ReferenceShakeAlgorithm.h

/* Portions copyright (c) 2006-2009 Stanford University and Simbios.
 * Contributors: 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
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 */

#ifndef __ReferenceShakeAlgorithm_H__
#define __ReferenceShakeAlgorithm_H__

#include "ReferenceConstraintAlgorithm.h"

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

class ReferenceShakeAlgorithm : public ReferenceConstraintAlgorithm {

   protected:

      int _maximumNumberOfIterations;
      RealOpenMM _tolerance;

      int _numberOfConstraints;
      int** _atomIndices;
      RealOpenMM* _distance;

      RealOpenMM** _r_ij;
      RealOpenMM* _d_ij2;
      RealOpenMM* _distanceTolerance;
      RealOpenMM* _reducedMasses;
      bool _hasInitializedMasses;
      
   public:

      /**---------------------------------------------------------------------------------------
      
         ReferenceShakeAlgorithm constructor
      
         @param numberOfConstraints      number of constraints 
         @param atomIndices              atom indices for contraints
         @param distance                 distances for constraints
         @param tolerance                constraint tolerance
      
         --------------------------------------------------------------------------------------- */
      
      ReferenceShakeAlgorithm( int numberOfConstraints, int** atomIndices, RealOpenMM* distance, RealOpenMM tolerance );

      /**---------------------------------------------------------------------------------------
      
         Destructor
      
         --------------------------------------------------------------------------------------- */

       ~ReferenceShakeAlgorithm( );

      /**---------------------------------------------------------------------------------------
      
         Get number of constraints
      
         @return number of constraints
      
         --------------------------------------------------------------------------------------- */
      
      int getNumberOfConstraints( void ) const;
      
      /**---------------------------------------------------------------------------------------
      
         Get maximum number of iterations
      
         @return maximum number of iterations
      
         --------------------------------------------------------------------------------------- */
      
      int getMaximumNumberOfIterations( void ) const;
      
      /**---------------------------------------------------------------------------------------
      
         Set maximum number of iterations
      
         @param maximumNumberOfIterations   new maximum number of iterations
      
         --------------------------------------------------------------------------------------- */
      
      void setMaximumNumberOfIterations( int maximumNumberOfIterations );
      
      /**---------------------------------------------------------------------------------------
      
         Get tolerance
      
         @return tolerance
      
         --------------------------------------------------------------------------------------- */
      
      RealOpenMM getTolerance( void ) const;
      
      /**---------------------------------------------------------------------------------------
      
         Set tolerance
      
         @param tolerance new tolerance
      
         --------------------------------------------------------------------------------------- */
      
      void setTolerance( RealOpenMM tolerance );

      /**---------------------------------------------------------------------------------------
      
         Apply Shake algorithm
      
         @param numberOfAtoms    number of atoms
         @param atomCoordinates  atom coordinates
         @param atomCoordinatesP atom coordinates prime
         @param inverseMasses    1/mass
      
         @return SimTKOpenMMCommon::DefaultReturn if converge; else
          return SimTKOpenMMCommon::ErrorReturn
      
         --------------------------------------------------------------------------------------- */
      
      int apply( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
                       std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses );
      
      /**---------------------------------------------------------------------------------------
      
         Report any violated constraints
      
         @param numberOfAtoms    number of atoms
         @param atomCoordinates  atom coordinates
         @param message          report
      
         @return number of violated constraints
      
         --------------------------------------------------------------------------------------- */
      
      int reportShake( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::stringstream& message );
};

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

#endif // __ReferenceShakeAlgorithm_H__