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lammps/lib/atc/SpeciesTimeIntegrator.h
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SpeciesTimeIntegrator.h
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#ifndef SPECIES_TIME_INTEGRATOR_H
#define SPECIES_TIME_INTEGRATOR_H
#include <map>
#include <utility>
#include <string>
// ATC headers
#include "TimeIntegrator.h"
namespace ATC {
// forward declarations
class ATC_CouplingMass;
class SpeciesIntegrationMethod;
/**
* @class SpeciesTimeIntegrator
* @brief Class for various time integrators for species FE quantities in the Eulerian frame
* (handles parsing and stores basic data structures)
*/
class SpeciesTimeIntegrator : public TimeIntegrator {
public:
// constructor
SpeciesTimeIntegrator(ATC_CouplingMass * atc,
TimeIntegrationType timeIntegrationType);
// destructor
virtual ~SpeciesTimeIntegrator(){};
/** parser/modifier */
virtual bool modify(int narg, char **arg);
/** create objects to implement requested numerical method */
virtual void construct_methods();
/** pack persistent fields */
virtual void pack_fields(RESTART_LIST & data);
DENS_MAN & nodal_atomic_species_concentration_filtered() { return nodalAtomicSpeciesConcentrationFiltered_; }
protected:
/** sets of molecules tracked */
const std::map<std::string,std::pair<MolSize,int> > & moleculeIds_;
/** data */
DENS_MAN nodalAtomicSpeciesConcentrationFiltered_;
private:
// DO NOT define this
SpeciesTimeIntegrator();
};
/**
* @class SpeciesIntegrationMethod
* @brief Class for species time integration methods which update FE quantities in time
*/
class SpeciesIntegrationMethod : public TimeIntegrationMethod {
public:
// constructor
SpeciesIntegrationMethod(SpeciesTimeIntegrator * speciesTimeIntegrator,
const std::map<std::string,std::pair<MolSize,int> > & moleculeIds);
// destructor
virtual ~SpeciesIntegrationMethod() {nodalAtomicMassDensity_=NULL;};
/** create and get necessary transfer operators */
virtual void construct_transfers();
protected:
/** time filtering object */
TimeFilter * timeFilter_;
/** finite element mass density field */
DENS_MAN & massDensity_;
/** atomic nodal mass density field */
// OBSOLETE?
DENS_MAN & nodalAtomicMassDensityOut_;
DENS_MAN * nodalAtomicMassDensity_;
/** finite element mass density field */
DENS_MAN & speciesConcentration_;
DENS_MAN * nodalAtomicSpeciesConcentration_;
DENS_MAN & nodalAtomicSpeciesConcentrationFiltered_;
/** sets of molecules tracked */
const std::map<std::string,std::pair<MolSize,int> > & moleculeIds_;
private:
// DO NOT define this
SpeciesIntegrationMethod();
};
/**
* @class SpeciesTimeIntegratorFractionalStep
* @brief FractionalStep integration for FE species quantities
* (Uses 2nd order FractionalStep integration to update
* the FE mass density field)
*/
class SpeciesTimeIntegratorFractionalStep : public SpeciesIntegrationMethod {
public:
// constructor
SpeciesTimeIntegratorFractionalStep(SpeciesTimeIntegrator * speciesTimeIntegrator,
const std::map<std::string,std::pair<MolSize,int> > & moleculeIds);
// destructor
virtual ~SpeciesTimeIntegratorFractionalStep(){};
/** pre time integration */
virtual void initialize();
// time step methods, corresponding to ATC_Transfer
virtual void pre_initial_integrate1(double dt);
virtual void pre_final_integrate1(double dt);
virtual void post_final_integrate2(double dt);
/** post processing step before output */
virtual void post_process();
private:
// DO NOT define this
SpeciesTimeIntegratorFractionalStep();
};
/**
* @class SpeciesTimeIntegratorFractionalStepFiltered
* @brief FractionalStep integration for FE species quantities
* (Uses 2nd order FractionalStep integration to update
* the FE mass density field)
*/
class SpeciesTimeIntegratorFractionalStepFiltered : public SpeciesTimeIntegratorFractionalStep {
public:
// constructor
SpeciesTimeIntegratorFractionalStepFiltered(SpeciesTimeIntegrator * speciesTimeIntegrator,
const std::map<std::string,std::pair<MolSize,int> > & moleculeIds);
// destructor
virtual ~SpeciesTimeIntegratorFractionalStepFiltered(){};
/** pre time integration */
virtual void initialize() {};
// time step methods, corresponding to ATC_Transfer
/** first part of pre_final_integrate */
virtual void pre_final_integrate1(double dt);
/** post processing step before output */
virtual void post_process(){};
private:
// DO NOT define this
SpeciesTimeIntegratorFractionalStepFiltered();
};
};
#endif
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