add PseudoDojo #387

superstar54 · 2023-04-26T14:20:31Z

Here, two pseudo families added:

PseudoDojo/0.4/PBE/SR/standard/upf
PseudoDojo/0.4/PBEsol/SR/standard/upf

I didn't touch the installation process, thus, it still uses the aiida-pseudo install method like that for SSSP.

GUI

The GUI of pseudo selection is now:

AndresOrtegaGuerrero · 2023-04-27T06:45:56Z

I think it would be worth to also include FR (though that will require that we add the SOC options for properties) and also to add the stringent accuracy

superstar54 · 2023-04-27T07:26:42Z

Hi @AndresOrtegaGuerrero, Thanks for your suggestions. It's good to add more pseudo-family, but this leads to a longer time for the installation, thus the user needs to wait in the first run. The idea here is only to install the most commonly used pseudo, and trigger additional downloads (FR, stringent) if an advanced calculation is needed. This may be added in a further PR. See discussion #386.

AndresOrtegaGuerrero · 2023-04-27T07:35:45Z

@superstar54 I agree, though it might be a good idea that the user gets some description that the PseudoDojo that they are using is SR, and that the accuracy is the standard

superstar54 · 2023-04-27T08:21:03Z

@superstar54 I agree, though it might be a good idea that the user gets some description that the PseudoDojo that they are using is SR, and that the accuracy is the standard

Thanks!. A description for Pseudodojo has been added.

unkcpz · 2023-05-24T21:59:00Z

Hi @superstar54, I change the base to branch main since I decided to deprecate master after the change in app registry is merged, I hope you don't mind.

Is there any block for this PR? Do we need more discussion on this? I remember we want to double-check the versioning of pseudo-dojo?

AndresOrtegaGuerrero · 2023-06-06T07:49:21Z

I think in a previous meeting, we discussed as well that it could be useful to have normal and stringent precision

superstar54 · 2023-06-06T08:06:18Z

it could be useful to have normal and stringent precision

Done

AndresOrtegaGuerrero · 2023-06-06T09:44:44Z

@superstar54 Since the code was re factored, you should do a rebased on this branch with main , since now there is a folder named app for the files you modified

aiidalab_qe/pseudos.py

codecov · 2023-06-08T06:54:29Z

Codecov Report

Patch coverage: 62.85% and project coverage change: +0.49 🎉

Comparison is base (827bb83) 52.13% compared to head (81b4529) 52.63%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #387      +/-   ##
==========================================
+ Coverage   52.13%   52.63%   +0.49%     
==========================================
  Files          16       17       +1     
  Lines        1849     1879      +30     
==========================================
+ Hits          964      989      +25     
- Misses        885      890       +5

Flag	Coverage Δ
python-3.10	`52.63% <62.85%> (+0.49%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
aiidalab_qe/app/report.py	`28.57% <ø> (ø)`
aiidalab_qe/app/sssp.py	`41.30% <12.50%> (-2.38%)`	⬇️
aiidalab_qe/app/steps.py	`68.91% <50.00%> (-0.16%)`	⬇️
aiidalab_qe/app/pseudos.py	`92.85% <75.00%> (+7.14%)`	⬆️
tests/test_pseudo.py	`100.00% <100.00%> (ø)`

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superstar54 · 2023-06-08T07:03:51Z

@AndresOrtegaGuerrero Thanks for the review. I addressed the issues and rebased the branch with the main branch.

AndresOrtegaGuerrero · 2023-06-08T07:40:56Z

@superstar54 Thank you it looks nice, I tested and didn't observe any issues, I only have one opinion an is regarding the widget.

I was wondering if we should use a Dropdown ? or maybe to make like a 2x2 grid to organize the buttons? What do you think?

superstar54 · 2023-06-08T09:04:44Z

I was wondering if we should use a Dropdown ? or maybe to make like a 2x2 grid to organize the buttons? What do you think?

Thanks for the suggestion. I updated the layout to show them in a 2x2 grid on a large screen and 4x1 on a small one.

AndresOrtegaGuerrero · 2023-06-08T09:10:26Z

@superstar54 It looks great to me ! thank you

aiidalab_qe/app/report.py

aiidalab_qe/app/steps.py

aiidalab_qe/app/sssp.py

unkcpz

Thanks @superstar54, some change requests.

superstar54 · 2023-06-08T11:50:25Z

@unkcpz thanks for the review, I have addressed all the requests.

unkcpz

Thanks a lot @superstar54, still have one thing want you to check. I approve it anyway so I do not block you for further progress.

BTW, do you think it is okay to add a test for checking using the other pseudofamily?

unkcpz · 2023-06-08T12:10:28Z

aiidalab_qe/app/pseudos.py

+        if self.override_protocol_pseudo_family.value:
+            if "PseudoDojo" in self.protocol_selection.value:
+                pseudo_family = f"PseudoDojo/0.4/{self.dft_functional.value}/SR/{self.protocol_selection.value.split()[1]}/upf"
+            elif "SSSP" in self.protocol_selection.value:
+                pseudo_family = f"SSSP/1.2/{self.dft_functional.value}/{self.protocol_selection.value.split()[1]}"
+            else:
+                raise ValueError(
+                    f"Unknown pseudo family {self.override_protocol_pseudo_family.value}"
+                )
+            self.value = pseudo_family
+        else:
+            self.value = DEFAULT_PARAMETERS["pseudo_family"]


I am a bit worried about the complex if..else nest here. Can you check it again if you can make it more clear?

@superstar54 perhaps you can use a dictionary to put the options an evaluate the dict[value] ?

@AndresOrtegaGuerrero, I don't quite understand what you mean. @superstar54, can you try to address it?
Then we can merge this PR.

@superstar54 you can ignore my suggestion and merge if you want

Thanks for the suggestions. I updated the code to make the string pretty and hopefully more clear. A test is also added for the PseudoFamilySelector widget.

Great! All good to me.

add PseudoDojo

b4319b3

superstar54 requested review from unkcpz and mbercx April 26, 2023 14:25

superstar54 linked an issue Apr 26, 2023 that may be closed by this pull request

Add PseudoDojo to the pseudopotential selection list #366

Closed

add description for PseudoDojo

5515e4a

unkcpz force-pushed the master branch from 3431f6f to 3ca6592 Compare May 17, 2023 12:47

unkcpz changed the base branch from master to main May 24, 2023 21:56

add stringent

a4111c8

superstar54 requested a review from AndresOrtegaGuerrero June 6, 2023 08:05

AndresOrtegaGuerrero reviewed Jun 6, 2023

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superstar54 added 2 commits June 8, 2023 06:21

update UI and logic

4ba9ce5

Merge branch 'main' into add_pseudo_dojo

9545126

update pseudo description

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superstar54 requested a review from AndresOrtegaGuerrero June 8, 2023 07:03

update layout

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AndresOrtegaGuerrero approved these changes Jun 8, 2023

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unkcpz requested changes Jun 8, 2023

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update psuedo instal cmds and move pseudo logic to steps

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superstar54 requested a review from unkcpz June 8, 2023 11:49

unkcpz approved these changes Jun 8, 2023

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superstar54 added 2 commits June 20, 2023 07:50

pretty the fromat

caeca17

add unit test for pseudo selector

81b4529

unkcpz merged commit d210b45 into main Jun 20, 2023
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unkcpz deleted the add_pseudo_dojo branch June 20, 2023 08:32

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add PseudoDojo #387

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add PseudoDojo #387

add PseudoDojo #387

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superstar54 commented Apr 26, 2023 • edited Loading

GUI

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