ReferenceCustomNonbondedIxn.cpp

/* Portions copyright (c) 2009 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
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, sublicense, and/or sell copies of the Software, and to
 * 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
 * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
 * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */

#include <string.h>
#include <sstream>

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

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

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

   ReferenceCustomNonbondedIxn constructor

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

ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::ExpressionProgram& energyExpression,
        const Lepton::ExpressionProgram& forceExpression, const vector<string>& parameterNames) :
            cutoff(false), useSwitch(false), periodic(false), energyExpression(energyExpression), forceExpression(forceExpression), paramNames(parameterNames) {

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

   // static const char* methodName = "\nReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn";

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

    for (int i = 0; i < (int) paramNames.size(); i++) {
        for (int j = 1; j < 3; j++) {
            stringstream name;
            name << paramNames[i] << j;
            particleParamNames.push_back(name.str());
        }
    }
}

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

   ReferenceCustomNonbondedIxn destructor

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

ReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn( ){

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

   // static const char* methodName = "\nReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn";

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

}

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

     Set the force to use a cutoff.

     @param distance            the cutoff distance
     @param neighbors           the neighbor list to use

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

  void ReferenceCustomNonbondedIxn::setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors ) {

    cutoff = true;
    cutoffDistance = distance;
    neighborList = &neighbors;
  }

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

   Restrict the force to a list of interaction groups.

   @param distance            the cutoff distance
   @param neighbors           the neighbor list to use

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

void ReferenceCustomNonbondedIxn::setInteractionGroups(const vector<pair<set<int>, set<int> > >& groups) {
    interactionGroups = groups;
}

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

   Set the force to use a switching function.

   @param distance            the switching distance

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

void ReferenceCustomNonbondedIxn::setUseSwitchingFunction( RealOpenMM distance ) {
    useSwitch = true;
    switchingDistance = distance;
}

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

     Set the force to use periodic boundary conditions.  This requires that a cutoff has
     also been set, and the smallest side of the periodic box is at least twice the cutoff
     distance.

     @param boxSize             the X, Y, and Z widths of the periodic box

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

  void ReferenceCustomNonbondedIxn::setPeriodic( RealVec& boxSize ) {

    assert(cutoff);
    assert(boxSize[0] >= 2.0*cutoffDistance);
    assert(boxSize[1] >= 2.0*cutoffDistance);
    assert(boxSize[2] >= 2.0*cutoffDistance);
    periodic = true;
    periodicBoxSize[0] = boxSize[0];
    periodicBoxSize[1] = boxSize[1];
    periodicBoxSize[2] = boxSize[2];

  }


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

   Calculate the custom pair ixn

   @param numberOfAtoms    number of atoms
   @param atomCoordinates  atom coordinates
   @param atomParameters   atom parameters                             atomParameters[atomIndex][paramterIndex]
   @param exclusions       atom exclusion indices
                           exclusions[atomIndex] contains the list of exclusions for that atom
   @param fixedParameters  non atom parameters (not currently used)
   @param globalParameters the values of global parameters
   @param forces           force array (forces added)
   @param energyByAtom     atom energy
   @param totalEnergy      total energy

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

void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<RealVec>& atomCoordinates,
                                             RealOpenMM** atomParameters, vector<set<int> >& exclusions,
                                             RealOpenMM* fixedParameters, const map<string, double>& globalParameters, vector<RealVec>& forces,
                                             RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const {

    map<string, double> variables = globalParameters;
    if (interactionGroups.size() > 0) {
        // The user has specified interaction groups, so compute only the requested interactions.
        
        for (int group = 0; group < (int) interactionGroups.size(); group++) {
            const set<int>& set1 = interactionGroups[group].first;
            const set<int>& set2 = interactionGroups[group].second;
            for (set<int>::const_iterator atom1 = set1.begin(); atom1 != set1.end(); ++atom1) {
                for (set<int>::const_iterator atom2 = set2.begin(); atom2 != set2.end(); ++atom2) {
                    if (*atom1 == *atom2 || exclusions[*atom1].find(*atom2) != exclusions[*atom1].end())
                        continue; // This is an excluded interaction.
                    if (*atom1 > *atom2 && set1.find(*atom2) != set1.end() && set2.find(*atom1) != set2.end())
                        continue; // Both atoms are in both sets, so skip duplicate interactions.
                    for (int j = 0; j < (int) paramNames.size(); j++) {
                        variables[particleParamNames[j*2]] = atomParameters[*atom1][j];
                        variables[particleParamNames[j*2+1]] = atomParameters[*atom2][j];
                    }
                    calculateOneIxn(*atom1, *atom2, atomCoordinates, variables, forces, energyByAtom, totalEnergy);
                }
            }
        }
    }
    else if (cutoff) {
        // We are using a cutoff, so get the interactions from the neighbor list.
        
        for (int i = 0; i < (int) neighborList->size(); i++) {
            OpenMM::AtomPair pair = (*neighborList)[i];
            for (int j = 0; j < (int) paramNames.size(); j++) {
                variables[particleParamNames[j*2]] = atomParameters[pair.first][j];
                variables[particleParamNames[j*2+1]] = atomParameters[pair.second][j];
            }
            calculateOneIxn(pair.first, pair.second, atomCoordinates, variables, forces, energyByAtom, totalEnergy);
        }
    }
    else {
        // Every particle interacts with every other one.
        
        for (int ii = 0; ii < numberOfAtoms; ii++) {
            for (int jj = ii+1; jj < numberOfAtoms; jj++) {
                if (exclusions[jj].find(ii) == exclusions[jj].end()) {
                    for (int j = 0; j < (int) paramNames.size(); j++) {
                        variables[particleParamNames[j*2]] = atomParameters[ii][j];
                        variables[particleParamNames[j*2+1]] = atomParameters[jj][j];
                    }
                    calculateOneIxn(ii, jj, atomCoordinates, variables, forces, energyByAtom, totalEnergy);
                }
            }
        }
    }
}

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

     Calculate one pair ixn between two atoms

     @param ii               the index of the first atom
     @param jj               the index of the second atom
     @param atomCoordinates  atom coordinates
     @param atomParameters   atom parameters (charges, c6, c12, ...)     atomParameters[atomIndex][paramterIndex]
     @param forces           force array (forces added)
     @param energyByAtom     atom energy
     @param totalEnergy      total energy

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

void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& atomCoordinates,
                        map<string, double>& variables, vector<RealVec>& forces,
                        RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const {

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

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

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

    // constants -- reduce Visual Studio warnings regarding conversions between float & double

    static const RealOpenMM zero        =  0.0;
    static const RealOpenMM one         =  1.0;
    static const RealOpenMM two         =  2.0;
    static const RealOpenMM three       =  3.0;
    static const RealOpenMM six         =  6.0;
    static const RealOpenMM twelve      = 12.0;
    static const RealOpenMM oneM        = -1.0;

    // get deltaR, R2, and R between 2 atoms

    RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
    if (periodic)
        ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxSize, deltaR );
    else
        ReferenceForce::getDeltaR( atomCoordinates[jj], atomCoordinates[ii], deltaR );
    RealOpenMM r = deltaR[ReferenceForce::RIndex];
    if (cutoff && r >= cutoffDistance)
        return;

    // accumulate forces

    variables["r"] = r;
    RealOpenMM dEdR = (RealOpenMM) (forceExpression.evaluate(variables)/(deltaR[ReferenceForce::RIndex]));
    RealOpenMM energy = (RealOpenMM) energyExpression.evaluate(variables);
    if (useSwitch) {
        if (r > switchingDistance) {
            RealOpenMM t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
            RealOpenMM switchValue = 1+t*t*t*(-10+t*(15-t*6));
            RealOpenMM switchDeriv = t*t*(-30+t*(60-t*30))/(cutoffDistance-switchingDistance);
            dEdR = switchValue*dEdR + energy*switchDeriv/r;
            energy *= switchValue;
        }
    }
    for( int kk = 0; kk < 3; kk++ ){
       RealOpenMM force  = -dEdR*deltaR[kk];
       forces[ii][kk]   += force;
       forces[jj][kk]   -= force;
    }

    // accumulate energies

    if( totalEnergy || energyByAtom ) {
        if( totalEnergy )
           *totalEnergy += energy;
        if( energyByAtom ){
           energyByAtom[ii] += energy;
           energyByAtom[jj] += energy;
        }
    }
  }