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AtomicRegulator.h
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AtomicRegulator.h
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/** Atomic Regulator : a base class class for atom-continuum control */
#ifndef ATOMICREGULATOR_H
#define ATOMICREGULATOR_H
#include "ATC_TypeDefs.h"
#include <map>
#include <set>
#include <vector>
#include <utility>
#include <string>
namespace ATC {
static const int myMaxIterations = 0;
static const double myTolerance = 1.e-10;
// forward declarations
class TimeFilter;
class RegulatorMethod;
class LambdaMatrixSolver;
class ATC_Coupling;
class NodeToSubset;
class SubsetToNode;
class RegulatedNodes;
class ElementMaskNodeSet;
class LargeToSmallAtomMap;
template <typename T>
class PerAtomQuantity;
template <typename T>
class ProtectedAtomQuantity;
template <typename T>
class PerAtomSparseMatrix;
/**
* @class AtomicRegulator
* @brief Base class for atom-continuum control
*/
//--------------------------------------------------------
//--------------------------------------------------------
// Class AtomicRegulator
//--------------------------------------------------------
//--------------------------------------------------------
class AtomicRegulator {
public:
/** linear solver types */
enum LinearSolverType {
NO_SOLVE=0,
CG_SOLVE, // conjugate gradient
RSL_SOLVE // row-sum lumping solution
};
/** regulator target variable */
enum RegulatorTargetType {
NONE=0,
FIELD,
DERIVATIVE,
DYNAMICS
};
enum RegulatorCouplingType {
UNCOUPLED=0,
FLUX,
GHOST_FLUX,
FIXED
};
// constructor
AtomicRegulator(ATC_Coupling * atc,
const std::string & regulatorPrefix = "");
// destructor
virtual ~AtomicRegulator();
/** parser/modifier */
virtual bool modify(int narg, char **arg);
/** instantiate up the desired method(s) */
virtual void construct_methods() = 0;
/** method(s) create all necessary transfer operators */
virtual void construct_transfers();
/** initialization of method data */
virtual void initialize();
/** add output information */
virtual void output(OUTPUT_LIST & outputData) const;
virtual double compute_vector(int n) const {return 0;}
/** final work at the end of a run */
virtual void finish();
/** reset number of local atoms, as well as atomic data */
virtual void reset_nlocal();
/** set up atom to material identification */
virtual void reset_atom_materials(const Array<int> & elementToMaterialMap,
const MatrixDependencyManager<DenseMatrix, int> * atomElement);
// application steps
/** apply the regulator in the pre-predictor phase */
virtual void apply_pre_predictor(double dt, int timeStep);
/** apply the regulator in the mid-predictor phase */
virtual void apply_mid_predictor(double dt, int timeStep);
/** apply the regulator in the post-predictor phase */
virtual void apply_post_predictor(double dt, int timeStep);
/** apply the regulator in the pre-correction phase */
virtual void apply_pre_corrector(double dt, int timeStep);
/** apply the regulator in the post-correction phase */
virtual void apply_post_corrector(double dt, int timeStep);
/** prior to exchanges */
virtual void pre_force();
/** prior to exchanges */
virtual void pre_exchange();
/** pack fields for restart */
virtual void pack_fields(RESTART_LIST & data);
/** thermo output */
virtual int size_vector(int s) const {return 0;};
// coupling to FE state
/** FE state variable regulator is applied to */
virtual RegulatorTargetType regulator_target() const {return regulatorTarget_;};
/** type of boundary coupling */
//TEMP_JAT field variable should be removed
virtual RegulatorCouplingType coupling_mode(const FieldName field=NUM_TOTAL_FIELDS) const {return couplingMode_;};
/** compute the thermal boundary flux, must be consistent with regulator */
virtual void compute_boundary_flux(FIELDS & fields);
/** add contributions (if any) to the finite element right-hand side */
virtual void add_to_rhs(FIELDS & rhs);
// data access, intended for method objects
/** returns a pointer to the DENS_MAN associated with the tag, creates a new data member if necessary */
DENS_MAN * regulator_data(const std::string tag, int nCols);
/** can externally set regulator dynamic contributions */
virtual void reset_lambda_contribution(const DENS_MAT & target, const FieldName field) {};
virtual void reset_lambda_contribution(const DENS_MAT & target) { reset_lambda_contribution(target,NUM_TOTAL_FIELDS); }
/** returns a const pointer to the DENS_MAN associated with the tag, or NULL */
const DENS_MAN * regulator_data(const std::string tag) const;
/** return the maximum number of iterations */
int max_iterations() {return maxIterations_;};
/** return the solver tolerance */
double tolerance() {return tolerance_;};
/** access for ATC transfer */
ATC_Coupling * atc_transfer() {return atc_;};
/** access for time filter */
TimeFilter * time_filter() {return timeFilter_;};
/** access for number of nodes */
int num_nodes() {return nNodes_;};
/** access for number of spatial dimensions */
int nsd() {return nsd_;};
/** access for number of local atoms */
int nlocal() {return nLocal_;};
/** access for boundary integration methods */
BoundaryIntegrationType boundary_integration_type()
{return boundaryIntegrationType_;};
/** access for boundary face sets */
const std::set< std::pair<int,int> > * face_sets()
{ return boundaryFaceSet_;};
/** access for needing a reset */
bool need_reset() const {return needReset_;};
/** force a reset to occur */
void force_reset() {needReset_ = true;};
/** check if lambda is localized */
bool use_localized_lambda() const {return useLocalizedLambda_;};
/** check if matrix should be lumpted for lambda solve */
bool use_lumped_lambda_solve() const {return useLumpedLambda_;};
/** check to see if this direction is being used */
bool apply_in_direction(int i) const {return applyInDirection_[i];};
/** checks if there are any fixed nodes in the MD region */
bool md_fixed_nodes(FieldName fieldName = NUM_TOTAL_FIELDS) const;
/** checks if there are any flux nodes in the MD region */
bool md_flux_nodes(FieldName fieldName = NUM_TOTAL_FIELDS) const;
/** returns prefix tag for regulator */
const std::string & regulator_prefix() const {return regulatorPrefix_;};
protected:
// methods
/** deletes the current regulator method */
void delete_method();
/** deletes all unused data */
void delete_unused_data();
/** sets all data to be unused */
void set_all_data_to_unused();
/** sets all data to be used */
void set_all_data_to_used();
// data
/** point to atc_transfer object */
ATC_Coupling * atc_;
/** how often in number of time steps regulator is applied */
int howOften_;
// reset/reinitialize flags
/** flag to reset data */
bool needReset_;
/** reinitialize method */
void reset_method();
// regulator data
/** container for all data, string is tag, bool is false if currently in use */
std::map<std::string, std::pair<bool,DENS_MAN * > > regulatorData_;
/** maximum number of iterations used in solving for lambda */
int maxIterations_;
/** tolerance used in solving for lambda */
double tolerance_;
/** regulator target flag */
RegulatorTargetType regulatorTarget_;
/** regulator fe coupling type flag */
RegulatorCouplingType couplingMode_;
/** number of nodes */
int nNodes_;
/** number of spatial dimensions */
int nsd_;
/** number of local atoms */
int nLocal_;
/** use of localization techniques */
bool useLocalizedLambda_;
bool useLumpedLambda_;
/** restrict application in certain directions */
std::vector<bool> applyInDirection_;
// method pointers
/** time filtering object */
TimeFilter * timeFilter_;
/** sets up and solves the regulator equations */
RegulatorMethod * regulatorMethod_;
// boundary flux information
BoundaryIntegrationType boundaryIntegrationType_;
const std::set< std::pair<int,int> > * boundaryFaceSet_;
/** prefix string for registering data */
const std::string regulatorPrefix_;
private:
// DO NOT define this
AtomicRegulator();
};
/**
* @class RegulatorMethod
* @brief Base class for implementation of control algorithms
*/
//--------------------------------------------------------
//--------------------------------------------------------
// Class RegulatorMethod
//--------------------------------------------------------
//--------------------------------------------------------
class RegulatorMethod {
public:
RegulatorMethod(AtomicRegulator * atomicRegulator,
const std::string & regulatorPrefix = "");
virtual ~RegulatorMethod(){};
/** instantiate all needed data */
virtual void construct_transfers(){};
/** pre-"run" initialization */
virtual void initialize(){};
/** reset number of local atoms, as well as atomic data */
virtual void reset_nlocal(){};
/** set up atom to material identification */
virtual void reset_atom_materials(const Array<int> & elementToMaterialMap,
const MatrixDependencyManager<DenseMatrix, int> * atomElement){};
/** applies regulator to atoms in the pre-predictor phase */
virtual void apply_pre_predictor(double dt){};
/** applies regulator to atoms in the mid-predictor phase */
virtual void apply_mid_predictor(double dt){};
/** applies regulator to atoms in the post-predictor phase */
virtual void apply_post_predictor(double dt){};
/** applies regulator to atoms in the pre-corrector phase */
virtual void apply_pre_corrector(double dt){};
/** applies regulator to atoms in the post-corrector phase */
virtual void apply_post_corrector(double dt){};
/** applies regulator to atoms in the pre-corrector phase */
virtual void apply_pre_force(double dt){};
/** applies regulator to atoms in the post-corrector phase */
virtual void apply_post_force(double dt){};
/** applies regulator in pre-force phase */
virtual void pre_force(){};
/** applies regulator in pre-exchange phase */
virtual void pre_exchange(){};
/** applies regulator in post-exchange phase */
virtual void post_exchange(){};
/** compute boundary flux, requires regulator input since it is part of the coupling scheme */
virtual void compute_boundary_flux(FIELDS & fields);
/** add contributions (if any) to the finite element right-hand side */
virtual void add_to_rhs(FIELDS & rhs){};
/** get data for output */
virtual void output(OUTPUT_LIST & outputData){};
virtual double compute_vector(int n) const {return 0;}
/** final work at the end of a run */
virtual void finish(){};
/** pack fields for restart */
virtual void pack_fields(RESTART_LIST & data){};
protected:
//data
/** pointer to atomic regulator object for data */
AtomicRegulator * atomicRegulator_;
/** pointer to ATC_transfer object */
ATC_Coupling * atc_;
/** boundary flux */
FIELDS & boundaryFlux_;
/** field mask for specifying boundary flux */
Array2D<bool> fieldMask_;
/** number of nodes */
int nNodes_;
/** prefix string for registering data */
const std::string regulatorPrefix_;
/** mapping for atom materials for atomic FE quadrature */
Array<std::set<int> > atomMaterialGroups_;
/** shape function derivative matrices for boundary atoms */
VectorDependencyManager<SPAR_MAT * > * shpFcnDerivs_;
private:
// DO NOT define this
RegulatorMethod();
};
/**
* @class RegulatorShapeFunction
* @brief Base class for implementation of regulation algorithms using the shape function matrices
*/
// DESIGN each regulator handles only one lambda, but solvers and data are added later
// add a new function to set the linear solver based on enum CG_SOLVE or RSL_SOLVE and shape function matrix
// followed by call to compute sparsity pattern
//--------------------------------------------------------
//--------------------------------------------------------
// Class RegulatorShapeFunction
// base class for all regulators of general form
// of N^T w N lambda = rhs
//--------------------------------------------------------
//--------------------------------------------------------
class RegulatorShapeFunction : public RegulatorMethod {
public:
RegulatorShapeFunction(AtomicRegulator * atomicRegulator,
const std::string & regulatorPrefix = "");
virtual ~RegulatorShapeFunction();
/** instantiate all needed data */
virtual void construct_transfers();
/** pre-"run" initialization */
virtual void initialize();
/** sets lambda to an initial value */
virtual void set_lambda_to_value(double value) {*lambda_ = value;}
/** reset number of local atoms, as well as atomic data */
virtual void reset_nlocal();
/** set up atom to material identification */
virtual void reset_atom_materials(const Array<int> & elementToMaterialMap,
const MatrixDependencyManager<DenseMatrix, int> * atomElement);
/** compute boundary flux, requires regulator input since it is part of the coupling scheme */
virtual void compute_boundary_flux(FIELDS & fields);
/** access to nodes the thermostat is applied to */
const SetDependencyManager<int> * application_nodes() const {return applicationNodes_;};
/** determine if local shape function matrices are needed */
virtual bool use_local_shape_functions() const {return false;};
protected:
// methods
/** compute sparsity for matrix */
void compute_sparsity(void);
/** solve matrix equation */
void solve_for_lambda(const DENS_MAT & rhs,
DENS_MAT & lambda);
/** set weighting factor for in matrix Nhat^T * weights * Nhat */
virtual void set_weights() = 0;
/** Mapping between unique nodes and nodes overlapping MD region */
void map_unique_to_overlap(const MATRIX & uniqueData,
MATRIX & overlapData);
/** Mapping between nodes overlapping MD region to unique nodes */
void map_overlap_to_unique(const MATRIX & overlapData,
MATRIX & uniqueData);
/** sets up the transfer which is the set of nodes being regulated */
virtual void construct_regulated_nodes();
/** creates data structure needed for all to regulated node maps */
virtual void create_node_maps();
// member data
/** lambda coupling parameter */
DENS_MAN * lambda_;
/** lambda at atomic locations */
PerAtomQuantity<double> * atomLambdas_;
/** shape function matrix for use in GLC solve */
PerAtomSparseMatrix<double> * shapeFunctionMatrix_;
/** algorithm being used for the linear solver */
AtomicRegulator::LinearSolverType linearSolverType_;
/** pre-templated sparsity pattern for N^T * T * N */
SPAR_MAN matrixTemplate_;
/** maximum number of iterations used in solving for lambda */
int maxIterations_;
/** tolerance used in solving for lambda */
double tolerance_;
/** matrix solver object */
LambdaMatrixSolver * matrixSolver_;
/** set of nodes used to construct matrix */
SetDependencyManager<int> * regulatedNodes_;
/** set of nodes on which lambda is non-zero */
SetDependencyManager<int> * applicationNodes_;
/** set of nodes needed for localized boundary quadrature */
SetDependencyManager<int> * boundaryNodes_;
/** mapping from all nodes to overlap nodes: -1 is no overlap, otherwise entry is overlap index */
NodeToSubset * nodeToOverlapMap_;
/** mapping from overlap nodes to unique nodes */
SubsetToNode * overlapToNodeMap_;
/** shape function matrix for boundary atoms */
SPAR_MAN * shpFcn_;
/** atomic weights for boundary atoms */
DIAG_MAN * atomicWeights_;
/** element mask for boundary elements corresponding to nodeToOverlapMap_ */
MatrixDependencyManager<ATC_matrix::DenseMatrix, bool> * elementMask_;
/** maps atoms from atc indexing to regulator indexing */
LargeToSmallAtomMap * lambdaAtomMap_;
/** weight per-atom transfer */
PerAtomQuantity<double> * weights_;
/** number of spatial dimensions */
int nsd_;
/** number of ATC internal atoms on this processor */
int nLocal_;
private:
// DO NOT define this
RegulatorShapeFunction();
};
//--------------------------------------------------------
//--------------------------------------------------------
// Class LambdaMatrixSolver
//--------------------------------------------------------
//--------------------------------------------------------
class LambdaMatrixSolver {
public:
LambdaMatrixSolver(SPAR_MAN & matrixTemplate, SPAR_MAN * shapeFunctionMatrix, int maxIterations, double tolerance);
virtual ~LambdaMatrixSolver(){};
/** assemble the matrix */
virtual void assemble_matrix(DIAG_MAT & weights);
/** execute the solver */
virtual void execute(VECTOR & rhs, VECTOR & lambda)=0;
protected:
/** sparse template for the matrix */
SPAR_MAN & matrixTemplate_;
/** non-symmetric part of the matrix */
SPAR_MAN * shapeFunctionMatrix_;
/** matrix used to solve for lambda */
SPAR_MAT lambdaMatrix_;
/** maximum number of iterations */
int maxIterations_;
/** relative tolerance to solve to */
double tolerance_;
private:
// DO NOT define this
LambdaMatrixSolver();
};
//--------------------------------------------------------
//--------------------------------------------------------
// Class LambdaMatrixSolverLumped
//--------------------------------------------------------
//--------------------------------------------------------
class LambdaMatrixSolverLumped : public LambdaMatrixSolver {
public:
LambdaMatrixSolverLumped(SPAR_MAN & matrixTemplate, SPAR_MAN * shapeFunctionMatrix, int maxIterations, double tolerance, const SetDependencyManager<int> * applicationNodes, const NodeToSubset * nodeToOverlapMap);
virtual ~LambdaMatrixSolverLumped(){};
/** assemble the matrix */
virtual void assemble_matrix(DIAG_MAT & weights);
/** execute the solver */
virtual void execute(VECTOR & rhs, VECTOR & lambda);
protected:
/** lumped version of the matrix governing lamda */
DIAG_MAT lumpedMatrix_;
/** set of regulated nodes */
const SetDependencyManager<int> * applicationNodes_;
/** mapping from all nodes to overlap nodes: -1 is no overlap, otherwise entry is overlap index */
const NodeToSubset * nodeToOverlapMap_;
private:
// DO NOT define this
LambdaMatrixSolverLumped();
};
//--------------------------------------------------------
//--------------------------------------------------------
// Class LambdaMatrixSolverCg
//--------------------------------------------------------
//--------------------------------------------------------
class LambdaMatrixSolverCg : public LambdaMatrixSolver {
public:
LambdaMatrixSolverCg(SPAR_MAN & matrixTemplate, SPAR_MAN * shapeFunctionMatrix, int maxIterations, double tolerance);
virtual ~LambdaMatrixSolverCg(){};
/** execute the solver */
virtual void execute(VECTOR & rhs, VECTOR & lambda);
protected:
private:
// DO NOT define this
LambdaMatrixSolverCg();
};
};
#endif

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