BrookIntegrateLangevinStepKernel.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) 2008 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
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 * 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,   *
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 * Software is furnished to do so, subject to the following conditions:       *
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 * The above copyright notice and this permission notice shall be included in *
 * all copies or substantial portions of the Software.                        *
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 * 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,    *
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#include "BrookIntegrateKernals.h"
#include "BrookStreamInternal.h"

using namespace OpenMM;
using namespace std;

BrookIntegrateLangevinStepKernel::BrookIntegrateLangevinStepKernel( std::string name, const Platform& platform ) :
                                IntegrateLangevinStepKernel( name, platform ){

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

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

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

   _numberOfConstraints            = -1;

   _brookStochasticDynamics        = NULL;
   _brookShakeAlgorithm            = NULL;
   _atomMasses                     = NULL;
   _shakeParameters                = NULL;
   _constraintIndices              = NULL;
   _shakeParameters                = NULL;
   
}

BrookIntegrateLangevinStepKernel::~BrookIntegrateLangevinStepKernel( ){

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

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

// ---------------------------------------------------------------------------------------
   
   delete _brookkStochasticDynamics;
   delete _brookShakeAlgorithm;
   delete _atomMasses;
   delete _shakeParameters;
   delete _constraintIndices;
   delete _shakeParameters;

}

void BrookIntegrateLangevinStepKernel::initialize( const vector<double>& masses,
                                                 const vector<vector<int> >& constraintIndices,
                                                 const vector<double>& constraintLengths ){

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

   // static const std::string methodName      = "BrookIntegrateLangevinStepKernel::initialize";

// ---------------------------------------------------------------------------------------
   
/*
    this->masses = new RealOpenMM[masses.size()];
    for (size_t i = 0; i < masses.size(); ++i)
        this->masses[i] = static_cast<RealOpenMM>( masses[i] );
    numConstraints = constraintIndices.size();
    this->constraintIndices = allocateIntArray(numConstraints, 2); 
    for (int i = 0; i < numConstraints; ++i) {
        this->constraintIndices[i][0] = constraintIndices[i][0];
        this->constraintIndices[i][1] = constraintIndices[i][1];
    }   
    shakeParameters = allocateRealArray(constraintLengths.size(), 1); 
    for (size_t i = 0; i < constraintLengths.size(); ++i)
        shakeParameters[i][0] = static_cast<RealOpenMM>( constraintLengths[i] );

*/
}

/** 
 * Execute kernel
 * 
 * @param positions          atom coordinates
 * @param velocities         atom velocities
 * @param forces             atom forces
 * @param temperature        heat bath temperature
 * @param friction           friction coefficient coupling the system to the heat bath
 * @param stepSize           integration step size
 *
 */

void BrookIntegrateLangevinStepKernel::execute( Stream& positions, Stream& velocities,
                                                const Stream& forces, double temperature,
                                                double friction, double stepSize ){

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

   //static const std::string methodName      = "BrookIntegrateLangevinStepKernel::execute";

// ---------------------------------------------------------------------------------------
   
   // first time through initialize _brookStochasticDynamics

   // for each subsequent call, check if parameters need to be updated due to a change
   // in T, gamma, or the step size

   // take step

   if( _brookStochasticDynamics == NULL ){
      _brookStochasticDynamics = new BrookStochasticDynamics( getNumberOfAtoms(), static_cast<RealOpenMM>(stepSize), 
                                                              static_cast<RealOpenMM>(tau), static_cast<RealOpenMM>(temperature) );
   } else {
      _brookStochasticDynamics->updateParameters( temperature, friction, stepSize );
   } 
   _brookStochasticDynamics->update( positions, velocities, forces );

}