forked from lijiext/lammps
804 lines
25 KiB
C++
804 lines
25 KiB
C++
#ifndef KINETOTHERMOSTAT_H
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#define KINETOTHERMOSTAT_H
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#include "AtomicRegulator.h"
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#include "PerAtomQuantityLibrary.h"
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#include "Kinetostat.h"
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#include "Thermostat.h"
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#include <map>
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#include <set>
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#include <string>
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namespace ATC {
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static const int myCouplingMaxIterations = 50;
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// forward declarations
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class MomentumTimeIntegrator;
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class ThermalTimeIntegrator;
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class AtfShapeFunctionRestriction;
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class FundamentalAtomQuantity;
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class PrescribedDataManager;
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/**
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* @class KinetoThermostat
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* @brief Manager class for atom-continuum simulataneous control of momentum and thermal energy
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*/
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class KinetoThermostat : public AtomicRegulator {
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public:
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// constructor
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KinetoThermostat(ATC_Coupling * atc,
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const std::string & regulatorPrefix = "");
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// destructor
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virtual ~KinetoThermostat(){};
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/** parser/modifier */
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virtual bool modify(int narg, char **arg);
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/** instantiate up the desired method(s) */
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virtual void construct_methods();
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// data access, intended for method objects
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/** reset the nodal power to a prescribed value */
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virtual void reset_lambda_contribution(const DENS_MAT & target,
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const FieldName field);
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/** return value for the max number of mechanical/thermal coupling iterations */
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int coupling_max_iterations() const {return couplingMaxIterations_;};
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protected:
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/** maximum number of iterations used to solved coupled thermo/mechanical problem */
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int couplingMaxIterations_;
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private:
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// DO NOT define this
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KinetoThermostat();
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};
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/**
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* @class KinetoThermostatShapeFunction
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* @brief Class for kinetostat/thermostat algorithms using the shape function matrices
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* (thermostats have general for of N^T w N lambda = rhs)
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*/
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class KinetoThermostatShapeFunction : public RegulatorMethod {
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public:
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KinetoThermostatShapeFunction(AtomicRegulator * kinetoThermostat,
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int couplingMaxIterations,
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const std::string & /* regulatorPrefix */) : RegulatorMethod(kinetoThermostat),
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couplingMaxIterations_(couplingMaxIterations) {};
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KinetoThermostatShapeFunction(AtomicRegulator * kinetoThermostat,
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int couplingMaxIterations)
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: RegulatorMethod(kinetoThermostat), couplingMaxIterations_(couplingMaxIterations) {};
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virtual ~KinetoThermostatShapeFunction() {};
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/** instantiate all needed data */
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virtual void construct_transfers() = 0;
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/** initialize all data */
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virtual void initialize() {tolerance_ = atomicRegulator_->tolerance();};
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protected:
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/** maximum number of iterations between energy and momentum regulators */
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int couplingMaxIterations_;
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/** tolerance */
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double tolerance_;
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private:
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// DO NOT define this
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KinetoThermostatShapeFunction();
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};
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/**
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* @class VelocityRescaleCombined
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* @brief Enforces constraints on atomic velocity based on FE temperature and velocity
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*/
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class VelocityRescaleCombined : public VelocityGlc {
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public:
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friend class KinetoThermostatRescale; // since this is basically a set of member functions for friend
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VelocityRescaleCombined(AtomicRegulator * kinetostat);
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virtual ~VelocityRescaleCombined(){};
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/** pre-run initialization of method data */
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virtual void initialize();
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/** applies kinetostat to atoms */
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virtual void apply_mid_predictor(double /* dt */){};
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/** applies kinetostat to atoms */
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virtual void apply_post_corrector(double /* dt */){};
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/** local shape function matrices are incompatible with this mode */
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virtual bool use_local_shape_functions() const {return false;};
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protected:
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// data
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/** reference to AtC FE velocity */
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DENS_MAN & velocity_;
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/** RHS correct based on thermostat */
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DENS_MAN * thermostatCorrection_;
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// methods
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/** sets up appropriate rhs for kinetostat equations */
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virtual void set_kinetostat_rhs(DENS_MAT & rhs, double dt);
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// disable un-needed functionality
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/** does initial filtering operations before main computation */
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virtual void apply_pre_filtering(double /* dt */){};
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/** applies kinetostat correction to atoms */
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virtual void apply_kinetostat(double /* dt */) {};
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/** computes the nodal FE force applied by the kinetostat */
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virtual void compute_nodal_lambda_force(double /* dt */){};
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/** apply any required corrections for localized kinetostats */
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virtual void apply_localization_correction(const DENS_MAT & /* source */,
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DENS_MAT & /* nodalField */,
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double /* weight */){};
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virtual void apply_localization_correction(const DENS_MAT & /* source */,
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DENS_MAT & /* nodalField */){};
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private:
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// DO NOT define this
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VelocityRescaleCombined();
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};
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/**
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* @class ThermostatRescaleCombined
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* @brief Enforces constraint on atomic kinetic energy based on FE temperature and velocity
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*/
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class ThermostatRescaleCombined : public ThermostatRescale {
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public:
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ThermostatRescaleCombined(AtomicRegulator * thermostat);
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virtual ~ThermostatRescaleCombined() {};
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/** pre-run initialization of method data */
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virtual void initialize();
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// deactivate un-needed methods
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/** applies thermostat to atoms in the post-corrector phase */
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virtual void apply_post_corrector(double /* dt */){};
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protected:
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// data
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/** RHS correct based on kinetostat */
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DENS_MAN * kinetostatCorrection_;
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// deactivate un-needed methods
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/** apply solution to atomic quantities */
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virtual void apply_to_atoms(PerAtomQuantity<double> * /* atomVelocities */){};
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/** construct the RHS vector */
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virtual void set_rhs(DENS_MAT & rhs);
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private:
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// DO NOT define this
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ThermostatRescaleCombined();
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};
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/**
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* @class KinetoThermostatRescale
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* @brief Enforces constraints on atomic kinetic energy and velocity based on FE temperature and velocity
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*/
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class KinetoThermostatRescale : public KinetoThermostatShapeFunction {
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public:
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KinetoThermostatRescale(AtomicRegulator * kinetoThermostat,
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int couplingMaxIterations);
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virtual ~KinetoThermostatRescale();
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/** instantiate all needed data */
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virtual void construct_transfers();
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/** pre-run initialization of method data */
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virtual void initialize();
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/** applies thermostat to atoms in the post-corrector phase */
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virtual void apply_post_corrector(double dt);
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/** compute boundary flux, requires thermostat input since it is part of the coupling scheme */
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virtual void compute_boundary_flux(FIELDS & /* fields */)
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{boundaryFlux_[TEMPERATURE] = 0.; boundaryFlux_[VELOCITY] = 0.;};
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/** get data for output */
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virtual void output(OUTPUT_LIST & outputData);
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protected:
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// methods
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/** apply solution to atomic quantities */
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virtual void apply_to_atoms(PerAtomQuantity<double> * atomVelocities);
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/** creates the appropriate rescaling thermostat */
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virtual ThermostatRescale * construct_rescale_thermostat();
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// data
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/** pointer to atom velocities */
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FundamentalAtomQuantity * atomVelocities_;
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/** clone of FE velocity field */
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DENS_MAN & nodalVelocities_;
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/** lambda coupling parameter for momentum */
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DENS_MAN * lambdaMomentum_;
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/** lambda coupling parameter for energy */
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DENS_MAN * lambdaEnergy_;
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/** pointer to rescaled velocity fluctuations */
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PerAtomQuantity<double> * atomicFluctuatingVelocityRescaled_;
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/** pointer to streaming velocity */
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PerAtomQuantity<double> * atomicStreamingVelocity_;
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/** rescaling thermostat */
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ThermostatRescale * thermostat_;
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/** velocity regulating kinetostat */
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VelocityRescaleCombined * kinetostat_;
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// workspace
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DENS_MAT _lambdaEnergyOld_, _lambdaMomentumOld_, _diff_;
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private:
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// DO NOT define this
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KinetoThermostatRescale();
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};
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/**
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* @class ThermostatRescaleMixedKePeCombined
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* @brief Enforces constraint on atomic kinetic energy based on FE temperature and velocity when the temperature is comprised of both KE and PE contributions
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*/
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class ThermostatRescaleMixedKePeCombined : public ThermostatRescaleMixedKePe {
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public:
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ThermostatRescaleMixedKePeCombined(AtomicRegulator * thermostat);
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virtual ~ThermostatRescaleMixedKePeCombined() {};
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/** pre-run initialization of method data */
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virtual void initialize();
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// deactivate un-needed methods
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/** applies thermostat to atoms in the post-corrector phase */
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virtual void apply_post_corrector(double /* dt */){};
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protected:
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// data
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/** RHS correct based on kinetostat */
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DENS_MAN * kinetostatCorrection_;
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// deactivate un-needed methods
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/** apply solution to atomic quantities */
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virtual void apply_to_atoms(PerAtomQuantity<double> * /* atomVelocities */){};
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/** construct the RHS vector */
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virtual void set_rhs(DENS_MAT & rhs);
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private:
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// DO NOT define this
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ThermostatRescaleMixedKePeCombined();
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};
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/**
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* @class KinetoThermostatRescaleMixedKePe
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* @brief Enforces constraint on atomic kinetic energy based on FE temperature
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* when the temperature is a mix of the KE and PE
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*/
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class KinetoThermostatRescaleMixedKePe : public KinetoThermostatRescale {
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public:
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KinetoThermostatRescaleMixedKePe(AtomicRegulator * kinetoThermostat,
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int couplingMaxIterations);
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virtual ~KinetoThermostatRescaleMixedKePe() {};
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protected:
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/** creates the appropriate rescaling thermostat */
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virtual ThermostatRescale * construct_rescale_thermostat();
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private:
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// DO NOT define this
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KinetoThermostatRescaleMixedKePe();
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};
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/**
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* @class KinetoThermostatGlcFs
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* @brief Class for regulation algorithms based on Gaussian least constraints (GLC) for fractional step (FS) algorithsm
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*/
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class KinetoThermostatGlcFs : public KinetoThermostatShapeFunction {
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public:
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KinetoThermostatGlcFs(AtomicRegulator * kinetoThermostat,
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int couplingMaxIterations,
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const std::string & regulatorPrefix = "");
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virtual ~KinetoThermostatGlcFs() {};
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/** instantiate all needed data */
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virtual void construct_transfers();
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/** pre-run initialization of method data */
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virtual void initialize();
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/** applies thermostat to atoms in the predictor phase */
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virtual void apply_pre_predictor(double dt);
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/** applies thermostat to atoms in the pre-corrector phase */
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virtual void apply_pre_corrector(double dt);
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/** applies thermostat to atoms in the post-corrector phase */
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virtual void apply_post_corrector(double dt);
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/** get data for output */
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virtual void output(OUTPUT_LIST & outputData);
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/* flag for performing the full lambda prediction calculation */
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bool full_prediction();
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protected:
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// methods
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/** apply forces to atoms */
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virtual void apply_to_atoms(PerAtomQuantity<double> * atomicVelocity,
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const DENS_MAN * nodalAtomicMomentum,
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const DENS_MAN * nodalAtomicEnergy,
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const DENS_MAT & lambdaForce,
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DENS_MAT & nodalAtomicLambdaForce,
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DENS_MAT & nodalAtomicLambdaPower,
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double dt);
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// USE BASE CLASSES FOR THESE
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/** add contributions from regulator to FE momentum */
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virtual void add_to_momentum(const DENS_MAT & nodalLambdaForce,
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DENS_MAT & deltaForce,
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double dt) = 0;
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/** add contributions from regulator to FE energy */
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virtual void add_to_energy(const DENS_MAT & nodalLambdaPower,
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DENS_MAT & deltaEnergy,
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double dt) = 0;
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/* sets up and solves the linear system for lambda */
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virtual void compute_lambda(double dt,
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bool iterateSolution = true);
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// member data
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/** reference to AtC FE velocity */
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DENS_MAN & velocity_;
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/** reference to AtC FE temperature */
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DENS_MAN & temperature_;
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/** pointer to a time filtering object */
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TimeFilter * timeFilter_;
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/** force induced by lambda */
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DENS_MAN * nodalAtomicLambdaForce_;
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/** filtered lambda force */
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DENS_MAN * lambdaForceFiltered_;
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/** power induced by lambda */
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DENS_MAN * nodalAtomicLambdaPower_;
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/** filtered lambda power */
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DENS_MAN * lambdaPowerFiltered_;
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/** atomic force induced by lambda */
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AtomicThermostatForce * atomRegulatorForces_;
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/** atomic force induced by thermostat lambda */
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AtomicThermostatForce * atomThermostatForces_;
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/** pointer to atom masses */
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FundamentalAtomQuantity * atomMasses_;
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/** pointer to atom velocities */
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FundamentalAtomQuantity * atomVelocities_;
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/** hack to determine if first timestep has been passed */
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bool isFirstTimestep_;
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/** nodal atomic momentum */
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DENS_MAN * nodalAtomicMomentum_;
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/** nodal atomic energy */
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DENS_MAN * nodalAtomicEnergy_;
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/** local version of velocity used as predicted final veloctiy */
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PerAtomQuantity<double> * atomPredictedVelocities_;
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/** predicted nodal atomic momentum */
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AtfShapeFunctionRestriction * nodalAtomicPredictedMomentum_;
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/** predicted nodal atomic energy */
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AtfShapeFunctionRestriction * nodalAtomicPredictedEnergy_;
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/** pointer for force applied in first time step */
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DENS_MAN * firstHalfAtomForces_;
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/** FE momentum change from regulator during predictor phase in second half of timestep */
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DENS_MAT deltaMomentum_;
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/** FE temperature change from regulator during predictor phase in second half of timestep */
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DENS_MAT deltaEnergy1_;
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/** FE temperature change from regulator during corrector phase in second half of timestep */
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DENS_MAT deltaEnergy2_;
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/** fraction of timestep over which constraint is exactly enforced */
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double dtFactor_;
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// workspace
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DENS_MAT _lambdaForceOutput_; // force applied by lambda in output format
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DENS_MAT _lambdaPowerOutput_; // power applied by lambda in output format
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DENS_MAT _velocityDelta_; // change in velocity when lambda force is applied
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private:
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// DO NOT define this
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KinetoThermostatGlcFs();
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};
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/* #ifdef WIP_JAT */
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/* /\** */
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/* * @class ThermostatFlux */
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/* * @brief Class enforces GLC on atomic forces based on FE power when using fractional step time integration */
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/* *\/ */
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/* class ThermostatFlux : public ThermostatGlcFs { */
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/* public: */
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/* ThermostatFlux(Thermostat * thermostat, */
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/* const std::string & regulatorPrefix = ""); */
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/* virtual ~ThermostatFlux() {}; */
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/* /\** instantiate all needed data *\/ */
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/* virtual void construct_transfers(); */
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/* /\** pre-run initialization of method data *\/ */
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/* virtual void initialize(); */
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/* protected: */
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/* /\** sets up appropriate rhs for thermostat equations *\/ */
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/* virtual void set_thermostat_rhs(DENS_MAT & rhs, */
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/* double dt); */
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/* /\** add contributions from thermostat to FE energy *\/ */
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/* virtual void add_to_energy(const DENS_MAT & nodalLambdaPower, */
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/* DENS_MAT & deltaEnergy, */
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/* double dt); */
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/* /\** sets up the transfer which is the set of nodes being regulated *\/ */
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/* virtual void construct_regulated_nodes(); */
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/* // data */
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/* /\** reference to ATC sources coming from prescribed data, AtC coupling, and extrinsic coupling *\/ */
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/* DENS_MAN & heatSource_; */
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/* private: */
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/* // DO NOT define this */
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/* ThermostatFlux(); */
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/* }; */
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/* /\** */
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/* * @class ThermostatFixed */
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/* * @brief Class enforces GLC on atomic forces based on FE power when using fractional step time integration */
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/* *\/ */
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/* class ThermostatFixed : public ThermostatGlcFs { */
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/* public: */
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/* ThermostatFixed(Thermostat * thermostat, */
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/* const std::string & regulatorPrefix = ""); */
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/* virtual ~ThermostatFixed() {}; */
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/* /\** instantiate all needed data *\/ */
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/* virtual void construct_transfers(); */
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/* /\** pre-run initialization of method data *\/ */
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/* virtual void initialize(); */
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/* /\** applies thermostat to atoms in the predictor phase *\/ */
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/* virtual void apply_pre_predictor(double dt); */
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/* /\** applies thermostat to atoms in the pre-corrector phase *\/ */
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/* virtual void apply_pre_corrector(double dt); */
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/* /\** applies thermostat to atoms in the post-corrector phase *\/ */
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/* virtual void apply_post_corrector(double dt); */
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/* /\** compute boundary flux, requires thermostat input since it is part of the coupling scheme *\/ */
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/* virtual void compute_boundary_flux(FIELDS & fields) */
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/* {boundaryFlux_[TEMPERATURE] = 0.;}; */
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/* /\** determine if local shape function matrices are needed *\/ */
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/* virtual bool use_local_shape_functions() const {return atomicRegulator_->use_localized_lambda();}; */
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/* protected: */
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/* // methods */
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/* /\** initialize data for tracking the change in nodal atomic temperature *\/ */
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/* virtual void initialize_delta_nodal_atomic_energy(double dt); */
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/* /\** compute the change in nodal atomic temperature *\/ */
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/* virtual void compute_delta_nodal_atomic_energy(double dt); */
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/* /\** sets up appropriate rhs for thermostat equations *\/ */
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/* virtual void set_thermostat_rhs(DENS_MAT & rhs, */
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/* double dt); */
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/* /\** add contributions from thermostat to FE energy *\/ */
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/* virtual void add_to_energy(const DENS_MAT & nodalLambdaPower, */
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/* DENS_MAT & deltaEnergy, */
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/* double dt); */
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/* /\* sets up and solves the linear system for lambda *\/ */
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/* virtual void compute_lambda(double dt, */
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/* bool iterateSolution = true); */
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/* /\** flag for halving the applied force to mitigate numerical errors *\/ */
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/* bool halve_force(); */
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/* /\** sets up the transfer which is the set of nodes being regulated *\/ */
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/* virtual void construct_regulated_nodes(); */
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/* // data */
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/* /\** change in FE energy over a timestep *\/ */
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/* DENS_MAT deltaFeEnergy_; */
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/* /\** initial FE energy used to compute change *\/ */
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/* DENS_MAT initialFeEnergy_; */
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/* /\** change in restricted atomic FE energy over a timestep *\/ */
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/* DENS_MAT deltaNodalAtomicEnergy_; */
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/* /\** initial restricted atomic FE energy used to compute change *\/ */
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/* DENS_MAT initialNodalAtomicEnergy_; */
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/* /\** filtered nodal atomic energy *\/ */
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/* DENS_MAN nodalAtomicEnergyFiltered_; */
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/* /\** forces depending on predicted velocities for correct updating with fixed nodes *\/ */
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/* AtomicThermostatForce * atomThermostatForcesPredVel_; */
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/* /\** coefficient to account for effect of time filtering on rhs terms *\/ */
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/* double filterCoefficient_; */
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/* /\** kinetic energy multiplier in total energy (used for temperature expression) *\/ */
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/* double keMultiplier_; */
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/* // workspace */
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/* DENS_MAT _tempNodalAtomicEnergyFiltered_; // stores filtered energy change in atoms for persistence during predictor */
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/* private: */
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/* // DO NOT define this */
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/* ThermostatFixed(); */
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/* }; */
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/* /\** */
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/* * @class ThermostatFluxFiltered */
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/* * @brief Class enforces GLC on atomic forces based on FE power when using fractional step time integration */
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/* * in conjunction with time filtering */
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/* *\/ */
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/* class ThermostatFluxFiltered : public ThermostatFlux { */
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/* public: */
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/* ThermostatFluxFiltered(Thermostat * thermostat, */
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/* const std::string & regulatorPrefix = ""); */
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/* virtual ~ThermostatFluxFiltered() {}; */
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/* /\** pre-run initialization of method data *\/ */
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/* virtual void initialize(); */
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/* /\** applies thermostat to atoms in the post-corrector phase *\/ */
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/* virtual void apply_post_corrector(double dt); */
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/* /\** get data for output *\/ */
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/* virtual void output(OUTPUT_LIST & outputData); */
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/* protected: */
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/* /\** sets up appropriate rhs for thermostat equations *\/ */
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/* virtual void set_thermostat_rhs(DENS_MAT & rhs, */
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/* double dt); */
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|
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/* /\** add contributions from thermostat to FE energy *\/ */
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/* virtual void add_to_energy(const DENS_MAT & nodalLambdaPower, */
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/* DENS_MAT & deltaEnergy, */
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|
/* double dt); */
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/* // data */
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/* /\** heat source time history required to get instantaneous heat sources *\/ */
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/* DENS_MAT heatSourceOld_; */
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/* DENS_MAT instantHeatSource_; */
|
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/* DENS_MAT timeStepSource_; */
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/* private: */
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/* // DO NOT define this */
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/* ThermostatFluxFiltered(); */
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/* }; */
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/* /\** */
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/* * @class ThermostatFixedFiltered */
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/* * @brief Class for thermostatting using the temperature matching constraint and is compatible with */
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|
/* the fractional step time-integration with time filtering */
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/* *\/ */
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/* class ThermostatFixedFiltered : public ThermostatFixed { */
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/* public: */
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/* ThermostatFixedFiltered(Thermostat * thermostat, */
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|
/* const std::string & regulatorPrefix = ""); */
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/* virtual ~ThermostatFixedFiltered() {}; */
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|
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/* /\** get data for output *\/ */
|
|
/* virtual void output(OUTPUT_LIST & outputData); */
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|
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/* protected: */
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|
|
/* // methods */
|
|
/* /\** initialize data for tracking the change in nodal atomic temperature *\/ */
|
|
/* virtual void initialize_delta_nodal_atomic_energy(double dt); */
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|
|
|
/* /\** compute the change in nodal atomic temperature *\/ */
|
|
/* virtual void compute_delta_nodal_atomic_energy(double dt); */
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|
|
/* /\** sets up appropriate rhs for thermostat equations *\/ */
|
|
/* virtual void set_thermostat_rhs(DENS_MAT & rhs, */
|
|
/* double dt); */
|
|
|
|
/* /\** add contributions from thermostat to temperature for uncoupled nodes *\/ */
|
|
/* virtual void add_to_energy(const DENS_MAT & nodalLambdaPower, */
|
|
/* DENS_MAT & deltaEnergy, */
|
|
/* double dt); */
|
|
|
|
/* private: */
|
|
|
|
/* // DO NOT define this */
|
|
/* ThermostatFixedFiltered(); */
|
|
|
|
/* }; */
|
|
|
|
/* /\** */
|
|
/* * @class ThermostatFluxFixed */
|
|
/* * @brief Class for thermostatting using the temperature matching constraint one one set of nodes and the flux matching constraint on another */
|
|
/* *\/ */
|
|
|
|
/* class ThermostatFluxFixed : public RegulatorMethod { */
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|
|
|
/* public: */
|
|
|
|
/* ThermostatFluxFixed(Thermostat * thermostat, */
|
|
/* bool constructThermostats = true); */
|
|
|
|
/* virtual ~ThermostatFluxFixed(); */
|
|
|
|
/* /\** instantiate all needed data *\/ */
|
|
/* virtual void construct_transfers(); */
|
|
|
|
/* /\** pre-run initialization of method data *\/ */
|
|
/* virtual void initialize(); */
|
|
|
|
/* /\** 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); */
|
|
|
|
/* /\** get data for output *\/ */
|
|
/* virtual void output(OUTPUT_LIST & outputData); */
|
|
|
|
/* /\** compute boundary flux, requires thermostat input since it is part of the coupling scheme *\/ */
|
|
/* virtual void compute_boundary_flux(FIELDS & fields) */
|
|
/* {thermostatBcs_->compute_boundary_flux(fields);}; */
|
|
|
|
/* protected: */
|
|
|
|
/* // data */
|
|
/* /\** thermostat for imposing the fluxes *\/ */
|
|
/* ThermostatFlux * thermostatFlux_; */
|
|
|
|
/* /\** thermostat for imposing fixed nodes *\/ */
|
|
/* ThermostatFixed * thermostatFixed_; */
|
|
|
|
/* /\** pointer to whichever thermostat should compute the flux, based on coupling method *\/ */
|
|
/* ThermostatGlcFs * thermostatBcs_; */
|
|
|
|
/* private: */
|
|
|
|
/* // DO NOT define this */
|
|
/* ThermostatFluxFixed(); */
|
|
/* }; */
|
|
|
|
/* /\** */
|
|
/* * @class ThermostatFluxFixedFiltered */
|
|
/* * @brief Class for thermostatting using the temperature matching constraint one one set of nodes and the flux matching constraint on another with time filtering */
|
|
/* *\/ */
|
|
|
|
/* class ThermostatFluxFixedFiltered : public ThermostatFluxFixed { */
|
|
|
|
/* public: */
|
|
|
|
/* ThermostatFluxFixedFiltered(Thermostat * thermostat); */
|
|
|
|
/* virtual ~ThermostatFluxFixedFiltered(){}; */
|
|
|
|
/* private: */
|
|
|
|
/* // DO NOT define this */
|
|
/* ThermostatFluxFixedFiltered(); */
|
|
|
|
/* }; */
|
|
/* #endif */
|
|
|
|
};
|
|
|
|
#endif
|