ReferenceVerletDynamics.cpp

/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
 * Contributors: Peter Eastman, Pande Group
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 * permit persons to whom the Software is furnished to do so, subject
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#include <cstring>
#include <sstream>

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

#include <cstdio>

using std::vector;
using namespace OpenMM;

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

   ReferenceVerletDynamics constructor

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

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

ReferenceVerletDynamics::ReferenceVerletDynamics(int numberOfAtoms, double deltaT) :
           ReferenceDynamics(numberOfAtoms, deltaT, 0.0) {
   xPrime.resize(numberOfAtoms);
   inverseMasses.resize(numberOfAtoms);
}

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

   ReferenceVerletDynamics destructor

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

ReferenceVerletDynamics::~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<Vec3>& atomCoordinates,
                                          vector<Vec3>& velocities,
                                          vector<Vec3>& forces, vector<double>& masses, double tolerance) {
   // first-time-through initialization

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

      for (int ii = 0; ii < numberOfAtoms; ii++) {
         if (masses[ii] == 0.0)
             inverseMasses[ii] = 0.0;
         else
             inverseMasses[ii] = 1.0/masses[ii];
      }
   }
   
   // Perform the integration.
   
   for (int i = 0; i < numberOfAtoms; ++i) {
       if (masses[i] != 0.0)
           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, tolerance);
   
   // Update the positions and velocities.
   
   double velocityScale = static_cast<double>(1.0/getDeltaT());
   for (int i = 0; i < numberOfAtoms; ++i) {
       if (masses[i] != 0.0)
           for (int j = 0; j < 3; ++j) {
               velocities[i][j] = velocityScale*(xPrime[i][j] - atomCoordinates[i][j]);
               atomCoordinates[i][j] = xPrime[i][j];
           }
   }

   getVirtualSites().computePositions(system, atomCoordinates);
   incrementTimeStep();
}