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Thermostat.h
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Thermostat.h
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/** Thermostat : a class for atom-continuum control of energy/temperature */
#ifndef THERMOSTAT_H
#define THERMOSTAT_H
// ATC_Transfer headers
#include "AtomicRegulator.h"
// other headers
#include <map>
#include <set>
namespace ATC {
/**
* @class Thermtostat
* @brief Manager class for atom-continuum control of thermal energy
*/
//--------------------------------------------------------
//--------------------------------------------------------
// Class Thermostat
//--------------------------------------------------------
//--------------------------------------------------------
class Thermostat : public AtomicRegulator {
public:
/** thermostat types */
enum ThermostatType {
NONE=0,
RESCALE,
HOOVER,
FLUX
};
// constructor
Thermostat(ATC_Transfer * atcTransfer);
// destructor
~Thermostat(){};
/** parser/modifier */
virtual bool modify(int narg, char **arg);
/** pre time integration */
virtual void initialize();
// data access, intended for method objects
/** reset the nodal power to a prescribed value */
void reset_lambda_power(DENS_MAT & target);
/** return the nodal power induced by lambda */
DENS_VEC & get_nodal_atomic_lambda_power(){return nodalAtomicLambdaPower_;};
/** return value filtered lambda */
DENS_VEC & get_filtered_lambda_power(){return lambdaPowerFiltered_;};
/** access to thermostat type */
ThermostatType get_thermostat_type() const {return thermostatType_;};
protected:
/** thermostat type flag */
ThermostatType thermostatType_;
// thermostat data
/** lambda power applied to atoms */
DENS_VEC nodalAtomicLambdaPower_;
/** filtered lambda power */
DENS_VEC lambdaPowerFiltered_;
private:
// DO NOT define this
Thermostat();
};
/**
* @class ThermostatShapeFunction
* @brief Base class for implementation of thermostat algorithms using the shape function matrices
*/
//--------------------------------------------------------
//--------------------------------------------------------
// Class ThermostatShapeFunction
// base class for all thermostats of general form
// of N^T w N lambda = rhs
//--------------------------------------------------------
//--------------------------------------------------------
class ThermostatShapeFunction : public RegulatorShapeFunction {
public:
ThermostatShapeFunction(Thermostat * thermostat);
~ThermostatShapeFunction(){};
/** reset number of local atoms, as well as atomic data */
virtual void reset_nlocal();
protected:
// methods
/** set weighting factor for in matrix Nhat^T * weights * Nhat */
virtual void set_weights(DIAG_MAT & weights);
// member data
/** pointer to thermostat object for data */
Thermostat * thermostat_;
/** pointer to lammps atomic velocities */
double ** v_;
/** MD mass matrix */
MATRIX & mdMassMatrix_;
/** mass of ATC internal atoms on this processor */
DENS_VEC atomicMass_;
private:
// DO NOT define this
ThermostatShapeFunction();
};
/**
* @class ThermostatRescale
* @brief Enforces constraint on atomic kinetic energy based on FE temperature
*/
//--------------------------------------------------------
//--------------------------------------------------------
// Class ThermostatRescale
//--------------------------------------------------------
//--------------------------------------------------------
class ThermostatRescale : public ThermostatShapeFunction {
public:
ThermostatRescale(Thermostat * thermostat);
~ThermostatRescale(){};
/** applies thermostat to atoms in the post-corrector phase */
virtual void apply_post_corrector(double dt);
/** get data for output */
virtual void output(double dt, OUTPUT_LIST & outputData);
protected:
/** apply solution to atomic quantities */
void apply_to_atoms(double ** atomicVelocity,
double dt);
/** FE temperature field */
DENS_MAT & nodalTemperature_;
private:
// DO NOT define this
ThermostatRescale();
};
/**
* @class ThermostatGlc
* @brief Base class for implementation of thermostat algorithms based on Gaussian least constraints (GLC)
*/
//--------------------------------------------------------
//--------------------------------------------------------
// Class ThermostatGlc
// base clas for all thermostats of general form of a
// Gaussian least constraint (GLC)
//--------------------------------------------------------
//--------------------------------------------------------
class ThermostatGlc : public ThermostatShapeFunction {
public:
ThermostatGlc(Thermostat * thermostat);
~ThermostatGlc(){};
protected:
// methods
/** compute force induced by lambda */
virtual void compute_lambda_force(double * const * atomicQuantity,
DENS_MAT & lambdaForce);
/** apply forces to atoms */
virtual void apply_to_atoms(double ** atomicVelocity,
const DENS_MAT & lambdaForce,
double dt);
// member data
/** pointer to a time filtering object */
TimeFilter * timeFilter_;
/** power induced by lambda */
DENS_VEC & nodalAtomicLambdaPower_;
/** filtered lambda power */
DENS_VEC & lambdaPowerFiltered_;
/** atomic force induced by lambda */
DENS_MAT & lambdaForce_;
/** bool to determine if node is fixed or not */
Array2D<bool> & isFixedNode_;
private:
// DO NOT define this
ThermostatGlc();
};
/**
* @class ThermostatPower
* @brief Enforces GLC on atomic forces based on FE power
* when using fractional step time integration
*/
//--------------------------------------------------------
//--------------------------------------------------------
// Class ThermostatPower
//--------------------------------------------------------
//--------------------------------------------------------
class ThermostatPower : public ThermostatGlc {
public:
ThermostatPower(Thermostat * thermostat);
~ThermostatPower();
/** reset number of local atoms, as well as atomic data */
virtual void reset_nlocal();
/** applies thermostat to atoms in the predictor phase */
virtual void apply_pre_predictor(double dt);
/** applies thermostat to atoms in the pre-corrector phase */
virtual void apply_pre_corrector(double dt);
/** applies thermostat to atoms in the post-corrector phase */
virtual void apply_post_corrector(double dt);
protected:
// methods
/** destroys allocated memory */
void destroy();
/** update the nodal quantities after predictor step */
virtual void update_nodal_quantities_predictor(double dt);
/** compute the change in nodal atomic temperature */
virtual void compute_delta_nodal_atomic_temperature(double dt);
/** update the nodal quantities after pre-corrector step */
virtual void update_nodal_quantities_pre_corrector(double dt);
/** undoes the update the nodal quantities after pre-corrector step */
virtual void undo_update_nodal_quantities_pre_corrector(double dt);
/** update the nodal quantities after post-corrector step */
virtual void update_nodal_quantities_post_corrector(double dt);
/** sets up appropriate rhs for thermostat equations */
virtual void set_thermostat_rhs(DENS_MAT & rhs_nodes,
double dt);
/** apply forces to atoms */
virtual void apply_to_atoms(double ** atomicVelocity,
const DENS_MAT & lambdaForce,
double dt);
/** solves the non-linear equation for lambda iteratively */
void iterate_lambda(const MATRIX & rhs,
double * const * atomicVelocity,
double dt);
/** set weighting factor for in matrix Nhat^T * weights * Nhat */
virtual void set_weights(DIAG_MAT & weights);
// data
/** reference to AtC FE temperature */
DENS_MAT & nodalTemperature_;
/** reference to AtC restricted atomic temperature */
DENS_MAT & nodalAtomicTemperature_;
/** reference to ATC sources coming from prescribed data, AtC coupling, and extrinsic coupling */
DENS_MAT & heatSource_;
/** reference to weights for Nhat */
DIAG_MAT & nodalWeights_;
/** change in FE temperature over a timestep */
DENS_MAT deltaTemperature_;
/** change in restricted atomic FE temperature over a timestep */
DENS_MAT deltaNodalAtomicTemperature_;
/** FE temperature rate of change */
DENS_MAT nodalTemperatureRoc_;
/** local version of velocity used as predicted final veloctiy */
double ** myAtomicVelocity_;
/** pointer to lammps atomic forces */
double ** f_;
/** number of total atoms on this processor */
int nLocalTotal_;
/** maximum number of iterations used in iterative solve for lambda */
int lambdaMaxIterations_;
/** tolerance used in iterative solve for lambda */
double lambdaTolerance_;
/** coefficient to account for effect of time filtering on rhs terms */
double filterCoefficient_;
/** reference to ATC unity shape function on ghost atoms */
SPAR_MAT & Nstar_;
/** maps ghost atom and LAMMPS atom ids */
Array<int> & ghostToAtom_;
private:
// DO NOT define this
ThermostatPower();
};
//--------------------------------------------------------
//--------------------------------------------------------
// Class ThermostatHoover
//--------------------------------------------------------
//--------------------------------------------------------
class ThermostatHoover : public ThermostatPower {
public:
ThermostatHoover(Thermostat * thermostat);
~ThermostatHoover();
/** reset number of local atoms, as well as atomic data */
virtual void reset_nlocal();
/** applies thermostat to atoms in the predictor phase */
virtual void apply_pre_predictor(double dt);
/** applies thermostat to atoms in the pre-corrector phase */
virtual void apply_pre_corrector(double dt);
/** applies thermostat to atoms in the post-corrector phase */
virtual void apply_post_corrector(double dt);
protected:
// methods
/** compute boundary flux, requires thermostat input since it is part of the coupling scheme */
virtual void compute_boundary_flux(FIELDS & fields) {boundaryFlux_[TEMPERATURE] = 0.;};
/** adds Hoover power terms to nodal variables after the predictor phase */
void add_to_lambda_power_predictor(double dt);
/** adds Hoover power terms to nodal variables after the pre-corrector phase */
void add_to_lambda_power_pre_corrector(double dt);
/** adds Hoover power terms to nodal variables after the post-corrector phase */
void add_to_lambda_power_post_corrector(double dt);
/** sets up appropriate rhs for thermostat equations */
virtual void set_hoover_rhs(DENS_MAT & rhs_nodes,
double dt);
/** add Hoover contributions to lambda power */
void add_to_lambda_power(DENS_MAT & myLambdaForce);
// data
/** force coming from Hoover contribution */
DENS_MAT lambdaForceHoover_;
/** reference to ATC map from global nodes to overlap nodes */
Array<int> & nodeToOverlapMap_;
private:
// DO NOT define this
ThermostatHoover();
};
//--------------------------------------------------------
//--------------------------------------------------------
// Class ThermostatPowerFiltered
//--------------------------------------------------------
//--------------------------------------------------------
class ThermostatPowerFiltered : public ThermostatPower {
public:
ThermostatPowerFiltered(Thermostat * thermostat);
~ThermostatPowerFiltered(){};
protected:
/** update the nodal quantities after predictor step */
virtual void update_nodal_quantities_predictor(double dt);
/** compute the change in nodal atomic temperature */
virtual void compute_delta_nodal_atomic_temperature(double dt);
/** update the nodal quantities after pre-corrector step */
virtual void update_nodal_quantities_pre_corrector(double dt);
/** update the nodal quantities after post-corrector step */
virtual void update_nodal_quantities_post_corrector(double dt);
/** sets up appropriate rhs for thermostat equations */
virtual void set_thermostat_rhs(DENS_MAT & rhs_nodes,
double dt);
private:
// DO NOT define this
ThermostatPowerFiltered();
};
//--------------------------------------------------------
//--------------------------------------------------------
// Class ThermostatPowerVerlet
//--------------------------------------------------------
//--------------------------------------------------------
class ThermostatPowerVerlet : public ThermostatGlc {
public:
ThermostatPowerVerlet(Thermostat * thermostat);
~ThermostatPowerVerlet(){};
/** applies thermostat to atoms in the predictor phase */
virtual void apply_pre_predictor(double dt);
/** applies thermostat to atoms in the pre-corrector phase */
virtual void apply_pre_corrector(double dt);
/** get data for output */
virtual void output(double dt, OUTPUT_LIST & outputData);
protected:
/** nodal temperature rate of change */
DENS_MAT & nodalTemperatureRoc_;
/** reference to ATC sources coming from prescribed data, AtC coupling, and extrinsic coupling */
DENS_MAT & heatSource_;
/** pointer to lammps atomic forces */
double ** f_;
/** sets up and solves thermostat equations */
virtual void compute_thermostat(double dt);
/** sets up appropriate rhs for thermostat equations */
virtual void set_thermostat_rhs(DENS_MAT & rhs_nodes);
/** computes the nodal FE power applied by the thermostat */
virtual void compute_nodal_lambda_power(double dt);
/** add contributions (if any) to the finite element right-hand side */
virtual void add_to_rhs(FIELDS & rhs);
private:
// DO NOT define this
ThermostatPowerVerlet();
};
//--------------------------------------------------------
//--------------------------------------------------------
// Class ThermostatHooverVerlet
//--------------------------------------------------------
//--------------------------------------------------------
class ThermostatHooverVerlet : public ThermostatPowerVerlet {
public:
ThermostatHooverVerlet(Thermostat * thermostat);
~ThermostatHooverVerlet(){};
protected:
/** reference to ATC map from global nodes to overlap nodes */
Array<int> & nodeToOverlapMap_;
/** sets up and solves thermostat equations */
virtual void compute_thermostat(double dt);
/** compute boundary flux, requires thermostat input since it is part of the coupling scheme */
virtual void compute_boundary_flux(FIELDS & fields) {boundaryFlux_[TEMPERATURE] = 0.;};
/** sets up Hoover component of the thermostat */
void set_hoover_rhs(DENS_MAT & rhs_nodes);
/** add Hoover contributions to lambda power */
void add_to_lambda_power(DENS_MAT & myLambdaForce,
double dt);
private:
// DO NOT implement this
ThermostatHooverVerlet();
};
//--------------------------------------------------------
//--------------------------------------------------------
// Class ThermostatPowerVerletFiltered
//--------------------------------------------------------
//--------------------------------------------------------
class ThermostatPowerVerletFiltered : public ThermostatPowerVerlet {
public:
ThermostatPowerVerletFiltered(Thermostat * thermostat);
~ThermostatPowerVerletFiltered(){};
/** compute boundary flux, requires thermostat input since it is part of the coupling scheme */
virtual void compute_boundary_flux(FIELDS & fields);
/** get data for output */
virtual void output(double dt, OUTPUT_LIST & outputData);
protected:
/** sets up appropriate rhs for thermostat equations */
virtual void set_thermostat_rhs(DENS_MAT & rhs_nodes);
/** add contributions (if any) to the finite element right-hand side */
virtual void add_to_rhs(FIELDS & rhs);
/** nodal temperature 2nd rate of change (i.e. second time derivative) */
DENS_MAT & nodalTemperature2Roc_;
/** reference to ATC rate of change sources coming from prescribed data, AtC coupling, and extrinsic coupling */
DENS_MAT heatSourceRoc_;
/** references to ATC field rates of changing for inverting the filtered heat sources */
FIELDS & fieldsRoc_;
/** flux rate of changes for inverting filtered fluxes */
FIELDS fluxRoc_;
/** time scale for the time filter */
double filterScale_;
private:
// DO NOT define this
ThermostatPowerVerletFiltered();
};
//--------------------------------------------------------
//--------------------------------------------------------
// Class ThermostatHooverVerletFiltered
//--------------------------------------------------------
//--------------------------------------------------------
class ThermostatHooverVerletFiltered : public ThermostatPowerVerletFiltered {
public:
ThermostatHooverVerletFiltered(Thermostat * thermostat);
~ThermostatHooverVerletFiltered(){};
protected:
/** reference to ATC map from global nodes to overlap nodes */
Array<int> & nodeToOverlapMap_;
/** sets up and solves thermostat equations */
virtual void compute_thermostat(double dt);
/** compute boundary flux, requires thermostat input since it is part of the coupling scheme */
virtual void compute_boundary_flux(FIELDS & fields) {boundaryFlux_[TEMPERATURE] = 0.;};
/** sets up Hoover component of the thermostat */
void set_hoover_rhs(DENS_MAT & rhs_nodes);
/** add Hoover contributions to lambda power */
void add_to_lambda_power(DENS_MAT & myLambdaForce,
double dt);
private:
// DO NOT implement this
ThermostatHooverVerletFiltered();
};
};
#endif

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