Add torsiondrive as a potential torsion scan tool. #43
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@selimsami Sorry, my fault. Forget to set |
This reverts commit 8c6f348.
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@selimsami The code is done now and I'm testing the robustness. Do you mind having a look and tell me your thought, please? Thanks. |
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Thanks a lot for this contribution, looks very nice. Sorry for the delay, had a really busy teaching week.
I made a few minor comments. And I have one more general one here: I think it would be nice to move xtb-torsiondrive reader/writer to a different module named torsiondrive or torsiondrive_xtb
qforce/qm/qm.py
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| try: | ||
| os.makedirs(f'{dir}/{scan_id}_torsiondrive') | ||
| except FileExistsError: | ||
| warn(f'Folder {dir}/{scan_id}_torsiondrive exists, remove the folder.') | ||
| shutil.rmtree(f'{dir}/{scan_id}_torsiondrive') | ||
| os.makedirs(f'{dir}/{scan_id}_torsiondrive') |
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why not just remove the directory if it exists?
if os.path.exists(name):
shutil.rmtree(name)
os.makedirs(name)
qforce/qm/qm.py
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| os.makedirs(f'{dir}/{scan_id}_torsiondrive') | ||
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| # Create the coordinate input file | ||
| with open(f'{dir}/{scan_id}_torsiondrive/input.xyz', 'w') as f: |
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perhaps you can use ASE here again to write the XYZ file?
See an example here.
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@selimsami Thanks. I was thinking of the same thing but I couldn't get the mol.info to write what I want. It is nice that I could just put it in the comment.
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@selimsami Sorry about more ase question. I wonder how do I create an ase mol object given ele_id and pos? see the input here https://github.com/selimsami/qforce/pull/43/files#diff-f579a382b4ca6ded95ab6837635635e6329d9fe38329927c5f4e2d8a4ff2b243R119
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from ase import Atoms
mol = Atoms(positions=pos, numbers=ele_id)
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@selimsami Thanks for the advice on ase. Once I have tested that it is robust, I will ping you and we can have this merged. |
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@selimsami I have tested this routine on 30 molecules and it seems fine. If you are happy, we can have this merged. |
@selimsami Do you mind help me on this?
I have allowed the torsiondrive to be used as torsion scan tool but it seems that the charge is not read in correctly.
https://github.com/Exscientia/qforce/blob/0fded8348d59a9967048f525c2fb766580162669/qforce/qm/qm.py#L122
I'm loading the charge from the torsion scan to be used as charge for the fitting.
But I found that the charge that I feed in to the
Qforce (propane_qforce/fragments/CC_H8C3_d91b46644317dee9c2b868166c66a18c~1.chargesis not the same as the topology that Qforce generates (Qforce (propane_qforce/fragments/CC_H8C3_d91b46644317dee9c2b868166c66a18c~1/step00/propane_qforce.itp) during the fitting.Please find the example.
Archive.zip