ReferenceBrownianDynamics.cpp

/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
 * Contributors: Peter Eastman, Pande Group
 *
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 * 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
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 *
 * 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
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#include <cstring>
#include <sstream>

#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMLog.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceBrownianDynamics.h"
#include "ReferenceVirtualSites.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,
                                                          RealOpenMM deltaT, RealOpenMM friction,
                                                          RealOpenMM temperature ) : 
           ReferenceDynamics( numberOfAtoms, deltaT, temperature ), friction( friction ) {

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

   static const char* methodName      = "\nReferenceBrownianDynamics::ReferenceBrownianDynamics";

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

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

   if( friction <= zero ){

      std::stringstream message;
      message << methodName;
      message << " input frction value=" << friction << " is invalid -- setting to 1.";
      SimTKOpenMMLog::printError( message );

      this->friction = one;
     
   }
   xPrime.resize(numberOfAtoms);
   inverseMasses.resize(numberOfAtoms);
}

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

   ReferenceBrownianDynamics destructor

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

ReferenceBrownianDynamics::~ReferenceBrownianDynamics( ){

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

   // static const char* methodName = "\nReferenceBrownianDynamics::~ReferenceBrownianDynamics";

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

}

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

   Get the friction coefficient

   @return friction

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

RealOpenMM ReferenceBrownianDynamics::getFriction( void ) const {

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

   // static const char* methodName  = "\nReferenceBrownianDynamics::getFriction";

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

   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<RealVec>& atomCoordinates,
                                          vector<RealVec>& velocities,
                                          vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {

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

   static const char* methodName      = "\nReferenceBrownianDynamics::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.
   
   const RealOpenMM noiseAmplitude = static_cast<RealOpenMM>( sqrt(2.0*BOLTZ*getTemperature()*getDeltaT()/getFriction()) );
   const RealOpenMM forceScale = getDeltaT()/getFriction();
   for (int i = 0; i < numberOfAtoms; ++i) {
       if (masses[i] != zero)
           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.
   
   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();
}