ReferenceDynamics.h 6.67 KB
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/* Portions copyright (c) 2006-2012 Stanford University and Simbios.
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 * 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
 * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
 * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */

#ifndef __ReferenceDynamics_H__
#define __ReferenceDynamics_H__

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#include "ReferenceConstraintAlgorithm.h"
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#include "ReferenceVirtualSites.h"
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#include "openmm/System.h"
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#include <cstddef>
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#include <vector>
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namespace OpenMM {
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/**---------------------------------------------------------------------------------------

Abstract class for dynamics

Main method (virtual) is update()

'Random' numbers are currently fixed to allow testing

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

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class OPENMM_EXPORT ReferenceDynamics {
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   private:

      int _numberOfAtoms;
      int _timeStep;

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      double _deltaT;
      double _temperature;
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      ReferenceConstraintAlgorithm* _referenceConstraint;
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      const ReferenceVirtualSites* virtualSites;
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   public:

      /**---------------------------------------------------------------------------------------
      
         Constructor
      
         @param numberOfAtoms  number of atoms
         @param deltaT         delta t for dynamics
         @param temperature    temperature

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

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       ReferenceDynamics(int numberOfAtoms, double _deltaT, double temperature);
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      /**---------------------------------------------------------------------------------------
      
         Destructor
      
         --------------------------------------------------------------------------------------- */

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       virtual ~ReferenceDynamics();
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      /**---------------------------------------------------------------------------------------
      
         Get number of atoms
      
         @return number of atoms
      
         --------------------------------------------------------------------------------------- */
      
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      int getNumberOfAtoms() const;
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      /**---------------------------------------------------------------------------------------
      
         Get time step
      
         @return time step
      
         --------------------------------------------------------------------------------------- */
      
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      int getTimeStep() const;
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      /**---------------------------------------------------------------------------------------
      
         Increment time step
      
         @return incremented time step
      
         --------------------------------------------------------------------------------------- */
      
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      int incrementTimeStep();
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      /**---------------------------------------------------------------------------------------
      
         Get delta t
      
         @return deltaT
      
         --------------------------------------------------------------------------------------- */
      
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      double getDeltaT() const;
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      /**---------------------------------------------------------------------------------------

         Set delta t

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

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      void setDeltaT(double deltaT);
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      /**---------------------------------------------------------------------------------------
      
         Get temperature
      
         @return temperature
      
         --------------------------------------------------------------------------------------- */
    
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      double getTemperature() const;
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      /**---------------------------------------------------------------------------------------
      
         Set the temperature
      
         --------------------------------------------------------------------------------------- */
    
      void setTemperature(double temperature);

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      /**---------------------------------------------------------------------------------------
      
         Update
      
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         @param system              the System to be integrated
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         @param atomCoordinates     atom coordinates
         @param velocities          velocities
         @param forces              forces
         @param masses              atom masses
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         @param tolerance           the constraint tolerance
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         --------------------------------------------------------------------------------------- */
      
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      virtual void update(const OpenMM::System& system, std::vector<OpenMM::Vec3>& atomCoordinates,
                          std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, double tolerance);
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      /**---------------------------------------------------------------------------------------
      
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         Get ReferenceConstraint
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         @return referenceConstraint  object
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         --------------------------------------------------------------------------------------- */
      
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      ReferenceConstraintAlgorithm* getReferenceConstraintAlgorithm() const;
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      /**---------------------------------------------------------------------------------------
      
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         Set ReferenceConstraint
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         @param referenceConstraint  referenceConstraint object
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         --------------------------------------------------------------------------------------- */
      
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      void setReferenceConstraintAlgorithm(ReferenceConstraintAlgorithm* referenceConstraint);
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      /**
       * Get the object used to compute virtual sites.
       */
      const ReferenceVirtualSites& getVirtualSites() const;

      /**
       * Set the object used to compute virtual sites.
       */
      void setVirtualSites(const ReferenceVirtualSites& sites);
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};

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} // namespace OpenMM

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#endif // __ReferenceDynamics_H__