Detailed Description

Relates to CASM project input/output.

Classes
struct	CASM::CompositionAxes

Functions
BasicStructure< Site >	CASM::read_prim (fs::path filename)

BasicStructure< Site >	CASM::read_prim (const jsonParser &json)
	Read prim.json. More...

void	CASM::write_prim (const BasicStructure< Site > &prim, fs::path filename, COORD_TYPE mode)
	Write prim.json to file. More...

void	CASM::write_prim (const BasicStructure< Site > &prim, jsonParser &json, COORD_TYPE mode)
	Write prim.json as JSON. More...

void	CASM::write_symop (const SymGroup &grp, Index i, jsonParser &j)

void	CASM::write_symgroup (const SymGroup &grp, jsonParser &json)

ChemicalReference	CASM::read_chemical_reference (fs::path filename, const Structure &prim, double tol)
	Read chemical reference states from JSON file. More...

ChemicalReference	CASM::read_chemical_reference (const jsonParser &json, const Structure &prim, double tol)
	Read chemical reference states from JSON. More...

void	CASM::write_chemical_reference (const ChemicalReference &chem_ref, fs::path filename)

void	CASM::write_chemical_reference (const ChemicalReference &chem_ref, jsonParser &json)

template<typename OutputIterator >
OutputIterator	CASM::read_composition_axes (OutputIterator result, const jsonParser &json)
	Read standard axes from JSON, and output to std::map<std::string, CompositionConverter> More...

void	CASM::write_basis (const SiteOrbitree &tree, const Structure &prim, jsonParser &json, double tol)
	Write summary of basis functions. More...

jsonParser &	CASM::to_json (const ChemicalReferenceState &ref_state, jsonParser &json)
	Write ChemicalReferenceState to: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'. More...

template<>
ChemicalReferenceState	CASM::from_json< ChemicalReferenceState > (const jsonParser &json)
	Read ChemicalReferenceState from: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'. More...

void	CASM::from_json (ChemicalReferenceState &ref_state, const jsonParser &json)
	Read ChemicalReferenceState from: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'. More...

jsonParser &	CASM::to_json (const HyperPlaneReference &ref, jsonParser &json)

void	CASM::from_json (HyperPlaneReference &ref, const jsonParser &json, HyperPlaneReference::InputFunction f)

jsonParser &	CASM::to_json (const ChemicalReference &ref, jsonParser &json)
	Write chemical reference. More...

std::pair< Eigen::VectorXd, std::vector < ChemicalReferenceState > >	CASM::one_chemical_reference_from_json (const Structure &prim, const jsonParser &json)
	Read chemical reference from one of 3 alternative forms. More...

void	CASM::from_json (ChemicalReference &ref, const jsonParser &json, const Structure &prim, double tol=1e-14)
	Read chemical reference from JSON. More...

Function Documentation

void CASM::from_json	(	ChemicalReferenceState &	ref_state,
		const jsonParser &	json
	)

Read ChemicalReferenceState from: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'.

Definition at line 44 of file clex.cc.

void CASM::from_json	(	HyperPlaneReference &	ref,
		const jsonParser &	json,
		HyperPlaneReference::InputFunction	f
	)

Definition at line 69 of file clex.cc.

void CASM::from_json	(	ChemicalReference &	ref,
		const jsonParser &	json,
		const Structure &	prim,
		double	tol = `1e-14`
	)

Read chemical reference from JSON.

Definition at line 297 of file clex.cc.

template<>

ChemicalReferenceState CASM::from_json< ChemicalReferenceState > ( const jsonParser & json )

Read ChemicalReferenceState from: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'.

std::pair< Eigen::VectorXd, std::vector< ChemicalReferenceState > > CASM::one_chemical_reference_from_json	(	const Structure &	prim,
		const jsonParser &	json
	)

Read chemical reference from one of 3 alternative forms.

This function returns a pair with only one element initialized. If alternative 1, then the vector is set. If alternative 2 or 3, then the Eigen::VectorXd is set.

Expected input form: 1)

[
  {"A": 3.4, "C": 2.0, "energy_per_species": 2.0},
  {"B": 2.0, "energy_per_species": 4.0},
  {"C": 1.0, "energy_per_species": 3.0}
]

2) Expects all species in prim, except vacancy:

{"A": X, "C": X, "D": X}

3) Expects one element for each species in prim, including 0.0 for vacancy:

[X, X, X, X]

Definition at line 180 of file clex.cc.

ChemicalReference CASM::read_chemical_reference	(	fs::path	filename,
		const Structure &	prim,
		double	tol
	)

Read chemical reference states from JSON file.

See documentation in related function for expected form of the JSON

re-throw exceptions

Definition at line 212 of file AppIO.cc.

ChemicalReference CASM::read_chemical_reference	(	const jsonParser &	json,
		const Structure &	prim,
		double	tol
	)

Read chemical reference states from JSON.

Example expected form:

{
  "chemical_reference" : {
    "global" : ...,
    "supercell": {
      "SCELX": ...,
      "SCELY": ...
    },
    "config": {
      "SCELX/I": ...,
      "SCELY/J": ...
    }
  }
}

See one_chemical_reference_from_json for documentation of the

{...}

expected form.

Definition at line 246 of file AppIO.cc.

template<typename OutputIterator >

OutputIterator CASM::read_composition_axes	(	OutputIterator	result,
		const jsonParser &	json
	)

Read standard axes from JSON, and output to std::map<std::string, CompositionConverter>

json Format: {"standard_axes": {"key0" : {CompositionConverter}, ... more axes ...}, "custom_axes": {"key0" : {CompositionConverter}, ... more axes ...}, "current_axes": "key"}
- "axes_type" is either "standard_axes" or "custom_axes"
- "key" is a string indicating which composition axes in the "standard_axes" or "custom_axes" JSON object
This read json["standard_axes"] or json["custom_axes"]

Definition at line 121 of file AppIO.hh.

BasicStructure< Site > CASM::read_prim ( fs::path filename )

re-throw exceptions

Definition at line 11 of file AppIO.cc.

BasicStructure< Site > CASM::read_prim ( const jsonParser & json )

Read prim.json.

re-throw exceptions

Definition at line 25 of file AppIO.cc.

jsonParser & CASM::to_json	(	const ChemicalReferenceState &	ref_state,
		jsonParser &	json
	)

Write ChemicalReferenceState to: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'.

Definition at line 12 of file clex.cc.

jsonParser & CASM::to_json	(	const HyperPlaneReference &	ref,
		jsonParser &	json
	)

Definition at line 51 of file clex.cc.

jsonParser & CASM::to_json	(	const ChemicalReference &	ref,
		jsonParser &	json
	)

Write chemical reference.

Write ChemicalReference.

Example form:

{
  "chemical_reference" : {
    "global" : ...,
    "supercell": {
      "SCELX": ...,
      "SCELY": ...
    },
    "config": {
      "SCELX/I": ...,
      "SCELY/J": ...
    }
  }
}

Each individual reference is a vector,

[X, X, X, X]

giving the hyperplane of the reference (each element is the reference value for pure Configurations of a given Molecule).

Definition at line 104 of file clex.cc.

void CASM::write_basis	(	const SiteOrbitree &	tree,
		const Structure &	prim,
		jsonParser &	json,
		double	tol
	)

Write summary of basis functions.

Format:

{
  "site_functions":[
    {
      "asym_unit": X,
      "sublat_indices: [2, 3],
      "phi_b_0": {"Va":0.0, "O":1.0},
      "phi_b_1": {"Va":0.0, "O":1.0},
       ...
    },
    ...
  ],
  "cluster_functions":[
    {
      "eci": X.XXXXX,
      "prototype_function": "\phi_b_i(s_j)...",
      "orbit": [branch_index, orbit_index],
      "linear_orbit_index": I,
      "mult": X,
      "prototype": [
        [b, i, j, k],
        ...
      ]
    },
    ...
  ]
}

Definition at line 474 of file AppIO.cc.

void CASM::write_chemical_reference	(	const ChemicalReference &	chem_ref,
		fs::path	filename
	)

Definition at line 258 of file AppIO.cc.

void CASM::write_chemical_reference	(	const ChemicalReference &	chem_ref,
		jsonParser &	json
	)

Definition at line 269 of file AppIO.cc.

void CASM::write_prim	(	const BasicStructure< Site > &	prim,
		fs::path	filename,
		COORD_TYPE	mode
	)

Write prim.json to file.

Definition at line 107 of file AppIO.cc.

void CASM::write_prim	(	const BasicStructure< Site > &	prim,
		jsonParser &	json,
		COORD_TYPE	mode
	)

Write prim.json as JSON.

Definition at line 120 of file AppIO.cc.

void CASM::write_symgroup	(	const SymGroup &	grp,
		jsonParser &	json
	)

Definition at line 183 of file AppIO.cc.

void CASM::write_symop	(	const SymGroup &	grp,
		Index	i,
		jsonParser &	j
	)

Definition at line 166 of file AppIO.cc.

Detailed Description

Classes

Functions

Function Documentation