bond_order_processing

Library for processing Mayer bond orders.

The current library allows you to process Mayer bond orders from the CPMD output file

Library version: 1.1.2

Coverage Report

File	Stmts	Miss	Cover	Missing
main/BondOrderProcessing/bond_order_processing
calculations.py	352	9	97%	40, 44, 51, 171, 324, 505, 660, 662–663
calculations_for_atoms_lists.py	166	3	98%	84–87
input_data.py	422	53	87%	88–100, 122–155, 185–189, 225, 234–238, 306, 319–320, 379–383, 430–441, 478–479, 485, 500, 507, 664, 671, 709, 738, 742, 765, 772, 818, 826, 872, 878, 892, 943, 955
TOTAL	941	65	93%

Links

• Documentation page
• Git repository
• More information about CPMD - https://github.com/CPMD-code

You can calculate from Mayer bond orders

• coordinations numbers,
• Qi units,
• Connections between atoms,
• Relation between bond order and length,
• Covalence (The sum of the bond orders of a given atom. This value is close to the valence if atom have only purely covalent bonds)

Example:

>>> from bond_order_processing.input_data import LoadedData
>>> from bond_order_processing.calculations import CoordinationNumbers
>>> from bond_order_processing.input_data import InputDataFromCPMD
>>> 
>>> path_to_input_file = r'./egzamples_instructions/cpmd_out1.txt'
>>> 
>>> input_data = InputDataFromCPMD()
>>> input_data.load_input_data(path_to_input_file, LoadedData.MayerBondOrders)
>>> mayer_bond_orders = input_data.return_data(LoadedData.MayerBondOrders)
>>>
>>> # Calculate percentage of coordination numbers of P
>>> coordinations_numbers_stats = CoordinationNumbers.calculate(mayer_bond_orders, 'P', 'O', 'INF', 0.2, 'P-O').calculate_statistics()
>>> coordinations_numbers_stats.statistics
{4: 100.0}

You can also use application using this library.

Check: https://github.com/pawelgoj/pyMayCoor

 1"""Library for processing Mayer bond orders.
 2
 3.. include:: ../README.md
 4
 5Example:
 6
 7    >>> from bond_order_processing.input_data import LoadedData
 8    >>> from bond_order_processing.calculations import CoordinationNumbers
 9    >>> from bond_order_processing.input_data import InputDataFromCPMD
10    >>> 
11    >>> path_to_input_file = r'./egzamples_instructions/cpmd_out1.txt'
12    >>> 
13    >>> input_data = InputDataFromCPMD()
14    >>> input_data.load_input_data(path_to_input_file, LoadedData.MayerBondOrders)
15    >>> mayer_bond_orders = input_data.return_data(LoadedData.MayerBondOrders)
16    >>>
17    >>> # Calculate percentage of coordination numbers of P
18    >>> coordinations_numbers_stats = CoordinationNumbers.calculate(mayer_bond_orders, 'P', 'O', 'INF', 0.2, 'P-O').calculate_statistics()
19    >>> coordinations_numbers_stats.statistics
20    {4: 100.0}
21    
22.. include:: ../app.md
23
24"""
25__docformat__ = "google"