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README.md

Hydraspa

Build Status codecov

Hydraspa (hydra + Raspa) is a Python package for preparing GCMC gas adsorption simulation inputs for the Raspa simulation package.

Permission to use the structures from the CoRe MOF Database has kindly been given by Dr. Yongchul G. Chung of Pusan National University.

Installing hydraspa

git clone https://github.com/richardjgowers/hydraspa.git

cd hydraspa

pip install -r requirements.txt .

Using hydraspa

hydraspa is designed to be used via the command line to prepare and analyse simulation inputs:

# Create a simulation template of CO2 in IRMOF-1
hydraspa create -s IRMOF-1 -g CO2 -f UFF -o myCO2sim

# Split the template into many temperatures and pressures
hydraspa split myCO2sim/ -p 10k,20k,30k -T  278.0,298.0 -c 20k

# Gather the results once the simulation has been done
hydraspa gather myCO2sim/

Citing

If this software is useful in your research, please consider citing the following sources:

D. Nazarian, J. Camp, Y.G. Chung, R.Q. Snurr, D.S. Sholl, "Large-Scale Refinement of Metal Organic Framework Structures Using DFT," Chemistry of Materials, 2016

Y.G. Chung, J. Camp, M. Haranczyk, B.J. Sikora, W. Bury, V. Krungleviciute, T. Yildirim, O.K. Farha, D.S. Sholl, R.Q. Snurr, "Computation-Ready, Experimental Metal-Organic Frameworks: A Tool to Enable High-Throughput Computation of Nanoporous Crystals," Chemistry of Materials, 2014, 26 (21), pp 6185–6192

A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard III, and W. M. Skiff "UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations" Journal of the American Chemical Society, 1992, 114 (25) pp 10024–10035

Contributing

Hydraspa is actively being used and developed, if you encounter any issues drop me a line on the issue tracker.

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