matador.crystal package¶

This module contains functionality for wrapping matador data dictionaries as Crystal objects, which possess several convenience methods.

class matador.crystal.Crystal(doc, voronoi=False, network_kwargs=None, mutable=False)[source]¶

Bases: DataContainer

Class that wraps the MongoDB document, providing useful interfaces for cell manipulation and validation.

elems¶

list of present elements in the crystal, sorted in alphabetical order.

Type: list of str

cell¶

the unit cell constructed from lattice vectors.

Type: UnitCell

Initialise Crystal object from matador document with Site list and any additional abstractions, e.g. voronoi or CrystalGraph.

Parameters

doc (dict) – document containing structural information, minimal requirement is for atom_types, one of lattice_abc or lattice_cart, and one of positions_frac or positions_abs to be present.

Keyword Arguments

voronoi (bool) – whether to compute Voronoi substructure for each site
network_kwargs (dict) – keywords to pass to the CrystalGraph initialiser

update(data)[source]¶: Update the underlying self._data dictionary with the passed data.

print_sites()[source]¶

set_positions(new_positions, fractional=True)[source]¶

property atom_types: List[str]¶: Return list of atom types.

property num_atoms: int¶: Return number of atoms in structure.

property num_elements: int¶: Return number of species in the structure.

property positions_frac: List[List[float]]¶: Return list of fractional positions.

property positions_abs: List[List[float]]¶: Return list of absolute Cartesian positions.

property site_occupancies: List[float]¶: Return a list of site occupancies.

property stoichiometry: List[List[Union[str, float]]]¶: Return stoichiometry in matador format: a list of two-member lists containing element symbol and number of atoms per formula unit, sorted in alphabetical order by element symbol).

property num_fu: int¶

property concentration: List[float]¶: Return concentration of each species in stoichiometry.

get_concentration(elements=None, include_end=True) → List[float][source]¶: Return concentration of each species in stoichiometry, and use this value for future calls to crystal.concentration.

property formula: str¶: Returns chemical formula of structure.

property formula_tex: str¶: Returns chemical formula of structure in LaTeX format.

property formula_unicode: str¶: Returns a unicode string for the chemical formula.

property cell_volume: float¶: Returns cell volume in Å³.

property lattice_cart: Tuple[Tuple[float, float, float], Tuple[float, float, float], Tuple[float, float, float]]¶: The Cartesian lattice vectors as a tuple.

property lattice_abc: Tuple[Tuple[float, float, float], Tuple[float, float, float]]¶: Lattice parameters as a tuple.

property bond_lengths: List[Tuple[Tuple[str, str], float]]¶: Returns a list of ((species_A, species_B), bond_length)), sorted by bond length, computed from the network structure of the crystal (i.e. first coordination sphere).

property voronoi_substructure¶: Returns, or calculates if not present, the Voronoi substructure of crystal.

property space_group: str¶: Return the space group symbol at the last-used symprec.

property space_group_tex: str¶

Returns the space group symbol at the last-used symprec, formatted for LaTeX.

The HM symbol is surrounded by $ and with ‘-’ replaced with overbars for rotoinversion axes, e.g., Fm-3m -> $Fmbar{3}m$.

get_space_group(symprec=0.01) → str[source]¶

Return the space group of the structure at the desired symprec. Stores the space group in a dictionary self._space_group under symprec keys. Updates self._data['space_group'] and self._data['symprec'] with the last value calculated.

Keyword Arguments: symprec (float) – spglib symmetry tolerance.

property pdf¶: Returns a PDF object (pair distribution function) for the structure, calculated with default PDF settings.

calculate_pdf(**kwargs)[source]¶: Calculate and set the PDF with the passed parameters.

property pxrd¶: Returns a PXRD object (powder xray diffraction) containing the XRD pattern for the structure.

calculate_pxrd(**kwargs)[source]¶: Compute and set PXRD with the passed parameters.

property coordination_stats¶: Returns stastistics on the coordination of each site, as computed from Voronoi decomposition.

property ase_atoms¶: Returns an ASE Atoms representation of the crystal.

property pmg_structure¶: Returns the pymatgen structure representation of the crystal.

classmethod from_ase(atoms)[source]¶

classmethod from_pmg(pmg)[source]¶

property coordination_lists¶: Returns a dictionary containing pairs of elements and the list of coordination numbers per site.

property unique_sites¶: Return unique sites using Voronoi decomposition.

property network¶: Returns/constructs a CrystalGraph object of the structure.

property network_stats¶: Return network-calculated coordnation stats.

property bonding_stats¶

Return network-calculated bonding stats.

Returns

sorted dictionary with root atom as keys and bond: information as values.

Return type

dict

draw_network(layout=None)[source]¶: Draw the CrystalGraph network.

supercell(extension=None, target=None)[source]¶: Returns a supercell of this crystal with the specified extension.

standardized(primitive=False)[source]¶: Returns a standardized cell for this crystal, optionally the primitive cell.

Submodules¶

matador.crystal.crystal module¶

This submodule implements the Crystal class, a wrapper to the raw dictionary stored in MongoDB that allows for validation, manipulation and analysis of the lattice.

class matador.crystal.crystal.UnitCell(lattice)[source]¶

Bases: object

This class describes a 3D periodic unit cell by its Cartesian lattice vectors or lattice parameters, in Å.

Initialise the cell from either Cartesian lattice vectors [[x1, y1, z1], [x2, y2, z2], [x3, y3, z3]], or lattice parameters [[a, b, c], [alpha, beta, gamma]].

Parameters: lattice (list or numpy.ndarray) – either Cartesian lattice vectors or lattice parameters, stored as lists or a numpy arrays.

property lattice_cart: Tuple[Tuple[float, float, float], Tuple[float, float, float], Tuple[float, float, float]]¶: The Cartesian lattice vectors as a tuple.

property lattice_abc: Tuple[Tuple[float, float, float], Tuple[float, float, float]]¶: Lattice parameters as a tuple.

property lengths: Tuple[float, float, float]¶: Lattice vector lengths.

property recip_lattice_cart: List[List[float]]¶

property angles: Tuple[float, float, float]¶: Lattice vector angles.

property volume: float¶: The cell volume in Å³.

class matador.crystal.crystal.Crystal(doc, voronoi=False, network_kwargs=None, mutable=False)[source]¶

Bases: DataContainer

Class that wraps the MongoDB document, providing useful interfaces for cell manipulation and validation.

elems¶

list of present elements in the crystal, sorted in alphabetical order.

Type: list of str

cell¶

the unit cell constructed from lattice vectors.

Type: UnitCell

Initialise Crystal object from matador document with Site list and any additional abstractions, e.g. voronoi or CrystalGraph.

Parameters

doc (dict) – document containing structural information, minimal requirement is for atom_types, one of lattice_abc or lattice_cart, and one of positions_frac or positions_abs to be present.

Keyword Arguments

voronoi (bool) – whether to compute Voronoi substructure for each site
network_kwargs (dict) – keywords to pass to the CrystalGraph initialiser

update(data)[source]¶: Update the underlying self._data dictionary with the passed data.

print_sites()[source]¶

set_positions(new_positions, fractional=True)[source]¶

property atom_types: List[str]¶: Return list of atom types.

property num_atoms: int¶: Return number of atoms in structure.

property num_elements: int¶: Return number of species in the structure.

property positions_frac: List[List[float]]¶: Return list of fractional positions.

property positions_abs: List[List[float]]¶: Return list of absolute Cartesian positions.

property site_occupancies: List[float]¶: Return a list of site occupancies.

property stoichiometry: List[List[Union[str, float]]]¶: Return stoichiometry in matador format: a list of two-member lists containing element symbol and number of atoms per formula unit, sorted in alphabetical order by element symbol).

property num_fu: int¶

property concentration: List[float]¶: Return concentration of each species in stoichiometry.

get_concentration(elements=None, include_end=True) → List[float][source]¶: Return concentration of each species in stoichiometry, and use this value for future calls to crystal.concentration.

property formula: str¶: Returns chemical formula of structure.

property formula_tex: str¶: Returns chemical formula of structure in LaTeX format.

property formula_unicode: str¶: Returns a unicode string for the chemical formula.

property cell_volume: float¶: Returns cell volume in Å³.

property lattice_cart: Tuple[Tuple[float, float, float], Tuple[float, float, float], Tuple[float, float, float]]¶: The Cartesian lattice vectors as a tuple.

property lattice_abc: Tuple[Tuple[float, float, float], Tuple[float, float, float]]¶: Lattice parameters as a tuple.

property bond_lengths: List[Tuple[Tuple[str, str], float]]¶: Returns a list of ((species_A, species_B), bond_length)), sorted by bond length, computed from the network structure of the crystal (i.e. first coordination sphere).

property voronoi_substructure¶: Returns, or calculates if not present, the Voronoi substructure of crystal.

property space_group: str¶: Return the space group symbol at the last-used symprec.

property space_group_tex: str¶

Returns the space group symbol at the last-used symprec, formatted for LaTeX.

The HM symbol is surrounded by $ and with ‘-’ replaced with overbars for rotoinversion axes, e.g., Fm-3m -> $Fmbar{3}m$.

get_space_group(symprec=0.01) → str[source]¶

Return the space group of the structure at the desired symprec. Stores the space group in a dictionary self._space_group under symprec keys. Updates self._data['space_group'] and self._data['symprec'] with the last value calculated.

Keyword Arguments: symprec (float) – spglib symmetry tolerance.

property pdf¶: Returns a PDF object (pair distribution function) for the structure, calculated with default PDF settings.

calculate_pdf(**kwargs)[source]¶: Calculate and set the PDF with the passed parameters.

property pxrd¶: Returns a PXRD object (powder xray diffraction) containing the XRD pattern for the structure.

calculate_pxrd(**kwargs)[source]¶: Compute and set PXRD with the passed parameters.

property coordination_stats¶: Returns stastistics on the coordination of each site, as computed from Voronoi decomposition.

property ase_atoms¶: Returns an ASE Atoms representation of the crystal.

property pmg_structure¶: Returns the pymatgen structure representation of the crystal.

classmethod from_ase(atoms)[source]¶

classmethod from_pmg(pmg)[source]¶

property coordination_lists¶: Returns a dictionary containing pairs of elements and the list of coordination numbers per site.

property unique_sites¶: Return unique sites using Voronoi decomposition.

property network¶: Returns/constructs a CrystalGraph object of the structure.

property network_stats¶: Return network-calculated coordnation stats.

property bonding_stats¶

Return network-calculated bonding stats.

Returns

sorted dictionary with root atom as keys and bond: information as values.

Return type

dict

draw_network(layout=None)[source]¶: Draw the CrystalGraph network.

supercell(extension=None, target=None)[source]¶: Returns a supercell of this crystal with the specified extension.

standardized(primitive=False)[source]¶: Returns a standardized cell for this crystal, optionally the primitive cell.

matador.crystal.crystal_site module¶

This submodule implements the Site class for handling atomic sites.

class matador.crystal.crystal_site.Site(species: str, position: list, lattice, position_unit='fractional', mutable: bool = False, **site_data)[source]¶

Bases: DataContainer

The Site class contains a description of an individual site within a 3D periodic Crystal.

Initialise a Site object from its species, position and a reference to the lattice it exists in. Any other keys will be made available as site-level values.

get(key, default=None)[source]¶

Overload dictionary.get() method.

Parameters: key (str) – key to try and obtain.
Keyword Arguments: default – return value raise if key is not present.
Returns: _data[key] if it exists, else None.

set_position(position, units)[source]¶

property coords¶

property coords_cartesian¶

property species¶

property lattice¶

property occupancy¶

property coordination¶

displacement_between_sites(other_site)[source]¶

distance_between_sites(other_site)[source]¶

matador.crystal.elastic module¶

This submodule contains functionality to fit E(V) equations of state to ab initio data, primarily to calculate bulk moduli.

matador.crystal.elastic.get_equation_of_state(seed, plot=False)[source]¶

Extract E(V) data from CASTEP files and perform fits for the equation of state and bulk moduli.

Parameters: seed (str/dict) – filename or scraped dictionary to fit.
Keyword Arguments: plot (bool) – plot the fitted EoS.

class matador.crystal.elastic.EquationOfState(E_0, V_0)[source]¶

Bases: object

Abstract class for E(V) isothermal equations of state. Used to perform least squares fitting to arbitrary functional form.

E_0¶

equilbirium lattice energy.

Type: float

V_0¶

equilibrium lattice volume.

Type: float

popt¶

fitting parameters for particular EOS.

Type: list of float

p0¶

initial guess at fitting parameters.

Type: list of float

rrmsd¶

relative root mean square deviation of fit, as defined by [2].

Type: float

Set up EOS ready for fit.

Parameters

E_0 (float) – equilibrium energy.
V_0 (float) – equilibrium volume.

fit(volumes, energies)[source]¶

Perform a least squares fit on the volumes and energies.

Parameters

volumes (list of float) – calculated volumes.
energies (list of float) – calculated energies.

evaluate(V, B, C)[source]¶

Evaluate the EOS.

Parameters

V (list of float) – volumes at which to test.
B (float) – the first fitting parameter defined in [2].
C (float) – the second fitting parameter defined in [2].

residual(guess, V, E)[source]¶

Calculate the resdiual of the current fit.

Parameters

guess (list of float) – interim fitting parameters.
V (list of float) – volumes at which to test.
E (list of float) – energies at the volumes V.

property bulk_modulus¶: Returns the bulk modulus predicted by the fit.

property bulk_modulus_err¶: Returns the estimated error on the bulk modulus.

property fit_parameters¶: Return list of final fitting parameters.

class matador.crystal.elastic.BirchMurnaghanEulerianEOS(E_0, V_0)[source]¶

Bases: EquationOfState

Implements the 3rd order Birch-Murnaghan EOS [1] for given data, as provided by Ref. [2] in the Eulerian frame.

[1]. Francis Birch, Phys. Rev. 71 809 (1947): DOI: 10.1103/PhysRev.71.809.
[2]. K. Latimer, S. Dwaraknath, K. Mathew, D. Winston, K. A. Persson,: npj Comput. Mater. 2018 41 2018, 4, 40. DOI: 10.1038/s41524-018-0091-x.

Set up EOS ready for fit.

Parameters

E_0 (float) – equilibrium energy.
V_0 (float) – equilibrium volume.

evaluate(V, B, C)[source]¶

Evaluate the EOS.

Parameters

V (list of float) – volumes at which to test.
B (float) – the first fitting parameter defined in [2].
C (float) – the second fitting parameter defined in [2].

get_bulk_modulus()[source]¶: Return the bulk modulus of this particular fit.

class matador.crystal.elastic.PoirerTarantolaEOS(E_0, V_0)[source]¶

Bases: EquationOfState

Implements the logarithmic Poirer-Tarantola [3] for given data, as provided by Ref. [2].

[2]. K. Latimer, S. Dwaraknath, K. Mathew, D. Winston, K. A. Persson,: npj Comput. Mater. 2018 41 2018, 4, 40. DOI: 10.1038/s41524-018-0091-x.

[3]. J. Poirer, A. Tarantola, Phys. Earth Planet. Inter. 109 1-8 (1998).

Set up EOS ready for fit.

Parameters

E_0 (float) – equilibrium energy.
V_0 (float) – equilibrium volume.

evaluate(V, B, C)[source]¶

Evaluate the EOS.

Parameters

V (list of float) – volumes at which to test.
B (float) – the first fitting parameter defined in [2].
C (float) – the second fitting parameter defined in [2].

get_bulk_modulus()[source]¶: Return the bulk modulus of this particular fit.

class matador.crystal.elastic.TaitEOS(E_0, V_0)[source]¶

Bases: EquationOfState

Implements the exponential Tait EOS [4] for given data, as provided by Ref. [2].

[2]. K. Latimer, S. Dwaraknath, K. Mathew, D. Winston, K. A. Persson,: npj Comput. Mater. 2018 41 2018, 4, 40. DOI: 10.1038/s41524-018-0091-x.

[4]. J. H. Dymond, R. Malhotra, Int. J. Thermophys. 9 941-951 (1988).

Set up EOS ready for fit.

Parameters

E_0 (float) – equilibrium energy.
V_0 (float) – equilibrium volume.

evaluate(V, B, C)[source]¶

Evaluate the EOS.

Parameters

V (list of float) – volumes at which to test.
B (float) – the first fitting parameter defined in [2].
C (float) – the second fitting parameter defined in [2].

get_bulk_modulus()[source]¶: Return the bulk modulus of this particular fit.

matador.crystal.elastic.plot_volume_curve(probes_all, labels, curves, volumes, energies, seed)[source]¶: Plot all fitted EOS curves for this structure and save as a PDF.

matador.crystal.network module¶

This file implements turning matador Crystal objects into CrystalGraph objects.

class matador.crystal.network.CrystalGraph(structure=None, graph=None, coordination_cutoff=1.1, bond_tolerance=1e+20, num_images=1, debug=False, separate_images=False, delete_one_way_bonds=False, max_bond_length=5)[source]¶

Bases: MultiDiGraph

Create networkx.MultiDiGraph object with extra functionality for atomic networks.

Keyword Arguments

structure (matador.Crystal) – crystal structure to network-ify
graph (nx.MultiDiGraph) – initialise from graph
coordination_cutoff (float) – max multiplier of first coordination sphere for edge drawing
num_images (int) – number of periodic images to include in each direction
separate_images (bool) – whether or not to include image atoms as new nodes

get_strongly_connected_component_subgraphs(delete_one_way_bonds=True)[source]¶: Return generator of strongly-connected subgraphs in CrystalGraph format.

get_communities(graph=None, **louvain_kwargs)[source]¶: Return list of community subgraphs in CrystalGraph format.

remove_directionality(graph=None)[source]¶

set_unique_subgraphs(method='community')[source]¶: Filter strongly connected component subgraphs for isomorphism with others inside CrystalGraph. Sets self.unique_subgraph to a set of such subgraphs.

get_bonds_per_atom()[source]¶

matador.crystal.network.node_match(n1, n2)[source]¶

matador.crystal.network.get_unique_subgraphs(subgraphs)[source]¶

Filter strongly connected component subgraphs for isomorphism with others.

Input:

subgraphs: list(CrystalGraph), list of subgraph objects to filter

Returns

set(CrystalGraph), set of unique subgraphs

Return type

unique_subgraphs

matador.crystal.network.are_graphs_the_same(g1, g2, edge_match=None)[source]¶

matador.crystal.network.draw_network(structure, layout=None, edge_labels=False, node_index=False, curved_edges=True, node_colour='elem', partition=None, ax=None)[source]¶