BrookRemoveCMMotionKernel.cpp

/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
 * -------------------------------------------------------------------------- *
 * This is part of the OpenMM molecular simulation toolkit originating from   *
 * Simbios, the NIH National Center for Physics-Based Simulation of           *
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
 *                                                                            *
 * Portions copyright (c) 2009 Stanford University and the Authors.           *
 * Authors: Mark Friedrichs, Mike Houston                                     *
 * Contributors:                                                              *
 *                                                                            *
 * This program is free software: you can redistribute it and/or modify       *
 * it under the terms of the GNU Lesser General Public License as published   *
 * by the Free Software Foundation, either version 3 of the License, or       *
 * (at your option) any later version.                                        *
 *                                                                            *
 * This program is distributed in the hope that it will be useful,            *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
 * GNU Lesser General Public License for more details.                        *
 *                                                                            *
 * You should have received a copy of the GNU Lesser General Public License   *
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
 * -------------------------------------------------------------------------- */

#include "openmm/internal/ContextImpl.h"
#include "openmm/System.h"
#include "BrookRemoveCMMotionKernel.h"
#include "BrookStreamInternal.h"

using namespace OpenMM;
using namespace std;

/** 
 * BrookRemoveCMMotionKernel constructor
 * 
 * @param name        name of the stream to create
 * @param platform    platform
 * @param openMMBrookInterface      OpenMM-Brook interface
 * @param System                    System reference
 *
 */
  
BrookRemoveCMMotionKernel::BrookRemoveCMMotionKernel( std::string name, const Platform& platform, OpenMMBrookInterface& openMMBrookInterface, System& system ) :
                              RemoveCMMotionKernel( name, platform ), _openMMBrookInterface( openMMBrookInterface ), _system( system ){

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

   // static const std::string methodName      = "BrookRemoveCMMotionKernel::BrookRemoveCMMotionKernel";

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

   _frequency                           = 0;
   _log                                 = NULL;
   _brookVelocityCenterOfMassRemoval    = NULL;

   const BrookPlatform& brookPlatform   = dynamic_cast<const BrookPlatform&> (platform);
   if( brookPlatform.getLog() != NULL ){
      setLog( brookPlatform.getLog() );
   }   
   _openMMBrookInterface.setNumberOfParticles( system.getNumParticles() );

}

/** 
 * BrookRemoveCMMotionKernel destructor
 * 
 */
  
BrookRemoveCMMotionKernel::~BrookRemoveCMMotionKernel( ){

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

   // static const std::string methodName      = "BrookRemoveCMMotionKernel::~BrookRemoveCMMotionKernel";

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

   delete _brookVelocityCenterOfMassRemoval;
}

/** 
 * Initialize the kernel
 * 
 * @param system   System reference
 * @param force    CMMotionRemover reference
 *
 */

void BrookRemoveCMMotionKernel::initialize( const System& system, const CMMotionRemover& force ){

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

   static const std::string methodName      = "BrookRemoveCMMotionKernel::initialize";
   static const int PrintOn                 = 0;
   FILE* log                                = getLog();

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

   _frequency = force.getFrequency();
   std::vector<double> masses;
   masses.resize( system.getNumParticles() );
   for( size_t ii = 0; ii < masses.size(); ii++ ){
      masses[ii] = system.getParticleMass(ii);
   }

   _brookVelocityCenterOfMassRemoval = new BrookVelocityCenterOfMassRemoval();
   _brookVelocityCenterOfMassRemoval->setup( masses, getPlatform() );

   if( PrintOn && log ){
      (void) fprintf( log, "%s\n", methodName.c_str() );
      (void) fflush( log );
   }

   return;

}

/** 
 * Get log file reference
 * 
 * @return  log file reference
 *
 */

FILE* BrookRemoveCMMotionKernel::getLog( void ) const {
   return _log;
}

/** 
 * Set log file reference
 * 
 * @param  log file reference
 *
 * @return  DefaultReturnValue
 *
 */

int BrookRemoveCMMotionKernel::setLog( FILE* log ){
   _log = log;
   return BrookCommon::DefaultReturnValue;
}


/** 
 * Get COM removal frequency
 * 
 * @return frequency 
 *
 */

int BrookRemoveCMMotionKernel::getFrequency( void ) const {
   return _frequency;
}

/** 
 * Execute kernel
 * 
 * @param context    ContextImpl reference
 *
 */

void BrookRemoveCMMotionKernel::execute( ContextImpl& context ){

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

   static const std::string methodName      = "BrookRemoveCMMotionKernel::execute";

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

   int step      = (int) floor( context.getTime()/context.getIntegrator().getStepSize() );
   int frequency = getFrequency();
   if( frequency <= 0 || (step % frequency) != 0 ){
        return;
   }

   BrookStreamImpl* velocities = _openMMBrookInterface.getParticleVelocities();
   _brookVelocityCenterOfMassRemoval->removeVelocityCenterOfMass( *velocities );

   return;
}