Generalize data creation for RSS workflow by JaGeo · Pull Request #397 · autoatml/autoplex

JaGeo · 2025-06-10T06:56:28Z

Make ML potential-based training in the RSS workflow available. This will then also allow to extend towards other data generation mechanisms.

…ex into generalize_data_creation

YuanbinLiu · 2025-07-11T20:27:51Z

The isolated atom maker has been added. Should we consider enabling the configuration of both static_energy_maker and static_energy_maker_isolated_atoms in the YAML file? It might make things more flexible.

JaGeo · 2025-07-11T20:57:11Z

@YuanbinLiu Great!

It would be great to add it to the yaml. But we can also first merge this PR and do this subsequently.

Bumps [numpydoc](https://github.com/numpy/numpydoc) from 1.8.0 to 1.9.0. - [Release notes](https://github.com/numpy/numpydoc/releases) - [Changelog](https://github.com/numpy/numpydoc/blob/main/RELEASE.rst) - [Commits](numpy/numpydoc@v1.8.0...v1.9.0) --- updated-dependencies: - dependency-name: numpydoc dependency-version: 1.9.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Pre commit update

YuanbinLiu · 2025-07-12T08:08:56Z

@YuanbinLiu Great!

It would be great to add it to the yaml. But we can also first merge this PR and do this subsequently.

Sounds good!

update mace version

--- updated-dependencies: - dependency-name: myst-nb dependency-version: 1.3.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>

--- updated-dependencies: - dependency-name: matgl dependency-version: 1.2.7 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]>

JaGeo · 2025-07-15T05:49:55Z

src/autoplex/data/common/jobs.py

            converged = check_convergence_vasp(os.path.join(val, "vasprun.xml.gz"))
-
-            if converged:
+        if (has_vasp_output and converged) or has_ase_output:


Likely my fault but I just realized that it is probably rather

Suggested change

if (has_vasp_output and converged) or has_ase_output:

if has_vasp_output or has_ase_output:

Bump matgl from 1.2.6 to 1.2.7

Bump myst-nb from 1.2.0 to 1.3.0

…ex into generalize_data_creation

JaGeo · 2025-07-15T11:16:40Z

Hi @YuanbinLiu ,
i made all changes, I think. Please check if everything works as intended. I changed logic with regard to the VASP convergence check.

I am attaching a script that allows you to run the workflow with Quantum Espresso. You need to install qe, get some pseudopotentials (set the path correctly) and figure out the run command locally to test it.
run.zip

YuanbinLiu · 2025-07-16T07:04:24Z

Hi @YuanbinLiu , i made all changes, I think. Please check if everything works as intended. I changed logic with regard to the VASP convergence check.

I am attaching a script that allows you to run the workflow with Quantum Espresso. You need to install qe, get some pseudopotentials (set the path correctly) and figure out the run command locally to test it. run.zip

Hi @JaGeo, I had a quick check. All look good to me! Thank you!

JaGeo · 2025-07-16T07:24:09Z

Awesome! Thank you @YuanbinLiu ! Merged! And ee can build upon the attached script to document the, so far, experimental support for other dft codes!

JaGeo and others added 30 commits May 30, 2025 16:28

add ml potentials to data creation

9e181ae

replace installation

44e5ea7

replace installation

4eaf4bb

pre-commit auto-fixes

2ccae6a

fix spelling error

8707ce2

Merge branch 'generalize_data_creation' of github.com:autoatml/autopl…

1029f62

…ex into generalize_data_creation

Update pyproject.toml

625501e

Update pyproject.toml

0767545

add AseMaker to documentation

7d5f6b4

Merge branch 'generalize_data_creation' of github.com:autoatml/autopl…

cc243d6

…ex into generalize_data_creation

pre-commit auto-fixes

871611c

make ml potential training available

172c56d

Merge branch 'generalize_data_creation' of github.com:autoatml/autopl…

f80ff1a

…ex into generalize_data_creation

pre-commit auto-fixes

e4f8274

fix maker

066fb52

add loadfn

2be6e23

pre-commit auto-fixes

230a6d5

revert

6fd4f7e

revert

38afb1d

pre-commit auto-fixes

cf78131

add additional maker

8d3c834

pre-commit auto-fixes

7d71a1a

add additional maker

f3f9816

Merge branch 'generalize_data_creation' of github.com:autoatml/autopl…

8098419

…ex into generalize_data_creation

add additional maker

26ed92b

fix maker definition

8ad50f4

pre-commit auto-fixes

8174847

fix calc

5c48e55

Merge branch 'generalize_data_creation' of github.com:autoatml/autopl…

d560af7

…ex into generalize_data_creation

pre-commit auto-fixes

da9ff30

YuanbinLiu and others added 2 commits July 11, 2025 20:58

Add argument static_energy_maker_isolated_atoms

176ca80

pre-commit auto-fixes

2cb0b60

dependabot bot and others added 8 commits July 12, 2025 09:15

update pre-commit and lint config

0c7f6a6

fix lint erros

b8a5d96

Merge branch 'autoatml:main' into pre_commit_update

95e53b9

Merge pull request #413 from naik-aakash/pre_commit_update

26e3c7b

Pre commit update

upgrade mace version

5a15afb

fix regrex for mace data extraction

a6c507f

Merge branch 'autoatml:main' into mace_update

f5fc969

naik-aakash and others added 5 commits July 12, 2025 08:44

fix failing test

13ad0ee

fix comment

e174d85

Merge pull request #414 from naik-aakash/mace_update

c7ce92a

update mace version

Bump myst-nb from 1.2.0 to 1.3.0

a19f467

--- updated-dependencies: - dependency-name: myst-nb dependency-version: 1.3.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>

Bump matgl from 1.2.6 to 1.2.7

cd9a44c

--- updated-dependencies: - dependency-name: matgl dependency-version: 1.2.7 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]>

JaGeo commented Jul 15, 2025

View reviewed changes

naik-aakash and others added 7 commits July 15, 2025 08:37

Merge pull request #416 from autoatml/dependabot/pip/matgl-1.2.7

6ed6ebd

Bump matgl from 1.2.6 to 1.2.7

Merge pull request #415 from autoatml/dependabot/pip/myst-nb-1.3.0

ee9fa95

Bump myst-nb from 1.2.0 to 1.3.0

fix fall backs

3f7a844

pre-commit auto-fixes

9e68456

Merge branch 'generalize_data_creation' of github.com:autoatml/autopl…

4f2dab6

…ex into generalize_data_creation

fix fall backs

a47b1a0

pre-commit auto-fixes

5024809

JaGeo merged commit 960da42 into main Jul 16, 2025
18 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Generalize data creation for RSS workflow#397

Generalize data creation for RSS workflow#397
JaGeo merged 84 commits intomainfrom
generalize_data_creation

JaGeo commented Jun 10, 2025

Uh oh!

YuanbinLiu commented Jul 11, 2025 •

edited

Loading

Uh oh!

JaGeo commented Jul 11, 2025

Uh oh!

YuanbinLiu commented Jul 12, 2025

Uh oh!

JaGeo Jul 15, 2025

Uh oh!

JaGeo commented Jul 15, 2025

Uh oh!

YuanbinLiu commented Jul 16, 2025

Uh oh!

Uh oh!

JaGeo commented Jul 16, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

	if (has_vasp_output and converged) or has_ase_output:
	if has_vasp_output or has_ase_output:

Conversation

JaGeo commented Jun 10, 2025

Uh oh!

YuanbinLiu commented Jul 11, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

JaGeo commented Jul 11, 2025

Uh oh!

YuanbinLiu commented Jul 12, 2025

Uh oh!

JaGeo Jul 15, 2025

Choose a reason for hiding this comment

Uh oh!

JaGeo commented Jul 15, 2025

Uh oh!

YuanbinLiu commented Jul 16, 2025

Uh oh!

Uh oh!

JaGeo commented Jul 16, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

YuanbinLiu commented Jul 11, 2025 •

edited

Loading