Reaction Feasibility Estimator

Estimate reaction feasibility by difference in energy between energy of reactants and products

Docker pull

timurious/estimator:latest

Docker build

To build an image:

docker build . -t estimator 

Input files

change directories in docker-compose file near to "source:" line, absolute path to dir with input.json should be provided. Example of json file is shown in example folder.

speed and precision of CREST calculations, possible options :

• crest_speed (https://github.com/grimme-lab/crest):

• • quick
• • squick
• • mquick (default)

• dft:

• • priroda - use priroda16 for dft calculations (PBEPBE 3z), programm developed by D. Laikov https://rad.chem.msu.ru/~laikov/ru/
• • pyscf (not finished) - use pyscf package for calculations (B3LYP) None or not mentioned in json (default) - do not perform DFT

• obabel_fast - speed vs precision in 3D generation by openbabel (http://openbabel.org/wiki/Main_Page)

• • True - can save some time in generation of 3D by mmff94
• • False or not mentioned in json (default)

Run calculations

docker compose up

or

docker stack deploy -c docker-compose.yaml estimator

The results will be stored in python .shelve file For each job several types of responses available:

• ReactionComponents (python named tuple):

• • index - serial number of reaction
• • smi - SMILES of reaction
• • reactants - list of CalcResult (python named tuple) for reactants
• • products - list of CalcResult (python named tuple) for products
• • energy_dif - difference in energies between products and reactants (Hartree)
• • comments
• • time_s - calculation execution time

• CalcResult (python named tuple) - result of successful calculations

• • data - list of strings as lines in XYZ file
• • min_energy - energy of converged structure
• • log - full output of calculations, if log option is None or omitted in json

• FailReport (python named tuple)

• • initial - initial file
• • log - output of calculations
• • step - at which step calculations failed