gojian / mlincrs

Code collection to fit KRR ML models

MLinCRS

Code collection to fit KRR ML models

Requirements

Requirements for Example_tutorial.ipynb are:

• python >= 3.7

• ase >= 3.19.1

• numpy >= 1.19.0

• scikit-learn >= 0.23.1

• jupyter-notebook >= 6.1.3

• matplotlib >= 3.3.0

• mltools https://github.com/simonwengert/mltools.git

• QUIP, quippy, GAP https://libatoms.github.io/GAP/installation.html

Data formats

Molecular database stored in an extended .xyz file. This file serves as input for the preparation of the kernel matrices. The molecule info line has to contain an id and AE keyword, which is the id of the molecule in the database and the atomization energy.

Reaction network with bond breaking reactions of types A - > B + C (reaction type I) or A -> B (reaction type II) stored in a .txt file. Each row is a sepatate reaction. The file consists of 4 columns.

Column	Content
1	Index of molecule A (molecule id in .xyz file)
2	Index of molecule B (molecule id in .xyz file)
3	Index of molecule C (molecule id in .xyz file), reaction type I or "[x]", reaction type II
4	DFT calculated Reaction energy (RE) [eV], RE = sum(AE(products)) - AE(educt)

Authors

Sina Stocker ([email protected])