Line data    Source code

       1              : // Copyright (C) 2015 Technische Universitaet Muenchen
       2              : // This file is part of the Mamico project. For conditions of distribution
       3              : // and use, please see the copyright notice in Mamico's main folder, or at
       4              : // www5.in.tum.de/mamico
       5              : #ifndef _MOLECULARDYNAMICS_MOLECULARDYNAMICSSIMULATION_H_
       6              : #define _MOLECULARDYNAMICS_MOLECULARDYNAMICSSIMULATION_H_
       7              : 
       8              : #include "simplemd/BoundaryTreatment.h"
       9              : #include "simplemd/MolecularDynamicsDefinitions.h"
      10              : #include "simplemd/ProfilePlotter.h"
      11              : #include "simplemd/cell-mappings/ComputeMeanVelocityMapping.h"
      12              : #include "simplemd/cell-mappings/ComputeTemperatureMapping.h"
      13              : #include "simplemd/molecule-with-cell-mappings/LennardJonesForceMapping.h"
      14              : #include "simplemd/cell-mappings/RDFMapping.h"
      15              : #include "simplemd/configurations/MolecularDynamicsConfiguration.h"
      16              : #include "simplemd/molecule-mappings/ConvertForcesFixedToFloatMapping.h"
      17              : #include "simplemd/molecule-mappings/InitialPositionAndForceUpdate.h"
      18              : #include "simplemd/molecule-mappings/VTKMoleculeWriter.h"
      19              : #if BUILD_WITH_ADIOS2
      20              : #include "simplemd/molecule-mappings/Adios2Writer.h"
      21              : #endif
      22              : #include "simplemd/molecule-mappings/VelocityStoermerVerletMapping.h"
      23              : #include "simplemd/services/ExternalForceService.h"
      24              : #include "simplemd/services/MolecularPropertiesService.h"
      25              : #include "simplemd/services/MoleculeService.h"
      26              : #include "simplemd/services/ParallelTopologyService.h"
      27              : #include "tarch/utils/MultiMDService.h"
      28              : #include "tarch/utils/RandomNumberService.h"
      29              : #include "simplemd/MoleculeContainer.h"
      30              : #include <iostream>
      31              : #include <sstream>
      32              : 
      33              : namespace simplemd {
      34              : class MolecularDynamicsSimulation;
      35              : }
      36              : 
      37              : /** steers the MD simulation.
      38              :  *
      39              :  *  @author Philipp Neumann
      40              :  */
      41              : class simplemd::MolecularDynamicsSimulation {
      42              : public:
      43              :   MolecularDynamicsSimulation(const simplemd::configurations::MolecularDynamicsConfiguration& configuration);
      44           12 :   virtual ~MolecularDynamicsSimulation() {}
      45              : 
      46              :   /** initialises all services */
      47              :   void initServices();
      48              :   /** variant for multi-MD simulations */
      49              :   void initServices(const tarch::utils::MultiMDService<MD_DIM>& multiMDService, unsigned int localMDSimulation);
      50              : 
      51              :   /** simulates one MD timestep. It's a virtual function as we (will definitely) need to extend this method when
      52              :    *  going to coupled LB-MD simulations.
      53              :    */
      54              :   void simulateOneTimestep(const unsigned int& t);
      55              : 
      56              :   /** runs the time loop for the MD simulation */
      57              :   void runSimulation();
      58              : 
      59              :   /** shuts down all services and deletes pointers */
      60              :   void shutdownServices();
      61              : 
      62              :   void evaluateStatistics(const unsigned int& t);
      63              : 
      64              : private:
      65              :   /** computes the number density for molecules given per direction and a certain domain size.
      66              :    *  This is only used during initialisation.
      67              :    */
      68              :   double getNumberDensity(unsigned int numberMolecules, const tarch::la::Vector<MD_DIM, double>& domainSize) const;
      69              : 
      70              :   class simplemd::moleculemappings::ConvertForcesFixedToFloatMapping _convertForcesFixedToFloatMapping;
      71              : 
      72              : protected:
      73              :   const simplemd::configurations::MolecularDynamicsConfiguration& _configuration;
      74              : 
      75              :   // molecule mappings
      76              :   simplemd::moleculemappings::VelocityStoermerVerletMapping* _timeIntegrator;
      77              :   simplemd::moleculemappings::VTKMoleculeWriter* _vtkMoleculeWriter;
      78              :   std::string _vtkFilestem;
      79              : 
      80              : #if BUILD_WITH_ADIOS2
      81              :   simplemd::moleculemappings::Adios2Writer* _Adios2Writer;
      82              : #endif
      83              : 
      84              :   // cell mappings
      85              :   simplemd::moleculewithcellmappings::LennardJonesForceMapping* _lennardJonesForce;
      86              :   simplemd::cellmappings::RDFMapping* _rdfMapping;
      87              : 
      88              :   // boundary treatment
      89              :   simplemd::BoundaryTreatment* _boundaryTreatment;
      90              :   tarch::la::Vector<MD_LINKED_CELL_NEIGHBOURS, simplemd::BoundaryType> _localBoundary;
      91              : 
      92              :   // number of this MD simulation on this local rank
      93              :   unsigned int _localMDSimulation;
      94              :   // for plotting
      95              :   simplemd::ProfilePlotter* _profilePlotter;
      96              :   // for parallel data exchange
      97              :   simplemd::services::ParallelTopologyService* _parallelTopologyService;
      98              :   // for molecule storage
      99              :   simplemd::services::MoleculeService* _moleculeService;
     100              :   std::string _checkpointFilestem;
     101              :   // for linked cell storage
     102              :   // molecular properties (potential parameters, mass etc)
     103              :   simplemd::services::MolecularPropertiesService* _molecularPropertiesService;
     104              :   // for external forces; has default constructor, hence we use it as object instead of ptr
     105              :   simplemd::services::ExternalForceService _externalForceService;
     106              : };
     107              : #endif // _MOLECULARDYNAMICS_MOLECULARDYNAMICSSIMULATION_H_