abics.applications.latgas_abinitio_interface.model_setup module

class abics.applications.latgas_abinitio_interface.model_setup.ObserverParams[source]

Bases: object

classmethod from_dict(d)[source]
Parameters

d (dict) – Dictionary

Returns

oparams – self

Return type

ObserverParams

classmethod from_toml(f)[source]
Parameters

f (str) – Name of input toml File

Returns

oparams – self

Return type

ObserverParams

abics.applications.latgas_abinitio_interface.model_setup.base_structure(lat, dict_str)[source]
Parameters

  • lat (pymatgen.Lattice) –

  • dict_str (dict) – Dictionary of base structure

Returns

st

Return type

pymatgen.Structure

class abics.applications.latgas_abinitio_interface.model_setup.config(base_structure, defect_sublattices, num_defects, cellsize=[1, 1, 1], perfect_structure=None)[source]

Bases: object

This class defines the config with lattice gas mapping

Parameters

  • base_structure (pymatgen.Structure) – Structure of base sites (unsampled sites)

  • defect_sublattices (defect_sublattice) – Structure of defects (sampled sites)

  • num_defects (dict) – {group name: number of defects}

  • cellsize (list, optional) – Cell size, by default [1, 1, 1]

  • perfect_structure (pymatgen.Structure, optional) – Strucure of all sites (union of base and defect), by default None

__init__(base_structure, defect_sublattices, num_defects, cellsize=[1, 1, 1], perfect_structure=None)[source]
Parameters

  • base_structure (pymatgen.Structure) – Structure of base sites (unsampled sites)

  • defect_sublattices (defect_sublattice) – Structure of defects (sampled sites)

  • num_defects (dict) – {group name: number of defects}

  • cellsize (list, optional) – Cell size, by default [1, 1, 1]

  • perfect_structure (pymatgen.Structure, optional) – Strucure of all sites (union of base and defect), by default None

count(group_name, orientation)[source]
Parameters

  • group_name (str) – The name of the group

  • orientation –

defect_sublattice_structure(sublat_id)[source]
Parameters

sublat_id (int) – index of sublattice

Returns

sublattice_structure – sublattice structure object

Return type

pymatgen.Structure

set_latgas(defect_sublattices=False)[source]
Parameters

defect_sublattices (pymatgen.Structure) –

shuffle()[source]
update_basestruct()[source]
property vacancy_structure
class abics.applications.latgas_abinitio_interface.model_setup.defect_sublattice(site_centers, groups)[source]

Bases: object

Parameters

  • site_centers (list) – Center coordinates at each groups

  • groups (list) – List of groups

__init__(site_centers, groups)[source]
Parameters

  • site_centers (list) – Center coordinates at each groups

  • groups (list) – List of groups

classmethod from_dict(d)[source]
Parameters

d (dict) –

Returns

  • site_centers (list) – Center coordinates at each groups

  • groups (list) – List of groups

class abics.applications.latgas_abinitio_interface.model_setup.dft_latgas(abinitio_run, save_history=True, l_update_basestruct=False, check_ion_move=False, ion_move_tol=0.7)[source]

Bases: abics.mc.model

This class defines the DFT lattice gas mapping model

Parameters

  • abinitio_run (runner object) – Runner (manager) of external solver program

  • save_history (boolean) –

  • l_update_basestruct (boolean) –

  • check_ion_move (boolean) –

  • ion_move_tol (float) –

__init__(abinitio_run, save_history=True, l_update_basestruct=False, check_ion_move=False, ion_move_tol=0.7)[source]
Parameters

  • abinitio_run (runner object) – Runner (manager) of external solver program

  • save_history (boolean) –

  • l_update_basestruct (boolean) –

  • check_ion_move (boolean) –

  • ion_move_tol (float) –

energy(config)[source]

Calculate total energy

Parameters

config (config object) – Configurations

Returns

energy

Return type

float

model_name = 'dft_latgas'
newconfig(config, dconfig)[source]

Update config by the trial step, dconfig

Parameters

  • config (config object) – Configuration

  • dconfig (config object) – Difference of configuration

Returns

config – New configuration

Return type

config object

trialstep(config, energy_now)[source]
Parameters

  • config (config object) – Configurations

  • energy_now (float) – Present energy

Returns

  • dconfig (float) – Difference of configurations

  • dE (float) – Difference of energies

class abics.applications.latgas_abinitio_interface.model_setup.energy_lst(calcode, vasp_run, base_vaspinput, matcher_base, queen, reps, energy_lst, matcher=None)[source]

Bases: abics.applications.latgas_abinitio_interface.model_setup.dft_latgas

Parameters

  • calcode –

  • vasp_run (runner object) – Runner (manager) of external solver program

  • base_vaspinput –

  • matcher_base –

  • queen –

  • reps –

  • energy_lst (list) – Energy list

  • matcher –

__init__(calcode, vasp_run, base_vaspinput, matcher_base, queen, reps, energy_lst, matcher=None)[source]
Parameters

  • calcode –

  • vasp_run (runner object) – Runner (manager) of external solver program

  • base_vaspinput –

  • matcher_base –

  • queen –

  • reps –

  • energy_lst (list) – Energy list

  • matcher –

energy(config, save_history=False)[source]
Parameters

  • config (config object) – Configuration

  • save_history (boolean) –

Returns

energy

Return type

float

abics.applications.latgas_abinitio_interface.model_setup.gauss(x, x0, sigma)[source]

Gaussian function

Parameters

  • x (float) – The position

  • x0 (float) – The position of the center of the peak

  • sigma (float) – The standard deviation

Returns

value

Return type

float

class abics.applications.latgas_abinitio_interface.model_setup.group(name, species, *, coords=None, relaxations=None, magnetizations=None)[source]

Bases: object

Parameters

  • name (str) – The name of atomic group

  • species (str) – The atomic species belonging to the atom group

  • coords (numpy array) – The coordinates of each atom in the atom group.

  • relaxations (numpy array) – Whether to perform structure optimization or not

  • magnetization (numpy array) – Magnetizations (inbalance of up/down spins)

__init__(name, species, *, coords=None, relaxations=None, magnetizations=None)[source]
Parameters

  • name (str) – The name of atomic group

  • species (str) – The atomic species belonging to the atom group

  • coords (numpy array) – The coordinates of each atom in the atom group.

  • relaxations (numpy array) – Whether to perform structure optimization or not

  • magnetization (numpy array) – Magnetizations (inbalance of up/down spins)

abics.applications.latgas_abinitio_interface.model_setup.match_id(lst, obj)[source]

Return the index list of lst which matches obj.

Parameters

  • lst (list) –

  • obj (object) –

Returns

Return type

The index list of lst which matches obj.

abics.applications.latgas_abinitio_interface.model_setup.match_latgas_group(latgas_rep, group)[source]

Return the index list of latgas_rep which matches group.name.

Parameters

  • latgas_rep (list) –

  • group (object) – Notes: the group must have name

Returns

Return type

The index list of latgas_rep which matches group.name.

abics.applications.latgas_abinitio_interface.model_setup.nomatch_id(lst, obj)[source]

Return the index list of lst which does not match obj.

Parameters

  • lst (list) –

  • obj (object) –

Returns

Return type

The index list of lst which does not match obj.

abics.applications.latgas_abinitio_interface.model_setup.perturb_structure(st: pymatgen.core.structure.Structure, distance: float) → None[source]

Perform random perturbation of the atomic coordinates. All atoms will be moved at the same distance.

Which components will be perturbed is specified by a boolean array stored as st.site_properties[“seldyn”]. If not stored, all the components will be perturbed. Argument st will be mutated.

Parameters

  • st (Structure) –

  • distance (float) – strength of perturb