pyKinML database

This is a set of SQL databases with information about molecules and radicals with the following database conventions and content.

Each database is named as “CnHm”, where n and m range from 1 to 5 and indicate the number of carbon (C) and hydrogen (H) atoms in the structures in the database.

Each database contains entries of a large number of “CnHm” geometries. Within each database are frous tables.

Table “meta”Contains the name of the database and the date it was created.Table “xyz”The columns of the “xyz” database are the following:

“id”: a numerical identification number, integer

“calc_params”: metadata describing the level of theory and other details of the quantum chemical calculations to generate the Hessian used for generating this structure, numpy array stored as a blob.

“calc”: software used to for the calculation, string

“temp”: the temperature used during the normal mode sampling process to generate the structure in K, outliers are assigned negative temperature, float

“name”: a unique name describing the anchor point the structure was generated from, string

“dist”: the normalized unitless distance of the structure from its anchor point at the temperature given in “temp”, float

“geometry”: atomic coordinates in angstroms, (n+m) by 3 numpy array of floats stored as a blob. Note that the atomic positions are listed with carbons first followed by hydrogens.

“created_at”: date the structure was generated

Table “energy”The columns of the “energy” database are the following:

“id”: a numerical identification number, not linked to the “id” in “xyz”, integer

“fidelity”: the fidelity level the energy was calculated at, integer

0 = B3LYP/6-31+G(d)

1 = wB97X-D/6-311++G(d,p)

2 = HF/6-31G

3 = B3LYP/6-31G

4 = B2PLYPD3/6-311++G(d,p)

“E”: molecular energy in eV, float

“xyz_id”: the “id” of the geometry in the “xyz” table this energy calculated for, integer

“hessian”: empty

“forces”: atomic forces in eV/angstrom, (n+m) by 3 numpy array of floats stored as a blob. Note that the atomic forces are listed in the same order as the atoms in the “geometry” in the “xyz” table

“calc_params”: metadata describing the level of theory and other details of the energy and force calculations of this entry, numpy array stored as a blob

“calc”: software used to for the energy and force calculation

“created_at”: date the energy and forces were calculated

“sample_set_id”: empty

Table “aev”: currently empty (edited)