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PR_kwDOACgets5-JfDv
| 4,099
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Ion: bugfix for CO2(aq) reduced formula
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[] | 2024-10-10T01:57:56
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2024-10-10T18:48:08Z
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CONTRIBUTOR
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My recent changes to `Ion` in #3991 introduced a problem in which the `reduced_formula` of `CO2(aq)` would incorrectly be shown as `C2O4(aq)`. Other properties such as `composition` etc were not affected.
```
>>> from pymatgen.core.ion import Ion
>>> Ion.from_formula('CO2').composition
Composition('C1 O2')
>>> Ion.from_formula('CO2').formula
'C1 O2 (aq)'
>>> Ion.from_formula('CO2').reduced_formula
'C2O4(aq)'
>>> Ion.from_formula('C2O4[-2]').composition
Composition('C2 O4')
>>> Ion.from_formula('C2O4[-2]').formula
'C2 O4 -2'
>>> Ion.from_formula('C2O4[-2]').reduced_formula
'C2O4[-2]'
```
This PR fixes the CO2(aq) problem and adds tests.
|
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Support python3.13
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[
"might close this one now as too many packages don't support python 3.13, feel free to take over this",
"Also cannot recreate the `Windows fatal exception: access violation` failure on my Windows machine (https://github.com/pytest-dev/pytest/issues/7634)",
"I'm pretty much stuck with the Windows runner failure, **help needed**\r\n\r\n- Cannot recreate locally with `pytest --splits 10 --group 1 --durations-path tests/files/.pytest-split-durations tests`\r\n- Cannot find much useful info, according to: https://github.com/pytest-dev/pytest/issues/12728 \r\n > this is certain to be a bug in one (or several) other libraries.\r\n\r\n As there're too many dependencies in `pymatgen`, it's super hard to identify which \"may\" have caused this failure",
"Would close this and open a new PR once #4361 is merged, this PR has been around for too long and I cannot remember everything here (plus most changes are related to pybtex)"
] | 2024-10-10T04:44:06
| 2025-04-17T20:00:42
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2025-04-17T20:00:24Z
|
CONTRIBUTOR
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### Summary
- Support python 3.13, to close #4284
- [ ] Remove all `pybtex` check after #4361
- [ ] Need to fix the EOS test failure on Ubuntu 3.13 (seemingly related to numerical precision but cannot recreate locally)
- [ ] Revert all platforms tested on Python 3.13 in `test.yml` test matrix (c9cc898301a7198488de660829a63ea62fafef3a)
#### Optional dependencies that miss Python 3.13 support:
- [ ] `openff-toolkit` (conda source)
- [ ] `chgnet`
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PR_kwDOACgets5-Ku55
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|
bump `chgnet` to support numpy 2, skip failing `matgl` test for `torch` 2.4.1
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[
"[The unit test failure](https://github.com/materialsproject/pymatgen/actions/runs/11269124025/job/31337138014?pr=4101):\r\n> E FileNotFoundError: Cannot find DGL C++ graphbolt library at /home/runner/micromamba/envs/pmg/lib/python3.12/site-packages/dgl/graphbolt/libgraphbolt_pytorch_2.4.1.so\r\n\r\nSeem to be related to DGL doesn't have that particular shared object for torch 2.4.1:\r\n```\r\n~/opt/miniconda3/envs/pymatgen/lib/python3.12/site-packages/dgl/graphbolt$ ls libgraphbolt_pytorch_2.*\r\nlibgraphbolt_pytorch_2.0.0.so libgraphbolt_pytorch_2.1.0.so libgraphbolt_pytorch_2.1.2.so libgraphbolt_pytorch_2.2.1.so\r\nlibgraphbolt_pytorch_2.0.1.so libgraphbolt_pytorch_2.1.1.so libgraphbolt_pytorch_2.2.0.so\r\n```\r\n\r\nshould be related to https://github.com/dmlc/dgl/issues/7247 and https://github.com/materialsvirtuallab/matgl/issues/296\r\n\r\n\r\n```\r\ndgl==2.1.0\r\nmatgl==1.1.3\r\n```",
"Since chgnet is already implemented in matgl, I would rather we unify support for everything that matgl supports using matgl. ",
"Great to know, thanks! But I don't any experience with matgl or chgnet, perhaps need someone with more expertise on this to migrate the implementation"
] | 2024-10-10T06:13:02
| 2024-10-22T03:03:58
|
2024-10-22T02:41:39Z
|
CONTRIBUTOR
|
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### Summary
- Bump `chgnet` to support Numpy2
### Conflicting `torch` version
- `chgnet 0.4.0` requires `torch > 2.4.1` to be NumPy2 compatible https://github.com/CederGroupHub/chgnet/pull/202#discussion_r1756944575
- `matgl` requires `torch <= 2.2.1` for `dgl` to work correctly https://github.com/materialsproject/pymatgen/pull/4101#issuecomment-2404278607
Should we skip two failing tests for `matgl` here as I assume this should be fixed from the `dgl` side?
Input appreciated.
|
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PR_kwDOACgets5-ME_8
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|
pin python 3.12 in CI and `requires-python`
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[
"The last set of tests never started. Thus, we are stuck here. Any thoughts, @DanielYang59 ?",
"> The last set of tests never started. Thus, we are stuck here. \r\n\r\nI don't know the exact reason, ~~but my guess is the unstarted set is the cached set for our current config (python > 3.10 for Ubuntu). As the finished number of tests is exactly what we asked ` 42 successful, 1 skipped, and 10 expected checks `, the last 10 expected checks look like some kind of \"ghost\" from previous cache. The [check panel](https://github.com/materialsproject/pymatgen/pull/4102/checks), however, does reflect this real number of tests required.~~\r\n\r\nI didn't find any related reports in GitHub Community so I might open one later, https://github.com/orgs/community/discussions/141301",
"@DanielYang59 @JaGeo I think that the branch protection rules require a check under the name `test (ubuntu-latest, >3.10, lowest-direct, ci,optional)` to pass (hence the \"Required\" tag at the end of the line) but since that doesn't exist anymore so it can't report its status. I saw the same thing in one of my projects. The only workaround I know is to temporarily remove that rule from the repo setting. ",
"@ab5424 Bravo! you are the savior.\r\n\r\n> I think that the branch protection rules require a check under the name\r\n\r\nI don't have write access to the repo, but sounds like the branch protection rules are dynamically generated based the test matrix config **from the master branch**?\r\n\r\n> The only workaround I know is to temporarily remove that rule from the repo setting.\r\n\r\nMaintainers should be able to do a manual (force) merge not using auto-merge? @shyuep \r\n\r\n",
"For some reason I'm still seeing \"ghost\" expected checks from other PR where the config should have been updated on master branch, perhaps the branch protection rule is hard coding to expect `ubuntu-latest, >3.10`? I cannot check myself as I don't have access "
] | 2024-10-10T09:06:01
| 2024-12-24T12:17:44
|
2024-10-21T20:58:32Z
|
CONTRIBUTOR
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### Summary
- Pin Python 3.12 in CI for now, as it seems a lot of dependencies don't support Python 3.13 yet #4100
|
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PR_kwDOACgets5-QPRE
| 4,103
|
Support to aims format from Structure instance
|
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[
"Thanks!"
] | 2024-10-10T17:45:19
| 2024-10-15T10:29:47
|
2024-10-10T18:35:49Z
|
CONTRIBUTOR
|
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## Summary
This pull request adds support for reading and writing files in FHI-aims `geometry.in` format to the `Structure` objects.
Major changes:
- Support for reading `geometry.in` file in `Structure.from_file` and `Structure.from_str` methods
- Support for writing FHI-aims formatted file in `Structure.to` method
## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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PR_kwDOACgets5-YxZo
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VASP Bugfixes: Volumetric data and XDATCAR parsing for monatomic structures
|
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[
"@shyuep and @mkhorton should be ready for review whenever you have time. I had to make some version changes to linting / testing in CI to get the tests to set up correctly and run (newer version of mypy throws a lot of errors that should be handled separately and the linux build failed because of py3.13)",
"Thanks. This looks good to me. Merged."
] | 2024-10-11T23:23:35
| 2024-11-15T18:08:49
|
2024-10-14T18:37:42Z
|
CONTRIBUTOR
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Two bug fixes:
- For VASP 6.4.2 and up, all POSCAR-style strings include both the POTCAR symbol (e.g., `Mg_pv` rather than the elemental symbol `Mg`) and part of the POTCAR hash (`Si/79d9987ad87` rather than `Si`). While the hashing is already accounted for, the underscore was not. Fixed here, impacts CONTCAR and all volumetric data (CHGCAR, LOCPOT, AECCAR*)
- For any monatomic XDATCAR where the title of the POSCAR substring is the same as the single chemical species, the XDATCAR parsing functionality of pymatgen doesn't work. This PR fixes that behavior, adds a test for it, and cleans up the XDATCAR parsing a bit
|
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PR_kwDOACgets5-aBSL
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Replace deprecated `ExpCellFilter` with `FrechetCellFilter`
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[
"Thanks for this @ab5424, appreciate you expanding the type hint too!",
"Still issues with these ghost tests",
"I minor head up though, the `ExpCellFilter` -> `FrechetCellFilter` change is more than an API migration, but involved behaviour change (sounds more like a bug fix), see [the implementation note](https://wiki.fysik.dtu.dk/ase/_modules/ase/filters.html) of `FrechetCellFilter`:\r\n> The initial implementation of ExpCellFilter gave inconsistent gradients\r\n for cell variables (matrix log of the deformation tensor). If you would\r\n like to keep the previous behavior, please use ExpCellFilter.\r\n\r\nI don't have enough knowledge in this regard to make meaningful comment though, just a gentle warning.\r\n",
"@DanielYang59 Yes, results might be different but better. Thus, it is an important change."
] | 2024-10-12T11:08:48
| 2024-10-22T21:47:17
|
2024-10-22T03:05:20Z
|
CONTRIBUTOR
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## Summary
Major changes:
- Replace deprecated `ase` `ExpCellFilter` with `FrechetCellFilter` for structure relaxation.
- `pre-commit` complained about outdated configuration so I updated it.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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I_kwDOACgets6Z9Nvk
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Replace POTCAR in MPRelaxSet
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[
"Yes this impacts compatibility with the Materials Project entries. You can use the `MPScanRelaxSet` which uses the PBE_54 pseudopotentials and will be compatible with the newer materials project r2SCAN data",
"Ok, thank you. I see. "
] | 2024-10-12T12:46:24
| 2024-10-14T17:05:57
|
2024-10-14T17:05:57Z
|
NONE
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### Feature Requested
When users run MPGGARelax or any other workflow requiring MPRelaxSet, and the structures contain elements like tungsten (W), they encounter a "POTCAR not found" error. This issue arises because the newer PBE 54 pseudopotential set no longer includes W_pv, which is still expected by MPRelaxSet. However, I am unsure if replacing W_pv with the newer W potential affects the compatibility of the results with those generated by the Materials Project.
### Proposed Solution
Update MPRelaxSet
### Relevant Information
_No response_
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PR_kwDOACgets5-cJKk
| 4,107
|
Properly test `ase` not installed error, use single `skip` mark for module level test skip
|
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[] | 2024-10-13T06:19:25
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2024-10-21T20:56:22Z
|
CONTRIBUTOR
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### Summary
- Properly test `ase` not installed error, the original test would not actually run because `ase` is installed in CI (ideally the test should be independent of whether that package is installed or not)
- Also fix not installed test for `seekpath` in `io.pwmat.inputs`
- Use module level skip when package not available
|
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I_kwDOACgets6aGurQ
| 4,108
|
pmg plot --dos ... errs in matplotlib call
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[
"Thanks for reporting this, this should be related to the change in return type from figure to axes in #3237. I would fix this."
] | 2024-10-14T09:47:55
| 2024-10-21T20:52:56
|
2024-10-21T20:52:56Z
|
CONTRIBUTOR
|
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### Python version
3.12.7
### Pymatgen version
2024.10.3
### Operating system version
_No response_
### Current behavior
```bash
pmg plot -d vasprun.xml --out_file dos.png
```
yields
```bash
Traceback (most recent call last):
File "/home/yantar92/Downloads/Nio.DOS/.venv/bin/pmg", line 8, in <module>
sys.exit(main())
^^^^^^
File "/home/yantar92/Downloads/Nio.DOS/.venv/lib/python3.12/site-packages/pymatgen/cli/pmg.py", line 448, in main
return args.func(args)
^^^^^^^^^^^^^^^
File "/home/yantar92/Downloads/Nio.DOS/.venv/lib/python3.12/site-packages/pymatgen/cli/pmg_plot.py", line 107, in plot
plt.savefig(args.out_file)
^^^^^^^^^^^
AttributeError: 'Axes' object has no attribute 'savefig'
```
### Expected Behavior
The DOS plot is generated.
### Minimal example
```Python
pip install matplotlib
cd /path/to/vasp/results
pmg plot -d vasprun.xml --out_file dos.png
```
I suspect that my Matplotlib Version: 3.9.2 might have changes in the API.
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets5-hFbb
| 4,109
|
Fix `savefig` in `pmg.cli.plot`
|
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[] | 2024-10-14T10:06:01
| 2024-10-22T02:09:25
|
2024-10-21T20:52:55Z
|
CONTRIBUTOR
|
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### Summary
- Fix `savefig` in pmg.cli.plot, to close #4108
- [x] Add unit test
- [x] Confirm `matplotlib` versions (oldest supported matplotlib 3.8 works)
- Split tests for `cli` module
- Fix `test_pkg` to use the `src` layout path
|
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PR_kwDOACgets5-h1Am
| 4,110
|
Remove all `no_type_check` mark, fix new `mypy` error in `1.12.0`
|
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[] | 2024-10-14T11:24:33
| 2024-11-02T03:02:58
|
2024-10-21T20:57:41Z
|
CONTRIBUTOR
|
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### Summary
- Remove all `no_type_check` mark, follow up #4109
- Fix new `mypy` errors in CI after [the `1.12.0` release](https://github.com/python/mypy/releases/tag/v1.12.0)
|
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PR_kwDOACgets5-qSov
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|
Add support for `use_structure_charge` keyword in FHI-aims input generator
|
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[
"Looks good to me!",
"Thanks."
] | 2024-10-15T11:25:30
| 2024-10-22T09:40:52
|
2024-10-21T20:55:12Z
|
CONTRIBUTOR
|
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## Summary
This PR adds support of `use_structure_charge` keyword to a base FHI-aims input generator to make it more consistent with VASP and `atomate2` common defect workflows.
Major changes:
- support of `use_structure_charge` keyword to a base FHI-aims input generator
## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
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I_kwDOACgets6aWhL1
| 4,112
|
Vampire_interface (pymatgen/analysis/magnetism/heisenberg.py:323:)
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[] | 2024-10-15T18:47:27
| 2024-11-12T18:02:07
|
2024-11-12T18:02:07Z
|
NONE
|
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### Python version
python 3.10
### Pymatgen version
2024.10.3
### Operating system version
ubuntu 20.04lts
### Current behavior
pymatgen/analysis/magnetism/heisenberg.py:323: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
temp_df = pd.concat([ex_mat, ex_row], ignore_index=True)
/home/ssd/.local/lib/python3.10/site-packages/pymatgen/analysis/magnetism/heisenberg.py:328: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
ex_mat = pd.concat([ex_mat, ex_row], ignore_index=True)
### Expected Behavior
pymatgen/analysis/magnetism/heisenberg.py:323: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
temp_df = pd.concat([ex_mat, ex_row], ignore_index=True)
/home/ssd/.local/lib/python3.10/site-packages/pymatgen/analysis/magnetism/heisenberg.py:328: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
ex_mat = pd.concat([ex_mat, ex_row], ignore_index=True)
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets5-04qu
| 4,113
|
Fix arg passing in `inverse` property of `SymmOp`
|
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[] | null |
[] | 2024-10-16T12:52:36
| 2024-10-22T02:07:04
|
2024-10-21T20:54:56Z
|
CONTRIBUTOR
|
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### Summary
- Fix arg passing in `inverse` property of `SymmOp`, to fix #4023
- Replace some `np.array` with `np.asarray` for efficiency where we don't rely on creating a copy
|
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I_kwDOACgets6ak--_
| 4,114
|
`io.pwscf.PWInput.from_file()` incorrectly reads decimal numbers and the `K_POINTS` card in `automatic` mode
|
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[
"Seems there is one more bug in parsing `K_POINTS` card, adding that to this issue"
] | 2024-10-17T01:38:04
| 2024-10-21T20:54:32
|
2024-10-21T20:54:32Z
|
CONTRIBUTOR
|
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### Python version
Python 3.12.4
### Pymatgen version
2024.10.3
### Operating system version
Ubuntu 22.04.5 LTS
### Current behavior
The `io.pwscf.PWInput.from_file()` method fails to correctly parse:
- decimal numbers written in scientific notation with exponent part prefixed with `e` or `E` (note that as of QE v7.3, `pw.x` can still parse such cases correctly; i.e., exponent prefix need not be `d`), and
- the `K_POINTS` card with mode set to `automatic`.
**Example input file `scf.in`:**
```
&CONTROL
calculation = 'scf',
/
&SYSTEM
ecutwfc = 100,
ibrav = 0,
nat = 2,
ntyp = 1,
/
&ELECTRONS
conv_thr = 2e-12, ! same behavior with 2E-12
/
ATOMIC_SPECIES
C 12.0107 C.upf
ATOMIC_POSITIONS crystal
C 0.2500000000 0.2500000000 0.2500000000
C -0.0000000000 -0.0000000000 0.0000000000
K_POINTS automatic
4 4 4 1 1 1
CELL_PARAMETERS angstrom
-1.786119886 0.000000000 1.786119886
-0.000000000 1.786119886 1.786119886
-1.786119886 1.786119886 0.000000000
```
**Current behavior:**
```
>>> from pymatgen.io.pwscf import PWInput
>>> pwi = PWInput.from_file("scf.in")
>>> print(pwi.sections["electrons"]["conv_thr"])
2.0
>>> print(pwi.kpoints_grid, pwi.kpoints_shift)
(1, 1, 1) (0, 0, 0)
```
### Expected Behavior
I expect both the `conv_thr` value and the `K_POINTS` card in the above example input file to be parsed correctly.
```
>>> from pymatgen.io.pwscf import PWInput
>>> pwi = PWInput.from_file("scf.in")
>>> print(pwi.sections["electrons"]["conv_thr"])
2e-12
>>> print(pwi.kpoints_grid, pwi.kpoints_shift)
(4, 4, 4) (1, 1, 1)
```
### Minimal example
```Python
contents = """&CONTROL
calculation = 'scf',
/
&SYSTEM
ecutwfc = 100,
ibrav = 0,
nat = 2,
ntyp = 1,
/
&ELECTRONS
conv_thr = 2e-12, ! same behavior with 2E-12
/
ATOMIC_SPECIES
C 12.0107 C.upf
ATOMIC_POSITIONS crystal
C 0.2500000000 0.2500000000 0.2500000000
C -0.0000000000 -0.0000000000 0.0000000000
K_POINTS automatic
4 4 4 1 1 1
CELL_PARAMETERS angstrom
-1.786119886 0.000000000 1.786119886
-0.000000000 1.786119886 1.786119886
-1.786119886 1.786119886 0.000000000
"""
with open("scf.in", "w") as fp:
fp.write(contents)
from pymatgen.io.pwscf import PWInput
pwi = PWInput.from_file("scf.in")
print(pwi.sections["electrons"]["conv_thr"]) # Prints "2.0", should print "2e-12"
print(pwi.kpoints_grid, pwi.kpoints_shift) # Prints "(1, 1, 1) (0, 0, 0)", should print "(4, 4, 4) (1, 1, 1)"
```
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets5-53uc
| 4,115
|
Bugfix: Parsing bugs in `io.pwscf.PWInput`
|
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[
"Thanks."
] | 2024-10-17T01:46:36
| 2024-10-21T20:54:35
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2024-10-21T20:54:31Z
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CONTRIBUTOR
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## Summary
A quick regexp fixes + strengthened test cases to close #4114
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PR_kwDOACgets5-6LhP
| 4,116
|
bump `networkx` to 2.7 to fix intermittent CI failure when `torch` install failed: `ImportError: cannot import name 'Mapping' from 'collections'`
|
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[] | null |
[
"Happened again in https://github.com/materialsproject/pymatgen/actions/runs/11383942907/job/31670629571",
"Looks like networkx 2.7 [causes test failure in MacOS CI](https://github.com/materialsproject/pymatgen/actions/runs/11432515352/job/31803122891) (if `torch` install failed of course), might need to bump it even further, sorry for the overlook (I tested on Ubuntu and thought MacOS would behave more or less the same):\r\n```\r\n> P = np.array(basis_change, dtype=float).T[0]\r\nE TypeError: MatrixBase.__array__() takes 1 positional argument but 2 were given\r\n```\r\n\r\n",
"Okay I was wrong here, it has nothing to do with `networkx 2.7`, it's `sympy 1.2` that causing this failure, and looks like we need to bump `sympy` to `>=1.3` to avoid this, I would do this in #4128.\r\n\r\n```\r\n>>> python3 --version\r\nPython 3.11.10\r\n\r\n>>> pip freeze | grep networkx\r\nnetworkx==2.7\r\n\r\n>>> pip install sympy==1.2\r\n>>> pytest tests/symmetry/test_maggroups.py\r\n\r\nFFFFFFF [100%]\r\n=============================================================================== FAILURES ================================================================================\r\n... (all failed)\r\n7 failed in 0.81s\r\n\r\n\r\n>>> pip install sympy==1.3\r\n\r\n....... [100%]\r\n\r\n(14 durations < 0.005s hidden. Use -vv to show these durations.)\r\n7 passed in 1.30s\r\n```\r\n\r\n"
] | 2024-10-17T03:08:29
| 2024-10-22T05:46:56
|
2024-10-21T20:52:35Z
|
CONTRIBUTOR
|
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### Summary
- Bump `networkx` to resolve [the following intermittent CI failure](https://github.com/materialsproject/pymatgen/actions/runs/11377302114/job/31651207689):
```
../../../micromamba/envs/pmg/lib/python3.11/site-packages/networkx/__init__.py:100: in <module>
import networkx.classes.filters
../../../micromamba/envs/pmg/lib/python3.11/site-packages/networkx/classes/__init__.py:1: in <module>
from .graph import Graph
../../../micromamba/envs/pmg/lib/python3.11/site-packages/networkx/classes/graph.py:23: in <module>
from collections import Mapping
E ImportError: cannot import name 'Mapping' from 'collections' (/Users/runner/micromamba/envs/pmg/lib/python3.11/collections/__init__.py)
```
networkx `3.4.1` is usually installed in CI:
> Collecting networkx (from torch==2.2.1)
Downloading networkx-3.4.1-py3-none-any.whl.metadata (6.3 kB)
But it might [fall back to very old versions (`networkx 2.2`) if torch install is unsuccessful](https://github.com/materialsproject/pymatgen/actions/runs/11377302114/job/31651207689), leading to above import failure, as after Python 3.10 the `Mapping `class has been moved to the [collections.abc](https://docs.python.org/3/library/collections.abc.html#collections.abc.Mapping) module. :
> Downloading torch-2.2.1-cp311-none-macosx_11_0_arm64.whl (59.7 MB)
━━━━━━━━━━━━╸ 18.9/59.7 MB 113.1 MB/s eta 0:00:01
> + networkx==2.2
---
For **networkx 2.3**, I got the following (with Python 3.12.7):
```
venv312/lib/python3.12/site-packages/networkx/algorithms/dag.py:23: in <module>
from fractions import gcd
E ImportError: cannot import name 'gcd' from 'fractions' (/usr/lib/python3.12/fractions.py)
```
**2.4-2.5 (2.6 yanked):**
```
venv312/lib/python3.12/site-packages/networkx/readwrite/graphml.py:345: in GraphML
(np.float16, "float"), (np.float_, "float"),
venv312/lib/python3.12/site-packages/numpy/__init__.py:397: in __getattr__
raise AttributeError(
E AttributeError: `np.float_` was removed in the NumPy 2.0 release. Use `np.float64` instead.. Did you mean: 'float16'?
```
2.7 seems to be the oldest working version at this moment.
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PR_kwDOACgets5-861J
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Migrate `ext.COD` from `mysql` to REST API
|
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[] | null |
[
"Thanks.",
"No problem, thanks for reviewing and for original bringing up the idea to migrate to REST API"
] | 2024-10-17T11:03:58
| 2024-10-22T02:08:11
|
2024-10-21T20:54:02Z
|
CONTRIBUTOR
|
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### Summary
- Migrate `ext.COD` from `mysql` to REST API, to close #4016
- [**Deprecation**] Deprecate `timeout` arg from `get_structure_by_id` method and use a single class level `timeout`
- [x] suppress timeout error in CI
|
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Support Pymatgen Species object in aims
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[] | 2024-10-17T12:36:36
| 2024-10-22T09:41:25
|
2024-10-22T02:39:35Z
|
CONTRIBUTOR
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## Summary
As of now, the basis set for the site in FHI-aims input files got chosen according to the site element. This PR enables the support of Species object when present in the structure, which should make setting up heterogeneous calculations with FHI-aims and Pymatgen easier.
Major changes:
- Support for `species_string` in `SpeciesDefaults` class added
- Simplified creating string representation for `geometry.in` file, adding support for `species_string` there as well
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I_kwDOACgets6apw25
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VaspInput setter and Incar.check_params() are inconsistent
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[
"Thanks for reporting this, I believe the warning on `GGA=PS` is owing to: https://github.com/materialsproject/pymatgen/blob/4f7aa35f15cb17a89209b955903c64b39e2fa922/src/pymatgen/io/vasp/inputs.py#L988\r\n\r\nI.e. any keyword not included inside the following and is not `boolean/float/int` (`str`) would be capitalized: https://github.com/materialsproject/pymatgen/blob/4f7aa35f15cb17a89209b955903c64b39e2fa922/src/pymatgen/io/vasp/inputs.py#L876-L932\r\n\r\n---\r\n\r\nThe warning on `ENCUT=550` should be owing to the incorrect classification of it into `int_keys` instead of `float_keys`: https://github.com/materialsproject/pymatgen/blob/4f7aa35f15cb17a89209b955903c64b39e2fa922/src/pymatgen/io/vasp/inputs.py#L910-L924\r\n\r\nI believe [it should be a float](https://www.vasp.at/wiki/index.php/ENCUT):\r\n> ENCUT = [real] \r\n\r\n",
"With Version: 2024.10.22, I am still getting\r\n\r\n```\r\n/net/home/plgrid/plgyantar92/groupdir/functional-input.py:70: BadIncarWarning: Cannot find ZAB_VDW in the list of INCAR tags\r\n vasp_input.incar.check_params()\r\n/net/home/plgrid/plgyantar92/groupdir/functional-input.py:70: BadIncarWarning: GGA: Cannot find Ml in the list of values\r\n vasp_input.incar.check_params()\r\n```",
"Hi thanks for following up. I just have a look and I believe it's a separate issue related to #4042, i.e. we need to update the `incar_parameters.json` record.\r\n\r\n`ZAB_VDW` is currently not in the recorded INCAR tags, and `GGA` doesn't have `ML` in the recording yet: https://github.com/materialsproject/pymatgen/blob/3ee17e2c346dea6e9248eb04c989e58880914650/src/pymatgen/io/vasp/incar_parameters.json#L191-L218\r\n\r\nBut currently I don't have a better way other than doing that manually (which would be very inefficiently) given the amount of possible INCAR tags and their values. Updating the tags should be easier with: https://github.com/materialsproject/pymatgen/blob/3ee17e2c346dea6e9248eb04c989e58880914650/src/pymatgen/io/vasp/help.py#L68-L83\r\n\r\nBut updating the values is a bit tricky so I assume we need to helper script to do this? Would you be interested? If not I'm happy to get my hands on this a bit later :)\r\n",
"> But updating the values is a bit tricky so I assume we need to helper script to do this? Would you be interested? If not I'm happy to get my hands on this a bit later :)\r\n\r\n```python\r\n @classmethod\r\n def get_incar_tags(cls) -> list[str]:\r\n \"\"\"Get a list of all INCAR tags from the VASP wiki.\"\"\"\r\n url = (\"https://www.vasp.at/wiki/api.php?\"\r\n \"action=query&list=categorymembers\"\r\n \"&cmtitle=Category:INCAR_tag\"\r\n \"&cmlimit=500&format=json\")\r\n response = requests.get(url, timeout=60)\r\n response_dict = json.loads(response.text)\r\n\r\n def extract_titles(data):\r\n \"\"\"Extract keywords from from Wikimedia response data.\r\n See https://www.vasp.at/wiki/api.php?action=help&modules=query\r\n Returns: List of keywords as strings.\r\n \"\"\"\r\n return [category_data['title'] for category_data\r\n in data['query']['categorymembers']]\r\n\r\n tags = extract_titles(response_dict)\r\n while 'continue' in response_dict:\r\n response = requests.get(\r\n url + f\"&cmcontinue={response_dict['continue']['cmcontinue']}\",\r\n timeout=60\r\n )\r\n response_dict = json.loads(response.text)\r\n tags = tags + extract_titles(response_dict)\r\n\r\n return tags\r\n```\r\nI can make it into pull request if you wish.",
"> I can make it into pull request if you wish.\r\n\r\nThat would be hugely appreciated! You might have misread my previous comment https://github.com/materialsproject/pymatgen/issues/4119#issuecomment-2432250673\r\n\r\nCurrent we already have a method to get the (tags/keywords/parameters): https://github.com/materialsproject/pymatgen/blob/0e65d35ae0b1df964639a48067b1a525979eec84/src/pymatgen/io/vasp/help.py#L68-L70\r\n\r\n---\r\n\r\nWhat we need is something to update the values, which is a bit tricky. Currently VASP wiki doesn't seem to provide an API to get possible values of a tag directly (do they?), and the webpage format seems pretty inconsistent and probably make scraping infeasible (I'm not a web scraping expert and I wish I'm wrong here).\r\n\r\nFor example the [ALGO tag page](https://www.vasp.at/wiki/index.php/ALGO) seems to list all possible values at the start:\r\n<img width=\"1318\" alt=\"image\" src=\"https://github.com/user-attachments/assets/a65bbb83-237d-4589-9728-822dd3d3af3e\">\r\n\r\nHowever the [GGA tag](https://www.vasp.at/wiki/index.php/GGA) only listed a small portion and left the rest inside a table: \r\n<img width=\"775\" alt=\"image\" src=\"https://github.com/user-attachments/assets/883a0336-2ded-4d5e-ae3c-5d5e26dcb1ed\">\r\n",
"> What we need is something to update the values, which is a bit tricky. Currently VASP wiki doesn't seem to provide an API to get possible values of a tag directly (do they?),\r\n\r\nI do not see anything either.\r\n\r\n> the webpage format seems pretty inconsistent and probably make scraping infeasible (I'm not a web scraping expert and I wish I'm wrong here).\r\n\r\nScaping is possible, but awkward. One will need to write the scaper specifically for this page and add a number of asserts to catch incompatible changes (those are unlikely in practice though).\r\n\r\nI looked into the source of the page at https://www.vasp.at/wiki/index.php?title=GGA&action=edit\r\nand it looks like they define the tag list simply within a table, not using a template (template would make scaping much easier).\r\n\r\nIt should be still possible to write a dedicated scraper, via pymediawiki + wikitexparser, but non-standard pages like the one for GGA will need to have a specially tailored handler.\r\n\r\nI think that the most productive course of action here would be asking VASP maintainers to list all the possible keys in their TAGDEF template (the template defining GGA = PE | ... line) for this page and maybe for other pages with the same problem.",
"> I think that the most productive course of action here would be asking VASP maintainers to list all the possible keys in their TAGDEF template\r\n\r\nIt sounds like the best option to me, not sure what is the best approach to reach out though, perhaps through [the VASP forum](https://www.vasp.at/forum/)?\r\n",
"Yup, the forum. I see no better options on https://www.vasp.at/wiki/index.php/The_VASP_Manual#Support",
"Following up on this since I just encountered exact same issue, but for different keyword: `IMAGES`. It is not listed in `proc_val` and cast as str (AFAIU), but `IMAGES` should be int, according to incar_parameters.json (and VASP wiki).\r\n\r\nI am wondering if incar_parameters.json can be used to populate `proc_val` key/type associations.",
"> I am wondering if incar_parameters.json can be used to populate proc_val key/type associations.\r\n\r\nThis absolutely makes sense, currently we have type recording in both `proc_val` method and `incar_parameters.json`, but both are not really updated/validated. But I guess currently the biggest issue is that we don't have a programmatic way to retrieve such entries from VASP wiki.\r\n\r\n> I think that the most productive course of action here would be asking VASP maintainers to list all the possible keys in their TAGDEF template (the template defining GGA = PE | ... line) for this page and maybe for other pages with the same problem.\r\n\r\nDid you have time to reach out to them and request such feactures maybe? I might have a closer look later and see if I could find some interface to do the job :) I lean less towards scraping unless we don't have a better option maybe\r\n",
"> Did you have time to reach out to them and request such feactures maybe?\r\n\r\nIt is on my todo list, but not a high priority. I will follow up if I post something on the forum."
] | 2024-10-17T12:46:59
| 2024-12-19T08:13:47
|
2024-10-21T19:05:19Z
|
CONTRIBUTOR
|
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### Python version
Python 3.12.4
### Pymatgen version
2024.7.18
### Operating system version
_No response_
### Current behavior
When I set INCAR parametrs via `vasp_input['INCAR']['PARAM']=value`, they do not always pass `Incar.check_params()` checks.
Using the example below, I am getting:
```
...: BadIncarWarning: ENCUT: 550 is not a float
vasp_input.incar.check_params()
...: BadIncarWarning: GGA: Cannot find Ps in the list of values
vasp_input.incar.check_params()
```
### Expected Behavior
Setting the parameters passes the checks.
### Minimal example
```Python
from pymatgen.io.vasp.inputs import VaspInput
vasp_input = VaspInput.from_directory('.')
vasp_input['INCAR']['GGA'] = "MK"
vasp_input['INCAR']['GGA']
```
### Relevant files to reproduce this bug
I used the following INCAR
```
ALGO = Normal
ENCUT = 550
ISMEAR = 0
NCORE = 16
SIGMA = 0.04
SYSTEM = C.hexagonal.191
```
Other requried inputs may be anything.
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I_kwDOACgets6atc7e
| 4,120
|
`AseAtomsAdaptor` conversions fail to preserve 1D or 2D PBC
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[] | 2024-10-17T19:50:52
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2024-10-17T20:09:06Z
|
CONTRIBUTOR
|
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### Python version
Python 3.12.4
### Pymatgen version
2024.10.3
### Operating system version
Ubuntu 22.04.5 LTS
### Current behavior
The `get_atoms()` and `get_structure()` methods defined in `pymatgen.io.ase.AseAtomsAdaptor` class both set PBC of output objects to `True` (i.e., periodic in all 3 directions) when given a periodic structure/atoms input, thereby failing to preserve 1D PBC (e.g., `pbc = (True, False, False)`) or 2D PBC (e.g., `pbc = (True, True, False)`).
### Expected Behavior
Given a structure containing a lattice/cell defined with an arbitrary PBC, I expect both `pymatgen.io.ase.AseAtomsAdaptor.get_atoms()` and `pymatgen.io.ase.AseAtomsAdaptor.get_structure()` methods to preserve the input argument PBC values in their respective outputs.
### Minimal example
```Python
import numpy as np
from pymatgen.core import Structure, Lattice
from ase import Atoms
from pymatgen.io.ase import AseAtomsAdaptor
# Create Structure and Atoms instances with identical info
structure_src = Structure(
lattice=Lattice(np.eye(3), pbc=(True, True, False)),
species=['C', 'C'],
coords=np.array([[0.0, 0.0, 0.0], [.25, .25, .25]]),
)
atoms_src = Atoms(
symbols=['C', 'C'],
positions=np.array([[0.0, 0.0, 0.0], [.25, .25, .25]]),
cell=np.eye(3),
pbc=(True, True, False),
)
# Convert
structure_dst = AseAtomsAdaptor.get_structure(atoms_src)
atoms_dst = AseAtomsAdaptor.get_atoms(structure_src)
print("Structure PBC expected:", structure_src.lattice.pbc) # (True, True, False)
print("Structure PBC observed:", structure_dst.lattice.pbc) # (True, True, True)
print("Atoms PBC expected:", atoms_src.get_pbc()) # [ True True False]
print("Atoms PBC observed:", atoms_dst.get_pbc()) # [ True True True]
```
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets5_AyvM
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Bugfix: Preserve PBC info in `AseAtomsAdaptor`
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[
"Thanks."
] | 2024-10-17T19:53:32
| 2024-10-17T20:09:06
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2024-10-17T20:09:05Z
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CONTRIBUTOR
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## Summary
The `get_atoms()` and `get_structure()` methods of the `pymatgen.io.ase.AseAtomsAdaptor` class now preserve PBC value of their input.
Intended to close #4120
|
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PR_kwDOACgets5_C8Eb
| 4,122
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Make `Incar` keys case insensitive, fix init `Incar` from dict val processing for str/float/int
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[
"ping the true expert @esoteric-ephemera in case you have any comments (perhaps deserve a separate PR):\r\n\r\n- ~~Do we want to cast INCAR keys to upper case (to be consistent with VASP behaviour, but potentially breaking)~~\r\n- ~~Do we want to automatically filter duplicated INCAR keys (with a warning of course), again to be consistent with VASP behaviour (this should be resolved by casting keys to upper, as we cannot have duplicated keys in dict)~~\r\n- Wondering why do we capitalize values for unknown string keys? https://github.com/materialsproject/pymatgen/blob/32d9bebbebf24043bdf56683333053dcb1980d23/src/pymatgen/io/vasp/inputs.py#L988\r\n\r\nThanks in advance :)",
"> Do we want to cast INCAR keys to upper case (to be consistent with VASP behaviour, but potentially breaking)\r\n\r\nWhy do this exactly? FORTRAN (unless you use specific compiler options) is case insensitive, and most FORTRAN code, VASP included, is case insensitive. `aLgO = aLL` should mean the same thing as `ALGO = ALL` to VASP\r\n\r\n> Do we want to automatically filter duplicated INCAR keys (with a warning of course), again to be consistent with VASP behaviour (this should be resolved by casting keys to upper, as we cannot have duplicated keys in dict)\r\n\r\nI would just throw a user warning. Because of how VASP parses an INCAR, I'm pretty sure you can write the same tag multiple times, and the bottom-most value is the one that's accepted\r\n\r\n> Wondering why do we capitalize values for unknown string keys? \r\n\r\nProbably just convention, again because FORTRAN is case insensitive\r\n\r\nAlso for the `check_incar` stuff: keep in mind that FORTRAN is very strictly typed. Even if I write `ENCUT = 500` in the INCAR, fortran will enforce this to be double precision because ENCUT is declared as a double",
"I btw recently had issues with updating the incar. I would have expected that sigma and SIGMA would simply modify SIGMA but they did not. Instead, i had two different sigmas in the incar. I did not have time to investigate but it was a very recent pymatgen version",
"@JaGeo did VASP parse them as different variables or just take the one defined furthest down the INCAR?",
"Yes, all tags are case insensitive. I don't think the Incar class actually checks. So if you set `sigma` and `SIGMA`, you end up with two sigma tags. The easiest solution is to automatically capitalize the key in setitem for Incar. I would use Camelcase for the values for Incar (even though it makes no difference where VASP is concerned). Usually VASP just looks at the first letter. E.g., ALGO = Accurate and ALGO=A means the same thing.",
"> Probably just convention, again because FORTRAN is case insensitive\r\n\r\nThanks that makes sense, and I don't think we need to change this as it wouldn't have any side effect.\r\n\r\n> I'm pretty sure you can write the same tag multiple times, and the bottom-most value is the one that's accepted\r\n\r\n> did VASP parse them as different variables or just take the one defined furthest down the INCAR?\r\n\r\nI believe VASP parses the first occurrence (can you confirm it's the bottom one? @esoteric-ephemera ), but I could be wrong here. I tested with INCAR:\r\n```\r\nencut = 500\r\nENCUT = 400\r\n``` \r\n\r\nAnd `grep ENCUT vasprun.xml` would return: `<i name=\"ENCUT\"> 500.00000000</i>`",
"@DanielYang59 @esoteric-ephemera Yes, it took the first one as far as I remember. \r\n\r\n@shyuep i might be wrong but I thought i modelled the lobsterin class after the incar at the time and i think it checked at some point. In any case, it would be great if this would be checked again (e.g., via Camelcase). \r\nEDIT: ah, already implemented 😀",
"> Why do this exactly?\r\n\r\n> I don't think the Incar class actually checks. So if you set sigma and SIGMA, you end up with two sigma tags. The easiest solution is to automatically capitalize the key in setitem for Incar. \r\n\r\nI proposed that we cast Incar keys to upper case internally in order to prevent such duplicate and make other internal checking/handling easier.\r\n\r\nAlso the reason I personally prefer upper case over others (capitalize/lower) being:\r\n- Most (if not all) our internal recordings (`incar_parameters.json`, and all kinds of recordings inside `vasp.inputs` class) use upper case, so we don't need to update them all\r\n- VASP internally cast all keys to upper case when parsing (see the top comment in VASP source code `drdatab.F`)\r\n- VASP wiki also use upper case, so I assume it's more or less a convention?\r\n",
"@JaGeo I just fix the upper case keys problem and added a test. It should no longer be a problem. As far as I can tell, the values are already properly capitalize and there is a test.",
"Thanks for the helpful discussion and the quick fix @shyuep \r\n\r\nI would finish the remaining part of this PR",
"@shyuep Thanks for the fast fix!",
"Just mention this in case you have any comments, it seems [the `ML_MODE` tag](https://www.vasp.at/wiki/index.php/ML_MODE) (which I never used) is an exception of the case insensitivity, added in #3625: https://github.com/materialsproject/pymatgen/blob/ed8542d8ebf18c0fa49e6d87386a52072bc31559/src/pymatgen/io/vasp/inputs.py#L932\r\n\r\nPer the above VASP wiki:\r\n> Warning: If any option other than the above is chosen or there is a spelling error (be careful to write everything in upper case or lower case letters) the code will exit with an error. ",
"Thanks.",
"No problem, thanks for the helpful discussion everyone",
"I think that one special key is SYSTEM - it is usually free text and capitalizing it can be awkward.",
"> I think that one special key is SYSTEM - it is usually free text and capitalizing it can be awkward.\r\n\r\nThat's a good point to me. \r\n\r\n\r\nUpdate: I released comparing two INCARs (especially to check if they produce the same result) through directly `==` may not make sense as the VASP default value handling, so it should be preferred to use `diff` for a manually inspection.\r\n\r\n\r\n<del>Meanwhile, I think the `__eq__` for `Incar/Kpoint` (perhaps `diff` as well? I don't have a strong opinion on `diff` though) should be overwritten to ignore the comment/`SYSTEM` for similar reason (docstring should be updated to reflect this behaviour of course). </del>\r\n"
] | 2024-10-18T03:28:51
| 2024-10-26T11:42:11
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2024-10-21T19:05:18Z
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CONTRIBUTOR
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### Summary
- Fix `Incar.check_params` handling of case sensitivity, to fix #4119, also add unit tests
- [x] Issue warning if duplicated keys found when init `Incar`
### Make more operations (get/update/setdefault) in `Incar` case insensitive
- [x] Init `Incar` from dict (also the `from_dict` method) doesn't seem to use setter method, might be better off subclass UserDict
- [x] Update Incar class docstring to record the change in behaviour
- [x] Test other dict methods like update/setdefault/...
### Init `Incar` from dict doesn't call setter method, leading to unprocessed str/float/int value
- [x] Setter method only trigger `proc_val` when val is string, leading to inconsistent behaviour when init from dict for int/float
- [x] Setter method not triggered on `update` method when subclassing builtin `dict`, leading to val not passing through `proc_val` when init from dict
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fix: preserve site properties over cell transform
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"Thanks"
] | 2024-10-18T16:05:50
| 2024-10-21T20:51:12
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2024-10-21T20:51:08Z
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CONTRIBUTOR
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Make sure site properties are properly transferred from the original cell to the primitive or refined one.
## Summary
Major changes:
- fix 1: in `SpacegroupAnalyzer.get_refined_cell`, the flag `keep_site_properties` (used notably by `get_conventional_standard_structure`) would not behave as expected before because it used `number` returned by `spglib.refine_cell` to index into the `properties` (`properties` has one element per site, but `number` indexes into `_unique_species` which has one element per occupied irreducible position).
- fix 2: I noticed the same pattern in `SpacegroupAnalyzer.find_primitive`
You can verify that the new tests wouldn't pass before the change to `SpacegroupAnalyzer`.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [-] (no relevant changes) Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [-] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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doc: make the test procedure explicit
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"I don't think we need to do both:\r\n- either we install pymatgen in editable mode to make the test files available (as test files are not included inside the distribution), OR\r\n- if for whatever reason you don't want to install in editable mode (test the distribution content for example), set `PMG_TEST_FILES_DIR` to point to the test file directory \r\n",
"You are supposed to install pymatgen in editable mode if you are a dev."
] | 2024-10-18T16:10:23
| 2024-10-19T16:06:45
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2024-10-19T16:06:45Z
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CONTRIBUTOR
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The most common usual workflow with `pytest` is just `pip install . && pytest`, but this doesn't apply to pymatgen because of the test files.
Since I had to dig (just a bit) in the sources to get `pytest` to run I figured I could help the next contributor by making it clear how to point to the files using an environment variable.
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Add CUDA functionality to `parse_lammps_dumps` to allow for NVIDIA GPU support when analyzing large dump files.
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[] | 2024-10-19T19:22:52
| 2024-10-19T19:25:33
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NONE
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### Feature Requested
I'd like to add GPU support for NVIDIA A100 GPUs for using `parse_lammps_dumps` from `pymatgen.io.lammps.outputs`.
### Proposed Solution
Use `cudf` instead of `pandas` to read and parse LAMMPS dump file.
### Relevant Information
Can increase efficiency of LAMMPS dump file reading significantly.
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I_kwDOACgets6a-AF3
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Question about conventional cell standards defined by `get_conventional_standard_structure` in pymatgen.
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[
"Dear @hongyi-zhao ,\r\n\r\nI think the different kpath scheme implementations have been made as a part of this publication: https://doi.org/10.1038/s41524-020-00383-7\r\n\r\nHistorically, MP used the scheme by 'setyawan_curtarolo first. That's why the prinitive and content cells are implemented like this. I assume implementing the different conventional cell types simply wasn't necessary for the publication above at the time.\r\n\r\nI am not aware of any plans to extend this. Tagging @mkhorton @tschaume @munrojm to see if they might know/remember more.\r\n\r\nPS: Most of the developments in pymatgen are part of projects/publications and pull requests are made for such specific projects.",
"Btw, https://github.com/materialsproject/pymatgen/blob/v2024.10.3/src/pymatgen/symmetry/bandstructure.py#L27-L391 also clearly says that the convention from setyawan_curtarolo is used as a starting point for the generation of all 3 schema in this class."
] | 2024-10-20T04:06:06
| 2024-10-20T08:26:02
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2024-10-20T08:26:02Z
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CONTRIBUTOR
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Hello pymatgen developers,
I've been examining the documentation for [`get_conventional_standard_structure`](https://pymatgen.org/pymatgen.symmetry.html#pymatgen.symmetry.analyzer.SpacegroupAnalyzer.get_conventional_standard_structure) and [`HighSymmKpath`](https://pymatgen.org/pymatgen.symmetry.html#pymatgen.symmetry.bandstructure.HighSymmKpath), and I've noticed a discrepancy that I'd like to understand better.
In [`HighSymmKpath`](https://pymatgen.org/pymatgen.symmetry.html#pymatgen.symmetry.bandstructure.HighSymmKpath), there are three options for the `path_type` parameter:
- 'setyawan_curtarolo'
- 'hinuma'
- 'latimer_munro'
These different conventions allow for flexibility in generating high symmetry paths.
However, in [`get_conventional_standard_structure`](https://pymatgen.org/pymatgen.symmetry.html#pymatgen.symmetry.analyzer.SpacegroupAnalyzer.get_conventional_standard_structure), the method seems to use only one standard, defined by [Setyawan & Curtarolo (2010)](https://doi.org/10.1016/j.commatsci.2010.05.010). The documentation states:
> The standards are defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: Challenges and tools. Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010
My question is: Why doesn't [`get_conventional_standard_structure`](https://pymatgen.org/pymatgen.symmetry.html#pymatgen.symmetry.analyzer.SpacegroupAnalyzer.get_conventional_standard_structure) offer similar options for different conventions, as seen in [`HighSymmKpath`](https://pymatgen.org/pymatgen.symmetry.html#pymatgen.symmetry.bandstructure.HighSymmKpath)?
Would it be beneficial to implement multiple standards for conventional cell generation, allowing users to choose between different conventions (e.g., Setyawan & Curtarolo, Hinuma et al., and Latimer & Munro) similar to how [`HighSymmKpath`](https://pymatgen.org/pymatgen.symmetry.html#pymatgen.symmetry.bandstructure.HighSymmKpath) operates?
I'm curious about the rationale behind this design decision and whether there are plans to expand the options for conventional cell standards in future versions of pymatgen.
Thank you for your time and consideration.
Best regards,
Zhao
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Fix gaussian input parser, and add test
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"Thanks"
] | 2024-10-21T13:15:22
| 2024-10-22T00:42:37
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2024-10-21T20:50:53Z
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CONTRIBUTOR
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## Summary
Major changes:
- fix 1: In src/pymatgen/io/gaussian.py, within the from_str() method, the variable route_index is initially set to None and later assigned an integer representing the line number in the file. The code used `if route_index:` to check if route_index was set to a value other than None. However, when route_index is assigned 0, the condition if route_index: incorrectly evaluates to False. To fix this, I changed the condition to `if route_index is not None:`. This bug occurred when the Gaussian input file has no Link0 section and has the route section spanned multiple lines with only the first line starting with #, the parser did not read the file correctly.
- fix 2: Added the test function test_from_str_no_link0() for a Gaussian input file that previously caused an error in from_str(). This test ensures that the parser correctly handles input files without a Link0 section and with multi-line route sections.
- fix 3: Included example Gaussian input file for the .com extension used on Linux. This file, as described in Fix 1, has no Link0 section, has a multi-line route section, and only the first line of the route section starts with #.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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PR_kwDOACgets5_Zilu
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|
bump `monty` to use the `monty.json` import speedup patch, add import time regression test, lazy load some rarely used but costly modules
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[
"Strange, I cannot [recreate this CI failure](https://github.com/materialsproject/pymatgen/actions/runs/11454074042/job/31867593537?pr=4128) on Ubuntu 22.04, python 3.12.7 (still trying) and h5py==3.11.0:\r\n\r\nMight be https://stackoverflow.com/questions/49317927/errno-101-netcdf-hdf-error-when-opening-netcdf-file\r\n\r\nhttps://github.com/Unidata/netcdf4-python/issues/1027\r\n\r\n",
"@mkhorton Can I lazy import `sympy` (it's used by only one method `symmetry.settings.JonesFaithfulTransformation.parse_transformation_string` and would give us a ~15% speed up on import `core.Structure`)?\r\n",
"> @mkhorton Can I lazy import `sympy` (it's used by only one method `symmetry.settings.JonesFaithfulTransformation.parse_transformation_string` and would give us a ~15% speed up on import `core.Structure`)?\r\n\r\nPlease! This method is very rarely used, lazy import preferred.",
"Thank you for the profiling, let me know when ready for review.",
"@mkhorton I believe this PR is already for view, let me know if you have any comment, thank you!\r\n\r\nCredit to @janosh for the motivation and helpful discussion!\r\n",
"thanks a lot for your extensive profiling work @DanielYang59! i expected there would be a some low-hanging fruit but not nearly as much as you found. you went above and beyond here. 👍 \r\nwill be big help in resolving https://github.com/janosh/pymatviz/issues/209",
"thanks @shyuep this hopefully would significantly speedup import "
] | 2024-10-22T03:52:11
| 2024-11-14T03:35:11
|
2024-11-13T17:49:45Z
|
CONTRIBUTOR
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## Summary
- Organize optional dependencies in `pyproject.toml` to avoid duplicate
- Bump `sympy >= 1.3` to resolve https://github.com/materialsproject/pymatgen/pull/4116#issuecomment-2428308320
- Avoid `from numpy.testing import assert_allclose` in production code
---
- bump `monty` to use [the latest json import speedup patch](https://github.com/materialsvirtuallab/monty/pull/713), partially fix #3793
- Have a quick look at other important modules (on cover those import other 3rd-party/non-core-pmg modules in this PR) and add import time test (profile: `python -X importtime -c "from pymatgen.core.structure import Structure" 2> pmg.log && tuna pmg.log`):
- [x] core.bonds: <img width="1475" alt="image" src="https://github.com/user-attachments/assets/50c868a2-5df4-4662-afd4-a68f4a70e8da">
- [x] core.composition: <img width="1475" alt="image" src="https://github.com/user-attachments/assets/d90d517c-aea2-4196-ac92-ed6e8e5846d9">
- [x] core.interface (**need attention**)
- [x] core.ion: <img width="1475" alt="image" src="https://github.com/user-attachments/assets/272f5489-0942-4767-8793-99aa780516d9">
- [x] core.lattice: <img width="1475" alt="image" src="https://github.com/user-attachments/assets/38978d49-5202-42ae-9a0c-a2dec86ba62a">
- [x] core.operations: <img width="1475" alt="image" src="https://github.com/user-attachments/assets/c194a5a3-f8a5-4d21-bf5d-23984ce65341">
- [x] core.periodic_table: <img width="1475" alt="image" src="https://github.com/user-attachments/assets/02a0fee0-588a-4688-ba53-e2b778b1a657">
- [x] core.sites: <img width="1475" alt="image" src="https://github.com/user-attachments/assets/080fe0d6-66d3-412e-85ce-92a6d04a0b78">
- [x] core.spectrum: <img width="1475" alt="image" src="https://github.com/user-attachments/assets/84f4550a-ce9b-42ad-8086-29a01f756a84">
- [x] core.structure
- [x] core.surface: <img width="1475" alt="image" src="https://github.com/user-attachments/assets/6adc138b-d224-4b42-b0cb-1778ede20d3f">
- [x] core.tensors: <img width="1475" alt="image" src="https://github.com/user-attachments/assets/1142ebe6-c762-4929-ab95-d2b8f66eec5b">
- [x] core.trajectory (`AseAtomsAdaptor` lazy imported)
- [x] io.vasp.inputs <img width="1475" alt="image" src="https://github.com/user-attachments/assets/67faa4fc-6126-4a1d-b79d-1cba30fcfd0b">
- [x] io.vasp.outputs: <img width="1475" alt="image" src="https://github.com/user-attachments/assets/7a0b705a-0458-482b-8e5f-e2247dc29d17">
- [For a follow up PR] looks like `scipy` across `core` need special attention
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I_kwDOACgets6bfCkV
| 4,130
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Kpoints.from_file sometimes override the comment
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[
"Thanks for reporting this, yes I could confirm this. \r\n\r\nMeanwhile it seems comments are not passed for some other modes as well, I would fix this.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/3ee17e2c346dea6e9248eb04c989e58880914650/src/pymatgen/io/vasp/inputs.py#L1594\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/3ee17e2c346dea6e9248eb04c989e58880914650/src/pymatgen/io/vasp/inputs.py#L1617"
] | 2024-10-23T13:26:20
| 2024-10-25T21:25:23
|
2024-10-25T21:25:23Z
|
CONTRIBUTOR
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### Python version
Python 3.12.4
### Pymatgen version
Version: 2024.10.22
### Operating system version
_No response_
### Current behavior
Given the following example KPOINTS file
```
pymatgen with grid density = 10000 / number of atoms
0
Gamma
19 19 6
```
Upon reading it, I am getting kpt.comment value 'Automatic kpoint scheme'
### Expected Behavior
I expect Kpoints object to capture the file comment and kpt.comment have the value "pymatgen with grid density = 10000 / number of atoms".
### Minimal example
```Python
from pymatgen.io.vasp.inputs import Kpoints
pt=Kpoints.from_file('KPOINTS')
pt.comment
```
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets5_nzMb
| 4,131
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Fix comment pass in `Kpoints` constructors
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[
"@yantar92 Thanks again for reporting, am I missing anything here?\r\n\r\nUpdate: I changed my mind, I would change the methods to take a `comment` arg instead of hard coding the comments.",
"> Thanks again for reporting, am I missing anything here?\r\n\r\nLooks reasonable from a quick glance. Thanks!",
"No problem, thanks for checking"
] | 2024-10-23T13:55:34
| 2024-10-27T03:15:53
|
2024-10-25T21:25:22Z
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CONTRIBUTOR
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### Summary
- Fix comment pass in `Kpoints` in auto/gamma/Monkhorst modes, to close #4130
- [x] Add unit test
|
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I_kwDOACgets6bgwuO
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assimilate method in SimpleVaspToComputedEntryDrone is not raising ValueError
|
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[
"Thanks for reporting this and your investigation. I could confirm this issue.\r\n\r\nOn top of the issue you discovered, there's another subtle bug in: https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/apps/borg/hive.py#L229-L239\r\n\r\nWhen `files` has no match, calling `files[0]` would trigger an IndexError, this should not be caught either.\r\n\r\n"
] | 2024-10-23T15:39:18
| 2024-11-12T18:01:08
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2024-11-12T18:01:08Z
|
NONE
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### Python version
Python 3.12.3
### Pymatgen version
2024.10.22
### Operating system version
Ubuntu 22.04 LTS
### Current behavior
assimilate method in apps.borg.hive.SimpleVaspToComputedEntryDrone is not raising the ValueError when checking if all the necessary files are present ("INCAR", "POTCAR", "CONTCAR", "OSZICAR", "POSCAR"). Instead, the method returns None, i think it happens because the raise keyword is placed inside the try statement.
### Expected Behavior
assimilate method should correctly detect the absence of required VASP files.
### Minimal example
```Python
from pymatgen.apps.borg.hive import SimpleVaspToComputedEntryDrone
drone = SimpleVaspToComputedEntryDrone()
entry = drone.assimilate(".")
print(entry)
```
### Relevant files to reproduce this bug
_No response_
|
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Add min "thickness" check in `CifParser` to filter invalid structure which leads to infinite loop
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[
"@anyangml I hope this looks good to you, with this patch your example would terminate gracefully:\r\n```python\r\n/Users/yang/developer/pymatgen/src/pymatgen/io/cif.py:1318: UserWarning: No structure parsed for section 1 in CIF.\r\nlattice.volume=2.2009330203855426e-06 ų below threshold, double check your structure.\r\n warnings.warn(msg)\r\n/Users/yang/developer/pymatgen/src/pymatgen/io/cif.py:1322: UserWarning: Issues encountered while parsing CIF: No structure parsed for section 1 in CIF.\r\nlattice.volume=2.2009330203855426e-06 ų below threshold, double check your structure.\r\n warnings.warn(\"Issues encountered while parsing CIF: \" + \"\\n\".join(self.warnings))\r\nTraceback (most recent call last):\r\n File \"/Users/yang/developer/pymatgen/debug/recreate_cif.py\", line 15, in <module>\r\n read_file(\"./example.cif\")\r\n File \"/Users/yang/developer/pymatgen/debug/recreate_cif.py\", line 6, in read_file\r\n structure = cif.parse_structures(primitive=True)[0]\r\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n File \"/Users/yang/developer/pymatgen/src/pymatgen/io/cif.py\", line 1325, in parse_structures\r\n raise ValueError(\"Invalid CIF file with no structures!\")\r\nValueError: Invalid CIF file with no structures!\r\n```\r\n",
"@anyangml May I have your permission to include your cif file as a test file for `pymatgen` for such cases?",
"> @anyangml May I have your permission to include your cif file as a test file for `pymatgen` for such cases?\r\n\r\nyes!",
"Cool thanks!"
] | 2024-10-25T10:26:50
| 2024-11-14T03:30:59
|
2024-11-13T17:49:17Z
|
CONTRIBUTOR
|
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### Summary
- Add min thickness check in `CifParser` to filter invalid structure which leads to infinite loop, to fix #4028
- [x] Add unit test
|
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PR_kwDOACgets5_4uJ-
| 4,134
|
Clean up `neighbors.pyx` variable name
|
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[] | 2024-10-25T10:49:17
| 2024-10-26T02:02:17
|
2024-10-25T21:24:53Z
|
CONTRIBUTOR
|
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### Summary
- Minor clean up `neighbors.pyx` variable name, remnant from #4028, **I don't expect any functional changes**
- Use `unsigned int` (`npy_uint32`) over `int` for variables that we're certain would not be negative (counter, index when looping through "number of points/dimensions")
|
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PR_kwDOACgets5_-NUh
| 4,136
|
Read INCAR `SYSTEM` as is, `check_params` use `proc_val`
|
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[
"@yantar92 Hope this looks good to you\r\n\r\nThe issue with `incar_parameters.json` is not completely resolved as we cannot reply on manual upgrade of tags and values, a script is certainly needed but I don't have time to work on this at this moment.\r\n",
"> a script is certainly needed but I don't have time to work on this at this moment.\r\n\r\nhttps://github.com/materialsproject/pymatgen/issues/4119#issuecomment-2439617604-permalink",
"I am merging this. In the end, we are using the 80/20 rule. VASP keys are always all caps. VASP values are a mess of different things (int, floats, case-insensitive strings, case-sensitive strings, etc.). For now, we will just use capitalize since that works for most of the cases, e.g., ALGO=Fast,Normal, etc. I get that BSE should be full caps since it is an acronym but since it makes no difference to actual functionality, we are going to live with it."
] | 2024-10-26T02:25:03
| 2024-11-13T01:46:18
|
2024-11-12T18:08:52Z
|
CONTRIBUTOR
|
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### Summary
- Manually update `incar_parameters.json`, to fix https://github.com/materialsproject/pymatgen/issues/4119#issuecomment-2431859839, need a more systematic script to update `incar_parameters.json` in the long run
- `check_params` use `proc_val`
- Remove some unnecessary casting in INCAR values as we're confident they are capitalized now
- Avoid casing INCAR `SYSTEM` keyword, to fix https://github.com/materialsproject/pymatgen/pull/4122#issuecomment-2431216473
|
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PR_kwDOACgets5_-PkH
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|
Preprocess Structure Reduction Before Bulk Match
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[
"Hi @mkhorton, This PR aims to enhance the performance of `AflowPrototypeMatcher` with a similar approach to `StructureMatcher.group_structures` (see https://github.com/materialsproject/pymatgen/pull/2490). It might be of interest to you. Could you please review this PR?\r\n",
"Merged. Thanks,"
] | 2024-10-26T03:01:55
| 2024-11-12T18:03:38
|
2024-11-12T18:03:30Z
|
CONTRIBUTOR
|
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## Summary
The `AflowPrototypeMatcher` matches a structure against predefined AFLOW prototype structures using `StructureMatcher`. `StructureMatcher` requires preprocessing via lattice reduction and primitive-cell conversion. This commit optimizes performance by preprocessing AFLOW prototype structures during the initialization of `AflowPrototypeMatcher`. This change eliminates redundant processing when `AflowPrototypeMatcher.get_prototypes` is called multiple times.
## Benchmark
I have checked the performance change by the following script, which calls `AflowPrototypeMatcher` with diamond-Si by 10 times.
```python
# debug.py
from __future__ import annotations
from pymatgen.analysis.prototypes import AflowPrototypeMatcher
from pymatgen.util.testing import PymatgenTest
class TestAflowPrototypeMatcher(PymatgenTest):
def test_prototype_matching(self):
af = AflowPrototypeMatcher()
struct = self.get_structure("Sn")
for _ in range(10):
prototype = af.get_prototypes(struct)[0]
assert prototype["tags"] == {
"aflow": "A_cF8_227_a",
"mineral": "diamond",
"pearson": "cF8",
"strukturbericht": "A4",
}
if __name__ == '__main__':
TestAflowPrototypeMatcher().test_prototype_matching()
```
The current master branch takes 20.4 s in total. `StructureMatcher._get_reduced_structure` takes most of the computational time.
This PR takes 2.48 s for the same workload. Now, the heavy primitive-cell conversion is called only once.
These profiles are generated with cProfile and SnakeViz as follows
```shell
python -m cProfile -s cumulative -o debug.prof debug.py
```
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- Tests added for new features/fixes.
- If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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PR_kwDOACgets5__Ofm
| 4,138
|
Show `FutureWarning` and `DeprecationWarning` for `pytest`
|
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[] | 2024-10-26T13:44:55
| 2024-11-13T01:44:34
|
2024-11-12T18:02:06Z
|
CONTRIBUTOR
|
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### Summary
- Show `FutureWarning` and `DeprecationWarning` for `pytest`, https://docs.pytest.org/en/stable/how-to/capture-warnings.html
- [x] Fix #4112
- [x] **For replacement of external APIs, double check the minimal version requirement** (scipy, phonopy and pandas)
- [ ] Are there alternatives for deprecated `scipy` functions?
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| 2,615,897,934
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I_kwDOACgets6b629O
| 4,139
|
How to transform elastic constants after a change of basis with the help of pymatgen?
|
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[
"Based on the related documentation [here](https://docs.materialsproject.org/methodology/materials-methodology/elasticity#derived-elastic-properties) and [here](https://materialsproject.github.io/atomate2/user/codes/vasp.html#elastic-constant), I got the following solution based on the method [here](https://pymatgen.org/pymatgen.core.html#pymatgen.core.tensors.Tensor.convert_to_ieee) in order to demonstrate some of the methodology conventions of simulating elasticity calculations adopted by [the materials project](https://docs.materialsproject.org/methodology/materials-methodology/elasticity#derived-elastic-properties). The details and parameter settings of the vasp calculations may not necessarily be consistent, so the final results cannot be directly and accurately compared with those in the Materials Project database.\r\n\r\nIn the following test, we use [the cif structure file from the legacy database](https://legacy.materialsproject.org/materials/mp-149/cif?type=primitive&download=true) to prepare the POSCAR, as shown below:\r\n\r\n```shell\r\n# Steps to do the test, using Si_mp-149_primitive.cif as an example:\r\n# Use your python venv accordingly:\r\n$ pyenv shell datasci \r\n$ python struct2conv.py -i Si_mp-149_primitive.cif -o Si_mp-149_conventional_standard.vasp\r\n$ mkdir Si_mp-149_conventional_standard && cd Si_mp-149_conventional_standard\r\n$ ln -sfr ../Si_mp-149_conventional_standard.vasp POSCAR\r\n$ (echo 101; echo DC)|vaspkit\r\n$ (echo 102; echo 2; echo 0.03)|vaspkit\r\n\r\n# Comment out the `NPAR` tag in INCAR and run the vasp calculation:\r\n$ mpirun -n 16 vasp_std\r\n\r\n# Extract the elastic tensor\r\n$ echo 203 |vaspkit\r\n\r\n# Convert elastic tensor to IEEE format\r\n$ python ../elastic2ieee.py\r\n```\r\nAll related necessary files and scripts are as follows:\r\n\r\n[elastic2ieee.zip](https://github.com/user-attachments/files/17542584/elastic2ieee.zip)\r\n\r\nSee below for the related discussions and tools:\r\n- https://www.vasp.at/forum/viewtopic.php?t=19829\r\n- https://github.com/libAtoms/matscipy/issues/271\r\n- https://github.com/materialsproject/pymatgen/discussions/4135\r\n- https://progs.coudert.name/elate"
] | 2024-10-26T14:23:50
| 2024-11-05T14:11:46
|
2024-10-28T02:43:31Z
|
CONTRIBUTOR
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Hi there,
I have a question about transforming elastic constants when changing the basis/coordinate system. Does pymatgen provide functionality for this kind of transformation?
Specifically, I want to:
1. Take a 6x6 elastic constant matrix in Voigt notation
2. Apply a basis transformation
3. Get the transformed elastic constants in the new basis
Is there a built-in method to do this in pymatgen? If not, what would be the recommended way to implement this?
Thanks in advance!
Zhao
P.S.:
The following things seem to have something to do with this problem:
1. https://pymatgen.org/pymatgen.core.html#pymatgen.core.operations.SymmOp.transform_tensor
2. https://github.com/materialsproject/pymatgen/blob/0e65d35ae0b1df964639a48067b1a525979eec84/src/pymatgen/core/tensors.py#L406
But [the documentation link](http://pymatgen.org/_modules/pymatgen/core/tensors.html) shown [here](https://docs.materialsproject.org/methodology/materials-methodology/elasticity#symmetrization) is outdated:
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I_kwDOACgets6b7EJe
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Poscar.from_file throws a cryptic error for VASP5-like POSCARs when POTCAR does not contain all the present elements
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[
"Thanks for reporting again. Yes I agree this error message is not semantic, and I'm happy to have a closer look later.\r\n\r\n> Ideally, I'd like Poscar.from_file fall back to using POSCAR symbols if POTCAR does not specify them all and throw a warning.\r\n\r\nI believe this \"not failing back to POSCAR symbol\" behaviour is intended when `check_for_potcar` is True.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/0e65d35ae0b1df964639a48067b1a525979eec84/src/pymatgen/io/vasp/inputs.py#L233-L245\r\n\r\nIf you want to read a POSCAR with an incompatible POTCAR in the same directory, you may want to use `check_for_potcar=False` to turn off the POTCAR check.\r\n\r\n```python\r\nposcar = Poscar.from_file(\"./POSCAR\", check_for_potcar=False)\r\n```\r\n",
"> If you want to read a POSCAR with an incompatible POTCAR in the same directory, you may want to use check_for_potcar=False to turn off the POTCAR check.\r\n\r\nUnfortunately, I have no such option.\r\n\r\nI think I need to elaborate on the _actual_ problem I encountered.\r\n\r\nMy code is the following\r\n\r\n```python\r\n # No VASP output found. Try to ingest VASP input.\r\n vasp_input = VaspInput.from_directory(self.directory)\r\n self.structure = vasp_input['POSCAR'].structure\r\n\r\n super().__post_init__()\r\n\r\n self.prev_incar = vasp_input['INCAR']\r\n self.prev_kpoints = vasp_input['KPOINTS']\r\n```\r\n\r\nAs you can see, I am not calling `Poscar.from_file` directly. I am using `VaspInput.from_directory`, which is then calling `Poscar.from_file` internally and throwing the observed error.\r\n\r\nThat's why I objected the existing behaviour and instead proposing throwing a warning and reading the POSCAR anyway (the POSCAR itself is perfectly valid).\r\n\r\nAnother option would be throwing some catchable error, so that I can at least handle this specific scenario via try/catch. For now, I cannot even do that because the observed error in indistinguishable from a real problem with POSCAR.",
"Thanks for the input!\r\n\r\n> I am using VaspInput.from_directory, which is then calling Poscar.from_file internally and throwing the observed error.\r\n\r\nI believe this is intended to \"force\" user to make a VASP runner \"VASP input set\" and therefore POTCAR check is mandatory, I cannot think of any reason not to use a \"good\" POTCAR in this regard?\r\n\r\nI agree the error message should be clarified, but I don't have a good reason to change the default POTCAR checking behaviour of `VaspInput.from_directory` \r\n\r\n\r\n",
"> I believe this is intended to \"force\" user to make a VASP runner \"VASP input set\" and therefore POTCAR check is mandatory, I cannot think of any reason not to use a \"good\" POTCAR in this regard?\r\n\r\nIn my case, there is an existing VASP input directory where the POSCAR is modified manually (well, using a custom script). Then, I wanted to re-generate the POTCAR according to the new POSCAR. I could read the files separately, but using VaspInput looked like a better option.\r\n\r\n> I agree the error message should be clarified, but I don't have a good reason to change the default POTCAR checking behaviour of VaspInput.from_directory\r\n\r\nYour call. Having a better error is good enough for my needs.",
"> Your call. Having a better error is good enough for my needs.\r\n\r\nI'm not a maintainer, nor the person to unilaterally say no to a possible feature and you are free to open a separate PR if you believe this is a needed :)\r\n\r\n",
"An alternative approach to turn off POTCAR checking globally might be the following (set `PMG_POTCAR_CHECKS` to False in your PMG config file):\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/4b10dd3fb37d8012d46dee58678ac3a695845104/src/pymatgen/io/vasp/inputs.py#L272-L276\r\n\r\nI believe this should work for your case.",
"\r\n\r\nUpdate: I guess it's intended to overwrite elements by POTCAR, but I would enhance the warning message and error handling\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/4b10dd3fb37d8012d46dee58678ac3a695845104/src/pymatgen/io/vasp/inputs.py#L418-L428"
] | 2024-10-26T15:44:23
| 2024-11-13T17:48:18
|
2024-11-13T17:48:18Z
|
CONTRIBUTOR
|
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### Python version
Python 3.12.7
### Pymatgen version
Version: 2024.10.22
### Operating system version
_No response_
### Current behavior
Consider the following scenario:
1. We have a POSCAR file in VASP5 format with, say, C and Na sites
2. We have an obsolete POTCAR file only specifying C potentials
3. We try to read the POSCAR using Poscar.from_file
When I do try it, I get an error like:
```
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/yantar92/.venv/lib/python3.12/site-packages/pymatgen/io/vasp/inputs.py", line 282, in from_file
return cls.from_str(file.read(), names, read_velocities=read_velocities)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/yantar92/.venv/lib/python3.12/site-packages/pymatgen/io/vasp/inputs.py", line 478, in from_str
struct = Structure(
^^^^^^^^^^
File "/home/yantar92/.venv/lib/python3.12/site-packages/pymatgen/core/structure.py", line 3956, in __init__
super().__init__(
File "/home/yantar92/.venv/lib/python3.12/site-packages/pymatgen/core/structure.py", line 1051, in __init__
raise StructureError(f"{len(species)=} != {len(coords)=}")
pymatgen.core.structure.StructureError: len(species)=1 != len(coords)=721
```
Such error is extremely hard to understand.
I note that the error is not exactly a bug - docstring of from_file method does say that POTCAR symbols take priority by default. However, (1) it is very hard to understand what is going on from the error thrown; (2) the existing behaviour does not make much sense for VASP5 POSCARs where the symbol names are explicitly specified.
### Expected Behavior
Ideally, I'd like Poscar.from_file fall back to using POSCAR symbols if POTCAR does not specify them all and throw a warning.
### Minimal example
```Python
from pymatgen.io.vasp.inputs import Poscar, Potcar
Poscar.from_file('POSCAR')
```
### Relevant files to reproduce this bug
[POSCAR.tar.gz](https://github.com/user-attachments/files/17531141/POSCAR.tar.gz)
I cannot share the POTCAR file because of license terms, but here is the spec:
```python
[PotcarSingle(symbol='C', functional='PBE', TITEL='PAW_PBE C 08Apr2002', VRHFIN='C: s2p2', n_valence_elec=4)]
```
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PR_kwDOACgets6AAhvz
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|
VaspDoc.get_incar_tags: Use Mediawiki API
|
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[
"Thanks!"
] | 2024-10-27T09:24:17
| 2024-10-29T00:06:01
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2024-10-29T00:05:56Z
|
CONTRIBUTOR
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* src/pymatgen/io/vasp/help.py (VaspDoc.get_incar_tags): Use Mediawiki API instead of parsing the HTML source directly. The old approach is not stable against changes in the tag list because of the way URLs are constructed. pagefrom= parameters start from certain tag, which is not guaranteed to provide the complete tag list as the new tags are added before that tag given in pagefrom=. At the moment of writing this commit, PRECFOCK tag is already missed using the old approach.
Following up: https://github.com/materialsproject/pymatgen/issues/4119#issuecomment-2439617604-permalink
- [X] Install `pre-commit` hooks to auto-check types and linting before every commit
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PR_kwDOACgets6ABkYE
| 4,142
|
Add a coerce formal charges method to openff code
|
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[
"Please add a unittest for the new method. Thanks."
] | 2024-10-27T21:55:45
| 2024-11-16T16:42:52
|
CONTRIBUTOR
|
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## Summary
Major changes:
Add a `coerce_formal_charges` method to the `pymatgen.io.openff` code, allowing molecules with formal charges to be more accurately parsed.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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PR_kwDOACgets6ACkTX
| 4,143
|
Improve element mismatch handling with POTCAR for `Poscar.from_file/str`
|
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[
"@yantar92 This situation seems a bit trickier than I thought (I don't have much experience handling an incompatible POTCAR). I'm still finding a cleaner way to handle this.\r\n\r\n`check_for_potcar` doesn't really check the content (elements matching) of a POTCAR, but more likely: \r\n1. check existence (by calling `Potcar.from_file`)\r\n2. Generate `default_names` which is the list of elements in POTCAR \r\nhttps://github.com/materialsproject/pymatgen/blob/4b10dd3fb37d8012d46dee58678ac3a695845104/src/pymatgen/io/vasp/inputs.py#L278-L280\r\n\r\n---\r\n\r\nAnd it turns out it's the `default_names` generated from the incompatible POTCAR that caused the cryptic error: https://github.com/materialsproject/pymatgen/blob/4b10dd3fb37d8012d46dee58678ac3a695845104/src/pymatgen/io/vasp/inputs.py#L418-L428\r\n\r\nIn your specific case, the `n_atoms` is `[1, 720]` (corresponding to your POSCAR) but the `default_names` is `[\"C\", ]` therefore there would be an `IndexError` raised but caught (I believe this is sort of intended, see the comment in the above code block)\r\n\r\nThis block also generates `atomic_symbols` as `[\"C\", ]`, and propagates to the `Structure` init and leads to the final exception we saw (as the lengths of `atomic_symbols` and `coords` mismatch).\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/4b10dd3fb37d8012d46dee58678ac3a695845104/src/pymatgen/io/vasp/inputs.py#L485-L492\r\n\r\n---\r\n\r\nAt this stage I believe not suppress the `IndexError` but re-raise as a semantic `ValueError` is the best solution (also confirmed this would not break any test so far), unless there're other cases that is not covered by tests?\r\n\r\n",
"> At this stage I believe not suppress the IndexError but re-raise as a semantic ValueError is the best solution\r\n\r\nWell. Reading again through the code of Poscar.from_str, it looks like its default behaviour is very permissive - it even assigns arbitrary elements in some scenarios:\r\n\r\n> ... This will ensure at least a\r\n> unique element is assigned to each site and any analysis that does not\r\n> require specific elemental properties should work fine.\r\n\r\nThrowing a warning as you did is 100% helpful.\r\nWhether to throw a ValueError or not, I am not sure. Maybe you can ask the maintainers?",
"Thanks for the comment.\r\n\r\n> Whether to throw a ValueError or not, I am not sure. Maybe you can ask the maintainers?\r\n\r\nI didn't fully understand the code when I left this comment, but I'm now pretty sure re-raising when not alter the original behaviour, only makes the error more understandable.\r\n\r\n---\r\n\r\nI rewrote the code logic to the following:\r\n\r\n```python\r\nif default_names is not None:\r\n # Use len(n_atoms) over len(symbols) as symbols is None for VASP 4 format\r\n if len(n_atoms) > len(default_names):\r\n raise ValueError(f\"{default_names=} (likely from POTCAR) has fewer elements than POSCAR {symbols}\")\r\n\r\n if symbols is None or default_names[: len(symbols)] != symbols:\r\n # After this VASP 4.x POSCAR would be converted to VASP 5/6 format\r\n vasp5or6_symbols = True\r\n\r\n atomic_symbols = []\r\n for idx, n_atom in enumerate(n_atoms):\r\n atomic_symbols.extend([default_names[idx]] * n_atom)\r\n\r\n warnings.warn(f\"Elements in POSCAR would be overwritten by {default_names=}\", stacklevel=2)\r\n```\r\n\r\nBasically there're three branches:\r\n- If the POTCAR (`default_names`) doesn't have enough elements, in the original code it could cause an `IndexError` which is suppressed. But this would leave a partially finished `atomic_symbols` which is then passed to `Structure` init and eventually leading to the cryptic error message you observed.\r\n- If the POTCAR has enough elements:\r\n - Elements would be overwritten if they're different, now a warning is inserted.\r\n - In the original implementation elements would be rewritten even if they're the same, this effectively does nothing but would now by skipped for efficiency.\r\n"
] | 2024-10-28T03:50:41
| 2024-11-14T03:30:46
|
2024-11-13T17:48:17Z
|
CONTRIBUTOR
|
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### Summary
- The glob logic of POTCAR matching might need some attention, as files other than `POTCAR` might take higher priority than `POTCAR`
- Suppress a lot of expected warning in VASP.inputs tests, to avoid warning pollution
### For element mismatch in POTCAR and POSCAR, to fix #4140:
- If is able to overwrite, a warning would be issued (previously would silently overwrite)
- If unable to overwrite as reported in #4140 (fewer elements in POTCAR than POSCAR), a more semantic value error would be raised
|
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I_kwDOACgets6cDmuq
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Some API from `scipy` is deprecated, no replacement inside `scipy`
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[
"Perhaps just copy the source code (and include the BSD license) as they're used only once. The original implementation just use `numpy`:\r\n\r\n\r\nhttps://github.com/scipy/scipy/blob/ea916c6f7f487bd53e98de082649d542cc6106ed/scipy/_lib/_finite_differences.py#L1-L144"
] | 2024-10-28T11:48:51
| 2024-10-29T08:10:38
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2024-10-29T05:01:42Z
|
CONTRIBUTOR
|
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The following two code pieces use deprecated `scipy.misc` API, but `scipy` doesn't provide replacement.
These API should have been removed ([1.12.0 was out in Jan 2024](https://pypi.org/project/scipy/#history)) but perhaps they postponed the removal?
```python
import scipy.misc
print(scipy.__version__) # 1.14.1
print(dir(scipy.misc)) # ['ascent', 'central_diff_weights', 'derivative', 'electrocardiogram', 'face']
```
---
https://github.com/materialsproject/pymatgen/blob/4b10dd3fb37d8012d46dee58678ac3a695845104/src/pymatgen/analysis/quasiharmonic.py#L302-L304
```
scipy.misc.central_diff_weights is deprecated in SciPy v1.10.0;
and will be completely removed in SciPy v1.12.0.
You may consider using findiff: https://github.com/maroba/findiff
or numdifftools: https://github.com/pbrod/numdifftools
```
https://github.com/materialsproject/pymatgen/blob/4b10dd3fb37d8012d46dee58678ac3a695845104/tests/analysis/elasticity/test_elastic.py#L468
```
scipy.misc.central_diff_weights is deprecated in SciPy v1.10.0;
and will be completely removed in SciPy v1.12.0.
You may consider using findiff: https://github.com/maroba/findiff
or numdifftools: https://github.com/pbrod/numdifftools
```
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PR_kwDOACgets6AGTrG
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|
Fixed execution of packmol in relative path.
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[
"Thanks."
] | 2024-10-28T13:04:28
| 2024-10-29T00:04:07
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2024-10-29T00:04:03Z
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CONTRIBUTOR
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## Summary
Major changes:
- fix 1: One could not do packmol_input_set.run("randomdirectory"). Code would fail.
This PR fixes this small issue. Added (actually adapted) a unit test to make sure it continues to work.
|
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I_kwDOACgets6cHYad
| 4,146
|
Memory leak with `Chgcar.from_dict`
|
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[
"Here is a test with `memory_profiler`:\r\n\r\n```python\r\nfrom memory_profiler import profile\r\nfrom monty.serialization import loadfn\r\n\r\n@profile\r\ndef test():\r\n for _ in range(100):\r\n loadfn(\"mp-1000005.json.gz\")\r\n\r\nif __name__ == \"__main__\":\r\n test()\r\n```\r\n\r\nDoing one iteration:\r\n\r\n```\r\nLine # Mem usage Increment Occurrences Line Contents\r\n=============================================================\r\n 5 201.2 MiB 201.2 MiB 1 @profile\r\n 6 def test():\r\n 7 333.6 MiB 0.0 MiB 2 for _ in range(1):\r\n 8 333.6 MiB 132.4 MiB 1 loadfn(\"mp-1000005.json.gz\")\r\n```\r\n\r\nDoing 100 iterations:\r\n\r\n```\r\nLine # Mem usage Increment Occurrences Line Contents\r\n=============================================================\r\n 5 201.2 MiB 201.2 MiB 1 @profile\r\n 6 def test():\r\n 7 450.3 MiB -608.8 MiB 101 for _ in range(100):\r\n 8 450.3 MiB -359.7 MiB 100 loadfn(\"mp-1000005.json.gz\")\r\n```",
"Chgcar inherits Volumetric data and that inherits from MSONable.from_dict. If there is a leak, it is in MSONable.",
"Yup, I am looking into it. I also am not yet convinced this is a \"bug\" or just a quirk of Python. I'm going to close this issue and see if I can reproduce the behavior with the `MSONable` class."
] | 2024-10-28T18:22:11
| 2024-10-28T22:48:58
|
2024-10-28T22:48:31Z
|
NONE
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### Python version
Python 3.12.4
### Pymatgen version
2024.10.27
### Operating system version
Linux
### Current behavior
I'm working with Professor Andrew Rosen @Andrew-S-Rosen. We found what appears to be a memory leak associated with `Chgcar.from_dict`. Even when deleting the object from memory we still witness an increase in memory.
### Expected Behavior
We expected to see no overall net increase in memory.
### Minimal example
```Python
import gzip
import json
import tracemalloc
import psutil
from pymatgen.io.vasp.outputs import Chgcar
# memory tracking functions and start
def get_memory_usage():
"""Get current process memory usage in MB"""
process = psutil.Process()
return process.memory_info().rss / (1024 * 1024)
def log_memory(message, log_file="memory_usage_testRead.log"):
"""Log memory usage to file and print to console"""
mem_usage = get_memory_usage()
log_message = f"{message}: {mem_usage:.2f} MB\n"
# Write to file
with open(log_file, "a") as f:
f.write(log_message)
# Also print to console
print(log_message, end="")
# Start memory tracking
tracemalloc.start()
print(f"Initial memory usage: {get_memory_usage():.2f} MB")
# Read in a CHGCAR several times
for i in range(10):
log_memory(f"Before gzip CHGCAR {i}")
with gzip.open("mp-1000005.json.gz", "rt", encoding="utf-8") as g:
chgcar_json = json.load(g)
log_memory(f"After gzip CHGCAR {i}")
log_memory(f"Before loading CHGCAR {i}")
chgcar = Chgcar.from_dict(chgcar_json["data"])
log_memory(f"After loading CHGCAR {i}")
del chgcar
log_memory(f"After deleting CHGCAR {i}")
print(f"Final memory usage: {get_memory_usage():.2f} MB")
```
### Relevant files to reproduce this bug
[mp-1000005.json.gz](https://github.com/user-attachments/files/17547198/mp-1000005.json.gz)
### Output
```
Initial memory usage: 161.57 MB
Before gzip CHGCAR 0: 161.57 MB
After gzip CHGCAR 0: 243.25 MB
Before loading CHGCAR 0: 243.25 MB
After loading CHGCAR 0: 250.32 MB
After deleting CHGCAR 0: 250.32 MB
Before gzip CHGCAR 1: 250.32 MB
After gzip CHGCAR 1: 359.54 MB
Before loading CHGCAR 1: 359.54 MB
After loading CHGCAR 1: 359.64 MB
After deleting CHGCAR 1: 359.64 MB
Before gzip CHGCAR 2: 359.64 MB
After gzip CHGCAR 2: 367.79 MB
Before loading CHGCAR 2: 367.79 MB
After loading CHGCAR 2: 367.89 MB
After deleting CHGCAR 2: 367.89 MB
Before gzip CHGCAR 3: 367.89 MB
After gzip CHGCAR 3: 320.54 MB
Before loading CHGCAR 3: 320.54 MB
After loading CHGCAR 3: 320.54 MB
After deleting CHGCAR 3: 320.54 MB
Before gzip CHGCAR 4: 320.54 MB
After gzip CHGCAR 4: 320.54 MB
Before loading CHGCAR 4: 320.54 MB
After loading CHGCAR 4: 320.54 MB
After deleting CHGCAR 4: 320.54 MB
Before gzip CHGCAR 5: 320.54 MB
After gzip CHGCAR 5: 324.48 MB
Before loading CHGCAR 5: 324.48 MB
After loading CHGCAR 5: 324.48 MB
After deleting CHGCAR 5: 324.48 MB
Before gzip CHGCAR 6: 324.48 MB
After gzip CHGCAR 6: 373.71 MB
Before loading CHGCAR 6: 373.71 MB
After loading CHGCAR 6: 373.71 MB
After deleting CHGCAR 6: 373.71 MB
Before gzip CHGCAR 7: 373.71 MB
After gzip CHGCAR 7: 324.38 MB
Before loading CHGCAR 7: 324.38 MB
After loading CHGCAR 7: 324.38 MB
After deleting CHGCAR 7: 324.38 MB
Before gzip CHGCAR 8: 324.38 MB
After gzip CHGCAR 8: 322.42 MB
Before loading CHGCAR 8: 322.42 MB
After loading CHGCAR 8: 322.42 MB
After deleting CHGCAR 8: 322.42 MB
Before gzip CHGCAR 9: 322.42 MB
After gzip CHGCAR 9: 324.38 MB
Before loading CHGCAR 9: 324.38 MB
After loading CHGCAR 9: 324.38 MB
After deleting CHGCAR 9: 324.38 MB
Final memory usage: 324.38 MB
```
This was for a different CHGCAR file, but the same behavior is observed for many CHGCARs we tried. In production calculations, the memory usage continually increased, although here it tends to fluctuate after a notable initial increase.
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PR_kwDOACgets6AJKqj
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Bump rexml from 3.3.6 to 3.3.9 in /docs
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[] | 2024-10-28T18:45:14
| 2024-10-29T00:03:47
|
2024-10-29T00:03:45Z
|
CONTRIBUTOR
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Bumps [rexml](https://github.com/ruby/rexml) from 3.3.6 to 3.3.9.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/ruby/rexml/releases">rexml's releases</a>.</em></p>
<blockquote>
<h2>REXML 3.3.9 - 2024-10-24</h2>
<h3>Improvements</h3>
<ul>
<li>Improved performance.
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/210">GH-210</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<h3>Fixes</h3>
<ul>
<li>
<p>Fixed a parse bug for text only invalid XML.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/215">GH-215</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Fixed a parse bug that <code>&#0x...;</code> is accepted as a character
reference.</p>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>NAITOH Jun</li>
</ul>
<h2>REXML 3.3.8 - 2024-09-29</h2>
<h3>Improvements</h3>
<ul>
<li>SAX2: Improve parse performance.
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/207">GH-207</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<h3>Fixes</h3>
<ul>
<li>Fixed a bug that unexpected attribute namespace conflict error for
the predefined "xml" namespace is reported.
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/208">GH-208</a></li>
<li>Patch by KITAITI Makoto</li>
</ul>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>
<p>NAITOH Jun</p>
</li>
<li>
<p>KITAITI Makoto</p>
</li>
</ul>
<h2>REXML 3.3.7 - 2024-09-04</h2>
<h3>Improvements</h3>
<ul>
<li>Added local entity expansion limit methods
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/192">GH-192</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/202">GH-202</a></li>
<li>Reported by takuya kodama.</li>
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/ruby/rexml/blob/master/NEWS.md">rexml's changelog</a>.</em></p>
<blockquote>
<h2>3.3.9 - 2024-10-24 {#version-3-3-9}</h2>
<h3>Improvements</h3>
<ul>
<li>Improved performance.
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/210">GH-210</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<h3>Fixes</h3>
<ul>
<li>
<p>Fixed a parse bug for text only invalid XML.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/215">GH-215</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Fixed a parse bug that <code>&#0x...;</code> is accepted as a character
reference.</p>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>NAITOH Jun</li>
</ul>
<h2>3.3.8 - 2024-09-29 {#version-3-3-8}</h2>
<h3>Improvements</h3>
<ul>
<li>SAX2: Improve parse performance.
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/207">GH-207</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<h3>Fixes</h3>
<ul>
<li>Fixed a bug that unexpected attribute namespace conflict error for
the predefined "xml" namespace is reported.
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/208">GH-208</a></li>
<li>Patch by KITAITI Makoto</li>
</ul>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>
<p>NAITOH Jun</p>
</li>
<li>
<p>KITAITI Makoto</p>
</li>
</ul>
<h2>3.3.7 - 2024-09-04 {#version-3-3-7}</h2>
<h3>Improvements</h3>
<ul>
<li>Added local entity expansion limit methods
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/192">GH-192</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/202">GH-202</a></li>
<li>Reported by takuya kodama.</li>
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/ruby/rexml/commit/38eaa86ac7abe0d31cf49d8df57ad239fdeb80e9"><code>38eaa86</code></a> Add 3.3.9 entry</li>
<li><a href="https://github.com/ruby/rexml/commit/ce59f2eb1aeb371fe1643414f06618dbe031979f"><code>ce59f2e</code></a> parser: fix a bug that &#0x...; is accepted as a character reference</li>
<li><a href="https://github.com/ruby/rexml/commit/a09646d395a07399cbf9bc3bc8d6d8bb1d13ecea"><code>a09646d</code></a> test: fix indent</li>
<li><a href="https://github.com/ruby/rexml/commit/cf0fb9c9ca3dc0d725c8e4644aa0e728025f42ce"><code>cf0fb9c</code></a> Fix <code>IOSource#readline</code> for <code>@pending_buffer</code> (<a href="https://redirect.github.com/ruby/rexml/issues/215">#215</a>)</li>
<li><a href="https://github.com/ruby/rexml/commit/1d0c362526f6e25e2abcd13e2fcefcc718c20e78"><code>1d0c362</code></a> Optimize <code>IOSource#read_until</code> method (<a href="https://redirect.github.com/ruby/rexml/issues/210">#210</a>)</li>
<li><a href="https://github.com/ruby/rexml/commit/622011f25ac1519fd553d6c56da52d7eba14a787"><code>622011f</code></a> Bump version</li>
<li><a href="https://github.com/ruby/rexml/commit/036d50851ce091c797db0b9ba3ed8e5a39c3918c"><code>036d508</code></a> test: avoid using needless non ASCII characters</li>
<li><a href="https://github.com/ruby/rexml/commit/4197054a19e65511fb51983518a134a5c65aa840"><code>4197054</code></a> Add 3.3.8 entry</li>
<li><a href="https://github.com/ruby/rexml/commit/78f8712dccad773a51dc5eef31c02d523e994570"><code>78f8712</code></a> Fix handling with "xml:" prefixed namespace (<a href="https://redirect.github.com/ruby/rexml/issues/208">#208</a>)</li>
<li><a href="https://github.com/ruby/rexml/commit/2e1cd64f2f9c0667a840a0e31f9bb99f9e1c2b33"><code>2e1cd64</code></a> Optimize SAX2Parser#get_namespace (<a href="https://redirect.github.com/ruby/rexml/issues/207">#207</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/ruby/rexml/compare/v3.3.6...v3.3.9">compare view</a></li>
</ul>
</details>
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</details>
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WIP: Fix consideration of translation symmetry for some (extremely rare) edge cases in LobsterEnv
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## Summary
- [ ] update documentation
- [ ] completely solve the translation question (i.e., figuring out the direction and origin)
- [ ] add a test case where this plays a role
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# Issue Metrics
| Metric | Average | Median | 90th percentile |
| --- | --- | --- | ---: |
| Time to first response | 11:32:34 | 2:26:24 | 1 day, 7:53:28 |
| Time to close | 2 days, 14:34:21 | 2 days, 4:19:33 | 5 days, 8:02:11 |
| Time to answer | None | None | None |
| Metric | Count |
| --- | ---: |
| Number of items that remain open | 6 |
| Number of items closed | 9 |
| Number of most active mentors | 0 |
| Total number of items created | 15 |
| Title | URL | Author | Time to first response | Time to close | Time to answer |
| --- | --- | --- | --- | --- | --- |
| Some API from `scipy` is deprecated, no replacement inside `scipy` | https://github.com/materialsproject/pymatgen/issues/4144 | [DanielYang59](https://github.com/DanielYang59) | None | 17:12:51 | None |
| Poscar.from_file throws a cryptic error for VASP5-like POSCARs when POTCAR does not contain all the present elements | https://github.com/materialsproject/pymatgen/issues/4140 | [yantar92](https://github.com/yantar92) | 11:44:38 | None | None |
| How to transform elastic constants after a change of basis with the help of pymatgen? | https://github.com/materialsproject/pymatgen/issues/4139 | [hongyi-zhao](https://github.com/hongyi-zhao) | None | 1 day, 12:19:41 | None |
| assimilate method in SimpleVaspToComputedEntryDrone is not raising ValueError | https://github.com/materialsproject/pymatgen/issues/4132 | [igor-s-tan](https://github.com/igor-s-tan) | None | None | None |
| Kpoints.from_file sometimes override the comment | https://github.com/materialsproject/pymatgen/issues/4130 | [yantar92](https://github.com/yantar92) | 0:21:32 | 2 days, 7:59:03 | None |
| Question about conventional cell standards defined by `get_conventional_standard_structure` in pymatgen. | https://github.com/materialsproject/pymatgen/issues/4126 | [hongyi-zhao](https://github.com/hongyi-zhao) | 3:09:53 | 4:19:56 | None |
| Add CUDA functionality to `parse_lammps_dumps` to allow for NVIDIA GPU support when analyzing large dump files. | https://github.com/materialsproject/pymatgen/issues/4125 | [kimiaGF](https://github.com/kimiaGF) | None | None | None |
| `AseAtomsAdaptor` conversions fail to preserve 1D or 2D PBC | https://github.com/materialsproject/pymatgen/issues/4120 | [jsukpark](https://github.com/jsukpark) | None | 0:18:14 | None |
| VaspInput setter and Incar.check_params() are inconsistent | https://github.com/materialsproject/pymatgen/issues/4119 | [yantar92](https://github.com/yantar92) | 1:42:56 | 4 days, 6:18:20 | None |
| `io.pwscf.PWInput.from_file()` incorrectly reads decimal numbers and the `K_POINTS` card in `automatic` mode | https://github.com/materialsproject/pymatgen/issues/4114 | [jsukpark](https://github.com/jsukpark) | None | 4 days, 19:16:28 | None |
| Vampire_interface (pymatgen/analysis/magnetism/heisenberg.py:323:) | https://github.com/materialsproject/pymatgen/issues/4112 | [ghlam14](https://github.com/ghlam14) | None | None | None |
| pmg plot --dos ... errs in matplotlib call | https://github.com/materialsproject/pymatgen/issues/4108 | [yantar92](https://github.com/yantar92) | 0:14:05 | 7 days, 11:05:01 | None |
| Replace POTCAR in MPRelaxSet | https://github.com/materialsproject/pymatgen/issues/4106 | [TDKOLI](https://github.com/TDKOLI) | 2 days, 4:02:19 | 2 days, 4:19:33 | None |
| Glob logic with `bader_analysis_from_path` is error-prone | https://github.com/materialsproject/pymatgen/issues/4089 | [Andrew-S-Rosen](https://github.com/Andrew-S-Rosen) | None | None | None |
| Monthly issue metrics report | https://github.com/materialsproject/pymatgen/issues/4088 | [github-actions[bot]](https://github.com/github-actions[bot]) | None | None | None |
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Added new Flag for `AutoOxiStateDecorationTransformation`
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[
"Merged. Thanks."
] | 2024-11-01T22:09:45
| 2024-12-23T16:38:19
|
2024-11-12T18:04:27Z
|
CONTRIBUTOR
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# New flag for `AutoOxiStateDecorationTransformation`
The situation we have in mind is `AutoOxiStateDecorationTransformation` -> `OrderDisorderedStructureTransformation` pipeline.
The `OrderDisorderedStructureTransformation` expects oxidation numbers to help rank the structure guesses. However, if you have metallic systems, the sequences of transformation breaks. In those cases it's not super clear how the ordered structures should be ranked anyways unless you start invoking more sqs-type logic. For the simple case I think we can allow the users to come up with some quick and dirty guess for ordered structures so they can start computing stuff before they might move on to more fine-grained structure selection.
Added a new `zeros_on_fail` flag.
If True and and the `BVAnalyzer` fails to come up with a guess for the oxidation guess, we will set the all the oxidation states to zero.
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Revert breaking `analysis.local_env` `default_op_params/cn_opt_params` rename
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[] | 2024-11-02T03:19:33
| 2024-11-14T03:31:34
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2024-11-13T17:53:46Z
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CONTRIBUTOR
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## Summary
- Reverse breaking `analysis.local_env` `default_op_params/cn_opt_params` rename, reported in https://github.com/materialsproject/pymatgen-analysis-defects/pull/206 and https://github.com/materialsproject/atomate2/pull/1030
- [x] Add unit test
- Minor format tweak
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<!--pre-commit.ci start-->
updates:
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- [github.com/pre-commit/mirrors-mypy: v1.12.0 → v1.13.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.12.0...v1.13.0)
- [github.com/adamchainz/blacken-docs: 1.19.0 → 1.19.1](https://github.com/adamchainz/blacken-docs/compare/1.19.0...1.19.1)
- [github.com/kynan/nbstripout: 0.7.1 → 0.8.0](https://github.com/kynan/nbstripout/compare/0.7.1...0.8.0)
- [github.com/RobertCraigie/pyright-python: v1.1.384 → v1.1.387](https://github.com/RobertCraigie/pyright-python/compare/v1.1.384...v1.1.387)
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PR_kwDOACgets6A7QT7
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Fix `borg.hive.SimpleVaspToComputedEntryDrone.assimilate` ValueError when core file missing
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2024-11-12T18:01:07Z
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CONTRIBUTOR
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### Summary
- Fix `borg.hive.SimpleVaspToComputedEntryDrone.assimilate` ValueError when core file missing, to fix #4132
- Add unit test
- Improve type annotation
|
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PR_kwDOACgets6A83rv
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Add informative error message to `SymmetryUndeterminedError`
|
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[
"Appreciate the improvement, thanks @kavanase !",
"Sorry for the delay in merging, auto-merge was broken and I hadn't realised. Should be fixed now."
] | 2024-11-05T16:07:50
| 2024-11-17T23:25:00
|
2024-11-17T23:24:47Z
|
CONTRIBUTOR
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After pulling my hair out for a little while, trying to figure out why I was getting `SymmetryUndeterminedError`s when trying to initialise `SpacegroupAnalyzer` with a particular structure (which currently don't come with any message), I realised that `spglib.get_error_message()` can be called to get an error message for why no result was obtained.
This is a small update to include the `spglib.get_error_message()` message in `SymmetryUndeterminedError`, so the user has some idea why it failed.
In action:
<img width="711" alt="image" src="https://github.com/user-attachments/assets/17ebbe2e-1571-4624-9d2a-3375eed9ff75">
<img width="741" alt="image" src="https://github.com/user-attachments/assets/f250b804-cd25-4bcb-8ab6-7d4540432a69">
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I_kwDOACgets6dlCLs
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tests use equality to compare floating point numbers
|
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[
"Thanks for reporting, would fix this."
] | 2024-11-08T11:20:50
| 2025-01-24T15:21:29
|
2025-01-24T15:21:28Z
|
CONTRIBUTOR
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Floating point numbers (angles) are compared in transformation tests at
https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/tests/transformations/test_advanced_transformations.py#L840
Using equality to compare floating point numbers inevitably fails
e.g. https://buildd.debian.org/status/fetch.php?pkg=pymatgen&arch=amd64&ver=2024.10.29%2Bdfsg1-1&stamp=1731061592&raw=0
```
# make sure that the orthorhombic supercell is different from the cubic cell
assert not np.array_equal(
supercell_generator_cubic.transformation_matrix,
supercell_generator_orthorhombic.transformation_matrix,
)
assert transformed_orthorhombic.lattice.abc != transformed_cubic.lattice.abc
# only angels are expected to be the same because of force_90_degrees = True
> assert transformed_cubic.lattice.angles == transformed_orthorhombic.lattice.angles
E assert (89.999970160...0000000086139) == (89.999970160...0000000086142)
E
E At index 2 diff: 90.00000000086139 != 90.00000000086142
E Use -v to get more diff
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:840: AssertionError
```
Floating point comparison needs to be used instead
```
assert_allclose(transformed_cubic.lattice.angles, lattice.angles)
```
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PR_kwDOACgets6BYpAL
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Avoid using full equality (`==`) to compare float, avoid `assert_array_equal` compare float array
|
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[] | 2024-11-09T03:04:29
| 2025-01-24T16:44:29
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2025-01-24T15:21:27Z
|
CONTRIBUTOR
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### Summary
- Avoid using full equality `==` to compare float, to fix #4158
- Avoid [`assert_array_equal` on int array](https://numpy.org/doc/stable/reference/generated/numpy.testing.assert_array_equal.html):
> Assert fails with numerical imprecision with floats:
> Use [assert_allclose](https://numpy.org/doc/stable/reference/generated/numpy.testing.assert_allclose.html#numpy.testing.assert_allclose) or one of the nulp (number of floating point values) functions for these cases instead:
- Tweak `_proj` implementation, ~3x speedup
- (Partially) Replace sequence of float comparison with `==` (list/tuple/dict ...): https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/tests/core/test_bonds.py#L56
- Other type/comment tweaks
|
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PR_kwDOACgets6BZKnC
| 4,160
|
Clean up `io.vasp.outputs.Outcar` docstring
|
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[] | 2024-11-09T09:41:40
| 2025-01-19T02:00:01
|
2025-01-18T16:23:16Z
|
CONTRIBUTOR
|
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### Clean up `io.vasp.outputs.Outcar` docstring/comment
- Greatly enhance type annotation for parsers in `Outcar` with more specific types, clarify docstring: `Renders accessible from self.data` (the internal `self.data` dictionary) vs `Renders accessible from attributes` (instance attributes)
- Other docstring/comment cleanups
### Others
- Change `getattr` default value to `False` instead of `None` when used for condition check
|
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I_kwDOACgets6du8zc
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coordination_geometry int64 indices breaks on 32-bit systems
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[
"Hi @drew-parsons thanks for reporting this and the analysis, sorry for the trouble caused.\r\n\r\nWe explicitly cast `int` to `int64` in a previous migration to NumPy 2.x #3992, as NumPy 2.x changed the default NumPy/Cython integer on 64-bit Windows platform to `int64` (was previously `int32`). Also `np.intp` was not used for the same reason (we want to consistently use `int64` onwards, over declaring fused type).\r\n\r\nThis decision was made with the assumption that very few, if any, users would still be running a 32-bit platform. However, it apparently you are using one. Currently, pymatgen’s CI does not cover 32-bit systems, and I don’t have access to one for testing. I’ll need to set up a 32-bit test environment to investigate this further later.\r\n\r\n",
"Not using it personally, and you're right in practice there are probably few users (maybe some on Raspberry Pi). But the Debian project tries to support as many architectures as feasible, including a few 32-bit ones. Our build logs across the various architectures are listed at https://buildd.debian.org/status/package.php?p=pymatgen.\r\n\r\nDebian hasn't migrated to numpy 2 yet, so those needful updates are still ahead for us.",
"> But the Debian project tries to support as many architectures as feasible, including a few 32-bit ones. \r\n\r\nYep I agree having better compatibility is almost always a good thing, as long as the price is not too high. I would have to look at this a bit later, thanks for sharing the info. ",
"Okay I just set up a Debian 12 32-bit VM and I could recreate this, would try to fix this soon.\r\n```\r\n def _cg_csm_separation_plane_optim2(\r\n self,\r\n coordination_geometry,\r\n sepplane,\r\n local_plane,\r\n points_perfect=None,\r\n separation_indices=None,\r\n ):\r\n argref_separation = sepplane.argsorted_ref_separation_perm\r\n permutations = []\r\n permutations_symmetry_measures = []\r\n stop_search = False\r\n # TODO: do not do that several times ... also keep in memory\r\n if sepplane.ordered_plane:\r\n> inp = self.local_geometry.coords.take(separation_indices[1], axis=0)\r\nE TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'\r\n\r\n/home/yang/pymatgen/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py:1979: TypeError\r\n\r\n4 failed, 20 passed, 2 skipped in 6.13s\r\n```"
] | 2024-11-09T17:17:11
| 2024-12-11T02:03:15
|
2024-12-11T02:03:15Z
|
CONTRIBUTOR
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### Python version
Python 3.12.7
### Pymatgen version
2024.10.29
### Operating system version
Debian unstable
### Current behavior
pymatgen coordination geometry sets an explicit `int64` for separation indices at
https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py#L1738
This breaks on 32-bit systems at
https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py#L1979
```
inp = self.local_geometry.coords.take(separation_indices[1], axis=0)
```
(also ll.1981,1989).
On 32-bit systems array indices are int32 (or more precisely, `np.intp`). So using `int64` as the argument to the `take()` function results in an error
```
if sepplane.ordered_plane:
> inp = self.local_geometry.coords.take(separation_indices[1], axis=0)
E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py:1979: TypeError
```
Error logs can be found at https://buildd.debian.org/status/fetch.php?pkg=pymatgen&arch=armel&ver=2024.10.29%2Bdfsg1-1&stamp=1731068454&raw=0
also [armhf](https://buildd.debian.org/status/fetch.php?pkg=pymatgen&arch=armhf&ver=2024.10.29%2Bdfsg1-1&stamp=1731065422&raw=0),
### Expected Behavior
The index type provided to `take()` needs to be compatible.
Down-conversion could be down by changing l.1979 to
```
inp = self.local_geometry.coords.take(separation_indices[1].astype(np.intp), axis=0)
```
(likewise at the other 2 lines).
Down conversion could be a problem if you really wanted to use 64-bit indexing on 32-bit systems, but perhaps that's unavoidable. One way of avoiding unexpected problems is to not use int64 in the first place, and define the separation indices at l.1738 as
```
_sep = [np.array(ss, dtype=np.intp) for ss in separation]
```
(in which case the `astype` patch at l.1979 would not be needed)
### Minimal example
```Python
pytest-3 -v -k "test_real_systems or TestCoordinationGeometryFinder or test_from_structure_environments" tests/analysis/chemenv
```
### Relevant files to reproduce this bug
_No response_
|
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I_kwDOACgets6dxUaL
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|
A few functions use unrounded `float` as `dict` keys
|
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[] | 2024-11-10T07:35:48
| 2024-11-13T02:55:59
|
CONTRIBUTOR
|
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Using `float` as `dict` keys can be prone to precision issues (especially when `float` is not rounded), a few functions operate on such `dict[float, Any]` (could be more not annotated):
### `core.bonds.obtain_all_bond_lengths`
https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/core/bonds.py#L122-L137
### `core.lattice.Lattie`
https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/core/lattice.py#L545-L557
### diffraction patterns
https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/analysis/diffraction/neutron.py#L135
https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/analysis/diffraction/xrd.py#L199
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https://github.com/materialsproject/pymatgen/pull/4163
| 2,647,079,612
|
PR_kwDOACgets6BbM7q
| 4,163
|
Clarify `util.string.formula_double_format` return type, fix using `int` to round to nearest int
|
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[] | 2024-11-10T10:32:11
| 2024-11-13T01:43:56
|
2024-11-12T18:00:48Z
|
CONTRIBUTOR
|
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### Summary
- [ ] Should `formula_double_format` return string instead of float?
- Clarify `util.string.formula_double_format` return type as `Literal[""] | float`
- Add types for `util.string`
- **Bug fix**: `int` would not round to nearest int (but truncate decimal part): https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/util/string.py#L136-L137
https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/util/string.py#L129
- **Two minor behavior changes** for `formula_double_format`:
1. Use `isclose` to round float very close to `1`:
```diff
- if ignore_ones and afloat == 1:
+ if ignore_ones and math.isclose(afloat, 1, abs_tol=tol):
```
2. `tol` now includes the boundary (unit test added):
```diff
- if abs(afloat - int(afloat)) < tol:
+ if math.isclose(afloat, round(afloat), abs_tol=tol):
```
```python
print(math.isclose(1, 1+1E-8, abs_tol=1E-8)) # True
```
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PR_kwDOACgets6Bbl1q
| 4,164
|
Replace hard-coded `np.allclose/isclose` and `math.isclose` (for complex expression)
|
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[] | 2024-11-10T15:17:21
| 2024-11-14T03:30:33
|
2024-11-13T17:45:49Z
|
CONTRIBUTOR
|
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### Summary
- Replace some hard-coded `np.allclose/isclose`
- Replace hard-coded `abs(a-b)<= tol` with`isclose` for **complex expressions**, **rationale**:
- better readability as `isclose` is more declarative, especially for complex expressions like `if abs(p1 - pos2[idx]) > tolerance[idx] and abs(p1 - pos2[idx]) < 1 - tolerance[idx]:`
- `isclose` is about 1.5x faster than `abs(a - b) <= abs_tol`, see following benchmark, presumably [`math` is implemented in C](https://github.com/python/cpython/blob/6ee542d491589b470ec7cdd353463ff9ff52d098/Modules/mathmodule.c#L3133-L3174)
- more consistent edge case handling on the boundary (`isclose` always includes boundary)
- [**WARNING**] For `abs(a - b) < abs_tol`, the behavior changes when `abs(a - b) == abs_tol` because `math.isclose` includes the boundary. However, this should be a **very rare edge case**.
#### Simplify some math expressions
- Avoid `int(round(x))` as `round(x)` already gives int, similar to `math.ceil/floor/gcd/...`
- Replace `int(len(something) / positive_number)` with `len(something) // positive_number`, as the latter is more concise and 2x faster (WARNING: their behaviours are different for negative numbers)
- Simplify comparison again zero: `abs(number - 0) [><]=? something`, simplify `1.0e-n` to `1e-n`
- Avoid `from math import xxx` when `xxx` is used only very few times, to declutter namespace
---
### Speed comparison
- [x] `math.isclose(a, b, abs_tol=abs_tol, rel_tol=0)` vs `abs(a - b) <= abs_tol`
```
Benchmark - math.isclose time: 0.028936 seconds
Benchmark - Custom Compare time: 0.036071 seconds
```
<details>
<summary> script(by GPT) </summary>
```python
import math
import time
import random
def custom_compare(a, b, abs_tol):
"""Custom comparison using absolute tolerance only."""
return abs(a - b) <= abs_tol
def test_comparisons(abs_tolerance, num_tests):
correct_count_isclose = 0
correct_count_custom = 0
for _ in range(num_tests):
# Generate two random floats and a tolerance
a = random.uniform(-1e6, 1e6)
b = a + random.uniform(-abs_tolerance * 2, abs_tolerance * 2) # b is within absolute tolerance range of a
# Using math.isclose with only absolute tolerance
if math.isclose(a, b, abs_tol=abs_tolerance, rel_tol=0):
correct_count_isclose += 1
# Using custom comparison
if custom_compare(a, b, abs_tolerance):
correct_count_custom += 1
return correct_count_isclose, correct_count_custom
def benchmark_comparisons(abs_tolerance, num_iterations):
a = random.uniform(-1e6, 1e6)
b = a + random.uniform(-abs_tolerance * 2, abs_tolerance * 2)
# Benchmark math.isclose
start_isclose = time.perf_counter()
for _ in range(num_iterations):
math.isclose(a, b, abs_tol=abs_tolerance)
end_isclose = time.perf_counter()
# Benchmark custom comparison
start_custom = time.perf_counter()
for _ in range(num_iterations):
custom_compare(a, b, abs_tolerance)
end_custom = time.perf_counter()
return (end_isclose - start_isclose), (end_custom - start_custom)
if __name__ == "__main__":
abs_tolerance = 1e-9
num_tests = 10000
num_iterations = 1000000
# Test correctness
correct_count_isclose, correct_count_custom = test_comparisons(abs_tolerance, num_tests)
print(f"Correctness Test - math.isclose: {correct_count_isclose}/{num_tests}")
print(f"Correctness Test - Custom Compare: {correct_count_custom}/{num_tests}")
# Benchmark performance
time_isclose, time_custom = benchmark_comparisons(abs_tolerance, num_iterations)
print(f"Benchmark - math.isclose time: {time_isclose:.6f} seconds")
print(f"Benchmark - Custom Compare time: {time_custom:.6f} seconds")
```
</details>
- [x] `np.allclose` vs `np.all(np.abs(array_a - array_b) <= abs_tol)` on 100x100 arrays
It seems custom implementation is faster, might need special attention
```
Benchmark - np.allclose time: 0.148381 seconds
Benchmark - Custom allclose time: 0.100266 seconds
```
<details>
<summary> script (by GPT) </summary>
```python
import numpy as np
import time
def custom_allclose(array_a, array_b, abs_tol):
"""Custom implementation of allclose using absolute tolerance."""
return np.all(np.abs(array_a - array_b) <= abs_tol)
def benchmark_np_allclose_and_custom(abs_tol, num_iterations):
# Benchmark numpy.allclose
start_np_allclose = time.perf_counter()
for _ in range(num_iterations):
# Generate two random 100x100 arrays for each iteration
array_a = np.random.uniform(-1e6, 1e6, (100, 100))
array_b = array_a + np.random.uniform(-abs_tol * 2, abs_tol * 2, (100, 100)) # Ensure b is within tolerance of a
np.allclose(array_a, array_b, atol=abs_tol, rtol=0)
end_np_allclose = time.perf_counter()
# Benchmark custom allclose
start_custom_allclose = time.perf_counter()
for _ in range(num_iterations):
# Generate two random 100x100 arrays for each iteration
array_a = np.random.uniform(-1e6, 1e6, (100, 100))
array_b = array_a + np.random.uniform(-abs_tol * 2, abs_tol * 2, (100, 100)) # Ensure b is within tolerance of a
custom_allclose(array_a, array_b, abs_tol)
end_custom_allclose = time.perf_counter()
return (end_np_allclose - start_np_allclose), (end_custom_allclose - start_custom_allclose)
if __name__ == "__main__":
abs_tolerance = 1e-9
num_iterations = 1000
# Run the benchmark
time_np_allclose, time_custom_allclose = benchmark_np_allclose_and_custom(abs_tolerance, num_iterations)
print(f"Benchmark - np.allclose time: {time_np_allclose:.6f} seconds")
print(f"Benchmark - Custom allclose time: {time_custom_allclose:.6f} seconds")
```
</details>
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| 2,648,294,170
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I_kwDOACgets6d2cMa
| 4,165
|
[BUG] Missing `()` in `electronic_structure.boltztrap.BoltztrapAnalyzer.get_extreme.is_isotropic`
|
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[] | 2024-11-11T06:21:03
| 2025-01-28T20:28:39
|
2025-01-28T20:28:39Z
|
CONTRIBUTOR
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Seemingly missing `()` in 744c7db9780a301e2f5fcdf1948a1b7a4d36a404: https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/electronic_structure/boltztrap.py#L1457-L1473
```diff
- and (abs(st[2] - st[0]) / st[2] <= isotropy_tolerance)
+ and (abs((st[2] - st[0]) / st[2]) <= isotropy_tolerance)
```
i.e.:
```diff
- abs(a) / b <= tol
+ abs(a / b) <= tol
```
Otherwise any vector with a negative z component would be considered isotropic along z direction.
Can you please comment on this? @computron
|
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[BUG] Incorrect usage of `np.all() > tol` for element-wise value comparison
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"@naik-aakash Could you kindly check this (after Thursday ;))? Thanks a lot. ",
"Hi @DanielYang59 , thanks for pointing this out. Indeed there seems to have been an error with comparison logic here. Using np.any should be preferable here as you suggested I think.\r\n\r\nI assume you have already started working on this issue, if not am also happy to raise a PR for this. Let me know.",
"Hi @naik-aakash greetings thanks for looking into this :)\r\n\r\n> Using np.any should be preferable here as you suggested I think.\r\n\r\nI might have caused confusion here, sorry. The main issue is not the usage of `any()` over `all()`, but the order of comparison vs `all/any` call. And we should do comparison **before** `all/any` evaluation:\r\n> Test whether all array elements along a given axis evaluate to True.\r\n\r\nCurrent implementation does the other way round, i.e. calling `array.all()` would evaluate the array to a `bool`, and we're basically comparing the bool (`0/1`) with `limit_deviation`.\r\n\r\n---\r\n\r\n> I assume you have already started working on this issue, if not am also happy to raise a PR for this. Let me know.\r\n\r\nI might need your help to fix this, and it's apparently not covered by unit test. Perhaps you could enhance the unit test on top of fixing the implementation? Thank you!\r\n\r\n",
"Hey 😃 ,\r\n\r\nI have an additional suggestion to improve this function further. Instead of looping through each value like that, \r\nhttps://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/io/lobster/outputs.py#L1713-L1735\r\nmaybe we could aim for a more compact comparison:\r\n```python\r\nimport numpy as np\r\n\r\ndef validate_band_overlaps(matrices, num_occ_bands, limit_deviation):\r\n \"\"\"\r\n Validate diagonal and off-diagonal elements for band overlaps.\r\n \"\"\"\r\n for matrix in matrices:\r\n matrix = np.array(matrix)\r\n # Limit matrix to occupied bands\r\n sub_matrix = matrix[:num_occ_bands, :num_occ_bands]\r\n\r\n # Check diagonal elements\r\n if np.any(np.abs(np.diag(sub_matrix) - 1.0) > limit_deviation):\r\n return False\r\n\r\n # Check off-diagonal elements\r\n if np.any(np.abs(sub_matrix - np.diag(np.diag(sub_matrix))) > limit_deviation):\r\n return False\r\n\r\n return True\r\n\r\n\r\ndef check_band_overlaps(band_overlaps_dict, number_occ_bands_spin_up, limit_deviation, spin_polarized=False, number_occ_bands_spin_down=None):\r\n \"\"\"\r\n Check band overlaps for spin-up and optionally spin-down configurations.\r\n \"\"\"\r\n # Validate spin-up matrices\r\n if not validate_band_overlaps(band_overlaps_dict[Spin.up][\"matrices\"], number_occ_bands_spin_up, limit_deviation):\r\n return False\r\n\r\n # Validate spin-down matrices if spin-polarized\r\n if spin_polarized:\r\n if number_occ_bands_spin_down is None:\r\n raise ValueError(\"number_occ_bands_spin_down must be specified.\")\r\n if not validate_band_overlaps(band_overlaps_dict[Spin.down][\"matrices\"], number_occ_bands_spin_down, limit_deviation):\r\n return False\r\n\r\n return True\r\n```\r\n(*Disclaimer*: this is ChatGPT-generated but looks about like the code structure I would have proposed, maybe one can condense it a little bit).\r\n\r\nWhat do you think about that, @naik-aakash ?\r\n",
"@QuantumChemist Brilliant idea, I didn't look closely into the code itself at the time of opening this issue, but I fully support your idea to reduce code repetition and nest level.\r\n\r\nI'm not quite familiar with the expected type and shape of the `matrix` from `band_overlaps_dict[Spin.up][\"matrices\"]`, but looks like it's a 2D square array of floats? If that's the case, perhaps comparing its top-left `num_occ_bands x num_occ_bands` leading principal sub-array with an identity array? Something like:\r\n\r\n```python\r\nif spin_polarized and number_occ_bands_spin_down is None:\r\n raise ValueError(\"number_occ_bands_spin_down has to be specified\")\r\n\r\nfor spin in (Spin.up, Spin.down) if spin_polarized else (Spin.up,):\r\n num_occ_bands = number_occ_bands_spin_up if spin == Spin.up else number_occ_bands_spin_down\r\n\r\n for array in self.band_overlaps_dict[spin][\"matrices\"]:\r\n # Looks like it is already np.array?\r\n sub_array = np.asarray(array)[:num_occ_bands, :num_occ_bands]\r\n\r\n if not np.allclose(sub_array, np.identity(num_occ_bands), atol=limit_deviation, rtol=0):\r\n return False\r\n\r\nreturn True\r\n```\r\n\r\n---\r\n\r\nI realized I might be misusing the word \"matrix\" as we're not doing linear algebra operations, I believe \"array\" might be a better term. I'm mentioning this because [NumPy is discouraging the usage of `np.matrix` even for real linear algebra usage](https://numpy.org/doc/stable/reference/generated/numpy.matrix.html):\r\n> It is no longer recommended to use this class, even for linear algebra. Instead use regular arrays. The class may be removed in the future.",
"Thank you so much, @QuantumChemist and @DanielYang59, for the suggestions to reduce the code complexity. I will implement the suggestions and raise a PR soon \r\n\r\nAnd @DanielYang59 , you are right, it is not using matrix but already an numpy array but the term \"matrix\" is used in Bandoverlaps class just to ensure consistency with actual output files from LOBSTER."
] | 2024-11-11T06:41:47
| 2024-11-18T13:32:59
|
2024-11-18T13:32:59Z
|
CONTRIBUTOR
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The following method: https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/io/lobster/outputs.py#L1694-L1737
Used a pattern like `np.array().all() > tolerance` with the intention to perform element-wise value comparison, however [this seems to be misused as `all()`](https://numpy.org/doc/stable/reference/generated/numpy.all.html#numpy.all):
> "Test whether all array elements along a given axis evaluate to True."
```python
import numpy as np
arr = np.array([1, 2, 3])
print(arr.all()) # True
print(np.array([False, 1, 2]).all()) # False
```
Should be something like:
```diff
- if abs(band2 - 1.0).all() > limit_deviation:
# However this logic might need double check as it only evaluates to True
# when ALL deviations are greater than threshold
+ if np.all(np.abs(band2 - 1) > limit_deviation):
# Perhaps it should be the following?
+ if np.any(np.abs(band2 - 1) > limit_deviation):
# The same to the other
- elif band2.all() > limit_deviation:
+ elif np.all(band2 > limit_deviation)
# The following seems more sensible?
+ elif np.any(band2 > limit_deviation)
```
I might go ahead and change this if I didn't misunderstand anything? @JaGeo
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PR_kwDOACgets6BmBv3
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Fix: BSPlotterProjected._Orbitals_SumOrbitals() method
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[
"And I also have a question, why we need run this\r\n\r\n```python\r\nelif len(dictio[elt][0]) > 1:\r\n```\r\nfor example code, the len(\"dxy\") = 3, what's meaning of this?"
] | 2024-11-12T07:35:01
| 2024-11-24T12:22:51
|
NONE
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**Fix**: Ensure BSPlotterProjected._Orbitals_SumOrbitals() checks if sum_morbs is not None, as a NoneType object cannot be iterated.
## Summary
### Major changes:
- Fixed the BSPlotterProjected._Orbitals_SumOrbitals() method to handle cases where sum_morbs is None.
## Description
When running the following code, I encountered an error in the get_projected_plots_dots_patom_pmorb() method, which uses _Orbitals_SumOrbitals(). The error occurred because sum_morbs was None, making it non-iterable.
This fix addresses the issue by ensuring that sum_morbs is checked to confirm it is not None before any iteration, especially when plotting a single orbital. The order of statements has been adjusted accordingly.
### Example Code to Reproduce:
```python
from pymatgen.electronic_structure.plotter import DosPlotter, BSPlotter, BSPlotterProjected, BSDOSPlotter
from pymatgen.io.vasp import BSVasprun, Vasprun
v = BSVasprun("./bs/vasprun.xml", parse_projected_eigen=True)
bs = v.get_band_structure(kpoints_filename="./bs/KPOINTS", line_mode=True)
plotter = BSPlotterProjected(bs)
plotter.get_projected_plots_dots_patom_pmorb({"Au": ["dxy"]}, {"Au": [1]}, ylim=[-5, 5])
```
This change ensures more robust handling of cases where sum_morbs is None to prevent runtime errors.
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PR_kwDOACgets6BmlDd
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`matplotlib` test use non-interactive `agg` backend
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[] | 2024-11-12T09:02:49
| 2024-11-13T01:43:45
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2024-11-12T18:00:28Z
|
CONTRIBUTOR
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### Summary
- I don't think we need `PMG_VASP_PSP_DIR` in editable mode
- [`matplotlib` test use non-interactive `agg` backend](https://matplotlib.org/stable/users/explain/figure/backends.html), as the [tk install for github windows runner seems pretty flaky](https://github.com/matplotlib/matplotlib/issues/29119#issuecomment-2469406065)
> The last, Agg, is a non-interactive backend that can only write to files. It is used on Linux, if Matplotlib cannot connect to either an X display or a Wayland display.
> The names of builtin backends are case-insensitive; e.g., 'QtAgg' and 'qtagg' are equivalent.
The tk backend might [emit intermittent failures](https://github.com/materialsproject/pymatgen/actions/runs/11771540044/job/32785607964?pr=4159) like:
```
> self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
E _tkinter.TclError: invalid command name "tcl_findLibrary"
```
[Or](https://github.com/materialsproject/pymatgen/actions/runs/11793603996/job/32849482132?pr=4164):
```
> self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
E _tkinter.TclError: Can't find a usable init.tcl in the following directories:
E C:/Users/runneradmin/micromamba/envs/pmg/Library/lib/tcl8.6 C:/Users/runneradmin/micromamba/envs/lib/tcl8.6 C:/Users/runneradmin/micromamba/lib/tcl8.6 C:/Users/runneradmin/micromamba/envs/library C:/Users/runneradmin/micromamba/library C:/Users/runneradmin/micromamba/tcl8.6.13/library C:/Users/runneradmin/tcl8.6.13/library
E
E C:/Users/runneradmin/micromamba/envs/pmg/Library/lib/tcl8.6/init.tcl: couldn't read file "C:/Users/runneradmin/micromamba/envs/pmg/Library/lib/tcl8.6/init.tcl": No error
E couldn't read file "C:/Users/runneradmin/micromamba/envs/pmg/Library/lib/tcl8.6/init.tcl": No error
E while executing
E "source C:/Users/runneradmin/micromamba/envs/pmg/Library/lib/tcl8.6/init.tcl"
E ("uplevel" body line 1)
E invoked from within
E "uplevel #0 [list source $tclfile]"
E
E
E This probably means that Tcl wasn't installed properly.
```
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CP2K fixes
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[] | null |
[
"Merged. Thanks. One option is to break this out as an add-on for separate management."
] | 2024-11-13T00:11:13
| 2024-11-13T02:11:34
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2024-11-13T02:05:11Z
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MEMBER
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this PR fixes several bugs encountered trying to use the `cp2k` modules in `pymatgen` which don't seem to have seen active development over the last 4 years (so some errors from upstream breaking changes expected)
## Key Changes
1. **Default Verbosity**: change `Keyword` + `Section` `verbose` default to `False` to stop printing explanatory comments for sections and flags into _every_ CP2K input file (don't explain stuff that can just be looked up in the docs)
2. **YAML Migration**: Switched from `ruamel.yaml` to `pyyaml` to resolve `AttributeError` in `setup_cp2k_data` function.
3. **Basis Set & Potential Handling**:
- Added support for string-based potential specifications (used to raise `AttributeError` no `.filename`)
- Added fallback to global basis sets and potentials in `get_basis_and_potential`
- Added `cp2k_data_dir` keyword parameter in `get_basis_and_potential` that takes precedence over `PMG_CP2K_DATA_DIR` from `pmgrc.yaml`
## Bug Fixes
- Fixed `KeyError` in `calculation_type` when `self.data.get("dft")` returns `None`
- Fixed trailing whitespace in `Section._get_str`
|
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https://github.com/materialsproject/pymatgen/pull/4170
| 2,659,852,600
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PR_kwDOACgets6B9vcY
| 4,170
|
CP2K allow specifying default initial element magmoms
|
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[] | 2024-11-14T19:28:16
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2024-11-17T23:20:50Z
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MEMBER
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`DftSet` in `src/pymatgen/io/cp2k/sets.py` gets a new `element_defaults: dict[str, dict[str, Any]] | None = None` keyword (format is `{element: {key: value}}`). includes new tests for this feature
`element_defaults` allows specifying e.g. initial magmoms/spins via the "magnetization" key for each element
this PR also adds corresponding env vars for all CP2K specific `.pmgrc.yaml` keys:
- `CP2K_DATA_DIR`
- `DEFAULT_CP2K_FUNCTIONAL`
- `DEFAULT_CP2K_BASIS_TYPE`
- `DEFAULT_CP2K_AUX_BASIS_TYPE`
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10 tests error out because they fail to find some files
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[
"Hi @yurivict thanks for asking.\r\n\r\nLooks like you installed `pymatgen` in non-editable mode, **`pymatgen` doesn't include test files as package data**, so you have to get the test files (usually by cloning the repo), and use one of the two ways to make test files available:\r\n- Install `pymatgen` in editable mode from cloned repo, i.e. `python -m pip install -e /path/to/cloned_pymatgen_repo`\r\n- Use the environment variable `PMG_TEST_FILES_DIR` to point to test files if you don't want to install in editable mode \r\n\r\n",
"PMG_TEST_FILES_DIR works, thanks!"
] | 2024-11-14T22:17:26
| 2025-01-24T07:36:23
|
2025-01-24T07:36:21Z
|
NONE
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### Python version
Python-3.11
### Pymatgen version
2024.11.13
### Operating system version
FreeBSD 14.1
### Current behavior
```
========================================================================================== ERRORS ===========================================================================================
___________________________________________________________ ERROR collecting tests/analysis/ferroelectricity/test_polarization.py ___________________________________________________________
analysis/ferroelectricity/test_polarization.py:23: in <module>
structures = [Structure.from_file(f"{TEST_DIR}/{folder}/POSCAR") for folder in bto_folders]
analysis/ferroelectricity/test_polarization.py:23: in <listcomp>
structures = [Structure.from_file(f"{TEST_DIR}/{folder}/POSCAR") for folder in bto_folders]
../../stage/usr/local/lib/python3.11/site-packages/pymatgen/core/structure.py:3175: in from_file
with zopen(filename, mode="rt", errors="replace") as file:
/usr/local/lib/python3.11/site-packages/monty/io.py:50: in zopen
return open(filename, *args, **kwargs)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/ports/science/py-pymatgen/work-py311/stage/usr/local/lib/python3.11/site-packages/../tests/files/io/vasp/fixtures/BTO_221_99_polarization/nonpolar_polarization/POSCAR'
___________________________________________________________________ ERROR collecting tests/analysis/xas/test_spectrum.py ____________________________________________________________________
analysis/xas/test_spectrum.py:17: in <module>
with open(f"{TEST_DIR}/LiCoO2_k_xanes.json") as file:
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/ports/science/py-pymatgen/work-py311/stage/usr/local/lib/python3.11/site-packages/../tests/files/analysis/spectrum_test/LiCoO2_k_xanes.json'
__________________________________________________________________ ERROR collecting tests/entries/test_computed_entries.py __________________________________________________________________
entries/test_computed_entries.py:29: in <module>
vasp_run = Vasprun(f"{VASP_OUT_DIR}/vasprun.xml.gz")
../../stage/usr/local/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:312: in __init__
with zopen(filename, mode="rt") as file:
/usr/local/lib/python3.11/site-packages/monty/io.py:47: in zopen
return gzip.open(filename, *args, **kwargs)
/usr/local/lib/python3.11/gzip.py:58: in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
/usr/local/lib/python3.11/gzip.py:174: in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/ports/science/py-pymatgen/work-py311/stage/usr/local/lib/python3.11/site-packages/../tests/files/io/vasp/outputs/vasprun.xml.gz'
______________________________________________________________________ ERROR collecting tests/io/feff/test_outputs.py _______________________________________________________________________
io/feff/test_outputs.py:11: in <module>
class TestFeffLdos(TestCase):
io/feff/test_outputs.py:14: in TestFeffLdos
ldos = LDos.from_file(filepath1, filepath2)
../../stage/usr/local/lib/python3.11/site-packages/pymatgen/io/feff/outputs.py:59: in from_file
header_str = Header.header_string_from_file(feff_inp_file)
../../stage/usr/local/lib/python3.11/site-packages/pymatgen/io/feff/inputs.py:249: in header_string_from_file
with zopen(filename, mode="r") as file:
/usr/local/lib/python3.11/site-packages/monty/io.py:50: in zopen
return open(filename, *args, **kwargs)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/ports/science/py-pymatgen/work-py311/stage/usr/local/lib/python3.11/site-packages/../tests/files/io/feff/feff.inp'
______________________________________________________________________ ERROR collecting tests/io/qchem/test_outputs.py ______________________________________________________________________
io/qchem/test_outputs.py:37: in <module>
SINGLE_JOB_DICT = loadfn(f"{TEST_DIR}/single_job.json")
/usr/local/lib/python3.11/site-packages/monty/serialization.py:70: in loadfn
with zopen(fn, "rt") as fp:
/usr/local/lib/python3.11/site-packages/monty/io.py:50: in zopen
return open(filename, *args, **kwargs)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/ports/science/py-pymatgen/work-py311/stage/usr/local/lib/python3.11/site-packages/../tests/files/io/qchem/single_job.json'
___________________________________________________________________________ ERROR collecting tests/io/test_ase.py ___________________________________________________________________________
io/test_ase.py:18: in <module>
STRUCTURE = Structure.from_file(f"{VASP_IN_DIR}/POSCAR")
../../stage/usr/local/lib/python3.11/site-packages/pymatgen/core/structure.py:3175: in from_file
with zopen(filename, mode="rt", errors="replace") as file:
/usr/local/lib/python3.11/site-packages/monty/io.py:50: in zopen
return open(filename, *args, **kwargs)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/ports/science/py-pymatgen/work-py311/stage/usr/local/lib/python3.11/site-packages/../tests/files/io/vasp/inputs/POSCAR'
________________________________________________________________________ ERROR collecting tests/io/test_optimade.py _________________________________________________________________________
io/test_optimade.py:9: in <module>
STRUCTURE = Structure.from_file(f"{VASP_IN_DIR}/POSCAR")
../../stage/usr/local/lib/python3.11/site-packages/pymatgen/core/structure.py:3175: in from_file
with zopen(filename, mode="rt", errors="replace") as file:
/usr/local/lib/python3.11/site-packages/monty/io.py:50: in zopen
return open(filename, *args, **kwargs)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/ports/science/py-pymatgen/work-py311/stage/usr/local/lib/python3.11/site-packages/../tests/files/io/vasp/inputs/POSCAR'
___________________________________________________________________________ ERROR collecting tests/io/test_res.py ___________________________________________________________________________
io/test_res.py:15: in <module>
@pytest.mark.parametrize("provider", [AirssProvider.from_file(res_coc, "strict")])
../../stage/usr/local/lib/python3.11/site-packages/pymatgen/io/res.py:433: in from_file
return cls(ResParser._parse_file(filename), parse_rems)
../../stage/usr/local/lib/python3.11/site-packages/pymatgen/io/res.py:252: in _parse_file
with zopen(filename, mode="r") as file:
/usr/local/lib/python3.11/site-packages/monty/io.py:50: in zopen
return open(filename, *args, **kwargs)
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/ports/science/py-pymatgen/work-py311/stage/usr/local/lib/python3.11/site-packages/../tests/files/io/res/coc-115925-9326-14.res'
__________________________________________________________ ERROR collecting tests/transformations/test_advanced_transformations.py __________________________________________________________
transformations/test_advanced_transformations.py:646: in <module>
class TestSQSTransformationIcet(PymatgenTest):
transformations/test_advanced_transformations.py:647: in TestSQSTransformationIcet
stored_run: dict = loadfn(f"{TEST_FILES_DIR}/transformations/icet-sqs-fcc-Mg_75-Al_25-scaling_8.json.gz")
/usr/local/lib/python3.11/site-packages/monty/serialization.py:70: in loadfn
with zopen(fn, "rt") as fp:
/usr/local/lib/python3.11/site-packages/monty/io.py:47: in zopen
return gzip.open(filename, *args, **kwargs)
/usr/local/lib/python3.11/gzip.py:58: in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
/usr/local/lib/python3.11/gzip.py:174: in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/ports/science/py-pymatgen/work-py311/stage/usr/local/lib/python3.11/site-packages/../tests/files/transformations/icet-sqs-fcc-Mg_75-Al_25-scaling_8.json.gz'
________________________________________________________________________ ERROR collecting tests/vis/test_plotters.py ________________________________________________________________________
vis/test_plotters.py:14: in <module>
with open(f"{TEST_FILES_DIR}/analysis/spectrum_test/LiCoO2_k_xanes.json") as file:
E FileNotFoundError: [Errno 2] No such file or directory: '/usr/ports/science/py-pymatgen/work-py311/stage/usr/local/lib/python3.11/site-packages/../tests/files/analysis/spectrum_test/LiCoO2_k_xanes.json'
===================================================================================== warnings summary ======================================================================================
../../../../../../local/lib/python3.11/site-packages/plotly/express/imshow_utils.py:24
/usr/local/lib/python3.11/site-packages/plotly/express/imshow_utils.py:24: DeprecationWarning: `np.bool8` is a deprecated alias for `np.bool_`. (Deprecated NumPy 1.24)
np.bool8: (False, True),
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================================================================================== short test summary info ==================================================================================
SKIPPED [1] analysis/test_functional_groups.py:16: could not import 'openbabel': No module named 'openbabel'
SKIPPED [1] electronic_structure/test_boltztrap2.py:27: No boltztrap2
SKIPPED [1] ext/test_matproj.py:44: MP API is down
SKIPPED [1] io/test_babel.py:17: could not import 'openbabel.pybel': No module named 'openbabel'
SKIPPED [1] io/test_openff.py:25: could not import 'openff.toolkit': No module named 'openff'
SKIPPED [1] io/test_packmol.py:23: packmol executable not present
SKIPPED [1] io/test_shengbte.py:9: could not import 'f90nml': No module named 'f90nml'
SKIPPED [1] io/test_zeopp.py:20: zeo not installed
SKIPPED [1] performance/test_import_time.py:32: ref time only comparable in CI runner
SKIPPED [1] symmetry/test_kpath_hin.py:11: seekpath not installed
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 10 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
======================================================================== 10 skipped, 1 warning, 10 errors in 19.15s =========================================================================
```
### Expected Behavior
n/a
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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I_kwDOACgets6ektGU
| 4,173
|
What's the correct way to use the `MAGMOM`'s value when using MP API data?
|
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[
"@hongyi-zhao , this is more of an atomate2 question, but the critical thing here is that the line `flow = update_user_incar_settings(flow, incar_settings)` is not needed. The `MPGGADoubleRelaxMaker` is constructed to use MP's settings by default\r\n\r\nIf you want to use the magmoms from the MP structure as the starting values of MAGMOM, then having \"magmom\" in the structure's site_properties is sufficient, atomate2 will use those\r\n\r\nTo be explicit, I recommend just the following:\r\n```\r\nfrom mp_api.client import MPRester\r\nfrom atomate2.vasp.flows.mp import MPGGADoubleRelaxMaker\r\nfrom atomate2.vasp.powerups import update_user_potcar_functional\r\nfrom jobflow import run_locally\r\n\r\n# Set POTCAR functional\r\nuser_potcar_functional = \"PBE_64\"\r\n\r\n# Get structure from MP\r\nmaterial_id = \"mp-126\"\r\nwith MPRester() as mpr:\r\n structure = mpr.get_structure_by_material_id(material_id)\r\n\r\n# If you really need the conventional structure, then uncomment this line. Otherwise, this adds unnecessary compute cost\r\n#structure = structure.to_conventional()\r\n\r\nflow = MPGGADoubleRelaxMaker().make(structure)\r\n\r\n# Update POTCAR settings\r\nflow = update_user_potcar_functional(flow, user_potcar_functional)\r\n\r\n# Run the flow\r\nresponses = run_locally(flow, create_folders=True, ensure_success=True)\r\n```",
"But, the above code will trigger several custodian errors:\r\n\r\n```python\r\n#$ pyenv shell datasci\r\n#$ module load vasp\r\n#$ ipython\r\nIn [1]: from mp_api.client import MPRester\r\n ...: from atomate2.vasp.flows.mp import MPGGADoubleRelaxMaker\r\n ...: from atomate2.vasp.powerups import update_user_potcar_functional\r\n ...: from jobflow import run_locally\r\n ...: \r\n ...: # Set POTCAR functional\r\n ...: user_potcar_functional = \"PBE_64\"\r\n ...: \r\n ...: # Get structure from MP\r\n ...: material_id = \"mp-126\"\r\n ...: with MPRester() as mpr:\r\n ...: structure = mpr.get_structure_by_material_id(material_id)\r\n ...: \r\n ...: # If you really need the conventional structure, then uncomment this line. Otherwise, this adds unnecessary compute cost\r\n ...: #structure = structure.to_conventional()\r\n ...: \r\n ...: flow = MPGGADoubleRelaxMaker().make(structure)\r\n ...: \r\n ...: # Update POTCAR settings\r\n ...: flow = update_user_potcar_functional(flow, user_potcar_functional)\r\n ...: \r\n ...: # Run the flow\r\n ...: responses = run_locally(flow, create_folders=True, ensure_success=True)\r\nRetrieving MaterialsDoc documents: 100%|█████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 13357.66it/s]\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/sets.py:288: BadInputSetWarning: Overriding the POTCAR functional is generally not recommended as it significantly affects the results of calculations and compatibility with other calculations done with the same input set. Note that some POTCAR symbols specified in the configuration file may not be available in the selected functional.\r\n warnings.warn(\r\n2024-12-20 09:20:02,603 INFO Started executing jobs locally\r\n2024-12-20 09:20:02,607 INFO Starting job - MP GGA relax 1 (1a81cdd6-3ab5-4165-aaf5-761fc4d7e45e)\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/sets.py:757: BadInputSetWarning: Relaxation of likely metal with ISMEAR < 0 (-5). See VASP recommendations on ISMEAR for metals (https://www.vasp.at/wiki/index.php/ISMEAR).\r\n warnings.warn(\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:2420: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:2985: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(os.path.join(output_dir, key), mode=\"wt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:908: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:1648: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:2826: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:287: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:908: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/custodian/vasp/handlers.py:185: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(os.path.join(directory, self.output_filename), mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:1648: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:2826: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:287: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:312: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:4356: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as fid:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2114: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2365: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(self.filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:895: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"wt\") as file:\r\nERROR:custodian.custodian:IncorrectSmearingHandler\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:908: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/custodian/vasp/handlers.py:185: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(os.path.join(directory, self.output_filename), mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:1648: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:2826: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:287: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:312: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:4356: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as fid:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2114: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2365: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(self.filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/core/structure.py:3175: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\", errors=\"replace\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:895: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"wt\") as file:\r\nERROR:custodian.custodian:LargeSigmaHandler\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:908: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/custodian/vasp/handlers.py:185: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(os.path.join(directory, self.output_filename), mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:1648: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:2826: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:287: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:312: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:4356: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as fid:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2114: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2365: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(self.filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/core/structure.py:3175: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\", errors=\"replace\") as file:\r\n2024-12-20 09:21:04,335 INFO Finished job - MP GGA relax 1 (1a81cdd6-3ab5-4165-aaf5-761fc4d7e45e)\r\nINFO:jobflow.core.job:Finished job - MP GGA relax 1 (1a81cdd6-3ab5-4165-aaf5-761fc4d7e45e)\r\n2024-12-20 09:21:04,335 WARNING Response.stored_data is not supported with local manager.\r\nWARNING:jobflow.managers.local:Response.stored_data is not supported with local manager.\r\n2024-12-20 09:21:04,335 INFO Starting job - MP GGA relax 2 (d7b7f3fd-53a5-4dc3-9188-c2bdd1a6bfc5)\r\nINFO:jobflow.core.job:Starting job - MP GGA relax 2 (d7b7f3fd-53a5-4dc3-9188-c2bdd1a6bfc5)\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/atomate2/common/files.py:268: UserWarning: /home/werner/test/job_2024-12-20-01-21-04-335517-47956/INCAR is not gzipped, skipping...\r\n file_client.gunzip(directory / file, host=host, force=force)\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/atomate2/common/files.py:268: UserWarning: /home/werner/test/job_2024-12-20-01-21-04-335517-47956/OUTCAR is not gzipped, skipping...\r\n file_client.gunzip(directory / file, host=host, force=force)\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/atomate2/common/files.py:268: UserWarning: /home/werner/test/job_2024-12-20-01-21-04-335517-47956/CONTCAR is not gzipped, skipping...\r\n file_client.gunzip(directory / file, host=host, force=force)\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/atomate2/common/files.py:268: UserWarning: /home/werner/test/job_2024-12-20-01-21-04-335517-47956/vasprun.xml is not gzipped, skipping...\r\n file_client.gunzip(directory / file, host=host, force=force)\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/atomate2/common/files.py:268: UserWarning: /home/werner/test/job_2024-12-20-01-21-04-335517-47956/WAVECAR is not gzipped, skipping...\r\n file_client.gunzip(directory / file, host=host, force=force)\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/atomate2/common/files.py:268: UserWarning: /home/werner/test/job_2024-12-20-01-21-04-335517-47956/CHGCAR is not gzipped, skipping...\r\n file_client.gunzip(directory / file, host=host, force=force)\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/atomate2/common/files.py:268: UserWarning: /home/werner/test/job_2024-12-20-01-21-04-335517-47956/POTCAR is not gzipped, skipping...\r\n file_client.gunzip(directory / file, host=host, force=force)\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/atomate2/common/files.py:268: UserWarning: /home/werner/test/job_2024-12-20-01-21-04-335517-47956/KPOINTS is not gzipped, skipping...\r\n file_client.gunzip(directory / file, host=host, force=force)\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/sets.py:757: BadInputSetWarning: Relaxation of likely metal with ISMEAR < 0 (-5). See VASP recommendations on ISMEAR for metals (https://www.vasp.at/wiki/index.php/ISMEAR).\r\n warnings.warn(\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:2420: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:2985: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(os.path.join(output_dir, key), mode=\"wt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:908: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/custodian/vasp/handlers.py:185: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(os.path.join(directory, self.output_filename), mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:1648: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:2826: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:287: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:312: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:4356: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as fid:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2114: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2365: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(self.filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:895: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"wt\") as file:\r\nERROR:custodian.custodian:IncorrectSmearingHandler\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:908: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/custodian/vasp/handlers.py:185: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(os.path.join(directory, self.output_filename), mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:1648: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:2826: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:287: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:312: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:4356: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as fid:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2114: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2365: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(self.filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/core/structure.py:3175: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\", errors=\"replace\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:895: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"wt\") as file:\r\nERROR:custodian.custodian:LargeSigmaHandler\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:908: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/custodian/vasp/handlers.py:185: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(os.path.join(directory, self.output_filename), mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:1648: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:2826: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:287: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:312: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:4356: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as fid:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2114: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:2365: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(self.filename, mode=\"rt\") as file:\r\n/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/core/structure.py:3175: EncodingWarning: We strongly encourage explicit `encoding`, and we would use UTF-8 by default as per PEP 686\r\n with zopen(filename, mode=\"rt\", errors=\"replace\") as file:\r\n2024-12-20 09:21:56,255 INFO Finished job - MP GGA relax 2 (d7b7f3fd-53a5-4dc3-9188-c2bdd1a6bfc5)\r\nINFO:jobflow.core.job:Finished job - MP GGA relax 2 (d7b7f3fd-53a5-4dc3-9188-c2bdd1a6bfc5)\r\n2024-12-20 09:21:56,255 WARNING Response.stored_data is not supported with local manager.\r\nWARNING:jobflow.managers.local:Response.stored_data is not supported with local manager.\r\n2024-12-20 09:21:56,255 INFO Finished executing jobs locally\r\nINFO:jobflow.managers.local:Finished executing jobs locally\r\n```\r\nWhile [custodian](http://materialsproject.github.io/custodian/#practical-example-electronic-structure-calculations) provides automated error handling and parameter adjustments, initial reasonable parameter settings are still important for obtaining meaningful calculation results.\r\n\r\nSee https://github.com/Neraaz/HTESP/issues/2#issuecomment-2480883486 for more tests and comments by me.",
"@hongyi-zhao, your job still runs successfully because of the changes made by custodian. The final results will still be meaningful because of those changes.\r\n\r\nYou can safely set `ISMEAR = 0` and `SIGMA = 0.05` as general defaults instead of the `MPRelaxSet`. This isn't a pymatgen bug\r\n\r\n@DanielYang59, these warnings about encoding from [monty #730](https://github.com/materialsvirtuallab/monty/pull/730) are a little disruptive. Can the default be to disable this, or at least explicitly set `utf-8` encoding in `loadfn`? We have so many places in the codebase where these warnings are getting thrown",
"> these warnings about encoding from https://github.com/materialsvirtuallab/monty/pull/730 are a little disruptive. Can the default be to disable this,\r\n\r\nYou're absolutely correct, I should have used the `PYTHONWARNDEFAULTENCODING` from PEP 597 for consistency (don't display encoding warning until `PYTHONWARNDEFAULTENCODING` is set), sorry for the trouble.\r\n\r\n> at least explicitly set utf-8 encoding in loadfn\r\n\r\nI just had a quick looks and it looks like [`loadfn` already use UTF-8 in text mode](https://github.com/materialsvirtuallab/monty/blob/26acf0b2900b5074143ed64ccd1bdea6ba9f6705/src/monty/serialization.py#L70) and [`zopen` would not issue an encoding warning for binary mode](https://github.com/materialsvirtuallab/monty/blob/26acf0b2900b5074143ed64ccd1bdea6ba9f6705/src/monty/io.py#L82-L83), can you show me what triggered this warning?\r\n\r\n\r\n",
"> @hongyi-zhao, your job still runs successfully because of the changes made by custodian. The final results will still be meaningful because of those changes.\r\n> \r\n> You can safely set `ISMEAR = 0` and `SIGMA = 0.05` as general defaults instead of the `MPRelaxSet`. This isn't a pymatgen bug\r\n\r\nFor certain types of computational tasks, such as elastic tensors, the small differences in the above parameters can make a big difference in the final result, as shown [here](https://github.com/Neraaz/HTESP/issues/2#issuecomment-2480883486).",
"@DanielYang59: most instances of `zopen` in the codebase don't use binary mode. You can see in the warnings that it's coming from `pymatgen.io` - every VASP input and output object, like [POSCAR's `from_file`](https://github.com/materialsproject/pymatgen/blob/da607e86f9ce8aec942067c6c1a4fda6e04915dd/src/pymatgen/io/vasp/inputs.py#L288) use `zopen(<path>,\"rt\")`. Probably goes for every `pymatgen.io` module too",
"@hongyi-zhao that's completely fair, but that's more of a scientific methodology question and not a pymatgen bug. FWIW, the experimental uncertainty in bulk moduli, especially after applying zero point corrections for the nuclear motion to better compare with zero-temperature DFT, can be on the order of 10 GPa if not more. The <10 GPa differences in your results is still less than the experimental uncertainty",
"@esoteric-ephemera But I have another question here: for the example of [\"mp-126\"](https://next-gen.materialsproject.org/materials/mp-126), the following values are used in the `input` filed of MP's database: [`{'ISMEAR': 2, 'SIGMA': 0.14}`](https://github.com/Neraaz/HTESP/issues/2#issuecomment-2480883486), which is different from the final values automatically adjusted by [custodian](http://materialsproject.github.io/custodian/#practical-example-electronic-structure-calculations) in [my previous example](https://github.com/materialsproject/pymatgen/issues/4173#issuecomment-2556075556), as shown below:\r\n```\r\nwerner@x13dai-t:~/test$ ug -ri 'ismear|sigma' -g INCAR\r\njob_2024-12-20-01-21-04-335517-47956/INCAR:ISMEAR = 2\r\njob_2024-12-20-01-21-04-335517-47956/INCAR:SIGMA = 0.07321952854558407\r\njob_2024-12-20-01-20-02-605601-93060/INCAR:ISMEAR = 2\r\njob_2024-12-20-01-20-02-605601-93060/INCAR:SIGMA = 0.07102306201943624\r\n```\r\nHowever, the MP database involves a huge amount of computations, so how are detailed parameter adjustments like this achieved if they are not based on [custodian](http://materialsproject.github.io/custodian/#practical-example-electronic-structure-calculations)'s automatic adjustments?",
"> most instances of zopen in the codebase don't use binary mode. \r\n\r\n@esoteric-ephemera Ah I got your point now so it's `zopen` instead of `loadfn` right? Don't worry about this then, it has been fixed by #4219, but was mistakenly reverted in #4221, would re-apply in #4222\r\n\r\nSorry for going astray in your thread @hongyi-zhao \r\n",
"@DanielYang59 \r\n> Sorry for going astray in your thread @hongyi-zhao\r\n\r\nNo worries, I understand. We can continue discussing the topic, or feel free to bring up any other questions you might have. 😊",
"@hongyi-zhao, since we add handlers to custodian over time, you might see different behavior in calculations run with a newer version of custodian. My guess is you're running a version of custodian that includes the `LargeSigmaHandler`, which checks to see if the electronic smearing pseudo-entropy is larger than 1 meV/atom, and reduces `SIGMA` if it is. That handler likely didn't exist when the MP calculation was performed"
] | 2024-11-15T00:30:18
| 2024-12-24T00:40:02
|
2024-12-24T00:40:01Z
|
CONTRIBUTOR
|
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The testing code below is adapted from my example [here](https://github.com/Neraaz/HTESP/issues/1#issuecomment-2451363600):
```python
from mp_api.client import MPRester
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from atomate2.vasp.flows.mp import MPGGADoubleRelaxMaker
from atomate2.vasp.powerups import (
update_user_incar_settings,
update_user_potcar_functional,
)
from jobflow import run_locally
# Set POTCAR functional
user_potcar_functional = "PBE_64"
# Get structure from MP
material_id = "mp-126"
with MPRester() as mpr:
# First get the task id from the materials doc
materials = mpr.materials.search(material_ids=[material_id], fields=["task_ids"])
task_id = materials[0].task_ids[0]
# Now get the calculation that includes MAGMOM settings
tasks = mpr.materials.tasks.search(task_ids=[task_id],
fields=["input.incar", "calcs_reversed"])
# Get the INCAR settings from the calculation
incar_settings = tasks[0].calcs_reversed[0].input.incar
# Get the structure and convert to conventional cell
structure = mpr.materials.get_structure_by_material_id(material_id)
structure = SpacegroupAnalyzer(structure).get_conventional_standard_structure()
# Convert MAGMOM list to dictionary format
#if "MAGMOM" in incar_settings:
# print("Original MAGMOM settings:", incar_settings["MAGMOM"])
# print("Number of sites in structure:", len(structure))
#
# # Get unique species list
# species_list = [site.species_string for site in structure]
# unique_species = sorted(set(species_list))
# print("Unique species in structure:", unique_species)
#
# # Set all species to the first MAGMOM value from the original calculation
# magmom_dict = {specie: incar_settings["MAGMOM"][0] for specie in unique_species}
# incar_settings["MAGMOM"] = magmom_dict
# print("MAGMOM dictionary:", magmom_dict)
# Create a simple flow with just the relax
flow = MPGGADoubleRelaxMaker().make(structure)
# Update POTCAR settings
flow = update_user_potcar_functional(flow, user_potcar_functional)
# Update INCAR settings
flow = update_user_incar_settings(flow, incar_settings)
# Run the flow
responses = run_locally(flow, create_folders=True, ensure_success=True)
```
But the above code will trigger the following error:
```python
Retrieving MaterialsDoc documents: 100%|████████████████████████████████| 1/1 [00:00<00:00, 12865.96it/s]
Retrieving TaskDoc documents: 100%|█████████████████████████████████████| 1/1 [00:00<00:00, 11715.93it/s]
Retrieving MaterialsDoc documents: 100%|████████████████████████████████| 1/1 [00:00<00:00, 11848.32it/s]
/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/sets.py:288: BadInputSetWarning: Overriding the POTCAR functional is generally not recommended as it significantly affects the results of calculations and compatibility with other calculations done with the same input set. Note that some POTCAR symbols specified in the configuration file may not be available in the selected functional.
warnings.warn(
2024-11-10 08:41:06,924 INFO Started executing jobs locally
2024-11-10 08:41:06,926 INFO Starting job - MP GGA relax 1 (ecdb12aa-5e73-4d2b-97b3-d6deb29ce066)
2024-11-10 08:41:06,928 INFO MP GGA relax 1 failed with exception:
Traceback (most recent call last):
File "/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/jobflow/managers/local.py", line 114, in _run_job
response = job.run(store=store)
^^^^^^^^^^^^^^^^^^^^
File "/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/jobflow/core/job.py", line 600, in run
response = function(*self.function_args, **self.function_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/werner/Public/repo/github.com/materialsproject/atomate2.git/src/atomate2/vasp/jobs/base.py", line 219, in make
write_vasp_input_set(
File "/home/werner/Public/repo/github.com/materialsproject/atomate2.git/src/atomate2/vasp/files.py", line 190, in write_vasp_input_set
vis = input_set_generator.get_input_set(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/sets.py", line 476, in get_input_set
incar=self.incar,
^^^^^^^^^^
File "/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/sets.py", line 572, in incar
if uic_magmom := self.user_incar_settings.get("MAGMOM", {}).get(site.species_string):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'list' object has no attribute 'get'
2024-11-10 08:41:06,928 INFO Finished executing jobs locally
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
Cell In[6], line 56
53 flow = update_user_incar_settings(flow, incar_settings)
55 # Run the flow
---> 56 responses = run_locally(flow, create_folders=True, ensure_success=True)
File ~/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/jobflow/managers/local.py:181, in run_locally(flow, log, store, create_folders, root_dir, ensure_success, allow_external_references, raise_immediately)
178 logger.info("Finished executing jobs locally")
180 if ensure_success and not finished_successfully:
--> 181 raise RuntimeError("Flow did not finish running successfully")
183 return dict(responses)
RuntimeError: Flow did not finish running successfully
```
Is there a proper way to handle `MAGMOM` settings when copying from MP calculations without requiring further user adjustment, say, the one done by the code snippet `Convert MAGMOM list to dictionary format` shown above?
See https://github.com/materialsproject/atomate2/issues/1049 for the related discussion.
Regards,
Zhao
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https://github.com/materialsproject/pymatgen/pull/4174
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PR_kwDOACgets6B_4De
| 4,174
|
Clean up `CONTRIBUTING.md` docs and change `_is_named_isotope` `getattr` default value
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[] | 2024-11-15T04:44:54
| 2024-11-16T02:38:51
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2024-11-15T16:56:37Z
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CONTRIBUTOR
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- [I believe this would not be breaking] The default value as `False` over `None` might be more conventional (we [should not use truthy to check `None`](https://docs.quantifiedcode.com/python-anti-patterns/readability/comparison_to_none.html)):
```diff
# When the `_is_named_isotope` doesn't have `_is_named_isotope`,
# we're effectively checking `if None`
- if getattr(obj, "_is_named_isotope", None):
+ if getattr(obj, "_is_named_isotope", False):
```
- Recommend Google Style Docstring in `CONTRIBUTING.md`
- Clarify usage of `PMG_TEST_FILES_DIR` when running unit test
- Fix internal indexes
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Cleanup `codespell` ignore patterns
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[
"Thanks! Currently `codespell` doesn't seem to support block/file level support with pattern, I would update once they do."
] | 2024-11-15T13:08:39
| 2024-11-16T13:40:42
|
2024-11-16T13:37:02Z
|
CONTRIBUTOR
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## Cleanup `codespell` ignore patterns
Currently a lot of global ignore patterns are very specific to a certain module (or even one line), there's no good reason to ignore a pattern globally for such cases. Admittedly it will be a balance between convenience (no one want to insert a `# codespell:ignore` tag every line) and correctness (some patterns are very specific to few lines across the code base, but are real typos elsewhere, like `lamda/coul`, do note).
Changes:
- Keep the global pattern when it's very common: Elements like `Nd/Te`, or very common for a commonly used module, `TITEL` for VASP for example, or our good friend `atomate`
- Rename some internal/test variables **when it's not breaking** (usually increase readability)
- Ignore all JSON files as comments are not allowed in JSON, we might safely assume everything is intended in JSON
### Follow up
- [ ] Is it possible to add file-specific ignore tags (for example ignore `ontop` for `adsorption.py`, or `coul` for `LAMMPS`)? Currently [`codespell` seems to provide block-level ignore tag](https://github.com/codespell-project/codespell/issues/3381) but doesn't take a pattern
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Change XAS behavior under negative frequencies
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[
"Thanks @esoteric-ephemera, appreciate the context with the matsci.org thread too",
"Thanks."
] | 2024-11-15T20:31:54
| 2024-11-18T18:15:42
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2024-11-18T13:35:12Z
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CONTRIBUTOR
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The XAS spectrum class used to not throw a `ValueError` when more than 5% of the user-input intensities are non-positive (cverified this was still the behavior as of v2020.4.29). More, the warning that is thrown is misleading, as it suggests that the majority of intensities are non-positive.
This change in behavior has led to issues with MP's API users, see [here for an example](https://matsci.org/t/avoiding-value-error-double-check-the-intensities-most-of-them-are-nonpositive/58748/2)
Changed this to throw a warning only when more than 5% of the intensities are ***negative***. Zero intensity shouldn't be penalized since this is physical (there's no absorption in that range, e.g. if a transition is forbidden)
Also added an option to zero out negative intensities (false by default)
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Modify FHI-aims inputs to not use species string
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[
"@ansobolev Does this work for your things?",
"@tpurcell90 This seems to work for the defect workflow, thanks; however, as aims accepts anything in the `species` line (it's just a label), I would rather use something like `site.label` for site description in `geometry.in`. This will allow more precise accounting for species defaults in heterogeneous calculations (something like adsorbate on the surface). But that's for sure open for discussion and not the blocking issue. ",
"FHI-aims can accept an arbitrary label, but pymatgen requires a `CompositionLike` or `SpeciesLike` object for species, which requires an element to be present from what I can tell.\r\n\r\nI think this is ready for review.",
"For writing `geometry.in` pymatgen perspective does not matter, as the file is intended for FHI-aims; when reading the element can be defined by species defaults in `control.in`, or element can be explicitly included (like `site.element_site.label`) in the species label.",
"ready for review",
"Thanks.",
"would it be possible to make a release with this soon? We need this fix for atomate2"
] | 2024-11-15T20:59:32
| 2024-12-11T20:31:24
|
2024-12-11T14:46:30Z
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CONTRIBUTOR
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FHI-aims does not read spin from the species and that causes issues with magnetic calculations
## Summary
Major changes:
- fix 1: Don't use species_string for FHI-aims
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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The inappropriate warnning info for `update_user_incar_settings`.
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[
"Hey Zhao,\r\nCould you elaborate a little bit why exactly this warning is inappropriate? ",
"I mean, this warning should be triggered by something like [`update_user_potcar_functional`](https://materialsproject.github.io/atomate2/reference/atomate2.vasp.powerups.update_user_potcar_functional.html#update-user-potcar-functional) instead of [`update_user_incar_settings`](https://materialsproject.github.io/atomate2/reference/atomate2.vasp.powerups.update_user_incar_settings.html#update-user-incar-settings).",
"Can you move this over to atomate2 with a complete code snippet? I don't think this is a pymatgen issue"
] | 2024-11-17T02:11:24
| 2024-11-19T07:05:02
|
2024-11-19T07:05:02Z
|
CONTRIBUTOR
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When I tested an atomate2 flow, I noticed the following information:
```shell
In [7]: flow = update_user_incar_settings(flow, { 'ALGO': 'Normal', 'EDIFF': 1e-06, 'ENCUT':700})
/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/sets.py:288: BadInputSetWarning: Overriding the POTCAR functional is generally not recommended as it significantly affects the results of calculations and compatibility with other calculations done with the same input set. Note that some POTCAR symbols specified in the configuration file may not be available in the selected functional.
warnings.warn(
```
This is an inappropriate warning message. Because I update INCAR here, the warning is indeed related to POTCAR.
Regards,
Zhao
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PR_kwDOACgets6CJYFN
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|
[Breaking/Fix] Skip isotopes when iterating through `core.Element`
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[
"I agree isotopes shouldn't appear as part of default behavior.",
"That was an oversight on my part, thanks for the fix! Also agree that enumerating over elements shouldn't list isotopes. Maybe adding a method to `Element` to show people which isotopes are available would be useful tho?",
"> That was an oversight on my part, thanks for the fix!\r\n\r\nNo problem at all, cannot blame anyone, it's the test that is missing, together we improve test coverage :)\r\n\r\n> Maybe adding a method to Element to show people which isotopes are available would be useful tho?\r\n\r\nFair point, is current implementation looking good to you @esoteric-ephemera (I don't have much experience overwriting an `Enum` so not sure if there's any pitfall like [builtin `dict/list/...`](https://docs.python.org/3/library/collections.html#module-collections), **do review with a pinch of salt**)?\r\n```python\r\nElement.named_isotopes # ---> (Element.D, Element.T)\r\n```\r\n\r\n\r\n",
"@janosh I believe you're very experienced with `Enum` (while I'm not), perhaps you could help me double-check the implementation?"
] | 2024-11-17T06:14:48
| 2025-01-10T02:27:51
|
2025-01-09T20:38:24Z
|
CONTRIBUTOR
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### Summary
- Skip isotopes when iterating through `core.Element`, to fix #4178, rationale:
- I might expect looping through `Element` to behave similarly to looping through the periodic table, i.e. isotopes should not sneak in here, do you like this idea @esoteric-ephemera?
- Implementation based on https://docs.python.org/3/library/enum.html:
> EnumType is responsible for setting the correct __repr__(), __str__(), __format__(), and __reduce__() methods on the final enum, as well as creating the enum members, properly handling duplicates, providing iteration over the enum class, etc.
- Add `property` `Element.named_isotopes` for all named_isotopes so far.
- Clean up `core.periodic_table` docstring (remove non-existent `PeriodicTable` class).
This **would be a breaking change** (also might be called a fix), so comments are hugely appreciated.
---
```python
from pymatgen.core import Element
for idx, ele in enumerate(Element):
print(idx, ele)
```
### Before
```
0 H
1 H # Deuterium
2 H # Tritium
3 He
4 Li
5 Be
6 B
7 C
......
```
### Now (nothing special, just skip isotopes of hydrogen)
```
0 H
1 He
2 Li
3 Be
4 B
5 C
......
```
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Fix incorrect comparison logic and update tests
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[
"@naik-aakash could you add a few more tests here next week (not today) and make sure it is working as intended? ",
"> @naik-aakash could you add a few more tests here next week (not today) and make sure it is working as intended?\r\n\r\nSure can do this 😄 ",
"Forgive me, I'm going slightly off-topic again (Haoyu the topic wanderer), perhaps also replace the tolerance (`limit_deviation`) with more readable scientific notation? https://github.com/materialsproject/pymatgen/blob/c72c9e93ca5922f8fbd1d0e0bb385cfc1ae26420/tests/io/lobster/test_outputs.py#L1545-L1604\r\n\r\nAlso perhaps separate the tests of `has_good_quality_maxDeviation` and `has_good_quality_check_occupied_bands` into two separate test methods? (I guess they're independent right?)",
"> Forgive me, I'm going slightly off-topic again, perhaps also replace the tolerance (`limit_deviation`) with more readable scientific notation?\r\n> \r\n> https://github.com/materialsproject/pymatgen/blob/c72c9e93ca5922f8fbd1d0e0bb385cfc1ae26420/tests/io/lobster/test_outputs.py#L1545-L1604\r\n> \r\n> Also perhaps separate the tests of `has_good_quality_maxDeviation` and `has_good_quality_check_occupied_bands` into two separate test methods? (I guess they're independent right?)\r\n\r\nHow about renaming `limit_deviation` to `identity_deviation_tol` ? Does this make it more readable scientific notation ?\r\n\r\nAnd regarding your second request, yes they are independent and thus have been seperated now in the tests.",
"> How about renaming limit_deviation to identitiy_deviation_tol ? Does this make it more readable scientific notation ?\r\n\r\nSorry I was trying to say replace values like `0.000001` with `1e-6`, renaming `limit_deviation` might be breaking I'm afraid (`has_good_quality_check_occupied_bands` is public right)?\r\n\r\n> And regarding your second request, yes they are independent and thus have been seperated now in the tests.\r\n\r\nThanks for the quick change!",
"> `has_good_quality_check_occupied_bands`\r\n\r\nAhh okay got what you meant. Was not clear to me it referred to numeric values and not vairable naming and Yess it is public, thus will lead to a breaking change. ",
"Thanks."
] | 2024-11-17T11:42:37
| 2024-11-18T13:33:03
|
2024-11-18T13:32:58Z
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CONTRIBUTOR
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## Closes #4166
## Changes
Based on the suggestions form @QuantumChemist ( https://github.com/materialsproject/pymatgen/issues/4166#issuecomment-2480508677) and @DanielYang59 (https://github.com/materialsproject/pymatgen/issues/4166#issuecomment-2480925279) , the code has been fixed to correctly evaluate whether the matrix values are above threshold and tests have been updated accordingly
# Todo
- [x] Add 1 or 2 more test cases
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Moved NUPDOWN from int_keys to float_keys
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[
"Thanks."
] | 2024-11-18T09:31:09
| 2024-11-18T13:32:23
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2024-11-18T13:32:20Z
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CONTRIBUTOR
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## Summary
`NUPDOWN` key in Incar can be set to floating point values in VASP (see https://gitlab.com/ase/ase/-/merge_requests/2580).
However, it is current treated as an int in `Incar.proc_val`.
This PR treats `NUPDOWN` as a float instead.
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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Compositions from weight str
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[
"Thanks. Merged."
] | 2024-11-18T20:07:06
| 2024-11-18T20:46:36
|
2024-11-18T20:41:04Z
|
CONTRIBUTOR
|
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Often in alloy literature we get composition strings given in weight rather than molar quantities. This PR extends upon the `from_weight_dict` method to give a more general `from_weights` method that will take strings as well as CompositionLike
|
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I_kwDOACgets6fTDzT
| 4,184
|
Default values replace the custom input ones in MagneticStructureEnumerator
|
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[] | 2024-11-19T15:32:22
| 2025-02-18T17:14:30
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2025-02-18T17:14:30Z
|
CONTRIBUTOR
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I think there is a bug in this line
https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/analysis/magnetism/analyzer.py#L657
The update method will overwrite the values in the keys of the 'transformation_kwargs' coming from the input, e.g. timeout cannot be changed because of this.
```
transformation_kwargs={"timeout":1}
default_transformation_kwargs = {"check_ordered_symmetry": False, "timeout": 5}
transformation_kwargs = transformation_kwargs or {}
print(transformation_kwargs)
transformation_kwargs.update(default_transformation_kwargs)
print(transformation_kwargs)
: {'timeout': 1}
: {'timeout': 5, 'check_ordered_symmetry': False}
```
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I_kwDOACgets6feyvz
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|
Timeout in MagneticStructureEnumerator (and EnumlibAdaptor) does not work
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[] | 2024-11-20T11:58:29
| 2025-02-18T17:11:31
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2025-02-18T17:11:30Z
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CONTRIBUTOR
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### Python version
3.11.5
### Pymatgen version
2024.11.13
### Operating system version
_No response_
### Current behavior
`enum = MagneticStructureEnumerator(structure)` should stop after 5 minutes by default,
but it does not. Passing a different timeout does not change anything. I'm now making sure that the timeout arg is passed to the EnumlibAdaptor (see bug in #4184).
I did some tests but I could not figure out why the enum.x process does not get killed.
The main logic from https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/command_line/enumlib_caller.py#L281 is here:
```
def _run_multienum(self):
with subprocess.Popen([enum_cmd], stdout=subprocess.PIPE, stdin=subprocess.PIPE, close_fds=True) as process:
if self.timeout:
timed_out = False
timer = Timer(self.timeout*60, lambda p: p.kill(), [process])
try:
timer.start()
output = process.communicate()[0].decode("utf-8")
finally:
if not timer.is_alive():
timed_out = True
timer.cancel()
if timed_out:
raise TimeoutError("Enumeration took too long")
else:
output = process.communicate()[0].decode("utf-8")
```
It seems the the process stops communicating. I tried to use the timeout argument
of the `process.communicate()` method but it does not work neither.
One thing that worked correctly is the same code above with
enum_cmd="/usr/bin/sleep 6000". This process gets killed as it should.
I have the same behavior both in my laptop and on perlmutter.
Any thoughts about what's causing this?
### Expected Behavior
`enum = MagneticStructureEnumerator(structure)` should stop after 5 minutes by default.
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
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I_kwDOACgets6fhcam
| 4,186
|
CP2K input set creation (error with basis set/potential finding for given structure)
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[
"I should add that I am using an older Pymatgen and older CP2K but this is the exact same error with newest Pymatgen and newest CP2K data directory."
] | 2024-11-20T15:48:22
| 2024-11-20T15:49:42
|
NONE
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### Python version
3.12
### Pymatgen version
v2024.9.17.1
### Operating system version
MacOSX
### Current behavior
Git clone cp2k v2022 for the data directory
Performed pmg config --cp2k /path/to/cp2k/data /path/to/pmg/cp2kdata
Doing any compounds mixed with In, O as species gives this error (also with other composition) while doing the elements alone do not give rise to any errors.
I attached the process basis set/potentials file from the pmg config --cp2k for In, O as example.
### Expected Behavior
```
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[28], line 1
----> 1 RelaxSet(structure=Structure([[4,0,0],[0,4,0],[0,0,4]],['In','O',],[[0,0,0,],[0,0,2],], coords_are_cartesian=True))
File [~/dev/pymatgen/src/pymatgen/io/cp2k/sets.py:1423](http://localhost:8889/lab/workspaces/auto-U/tree/dev/scratch/~/dev/pymatgen/src/pymatgen/io/cp2k/sets.py#line=1422), in RelaxSet.__init__(self, **kwargs)
1422 def __init__(self, **kwargs) -> None:
-> 1423 super().__init__(run_type="GEO_OPT", **kwargs)
1424 self.activate_motion()
File [~/dev/pymatgen/src/pymatgen/io/cp2k/sets.py:296](http://localhost:8889/lab/workspaces/auto-U/tree/dev/scratch/~/dev/pymatgen/src/pymatgen/io/cp2k/sets.py#line=295), in DftSet.__init__(self, structure, project_name, basis_and_potential, element_defaults, xc_functionals, multiplicity, ot, energy_gap, qs_method, eps_default, eps_scf, max_scf, minimizer, preconditioner, algorithm, linesearch, rotation, occupation_preconditioner, cutoff, rel_cutoff, ngrids, progression_factor, override_default_params, wfn_restart_file_name, kpoints, smearing, cell, **kwargs)
293 scf["MAX_DIIS"] = Keyword("MAX_DIIS", 15)
295 # Get basis, potential, and XC info
--> 296 self.basis_and_potential = DftSet.get_basis_and_potential(self.structure, self.basis_and_potential)
297 self.basis_set_file_names = self.basis_and_potential.get("basis_filenames", ())
298 self.potential_file_name = self.basis_and_potential.get("potential_filename")
File [~/dev/pymatgen/src/pymatgen/io/cp2k/sets.py:574](http://localhost:8889/lab/workspaces/auto-U/tree/dev/scratch/~/dev/pymatgen/src/pymatgen/io/cp2k/sets.py#line=573), in DftSet.get_basis_and_potential(structure, basis_and_potential, cp2k_data_dir)
572 pfn2 = getattr(potential, "filename", None)
573 if pfn1 and pfn2 and pfn1 != pfn2:
--> 574 raise ValueError(
575 "Provided potentials have more than one corresponding file."
576 "CP2K does not support multiple potential filenames"
577 )
578 data["potential_filename"] = pfn2
580 data[el] = {"basis": basis, "aux_basis": aux_basis, "potential": potential}
ValueError: Provided potentials have more than one corresponding file.CP2K does not support multiple potential filenames
```
### Minimal example
```Python
from pymatgen.core import Structure
from pymatgen.io.cp2k.sets import RelaxSet
RelaxSet(structure=Structure([[4,0,0],[0,4,0],[0,0,4]],['In',],[[0,0,0,]],], coords_are_cartesian=True)) # works well
RelaxSet(structure=Structure([[4,0,0],[0,4,0],[0,0,4]],['In','O',],[[0,0,0,],[0,0,2],], coords_are_cartesian=True)) # does not work
```
### Relevant files to reproduce this bug
[Archive.zip](https://github.com/user-attachments/files/17833141/Archive.zip)
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PR_kwDOACgets6Cut2P
| 4,187
|
Addition of "valences" property to ElementBase and Species for mixed-valence ions
|
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[
"closing this until I make those fixes"
] | 2024-11-21T21:23:22
| 2024-12-12T22:47:18
|
2024-11-26T22:47:19Z
|
CONTRIBUTOR
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## Summary
Note: This code change is **no longer required for #4078** and the `valences` property does **not** return `(idx, ne)` for every valence subshell but only **every partially filled valence subshell** (unless all subshells are filled, which causes only the last subshell to be returned). I don't see a use for this criteria, so I will fix this to behave as intended. I am also okay with letting this PR be closed and abandoned since it is no longer needed for #4078.
Major changes:
- feature 1: For both ElementBase and Species class, the code within the "valence" property was copy-pasted into a new "valences" property, with the error raised for ambiguous valence (more than one valence subshell) removed
(`if len(valence) > 1:
raise ValueError(f"{self} has ambiguous valence")`)
and return signature changed from `tuple[int | np.nan, int]` to `list[tuple[int | np.nan, int]]` (`return valence` instead of `return valence[0]`)
- fix 1: To remove redundancy, the "valence" property for `ElementBase` and `Species` was re-written to raise the ambiguous valence ValueError if `len(self.valences) > 1`, and otherwise return `self.valences[0]`
## TODO
- Loosen return criteria for `valences` to return all valence subshells while maintaining selectivity of `valence`
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Poscar.get_str() cartesian vs direct coords
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[
"Erm, I am not sure what you mean. I don't think you can use 0, 0, 0 as the example. Those coordinates are the same whether in direct or cartesian coords by definition. Also, your code is confusing because your comment says \"Position of the atom in Cartesian coordinates\" and yet you set `coords_are_cartesian` to False. Those are contradictory.\r\n\r\nYou will need to show an example where the Cartesian coords lead to the wrong direct coordinates. The Poscar always write direct coordinates by default because that is usually the way people define coordinates in crystals. But you can set cartesian output if you'd like.",
"My bad, I double checked it, everything works as expected. Gotta remember not to submit issues late in the night."
] | 2024-11-21T21:46:19
| 2025-03-13T19:32:40
|
2025-03-13T19:32:39Z
|
NONE
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First of all, thank you for this incredible library!
### Python version
Python 3.12.7
### Pymatgen version
2024.11.13
### Operating system version
Pop!_OS 22.04 LTS
### Current behavior
**Steps to reproduce**
- define structure in cartesian coords
- create Poscar object from structure
- wirte poscar to file
-⚡ POSCAR file contains __cartesian coords__ with a vasp flag `direct`
-⚡ POSCAR `__repr__` & `__str__` show `direct` coords.
### Expected Behavior
- POSCAR file contains cartesian coords with a vasp flag `cartesian`
- POSCAR `__repr__` & `__str__` shows `cartesian` coords.
### Additional info
Imho, this is a contrintuitive behavior.
In order for this to work one should explicitly call `poscar.write_file()` with `direct=False` argument: `poscar.write_file("POSCAR", direct=False)`. However, it will not affect `__repr__` & `__str__` behavior. Reason being: `direct` property is not passed to dunder methods, but is overwritten by default `get_str` declaration.
https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/io/vasp/inputs.py#L158-L163
https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/io/vasp/inputs.py#L565-L570
https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/io/vasp/inputs.py#L656-L661
### Minimal example
```Python
from pymatgen.io.vasp import Poscar
from pymatgen.core import Structure, Lattice
lattice = Lattice.cubic(10.0)
species = ["Al"] # Single aluminum atom
coords = [[0, 0, 0]] # Position of the atom in Cartesian coordinates
structure = Structure(
lattice,
species,
coords,
coords_are_cartesian=False,
)
poscar = Poscar(structure)
poscar.write_file("POSCAR")
```
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[
"@mkhorton , are you OK with merging this change?\r\n\r\n@shyuep I am not sure why some of the optional checks are not running, I started the tests a couple of days ago.\r\n\r\nLooks like all changes are restricted to the io/jdftx module, so not much likelihood of things breaking",
"Thanks for your patience with this one, long PRs adding a big new feature are always more difficult to review. I think this nicely self-contained and is in good shape to merge in. We can save further improvements for follow-up PRs that we can review/merge more quickly, and we can take the same approach with #4190 too.\r\n\r\nOne thing that wasn't obvious to me, why the `/tmp` directory in the test files? I couldn't see where it was used in the diff.",
"> Thanks for your patience with this one, long PRs adding a big new feature are always more difficult to review. I think this nicely self-contained and is in good shape to merge in. We can save further improvements for follow-up PRs that we can review/merge more quickly, and we can take the same approach with #4190 too.\r\n> \r\n> One thing that wasn't obvious to me, why the `/tmp` directory in the test files? I couldn't see where it was used in the diff.\r\n\r\nAwesome thank you! Sorry for the new push - had a minor bug from inconsistent tracking of units. And the `tmp` directory is used to hold files that are created and deleted during the tests (ie testing that an input file can be written and then read correctly). I thought it would make the tests run quicker to have the directory exist permanently instead of created when needed but I can change that if the alternative is better.\r\n\r\nEdit: The new push is actually restricted to #4078 - \r\n\r\n> We can save further improvements for follow-up PRs that we can review/merge more quickly\r\n\r\nSo edits for minor bugs I should keep within #4078 and leave #4189 and #4190 untouched, right?",
"> I thought it would make the tests run quicker to have the directory exist permanently instead of created when needed but I can change that if the alternative is better.\r\n\r\nIt'd be better to remove it :) Creating a directory doesn't take much time, and might add some confusion to others to see it there. Tests should do \"set up\" and \"tear down\" as needed.\r\n\r\n> So edits for minor bugs I should keep within https://github.com/materialsproject/pymatgen/pull/4078 and leave https://github.com/materialsproject/pymatgen/pull/4189 and https://github.com/materialsproject/pymatgen/pull/4190 untouched, right?\r\n\r\nAs long as you merge in changes from the main branch (or rebase) #4078 once #4189 and #4190 are merged, or you can create new PRs. Either way is fine, I will try and be responsive!",
"@mkhorton Sorry for the delay! \"tmp\" directory now only exists during the execution of the required tests by defining it as a module-scope fixture defined in [`tests.io.jdftx.shared_test_utils`](https://github.com/benrich37/pymatgen/blob/feature-jdftx-inputs/tests/io/jdftx/shared_test_utils.py#L38-L42). I tried using the `tmp_path` class variable in the `PymatgenTest` class but I discovered that test methods within test classes inheriting `unittest.TestCase` cannot use the `pytest.mark.parametrize` decorator so the fixture-approach ended up working out better.",
"Is htis ready to be merged?",
"> Is htis ready to be merged?\r\n\r\nyes! @mkhorton let me know if it looks good!"
] | 2024-11-21T23:20:36
| 2025-01-24T17:48:18
|
2025-01-24T00:21:07Z
|
CONTRIBUTOR
|
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## Summary
Major changes:
- feature 1: `inputs.py` module containing `JDFTXInfile` class to give pythonic representation to the inputs for a JDFTx calculation
- feature 2: "helper" module `generic_tags.py` holding "Tag" objects (`AbstractTag` and inheritors of `AbstractTag`) to represent the different data structures JDFTx expects for inputs
- feature 3: "helper" module `jdftxinfile_master_format.py` to create proper "Tag" objects for input tags
- feature 4: "helper" module `jdftxinfile_ref_options.py` to hold lists of acceptable input strings for different input tags (ie list of acceptable XC functionals for the tag "elec-ex-corr")
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[
"@mkhorton , are you OK with merging this change?\r\n\r\n@shyuep I am not sure why some of the optional checks are not running, I started the tests a couple of days ago.\r\n\r\nLooks like all changes are restricted to the io/jdftx module, so not much likelihood of things breaking",
"I’ll try and review this later today, thanks @benrich37 "
] | 2024-11-22T00:34:16
| 2025-01-24T17:48:09
|
2025-01-24T15:05:39Z
|
CONTRIBUTOR
|
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## Summary
Major changes:
-feature 0: hierarchy of class objects used to represent the data contained within a JDFTx out file. Hierarchy here is used to represent where each class object is stored - none of these classes inherit the class below it. Classes stored within a list in its parent are indicated by "[i]" (ie below where `JDFTXOutfile.slices` is a list of `JDFTXOutfileSlice`). Descriptions of each class are given below the tree.
JDFTXOutputs
|
JDFTXOutputs.outfile
|
JDFTXOutfile
|
JDFTXOutfile.slices[i]
|
JDFTXOutfileSlice
/ \
JDFTXOutfileSlice.jstrucs JDFTXOutfileSlice.jsettings_(fluid, electronic, lattice, or ionic)
| |
JOutStructures JMinSettings
|
JOutStructures.slices[i]
|
JOutStructure(Structure)
|
JOutStructure.elecmindata
|
JElSteps
|
JElSteps.slices[i]
|
JElStep
- feature 1: `outputs.py` module containing `JDFTXOutfile` class to give robust pythonic representation of to a JDFTx "out" file. This class is initialized from the path to a JDFTx "out" file by the user. The initialization of a `JDFTXOutfile` will initialize the following JDFTx IO classes by
- feature 2: `jdftxoutfileslice.py` module containing `JDFTXOutfileSlice` class representing a "slice" of a JDFTx "out" file corresponding to a single call of the JDFTx executable (subsequent calls will append the same "out" file). This class is initialized for every call from an "out" file when `JDFTXOutfile` is initialized and stored in the list `JDFTXOutfile.slices`
- feature 3: `joutstructures.py` module containing `JOutStructures` class representing a series of structures from an "out" file "slice". This class is primarily helpful for representing a geometric optimization during a single call. This class is initialized once during the initialization of a `JDFTXOutfileSlice` and is stored in `JDFTXOutfileSlice.jstrucs`
- feature 4: `joutstructure.py` module containing `JOutStructure` class representing a single structure within an "out" file (specifically from a portion of the "out" file starting from the beginning of an SCF optimization down to the next log of Lowdin charges as the flag for the end of geometric optimization step). This class initialized once for every structure update when initializing `JOutStructures`, and is stored within the list `JOutStructures.slices`. An initial structure is given for initialization in the case that either lattice or ion positions are not being updated (and therefore not printed for parsing within the given slice of the "out" file "slice".
- feature 5: `jelstep.py` module containing `JElStep` and `JElSteps` class representing a single SCF step and a series of SCF steps, respectively. The `JElSteps` class is helpful for getting SCF convergence data. The `JElSteps` class is initialized once for every initialization of a `JOutStructure`, and is stored within `JOutStructure.elecmindata`. The `JElStep` class is helpful for analyzing the logged SCF optimization data (energy, chemical potential, line-minimization values, etc) for a single SCF step. The `JElStep` class initialized once for every SCF step when initializing a `JElSteps`, and is stored within `JElSteps.slices`.
- feature 6: `jminsettings.py` module containing `JMinSettings` abstract class for representing the input minimization settings of a JDFTx call. `JMinSettings` is inherited by the following classes within `jminsettings.py` - `JMinSettingsElectronic` to represent electronic minimization settings, `JMinSettingsFluid` for implicit fluid minimization, `JMinSettingsLattice` for lattice minimization, and `JMinSettingsIonic` for ionic minimization.
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PR_kwDOACgets6C5MEq
| 4,192
|
Clean up `util.num.make_symmetric_matrix_from_upper_tri` and `util.io_util.micro_pyawk`, fix new `ruff` errors
|
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[] | 2024-11-23T03:56:51
| 2025-01-10T02:27:30
|
2025-01-09T20:34:55Z
|
CONTRIBUTOR
|
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### Simplify/clarify `util.num.make_symmetric_matrix_from_upper_tri` and add tests
> [!CAUTION]
> `make_symmetric_matrix_from_upper_tri` now raise `ValueError` for non 3x3 array
I believe `utils.num.make_symmetric_matrix_from_upper_tri` is designed to [work on 3x3 matrix alone](https://github.com/materialsproject/pymatgen/pull/4192#discussion_r1855063190) (the new index is hard-coded): https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/util/num.py#L31-L32
As such I might greatly simplify the implementation f2c325299aa0162f0ee3f0a50507ab95991363bb which [gives ~3x speedup](https://github.com/materialsproject/pymatgen/pull/4192#discussion_r1855063190) and much better readability.
### Clean up `util.io_util.micro_pyawk`
> [!WARNING]
> The `debug/postdebug` is likely debug args, no usage across the entire code bass, schedule them for removal after one-year grace period in case someone really need them.
### Others
- Remove: https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/util/io_utils.py#L98-L99
I believe this is doing nothing (set umask to 0, but reset it back the original umask immediately)
- Fix new `ruff` errors and bump `pre-commit` accordingly
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PR_kwDOACgets6C5WmV
| 4,193
|
Remove unnecesary isotope conversion in `core.periodic_table.get_el_sp`
|
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[] | null |
[
"@esoteric-ephemera Do we have further concerns on this change here? If not I might mark as ready?",
"If you mark as ready I'm happy to merge @DanielYang59, thank you!",
"Good to go from my side, not sure these lines are needed anymore. Thanks for checking!",
"No problem guys, happy holiday :)"
] | 2024-11-23T05:20:49
| 2025-01-10T02:27:23
|
2025-01-09T20:34:32Z
|
CONTRIBUTOR
|
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To close #4171.
This isotope conversion may not be working as we expected as the `name` of an isotope `Element/Species` is the "isotope name" (e.g. `"D"` for `Element.D` and `Species("D")` instead of `"H"`):
https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/core/periodic_table.py#L1649
https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/core/periodic_table.py#L1105-L1106
```python
from pymatgen.core.periodic_table import Element, Species, get_el_sp
print(get_el_sp(Element.D).name) # D
print(get_el_sp(Element.D) == Element.D) # True
print(get_el_sp(Species("D")).name) # D
print(get_el_sp(Species("D")) == Species("D")) # True
print(get_el_sp(Species("D", 1)).name) # D
print(get_el_sp(Species("D", 1)) == Species("D", 1)) # True
```
---
Meanwhile the [isotope characteristic removing in `Composition.add_charges_from_oxi_state_guesses`](https://github.com/materialsproject/pymatgen/discussions/4171#discussioncomment-11342357) is not done by this but `Composition.get_el_amt_dict`, full analysis in https://github.com/materialsproject/pymatgen/discussions/4171#discussioncomment-11355744.
This could also be confirmed by all unit tests passing including: https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/tests/core/test_composition.py#L845-L856
credit to @esoteric-ephemera for providing the context and the helpful discussion as always, and @benrich37 @mkhorton for bringing up the topic
|
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PR_kwDOACgets6C7zXs
| 4,194
|
Fix NumPy array indexing in 32-bit system in `analysis.chemenv.coordination_environments`
|
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[] | null |
[
"@drew-parsons I believe this resolved the index dtype issue in 32-bit systems (tested on Debian 12 32-bit with NumPy 1.26.4 and Python 3.11), let me know if you notice any issues :)",
"Thanks. This patch seems to be working well, applied to debian build 2024.10.29+dfsg1-4\t\r\nhttps://buildd.debian.org/status/package.php?p=pymatgen",
"No problem, great to know, thanks for confirming this!"
] | 2024-11-24T10:39:52
| 2024-12-11T02:29:36
|
2024-12-11T02:03:14Z
|
CONTRIBUTOR
|
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### Summary
- Fix NumPy array indexing in 32-bit system, to close #4161
> https://numpy.org/doc/1.21/reference/arrays.scalars.html
I may use `intp` instead of `uintp` as I'm not 100% sure if the indexes could be negative or not in the code design.
### Run unit tests locally as GitHub doesn't provide 32-bit runner
Test platform:
- `Linux debian32bit 6.1.0-27-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) i686 GNU/Linux`
- Python 3.11.2
#### Numpy 1.26.4
I don't think those three test failures are related to this PR.
```
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..............................................................................s................s..sssss..ssssssss...ssssss....s...........s.. [ 96%]
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===================================================================== FAILURES ======================================================================
_________________________________________________________ TestEOS.test_numerical_eos_values _________________________________________________________
self = <analysis.test_eos.TestEOS testMethod=test_numerical_eos_values>
def test_numerical_eos_values(self):
assert_allclose(self.num_eos_fit.e0, -10.84749, atol=1e-3)
assert_allclose(self.num_eos_fit.v0, 40.857201, atol=1e-1)
assert_allclose(self.num_eos_fit.b0, 0.55, atol=1e-2)
> assert_allclose(self.num_eos_fit.b0_GPa, 89.0370727, atol=1e-1)
/home/yang/pymatgen/tests/analysis/test_eos.py:429:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_allclose.<locals>.compare at 0x9a968d48>, array(88.86413), array(89.0370727))
kwds = {'equal_nan': True, 'err_msg': '', 'header': 'Not equal to tolerance rtol=1e-07, atol=0.1', 'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
> return func(*args, **kwds)
E AssertionError:
E Not equal to tolerance rtol=1e-07, atol=0.1
E
E Mismatched elements: 1 / 1 (100%)
E Max absolute difference: 0.1729427
E Max relative difference: 0.00194237
E x: array(88.86413)
E y: array(89.037073)
/usr/lib/python3.11/contextlib.py:81: AssertionError
__________________________________________________________ TestBalancedReaction.test_hash ___________________________________________________________
self = <analysis.test_reaction_calculator.TestBalancedReaction testMethod=test_hash>
def test_hash(self):
> assert hash(self.rxn) == 4774511606373046513
E assert 221359835 == 4774511606373046513
E + where 221359835 = hash(24 Li + Na2S + 3 K2SO4 -> 2 KNaS + 2 K2S + 12 Li2O)
E + where 24 Li + Na2S + 3 K2SO4 -> 2 KNaS + 2 K2S + 12 Li2O = <analysis.test_reaction_calculator.TestBalancedReaction testMethod=test_hash>.rxn
tests/analysis/test_reaction_calculator.py:334: AssertionError
_______________________________________________________________ TestLattice.test_init _______________________________________________________________
self = <core.test_lattice.TestLattice testMethod=test_init>
def test_init(self):
len_a = 9.026
lattice = Lattice.cubic(len_a)
assert lattice is not None, "Initialization from new_cubic failed"
assert_array_equal(lattice.pbc, (True, True, True))
> assert hash(lattice) == -6887896986157825384
E assert 50099439 == -6887896986157825384
E + where 50099439 = hash(Lattice\n abc : 9.026 9.026 9.026\n angles : 90.0 90.0 90.0\n volume : 735.336269576\n A : 9.026 0.0 0.0\n B : 0.0 9.026 0.0\n C : 0.0 0.0 9.026\n pbc : True True True)
/home/yang/pymatgen/tests/core/test_lattice.py:43: AssertionError
3 failed, 2719 passed, 205 skipped, 54 warnings in 1223.52s (0:20:23)
```
#### NumPy 2
Cannot install:
```
ERROR: Cannot install monty==2024.10.21, pymatgen and pymatgen==2024.11.13 because these package versions have conflicting dependencies.
The conflict is caused by:
pymatgen 2024.11.13 depends on numpy<3 and >=2.0.0
matplotlib 3.9.0 depends on numpy>=1.23
monty 2024.10.21 depends on numpy<2.0.0
```
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PR_kwDOACgets6C90_1
| 4,195
|
Read NBANDS in `io.vasp.outputs.Outcar` init
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[
"@Andrew-S-Rosen Is currently implementation looking good to you? :)",
"Due to time commitments, I can just say that I trust you. 👍 Happy to report if something comes up. ",
"Thanks for saying that, I tested on multiple VASP versions (included in unit test) and didn't find any issue for now, do let me know if you notice any :)\r\n"
] | 2024-11-25T03:27:47
| 2024-12-11T02:29:56
|
2024-12-11T02:01:55Z
|
CONTRIBUTOR
|
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### Summary
- Read NBANDS in `io.vasp.outputs.Outcar` init, to close #3843
- Add overwriting tests and test file (355 KB), I didn't find any reusable file (`zgrep 'I found NBANDS' OUTCAR*` returns nothing)
#### VASP version stability
- 5.2.11 (unit test)
- 5.4.4 (unit test)
- 6.3.0 (unit test)
- 6.3.2 (unit test, overridden)
#### Reason for using current pattern instead of `NBANDS = (\d+)`
As mentioned in https://github.com/materialsproject/pymatgen/issues/3843#issue-2308586992, the NBANDS could be modified to be "number of cores compatible". [More specifically](https://www.vasp.at/wiki/index.php/NBANDS):
> When executed on multiple CPUs, VASP automatically increases the number of bands, so that NBANDS is divisible by the number of CPU cores. If [NCORE](https://www.vasp.at/wiki/index.php/NCORE) > 1, NBANDS is increased until it is divisible by the number of cores in a group ([NCORE](https://www.vasp.at/wiki/index.php/NCORE)). If [KPAR](https://www.vasp.at/wiki/index.php/KPAR) > 1, NBANDS is increased until it is divisible by the number of cores in a group.
For example if I set NBANDS to 30 on a 64-core job, it would be modified to 32 with the following message:
```
>>> grep NBANDS OUTCAR_set_30_but_changed_to_32
NBANDS = 30
| I found NBANDS = 30. Now, NBANDS = 32. |
k-points NKPTS = 126 k-points in BZ NKDIM = 126 number of bands NBANDS= 32
```
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PR_kwDOACgets6C_OFX
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Change `get` default from empty list (`[]`) to `False` when used as `bool` or condition check for `Outcar` parsing methods
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[] | 2024-11-25T07:20:56
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2025-01-09T18:14:21Z
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CONTRIBUTOR
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### Summary
- Change `get` default from empty list (`[]`) to `False` when used as `bool` or condition check for `Outcar` parsing methods
This is slightly more readable as `bool([])` is `False`, also this would not be breaking as the evaluation result is not assigned (condition check only)
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I_kwDOACgets6gVKuy
| 4,197
|
Structure.merge_sites fails when selective_dynamics is property present
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[
"Thanks for reporting and for including a code snippet again, I would take care of this"
] | 2024-11-25T09:13:34
| 2025-01-09T20:35:17
|
2025-01-09T20:35:17Z
|
CONTRIBUTOR
|
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### Python version
Python 3.12.7
### Pymatgen version
Version: 2024.10.22
### Operating system version
_No response_
### Current behavior
Error is thrown when I try to run merge_sites.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/yantar92/.venv/lib/python3.12/site-packages/pymatgen/core/structure.py", line 4604, in merge_sites
if props[key] is not None and self[i].properties[key] != props[key]:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
### Expected Behavior
merge_sites works without errors :)
### Minimal example
```Python
import pymatgen.core as pmg
str1 = pmg.Structure.from_file('POSCAR1')
str2 = pmg.Structure.from_file('POSCAR2')
merge = str1.copy()
for site in str2:
merge.append(site.species, site.frac_coords, properties=site.properties)
merge.merge_sites(mode='average')
```
### Relevant files to reproduce this bug
[POSCAR2.gz](https://github.com/user-attachments/files/17900367/POSCAR2.gz)
[POSCAR1.gz](https://github.com/user-attachments/files/17900368/POSCAR1.gz)
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PR_kwDOACgets6DBRvD
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|
Fix array comparison in `core.Structure.merge_sites`, also allow `int` property to be merged instead of `float` alone, `mode` only allow full name
|
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[] | 2024-11-25T11:06:50
| 2025-01-10T02:27:40
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2025-01-09T20:35:16Z
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CONTRIBUTOR
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### Summary
- Fix array comparison in `core.Structure.merge_sites`, to fix #4197
- [x] Test for property reset warning is missing
- [x] Add test for `is_np_dict_equal ` for custom `__eq__`
- Add check for illegal `mode` initials (not starting with `a/s/d`, currently don't check full name yet)
---
> [!WARNING]
> Minor behaviour change (fix) in `merge_sites` property handling
Only allowing `float` to be averaged may not be a good idea, we should include `int` as well, otherwise `properties={"prop1": 100}` would lead to the site property being reset to `None` while `properties={"prop1": 100.0}` doesn't, which is super confusing
https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/tests/core/test_structure.py#L1677-L1679
Also the docstring is clarified to explain this behaviour.
---
> [!WARNING]
> `mode` only allow "full name" instead of initials after an one-year deprecation period
I believe it's beneficial to allow only full name (`"sum", "delete", "average"`) instead of checking first letter only:
- more readable: `mode="sum"` instead of `mode="s"`
- consistent with currently type annotation: https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/core/structure.py#L4719
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PR_kwDOACgets6DHyo7
| 4,199
|
Fix `py.typed` usage for namespace packages
|
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[
"Still I would prefer closing this and let maintainers take over, esp. around the migration from namespace system to entry points."
] | 2024-11-26T02:54:26
| 2024-12-01T07:50:34
|
2024-12-01T07:50:05Z
|
CONTRIBUTOR
|
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- [ ] [Fix `py.typed` marker file placement](https://typing.readthedocs.io/en/latest/spec/distributing.html#packaging-typed-libraries) to close #3413:
> For namespace packages (see [PEP 420](https://peps.python.org/pep-0420/)), the py.typed file should be in the submodules of the namespace, to avoid conflicts and for clarity.
- [ ] Add a test for `py.typed` files, verify the original reported issue is gone (`Skipping analyzing "pymatgen.io.vasp.inputs": module is installed, but missing library stubs or py.typed marker [import]`)
- [ ] Double check config of `analysis / ext / io`, are they meant to be namespace packages as well?
---
Looks like some sub-modules (`analysis / ext / io`) are implicit namespace packages as well (no `__init__.py`)? i.e. `pymatgen` is namespace package, so do `pymatgen.ext/pymatgen.analysis/pymatgen.io`. Not sure if this is intended, AFAIK sharing the `pymatgen` namespace is sufficient to support `pymatgen-analysis-defects/analysis/diffusion`, `pymatgen-io-validation`?
Also quote [Anthony Sottile](https://www.youtube.com/watch?v=2Xvb79hOUdM):
> imo a namespace package is just always a bad idea -- you're better to use a plugin system -- here's an example of how to set one up: [https://youtu.be/fY3Y_xPKWNA](https://www.youtube.com/watch?v=fY3Y_xPKWNA)
```
>>> import pymatgen
>>> pymatgen
<module 'pymatgen' (namespace) from ['/home/yang/developer/pymatgen/src/pymatgen']>
>>> import pymatgen.io
>>> pymatgen.io
<module 'pymatgen.io' (namespace) from ['/home/yang/developer/pymatgen/src/pymatgen/io']>
>>> import pymatgen.ext
>>> pymatgen.ext
<module 'pymatgen.ext' (namespace) from ['/home/yang/developer/pymatgen/src/pymatgen/ext']>
>>> import pymatgen.analysis
>>> pymatgen.analysis
<module 'pymatgen.analysis' (namespace) from ['/home/yang/developer/pymatgen/src/pymatgen/analysis']>
```
https://github.com/materialsproject/pymatgen/tree/master/src/pymatgen/ext
https://github.com/materialsproject/pymatgen/tree/master/src/pymatgen/io
https://github.com/materialsproject/pymatgen/tree/master/src/pymatgen/analysis
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I_kwDOACgets6gq948
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Parsing Failure of vasprun.xml from MD Simulations Using MLFF
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[] | 2024-11-26T17:58:09
| 2024-11-26T17:58:09
|
NONE
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### Python version
Python 3.10.14
### Pymatgen version
Version: 2024.11.13
### Operating system version
Red Hat Enterprise Linux Ver 8.6
### Current behavior
When trying to parse the `vasprun.xml` file generated from calculations using MLFF with the `Vasprun` class, an `IndexError: list index out of range` is raised at line 625 of `pymatgen.io.vasp.outputs.py` when accessing `self.ionic_steps[-1]["electronic_steps"]`. This seems to occur because, in MLFF calculations, data is stored in `md_data` instead of `ionic_steps`, leaving `ionic_steps` empty. Additionally, when `ionic_step_offset` or `ionic_step_skip` is specified during the creation of a Vasprun object, parsing fails because the `vasprun.xml` generated by MLFF calculations does not contain the `<calculation>` tag, which prevents parsing from working as expected.
### Expected Behavior
Parsing the `vasprun.xml` file generated from MD calculations using MLFF should not result in an error. While I am not entirely familiar with the code, changing the condition at line 348 in `outputs.py` from
```python
if self.incar.get("ALGO") not in {"Chi", "Bse"} and not self.converged and self.parameters.get("IBRION") != 0:
```
to
```python
if self.incar.get("ALGO") not in {"Chi", "Bse"} and self.parameters.get("IBRION") != 0 and not self.converged:
```
allowed me to parse the file successfully for now. However, errors still occur when `ionic_step_offset` or `ionic_step_skip` are used, and it is possible that there are other parts of the code where `ionic_steps` are referenced when `md_data` should be used instead.
### Minimal example
```Python
from pymatgen.io.vasp.outputs import Vasprun
vasprun_xml = Vasprun("vasprun.xml")
```
### Relevant files to reproduce this bug
I am attaching a sample vasprun.xml file created for the purpose of reproducing this issue.
[vasprun.zip](https://github.com/user-attachments/files/17923967/vasprun.zip)
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PR_kwDOACgets6DbBlq
| 4,201
|
Fix VASP/ABINIT link in main `README.md`
|
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[
"Seems the following is now recommended https://github.com/gaurav-nelson/github-action-markdown-link-check: \r\n\r\n> 🚨 Update (May 2024)\r\n\r\n>I have developed a new tool called [Linkspector](https://github.com/UmbrellaDocs/linkspector), which offers improved functionality and reduced false positives. I recommend using Linkspector for your needs, which is now the preferred and supported option.\r\nTry [GitHub action Linkspector](https://github.com/UmbrellaDocs/action-linkspector)!",
"I would put the markdown link checker on holder as it seems too fragile right now"
] | 2024-11-28T05:09:21
| 2024-12-11T02:29:42
|
2024-12-11T02:02:11Z
|
CONTRIBUTOR
|
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### Summary
- Fix VASP/ABINIT hyperlink in main `README.md`
Can someone help me double check to **make sure this is not my network issue**?
```diff
# VASP
- https://cms.mpi.univie.ac.at/vasp
+ https://www.vasp.at/
# ABINIT
- https://abinit.org
+ https://abinit.github.io/abinit_web/
```
|
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I_kwDOACgets6hAVFI
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|
[Dev/Test] Migrate `PymatgenTest` from `unittest.TestCase` to `pytest`
|
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[] | 2024-11-28T07:59:03
| 2025-04-17T14:43:55
|
2025-04-17T14:43:55Z
|
CONTRIBUTOR
|
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Current [`pytest` framework isn't fully compatible with `unittest.TestCase`](https://docs.pytest.org/en/stable/how-to/unittest.html#pytest-features-in-unittest-testcase-subclasses), we should consider migrate to `pytest` framework:
> The following pytest features do not work, and probably never will due to different design philosophies:
> [Fixtures](https://docs.pytest.org/en/stable/reference/fixtures.html#fixture) (except for autouse fixtures, see [below](https://docs.pytest.org/en/stable/how-to/unittest.html#mixing-fixtures));
> [Parametrization](https://docs.pytest.org/en/stable/how-to/parametrize.html#parametrize);
> [Custom hooks](https://docs.pytest.org/en/stable/how-to/writing_plugins.html#writing-plugins);
---
For example `pytest.mark.parametrize` doesn't work:
- https://github.com/pytest-dev/pytest/issues/5382
```python
from unittest import TestCase
import pytest
class TestPytest(TestCase):
@pytest.mark.parametrize("foo", ["hello", "world"])
def test_demo(self, foo):
assert isinstance(foo, str)
```
Gives:
```
def _callTestMethod(self, method):
> if method() is not None:
E TypeError: TestPytest.test_demo() missing 1 required positional argument: 'foo'
```
While the following works just fine:
```diff
- class TestPytest(TestCase):
+ class TestPytest:
```
|
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https://github.com/materialsproject/pymatgen/pull/4203
| 2,701,820,296
|
PR_kwDOACgets6DdZdG
| 4,203
|
Remove redundant `total_ordering` decorator usage
|
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[] | 2024-11-28T11:22:15
| 2024-12-11T02:30:13
|
2024-12-11T01:59:11Z
|
CONTRIBUTOR
|
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### Summary
- Remove redundant `total_ordering` decorator usage, as `total_ordering` is already applied on superclasses and child classes did not redefine any rich comparison operations.
- Clean up comment of equality definition of `core.IStructure`
- Minor import clean up (avoid `from io import StringIO` when it's used only twice as `io` is already imported)
- Minor docstring clean up
|
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I_kwDOACgets6hDQuq
| 4,204
|
Bugs in Composition().__ge__() method
|
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[
"Admittedly the behaviour is surprising, but I believe this is expected, I had the same question in https://github.com/materialsproject/pymatgen/pull/3895\r\n\r\nThis comparison operation is not defined to really \"compare\" `Composition` (it might not make chemical sense to order compositions in the first place), but more to provide a stable ordering reference (such that when you sort compositions, they don't came out in a unpredictable/random pattern).\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/core/composition.py#L234-L241\r\n\r\nNote [the elements are sorted by **electronegativity**](https://chemistry.stackexchange.com/a/538), in this case the comparing order is `[Element Li, Element Fe, Element P, Element H, Element O]`.\r\n\r\nFor the first comparison, the oxygen in \"LiFeP\" has an implied amount of zero (LiFePO<sub>0</sub>), it's therefore considered \"smaller\" than \"LiFePO\".\r\n\r\nFor the second case, the amount of P is greater in \"LiFePO\" than \"LiFeH\" (effectively LiFePH<sub>0</sub>O vs LiFeP<sub>0</sub>HO<sub>0</sub>) and thus the short-circuit: https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/core/composition.py#L245-L249\r\n"
] | 2024-11-28T12:19:45
| 2024-11-28T15:48:21
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NONE
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### Python version
Python 3.9
### Pymatgen version
2024.3.1
### Operating system version
macos
### Current behavior
<img width="455" alt="image" src="https://github.com/user-attachments/assets/cbf2053e-5d93-4157-abc9-9124fc4ee1ba">
### Expected Behavior
The second one should output False.
### Minimal example
```Python
from pymatgen.core import Composition
Composition("LiFePO") >= Composition("LiFeP")
Composition("LiFePO") >= Composition("LiFeH")
```
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets6Dh8vq
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|
Fix `assert_str_content_equal`, add tests for testing utils
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[] | 2024-11-29T05:52:56
| 2024-12-11T02:31:04
|
2024-12-11T01:53:22Z
|
CONTRIBUTOR
|
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### Summary
- Fix `assert_str_content_equal` not raising `AssertionError`
- Add unit tests for `util.testing` as it's intended for public usage (and [quite some external code use `PymatgenTest`](https://github.com/search?q=%22%28PymatgenTest%29%3A%22&type=code))
- More human-readable error messages for assert methods in `PymatgenTest`
- [**NEED CONFIRM**] Simplify single-file module `testing/__init__.py` to `testing.py`
---
> [!WARNING]
> [**NEED CONFIRM**] Simplify single-file module `testing/__init__.py` to `testing.py` (**Is this intended for some purpose?**), I don't think this would be breaking (though the definition of `MODULE_DIR` would change from `util/testing` to `util`, but no code import this AFAIK as the `util/testing` has nothing else, I believe it's intended for `STRUCTURES_DIR` and I have updated this)
---
### Fix `assert_str_content_equal` not raising `AssertionError`
Current implementation **would not raise `AssertionError` when two strings are not equal** (it only returns a bool): https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/util/testing/__init__.py#L66-L69
And [current usage of it](https://github.com/search?q=repo%3Amaterialsproject%2Fpymatgen%20self.assert_str_content_equal&type=code) take the pattern of `self.assert_str_content_equal` without `assert`.
Several issues found:
- #4206
- #4207
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I_kwDOACgets6hL34y
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|
`test_str` and `test_mul` for `TestStructureGraph` of `analysis.graphs` are failing
|
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[] | 2024-11-29T07:40:17
| 2025-01-28T17:41:30
|
CONTRIBUTOR
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After fixing `assert_str_content_equal` implementations in #4205, noticed the following tests for `TestStructureGraph` of `analysis.graphs` are failing.
cc @mkhorton
### `pytest tests/analysis/test_graphs.py::TestStructureGraph::test_str`
```
E AssertionError: Strings are not equal (whitespaces ignored):
E ===================== Actual =====================
E Structure Graph
E Structure:
E Full Formula (H1)
E Reduced Formula: H2
E abc : 5.000000 5.000000 50.000000
E angles: 90.000000 90.000000 90.000000
E pbc : True True True
E Sites (1)
E # SP a b c
E --- ---- --- --- ---
E 0 H 0 0 0
E Graph: bonds
E from to to_image
E ---- ---- ------------
E 0 0 (1, 0, 0)
E 0 0 (0, 1, 0)
E
E ==================== Expected ====================
E Structure Graph
E Structure:
E Full Formula (H1)
E Reduced Formula: H2
E abc : 5.000000 5.000000 50.000000
E angles: 90.000000 90.000000 90.000000
E Sites (1)
E # SP a b c
E --- ---- --- --- ---
E 0 H 0 0 0
E Graph: bonds
E from to to_image
E ---- ---- ------------
E 0 0 (1, 0, 0)
E 0 0 (-1, 0, 0)
E 0 0 (0, 1, 0)
E 0 0 (0, -1, 0)
```
### `pytest tests/analysis/test_graphs.py::TestStructureGraph::test_mul`
```
E AssertionError: Strings are not equal (whitespaces ignored):
E ===================== Actual =====================
E 1 H 0.5 0 -0
E Graph: bonds
E from to to_image
E ---- ---- ------------
E 0 0 (0, 1, 0)
E 0 1 (0, 0, 0)
E 0 1 (-1, 0, 0)
E 1 1 (0, 1, 0)
E ==================== Expected ====================
E Graph: bonds
E from to to_image
E ---- ---- ------------
E 0 0 (0, 1, 0)
E 0 0 (0, -1, 0)
E 0 1 (0, 0, 0)
E 0 1 (-1, 0, 0)
E 1 1 (0, 1, 0)
E 1 1 (0, -1, 0)
```
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