Implement batch_run #22
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@selimsami I think you have added some comments early this morning, but they are gone now. |
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Yes I saw a problem somewhere but then I realized my solution was not good. I'll have another look soon. |
qforce/fragment.py
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| @@ -357,26 +369,31 @@ def check_for_qm_data(self, job, config, mol, qm): | |||
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| else: | |||
| self.check_new_scan_data(job, mol, config, qm) | |||
| self.write_have_or_missing(job) | |||
| self.write_have_or_missing(job, config) | |||
| nx.write_gpickle(self.graph, f"{self.dir}/identifier_{self.hash_idx}") | |||
| self.write_xyz() | |||
| with open(f"{self.dir}/qm_method_{self.hash_idx}", 'w') as file: | |||
| json.dump(self.graph.graph['qm_method'], file, sort_keys=True, indent=4) | |||
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| if not self.has_data: | |||
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if not (self.has_data or (config.batch_run and self.has_inp)):
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Sorry, I don't quite understand this part.
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Sorry that was a bit ambiguous. I meant replace:
if not self.has_data:
self.make_qm_input(job, qm)
if not (config.batch_run and self.has_inp):
self.make_qm_input(job, qm)
with:
if not (self.has_data or (config.batch_run and self.has_inp)):
self.make_qm_input(job, qm)
qforce/fragment.py
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| if self.has_data: | ||
| status = 'have' | ||
| else: | ||
| status = 'missing' | ||
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| if config.batch_run and self.has_inp: |
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this should be an elif before the else above
qforce/fragment.py
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| check_and_notify(job, config.scan, len(unique_dihedrals), len(fragments)) | ||
| check_and_notify(job, config.scan, len(unique_dihedrals), len(fragments), | ||
| len(generated)) |
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Not too important but: I use line length of max 100, would be good to be consistent with that. (might apply elsewhere also)
qforce/fragment.py
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| for name, atomids in unique_dihedrals.items(): | ||
| frag = Fragment(job, config, mol, qm, atomids, name) | ||
| if frag.has_data: | ||
| fragments.append(frag) | ||
| if frag.has_inp: |
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elif config.batch_run and frag.has_inp:
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The config here is the fragment config and doesn't have the batch_run attribute.
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hmm I think it's the general config. Then you need: config.scan.batch_run
qforce/fragment.py
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| @@ -60,6 +63,8 @@ def check_and_notify(job, config, n_unique, n_have): | |||
| print("All scan data is available. Fitting the dihedrals...\n") | |||
| else: | |||
| print(f"{n_missing} of them are missing the scan data.") | |||
| if config.batch_run: | |||
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if n_generated > 0:
print(f"{n_generated} of them generated previously (Batch run enabled).")
if n_missing - n_generated > 0:
print(f"QM input files for them are created in: {job.frag_dir}")
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@selimsami Thanks for the review. I have addressed the points that I can address. |
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@selimsami Thanks for the review, all of the points have been addressed. |
FIx #15
The test is written against the qforce-example selimsami/qforce_examples#1