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ATB-UQ / PyThinFilm

GNU General Public License v3.0
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Using solvent_delete error #8

Open kkivg opened 10 months ago

kkivg commented 10 months ago

[INFO] - Running solvent_evaporation simulation #1 Traceback (most recent call last): File "/root/anaconda3/bin/pytf", line 8, in sys.exit(cli()) ^^^^^ File "/root/anaconda3/lib/python3.11/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/root/anaconda3/lib/python3.11/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/root/anaconda3/lib/python3.11/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/root/anaconda3/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/root/anaconda3/lib/python3.11/site-packages/PyThinFilm/pytf.py", line 30, in cli main(config, debug) File "/root/anaconda3/lib/python3.11/site-packages/PyThinFilm/pytf.py", line 17, in main while deposition.cycle(): ^^^^^^^^^^^^^^^^^^ File "/root/anaconda3/lib/python3.11/site-packages/PyThinFilm/deposition.py", line 195, in cycle self.solvent_delete() File "/root/anaconda3/lib/python3.11/site-packages/PyThinFilm/deposition.py", line 561, in solvent_delete thresh = del_config["density_thresh"]


KeyError: 'density_thresh'
kkivg commented 10 months ago

Additionally, what parameters can be used to fully simulate the solution deposition process described in the paper

ssande7 commented 10 months ago

It looks like there was a mis-indentation in the example file. Reducing the indentation of the solvent_delete line by one should fix it, assuming your input file is based on that example (see PR #9 for the change if that's unclear). If that doesn't work, a copy of your input script would be helpful for debugging.

The simulation in the paper started with a partially evaporated film from Lee et al., and the insertion/deletion protocols used are described in section 2A here. The comments in the example file should help with mapping the protocol in the paper to the parameters - I'd recommend going through that process to understand them since your system may need different ones to behave well, but for the most part the parameters used are the same as in the example, except for density_thresh which was initially 40 atoms / nm^-3 (0.04 A^-3) and slab_height which was initially 12.5 nm. These were adjusted as per the paper as the surface of the film approached the substrate for final drying (you'll need to stop/restart to do this). Note that if the bottom of the slab containing deletion candidates falls below slab_lower_limit then the slab height will be reduced, and the number of deleted atoms adjusted proportionally (as described in the paper).