ReferenceVerletDynamics.cpp

/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
 * Contributors: Peter Eastman, Pande Group
 *
 * 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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 * 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
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 */

#include <cstring>
#include <sstream>

#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMLog.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceVerletDynamics.h"
#include "ReferenceVirtualSites.h"

#include <cstdio>

using std::vector;
using OpenMM::RealVec;

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

   ReferenceVerletDynamics constructor

   @param numberOfAtoms  number of atoms
   @param deltaT         delta t for dynamics
   @param friction       friction coefficient
   @param temperature    temperature

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

ReferenceVerletDynamics::ReferenceVerletDynamics( int numberOfAtoms,
                                                          RealOpenMM deltaT ) : 
           ReferenceDynamics( numberOfAtoms, deltaT, 0.0 ) {

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

   static const char* methodName      = "\nReferenceVerletDynamics::ReferenceVerletDynamics";

   static const RealOpenMM zero       =  0.0;
   static const RealOpenMM one        =  1.0;

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

   xPrime.resize(numberOfAtoms);
   inverseMasses.resize(numberOfAtoms);
}

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

   ReferenceVerletDynamics destructor

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

ReferenceVerletDynamics::~ReferenceVerletDynamics( ){

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

   // static const char* methodName = "\nReferenceVerletDynamics::~ReferenceVerletDynamics";

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

}

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

   Update -- driver routine for performing Verlet dynamics update of coordinates
   and velocities

   @param system              the System to be integrated
   @param atomCoordinates     atom coordinates
   @param velocities          velocities
   @param forces              forces
   @param masses              atom masses

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

void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
                                          vector<RealVec>& velocities,
                                          vector<RealVec>& forces, vector<RealOpenMM>& masses ){

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

   static const char* methodName      = "\nReferenceVerletDynamics::update";

   static const RealOpenMM zero       =  0.0;
   static const RealOpenMM one        =  1.0;

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

   // first-time-through initialization

   int numberOfAtoms = system.getNumParticles();
   if( getTimeStep() == 0 ){
      // invert masses

      for( int ii = 0; ii < numberOfAtoms; ii++ ){
         if (masses[ii] == zero)
             inverseMasses[ii] = zero;
         else
             inverseMasses[ii] = one/masses[ii];
      }
   }
   
   // Perform the integration.
   
   for (int i = 0; i < numberOfAtoms; ++i) {
       if (masses[i] != zero)
           for (int j = 0; j < 3; ++j) {
               velocities[i][j] += inverseMasses[i]*forces[i][j]*getDeltaT();
               xPrime[i][j] = atomCoordinates[i][j] + velocities[i][j]*getDeltaT();
           }
   }
   ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
   if (referenceConstraintAlgorithm)
      referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
   
   // Update the positions and velocities.
   
   RealOpenMM velocityScale = static_cast<RealOpenMM>( 1.0/getDeltaT() );
   for (int i = 0; i < numberOfAtoms; ++i) {
       if (masses[i] != zero)
           for (int j = 0; j < 3; ++j) {
               velocities[i][j] = velocityScale*(xPrime[i][j] - atomCoordinates[i][j]);
               atomCoordinates[i][j] = xPrime[i][j];
           }
   }

   ReferenceVirtualSites::computePositions(system, atomCoordinates);
   incrementTimeStep();
}