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ATC_TransferThermal.h
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Fri, Jun 21, 03:03

ATC_TransferThermal.h
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/** ATC_TransferThermal : a class for atom-continuum transfers &
control involving heat transport */
#ifndef ATC_TRANSFER_THERMAL_H
#define ATC_TRANSFER_THERMAL_H
// ATC_Transfer headers
#include "ATC_Transfer.h"
#include "Thermostat.h"
#include "TimeIntegrator.h"
// Other headers
#include <map>
namespace ATC {
class ATC_TransferThermal : public ATC_Transfer {
public:
// constructor
ATC_TransferThermal(std::string groupName, std::string matParamFile,
ExtrinsicModelType extrinsic = NO_MODEL);
// destructor
~ATC_TransferThermal();
/** parser/modifier */
virtual bool modify(int narg, char **arg);
/** pre time integration */
virtual void initialize();
/** post time integration */
virtual void finish();
/** first time substep routines */
virtual void pre_init_integrate();
virtual void mid_init_integrate(){};
virtual void post_init_integrate();
/** second time substep routine */
virtual void pre_final_integrate();
virtual void post_final_integrate();
/** compute vector for output */
virtual double compute_vector(int n);
private:
/** sets the position/velocity of the ghost atoms */
virtual void set_ghost_atoms();
/** resets any arrays associated with local atom count */
virtual void reset_nlocal();
/** compute the mass matrix components coming from MD integration */
virtual void compute_md_mass_matrix(FieldName thisField,
map<FieldName,DIAG_MAT> & massMats);
/** time integration flag and access method */
TimeIntegrator::TimeIntegrationType integrationType_;
virtual TimeIntegrator::TimeIntegrationType get_integration_type(){return integrationType_;};
/** fractional step auxilliary storage */
DENS_MAT delTheta;
DENS_MAT delThetaV;
DENS_MAT dot_atomicTemp;
DENS_MAT dot_atomicTempOld;
DENS_MAT dot_dot_atomicTemp;
DENS_MAT dot_dot_atomicTempOld;
/** physics specific filter initialization */
void init_filter();
/** field mask for velocity integration */
Array2D<bool> temperatureMask_;
void output();
/** thermostat manager */
Thermostat thermostat_;
// Data for poor man's fractional step
bool pmfcOn_;
DENS_MAT oldFieldTemp_;
// Add in fields for restarting
virtual void read_restart_data(string fileName_, OUTPUT_LIST & data);
virtual void write_restart_data(string fileName_, OUTPUT_LIST & data);
void pack_thermal_fields(OUTPUT_LIST & data);
};
};
#endif

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