ReferenceBrownianDynamics.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
 * "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 <cstring>
#include <sstream>

#include "SimTKOpenMMUtilities.h"
#include "ReferenceBrownianDynamics.h"
#include "openmm/OpenMMException.h"

#include <cstdio>

using std::vector;
using namespace OpenMM;

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

   ReferenceBrownianDynamics constructor

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

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

ReferenceBrownianDynamics::ReferenceBrownianDynamics(int numberOfAtoms,
                                                          double deltaT, double friction,
                                                          double temperature) : 
           ReferenceDynamics(numberOfAtoms, deltaT, temperature), friction(friction) {

   if (friction <= 0) {
      std::stringstream message;
      message << "illegal friction value: " << friction;
      throw OpenMMException(message.str());
   }
   xPrime.resize(numberOfAtoms);
   inverseMasses.resize(numberOfAtoms);
}

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

   ReferenceBrownianDynamics destructor

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

ReferenceBrownianDynamics::~ReferenceBrownianDynamics() {
}

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

   Get the friction coefficient

   @return friction

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

double ReferenceBrownianDynamics::getFriction() const {
   return friction;
}

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

   Update -- driver routine for performing Brownian 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 ReferenceBrownianDynamics::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.
   
   const double noiseAmplitude = sqrt(2.0*BOLTZ*getTemperature()*getDeltaT()/getFriction());
   const double forceScale = getDeltaT()/getFriction();
   for (int i = 0; i < numberOfAtoms; ++i) {
       if (masses[i] != 0.0)
           for (int j = 0; j < 3; ++j) {
               xPrime[i][j] = atomCoordinates[i][j] + forceScale*inverseMasses[i]*forces[i][j] + noiseAmplitude*sqrt(inverseMasses[i])*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
           }
   }
   ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
   if (referenceConstraintAlgorithm)
      referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
   
   // Update the positions and velocities.
   
   double velocityScale = 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();
}