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lammps/lib/atc/ATC_TypeDefs.h
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ATC_TypeDefs.h
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#ifndef ATC_TYPEDEFS_H
#define ATC_TYPEDEFS_H
#include <set>
#include <vector>
#include <map>
#include <utility>
#include <string>
#ifdef NEW_LAMMPS
#include "lmptype.h"
#endif
#include "Array.h"
#include "Array2D.h"
#include "MatrixLibrary.h"
#include "DependencyManager.h"
namespace ATC
{
/** physical constants */
static const double kBeV_ = 8.617343e-5;// [eV/K]
/** unsigned ints, when needed */
typedef int INDEX;
/** elementset integral */
enum ElementsetOperationType {
ELEMENTSET_TOTAL=0,
ELEMENTSET_AVERAGE
};
/** faceset integral */
enum FacesetIntegralType {
BOUNDARY_INTEGRAL=0,
CONTOUR_INTEGRAL
};
/** nodeset operation */
enum NodesetOperationType {
NODESET_SUM=0,
NODESET_AVERAGE
};
/** boundary integration */
enum BoundaryIntegrationType {
NO_QUADRATURE=0,
FE_QUADRATURE,
FE_INTERPOLATION
};
/** domain integration */
enum IntegrationDomainType {
FULL_DOMAIN=0,
ATOM_DOMAIN,
FE_DOMAIN,
FULL_DOMAIN_ATOMIC_QUADRATURE_SOURCE,
FULL_DOMAIN_FREE_ONLY
};
/** domain decomposition */
enum DomainDecompositionType {
REPLICATED_MEMORY=0,
DISTRIBUTED_MEMORY
};
/** atomic weight specification */
enum AtomicWeightType {
USER=0,
LATTICE,
ELEMENT,
REGION,
GROUP,
MULTISCALE,
NODE,
NODE_ELEMENT,
READ_IN
};
/** geometry location with respect to MD domain */
enum GeometryType {
FE_ONLY = 0,
MD_ONLY,
BOUNDARY
};
/** enumerated type for atomic reference frame */
enum AtomToElementMapType {
LAGRANGIAN=0,
EULERIAN
};
/* enumerated type for coupling matrix structure */
enum MatrixStructure {
FULL=0, // contributions from all nodes
LOCALIZED, // contributions only from nodes with sources
LUMPED // row-sum lumped version of full matrix
};
/* enumerated type for distinguishing ghost from internal atoms */
enum AtomType {
INTERNAL=0,
GHOST,
ALL,
PROC_GHOST,
NO_ATOMS,
NUM_ATOM_TYPES
};
/** field types */
enum FieldName {
TIME=-2,
POSITION=-1,
TEMPERATURE=0, // Intrinsic Fields
DISPLACEMENT,
VELOCITY,
MASS_DENSITY,
CHARGE_DENSITY,
SPECIES_CONCENTRATION,
ELECTRON_DENSITY, // Extrinsic Fields
ELECTRON_VELOCITY,
ELECTRON_TEMPERATURE,
ELECTRIC_POTENTIAL,
ELECTRON_WAVEFUNCTION,
ELECTRON_WAVEFUNCTIONS,
ELECTRON_WAVEFUNCTION_ENERGIES,
FERMI_ENERGY,
MOMENTUM,
PROJECTED_VELOCITY,
KINETIC_TEMPERATURE,
THERMAL_ENERGY,
KINETIC_ENERGY,
STRESS,
KINETIC_STRESS,
HEAT_FLUX,
CHARGE_FLUX,
SPECIES_FLUX,
INTERNAL_ENERGY,
REFERENCE_POTENTIAL_ENERGY,
POTENTIAL_ENERGY,
ENERGY,
NUMBER_DENSITY,
ESHELBY_STRESS,
CAUCHY_BORN_STRESS,
CAUCHY_BORN_ENERGY,
CAUCHY_BORN_ESHELBY_STRESS,
TRANSFORMED_STRESS,
VACANCY_CONCENTRATION,
ROTATION,
STRETCH,
DIPOLE_MOMENT,
QUADRUPOLE_MOMENT,
CAUCHY_BORN_ELASTIC_DEFORMATION_GRADIENT,
DISLOCATION_DENSITY,
NUM_TOTAL_FIELDS
};
const int NUM_FIELDS = ELECTRON_WAVEFUNCTION+1;
#define NDIM 3
static const int FieldSizes[NUM_TOTAL_FIELDS] = {
1, // TEMPERATURE
NDIM, // DISPLACEMENT
NDIM, // VELOCITY
1, // MASS_DENSITY
1, // CHARGE_DENSITY
0, // SPECIES_CONCENTRATION - VARIABLE
1, // ELECTRON_DENSITY
NDIM, // ELECTRON_VELOCITY
1, // ELECTRON_TEMPERATURE
1, // ELECTRIC_POTENTIAL
1, // ELECTRON_WAVEFUNCTION ?
0, // ELECTRON_WAVEFUNCTIONS - VARIABLE
0, // ELECTRON_WAVEFUNCTION_ENERGIES - VARIABLE
1, // FERMI_ENERGY
NDIM, // MOMENTUM
NDIM, // PROJECTED_VELOCITY
1, // KINETIC_TEMPERATURE
1, // THERMAL_ENERGY
1, // KINETIC_ENERGY
NDIM*NDIM, // STRESS
NDIM*NDIM, // KINETIC_STRESS
NDIM, // HEAT_FLUX
NDIM, // CHARGE_FLUX
0, // SPECIES_FLUX - VARIABLE
1, // INTERNAL_ENERGY
1, // REFERENCE_POTENTIAL_ENERGY
1, // POTENTIAL_ENERGY
1, // ENERGY
1, // NUMBER_DENSITY
NDIM*NDIM, // ESHELBY_STRESS
NDIM*NDIM, // CAUCHY_BORN_STRESS,
1, // CAUCHY_BORN_ENERGY,
NDIM*NDIM, // CAUCHY_BORN_ESHELBY_STRESS,
NDIM*NDIM, // TRANSFORMED_STRESS,
1, // VACANCY_CONCENTRATION,
NDIM*NDIM, // ROTATION,
NDIM*NDIM, // STRETCH,
NDIM, // DIPOLE_MOMENT,
NDIM, // QUADRUPOLE_MOMENT,
NDIM*NDIM, // CAUCHY_BORN_ELASTIC_DEFORMATION_GRADIENT,
NDIM*NDIM // DISLOCATION_DENSITY
};
enum NodalAtomicFieldNormalization {
NO_NORMALIZATION=0,
VOLUME_NORMALIZATION, NUMBER_NORMALIZATION, MASS_NORMALIZATION,
MASS_MATRIX
};
inline FieldName use_mass_matrix(FieldName in) {
if (in == TEMPERATURE) return in;
else return MASS_DENSITY;
}
/** enums for FE Element and Interpolate classes */
enum FeEltGeometry {HEXA, TETRA};
enum FeIntQuadrature {NODAL, GAUSS1, GAUSS2, GAUSS3, FACE};
/** field name enum to string */
inline FeIntQuadrature string_to_FIQ(const std::string &str)
{
if (str == "nodal")
return NODAL;
else if (str == "gauss1")
return GAUSS1;
else if (str == "gauss2")
return GAUSS2;
else if (str == "gauss3")
return GAUSS3;
else if (str == "face")
return FACE;
else
throw ATC_Error("Bad quadrature input" + str + ".");
}
/** field name enum to string */
inline std::string field_to_string(const FieldName index)
{
switch (index) {
case TEMPERATURE:
return "temperature";
case DISPLACEMENT:
return "displacement";
case VELOCITY:
return "velocity";
case MASS_DENSITY:
return "mass_density";
case CHARGE_DENSITY:
return "charge_density";
case ELECTRON_DENSITY:
return "electron_density";
case ELECTRON_VELOCITY:
return "electron_velocity";
case ELECTRON_TEMPERATURE:
return "electron_temperature";
case ELECTRIC_POTENTIAL:
return "electric_potential";
case ELECTRON_WAVEFUNCTION:
return "electron_wavefunction";
case ELECTRON_WAVEFUNCTIONS:
return "electron_wavefunctions";
case ELECTRON_WAVEFUNCTION_ENERGIES:
return "electron_wavefunction_energies";
case FERMI_ENERGY:
return "fermi_energy";
case MOMENTUM:
return "momentum";
case PROJECTED_VELOCITY:
return "projected_velocity";
case KINETIC_TEMPERATURE:
return "kinetic_temperature";
case THERMAL_ENERGY:
return "thermal_energy";
case KINETIC_ENERGY:
return "kinetic_energy";
case STRESS:
return "stress";
case KINETIC_STRESS:
return "kinetic_stress";
case ESHELBY_STRESS:
return "eshelby_stress";
case CAUCHY_BORN_STRESS:
return "cauchy_born_stress";
case CAUCHY_BORN_ENERGY:
return "cauchy_born_energy";
case CAUCHY_BORN_ESHELBY_STRESS:
return "cauchy_born_eshelby_stress";
case HEAT_FLUX:
return "heat_flux";
case CHARGE_FLUX:
return "charge_flux";
case SPECIES_FLUX:
return "species_flux";
case INTERNAL_ENERGY:
return "internal_energy";
case POTENTIAL_ENERGY:
return "potential_energy";
case REFERENCE_POTENTIAL_ENERGY:
return "reference_potential_energy";
case ENERGY:
return "energy";
case NUMBER_DENSITY:
return "number_density";
case TRANSFORMED_STRESS:
return "transformed_stress";
case VACANCY_CONCENTRATION:
return "vacancy_concentration";
case SPECIES_CONCENTRATION:
return "species_concentration";
case ROTATION:
return "rotation";
case STRETCH:
return "stretch";
case DIPOLE_MOMENT:
return "dipole_moment";
case QUADRUPOLE_MOMENT:
return "quadrupole_moment";
default:
throw ATC_Error("field not found in field_to_string");
}
}
/** string to field enum */
inline FieldName string_to_field(const std::string & name)
{
if (name=="temperature")
return TEMPERATURE;
else if (name=="displacement")
return DISPLACEMENT;
else if (name=="velocity")
return VELOCITY;
else if (name=="mass_density")
return MASS_DENSITY;
else if (name=="charge_density")
return CHARGE_DENSITY;
else if (name=="electron_density")
return ELECTRON_DENSITY;
else if (name=="electron_velocity")
return ELECTRON_VELOCITY;
else if (name=="electron_temperature")
return ELECTRON_TEMPERATURE;
else if (name=="electric_potential")
return ELECTRIC_POTENTIAL;
else if (name=="electron_wavefunction")
return ELECTRON_WAVEFUNCTION;
else if (name=="electron_wavefunctions")
return ELECTRON_WAVEFUNCTIONS;
else if (name=="electron_wavefunction_energies")
return ELECTRON_WAVEFUNCTION_ENERGIES;
else if (name=="fermi_energy")
return FERMI_ENERGY;
else if (name=="momentum")
return MOMENTUM;
else if (name=="projected_velocity")
return PROJECTED_VELOCITY;
else if (name=="kinetic_temperature")
return KINETIC_TEMPERATURE; // temperature from total KE
else if (name=="thermal_energy")
return THERMAL_ENERGY;
else if (name=="kinetic_energy")
return KINETIC_ENERGY;
else if (name=="stress")
return STRESS;
else if (name=="kinetic_stress")
return KINETIC_STRESS;
else if (name=="eshelby_stress")
return ESHELBY_STRESS;
else if (name=="cauchy_born_stress")
return CAUCHY_BORN_STRESS;
else if (name=="cauchy_born_energy")
return CAUCHY_BORN_ENERGY;
else if (name=="cauchy_born_eshelby_stress")
return CAUCHY_BORN_ESHELBY_STRESS;
else if (name=="heat_flux")
return HEAT_FLUX;
else if (name=="charge_flux")
return CHARGE_FLUX;
else if (name=="species_flux")
return SPECIES_FLUX;
else if (name=="internal_energy")
return INTERNAL_ENERGY;
else if (name=="reference_potential_energy")
return REFERENCE_POTENTIAL_ENERGY;
else if (name=="potential_energy")
return POTENTIAL_ENERGY;
else if (name=="energy")
return ENERGY;
else if (name=="number_density")
return NUMBER_DENSITY;
else if (name=="transformed_stress")
return TRANSFORMED_STRESS;
else if (name=="vacancy_concentration")
return VACANCY_CONCENTRATION;
else if (name=="species_concentration")
return SPECIES_CONCENTRATION;
else if (name=="rotation")
return ROTATION;
else if (name=="stretch")
return STRETCH;
else if (name=="dipole_moment")
return DIPOLE_MOMENT;
else if (name=="quadrupole_moment")
return QUADRUPOLE_MOMENT;
else
throw ATC_Error(name + " is not a valid field");
}
inline bool is_intrinsic(const FieldName & field_enum)
{
if (field_enum==TEMPERATURE
|| field_enum==DISPLACEMENT
|| field_enum==VELOCITY
|| field_enum==MASS_DENSITY
|| field_enum==CHARGE_DENSITY
|| field_enum==SPECIES_CONCENTRATION
|| field_enum==KINETIC_TEMPERATURE
|| field_enum==POTENTIAL_ENERGY
|| field_enum==REFERENCE_POTENTIAL_ENERGY
) return true;
else return false;
}
inline std::string field_to_intrinsic_name(const FieldName index)
{
if (is_intrinsic(index)) {
return "NodalAtomic"+ATC_Utility::to_cap(field_to_string(index));
}
else {
throw ATC_Error("field "+field_to_string(index)+" is not an intrinsic field");
}
}
inline std::string field_to_restriction_name(const FieldName index)
{
if (is_intrinsic(index)) {
return "Restricted"+ATC_Utility::to_cap(field_to_string(index));
}
else {
throw ATC_Error("field "+field_to_string(index)+" is not an intrinsic field");
}
}
inline std::string field_to_prolongation_name(const FieldName index)
{
return "Prolonged"+ATC_Utility::to_cap(field_to_string(index));
}
/** types of temperature definitions */
enum TemperatureDefType {
NONE = 0,
KINETIC,
TOTAL
};
/** string to temperature definition enum */
inline bool string_to_temperature_def(const std::string & name, TemperatureDefType & index) {
if (name=="none")
index = NONE;
else if (name=="kinetic")
index = KINETIC;
else if (name=="total")
index = TOTAL;
else {
throw ATC_Error("temperature operator type "+name+" not valid");
return false;
}
return true;
}
/** solver types */
enum SolverType { DIRECT=0, ITERATIVE};
enum DirichletType {DIRICHLET_PENALTY=0, DIRICHLET_CONDENSE};
/** physics types */
enum PhysicsType
{
NO_PHYSICS=0, // for post-processing only
THERMAL,
ELASTIC,
SHEAR,
THERMO_ELASTIC,
SPECIES // aka Mass
};
/** rhs types */
enum FluxType
{
FLUX = 0, // has a source weighted by gradient of shape function
SOURCE, // has a source term weighted by the shape function
PRESCRIBED_SOURCE, // has a prescribed source term
ROBIN_SOURCE, // has a Robin source term
OPEN_SOURCE, // has a open boundary source term
EXTRINSIC_SOURCE, // has an extrinsic source term
NUM_FLUX
};
/** stiffness/ derivative of rhs types */
enum StiffnessType
{
BB_STIFFNESS = 0,
NN_STIFFNESS,
BN_STIFFNESS,
NB_STIFFNESS,
NUM_STIFFNESS
};
/** LAMMPS atom type identifiers */
enum IdType {
ATOM_TYPE=0,
ATOM_GROUP
};
/** molecule size identifiers */
enum MolSize {
MOL_SMALL=0,
MOL_LARGE
};
/** basic */
typedef std::pair<int, int> PAIR;
/** typedefs for compact set of bc values */
typedef std::set < std::pair < int, double> > BC_SET; // node, value
typedef std::vector< BC_SET > BCS; // dof (node, value)
typedef std::set<int> NSET; // nodeset
typedef std::set<PAIR> FSET; // faceset
typedef std::set<int> ESET; // elementset
/** typedefs for N and B integrand functions */
typedef std::set<FieldName> ARG_NAMES;
typedef std::map<FieldName, ATC_matrix::DenseMatrix<double> > ARGS;
typedef ATC::MatrixDependencyManager<ATC_matrix::DenseMatrix, double> FIELD;
typedef std::vector<ATC::MatrixDependencyManager<ATC_matrix::DenseMatrix, double> > GRAD_FIELD;
typedef std::map<FieldName, ATC::MatrixDependencyManager<ATC_matrix::DenseMatrix, double> > FIELDS;
typedef std::map<FieldName, ATC::MatrixDependencyManager<ATC_matrix::DenseMatrix, double> * > FIELD_POINTERS;
typedef std::map<FieldName, ATC_matrix::DenseMatrix<double> > FIELD_MATS;
typedef std::map<std::string, ATC::MatrixDependencyManager<ATC_matrix::DenseMatrix, double> > TAG_FIELDS;
typedef std::map<FieldName, std::vector<ATC::MatrixDependencyManager<ATC_matrix::DenseMatrix, double> > > GRAD_FIELDS;
typedef std::map<FieldName, std::vector<ATC_matrix::DenseMatrix<double> > > GRAD_FIELD_MATS;
typedef std::map<FieldName, ATC::MatrixDependencyManager<DiagonalMatrix, double> > MASS_MATS;
typedef std::map<FieldName, ATC::MatrixDependencyManager<SparseMatrix, double> > CON_MASS_MATS;
typedef ATC::MatrixDependencyManager<ATC_matrix::DenseMatrix, double> DENS_MAN;
typedef ATC::MatrixDependencyManager<SparseMatrix, double> SPAR_MAN;
typedef ATC::MatrixDependencyManager<ParSparseMatrix, double> PAR_SPAR_MAN;
typedef ATC::MatrixDependencyManager<DiagonalMatrix, double> DIAG_MAN;
typedef ATC::MatrixDependencyManager<ParDiagonalMatrix, double> PAR_DIAG_MAN;
/** typedefs for WeakEquation evaluation */
typedef Array2D<bool> RHS_MASK;
/** typedefs for input/output */
typedef std::map<std::string, const ATC_matrix::Matrix<double>*> OUTPUT_LIST;
typedef std::map<std::string, ATC_matrix::Matrix<double>*> RESTART_LIST;
typedef std::pair<int, int> ID_PAIR;
typedef std::vector< std::pair<int, int> > ID_LIST;
/** misc typedefs */
class XT_Function;
class UXT_Function;
typedef std::map<FieldName, std::map<PAIR, Array<XT_Function*> > > SURFACE_SOURCE;
typedef std::map<FieldName, std::map<PAIR, Array<UXT_Function*> > > ROBIN_SURFACE_SOURCE;
typedef std::map<FieldName, std::set<PAIR> > OPEN_SURFACE;
typedef std::map<FieldName, Array2D<XT_Function *> > VOLUME_SOURCE;
typedef std::map<std::string, ATC::MatrixDependencyManager<ATC_matrix::DenseMatrix, double> > ATOMIC_DATA;
/** typedefs for FE_Mesh */
typedef std::map<std::string, std::set<int > > NODE_SET_MAP;
typedef std::map<std::string, std::set<int > > ELEMENT_SET_MAP;
typedef std::map<std::string, std::set<PAIR> > FACE_SET_MAP;
/** string to index */
// inline vs. static is used to avoid compiler warnings that the function isn't used
// the compiler seems to just check if static functions are used in the file they're
// declared in rather than all the files that include the header,
// same for arrays (but not primitives, e.g. ints) hopefully this also speeds up the code
inline bool string_to_index(const std::string & dim, int & index, int & sgn)
{
char dir;
if (dim.empty()) return false;
sgn = (dim[0] == '-') ? -1 : 1;
dir = dim[dim.size()-1]; // dir is last character
if (dir == 'x') index = 0;
else if (dir == 'y') index = 1;
else if (dir == 'z') index = 2;
else return false;
return true;
}
/** string to index */
inline std::string index_to_string(const int &index)
{
if (index==0) return "x";
else if (index==1) return "y";
else if (index==2) return "z";
return "unknown";
}
/** string to index */
inline bool string_to_index(const std::string &dim, int &index)
{
if (dim=="x")
index = 0;
else if (dim=="y")
index = 1;
else if (dim=="z")
index = 2;
else
return false;
return true;
}
inline std::string print_mask(const Array2D<bool> & rhsMask)
{
std::string msg;
for (int i = 0; i < NUM_FIELDS; i++) {
FieldName field = (FieldName) i;
std::string name = field_to_string(field);
if (rhsMask(field,FLUX)
|| rhsMask(field,SOURCE)
|| rhsMask(field,PRESCRIBED_SOURCE)
|| rhsMask(field,ROBIN_SOURCE)
|| rhsMask(field,OPEN_SOURCE)
|| rhsMask(field,EXTRINSIC_SOURCE)) {
msg = "RHS_MASK: " + name;
if (rhsMask(field,FLUX)) msg += " flux";
if (rhsMask(field,SOURCE)) msg += " source";
if (rhsMask(field,PRESCRIBED_SOURCE)) msg += " prescribed_src";
if (rhsMask(field,ROBIN_SOURCE)) msg += " robin_src";
if (rhsMask(field,OPEN_SOURCE)) msg += " open_src";
if (rhsMask(field,EXTRINSIC_SOURCE)) msg += " extrinsic_src";
}
}
return msg;
}
}
#endif
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