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lammps/lib/atc/FE_Engine.h
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FE_Engine.h
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/** fe_engine :
* computes and assembles mass matrix, rhs vectors
* initial conditions handled in atc_transfer
*/
/** field structure:
a field is a dense matrix of numPoints X number of DOF in the field
a gradient is a std::vector of fields of length numSpatialDimensions
a set of fields is a map of fieldName->field of length numFields
a set of gradients is a map of fieldName->gradient of length numFields
Note: shape functions follow similar conventions with a shape function being
a field of numPoints X numNodes
and a shape function gradient being a std::vector of shape functions
of length numSpatialDimensions, although this is modified in calls when
numPoints = 1
Note: the convention between shape function format and field format allows
for shape functions to matmat nodal fields, creating matrices of
numPoints X numElementsInField for evaluating data at atomic/quadarture points
*/
/** current internal limitations:
* 3 spatial dimensions
* 8 node bricks
* structured mesh
* no stiffness matrix
(i.e. no implicit integration or special treatment of linear problems)
* lumped mass
*/
/** terminology:
density rate = flux
= Grad.FLUX(f,D_x f)
+ SOURCE(f,D_x f) + PRESCRIBED_SOURCE(x,t)
+ EXTRINSIC_SOURCE(f,D_x f,f_e,D_x f_e)
*/
#ifndef FE_ENGINE_H
#define FE_ENGINE_H
// Other headers
#include <vector>
#include <map>
// ATC_Transfer headers
#include "Array.h"
#include "Array2D.h"
#include "FE_Mesh.h"
#include "PhysicsModel.h"
#include "OutputManager.h"
using namespace std;
namespace ATC {
// Forward declarations
class ATC_Transfer;
class FE_Element;
class XT_Function;
class FE_Engine{
public:
/** constructor/s */
FE_Engine(ATC_Transfer * atcTransfer);
/** destructor */
~FE_Engine();
/** initialize */
void initialize();
/** parser/modifier */
bool modify(int narg, char **arg);
/** finish up */
void finish();
//----------------------------------------------------------------
/** \name output */
//----------------------------------------------------------------
/*@{*/
/** these assume the caller is handling the parallel collection */
void initialize_output(int rank,
string outputPrefix, OutputType otype = ENSIGHT);
/** write geometry */
void write_geometry(void);
/** write data: data is arrayed over _unique_ nodes
& then mapped by the engine */
void write_data(double time, FIELDS &soln, OUTPUT_LIST *data=NULL);
void write_data(double time, OUTPUT_LIST *data);
void write_restart_file(string fileName, OUTPUT_LIST *data)
{outputManager_.write_restart_file(fileName,data);};
void read_restart_file(string fileName, OUTPUT_LIST *data)
{outputManager_.read_restart_file(fileName,data);};
void delete_elements(const set<int> & elementList);
void add_global(string name, double value)
{outputManager_.add_global(name,value);}
void reset_globals() {outputManager_.reset_globals();}
/** pass through to access output manager */
OutputManager* output_manager() {return &outputManager_;}
/*@}*/
//----------------------------------------------------------------
/** \name assembled matrices and vectors */
//----------------------------------------------------------------
/*@{*/
/** compute a dimensionless stiffness matrix */
void compute_stiffness_matrix(SPAR_MAT &matrix) const;
/** compute a dimensionless mass matrix */
void compute_mass_matrix(SPAR_MAT &mass_matrix) const;
/** computes a dimensionless mass matrix for the given-quadrature */
void compute_mass_matrix(const DIAG_MAT &weights,
const SPAR_MAT &N,
SPAR_MAT &mass_matrix) const;
/** compute a single dimensionless mass matrix */
void compute_lumped_mass_matrix(DIAG_MAT &lumped_mass_matrix) const;
/** compute lumped mass matrix = diag (\int \rho N_I dV) */
void compute_lumped_mass_matrix(const Array<FieldName> &mask,
const FIELDS &fields,
const PhysicsModel * physicsModel,
const Array<int> & elementMaterials,
map<FieldName, DIAG_MAT> &mass_matrix,
const Array<bool> *element_mask=NULL) const;
/** compute dimensional lumped mass matrix using given quadrature */
void compute_lumped_mass_matrix(const Array<FieldName> &mask,
const FIELDS &fields,
const PhysicsModel * physicsModel,
const Array<set<int> > & pointMaterialGroups,
const DIAG_MAT &weights,
const SPAR_MAT &N,
map<FieldName, DIAG_MAT> &mass_matrix) const;
/** compute an approximation to a finite difference gradient from mesh */
void compute_gradient_matrix(GRAD_SHPFCN &grad_matrix) const;
/** compute energy */
void compute_energy(const Array<FieldName> &mask,
const FIELDS &fields,
const PhysicsModel * physicsModel,
const Array<int> & elementMaterials,
FIELDS &energy,
const Array<bool> *element_mask=NULL) const;
/** compute residual or RHS of the dynamic weak eqn */
void compute_rhs_vector(const Array2D<bool> &rhs_mask,
const FIELDS &fields,
const PhysicsModel * physicsModel,
const Array<int> & elementMaterials,
FIELDS &rhs,
const Array<bool> *element_mask=NULL) const;
/** compute RHS for given quadrature */
void compute_rhs_vector(const Array2D<bool> &rhs_mask,
const FIELDS &fields,
const PhysicsModel * physicsModel,
const Array<set<int> > & pointMaterialGroups,
const DIAG_MAT &weights,
const SPAR_MAT &N,
const GRAD_SHPFCN &dN,
FIELDS &rhs) const;
/** compute flux in domain i.e. N^T B_integrand */
void compute_flux(const Array2D<bool> & rhs_mask,
const FIELDS &fields,
const PhysicsModel * physicsModel,
const Array<int> & elementMaterials,
GRAD_FIELDS &flux,
const Array<bool> *element_mask=NULL) const;
/** compute the flux on the MD/FE boundary */
void compute_boundary_flux(
const Array2D<bool> & rhs_mask,
const FIELDS & fields,
const PhysicsModel * physicsModel,
const Array<int> & elementMaterials,
const set<PAIR> & faceSet,
FIELDS & rhs) const;
/** compute the flux on using an L2 interpolation of the flux */
void compute_boundary_flux(
const Array2D<bool> & rhs_mask,
const FIELDS & fields,
const PhysicsModel * physicsModel,
const Array<int> & elementMaterials,
const Array<set<int> > & pointMaterialGroups,
const DIAG_MAT & weights,
const SPAR_MAT & N,
const GRAD_SHPFCN & dN,
const DIAG_MAT & flux_mask,
FIELDS & rhs ) const;
/** compute prescribed flux given an array of functions of x & t */
void add_fluxes(const Array<bool> &fieldMask,
const double time,
const SURFACE_SOURCE & sourceFunctions,
FIELDS &nodalSources) const;
/** compute nodal vector of volume based sources */
void add_sources(const Array<bool> &fieldMask,
const double time,
const VOLUME_SOURCE &sourceFunctions,
FIELDS &nodalSources) const;
/** compute surface flux of a nodal field */
void field_surface_flux(const DENS_MAT & field,
const set<PAIR> &faceSet,
DENS_MAT & values,
const bool contour = false,
const int axis = 2) const;
/*@}*/
//----------------------------------------------------------------
/** \name shape functions */
//----------------------------------------------------------------
/*@{*/
/** evaluate shape function at a list of points in R^3 */
void evaluate_shape_functions(const MATRIX &coords,
SPAR_MAT &N,
Array<int> & pointToEltMap) const;
/** evaluate shape function & derivatives at a list of points in R^3 */
void evaluate_shape_functions( const MATRIX &coords,
SPAR_MAT &N,
GRAD_SHPFCN &dN,
Array<int> & pointToEltMap) const;
/** evaluate all shape function & derivatives at a specific R^3 location */
void evaluate_shape_functions(const VECTOR & x,
Array<int>& node_index,
DENS_VEC& shp,
DENS_MAT& dshp,
int & eltID) const;
/** pass through */
void shape_functions(const VECTOR &x,
DENS_VEC& shp,
int & eltID,
Array<int>& node_list) const
{ feMesh_->shape_functions(x,shp,eltID,node_list); }
void shape_functions(const VECTOR &x,
DENS_VEC& shp,
int & eltID,
Array<int>& node_list,
const Array<bool>& periodicity) const
{ feMesh_->shape_functions(x,shp,eltID,node_list, periodicity); }
/*@}*/
//----------------------------------------------------------------
/** \name accessors */
//----------------------------------------------------------------
/*@{*/
/** even though these are pass-throughs there is a necessary translation */
/** return number of unique nodes */
int get_nNodes() const { return feMesh_->get_nNodesUnique(); };
/** return number of total nodes */
int get_nNodesTotal() const { return feMesh_->get_nNodes(); };
/** return number of elements */
int get_nElements() const { return feMesh_->get_nElements(); };
/** return element connectivity */
void element_connectivity(const int eltID, Array<int> & nodes) const
{ feMesh_->element_connectivity_unique(eltID, nodes); }
/** return face connectivity */
void face_connectivity(const PAIR &faceID, Array<int> &nodes) const
{ feMesh_->face_connectivity_unique(faceID, nodes); }
/** in lieu of pass-throughs const accessors ... */
// return const ptr to mesh
const FE_Mesh* get_feMesh() const { return feMesh_;}
// return number of spatial dimensions
int get_nsd() const { return feMesh_->get_nSpatialDimensions(); }
// return if the FE mesh has been created
int fe_mesh_exist() const { return feMesh_!=NULL; }
// get nodal coordinates for a given element
void element_coordinates(const int eltIdx, DENS_MAT &coords)
{ feMesh_->element_coordinates(eltIdx,coords); }
// access list of elements to be deleted
set<int> & null_elements(void) { return nullElements_; }
/*@}*/
private:
//----------------------------------------------------------------
/** mesh setup commands (called from modify) */
//----------------------------------------------------------------
/*@{*/
/** initialized flag */
bool initialized_;
/** create a uniform, structured mesh */
void create_mesh(int nx, int ny, int nz, char * regionName,
int xperiodic, int yperiodic, int zperiodic);
/*@}*/
/** ATC transfer object */
ATC_Transfer * atcTransfer_;
/** finite element mesh */
FE_Mesh * feMesh_;
/** data that can be used for a subset of original mesh */
set<int> nullElements_;
bool amendedMeshData_;
const Array2D<int> * connectivity_;
const Array<int> * nodeMap_;
const DENS_MAT * coordinates_;
/** workspace */
int nNodesPerElement_;
int nIPsPerElement_;
int nIPsPerFace_;
int nSD_;
int nElems_;
/** output object */
OutputManager outputManager_;
/** base name for output files */
string outputPrefix_;
/** output frequency (NOTE will move to "Transfer") */
int outputFrequency_;
/** list of output timesteps */
vector<double> outputTimes_;
};
}; // end namespace ATC
#endif
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