delta1, &signOfDihedral, 1);
    }

    // Apply forces based on individual particle coordinates.

    for (int i = 0; i < (int) positionTerms.size(); i++) {
        const PositionTermInfo& term = positionTerms[i];
        forces[groups[term.group]][term.component] -= term.forceExpression.evaluate(variables);
    }

    // Apply forces based on distances.

    for (int i = 0; i < (int) distanceTerms.size(); i++) {
        const DistanceTermInfo& term = distanceTerms[i];
        RealOpenMM dEdR = (RealOpenMM) (term.forceExpression.evaluate(variables)/(term.delta[ReferenceForce::RIndex]));
        for (int i = 0; i < 3; i++) {
           RealOpenMM force  = -dEdR*term.delta[i];
           forces[groups[term.g1]][i] -= force;
           forces[groups[term.g2]][i] += force;
        }
    }

    // Apply forces based on angles.

    for (int i = 0; i < (int) angleTerms.size(); i++) {
        const AngleTermInfo& term = angleTerms[i];
        RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
        RealOpenMM thetaCross[ReferenceForce::LastDeltaRIndex];
        SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
        RealOpenMM lengthThetaCross = SQRT(DOT3(thetaCross, thetaCross));
        if (lengthThetaCross < 1.0e-06)
            lengthThetaCross = (RealOpenMM) 1.0e-06;
        RealOpenMM termA = dEdTheta/(term.delta1[ReferenceForce::R2Index]*lengthThetaCross);
        RealOpenMM termC = -dEdTheta/(term.delta2[ReferenceForce::R2Index]*lengthThetaCross);
        RealOpenMM deltaCrossP[3][3];
        SimTKOpenMMUtilities::crossProductVector3(term.delta1, thetaCross, deltaCrossP[0]);
        SimTKOpenMMUtilities::crossProductVector3(term.delta2, thetaCross, deltaCrossP[2]);
        for (int i = 0; i < 3; i++) {
            deltaCrossP[0][i] *= termA;
            deltaCrossP[2][i] *= termC;
            deltaCrossP[1][i] = -(deltaCrossP[0][i]+deltaCrossP[2][i]);
        }
        for (int i = 0; i < 3; i++) {
            forces[groups[term.g1]][i] += deltaCrossP[0][i];
            forces[groups[term.g2]][i] += deltaCrossP[1][i];
            forces[groups[term.g3]][i] += deltaCrossP[2][i];
        }
    }

    // Apply forces based on dihedrals.

    for (int i = 0; i < (int) dihedralTerms.size(); i++) {
        const DihedralTermInfo& term = dihedralTerms[i];
        RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
        RealOpenMM internalF[4][3];
        RealOpenMM forceFactors[4];
        RealOpenMM normCross1 = DOT3(term.cross1, term.cross1);
        RealOpenMM normBC = term.delta2[ReferenceForce::RIndex];
        forceFactors[0] = (-dEdTheta*normBC)/normCross1;
        RealOpenMM normCross2 = DOT3(term.cross2, term.cross2);
                   forceFactors[3] = (dEdTheta*normBC)/normCross2;
                   forceFactors[1] = DOT3(term.delta1, term.delta2);
                   forceFactors[1] /= term.delta2[ReferenceForce::R2Index];
                   forceFactors[2] = DOT3(term.delta3, term.delta2);
                   forceFactors[2] /= term.delta2[ReferenceForce::R2Index];
        for (int i = 0; i < 3; i++) {
            internalF[0][i] = forceFactors[0]*term.cross1[i];
            internalF[3][i] = forceFactors[3]*term.cross2[i];
            RealOpenMM s = forceFactors[1]*internalF[0][i] - forceFactors[2]*internalF[3][i];
            internalF[1][i] = internalF[0][i] - s;
            internalF[2][i] = internalF[3][i] + s;
        }
        for (int i = 0; i < 3; i++) {
            forces[groups[term.g1]][i] += internalF[0][i];
            forces[groups[term.g2]][i] -= internalF[1][i];
            forces[groups[term.g3]][i] -= internalF[2][i];
            forces[groups[term.g4]][i] += internalF[3][i];
        }
    }

    // Add the energy

    if (totalEnergy)
        *totalEnergy += (RealOpenMM) energyExpression.evaluate(variables);
}

void ReferenceCustomCentroidBondIxn::computeDelta(int group1, int group2, RealOpenMM* delta, vector<RealVec>& groupCenters) const {
    if (usePeriodic)
        ReferenceForce::getDeltaRPeriodic(groupCenters[group1], groupCenters[group2], boxVectors, delta);
    else
        ReferenceForce::getDeltaR(groupCenters[group1], groupCenters[group2], delta);
}

RealOpenMM ReferenceCustomCentroidBondIxn::computeAngle(RealOpenMM* vec1, RealOpenMM* vec2) {
    RealOpenMM dot = DOT3(vec1, vec2);
    RealOpenMM cosine = dot/SQRT((vec1[ReferenceForce::R2Index]*vec2[ReferenceForce::R2Index]));
    RealOpenMM angle;
    if (cosine >= 1)
        angle = 0;
    else if (cosine <= -1)
        angle = PI_M;
    else
        angle = ACOS(cosine);
    return angle;
}