`aim2dat.utils.chem_formula`¶

Module to parse representations of chemical formulas into each other.

Module Contents¶

`compare_formulas`(chem_formula1, chem_formula2[, ...])	Check if two chemical formulas are identical.
`reduce_formula`(formula_dict[, tolerance])	Try to find a reduced formula only having natural numbers as quantities
`transform_dict_to_latexstr`(formula_dict)	Create a string from a formula dictionary, fractional quantities are rounded.
`transform_dict_to_str`(formula_dict[, output_type])	Create a string from a formula dictionary, fractional quantities are rounded.
`transform_list_to_dict`(formula_list)	Convert a list of elements to a dictionary.
`transform_list_to_str`(formula_list)	Convert a list of elements to a dictionary.
`transform_str_to_dict`(formula_str)	Create a dictionary from a formula string. The function supports round, squared and curly

aim2dat.utils.chem_formula.compare_formulas(chem_formula1, chem_formula2, reduce_formulas=False)[source]¶

Check if two chemical formulas are identical.

Parameters:¶

chem_formula1 (dict) – Chemical formula as dictionary, e.g. {'Fe' : 4.0, 'O' : 6.0} or {'H' : 2.0, 'O' : 1.0}.
chem_formula2 (dict) – Chemical formula as dictionary, e.g. {'Fe' : 4.0, 'O' : 6.0} or {'H' : 2.0, 'O' : 1.0}.
reduce_formulas (bool) – Whether to reduce the formulas before comparison.

Returns:¶

match (bool) – True if the two forumals are identical

aim2dat.utils.chem_formula.reduce_formula(formula_dict, tolerance=0.0001)[source]¶

Try to find a reduced formula only having natural numbers as quantities

Parameters:¶

formula_dict (dict) – Chemical formula as dictionary, e.g. {'Fe' : 4.0, 'O' : 6.0} or {'H' : 2.0, 'O' : 1.0}
tolerance (float) – Tolerance to determine fractions, e.g., 0.33333 is intepreted as 1/3 for a tolerance of 1.0e-4.

Returns:¶

formula_red (dict) – Chemical formula as dictionary, e.g. {'Fe' : 2, 'O' : 3} or {'H' : 2, 'O' : 1}

aim2dat.utils.chem_formula.transform_dict_to_latexstr(formula_dict)[source]¶

Create a string from a formula dictionary, fractional quantities are rounded.

Parameters:¶: formula_dict (dict) – Chemical formula as dictionary, e.g. {'Fe' : 2.0, 'O' : 3.0} or {'H' : 2.0, 'O' : 1.0}.
Returns:¶: formula_str (str) – Chemical formula as string with latex formating, e.g. r'$\mathrm{Fe}_{\mathrm{2}}\mathrm{O3}$', r'$\mathrm{H}_{\mathrm{2}}\mathrm{O}$'.

aim2dat.utils.chem_formula.transform_dict_to_str(formula_dict, output_type=None)[source]¶

Create a string from a formula dictionary, fractional quantities are rounded.

Parameters:¶

formula_dict (dict) – Chemical formula as dictionary, e.g. {'Fe' : 2.0, 'O' : 3.0} or {'H' : 2.0, 'O' : 1.0}
output_type (None or str) – If set to 'alphabetic' the output formula will be alphabetically ordered.

Returns:¶

formula_str (str) – Chemical formula as string, e.g. Fe2O3`, ``H2O

aim2dat.utils.chem_formula.transform_list_to_dict(formula_list)[source]¶

Convert a list of elements to a dictionary.

Parameters:¶: formula_list (list) – Chemical formula as list, e.g. ['Fe', 'Fe', 'O', 'O', 'O'] or ['H', 'O', 'H']
Returns:¶: formula_dict (dict) – Chemical formula as dictionary, e.g. {'Fe' : 2.0, 'O' : 3.0} or {'H' : 2.0, 'O' : 1.0}

aim2dat.utils.chem_formula.transform_list_to_str(formula_list)[source]¶

Convert a list of elements to a dictionary.

Parameters:¶: formula_list (list) – Chemical formula as list, e.g. ['Fe', 'Fe', 'O', 'O', 'O'] or ['H', 'O', 'H']
Returns:¶: formula_str (str) – Chemical formula as string, e.g. Fe2O3`, ``H2O

aim2dat.utils.chem_formula.transform_str_to_dict(formula_str)[source]¶

Create a dictionary from a formula string. The function supports round, squared and curly brackets as well as recurring elements.

Examples

>>> transform_str_to_dict('HOH')
{'H': 2.0, 'O': 1.0}

>>> transform_str_to_dict("H.5(CO)CH3{OH[CH]4}3.5")
{'C': 16.0, 'O': 4.5, 'H': 21.0}

Parameters:¶: formula_str (str) – Chemical formula as string, e.g. Fe2O3`, ``H2O
Returns:¶: formula_dict (dict) – Chemical formula as dictionary, e.g. {'Fe' : 2.0, 'O' : 3.0} or {'H' : 2.0, 'O' : 1.0}