FHI-aims IO Parsers #3435

tpurcell90 · 2023-10-30T20:12:13Z

Summary

Creates an FHI-aims interface for pymatgen based off of the ASE parser and input generating structures. Part of this work was done in atomate2 originally for this PR (materialsproject/atomate2#562) where @ansobolev contributed.

This PR was made by the request of atomate2 so the IO can remain with pymatgen and not in that repoistory.

Major changes:

feature 1: IO objects for FHI-aims

Todos

Check how stress is stored as a property in structure
Confirm naming consistency
Convert doc strings from numpy format to Google format
Double check all type annotations are present

Checklist

Google format doc strings added. Check with ruff.
Type annotations included. Check with mypy.
Tests added for new features/fixes.
If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

1) parsers and AimsOuput ojbects moved over 2) All ASE Atoms objects removed in favor of pymatgen structures 3) TO DO: Check name schemes 4) Create an AimsInputs object in the future

1) remove aims_outputs naming convention 2) Add AimsGeometryIn and AimsControlIn classes

Adjusted from ASE parser tests

1) How to handle stress in properties?

For aims outputs checks

Test for both Si and H2O

Make sure that the AimsCubes are properly formatted

Add test for aims control.in file generators

tests/io/aims/aims_input_files/control.in.h2o

as requested all output files are gzipped

1) Species blocks can now read from gzipped file 2) geometry.in can now read a gzip file

Error in the Actions from rounding errors, do more explicit test for as_dict

1) Docstrings are googledoc format 2) All type hinting is done

Everything is also type hintted now

tpurcell90 · 2023-11-02T06:31:39Z

I think everything is now typehinted with google docstrings

JaGeo · 2023-11-02T20:45:46Z

@janosh I think this is ready to review as well

Forgot pip install in the last commit

tpurcell90 · 2023-11-03T07:38:31Z

Tests should now work

tpurcell90 · 2023-11-05T07:05:49Z

I updated to master if those changes are needed for the docker images (errors are in tests I did not touch)

janosh

Nice work @tpurcell90! 👍 🚀

Left a few comments.

tests/io/aims/test_aims_parsers.py

tests/io/aims/test_aims_inputs.py

1) Moved lines objects to seperate files 2) inline k_point_weights 3) Remove trailing comma 4) tmpdir -> tmp_path

tpurcell90 · 2023-11-07T10:11:34Z

Do we need to write a tutorial for the aims IO or are the docstrings good enough?

tpurcell90 · 2023-11-07T11:17:56Z

Also do I update the ChangeLog in a commit or is this done by the maintainers?

janosh · 2023-11-07T14:48:27Z

Do we need to write a tutorial for the aims IO or are the docstrings good enough?

You are very welcome to write a tutorial! 👍 Were you thinking a Jupyter notebook? I've been thinking about starting a /examples folder with tutorial notebooks in pymatgen.

Also do I update the ChangeLog in a commit or is this done by the maintainers?

We'll handle that.

pymatgen/io/aims/inputs.py

use numpy eye instead of a full list Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com> Signed-off-by: Thomas Purcell <tpurcell90@users.noreply.github.com>

tpurcell90 · 2023-11-07T15:06:35Z

Do we need to write a tutorial for the aims IO or are the docstrings good enough?

You are very welcome to write a tutorial! 👍 Were you thinking a Jupyter notebook? I've been thinking about starting a /examples folder with tutorial notebooks in pymatgen.

Also do I update the ChangeLog in a commit or is this done by the maintainers?

We'll handle that.

Ya I was thinking a basic jupyter notebook. I'll take a look at the examples tomorrow and make one up in the office (I am doing data transfer so I am not bringing my work computer home with me this week)

Keep it consistent with inputs naming scheme

tpurcell90 · 2023-11-08T12:43:17Z

Do we need to write a tutorial for the aims IO or are the docstrings good enough?

You are very welcome to write a tutorial! 👍 Were you thinking a Jupyter notebook? I've been thinking about starting a /examples folder with tutorial notebooks in pymatgen.

Also do I update the ChangeLog in a commit or is this done by the maintainers?

We'll handle that.

Ya I was thinking a basic jupyter notebook. I'll take a look at the examples tomorrow and make one up in the office (I am doing data transfer so I am not bringing my work computer home with me this week)

I added an example file. I think everything is finished now

examples/aims_io/species_dir/14_Si_default.gz

pymatgen/io/aims/inputs.py

tests/io/aims/test_aims_inputs.py

1) Remove copy of species file in examples 2) Typo corrections in docstrings 3) d -> dct for `from_dict` methods 4) error mesages for AimsCube 5) Shortened default checks in Inputs 6) Removal of chdir in tests

…ut_files tests/io/aims/(aims_->'')parser_checks

janosh

Thanks so much @tpurcell90! This was a big PR with nice docs and excellent test coverage, esp. for a 1st-time contributor! 👍

tpurcell90 · 2023-11-08T19:46:45Z

No problem happy to add this into pymatgen! @janosh thanks for reviewing this!

aims.output -> aims.outputs module name

tpurcell90 · 2023-11-08T19:57:33Z

Corrected the module name in the test ref files, all tests should now pass. I forgot to do a final clean install of pymatgen when I made the names of the modules consistent.

tpurcell90 added 8 commits October 23, 2023 16:24

Move FHI-aims io from atomate2 into pymatgen

8c677be

1) parsers and AimsOuput ojbects moved over 2) All ASE Atoms objects removed in favor of pymatgen structures 3) TO DO: Check name schemes 4) Create an AimsInputs object in the future

Initial aims input files

3b152d1

1) remove aims_outputs naming convention 2) Add AimsGeometryIn and AimsControlIn classes

Add test for the aims parsers

e3d1daa

Adjusted from ASE parser tests

Add tests for AimsOutputs

b311ac4

1) How to handle stress in properties?

Add aims output refrence files

2088fc8

For aims outputs checks

Add tests for AimsGeometryIn inputs

ea95182

Test for both Si and H2O

Add tests for AimsCube

41ac7bd

Make sure that the AimsCubes are properly formatted

Add tests for aims_control_in

d9e3041

Add test for aims control.in file generators

tpurcell90 mentioned this pull request Oct 30, 2023

Add FHI-aims DFT calculator materialsproject/atomate2#562

Merged

5 tasks

janosh requested changes Oct 30, 2023

View reviewed changes

tests/io/aims/aims_input_files/control.in.h2o Outdated Show resolved Hide resolved

tpurcell90 added 6 commits October 31, 2023 06:52

gzip all output files

9da0f6f

as requested all output files are gzipped

Gzip all refrence files

e633e6f

1) Species blocks can now read from gzipped file 2) geometry.in can now read a gzip file

Remove json dict comparision

4e390f6

Error in the Actions from rounding errors, do more explicit test for as_dict

Add full type hinting for inputs.py and convert docstrings

7d85afd

1) Docstrings are googledoc format 2) All type hinting is done

Convert all AimsOutput docstrings to google doc

168baba

Everything is also type hintted now

Add type hining and google doc strings to parsers

0406a95

Fix tests

0d368cd

Forgot pip install in the last commit

janosh added enhancement A new feature or improvement to an existing one io Input/output functionality labels Nov 5, 2023

Merge branch 'master' into aims_io

ff1a7ff

janosh requested changes Nov 6, 2023

View reviewed changes

tpurcell90 added 2 commits November 7, 2023 11:08

Requested changes to tests

ed4e09c

1) Moved lines objects to seperate files 2) inline k_point_weights 3) Remove trailing comma 4) tmpdir -> tmp_path

Merge branch 'aims_io' of github.com:tpurcell90/pymatgen into aims_io

7f5c675

janosh requested changes Nov 7, 2023

View reviewed changes

pymatgen/io/aims/inputs.py Outdated Show resolved Hide resolved

pymatgen/io/aims/inputs.py Outdated Show resolved Hide resolved

pymatgen/io/aims/inputs.py Outdated Show resolved Hide resolved

pymatgen/io/aims/inputs.py Outdated Show resolved Hide resolved

Update pymatgen/io/aims/inputs.py

9c8b42c

use numpy eye instead of a full list Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com> Signed-off-by: Thomas Purcell <tpurcell90@users.noreply.github.com>

pre-commit-ci bot and others added 5 commits November 7, 2023 15:06

pre-commit auto-fixes

a5823bb

Make more changes requested

6da5e9d

Merge branch 'master' into aims_io

90968cc

Rename io.aims.output to io.aims.outputs

bc0b4d6

Keep it consistent with inputs naming scheme

Add example for FHI-aims io

c82cd43

Merge branch 'master' into aims_io

0a36fef

janosh requested changes Nov 8, 2023

View reviewed changes

tpurcell90 and others added 9 commits November 8, 2023 20:14

Make corrections suggested by @janosh

3adc5cc

1) Remove copy of species file in examples 2) Typo corrections in docstrings 3) d -> dct for `from_dict` methods 4) error mesages for AimsCube 5) Shortened default checks in Inputs 6) Removal of chdir in tests

Merge branch 'aims_io' of github.com:tpurcell90/pymatgen into aims_io

5f37cff

add nbstripout to pre-commit hooks apply to FHI-aims-example.ipynb

7761e4a

class AimsCube snake_case spin_state

d457393

fix doc str

5c2e354

refactor AimsCube.from_dict

ad24261

fix typo

2756467

fix tests

b45b71f

mv tests/io/aims/(aims_->'')input_files tests/io/aims/(aims_->'')outp…

1563c82

…ut_files tests/io/aims/(aims_->'')parser_checks

janosh approved these changes Nov 8, 2023

View reviewed changes

janosh enabled auto-merge (squash) November 8, 2023 19:40

Correct refrence json files for aims_outputs

89c29a9

aims.output -> aims.outputs module name

auto-merge was automatically disabled November 8, 2023 19:56
Head branch was pushed to by a user without write access

janosh enabled auto-merge (squash) November 8, 2023 20:04

janosh merged commit d4e253d into materialsproject:master Nov 8, 2023
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FHI-aims IO Parsers #3435

FHI-aims IO Parsers #3435

tpurcell90 commented Oct 30, 2023 •

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tpurcell90 commented Nov 8, 2023

FHI-aims IO Parsers #3435

FHI-aims IO Parsers #3435

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tpurcell90 commented Oct 30, 2023 • edited Loading

Summary

Todos

Checklist

tpurcell90 commented Nov 2, 2023

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tpurcell90 commented Oct 30, 2023 •

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