Running PDOS workchain and plot bands + pdos #159

unkcpz · 2021-11-19T17:06:52Z

Fixes #62

The PR is blocked by NodesTreeWidget: find outputs not working for nested namespace aiidalab-widgets-base#262 since pdos workchain have outputs in namespace.
Clean qe.ipynb
add checkbox and able to run PDOS workchain when the box checked
newly added pdos and projwfc code setting will break backward compatibility.
newly added codes is not default set for the code dropdown widget.
Dependency: new aiida-quantumespresso plugin otherwise will raise tetrahydro setting error.
bands+pdos plot
show_band_structure widget tab name change. When only one bands or pdos calculation run.
aiida-quantumespresso 3.5.0 for the tetrahedra override

mbercx · 2021-11-25T14:37:34Z

@unkcpz aiida-quantumespresso 3.5.0 is now released with the fix you need for the tetrahedra override, so you can update the dependency.

unkcpz · 2021-11-25T16:24:07Z

For the band structure output view widget tab name, it is only a good to have feature. So I think this PR is ready to review.

mbercx

Thanks @unkcpz! Just left some minor comments. Two other things:

The dependency version of aiida-quantumespresso doesn't seem to be upgraded to 3.5.0?
When I refresh the app, the dos.x and projwfc.x codes weren't automatically set to the defaults. But this is most likely because I didn't install the app with this branch, since if I understand correctly the default are set upon installation.

aiidalab_qe/steps.py

aiidalab_qe/node_view.py

unkcpz · 2021-11-29T17:52:53Z

@mbercx Thanks a lot for the review.

The dependency version of aiida-quantumespresso doesn't seem to be upgraded to 3.5.0?

Ah, true. I forget to push the latest commits with some other changes.

I refresh the app, the dos.x and projwfc.x codes weren't automatically set to the defaults. But this is most likely because I didn't install the app with this branch, since if I understand correctly the default are set upon installation

This is an issue, I think the dos.x and projwfc.x were installed with pw.x. Just not sure which line of code influence this default fresh and setting behavior. I need to check this more.

aiidalab_qe/steps.py

unkcpz · 2021-12-09T09:21:09Z

I make all the changes you mentioned in the review, but I need to give it a final run and test. Will request another review after it.

unkcpz · 2022-01-05T13:05:14Z

When I refresh the app, the dos.x and projwfc.x codes weren't automatically set to the defaults. But this is most likely because I didn't install the app with this branch, since if I understand correctly the default are set upon installation.

I am not sure since I create a new container with install the app with this branch but got the QE setup error 'NoneType' object has no attribute 'uuid'. @csadorf I am a bit lot in the QESetupWidget code. Could you tell me where this error might come from? The thing confuse me is in the method SubmitQeAppWorkChainStep:_auto_select_code it calls get_input_parameters which need the corresponding code selector being set?

Moreover, I can not figure out how to retrigger the codes install and code setup or maybe just manually set the related parameters for code dos and projwfc? I don't think create a new container to get the code set is a convenient way to do this.

unkcpz · 2022-01-07T10:37:24Z

The only block of this is the code selector not setting the default code as expected.

csadorf · 2022-01-07T10:39:47Z

The only block of this is the code selector not setting the default code as expected.

I will try to reproduce the issue.

csadorf · 2022-01-07T11:21:40Z

I think we should have a bot that automatically generates the following command for us 😁 :

aiidalab install quantum-espresso@git+https://github.com/unkcpz/aiidalab-qe@pdos --yes

csadorf · 2022-01-07T11:45:44Z

I am still investigating, but I will start to try to answer some of your questions.

When I refresh the app, the dos.x and projwfc.x codes weren't automatically set to the defaults. But this is most likely because I didn't install the app with this branch, since if I understand correctly the default are set upon installation.

I just installed this app version in a new environment and did not experience any issues with the qe installation. However, I also found that the codes were not selected by default.

I am not sure since I create a new container with install the app with this branch but got the QE setup error 'NoneType' object has no attribute 'uuid'. @csadorf I am a bit lot in the QESetupWidget code. Could you tell me where this error might come from?

I am not able to reproduce this problem.

The thing confuse me is in the method SubmitQeAppWorkChainStep:_auto_select_code it calls get_input_parameters which need the corresponding code selector being set?

Indeed, I am not exactly sure how that currently works either. I will keep investigating.

Moreover, I can not figure out how to retrigger the codes install and code setup or maybe just manually set the related parameters for code dos and projwfc? I don't think create a new container to get the code set is a convenient way to do this.

To re-trigger the setup process just remove the AiiDA codes with the corresponding labels (pw-6.7@localhost etc.) and optionally also remove the quantum-espresso-6.7 conda environment.

Edit: You also have to remove the .do-not-setup-on-localhost file in the app folder. The file is created whenever a previous setup attempt failed to avoid that the setup process starts every single time the app is opened.

csadorf · 2022-01-07T13:52:02Z

I can confirm that the pw.x code is currently not automatically selected, not even on the "master" branch. Trying to figure out when and how this regression was introduced.

I have reported the issue here: #164

csadorf · 2022-01-07T16:05:09Z

Please rebase this branch after merging #167 .

csadorf

Please apply my suggestion on how to fix the remaining code selection issue and then rebase on master after #167 has been merged.

aiidalab_qe/steps.py

csadorf · 2022-01-07T15:24:33Z

aiidalab_qe/steps.py

+            self.codes_selector.pw.selected_code = _load_code(parameters["pw_code"])
+            self.codes_selector.dos.selected_code = _load_code(parameters["dos_code"])
+            self.codes_selector.projwfc.selected_code = _load_code(
+                parameters["projwfc_code"]
+            )


I would recommend to refactor this into a loop and keep the catch of the NotExistent exception for robustness:

for code in ("pw_code", "dos_code", ...): try: ... except NotExistent: pass

unkcpz · 2022-01-10T09:47:46Z

Hi @csadorf, I have run bumpver update to create a new tag: v22.01.0. I need then push this tag? Or do this after pr #169 merged?

csadorf · 2022-01-10T10:14:39Z

Hi @csadorf, I have run bumpver update to create a new tag: v22.01.0. I need then push this tag? Or do this after pr #169 merged?

As discussed offline, we should not bump the version on the feature branch. That said, bumpver should have pushed the tag, not sure why that did not happen.

csadorf

I tested this on the latest aiidalab version and everything appeared to work fine, however the DOS and the Projwfc calculations never appeared to fully finish:

That's despite the fact the logs appear completed:

I have one last question regarding the widgets base requirement, but other than that this is good to go.

setup.cfg

Add features to submit widget and output view widget to support running PdosWorkChain and show the pdos results.

csadorf

I reviewed the code and just ran a pdos work chain for testing on Si.

Everything appears to be working. 👍

unkcpz marked this pull request as draft November 19, 2021 17:07

unkcpz requested review from mbercx and csadorf and removed request for mbercx November 25, 2021 16:22

unkcpz marked this pull request as ready for review November 25, 2021 16:24

mbercx requested changes Nov 26, 2021

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unkcpz mentioned this pull request Nov 29, 2021

Improve the band structure plotting #104

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unkcpz force-pushed the pdos branch 4 times, most recently from 81a6161 to 984cba0 Compare January 10, 2022 08:42

unkcpz requested a review from csadorf January 10, 2022 08:45

unkcpz force-pushed the pdos branch from 6ac84c8 to 984cba0 Compare January 10, 2022 10:01

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Bug report: Application crashed with AttributeError #172

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Support PdosWorkChain

3dca9b8

Add features to submit widget and output view widget to support running PdosWorkChain and show the pdos results.

unkcpz force-pushed the pdos branch from 77215b6 to 3dca9b8 Compare January 17, 2022 22:14

unkcpz requested a review from csadorf January 17, 2022 22:15

csadorf approved these changes Jan 19, 2022

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csadorf merged commit 4d81d64 into aiidalab:master Jan 19, 2022

unkcpz deleted the pdos branch May 18, 2023 10:09

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Running PDOS workchain and plot bands + pdos #159

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Running PDOS workchain and plot bands + pdos #159

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