ReferenceCustomCompoundBondIxn.cpp

/* Portions copyright (c) 2009-2015 Stanford University and Simbios.
 * Contributors: Peter Eastman
 *
 * Permission is hereby granted, free of charge, to any person obtaining
 * a copy of this software and associated documentation files (the
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 * permit persons to whom the Software is furnished to do so, subject
 * to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included
 * in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
 * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
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#include <string.h>
#include <sstream>
#include <utility>

#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMLog.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "ReferenceCustomCompoundBondIxn.h"

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

/**---------------------------------------------------------------------------------------

   ReferenceCustomCompoundBondIxn constructor

   --------------------------------------------------------------------------------------- */

ReferenceCustomCompoundBondIxn::ReferenceCustomCompoundBondIxn(int numParticlesPerBond, const vector<vector<int> >& bondAtoms,
            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) :
            bondAtoms(bondAtoms), energyExpression(energyExpression.createProgram()), bondParamNames(bondParameterNames) {
    for (int i = 0; i < numParticlesPerBond; i++) {
        stringstream xname, yname, zname;
        xname << 'x' << (i+1);
        yname << 'y' << (i+1);
        zname << 'z' << (i+1);
        particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(xname.str(), i, 0, energyExpression.differentiate(xname.str()).optimize().createProgram()));
        particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).optimize().createProgram()));
        particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(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(ReferenceCustomCompoundBondIxn::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(ReferenceCustomCompoundBondIxn::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(ReferenceCustomCompoundBondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
}

/**---------------------------------------------------------------------------------------

   ReferenceCustomCompoundBondIxn destructor

   --------------------------------------------------------------------------------------- */

ReferenceCustomCompoundBondIxn::~ReferenceCustomCompoundBondIxn( ){
}

/**---------------------------------------------------------------------------------------

   Calculate custom hbond interaction

   @param atomCoordinates    atom coordinates
   @param bondParameters     bond parameters values       bondParameters[bondIndex][parameterIndex]
   @param globalParameters   the values of global parameters
   @param forces             force array (forces added)
   @param totalEnergy        total energy

   --------------------------------------------------------------------------------------- */

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

    map<string, double> variables = globalParameters;
    int numBonds = bondAtoms.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, atomCoordinates, variables, forces, totalEnergy);
    }
}

  /**---------------------------------------------------------------------------------------

     Calculate interaction for one bond

     @param bond             the index of the bond
     @param atomCoordinates  atom coordinates
     @param variables        the values of variables that may appear in expressions
     @param forces           force array (forces added)
     @param energyByAtom     atom energy
     @param totalEnergy      total energy

     --------------------------------------------------------------------------------------- */

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

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

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

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

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

    const vector<int>& atoms = bondAtoms[bond];
    for (int i = 0; i < (int) particleTerms.size(); i++) {
        const ParticleTermInfo& term = particleTerms[i];
        variables[term.name] = atomCoordinates[atoms[term.atom]][term.component];
    }
    for (int i = 0; i < (int) distanceTerms.size(); i++) {
        const DistanceTermInfo& term = distanceTerms[i];
        computeDelta(atoms[term.p1], atoms[term.p2], term.delta, atomCoordinates);
        variables[term.name] = term.delta[ReferenceForce::RIndex];
    }
    for (int i = 0; i < (int) angleTerms.size(); i++) {
        const AngleTermInfo& term = angleTerms[i];
        computeDelta(atoms[term.p1], atoms[term.p2], term.delta1, atomCoordinates);
        computeDelta(atoms[term.p3], atoms[term.p2], term.delta2, atomCoordinates);
        variables[term.name] = computeAngle(term.delta1, term.delta2);
    }
    for (int i = 0; i < (int) dihedralTerms.size(); i++) {
        const DihedralTermInfo& term = dihedralTerms[i];
        computeDelta(atoms[term.p2], atoms[term.p1], term.delta1, atomCoordinates);
        computeDelta(atoms[term.p2], atoms[term.p3], term.delta2, atomCoordinates);
        computeDelta(atoms[term.p4], atoms[term.p3], term.delta3, atomCoordinates);
        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) particleTerms.size(); i++) {
        const ParticleTermInfo& term = particleTerms[i];
        forces[atoms[term.atom]][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[atoms[term.p1]][i] -= force;
           forces[atoms[term.p2]][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[atoms[term.p1]][i] += deltaCrossP[0][i];
            forces[atoms[term.p2]][i] += deltaCrossP[1][i];
            forces[atoms[term.p3]][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[atoms[term.p1]][i] += internalF[0][i];
            forces[atoms[term.p2]][i] -= internalF[1][i];
            forces[atoms[term.p3]][i] -= internalF[2][i];
            forces[atoms[term.p4]][i] += internalF[3][i];
        }
    }

    // Add the energy

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

void ReferenceCustomCompoundBondIxn::computeDelta(int atom1, int atom2, RealOpenMM* delta, vector<RealVec>& atomCoordinates) const {
    ReferenceForce::getDeltaR(atomCoordinates[atom1], atomCoordinates[atom2], delta);
}

RealOpenMM ReferenceCustomCompoundBondIxn::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;
}