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Add Feature: XAS Plugin #580

Merged
merged 13 commits into from
Jan 29, 2024
Merged

Add Feature: XAS Plugin #580

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9b965f8
XAS: Add XAS Plugin
PNOGillespie Nov 21, 2023
1d1f3e7
XAS: Refactor CH Pseudo System
PNOGillespie Dec 4, 2023
bc38545
XAS: Migrate CLS Pseudos Directory
PNOGillespie Dec 4, 2023
cc9785a
Merge remote-tracking branch 'origin/main' into xas_plugin
PNOGillespie Dec 13, 2023
a980dcf
XAS Plugin: Various Improvements
PNOGillespie Dec 13, 2023
ed59020
XAS: Fix for Pre-Commit Checks
PNOGillespie Dec 13, 2023
3f6acbc
XAS: Fix Typo in `variable_broad_select_help`
PNOGillespie Dec 13, 2023
9a9f162
`XAS`: Enable `supercell_min_parameter` and Clean Code
PNOGillespie Jan 24, 2024
1b24462
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 24, 2024
57ceb0d
`XAS`: Move Pseudo Load to `setting.py` and clean code
PNOGillespie Jan 26, 2024
3ac8b6e
Merge branch 'main' into xas_plugin
superstar54 Jan 29, 2024
cc963d4
fix set_panel_value
superstar54 Jan 29, 2024
b0a80ac
add test for xas app's setting panel
superstar54 Jan 29, 2024
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1 change: 1 addition & 0 deletions setup.cfg
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Expand Up @@ -57,6 +57,7 @@ aiidalab_qe.properties =
bands = aiidalab_qe.plugins.bands:bands
pdos = aiidalab_qe.plugins.pdos:pdos
electronic_structure = aiidalab_qe.plugins.electronic_structure:electronic_structure
xas = aiidalab_qe.plugins.xas:xas

[aiidalab]
title = Quantum ESPRESSO
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31 changes: 31 additions & 0 deletions src/aiidalab_qe/plugins/xas/__init__.py
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@@ -0,0 +1,31 @@
from importlib import resources

import yaml
from aiidalab_widgets_base import ComputationalResourcesWidget

from aiidalab_qe.common.panel import OutlinePanel
from aiidalab_qe.plugins import xas as xas_folder

from .result import Result
from .setting import Setting
from .workchain import workchain_and_builder

PSEUDO_TOC = yaml.safe_load(resources.read_text(xas_folder, "pseudo_toc.yaml"))


class XasOutline(OutlinePanel):
title = "X-ray absorption spectroscopy (XAS)"
help = """"""


xs_code = ComputationalResourcesWidget(
description="xspectra.x", default_calc_job_plugin="quantumespresso.xspectra"
)

xas = {
"outline": XasOutline,
"code": {"xspectra": xs_code},
"setting": Setting,
"result": Result,
"workchain": workchain_and_builder,
}
26 changes: 26 additions & 0 deletions src/aiidalab_qe/plugins/xas/pseudo_toc.yaml
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---
xas_xch_elements: [C, Li]
pseudos:
pbe:
gipaw_pseudos:
C: C.pbe-n-kjgipaw_psl.1.0.0.UPF
Cu: Cu.pbe-n-van_gipaw.UPF
F: F.pbe-gipaw_kj_no_hole.UPF
Li: Li.pbe-s-rrkjus-gipaw.UPF
O: O.pbe-n-kjpaw_gipaw.UPF
Si: Si.pbe-van_gipaw.UPF
Comment on lines +6 to +11
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I don't want to slow down the progress, is that possible to integrate this to aiida-pseudo?

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So, I will say for this that the solution being used here is not necessarily intended as a permanent solution to providing pseudopotentials for these types of calculations. In principle, integrating some sort of family in aiida-pseudo for core-hole pseudopotentials is the ideal long-term objective here - since then the procedure for assigning pseudos obviously follows that of other plugins.

The two issues I see with integrating the current library with aiida-pseudo are:

  1. Some sort of new Class or other new feature will need to be made for aiida-pseudo in order to work with these types of pseudopotentials: for instance to ensure the correct core wavefunction data file is matched to the correct GIPAW pseudo, also that the core-hole and GIPAW pseudos are matched correctly.
  2. The current library is a stub which covers only some elements, therefore potentially not enough to make it worth pursuing with just what's there at the moment.

I would be interested in your thoughts on this in any case @unkcpz.

core_wavefunction_data:
C: C.pbe-n-kjgipaw_psl.1.0.0.dat
Cu: Cu.pbe-n-van_gipaw.dat
F: F.pbe-gipaw_kj_no_hole.dat
Li: Li.pbe-s-rrkjus-gipaw.dat
O: O.pbe-n-kjpaw_gipaw.dat
Si: Si.pbe-van_gipaw.dat
core_hole_pseudos:
1s:
C: C.star1s.pbe-n-kjgipaw_psl.1.0.0.UPF
Cu: Cu.star1s-pbe-n-van_gipaw.UPF
F: F.star1s-pbe-gipaw_kj.UPF
Li: Li.star1s-pbe-s-rrkjus-gipaw-test_2.UPF
O: O.star1s.pbe-n-kjpaw_gipaw.UPF
Si: Si.star1s-pbe-van_gipaw.UPF
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