calypso.formula module

class calypso.formula.Formula(formula)

Bases: UserDict, MSONable

Formula object

A dict with blocks and its amounts eg. {“Cl”:1, “Na”:1}

Examples

>>> formula = Formula({"Cl":1, "Na":1})
>>> formula.format()
NaCl
>>> formula = Formula([1, 2, 3, 4, 5])
>>> formula.format()
HHeLiBeB
>>> formula = Formula("H3O")
>>> formula
H3O
>>> formula.count
{'H': 3, 'O': 1}

__str__(): Return unstacked formula with no brasket.

count(): Return number of each atoms as dict.

format(mode='')

get_anonymous_formula(reduce=False)

get_reduced_formula()

property anonymous_formula

property count: dict[str, int]

property elements: list[str]: return each element symbol

property reduce: tuple[Formula, int]

class calypso.formula.FormulaFmt(*values)

Bases: StrEnum

_summary_

# TODO: finish the docstring

Parameters:: StrEnum (_type_) – _description_

ALPHABET = 'alphabet'

HILL = 'hill'

METAL = 'metal'

PERIODIC = 'periodic'

class calypso.formula.FormulaUnit(formulaunit: str | list[str])

Bases: object

FormulaUnit for reading from config

Examples

assume file a.xyz .. code-block:

2
comment
C 0 0 0
H 1 1 1

>>> formulaunit = FormulaUnit("B1-2{{file:a.xyz}}2-3")
>>> formulaunit.get_structure_template()
StructureTemplate(
    element_numbers=[5, 5, 6, 1],
    coords_template=[None, None, array([[0., 0., 0.],
                                        [1., 1., 1.]])]
)

static sample_range(formulaunit)

find each range and sample from it, return a dict with unit and value and a str.

`python > formula_str = sample_range("Mg2Al") > formula_str Mg2Al > sample_range("(Mg)23(Al)3") (Mg)23(Al)3 > sample_range("Mg3Al2") Mg3Al2 > sample_range("Mg3Al0-3") Mg3Al1 > sample_range("Mg3Al0-3") Mg3Al0 > sample_range("Mg3Al0-3") Mg3Al2 > sample_range("Mg3Al2-1") ValueError > sample_range("Mg0-0Al") ValueError > sample_range("(Mg)1(Al)0-1") (Mg)1(Al)0 > sample_range("A43B(2-5)") 'A43B(4)' > d = ["A43B(2-5)(C4(2-3)D45)1-2", "Ab43B(2-5)"] > sample_range(d) ['A43B(2)(C4(3)D45)1', 'Ab43B(2)'] `

Parameters:: formulaunit (list[str] | str) – “(B)2-3(N)3-4(N5)1-3”
Returns:: str like: (B)3(N)2(N5)3
Return type:: str

find_file_map() → dict[str, tuple[str, CalyData]]: Find the mapping from file label to pseudo element and structure

See also

_find_file_map()

get_pseudo_formula() → Formula | list[Formula]

Substitute the ambiguous marker into pseudo element

Returns:: pseudo_formula – Instance or list of instance of Formula with pseudo elements.
Return type:: Formula | list[Formula]