CASM
AClustersApproachtoStatisticalMechanics
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Relates to Molecule.
Classes | |
singleton | CASM::OccupantDoF< T > |
class | CASM::Specie |
class | CASM::AtomPosition |
class | CASM::Molecule |
Typedefs | |
typedef OccupantDoF< Molecule > | CASM::MoleculeOccupant |
typedef std::array< bool, 3 > | CASM::AtomPosition::sd_type |
Functions | |
bool | CASM::is_vacancy (const std::string &name) |
A vacancy is any Specie/Molecule with (name == "VA" || name == "va" || name == "Va") More... | |
CASM::Specie::Specie () | |
CASM::Specie::Specie (std::string init_name) | |
bool | CASM::Specie::is_vacancy () const |
bool | CASM::Specie::operator== (const Specie &RHS) const |
jsonParser & | CASM::to_json (const Specie &specie, jsonParser &json) |
void | CASM::from_json (Specie &specie, const jsonParser &json) |
CASM::AtomPosition::AtomPosition (const Lattice &init_lattice) | |
CASM::AtomPosition::AtomPosition (double elem1, double elem2, double elem3, std::string sp_name, const Lattice &init_lattice, COORD_TYPE mode, sd_type _SD_flag=sd_type{{false, false, false}}) | |
bool | CASM::AtomPosition::operator== (const AtomPosition &RHS) const |
void | CASM::AtomPosition::print (std::ostream &stream, const Coordinate &trans, int spaces, bool SD_is_on=false) const |
AtomPosition & | CASM::AtomPosition::apply_sym (const SymOp &op) |
AtomPosition & | CASM::AtomPosition::apply_sym_no_trans (const SymOp &op) |
jsonParser & | CASM::to_json (const AtomPosition &apos, jsonParser &json) |
void | CASM::from_json (AtomPosition &apos, const jsonParser &json) |
CASM::Molecule::Molecule (const Lattice &init_home) | |
Lattice const * | CASM::Molecule::home () const |
void | CASM::Molecule::get_center () |
void | CASM::Molecule::generate_point_group () |
bool | CASM::Molecule::is_vacancy () const |
Molecule & | CASM::Molecule::apply_sym (const SymOp &op) |
Molecule & | CASM::Molecule::apply_sym_no_trans (const SymOp &op) |
void | CASM::Molecule::set_lattice (const Lattice &new_lat, COORD_TYPE invariant_mode) |
Molecule | CASM::Molecule::get_union (const Molecule &RHS) |
Molecule & | CASM::Molecule::operator*= (const SymOp &RHS) |
Molecule & | CASM::Molecule::operator+= (const Coordinate &RHS) |
bool | CASM::Molecule::operator== (const Molecule &RHS) const |
bool | CASM::Molecule::contains (const std::string &name) const |
void | CASM::Molecule::read (std::istream &stream) |
void | CASM::Molecule::print (std::ostream &stream, const Coordinate &trans, int spaces, char delim, bool SD_is_on=false) const |
jsonParser & | CASM::Molecule::to_json (jsonParser &json) const |
void | CASM::Molecule::from_json (const jsonParser &json) |
Molecule | CASM::operator* (const SymOp &LHS, const Molecule &RHS) |
Molecule | CASM::operator+ (const Coordinate &LHS, const Molecule &RHS) |
Molecule | CASM::operator+ (const Molecule &LHS, const Coordinate &RHS) |
Molecule | CASM::make_atom (std::string atom_name, const Lattice &lat) |
Return an atomic Molecule with specified name and Lattice. More... | |
Molecule | CASM::make_vacancy (const Lattice &lat) |
Return an vacancy Molecule with specified Lattice. More... | |
bool | CASM::is_molecule_name (const Molecule &mol, std::string name) |
Return true if Molecule name matches 'name', including Va checks. More... | |
jsonParser & | CASM::to_json (const Molecule &mol, jsonParser &json) |
void | CASM::from_json (Molecule &mol, const jsonParser &json) |
Variables | |
std::string | CASM::Specie::name |
double | CASM::Specie::mass |
double | CASM::Specie::magmom |
double | CASM::Specie::U |
double | CASM::Specie::J |
Specie | CASM::AtomPosition::specie |
sd_type | CASM::AtomPosition::SD_flag |
Lattice const * | CASM::Molecule::m_home |
Array< SymOp > | CASM::Molecule::point_group |
Coordinate | CASM::Molecule::center |
std::string | CASM::Molecule::name |
typedef OccupantDoF<Molecule> CASM::MoleculeOccupant |
Definition at line 22 of file Molecule.hh.
typedef std::array<bool, 3> CASM::AtomPosition::sd_type |
Definition at line 58 of file Molecule.hh.
AtomPosition & CASM::AtomPosition::apply_sym | ( | const SymOp & | op | ) |
Definition at line 79 of file Molecule.cc.
Molecule & CASM::Molecule::apply_sym | ( | const SymOp & | op | ) |
Applies symmetry operation to a Molecule
SymOp | &op |
Definition at line 128 of file Molecule.cc.
AtomPosition & CASM::AtomPosition::apply_sym_no_trans | ( | const SymOp & | op | ) |
Definition at line 90 of file Molecule.cc.
Molecule & CASM::Molecule::apply_sym_no_trans | ( | const SymOp & | op | ) |
Applies symmetry operation to a Molecule without adding translation
SymOp | &op |
Definition at line 148 of file Molecule.cc.
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inlineexplicit |
Definition at line 63 of file Molecule.hh.
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inline |
Definition at line 64 of file Molecule.hh.
bool CASM::Molecule::contains | ( | const std::string & | name | ) | const |
Definition at line 207 of file Molecule.cc.
void CASM::from_json | ( | Specie & | specie, |
const jsonParser & | json | ||
) |
void CASM::from_json | ( | AtomPosition & | apos, |
const jsonParser & | json | ||
) |
void CASM::Molecule::from_json | ( | const jsonParser & | json | ) |
Read Molecule from json. Assumes current lattice.
re-throw exceptions
Definition at line 252 of file Molecule.cc.
void CASM::from_json | ( | Molecule & | mol, |
const jsonParser & | json | ||
) |
void CASM::Molecule::generate_point_group | ( | ) |
void CASM::Molecule::get_center | ( | ) |
Molecule CASM::Molecule::get_union | ( | const Molecule & | RHS | ) |
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inline |
Definition at line 116 of file Molecule.hh.
bool CASM::is_molecule_name | ( | const Molecule & | mol, |
std::string | name | ||
) |
Return true if Molecule name matches 'name', including Va checks.
Return true if Molecule name matches 'name', including Va name checks.
Equivalent to:
Definition at line 298 of file Molecule.cc.
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inline |
A vacancy is any Specie/Molecule with (name == "VA" || name == "va" || name == "Va")
Definition at line 27 of file Molecule.hh.
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inline |
Definition at line 38 of file Molecule.hh.
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inline |
Definition at line 124 of file Molecule.hh.
Molecule CASM::make_atom | ( | std::string | atom_name, |
const Lattice & | lat | ||
) |
Return an atomic Molecule with specified name and Lattice.
Definition at line 279 of file Molecule.cc.
Molecule CASM::make_vacancy | ( | const Lattice & | lat | ) |
Return an vacancy Molecule with specified Lattice.
Definition at line 287 of file Molecule.cc.
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inlineexplicit |
Definition at line 114 of file Molecule.hh.
Molecule CASM::operator* | ( | const SymOp & | LHS, |
const Molecule & | RHS | ||
) |
Molecule& CASM::Molecule::operator*= | ( | const SymOp & | RHS | ) |
Molecule CASM::operator+ | ( | const Coordinate & | LHS, |
const Molecule & | RHS | ||
) |
Molecule CASM::operator+ | ( | const Molecule & | LHS, |
const Coordinate & | RHS | ||
) |
Molecule& CASM::Molecule::operator+= | ( | const Coordinate & | RHS | ) |
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inline |
Definition at line 43 of file Molecule.hh.
bool CASM::AtomPosition::operator== | ( | const AtomPosition & | RHS | ) | const |
Definition at line 42 of file Molecule.cc.
bool CASM::Molecule::operator== | ( | const Molecule & | RHS | ) | const |
Definition at line 183 of file Molecule.cc.
void CASM::AtomPosition::print | ( | std::ostream & | stream, |
const Coordinate & | trans, | ||
int | spaces, | ||
bool | SD_is_on = false |
||
) | const |
Definition at line 54 of file Molecule.cc.
void CASM::Molecule::print | ( | std::ostream & | stream, |
const Coordinate & | trans, | ||
int | spaces, | ||
char | delim, | ||
bool | SD_is_on = false |
||
) | const |
Definition at line 220 of file Molecule.cc.
void CASM::Molecule::read | ( | std::istream & | stream | ) |
void CASM::Molecule::set_lattice | ( | const Lattice & | new_lat, |
COORD_TYPE | invariant_mode | ||
) |
Definition at line 168 of file Molecule.cc.
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inline |
Definition at line 35 of file Molecule.hh.
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inlineexplicit |
Definition at line 36 of file Molecule.hh.
jsonParser & CASM::to_json | ( | const Specie & | specie, |
jsonParser & | json | ||
) |
Definition at line 10 of file Molecule.cc.
jsonParser & CASM::to_json | ( | const AtomPosition & | apos, |
jsonParser & | json | ||
) |
Definition at line 96 of file Molecule.cc.
jsonParser & CASM::Molecule::to_json | ( | jsonParser & | json | ) | const |
Write Molecule to json. Does not write lattice.
Definition at line 234 of file Molecule.cc.
jsonParser & CASM::to_json | ( | const Molecule & | mol, |
jsonParser & | json | ||
) |
Definition at line 302 of file Molecule.cc.
Coordinate CASM::Molecule::center |
Definition at line 111 of file Molecule.hh.
double CASM::Specie::J |
Definition at line 34 of file Molecule.hh.
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private |
Definition at line 102 of file Molecule.hh.
double CASM::Specie::magmom |
Definition at line 34 of file Molecule.hh.
double CASM::Specie::mass |
Definition at line 34 of file Molecule.hh.
std::string CASM::Specie::name |
Definition at line 33 of file Molecule.hh.
std::string CASM::Molecule::name |
Definition at line 112 of file Molecule.hh.
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private |
Definition at line 104 of file Molecule.hh.
sd_type CASM::AtomPosition::SD_flag |
Definition at line 61 of file Molecule.hh.
Specie CASM::AtomPosition::specie |
Definition at line 59 of file Molecule.hh.
double CASM::Specie::U |
Definition at line 34 of file Molecule.hh.