airsspy.seed

Classes for preparing AIRSS seed

Module Contents

Classes

SeedAtoms	Subclass of ase.atoms.Atoms object. Template for generating random cells
BoolTag	Descriptor for tag-like properties (boolean flags)
GenericTag	Descriptor for generic properties (any value type)
RangeTag	Descriptor for range properties (number or tuple of two numbers)
NestedRangeTag	Descriptor for nested range properties (tuple/list of two elements)
TagHolder	Container for the tags
BuildcellParam	A class for storing parameters for the Buldcell program
SeedAtomTag	Tags for a single atom
SeedAtom	Element atoms in a AIRSS seed

Functions

tuple2range	Return the string for a given value. If the value is a tuple make it a range.
get_cell_inp	Get the CellInput holder for a given seed
get_cell_inp_lines	Write the seed to a file handle

API

class airsspy.seed.SeedAtoms(*args: Any, **kwargs: Any)

Bases: ase.Atoms

Subclass of ase.atoms.Atoms object. Template for generating random cells

Initialization

Initialise an SeedAtoms for buildcell. Same arguments signature as ase.Atoms object

Special attribute: gentags : BuildcellParam instance for storing parameter of buildcell

You can set the global buildcell tags by setting attributes of the gentags instance.

Per-atom generation tags are saved in an array called ‘atom_gentags’. They can be retrieved using get_atom_tag or set with set_atom_tag. The atom_tags attribute also provide a convient way of accessing.

set_atom_tag(tag: airsspy.seed.SeedAtomTag, index: int) → None

Set buildcell tags for individual atom if the SeedAtomTag object has no tagname, set automatically

get_atom_tag(index: int) → Any

Return the buildcell tag for the atom of the index. Can be used for in-place change

property atom_tags: numpy.ndarray

Array of tags, each for one Atom

write_seed(fpath: str) → None

Write the seed to file

get_cell_inp() → castepinput.CellInput

Return the python object represent the cell

get_cell_inp_lines() → List[str]

Return a list of strings of the seed file

build_random_atoms(timeout: int = 10, also_buildcell: bool = False, fail_ok: bool = True) → Optional[Union[ase.atoms.Atoms, Tuple[ase.atoms.Atoms, Any]]]

Returns the randomize Atoms built using buildcell program

__getitem__(i: Union[int, Sequence[int], slice]) → Union[airsspy.seed.SeedAtom, airsspy.seed.SeedAtoms]

Return a subset of the atoms.

i – scalar integer, list of integers, or slice object describing which atoms to return.

If i is a scalar, return an Atom object. If i is a list or a slice, return an Atoms object with the same cell, pbc, and other associated info as the original Atoms object. The indices of the constraints will be shuffled so that they match the indexing in the subset returned.

class airsspy.seed.BoolTag(doc: str = '', storage_name: Optional[str] = None)

Descriptor for tag-like properties (boolean flags)

Initialization

__set_name__(owner: type, name: str) → None

property storage_name: str

Storage name for the property, guaranteed to be set after set_name

__get__(instance: Optional[airsspy.seed.TagHolder], owner: type) → Optional[bool]

__set__(instance: airsspy.seed.TagHolder, value: bool) → None

__delete__(instance: airsspy.seed.TagHolder) → None

class airsspy.seed.GenericTag(doc: str = '', storage_name: Optional[str] = None)

Descriptor for generic properties (any value type)

Initialization

__set_name__(owner: type, name: str) → None

property storage_name: str

Storage name for the property, guaranteed to be set after set_name

__get__(instance: Optional[airsspy.seed.TagHolder], owner: type) → Any

__set__(instance: airsspy.seed.TagHolder, value: Any) → None

__delete__(instance: airsspy.seed.TagHolder) → None

class airsspy.seed.RangeTag(doc: str = '', storage_name: Optional[str] = None)

Descriptor for range properties (number or tuple of two numbers)

Initialization

__set_name__(owner: type, name: str) → None

property storage_name: str

Storage name for the property, guaranteed to be set after set_name

__get__(instance: Optional[airsspy.seed.TagHolder], owner: type) → Any

__set__(instance: airsspy.seed.TagHolder, value: Union[numbers.Number, Tuple[numbers.Number, numbers.Number], List[numbers.Number], Dict[str, List[int]]]) → None

__delete__(instance: airsspy.seed.TagHolder) → None

class airsspy.seed.NestedRangeTag(doc: str = '', storage_name: Optional[str] = None)

Descriptor for nested range properties (tuple/list of two elements)

Initialization

__set_name__(owner: type, name: str) → None

property storage_name: str

Storage name for the property, guaranteed to be set after set_name

__get__(instance: Optional[airsspy.seed.TagHolder], owner: type) → Any

__set__(instance: airsspy.seed.TagHolder, value: Union[Tuple[Any, Any], List[Any]]) → None

__delete__(instance: airsspy.seed.TagHolder) → None

class airsspy.seed.TagHolder(*args: Any, **kwargs: Any)

Container for the tags

Initialization

A container for tags of a single SeedAtom

get_prop_dict() → Dict[str, Any]

clear_all() → None

Set all property to be None

get_prop(value: str) → Any

Get property

set_prop(name: str, value: Any) → None

Set property

set_tag(tag: str) → None

Set a tag-like property

get_tag(tag: str) → Optional[bool]

Set a tag-like property

delete_prop(name: str) → None

Deleta a property

delete(name: str) → None

Delete a property by name

abstractmethod to_string() → str

__repr__() → str

class airsspy.seed.BuildcellParam(*args: Any, **kwargs: Any)

Bases: airsspy.seed.TagHolder

A class for storing parameters for the Buldcell program

Initialization

A container for tags of a single SeedAtom

populate_defaults() → airsspy.seed.BuildcellParam

Apply the active cell-level defaults used by AIRSS gencell.

to_string() → str

Return the string that should go into the .cell file

fix

‘BoolTag(…)’

abfix

‘BoolTag(…)’

adjgen

‘GenericTag(…)’

autoslack

‘BoolTag(…)’

breakamp

‘GenericTag(…)’

celladapt

‘BoolTag(…)’

cellamp

‘GenericTag(…)’

cellcon

‘GenericTag(…)’

coord

‘RangeTag(…)’

cylinder

‘GenericTag(…)’

flip

‘BoolTag(…)’

maxbangle

‘GenericTag(…)’

maxtime

‘GenericTag(…)’

minbangle

‘GenericTag(…)’

focus

‘GenericTag(…)’

molecules

‘GenericTag(…)’

nocompact

‘GenericTag(…)’

nopush

‘GenericTag(…)’

octet

‘GenericTag(…)’

permfrac

‘GenericTag(…)’

permute

‘GenericTag(…)’

rad

‘GenericTag(…)’

rash

‘GenericTag(…)’

rash_angamp

‘GenericTag(…)’

rash_posamp

‘GenericTag(…)’

remove

‘GenericTag(…)’

slab

‘GenericTag(…)’

species

‘GenericTag(…)’

sphere

‘GenericTag(…)’

spin

‘GenericTag(…)’

supercell

‘GenericTag(…)’

surface

‘BoolTag(…)’

symm

‘GenericTag(…)’

symmno

‘GenericTag(…)’

symmorphic

‘BoolTag(…)’

system

‘GenericTag(…)’

targvol

‘RangeTag(…)’

three

‘GenericTag(…)’

tight

‘BoolTag(…)’

vacancies

‘GenericTag(…)’

vacuum

‘GenericTag(…)’

width

‘GenericTag(…)’

cfix

‘BoolTag(…)’

cluster

‘BoolTag(…)’

nform

‘RangeTag(…)’

minsep

‘NestedRangeTag(…)’

posamp

‘NestedRangeTag(…)’

symmops

‘RangeTag(…)’

minamp

‘RangeTag(…)’

zamp

‘RangeTag(…)’

xamp

‘RangeTag(…)’

yamp

‘RangeTag(…)’

angamp

‘RangeTag(…)’

sgrank

‘RangeTag(…)’

varvol

‘GenericTag(…)’

slack

‘RangeTag(…)’

overlap

‘RangeTag(…)’

compact

‘BoolTag(…)’

cons

‘GenericTag(…)’

natom

‘RangeTag(…)’

formula

‘GenericTag(…)’

seed

‘GenericTag(…)’

vol

‘RangeTag(…)’

nfails

‘GenericTag(…)’

hole

‘GenericTag(…)’

holepos

‘GenericTag(…)’

shift

‘GenericTag(…)’

class airsspy.seed.SeedAtomTag(*args: Any, **kwargs: Any)

Bases: airsspy.seed.TagHolder

Tags for a single atom

Initialization

A container for tags of a single SeedAtom

tagname

‘GenericTag(…)’

posamp

‘RangeTag(…)’

minamp

‘RangeTag(…)’

zamp

‘RangeTag(…)’

xamp

‘RangeTag(…)’

yamp

‘RangeTag(…)’

num

‘RangeTag(…)’

adatom

‘BoolTag(…)’

fix

‘BoolTag(…)’

nomove

‘BoolTag(…)’

rad

‘GenericTag(…)’

occ

‘GenericTag(…)’

perm

‘BoolTag(…)’

athole

‘BoolTag(…)’

coord

‘RangeTag(…)’

angamp

‘RangeTag(…)’

vol

‘GenericTag(…)’

mult

‘GenericTag(…)’

spin

‘GenericTag(…)’

to_string() → str

Return the per entry string for this atom to be appended after its line in POSITIONS_FRAC / POSITIONS_ABS block

class airsspy.seed.SeedAtom(*args: Any, **kwargs: Any)

Bases: ase.Atom, airsspy.seed.SeedAtomTag

Element atoms in a AIRSS seed

Initialization

A container for tags of a single SeedAtom

airsspy.seed.tuple2range(value: Union[numbers.Number, List[numbers.Number], Tuple[numbers.Number, ...]]) → str

Return the string for a given value. If the value is a tuple make it a range.

airsspy.seed.get_cell_inp(atoms: airsspy.seed.SeedAtoms) → castepinput.CellInput

Get the CellInput holder for a given seed

airsspy.seed.get_cell_inp_lines(atoms: airsspy.seed.SeedAtoms) → List[str]

Write the seed to a file handle