atb-uq / pythinfilm Goto Github PK

What parameters do I need to change if I want to delete the solvent faster
I ran a 10ns MD test case and couldn't see the process of solvent removal

Accept a list of names for cases where users want to run simulations with a mix of solvent molecules.

[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'

We still need to add the forked pmx version (https://github.com/ATB-UQ/pmx-pytf) as an installation dependency.

Add a warning that the specified over-head void space is insufficient based on: overhead void hight < insertion hight + (molecule's longest dimension) / 2

When molecules are inserted, they are rotated to a random orientation around their origin, but that origin could be anywhere relative to the molecule, leading to the possibility that it overlaps the z boundary and clips into the electrode, and also making it more difficult to place multiple molecules in such a way that they don't overlap.

This can be fixed by shifting the origin of inserted molecules to be their geometric centre before they are inserted and rotated. Doing this calculation would also give the spatial extents of the molecule with little extra effort, meaning the z dimension of the simulation box could be set automatically based on a "minimum gap between the highest possible inserted atom and the top of the box" parameter, which can probably be given a sane default. A manual override for the z dimension would also be useful in some cases though (eg. simulations where some deposited molecules could bounce back up, or solvent evaporation simulations).