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):
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- quick
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- squick
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- mquick (default)
-
dft:
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- priroda - use priroda16 for dft calculations (PBEPBE 3z), programm developed by D. Laikov https://rad.chem.msu.ru/~laikov/ru/
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- 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)
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- 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):
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- index - serial number of reaction
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- smi - SMILES of reaction
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- reactants - list of CalcResult (python named tuple) for reactants
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- products - list of CalcResult (python named tuple) for products
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- energy_dif - difference in energies between products and reactants (Hartree)
-
- comments
-
- time_s - calculation execution time
-
CalcResult (python named tuple) - result of successful calculations
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- data - list of strings as lines in XYZ file
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- min_energy - energy of converged structure
-
- log - full output of calculations, if log option is None or omitted in json
-
FailReport (python named tuple)
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- initial - initial file
-
- log - output of calculations
-
- step - at which step calculations failed