Add support for vaspout.h5, improvements to potcar handling #3680

esoteric-ephemera · 2024-03-09T00:06:36Z

Summary

The vaspout.h5 file appears to be a replacement for / supplement to the vasprun.xml file, and has been available in certain VASP versions >= 6. This PR aims to add support for parsing this file.

However the vaspout.h5 file appears to be still in development. For example, no electronic self-consistency info is included in it as of 11 April, 2024, but there is a PR on VASP's py4vasp GH to add OSZICAR info to vaspout.h5

Major changes:

Add support for parsing vaspout.h5 through pymatgen.io.vasp.outputs.Vaspout. This subclasses Vasprun in the spirit that the two should contain roughly the same information now.
Add .from_str method to pymatgen.io.vasp.inputs.Potcar (needed because vaspout.h5 stores the complete potcar as a str)
- To avoid issues of copyright, there's a kwarg, store_potcar, to enable/disable storing the full POTCAR or its just spec
The structure at each ionic_step now has site_properties with the s, p, d,...-resolved and tot charge / magnetization, if applicable. This is the same format as Outcar.charge and Outcar.magnetization, but added as a site property at each ionic step instead of a top-level attr for only the final structure

Some related changes for VASP I/O

Add spec attr to PotcarSingle and Potcar. This standardizes the POTCAR spec attr added to vasprun.xml and vaspout.h5 objects
Add from_spec method to Potcar, which attempts to generate a POTCAR with a consistent functional just from the spec. Note that multiple matches are possible, this only takes the first consistent match.

Todos

Some information currently contained in vasprun.xml appears not to be available in vaspout.h5. That might change in the near future, or I may be mistaken
Support for selective dynamics (if applicable)
Various TODO's sprinkled through current code
Tests

…tcar class, standardize potcar checking

Signed-off-by: Aaron Kaplan <33381112+esoteric-ephemera@users.noreply.github.com>

janosh · 2024-04-11T08:34:01Z

there's going to be a new pmg release soon to close #3744. do we want to get this in before that? let us know if others can help with this PR

Signed-off-by: Aaron Kaplan <33381112+esoteric-ephemera@users.noreply.github.com>

coderabbitai · 2024-04-11T15:47:25Z

Important

Auto Review Skipped

Draft detected.

Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository.

To trigger a single review, invoke the @coderabbitai review command.

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

Share

Tips

Chat

There are 3 ways to chat with CodeRabbit:

Review comments: Directly reply to a review comment made by CodeRabbit. Example:
- I pushed a fix in commit <commit_id>.
- Generate unit testing code for this file.
- Open a follow-up GitHub issue for this discussion.
Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
- @coderabbitai generate unit testing code for this file.
- @coderabbitai modularize this function.
PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
- @coderabbitai generate interesting stats about this repository and render them as a table.
- @coderabbitai show all the console.log statements in this repository.
- @coderabbitai read src/utils.ts and generate unit testing code.
- @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (invoked as PR comments)

@coderabbitai pause to pause the reviews on a PR.
@coderabbitai resume to resume the paused reviews.
@coderabbitai review to trigger a review. This is useful when automatic reviews are disabled for the repository.
@coderabbitai resolve resolve all the CodeRabbit review comments.
@coderabbitai help to get help.

Additionally, you can add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.

CodeRabbit Configration File (`.coderabbit.yaml`)

You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
Please see the configuration documentation for more information.
If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

Visit our Documentation for detailed information on how to use CodeRabbit.
Join our Discord Community to get help, request features, and share feedback.
Follow us on X/Twitter for updates and announcements.

esoteric-ephemera · 2024-04-11T15:58:29Z

This isn't super urgent for release. What I'd like to do is ensure that this works across a wider variety of vaspout's, and make sure that all fields currently included in the vaspout are being mapped correctly to the PMG object

Rn, it doesn't seems like vaspout.h5 has the same level of detail as vasprun.xml so figuring out a way to handle that would also be good

…in Vaspout.ionic_steps

Shibu778

Following features can be included to extract information from one-shot band-structure calculation.

Shibu778 · 2024-04-17T20:51:41Z

pymatgen/io/vasp/outputs.py

+
+
+@requires(h5py is not None, "h5py must be installed to read vaspout.h5")
+class Vaspout(Vasprun):


You can add following parameter and attributes to the class.

dos_kpoints_opt

eigenvalues_kpoints_opt

projectors_kpoints_opt
It will be useful in case of one-shot calculation of bandstructure. Particularly, it is useful while doing HSE calculations (ref), which requires adding the kpoints with fake weights for hartree-fock calculations(ref). One-shot calculations reduces the two step calculations to one-step with two kpoints file, i.e., KPOINTS and KPOINTS_OPT.

Yeah I'll get on this next, will also bring the PR up to date with #3509

Shibu778 · 2024-04-17T22:51:47Z

pymatgen/io/vasp/outputs.py

+        self._parse(parse_dos, parse_eigen, parse_projected_eigen)
+
+    @classmethod
+    def _parse_hdf5_value(cls, val: Any) -> Any:


Instead of parsing the whole vaspout.h5 at once and creating a dictionary. The required information can be parsed directly using the full string as follows.

To extract the ENCUT from the input/incar we can use np.float64(h5_file['input/incar/ENCUT']) or np.float64(h5_file['input']['incar']['ENCUT'])

To extract array like data, use np.array(h5_file[...]), etc

This will not require lot of memory. Only the data needed will be accessed instead of storing the whole file as dictionary in memory. What do you think?

Essentially all attributes of the HDF5 file are accessed by the Vaspout object so I think it's more natural just to read the whole file in as a python dict. This also makes the code cleaner/more consistent than an approach which cherry picks different attr's with different types

First pass add functional Vaspout parser

700d255

esoteric-ephemera requested review from shyuep, janosh and mkhorton as code owners March 9, 2024 00:06

esoteric-ephemera marked this pull request as draft March 9, 2024 00:06

janosh added io Input/output functionality vasp Vienna Ab initio Simulation Package feature PRs with new features, not enhancements to existing features labels Mar 9, 2024

esoteric-ephemera and others added 3 commits March 20, 2024 14:47

Merge branch 'materialsproject:master' into vaspout

6231f44

Add POTCAR spec attrs to standardize spec, add from_spec method to Po…

dbea9d8

…tcar class, standardize potcar checking

pre-commit auto-fixes

31ba296

esoteric-ephemera changed the title ~~Add support for vaspout.h5~~ Add support for vaspout.h5, improvements to potcar handling Mar 21, 2024

esoteric-ephemera and others added 7 commits March 21, 2024 11:07

fix failing lobster tests

4b792ff

pre-commit auto-fixes

c1fde3c

Merge branch 'master' into vaspout

eef3ee3

Signed-off-by: Aaron Kaplan <33381112+esoteric-ephemera@users.noreply.github.com>

pre-commit auto-fixes

99dfb9a

Add Vaspout tests, fix method

e107740

pre-commit and fix test names

6a60d61

fix remaining linting and mypy errors

2cc49ed

Merge branch 'master' into vaspout

4261948

Signed-off-by: Aaron Kaplan <33381112+esoteric-ephemera@users.noreply.github.com>

pre-commit auto-fixes

d6a616b

esoteric-ephemera and others added 5 commits April 11, 2024 10:07

Fix python 3.9 support, add charge and magnetization site_properties …

c3d29d5

…in Vaspout.ionic_steps

pre-commit auto-fixes

5a0c985

Fix projected DOS parsing

dd4fceb

linting / typing

bd6792a

remove dunder methods from potcar spec

aa7c013

Shibu778 reviewed Apr 17, 2024

View reviewed changes

esoteric-ephemera added 4 commits April 26, 2024 13:49

resolve merge conflicts

68ee0ff

linting

ee05396

increase support for auto k point generation

0bafff1

linting

b6427a6

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add support for vaspout.h5, improvements to potcar handling #3680

Add support for vaspout.h5, improvements to potcar handling #3680

esoteric-ephemera commented Mar 9, 2024 •

edited

janosh commented Apr 11, 2024

coderabbitai bot commented Apr 11, 2024

Auto Review Skipped

Chat

CodeRabbit Commands (invoked as PR comments)

CodeRabbit Configration File (`.coderabbit.yaml`)

Documentation and Community

esoteric-ephemera commented Apr 11, 2024

Shibu778 left a comment •

edited

Shibu778 Apr 17, 2024

esoteric-ephemera Apr 29, 2024

Shibu778 Apr 17, 2024

esoteric-ephemera Apr 29, 2024



		@requires(h5py is not None, "h5py must be installed to read vaspout.h5")
		class Vaspout(Vasprun):

Add support for vaspout.h5, improvements to potcar handling #3680

Are you sure you want to change the base?

Add support for vaspout.h5, improvements to potcar handling #3680

Conversation

esoteric-ephemera commented Mar 9, 2024 • edited

Summary

Some related changes for VASP I/O

Todos

janosh commented Apr 11, 2024

coderabbitai bot commented Apr 11, 2024

Auto Review Skipped

Chat

CodeRabbit Commands (invoked as PR comments)

CodeRabbit Configration File (.coderabbit.yaml)

Documentation and Community

esoteric-ephemera commented Apr 11, 2024

Shibu778 left a comment • edited

Choose a reason for hiding this comment

Shibu778 Apr 17, 2024

Choose a reason for hiding this comment

esoteric-ephemera Apr 29, 2024

Choose a reason for hiding this comment

Shibu778 Apr 17, 2024

Choose a reason for hiding this comment

esoteric-ephemera Apr 29, 2024

Choose a reason for hiding this comment

esoteric-ephemera commented Mar 9, 2024 •

edited

CodeRabbit Configration File (`.coderabbit.yaml`)

Shibu778 left a comment •

edited