BrookCalcGBSAOBCForceKernel.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/OpenMMException.h"

#include "BrookStreamImpl.h"
#include "BrookCalcGBSAOBCForceKernel.h"
#include "kernels/kgbsa.h"
#include "kernels/kforce.h"

#include <cmath>
#include <limits>
#include <sstream>

using namespace OpenMM;
using namespace std;

/** 
 * BrookCalcGBSAOBCForceKernel constructor
 * 
 * @param name                      kernel name
 * @param platform                  platform
 * @param OpenMMBrookInterface      OpenMM-Brook interface
 * @param System                    System reference
 *
 */

BrookCalcGBSAOBCForceKernel::BrookCalcGBSAOBCForceKernel( std::string name, const Platform& platform, OpenMMBrookInterface& openMMBrookInterface, System& system ) :
                             CalcGBSAOBCForceKernel( name, platform ), _openMMBrookInterface( openMMBrookInterface ), _system( system ){

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

   // static const std::string methodName      = "BrookCalcGBSAOBCForceKernel::BrookCalcGBSAOBCForceKernel";
   // static const int debug                   = 1;

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

   _numberOfParticles                 = 0;
   _log                               = NULL;

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

/** 
 * BrookCalcGBSAOBCForceKernel destructor
 * 
 */

BrookCalcGBSAOBCForceKernel::~BrookCalcGBSAOBCForceKernel( ){

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

   // static const std::string methodName      = "BrookCalcGBSAOBCForceKernel::BrookCalcGBSAOBCForceKernel";
   // static const int debug                   = 1;

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

}

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

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

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

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

/** 
 * Initialize the kernel, setting up the values of all the force field parameters.
 * 
 * @param system     system this kernel will be applied to
 * @param force      GBSAOBCForce this kernel will be used for
 *
 */

void BrookCalcGBSAOBCForceKernel::initialize( const System& system, const GBSAOBCForce& force ){

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

   static const std::string methodName      = "BrookCalcGBSAOBCForceKernel::initialize";
   int printOn                              = 0;
   FILE* log;

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

   if( printOn && getLog() ){
       log = getLog();
   } else {
      printOn = 0;
   } 

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

   BrookGbsa& brookGbsa      = _openMMBrookInterface.getBrookGbsa();
    
   // get parameters from force object
   // and initialize brookGbsa

   _numberOfParticles = system.getNumParticles();
   std::vector<std::vector<double> > particleParameters( _numberOfParticles );

   for( int ii = 0; ii < _numberOfParticles; ii++ ){

      double charge, radius, scalingFactor;
      force.getParticleParameters( ii, charge, radius, scalingFactor );

      particleParameters[ii].push_back( charge );
      particleParameters[ii].push_back( radius );
      particleParameters[ii].push_back( scalingFactor );
   }   
   brookGbsa.setup( particleParameters, force.getSolventDielectric(), force.getSoluteDielectric(), getPlatform() );
   brookGbsa.setIsActive( 1 );

   _openMMBrookInterface.setTriggerForceKernel( this );
   _openMMBrookInterface.setTriggerEnergyKernel( this );

   if( printOn ){
      std::string contents = brookGbsa.getContentsString( ); 
      (void) fprintf( log, "%s brookGbsa::contents\n%s", methodName.c_str(), contents.c_str() );
      (void) fflush( log );
   }

   // ---------------------------------------------------------------------------------------
    
}

/** 
 * Compute forces given particle coordinates
 * 
 * @param context OpenMMContextImpl context
 *
 */

void BrookCalcGBSAOBCForceKernel::executeForces( OpenMMContextImpl& context ){

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

   //static const std::string methodName   = "BrookCalcGBSAOBCForceKernel::executeForces";

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

   if( _openMMBrookInterface.getTriggerForceKernel() == this ){
      _openMMBrookInterface.computeForces( context );
   }   

}

/**
 * Execute the kernel to calculate the OBC energy
 * 
 * @param context OpenMMContextImpl context
 *
 * @return energy
 *
 */

double BrookCalcGBSAOBCForceKernel::executeEnergy( OpenMMContextImpl& context ){

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

   //static const std::string methodName      = "BrookCalcGBSAOBCForceKernel::executeEnergy";

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

   if( _openMMBrookInterface.getTriggerEnergyKernel() == this ){
      return (double) _openMMBrookInterface.computeEnergy( context, _system );
   } else {
      return 0.0;
   }

}