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I_kwDOACgets6MbJK1
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Numpy 2.0 incompatability
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[
"Already fixed in the last commit. But there are some issues with CI on windows I am working on. ",
"Ah, very speedy! I missed that. Thanks for patching!",
"I noticed that Pymatgen is still built against the old version of NumPy.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/2b53fb1cdf08d5022894c0cb4e6960f3c4edcf81/pyproject.toml#L4-L5\r\n\r\nIn https://numpy.org/devdocs/dev/depending_on_numpy.html#numpy-2-0-specific-advice, it's recommended built against `numpy>=2.0.0rc1`.\r\n"
] | 2024-06-16T18:52:54
| 2024-06-19T02:29:36
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2024-06-16T19:44:32Z
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MEMBER
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### Python version
3.11
### Pymatgen version
2024.6.10
### Operating system version
Ubuntu
### Current behavior
When doing `pip install pymatgen`, you get `numpy==2.0` right now. This breaks Pymatgen, so we in the short-term we need to pin `pyproject.toml` to have numpy<2 and longer term we need to fix the underlying issues.
```python
from pymatgen.core import Structure
```
```
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.0 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "<stdin>", line 1, in <module>
File "/home/rosen/software/miniconda/envs/test/lib/python3.11/site-packages/pymatgen/core/__init__.py", line 13, in <module>
from pymatgen.core.lattice import Lattice
File "/home/rosen/software/miniconda/envs/test/lib/python3.11/site-packages/pymatgen/core/lattice.py", line 21, in <module>
from pymatgen.util.coord import pbc_shortest_vectors
File "/home/rosen/software/miniconda/envs/test/lib/python3.11/site-packages/pymatgen/util/coord.py", line 15, in <module>
from pymatgen.util import coord_cython
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/rosen/software/miniconda/envs/test/lib/python3.11/site-packages/pymatgen/core/__init__.py", line 13, in <module>
from pymatgen.core.lattice import Lattice
File "/home/rosen/software/miniconda/envs/test/lib/python3.11/site-packages/pymatgen/core/lattice.py", line 21, in <module>
from pymatgen.util.coord import pbc_shortest_vectors
File "/home/rosen/software/miniconda/envs/test/lib/python3.11/site-packages/pymatgen/util/coord.py", line 15, in <module>
from pymatgen.util import coord_cython
File "pymatgen/util/coord_cython.pyx", line 1, in init pymatgen.util.coord_cython
ImportError: numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use '<void>numpy._import_array' to disable if you are certain you don't need it).
```
### Expected Behavior
No crash.
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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[CI] Unit test from PR failing owing to inaccessible MP API keys
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2024-06-17T14:52:44Z
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CONTRIBUTOR
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[Unit test from PR are now failing](https://github.com/materialsproject/pymatgen/actions/runs/9538982150/job/26288803831?pr=3880) from the new unit test added in e572d34b206f48a43fe102a1c46e0532a60ff7de. (Presumably) owing to [inaccessible MP API keys](https://stackoverflow.com/questions/73866908/github-actions-main-repository-secret-not-picked-up-from-pull-request-build):
> Due to the dangers inherent to automatic processing of PRs, GitHub’s standard pull_request workflow trigger by default prevents write permissions and secrets access to the target repository.
According to the previous thread, using target `pull_request_target` might resolve this but **might post security risks** (GitHub secrets being exposed).
|
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Numpy 2.0 support
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[
"> As of now, tests pass on most systems except for some binary incompatibility issues. \r\n\r\nThanks for taking us to NumPy 2! Just a gentle reminder, the actual [installed `numpy` in CI tests for Ubuntu](https://github.com/materialsproject/pymatgen/actions/runs/9933938968/job/27437503821?pr=3885) is still version `1.26.4`:\r\n<img width=\"557\" alt=\"image\" src=\"https://github.com/user-attachments/assets/5bd3c849-3d39-419c-b838-aace86df7ca3\">\r\n\r\nAnd the [numpy installed for macos is `1.25.0`](https://github.com/materialsproject/pymatgen/actions/runs/9933938968/job/27437505022):\r\n\r\n<img width=\"598\" alt=\"image\" src=\"https://github.com/user-attachments/assets/c746cd6a-33d1-48ef-b361-28a1baab7cb6\">\r\n",
"obsolete with merging of https://github.com/materialsproject/pymatgen/pull/3894"
] | 2024-06-17T14:47:53
| 2024-08-22T10:54:11
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2024-08-22T10:52:45Z
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MEMBER
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This PR updates pymatgen to support np 2.0. As of now, tests pass on most systems except for some binary incompatibility issues. This PR should be merged only when all tests pass.
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Correcting lll_reduce execution and allow setting ftol for termination searching making heterogeneous interfaces
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[
"Thanks for catching this. However I don't think this should be removed, instead should put it after the following (I think I accidentally swapped their order in #3691 🙈, sorry): https://github.com/materialsproject/pymatgen/blob/d1fac20381f75773f23258f57b283d850a2f58c2/pymatgen/core/surface.py#L1147 \r\n\r\nAs the following lines: https://github.com/materialsproject/pymatgen/blob/9719845b1b449741c8ec661d6c09a443c982213a/pymatgen/core/surface.py#L1135-L1137\r\n\r\nDo more than just copying the `struct` (`copy` is not in-place), but sanitize it (note the `sanitize=True`): https://github.com/materialsproject/pymatgen/blob/9719845b1b449741c8ec661d6c09a443c982213a/pymatgen/core/structure.py#L2287-L2292\r\n\r\n",
"@janosh Sorry this indeed looks like an accidental bug I introduced.",
"Many thanks for the reviewing. I have swapped the order to rewrite struct into lll_reduced one after doing mapping.\r\n\r\nI also added another property for the CoherentInterfaceBuilder class to allow to set the ftol searching for different terminations. Sometimes a very small ftol is needed to shift the termination into different atomic planes as shown here.\r\n\r\n",
"Also added some features to allow 2D-identical terminations which might be 3D-non-identical to be saved as shown in the examples below:\r\n\r\n\r\n\r\n\r\nAs can be seen, the first and second terminations will be merged into one in the old version. I added an extra index before the label of the slab termination so that they can be distinguished to avoid merging.",
"Dear developers it seems there are some conflicts cannot be resolved automatically, could you please have a check?",
"Sorry I'm unable to resolve conflicts for you as I don't have write access.\r\n\r\nYou might want to look at [this tutorial](https://code.visualstudio.com/docs/sourcecontrol/overview#_merge-conflicts) to resolve merge conflicts with VSCode with a GUI, and [this](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/addressing-merge-conflicts/resolving-a-merge-conflict-on-github) from the web. \r\n\r\n@janosh Can you please review this? ",
"It seems that I do not have write access to resolve the conflicts on the web. I am using the github desktop and I have resolved it locally before commiting this version. I have no idea why the check still reported conflicts...",
"I [didn't see any merge conflicts from my side](https://github.com/DanielYang59/pymatgen/tree/help-fix-3886) for some reason, when you merge (and resolve conflicts during merge), you would also need to push the merge commit (just like any other commit). I didn't see the merge being pushed, can you please confirm this?\r\n\r\nAlso your fork is not up to date with remote, perhaps you should consider [syncing it](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork)?",
"Actually I have solved the conflict from my side before push it. I clicked syncing just now but it also says conflict remaining"
] | 2024-06-18T03:42:30
| 2024-07-17T04:51:09
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2024-07-17T04:51:09Z
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CONTRIBUTOR
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Why setting the two structures the same before finding the mappings between them?
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Improve type annotations for `io.lobster.{lobsterenv/outputs}`
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"@JaGeo Would appreciate it if you could review this. The `LobsterPy` tests passed, full test log:\r\n\r\n<details>\r\n\r\n```\r\nyang@Yang-NUC:~/test_lobsterpy$ bash run_test.sh \r\nChannels:\r\n - conda-forge\r\n - nodefaults\r\nPlatform: linux-64\r\nCollecting package metadata (repodata.json): done\r\nSolving environment: done\r\n\r\n## Package Plan ##\r\n\r\n environment location: /home/yang/opt/miniconda3/envs/test_lobster\r\n\r\n added / updated specs:\r\n - python=3.11\r\n\r\n\r\nThe following NEW packages will be INSTALLED:\r\n\r\n _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge \r\n _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu \r\n bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 \r\n ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 \r\n ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 \r\n libexpat conda-forge/linux-64::libexpat-2.6.2-h59595ed_0 \r\n libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 \r\n libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 \r\n libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 \r\n libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 \r\n libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 \r\n libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 \r\n libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 \r\n libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 \r\n ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 \r\n openssl conda-forge/linux-64::openssl-3.3.1-h4bc722e_2 \r\n pip conda-forge/noarch::pip-24.2-pyhd8ed1ab_0 \r\n python conda-forge/linux-64::python-3.11.9-hb806964_0_cpython \r\n readline conda-forge/linux-64::readline-8.2-h8228510_1 \r\n setuptools conda-forge/noarch::setuptools-72.1.0-pyhd8ed1ab_0 \r\n tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 \r\n tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 \r\n wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 \r\n xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0 \r\n\r\n\r\n\r\nDownloading and Extracting Packages:\r\n\r\nPreparing transaction: done\r\nVerifying transaction: done\r\nExecuting transaction: done\r\n#\r\n# To activate this environment, use\r\n#\r\n# $ conda activate test_lobster\r\n#\r\n# To deactivate an active environment, use\r\n#\r\n# $ conda deactivate\r\n\r\nfatal: destination path 'pymatgen' already exists and is not an empty directory.\r\nLooking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple\r\nProcessing /home/yang/test_lobsterpy/pymatgen\r\n Installing build dependencies ... done\r\n Getting requirements to build wheel ... done\r\n Preparing metadata (pyproject.toml) ... done\r\nCollecting joblib>=1 (from pymatgen==2024.7.18)\r\n Using cached https://pypi.tuna.tsinghua.edu.cn/packages/91/29/df4b9b42f2be0b623cbd5e2140cafcaa2bef0759a00b7b70104dcfe2fb51/joblib-1.4.2-py3-none-any.whl (301 kB)\r\nCollecting matplotlib<3.9.1,>=3.8 (from pymatgen==2024.7.18)\r\n Using cached 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requests>=2.32->pymatgen>=2024.5.1->lobsterpy==0.4.7) (3.7)\r\nRequirement already satisfied: urllib3<3,>=1.21.1 in /home/yang/opt/miniconda3/envs/test_lobster/lib/python3.11/site-packages (from requests>=2.32->pymatgen>=2024.5.1->lobsterpy==0.4.7) (2.2.2)\r\nRequirement already satisfied: certifi>=2017.4.17 in /home/yang/opt/miniconda3/envs/test_lobster/lib/python3.11/site-packages (from requests>=2.32->pymatgen>=2024.5.1->lobsterpy==0.4.7) (2024.7.4)\r\nRequirement already satisfied: ruamel.yaml.clib>=0.2.7 in /home/yang/opt/miniconda3/envs/test_lobster/lib/python3.11/site-packages (from ruamel.yaml>=0.17.0->pymatgen>=2024.5.1->lobsterpy==0.4.7) (0.2.8)\r\nCollecting typing-extensions>=4.6.0 (from SQLAlchemy>=1.4.0->mendeleev==0.17.0->lobsterpy==0.4.7)\r\n Using cached https://pypi.tuna.tsinghua.edu.cn/packages/26/9f/ad63fc0248c5379346306f8668cda6e2e2e9c95e01216d2b8ffd9ff037d0/typing_extensions-4.12.2-py3-none-any.whl (37 kB)\r\nCollecting greenlet!=0.4.17 (from 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kB)\r\nCollecting platformdirs<5,>=3.9.1 (from virtualenv>=20.10.0->pre-commit>=2.12.1->lobsterpy==0.4.7)\r\n Using cached https://pypi.tuna.tsinghua.edu.cn/packages/68/13/2aa1f0e1364feb2c9ef45302f387ac0bd81484e9c9a4c5688a322fbdfd08/platformdirs-4.2.2-py3-none-any.whl (18 kB)\r\nBuilding wheels for collected packages: lobsterpy\r\n Building editable for lobsterpy (pyproject.toml) ... done\r\n Created wheel for lobsterpy: filename=lobsterpy-0.4.7-0.editable-py3-none-any.whl size=6275 sha256=5c186ce7d01b93204900039d963a6a069b09542b6aeb4ddb000253a9a8c28d01\r\n Stored in directory: /tmp/pip-ephem-wheel-cache-cc8p0kny/wheels/7e/7b/84/024361668e6e29c16a15d6da4bf8f3704965685e150ddfece5\r\nSuccessfully built lobsterpy\r\nInstalling collected packages: pyfiglet, distlib, typing-extensions, typing, types-setuptools, Pygments, pyflakes, pycodestyle, pluggy, platformdirs, numpy, nodeenv, mccabe, iniconfig, identify, greenlet, filelock, coverage, colorama, cfgv, virtualenv, SQLAlchemy, pytest, flake8, pytest-split, pytest-mock, pytest-cov, pre-commit, mendeleev, lobsterpy\r\n Attempting uninstall: numpy\r\n Found existing installation: numpy 2.0.1\r\n Uninstalling numpy-2.0.1:\r\n Successfully uninstalled numpy-2.0.1\r\nSuccessfully installed Pygments-2.18.0 SQLAlchemy-2.0.31 cfgv-3.4.0 colorama-0.4.6 coverage-7.6.0 distlib-0.3.8 filelock-3.15.4 flake8-7.1.0 greenlet-3.0.3 identify-2.6.0 iniconfig-2.0.0 lobsterpy-0.4.7 mccabe-0.7.0 mendeleev-0.17.0 nodeenv-1.9.1 numpy-1.26.4 platformdirs-4.2.2 pluggy-1.5.0 pre-commit-3.8.0 pycodestyle-2.12.0 pyfiglet-0.8.post1 pyflakes-3.2.0 pytest-8.3.2 pytest-cov-5.0.0 pytest-mock-3.14.0 pytest-split-0.9.0 types-setuptools-71.1.0.20240726 typing-3.7.4.3 typing-extensions-4.12.2 virtualenv-20.26.3\r\nLooking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple\r\nCollecting pytest-xdist\r\n Using cached 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pytest>=7.0.0->pytest-xdist) (1.5.0)\r\nInstalling collected packages: execnet, pytest-xdist\r\nSuccessfully installed execnet-2.1.1 pytest-xdist-3.6.1\r\n.........................................s............................................................................ [ 87%]\r\n................. [100%]\r\n==================================================== slowest 30 durations ====================================================\r\n41.18s setup tests/cohp/test_describe.py::TestDescribe::test_text\r\n27.66s call tests/featurize/test_batch.py::TestExceptions::test_batch_summary_featurizer_exception\r\n18.10s call tests/featurize/test_batch.py::TestBatchSummaryFeaturizer::test_summary_featurize_with_json_overall\r\n15.76s call tests/cli/test_cli.py::TestCLI::test_cli_interactive_plotter_coops\r\n15.48s setup tests/cohp/test_analyze.py::TestAnalyse::test_all_attributes_nacl_pymatgen_objs\r\n15.45s setup tests/cohp/test_analyze.py::TestAnalyse::test_all_attributes_cdf_comp_range_coop\r\n13.06s call tests/featurize/test_batch.py::TestBatchSummaryFeaturizer::test_summary_featurize_orbitalwise\r\n12.91s call tests/featurize/test_batch.py::TestBatchSummaryFeaturizer::test_summary_featurize_without_json\r\n11.65s call tests/cohp/test_describe.py::TestCalcQualityDescribeWarnings::test_warnings\r\n8.31s setup tests/cohp/test_describe.py::TestDescribe::test_write_description\r\n7.49s call tests/featurize/test_batch.py::TestBatchCoxxFingerprint::test_fp_cohp_overall\r\n6.57s call tests/featurize/test_batch.py::TestBatchStructureGraphs::test_batch_structure_graphs_cation_anion_bonds\r\n6.57s call tests/featurize/test_batch.py::TestBatchSummaryFeaturizer::test_summary_featurize_with_json_bonding\r\n6.56s call tests/featurize/test_batch.py::TestBatchSummaryFeaturizer::test_summary_featurize_with_json_antibonding\r\n6.36s call tests/featurize/test_batch.py::TestBatchSummaryFeaturizer::test_summary_featurize_with_json\r\n6.34s call tests/featurize/test_core.py::TestFeaturizeLobsterpy::test_featurize_mp463\r\n6.28s call tests/featurize/test_batch.py::TestBatchCoxxFingerprint::test_fp_cohp_bonding\r\n6.02s call tests/featurize/test_batch.py::TestBatchStructureGraphs::test_batch_structure_graphs_all_bonds\r\n5.84s call tests/featurize/test_batch.py::TestBatchCoxxFingerprint::test_fp_cobi\r\n5.77s call tests/featurize/test_batch.py::TestBatchCoxxFingerprint::test_fp_coop\r\n5.52s call tests/cli/test_cli.py::TestCLI::test_nongz_file_cli\r\n5.40s call tests/cli/test_cli.py::TestCLI::test_cli_with_poscar_lobster\r\n5.31s call tests/cli/test_cli.py::TestCLI::test_calc_quality_summary_nacl\r\n5.19s call tests/plotting/test_plotting.py::TestInteractiveCohpPlotter::test_plot_colors\r\n5.07s call tests/featurize/test_batch.py::TestBatchSummaryFeaturizer::test_summary_featurize_with_no_bonds\r\n4.68s call tests/cohp/test_analyze.py::TestAnalyseCalcQuality::test_calc_quality_summary_with_objs\r\n4.52s setup tests/cohp/test_analyze.py::TestAnalyse::test_final_dicts\r\n4.52s call tests/structuregraph/test_graph.py::TestGraph::test_graph_nacl_close_fermi\r\n4.48s setup tests/plotting/test_plotting.py::TestInteractiveCohpPlotter::test_add_all_relevant_cohps_nacl_cobi_orb\r\n4.43s setup tests/cohp/test_analyze.py::TestAnalyse::test_all_attributes_nacl_comp_range_cobi_orbital\r\n================================================== short test summary info ===================================================\r\nSKIPPED [1] tests/cli/test_cli.py:711: Only enable this test to regenerate test data\r\n134 passed, 1 skipped in 416.51s (0:06:56)\r\n\r\nRemove all packages in environment /home/yang/opt/miniconda3/envs/test_lobster:\r\n```\r\n\r\n</details>",
"@JaGeo Look like last ping much have been missed, just a gentle reminder for review (and no rush of course). Thanks in advance!",
"@DanielYang59 i am on vacation. 😅 I had seen it. Maybe send me a reminder in 1.5 weeks.",
"Sorry! Enjoy your vacation :)",
"@DanielYang59 I think I am fine with this. Thank you! :)\r\n\r\nOne point, however: It is really hard to see the diff on the tests. Can you just make sure everything has been moved and that all tests are still in place?",
"> @DanielYang59 I think I am fine with this. Thank you! :)\r\n\r\nThanks a lot for reviewing! No problem.\r\n\r\n> One point, however: It is really hard to see the diff on the tests. Can you just make sure everything has been moved and that all tests are still in place?\r\n\r\nI'm pretty sure I didn't touch the actual content of those tests, just splitting acc9a1f2706b1ed9471f494d24762f308e75809d. The slight difference in number of lines should be related to imports.\r\n\r\n",
"@DanielYang59 Great! Thank you :). ",
"No problem, also pinging @janosh for review. Thanks!",
"> can we change the `Literal` doc string format to just use pipes? \r\n\r\nYep that's a good point (dropping the `Literal` is more concise, also just use human-readable things), Google docstring standard doesn't seem to have such detailed rules on typing yet.\r\n\r\nI believe there will be other violations, in this case are you aware of any IDE functionality to search for something only in code/comment, which would be very useful if we want to search for `Literal` in comment only for example (or replace `numpy` with `NumPy` but just in comments). I didn't really find one for VScode, excepting for [using regular expression](https://stackoverflow.com/questions/11314366/exclude-comments-when-searching-in-visual-studio) but is not very straightforward.\r\n\r\nA similar feature request https://github.com/microsoft/vscode/issues/55832 but didn't seem to get implemented.\r\n\r\n\r\n",
"No problem. Thanks for reviewing @JaGeo (hope you had a wonderful vacation)",
"\r\n> are you aware of any IDE functionality to search for something only in code/comment\r\n\r\nI did some search on this, seemingly VS Code doesn't seem to have the feature or from extensions (yet), though there is a [related feature request on 2016](https://github.com/microsoft/vscode/issues/11688).\r\n\r\nThe good news being [PyCharm](https://www.jetbrains.com.cn/en-us/pycharm/editions/) does have this functionality (even for the free community version):\r\n\r\n<img width=\"805\" alt=\"image\" src=\"https://github.com/user-attachments/assets/8156903a-29bd-4359-ab64-ce1c2fb68707\">\r\n\r\n"
] | 2024-06-19T02:59:30
| 2024-08-31T03:13:24
|
2024-08-30T05:59:36Z
|
CONTRIBUTOR
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## Summary
- Improve type annotations and docstring tweaks for `io.lobster.{lobsterenv/outputs}`.
- Separate unit tests for lobster inputs and outputs in acc9a1f2706b1ed9471f494d24762f308e75809d.
TODOs:
- [x] Test downstream `LobsterPy` with the script from #3873
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CrystalNN bug with atom bonded to its own images
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"Parts of CrystalNN get the right information. For example:\r\n\r\n- `crystallnn.get_cn(structure, 0)` returns `8`, which is correct\r\n- `crystallnn.get_cn_dict(structure, 0)` returns `{'Co': 8}`, also correct\r\n\r\nThe StructureGraph is created in `get_bonded_structure()` which calls `from_local_env_strategy()`. In that function (https://github.com/materialsproject/pymatgen/blob/24f7ae09125b115fdf13cb643ba5c3023c08e0d7/pymatgen/analysis/graphs.py#L273C9-L273C32) the structure graph is populated from the result of `get_all_nn_info()`, which is correct.\r\n\r\n```\r\n for idx, neighbors in enumerate(strategy.get_all_nn_info(structure)):\r\n for neighbor in neighbors:\r\n # local_env will always try to add two edges\r\n # for any one bond, one from site u to site v\r\n # and another form site v to site u: this is\r\n # harmless, so warn_duplicates=False\r\n struct_graph.add_edge(\r\n from_index=idx,\r\n from_jimage=(0, 0, 0),\r\n to_index=neighbor[\"site_index\"],\r\n to_jimage=neighbor[\"image\"],\r\n weight=neighbor[\"weight\"] if weights else None,\r\n edge_properties=neighbor[\"edge_properties\"] if edge_properties else None,\r\n warn_duplicates=False,\r\n )\r\n```\r\n\r\nFor our Co atom, we iterate over all 8 images, but half of the edges are detected as duplicates:\r\n\r\n```\r\n[/Users/fx/miniforge3/envs/matten/lib/python3.10/site-packages/pymatgen/analysis/graphs.py:437](http://localhost:8888/Users/fx/miniforge3/envs/matten/lib/python3.10/site-packages/pymatgen/analysis/graphs.py#line=436): UserWarning: Trying to add an edge that already exists from site 0 to site 0 in (1, 1, 1).\r\n warnings.warn(\r\n[/Users/fx/miniforge3/envs/matten/lib/python3.10/site-packages/pymatgen/analysis/graphs.py:437](http://localhost:8888/Users/fx/miniforge3/envs/matten/lib/python3.10/site-packages/pymatgen/analysis/graphs.py#line=436): UserWarning: Trying to add an edge that already exists from site 0 to site 0 in (1, 0, 0).\r\n warnings.warn(\r\n[/Users/fx/miniforge3/envs/matten/lib/python3.10/site-packages/pymatgen/analysis/graphs.py:437](http://localhost:8888/Users/fx/miniforge3/envs/matten/lib/python3.10/site-packages/pymatgen/analysis/graphs.py#line=436): UserWarning: Trying to add an edge that already exists from site 0 to site 0 in (0, 1, 0).\r\n warnings.warn(\r\n[/Users/fx/miniforge3/envs/matten/lib/python3.10/site-packages/pymatgen/analysis/graphs.py:437](http://localhost:8888/Users/fx/miniforge3/envs/matten/lib/python3.10/site-packages/pymatgen/analysis/graphs.py#line=436): UserWarning: Trying to add an edge that already exists from site 0 to site 0 in (0, 0, 1).\r\n warnings.warn(\r\n```\r\n\r\nSo this is where we are loosing half of the information. The `(-1, -1, -1)` edge is considered a duplicated of `(1, 1, 1)`, and so on.",
"Thanks for reporting this. \r\n\r\nI am not too familiar with the CrystalNN graph objects. We might need to check if someone else has some time to check this.\r\n\r\n@mkhorton @utf maybe?",
"@fxcoudert is there a chance that you could provide a fix?\r\n\r\n@shyuep any suggestions from your side?",
"I don't think I can provide a fix because I don't understand the intent of the code. It is apparently done on purpose at https://github.com/materialsproject/pymatgen/blob/d3c3b65826f29b485a141649db913db742502a55/pymatgen/analysis/graphs.py#L412\r\n\r\n```\r\n # if edge is from site i to site i, constrain direction of edge\r\n # this is a convention to avoid duplicate hops\r\n if to_index == from_index:\r\n if to_jimage == (0, 0, 0):\r\n warnings.warn(\"Tried to create a bond to itself, this doesn't make sense so was ignored.\")\r\n return\r\n\r\n # ensure that the first non-zero jimage index is positive\r\n # assumes that at least one non-zero index is present\r\n is_positive = next(idx for idx in to_jimage if idx != 0) > 0\r\n\r\n if not is_positive:\r\n # let's flip the jimage,\r\n # e.g. (0, 1, 0) is equivalent to (0, -1, 0) in this case\r\n to_jimage = tuple(-idx for idx in to_jimage) # type: ignore[assignment]\r\n```\r\n\r\nSo maybe it was considered a feature, but I don't understand why. It was apparently added in https://github.com/materialsproject/pymatgen/commit/732622f4fbec6b64eb38aa86b544b04de3d5656d by @mkhorton \r\n\r\nThe original PR at https://github.com/materialsproject/pymatgen/pull/2095 is not very clear about what it tries to fix. It may also be an incomplete fix, because the PR says:\r\n\r\n> While this convention fixes the present issue, I'm not convinced it's sufficient in all cases and will give it some further thought.\r\n\r\nBut I don't think the code was later improved.",
"@fxcoudert I see. Thanks!",
"@tschaume maybe you have an idea who to tag as this bug might affect structure graph objects in general. ",
"Good question :) Thanks @fxcoudert for digging into this and providing detailed information. @jmmshn and @kim-jiyoon were tagged in the original PR #2095. Maybe they can help or explain the intention here. Also tagging @munrojm and @esoteric-ephemera to see if they have any opinions on how this issue should be dealt with.",
"I believe the motivation was to create an undirected migration graph and prevent double-counting (Graph Analysis section in publication: https://www.nature.com/articles/s41524-023-01051-2) @jmmshn @hmlli",
"Ditto on what @kim-jiyoon mentioned.\r\nI'll post the text here:\r\n<img width=\"776\" alt=\"image\" src=\"https://github.com/materialsproject/pymatgen/assets/14003693/d2535005-80fd-4419-96a2-40b04632d2c0\">\r\n\r\nSo we were using the crystal graph to represent symmetry-distinct migration events and the issues of migration events that are equivalent up to lattice translation came up. I think the original PR was meant to address this issue.\r\n\r\nSo the opinion at the time was that whatever abstract object used to represent bonds or migration events should not consider two events that only differ by a lattice vector to be distinct objects so a canonical version chosen.\r\n",
"I see. But it seems that this leads to other bugs. Or: are you saying it is not a bug? In my opinion, the numbers should not change if you switch to a supercell. \r\n\r\nAnyone able to tackle this? (Maybe someone that still uses it and profits from its solution as this will likely take a day or two to figure out... maybe more). ",
"How about, as a middle ground solution and easy fix, we just make this duplicate detection optional? \r\n\r\n@fxcoudert would this work for you?",
"I see the intent, but it seems rather specific to the application in that paper. Generally speaking, the bond graph should have as many bonds as are indicated by the coordination number.\r\n\r\nYes, having an option would be good. I would argue that the default should be to count the bounds \"naturally\". Also, because it's easier to filter out the graph afterwards, rather than recreated edges.",
"@fxcoudert I agree about the default. Would you be willing to implement this? Otherwise, I fear this could take a while. \r\n\r\n@shyuep any opinion on this from your side? Also with emphasis on backward compability. Thanks in advance.",
"I would not suggest any change, it’s actually quite important.\r\n\r\n@fxcoudert it is correct, it is also a choice, but I can motivate it by analogy: consider an atom that is on the boundary of a unit cell and has periodic repeats. You would not expect the periodic repeats to be within the `Structure` definition. You can consider the edges/bonds similarly, and only want to store the unique edges.\r\n\r\nHowever, there is good news in the sense that this was considered during the writing of `StructureGraph`. If you take a look at the other methods there there are methods that will get you all 8 neighbours, I think the method is called `get_connected_sites`.\r\n\r\nI have not taken a look at this specific example, I am away from an IDE at present, but will do so next time I am doing maintenance work in case I have missed something important in this discussion.",
"> If you take a look at the other methods there there are methods that will get you all 8 neighbours, I think the method is called get_connected_sites.\r\n\r\nHum, thanks for pointing that out to me. Maybe it can make sense that the storage of the graph can be considered an implementation detail, and the user may not know what is inside or how it's stored.\r\n\r\nIn any case, I would definitely add it to the documentation, but it was really surprising to me and too me a while to figure out.",
"@mkhorton I don't have a strong opinion here but maybe you would like to document this once you have access to an IDE. ",
"So this is less of an implementation detail and more of something that is is very deliberate and fundamental to how these objects should be defined without a super clear UI interface. \r\nI think we need some way to discourage users from using the graph object for coordination analysis.\r\nJust a thought, we could just put a reference to this discussion inside of the documentation for `get_bonded_structure`.",
"OK, actually even with this definition there is a bug. Take this example:\r\n\r\n```py\r\nwith MPRester(apikey) as mpr:\r\n mp_data = mpr.materials.summary.search(\r\n material_ids=[\"mp-2647057\"],\r\n fields=[\"material_id\", \"formula\", \"formula_pretty\", \"nelements\", \"structure\"]\r\n )\r\n\r\nstructure = mp_data[0].structure\r\nbonded_struct = crystallnn.get_bonded_structure(structure)\r\n\r\nfor n, site in enumerate(bonded_struct.structure.sites):\r\n print(site.specie)\r\n print(bonded_struct.get_coordination_of_site(n))\r\n print(len(bonded_struct.get_connected_sites(n)))\r\n```\r\n\r\nIt outputs:\r\n\r\n```\r\nCo\r\n4\r\n8\r\n```\r\n\r\nThere is only one site, Co, eight-coordinated. `get_connected_sites()` returns a list of length 8, but `get_coordination_of_site()` returns 4, which is incorrect. The source for that function is at \r\nhttps://github.com/materialsproject/pymatgen/blob/d1361099331ba6c5217cbfc5a17c77dcdf4918a9/pymatgen/analysis/graphs.py#L803-L814\r\n\r\n_“Get the number of neighbors of site n.”_: the doc is clear that the answer should be 8. \r\n\r\n```py\r\nn_self_loops = sum(1 for n, v in self.graph.edges(n) if n == v)\r\nreturn self.graph.degree(n) - n_self_loops\r\n```\r\n\r\nI can't say I understand the logic here.",
"Anyone from the original developtment team able to comment on this? @jmmshn @mkhorton ?",
"@JaGeo, this definitely looks like a bug.\r\n\r\nSo it looks like this is happening:\r\n\r\n<img width=\"898\" alt=\"image\" src=\"https://github.com/user-attachments/assets/3d4ea683-c2fc-4fa0-a6b5-d7d4d470efe6\">\r\n\r\nThe full graph is just the node linking to itself 4 times, and the code assumes that all self-connections are double-counted.\r\nHowever, since we have ensured that there is no actual double counting from the way we defined the graph the ` - n_self_loops` part of the expression should not be needed.\r\n\r\nI think the fix here is just to remove the double-counting variable.\r\n@mkhorton let me know what you think. I can fix it in a PR.\r\n\r\nI also propose that we change `get_coordination_of_site` to something akin to `len(self.get_connected_sites(n))` so that we have only a single point of failure.\r\n",
"Thanks for continuing to chase this question @fxcoudert @JaGeo @jmmshn and for investigating, I'm glad this bug was caught. I'll merge @jmmshn's PR so we can fix.\r\n\r\nI know the original implementation was `self.graph.degree(n)` too. I committed the change to `self.graph.degree(n) - n_self_loops` myself, but at the time this was with the correct test value, and the error was introduced later. I do not recall the reason. Mea culpa on this."
] | 2024-06-21T12:10:31
| 2024-07-26T22:00:04
|
2024-07-26T22:00:04Z
|
NONE
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### Python version
3.11.2
### Pymatgen version
2024.6.10
### Operating system version
macOS 14.5
### Current behavior
Take a structure with only one atom per cell, which bonds to its own images in neighboring cells. Many simple metals do that, like mp-2647057.
Apply CrystalNN to get a bonded structure. The structure for mp-2647057 looks like this:
```
Structure Graph
Structure:
Structure Summary
Lattice
abc : 2.428889488469988 2.428889488469988 2.428889488469988
angles : 109.47122063449069 109.47122063449069 109.47122063449069
volume : 11.030656874268672
A : -1.40232 1.40232 1.40232
B : 1.40232 -1.40232 1.40232
C : 1.40232 1.40232 -1.40232
pbc : True True True
PeriodicSite: Co0 (Co) (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]
Graph: bonds
from to to_image
---- ---- ------------
0 0 (1, 1, 1)
0 0 (1, 0, 0)
0 0 (0, 0, 1)
0 0 (0, 1, 0)
```
The bonds graph is incorrect. The Co atom should be 8-connected, and there should be bonds to atoms at positions `(-1, -1, -1) (-1, 0, 0) (0, 0, -1) (0, -1, 0)`. These missing bonds have the exact same length and characteristics as the ones present, in fact they are equivalent by symmetry.
If you make a 2x2x2 supercell and apply CrystalNN, you get the correct coordination.
### Expected Behavior
The Co atom should be 8-coordinated.
### Minimal example
```Python
crystallnn = CrystalNN()
from pymatgen.analysis.local_env import CrystalNN
from pymatgen.ext.matproj import MPRester
with MPRester(apikey) as mpr:
mp_data = mpr.materials.summary.search(
material_ids=["mp-2647057"],
fields=["material_id", "formula", "formula_pretty", "nelements", "structure"]
)
structure = mp_data[0].structure
bonded_struct = crystallnn.get_bonded_structure(structure)
bonded_struct
```
```
### Relevant files to reproduce this bug
_No response_
|
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I_kwDOACgets6NImvx
| 3,889
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Add VASP setting for the dftd4 vdW functional.
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[
"Hi @hongyi-zhao, for the time being: you can pass `{\"IVDW\" : 13}` to the `user_incar_settings` of any VASP input set and this will accomplish the same thing. The `vdW_parameters.yaml` file is more of a convenience thing than a required one\r\n\r\nBut this should be a quick add to pymatgen. The base sets file you linked in atomate2 is [being overhauled to inherit directly from pymatgen](https://github.com/materialsproject/atomate2/pull/854) so no changes will be needed there\r\n\r\n",
"> But this should be a quick add to pymatgen.\r\n\r\nSo, a quick PR is appropriate, in this case.\r\n\r\nDone in https://github.com/materialsproject/pymatgen/pull/3891."
] | 2024-06-22T14:12:54
| 2024-06-24T23:56:40
|
CONTRIBUTOR
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### Feature Requested
VASP has implemented support for [dftd4](https://github.com/dftd4/dftd4#building-vasp-with-support-for-d4), as stated on [VASP wiki](https://www.vasp.at/wiki/index.php/DFT-D4).
On the other hand, pymatgen still doesn't support dftd4, as shown [here](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/vasp/vdW_parameters.yaml). So, I think it should be better if we can add support for dftd4 in pymatgen.
### Proposed Solution
According to the description [here](https://www.vasp.at/wiki/index.php/DFT-D4), it seems adding the following into https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/vasp/vdW_parameters.yaml should be enough:
```
dftd4:
IVDW: 13
```
### Relevant Information
The related packages, such as [this file](https://github.com/materialsproject/atomate2/blob/50ae3c05daa5d6e2deaeda4c37a4277e7b7ac4f5/src/atomate2/vasp/sets/base.py#L277) in the atomate2, should also be updated accordingly.
If there are any omissions or considerations I have overlooked, please feel free to point them out.
Regards,
Zhao
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Add SOC & multiple `PROCAR` parsing functionalities
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"Thanks for the PR @kavanase! It looks like we have a merge conflict before we can merge, otherwise this looks great.",
"No worries! Yep merge conflict came from some updates in the master branch since opening this, resolved now!",
"Just to bump, I think this PR is all ready to go. Fixed the merge conflict that had been introduced with the updated `master` branch"
] | 2024-06-22T20:54:07
| 2024-08-30T06:27:46
|
2024-08-30T06:27:46Z
|
CONTRIBUTOR
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This PR implements the `PROCAR` parsing functionality from [`easyunfold`](https://smtg-bham.github.io/easyunfold/) discussed in #3722; namely the ability to parse `PROCAR`s from spin-orbit coupling (SOC) VASP calculations (i.e. with `LSORBIT = True`), and the ability to parse multiple `PROCAR` files together (without wasting time parsing duplicate k-points etc; e.g. if the user has performed split hybrid DFT band structure calculations).
Also adds some further attributes to `Procar`; `is_soc`, `kpoints`, `occupancies`, `eigenvalues` and (when `is_soc` is `True`) `xyz_data` which gives the projections data along the x/y/z magnetisation projections.
Tests added for parsing SOC `PROCAR`s, and parsing multiple `PROCAR`s – including when they are SOC and `LORBIT = 14` (so phase factors also included and being parsed correctly).
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PR_kwDOACgets5zQ8Q1
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Improvement on loading and expanding YAML setting variables.
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[
"Maybe I am a bit unclear of the use case for this. What problem is this trying to solve? ",
"@shyuep \r\nFor improvement on loading and expanding YAML setting variables, see here: \r\nhttps://github.com/hongyi-zhao/pymatgen/blob/d4e85a81c0004a858155cf4e39267dcdfc0d1df0/tests/core/test_settings.py#L47-L63\r\n\r\nFor adding VASP setting for the dftd4 vdW functional, see here:\r\nhttps://github.com/hongyi-zhao/pymatgen/blob/d4e85a81c0004a858155cf4e39267dcdfc0d1df0/pymatgen/io/vasp/vdW_parameters.yaml#L8-L9",
"I understand the proposed improvement. I am just not clear on the benefits over the current settings YAML loading. As far as I know, no one has ever had any issue with the current settings file with regards to things like path expansion etc. ",
"For example, in my case, the following configuration doesn't work without my PR due to the `~` not being expanded correctly:\r\n```\r\nwerner@x13dai-t:~$ cat ~/.config/.pmgrc.yaml\r\nPMG_DEFAULT_FUNCTIONAL: PBE_64\r\nPMG_MAPI_KEY: <my-mapi-key>\r\nPMG_VASP_PSP_DIR: ~/Public/hpc/vasp/pot/pmg_potcar\r\n```\r\n",
"When you create the yaml file using the pmg config command, all paths are absolute. Anyway, I don't have a problem with adding path expansion. But this is a lot of additional code for a simple variable expansion.",
"> When you create the yaml file using the pmg config command, all paths are absolute.\r\n\r\nI agree with you: the path should be checked and correctly expanded with the absolute path when running the `pmg` config command and then stored in the `yaml` config file. Therefore, perhaps the logic I proposed here is not appropriate.",
"@shyuep @janosh Anyway, I just canceled this PR on my local machine and kept it in my GitHub repo and here, so that everyone can discuss and deliberate on how to handle it.\r\n\r\nThe sub-commit in this PR for `Add VASP setting for the dftd4 vdW functional.` has been re-issued separately to facilitate the development workflow: https://github.com/materialsproject/pymatgen/pull/3899.",
"i think this PR is worth having. `$HOME` expansion makes the `.pmgrc.yml` more transferable if you keep the same directory structure relative to `~` for `PMG_VASP_PSP_DIR` e.g. between clusters.",
"> i think this PR is worth having. `$HOME` expansion makes the `.pmgrc.yml` more transferable if you keep the same directory structure relative to `~` for `PMG_VASP_PSP_DIR` e.g. between clusters.\r\n\r\nHowever, this also brings up the following issue: when using `pmg` command to add configuration options, how should the corresponding values be added to the configuration file? Specifically, how to deal with the following problem: should the variables be expanded, or should the validity of the expanded variables be checked first and then still stored in the `.pmgrc.yml` file in their original variable form?\r\n\r\nIn any case, supporting as many possible forms as possible, including both the actual variable values and their unexpanded forms, should be the most flexible solution.",
"In general, config files are supposed to be machine specific. It is reasonable to assume that a person would take the one time effort to set up .pmgrc.yaml for each cluster. Also, most people keep the same user name across different clusters, in which case even the absolute paths would be the same. ",
"> in which case even the absolute paths would be the same.\r\n\r\nnot the case e.g. for Lambda, GCP and AWS. they have different root directories preceding the user name for $HOME and $SCRATCH. would be nice if you could just carbon copy the `pmgrc` across HPC providers",
"I reiterate my final point: In any case, supporting as many possible forms as possible, including the actual variable values and their unexpanded forms, should be the most flexible solution.\r\n",
"I am fine with adding path expansion. But the solution implemented is just too complicated. There are very minimal settings in the pmgrc file. We do not need a recursive function to handle lists, dicts, etc. \r\n\r\nI am a believer in implementing the **simplest** solution possible for **practical** problems. Personally, I am not convinced that being able to scp setting files over from machine to machine is a must-have. Like I said - it is a one time setup per machine, not something you do on a daily basis. But I will live with supporting path and user expansion for that esoteric purpose. However, that's all the support I am willing to add the the settings file. nested lists and dicts should not exist in the settings at the present moment. Until the day that that particular scenario actually manifests itself, we do not write code for hypothetical things."
] | 2024-06-23T01:59:51
| 2024-06-27T15:36:49
|
2024-06-26T23:35:23Z
|
CONTRIBUTOR
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- Added `_expand_strings` to handle environment and user variables in YAML.
- Introduced `_load_yaml_file` for loading YAML files with variable expansion.
- Updated `_load_pmg_settings` to use `_load_yaml_file`.
- Added tests for variable expansion, including $HOME, user-defined variables, and tilde (~) expansion.
|
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PR_kwDOACgets5zQ9eA
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|
Enable Ruff rule family "N" and "S"
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[
"Thanks for saying that and reviewing.\r\n\r\nCan I get a quick comment on https://github.com/materialsproject/pymatgen/pull/3892#discussion_r1649879457 please? I don't expect a unit test to pass only on some certain random seed :)"
] | 2024-06-23T02:12:20
| 2024-08-09T00:12:29
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2024-08-07T20:06:26Z
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CONTRIBUTOR
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## Summary
Follow up #3871:
- Enable [Ruff rule family "N"](https://docs.astral.sh/ruff/rules/#pep8-naming-n), fix violation of [NPY002](https://docs.astral.sh/ruff/rules/numpy-legacy-random/) (the use of legacy `np.random`)
> NumPy recommends using a dedicated Generator instance rather than the random variate generation methods exposed directly on the random module, as the new Generator is both faster and has better statistical properties.
- Enable [Ruff rule family "S"](https://docs.astral.sh/ruff/rules/#flake8-bandit-s), for security related checks.
- Replace standard lib `random` with `np.random`
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ValueError: Missing basis information for POTCAR symbol: Cd_GW. Please provide the basis manually.
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[
"We are a team of 2-3 people working on this. It is simply not yet implemented. \r\n\r\nThe code has been built for PBE POTCARs, 54. This is also the default in the LOBSTER input sets.",
"We could add a note that it has only been implemented for PBE_54 if there isn't already.",
"> We could add a note that it has only been implemented for PBE_54 if there isn't already.\r\n\r\nI think, for this purpose, you only need to adapt/update/enhance the following information accordingly:\r\n\r\n> ValueError: Missing basis information for POTCAR symbol: Cd_GW. Please provide the basis manually.\r\n\r\n\r\n"
] | 2024-06-25T04:20:41
| 2024-06-25T05:03:46
|
CONTRIBUTOR
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I tried to create the input files using [this example](https://github.com/JaGeo/LobsterPy/tree/main/examples/Create_inputs_example) for vasp and lobster via lobsterpy as follows, but failed:
```python
$ cat create_and_test_potcar.py
from pymatgen.io.vasp.inputs import Potcar, PotcarSingle
import os
# Specify the required elements
potcar_symbols = ["Cd_GW", "F"]
# Specify the POTCAR functional
functional = "PBE_64" # Ensure using the correct functional set
# Print the POTCAR file path for each element
for symbol in potcar_symbols:
try:
# Create PotcarSingle object for the symbol and functional
potcar_single = PotcarSingle.from_symbol_and_functional(symbol, functional)
if potcar_single:
functional_dir_dict = potcar_single.functional_dir
if functional in functional_dir_dict:
functional_dir = functional_dir_dict[functional]
potcar_path = os.path.join(functional_dir, symbol, "POTCAR")
print(f"{symbol} POTCAR created successfully.")
print(f"Element: {potcar_single.element}")
print(f"Symbol: {potcar_single.symbol}")
print(f"Functional: {potcar_single.functional}")
print(f"Number of electrons: {potcar_single.nelectrons}")
print(f"Potential type: {potcar_single.potential_type}")
print(f"POTCAR file path: {potcar_path}")
else:
print(f"Functional {functional} not found in directory dictionary.")
else:
print(f"POTCAR file for {symbol} with functional {functional} not found.")
except Exception as e:
print(f"Error occurred for symbol {symbol}: {e}")
# Create Potcar object
try:
potcar = Potcar(potcar_symbols, functional)
# Write the Potcar to a file
potcar.write_file("POTCAR")
# Read the generated POTCAR file
potcar_read = Potcar.from_file("POTCAR")
# Print POTCAR information
# print(potcar_read)
except Exception as e:
print(f"Error occurred while creating or reading POTCAR: {e}")
```
```shell
$ python create_and_test_potcar.py
Cd_GW POTCAR created successfully.
Element: Cd
Symbol: Cd_GW
Functional: PBE
Number of electrons: 12.0
Potential type: PAW
POTCAR file path: POT_PAW_PBE_64/Cd_GW/POTCAR
F POTCAR created successfully.
Element: F
Symbol: F
Functional: PBE
Number of electrons: 7.0
Potential type: PAW
POTCAR file path: POT_PAW_PBE_64/F/POTCAR
$ lobsterpy create-inputs --overwrite
/home/werner/Public/repo/github.com/materialsproject/pymatgen.git/pymatgen/io/lobster/inputs.py:642: UserWarning: These POTCARs are not compatible with Lobster up to version 4.1.0.
The keywords SHA256 and COPYR cannot be handled by Lobster
and will lead to wrong results.
warnings.warn(
Traceback (most recent call last):
File "/home/werner/.pyenv/versions/datasci/bin/lobsterpy", line 8, in <module>
sys.exit(main())
^^^^^^
File "/home/werner/Public/repo/github.com/JaGeo/LobsterPy.git/lobsterpy/cli.py", line 33, in main
run(args)
File "/home/werner/Public/repo/github.com/JaGeo/LobsterPy.git/lobsterpy/cli.py", line 987, in run
list_basis_dict = Lobsterin.get_all_possible_basis_functions(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/werner/Public/repo/github.com/materialsproject/pymatgen.git/pymatgen/io/lobster/inputs.py", line 401, in get_all_possible_basis_functions
max_basis = Lobsterin.get_basis(
^^^^^^^^^^^^^^^^^^^^
File "/home/werner/Public/repo/github.com/materialsproject/pymatgen.git/pymatgen/io/lobster/inputs.py", line 376, in get_basis
raise ValueError(
ValueError: Missing basis information for POTCAR symbol: Cd_GW. Please provide the basis manually.
```
See https://github.com/JaGeo/LobsterPy/issues/304#issuecomment-2187919611 for the related discussion.
Regards,
Zhao
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build against NPY2
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[
"Unluckily, there are still several errors. Some are related to the upstream chgnet and scipy and cannot be fixed here.",
"@njzjz sorry for the lack of reply here! looks like this is almost finished. thanks for the effort! feel free to skip the failing chgnet tests for now. re `scipy`, we'll have to pin to `<1.14` as the [newest release dropped Python 3.9 support](https://docs.scipy.org/doc/scipy/release/1.14.0-notes.html). but 1.13.0 already supports `numpy` v2",
"I really appreciate the pioneering work @njzjz! Meanwhile in case anyone missed this, [`ruff` now has a dedicated rule `NPY201`](https://numpy.org/doc/stable/numpy_2_0_migration_guide.html) to handle API migration automatically :)\r\n> `ruff check path/to/code/ --select NPY201`",
"For cross reference, I've submitted the SciPy issue to https://github.com/scipy/scipy/issues/21052",
"I do not know how to fix the rest of the errors and need help.",
"@njzjz feel free to skip the two failing `chgnet` tests. we'll migrate it to `numpy` v2 once `pymatgen` has. for `test_delta_func`, you can conditionally skip it like this:\r\n\r\n```py\r\n@pytest.mark.skipif(sys.platform == \"win32\" and np.__version__ > \"2.0.0\", reason=\"Fails on Windows with numpy > 2.0.0, awaiting https://github.com/scipy/scipy/issues/21052 resolution\")\r\ndef test_delta_func():\r\n x = np.array([0, 1, 2, 3, 4, 5])\r\n```\r\n\r\nnot sure about `TestWavecar.test_get_parchg`. that might need a closer look. maybe @esoteric-ephemera has some ideas on what's going wrong?",
"@njzjz this line is failing because of hundreds of new numpy warnings. we can make it more robust:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/4ffec03c93a513a58a0e48814d1f1eef7ce1e59b/tests/analysis/elasticity/test_elastic.py#L223\r\n\r\n```py\r\nassert sum(\"No eq state found\" in str(warn) for warn in warns) == 1\r\nassert sum(\"Extra strain states in strain-\" in str(warn) for warn in warns) == 1\r\n```",
"Just did some investigation on the failure of `TestWavecar.test_get_parchg`, unfortunately I wasn't able to come to a definite conclusion, but still share my findings in case it's helpful.\r\n\r\nI believe this failure has something to do with the float point precision (though I don't know exactly how), with the following script on Windows Python 3.12:\r\n```python\r\nimport numpy as np\r\n\r\nfrom pymatgen.io.vasp import Poscar, Wavecar\r\n\r\n\r\nTEST_DIR = \"tests/files/io/vasp\"\r\nposcar = Poscar.from_file(f\"{TEST_DIR}/inputs/POSCAR\")\r\nw = Wavecar(f\"{TEST_DIR}/outputs/WAVECAR.H2.ncl\")\r\n\r\nw.coeffs.append([np.ones((2, 100))])\r\nc = w.get_parchg(poscar, -1, 0, phase=False, spinor=None)\r\n\r\nprint(np.min(c.data[\"total\"])) # 0.0 in NumPy 1.x, 8.738907122657083e-33 in NumPy 2.x\r\nassert not np.all(c.data[\"total\"] > 0.0) # AssertionError\r\n```\r\n\r\nNote the min value in `c.data[\"total\"]` is very close to zero ([the min positive value with `float32` is around 10<sup>-38</sup>](https://en.wikipedia.org/wiki/Single-precision_floating-point_format)).\r\n\r\nFrom the [\"NumPy 2.0 migration guide\"](https://numpy.org/doc/stable/numpy_2_0_migration_guide.html), there seems to be two changes related to this:\r\n1. The default Windows integer was `int32` for NumPy 1.x, and is now `int64` (confirmed on my Windows PC), for Linux/Mac it's always `int64`\r\n2. [The change in the scalar promotion rules](https://numpy.org/neps/nep-0050-scalar-promotion.html#nep50)\r\n\r\nHowever, with these changes, I would expect the precision on Windows to be consistent with Linux on NumPy 2.x. Perhaps someone more familiar with the internal workings of `Wavecar` would know the reason :)\r\n \r\n",
"The failing tests for `tests/io/abinit/test_abiobjects.py` looks like another randomly failing test. I cannot recreate it on my Windows PC.",
"> The failing tests for tests/io/abinit/test_abiobjects.py looks like another randomly failing test. I cannot recreate it on my Windows PC.\r\n\r\nprobably something to report to https://github.com/Unidata/netcdf4-python, even if just to say the error message is self-contradictory...\r\n\r\n> E OSError: Error loading charset-233f44715e5aacaf3a688c2faff5ddf7.dll; The operation completed successfully.\r\n",
"> > The failing tests for tests/io/abinit/test_abiobjects.py looks like another randomly failing test. I cannot recreate it on my Windows PC.\r\n> \r\n> probably something to report to https://github.com/Unidata/netcdf4-python, even if just to say the error message is self-contradictory...\r\n\r\nAgreed, just for my own record, it failed in another PR randomly https://github.com/materialsproject/pymatgen/actions/runs/10268736299/job/28412461926?pr=3892\r\n\r\n",
"> E OSError: Error loading charset-233f44715e5aacaf3a688c2faff5ddf7.dll; The operation completed successfully.\r\n\r\nThis part of the code is generated by [delvewheel](https://github.com/adang1345/delvewheel) [here](https://github.com/adang1345/delvewheel/blob/e74686253154416dcba7c0cfd644f3b847bf267c/delvewheel/_wheel_repair.py#L74). I think I can report there.\r\n\r\nAccording to the [Windows documentation](https://learn.microsoft.com/en-us/windows/win32/debug/system-error-codes--0-499-), this error message means no error. So it may be incorrect to throw an error (while it is also strange that `LoadLibraryExW` returns nothing but gives `ERROR_SUCCESS`).\r\n\r\n> ERROR_SUCCESS\r\n> 0 (0x0)\r\n> The operation completed successfully.\r\n\r\nSee also https://stackoverflow.com/questions/7524142/what-does-windows-error-0-error-success-mean",
"> E OSError: Error loading charset-233f44715e5aacaf3a688c2faff5ddf7.dll; The operation completed successfully.\r\n\r\nSubmitted to https://github.com/adang1345/delvewheel/issues/51",
"@njzjz can you pin pyproject to the fixed [`delvewheel>=1.7.4`](https://pypi.org/project/delvewheel/1.7.4/)",
"> @njzjz can you pin pyproject to the fixed [`delvewheel>=1.7.4`](https://pypi.org/project/delvewheel/1.7.4/)\r\n\r\nThis may not work, as delvewheel is a build-time dependency, not a runtime dependency.",
"> This may not work, as delvewheel is a build-time dependency, not a runtime dependency.\r\n\r\nah, didn't realize that. so the place to pin that would be here\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/1dfc9e4f7bbddaf5d93fe9b09b425ca1be6a58f4/pyproject.toml#L1-L4\r\n\r\nbut looks like we're in the green anyway so would be good to remove the temp install command in `test.yml`",
"thanks again @njzjz! 👍 ",
"Just recorded another failure in https://github.com/materialsproject/pymatgen/actions/runs/10319015504/job/28566565139:\r\n> OSError: Error loading libxml2-14375db763c77d38e40bbe5c028add84.dll; The operation completed successfully."
] | 2024-06-25T20:31:21
| 2024-10-23T02:21:46
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2024-08-08T23:03:18Z
|
CONTRIBUTOR
|
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## Summary
Major changes:
- fix 1: Build against NPY2 instead of NPY1. This will support both NPY1 and NPY2. See https://numpy.org/devdocs/dev/depending_on_numpy.html#numpy-2-0-specific-advice.
- fix 2: Replace `np.int_t` (missing in NPY2) with `np.int64_t` and `np.float_` with `np.float64`.
- fix 3: Replace `long` with `np.int64_t`, as "The default integer type on Windows is now int64 rather than
int32, matching the behavior on other platforms" per the change log of NPY2.
## Todos
If this is work in progress, what else needs to be done?
- feature 2: ...
- fix 2:
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](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_kwDOACgets5zklwj
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[Breaking] Fix comparision for `core.Composition`
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[
"Can I have your advice on defining the comparability here please? Thanks a lot in advance. @shyuep @mkhorton @janosh ",
"There is no meaning to comparing compositions.",
"Thanks for your quick response. I assume you mean we don't define comparison to be chemically meaningful, but just for sorting purpose (as per the docstring)? Am I understanding that correct?\r\nhttps://github.com/materialsproject/pymatgen/blob/fbf8ec0a5a9c0fb649975d66dedb31b17bcc9dfc/pymatgen/core/composition.py#L195-L202",
"I would say unless there is some good reason, ie some broken randomness in the comparison or sorting, I would leave it be. This is purely a non meaningful sorting thing and there is no reason to cause any upstream breakage by changing it. ",
"Thanks for your reply, I really appreciate that. Here are currently two reasons:\r\n1. `True` is returned early for multi-element `Composition`:\r\n https://github.com/materialsproject/pymatgen/blob/fbf8ec0a5a9c0fb649975d66dedb31b17bcc9dfc/pymatgen/core/composition.py#L206-L212\r\n\r\n And lead to the following false positive:\r\n ```python\r\n print(Composition({\"Fe\": 4, \"S\": 2}) > Composition({\"Fe\": 3, \"S\": 4})) # True\r\n ```\r\n\r\n2. For the single-element case, currently the implementation doesn't agree with the docstring: \r\n ```python\r\n print(Composition({\"S\": 1}) > Composition({\"O\": 1})) # True\r\n ```\r\n And as per the docstring, \r\n > We consider compositions A >= B if all elements in B are in A and the amount of each element in A is greater than or equal to the amount of the element in B\r\n \r\n This does not satisfy the condition that \"all elements in B are in A\" and should be `False` instead.\r\n\r\nWhat do you think?",
"Well, there really isn't any meaning to it. An element not present in a composition has an implied amount of 0. The intent is to sort all elements by electronegativity order. We compare the most electropositive element first. If one amount is greater than the other, we make a conclusion. If not, we compare the next element. In your example, we will only consider S if the amounts of Fe are the same within tolerance.\r\n\r\nIn the second case, there are two elements to be compared - S and O. Since S is more electropositive, it is compared first. The first one has 1 S and the second one has 0 S. So it is >.\r\n\r\nThe docstring can be clarified to be clearer. But I don't think there is much to do in terms of actual code since there is no rigorous way to define comparisons for Compositions. It is what it is.",
"I push a docstring correction. Since this is a nonsense comparison to begin with, let's not spend too much time dwelling on it.",
"Okay sure. Thanks for the explanation and clarifying the docstring. \r\n\r\nPerhaps we want to remove this TODO tag as well?\r\nhttps://github.com/materialsproject/pymatgen/blob/f10ace8809765ce573fb334269ee199d59b2dbb8/pymatgen/core/composition.py#L206-L212"
] | 2024-06-26T03:17:44
| 2024-06-26T11:16:11
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2024-06-26T05:20:07Z
|
CONTRIBUTOR
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## Summary
- Fix #3815.
### Unchanged behavior
```python
# Single element
print(Composition({"O": 2}) > Composition({"O": 1})) # True
# Multiple shared elements
print(Composition({"Fe": 3, "O": 4}) > Composition({"Fe": 2, "O": 3})) # True
# Superset
print(Composition({"C":1, "O": 2}) > Composition({"O": 2})) # True
```
### Breaking change (fix)
As per the docstring: https://github.com/materialsproject/pymatgen/blob/fbf8ec0a5a9c0fb649975d66dedb31b17bcc9dfc/pymatgen/core/composition.py#L195-L202
```python
# The followings would now be False (with a warning)
# Single element
print(Composition({"S": 1}) > Composition({"O": 1})) # False, with a warning
print(Composition({"O": 1}) > Composition({"S": 1})) # False, with a warning
# Multiple elements but not superset
print(Composition({"S": 1, "O": 2}) > Composition({"C": 1, "O": 2})) # False, with a warning
print(Composition({"C": 1, "O": 2}) > Composition({"S": 1, "O": 2})) # False, with a warning
```
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PR_kwDOACgets5znzcg
| 3,896
|
Adding MD input set to FHI-aims
|
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[
"Is there anything that should be done here? (besides removing `src/pymatgen/analysis/aflow_prototypes.json` file from codespell :))",
"MErged. Thanks."
] | 2024-06-26T11:40:14
| 2024-07-08T12:37:12
|
2024-07-03T18:34:05Z
|
CONTRIBUTOR
|
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## Summary
This PR adds a Molecular Dynamics input set generator for FHI-aims, making it possible to build input files for the internal implementation of MD in aims.
Major changes:
- An `MDSetGenerator` class is added for FHI-aims, with API resembling that of Vasp MD input set
## Todos
None
## 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_kwDOACgets5zqw6j
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|
Bug fix for ComputedEntry from_dict
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[
"Thanks for the fix."
] | 2024-06-26T18:01:40
| 2024-09-25T17:54:09
|
2024-06-26T18:58:56Z
|
CONTRIBUTOR
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In `pymatgen.entries.computed_entries`, `ComputedEntry` takes three optional fields: `energy_adjustments`, `parameters`, `data`, which are not correctly read in by its `from_dict` method. This is because, for example:
```
parameters = {k: MontyDecoder().process_decoded(v) for k, v in (dct.get("parameters", {})}
```
will throw `AttributeError: 'NoneType' object has no attribute 'items'` if the input `ComputedEntry` dict has `parameters = None`.
Because the typing of `ComputedEntry` suggests that these fields can be `None`, this PR ensures that the `from_dict` can properly handle null fields and also ensures correct param defaults (`energy_adjustments` incorrectly defaults to an empty `dict` instead of `list`).
Also added a test for this behavior. cc @tsmathis who found this behavior
|
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I_kwDOACgets6NoXQn
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|
@cached_class decorator prevents class methods of Compatibility objects from being used in multiprocessing as they can't be pickled
|
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[
"This seems to be the motivation for the decorator: https://github.com/materialsproject/pymatgen/pull/2450 suggesting it may be necessary, pinging @munrojm for input on whether this is likely still potential issue given changes to the api/rester",
"Talked to @janosh and he thinks we can probably resolve this with a PR to `monty` to sort out the pickling behavior of the decorator",
"Closing as fixed by https://github.com/materialsproject/pymatgen/pull/2450"
] | 2024-06-26T20:03:50
| 2024-07-19T17:47:08
|
2024-07-19T17:47:08Z
|
CONTRIBUTOR
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The use of this decorator leads to the error message:
```python
self = <joblib.parallel.BatchCompletionCallBack object at 0x3376ec590>
def _return_or_raise(self):
try:
if self.status == TASK_ERROR:
> raise self._result
E AttributeError: Can't pickle local object 'cached_class.<locals>._decorated'
```
I'm unsure what problem this decorator is solving in this instance. If there's no reason to keep these decorators I can to submit PR of local edits to use joblib to parallelize applying compatibility settings to large numbers of entries.
https://github.com/materialsproject/pymatgen/blob/fbf8ec0a5a9c0fb649975d66dedb31b17bcc9dfc/pymatgen/entries/compatibility.py#L838-L840
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PR_kwDOACgets5zsbF0
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Add VASP setting for the dftd4 vdW functional.
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[
"This PR is fine but there are failing tests.",
"@shyuep these failing tests seem to be \"tests\" that make sure the input sets stay the same. Some hashes are out of date. \r\n\r\nThey say one should notify all input set owners: \r\n@mkhorton @janosh and you as well @shyuep \r\n\r\n",
"Thanks for the PR @hongyi-zhao!\r\n\r\nIndeed, the hash failures as @JaGeo are a safety mechanism to make sure that we are intentional when changing input sets. Since this is an additive change this is all good. I have committed a change to update the test.\r\n\r\nOnce the tests pass I would be happy to merge."
] | 2024-06-26T23:44:50
| 2024-07-23T10:43:14
|
2024-07-23T10:43:14Z
|
CONTRIBUTOR
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Add VASP setting for the dftd4 vdW functional, as discussed in https://github.com/materialsproject/pymatgen/issues/3889.
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Improve Keep Redundant Spaces algorithm for PatchedPhaseDiagram
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"Thanks @CompRhys!\r\n\r\nI think some comment strings need to be updated: for example, there is a claim that `PatchedPhaseDiagram` uses the same `as_dict()` as `PhaseDiagram` but this is not the case (`computed_data`, i.e. including the qhull entries, are not stored). Otherwise this looks great."
] | 2024-06-28T16:12:30
| 2024-07-17T14:59:37
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2024-07-17T14:59:37Z
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CONTRIBUTOR
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## Summary
- modularize the keep redundant spaces code, and fix the algorithm which previously didn't get rid of all the redundant spaces.
## 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))
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prettify periodic_table.json for readability
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[
"Pls test the loading speeds on the pretty vs non pretty version. This is something that is loaded often. So every millisecond counts. I would not prioritize being able to read the JSON directly since people seldom do it and it can always be pretty printed if needed. ",
"@shyuep good point; the impact does not appear significant. See timing results below. I will note that I repeated these tests multiple times manually, with multiple kernel restarts, etc. and the results were noisy, with load times always within +/- 1.5 ms of each other. Sometimes the pretty version loaded faster, sometimes the non-pretty version loaded faster.\r\n\r\nRun on python 3.12.0 on a windows laptop (WSL2) on battery power, restarting a fresh kernel before running.\r\n```\r\n%%timeit -n 10 -r 500\r\nimport json\r\n\r\n# Step 1: Load the JSON file\r\nwith open('/home/ryan/mambaforge/envs/pbx/code/pymatgen/src/pymatgen/core/periodic_table.json', 'r') as file:\r\n data = json.load(file)\r\n```\r\n\r\nResults (output of 3 successive runs for each condition is shown)\r\n**Current `master` (not pretty)**:\r\n`3.51 ms ± 790 µs per loop (mean ± std. dev. of 500 runs, 10 loops each)`\r\n```\r\nThe slowest run took 4.67 times longer than the fastest. This could mean that an intermediate result is being cached.\r\n2.77 ms ± 622 µs per loop (mean ± std. dev. of 500 runs, 10 loops each)\r\n```\r\n```\r\nThe slowest run took 5.98 times longer than the fastest. This could mean that an intermediate result is being cached.\r\n3.93 ms ± 1.45 ms per loop (mean ± std. dev. of 500 runs, 10 loops each)\r\n```\r\n\r\n\r\n\r\n**This PR (pretty)**\r\n`3.61 ms ± 718 µs per loop (mean ± std. dev. of 500 runs, 10 loops each)`\r\n```\r\nThe slowest run took 4.39 times longer than the fastest. This could mean that an intermediate result is being cached.\r\n3.25 ms ± 868 µs per loop (mean ± std. dev. of 500 runs, 10 loops each)\r\n```\r\n`3.64 ms ± 875 µs per loop (mean ± std. dev. of 500 runs, 10 loops each)`\r\n\r\n\r\n",
"Thanks"
] | 2024-07-01T02:25:03
| 2024-10-10T01:54:23
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2024-07-02T12:49:12Z
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CONTRIBUTOR
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Prettify `periodic_table.json` to improve its readability. (using the Prettify JSON VS Code extension)
I considered the alternative of converting to YAML so that comments could be inserted (see #3851 ), but I found the following way back in the git log from 2011:
```
--
Date: Mon Nov 14 13:19:54 2011 -0500
Move periodicTable back to json format for actual loading. Loading times ~ 200x
--
Date: Thu Nov 10 12:07:13 2011 -0500
Further sanitize yaml for periodic table to be proper sentence case keys.
--
Date: Thu Nov 10 10:40:16 2011 -0500
Switch periodic table data format to YAML for easier maintenance.
```
I'm not up to date on whether in modern times YAML is still much slower to read than .json, but I thought it best to stick with .json for now.
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Add electronic structure methods for Species
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[
"@shyuep can I have your thoughts on this implementation? I think all that remains to finish the PR is entering data for the rest of the common oxidation states, but before I spend time on that I want to make sure this looks workable to you. Thanks!",
"> @shyuep can I have your thoughts on this implementation? I think all that remains to finish the PR is entering data for the rest of the common oxidation states, but before I spend time on that I want to make sure this looks workable to you. Thanks!\r\n\r\n@shyuep friendly reminder about this - once I get your blessing on the approach I've taken, I'll populate the remaining data.",
"Also just a note that the pre-commit tests are currently unhappy about some spellings in `aflow_prototypes`\r\n\r\n```\r\nsrc/pymatgen/analysis/aflow_prototypes.json:1: cristalline ==> crystalline\r\nsrc/pymatgen/analysis/aflow_prototypes.json:1: Ond ==> One, And\r\nsrc/pymatgen/analysis/aflow_prototypes.json:1: Bever ==> Never\r\nsrc/pymatgen/analysis/aflow_prototypes.json:1: CaCl ==> calc\r\nsrc/pymatgen/analysis/aflow_prototypes.json:1: Parth ==> Path\r\nsrc/pymatgen/analysis/aflow_prototypes.json:1: cristalline ==> crystalline\r\nsrc/pymatgen/analysis/aflow_prototypes.json:1: CaF ==> calf\r\nsrc/pymatgen/analysis/aflow_prototypes.json:1: Sclar ==> Scalar\r\nsrc/pymatgen/analysis/aflow_prototypes.json:1: Zink ==> Zinc\r\nsrc/pymatgen/analysis/aflow_prototypes.json:1: Pease ==> Peace, Piece, Please, Lease\r\n```",
"Seems ok to me. Ignore the spelling issues.",
"@shyuep @mkhorton this is ready for review / merge!",
"Merged. Thanks!"
] | 2024-07-01T14:32:44
| 2024-07-16T20:27:36
|
2024-07-16T20:27:36Z
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CONTRIBUTOR
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## Summary
Replacing #3851 , this PR implements `electronic_structure`, `full_electronic_structure`, and `valence` methods for `Species`.
Major changes:
- Electronic configurations of ions is added to `periodic_table.json`. Instead of a single string, the `["Electronic structure"]` key for each element is now a `dict` keyed by oxidation state, so the elemental electronic structures are found in `["Electronic structure"]["0"]`. Those of ions corresponding to the common oxidation states are added accordingly, e.g. under `["Electronic structure"]["2"]`. This parallels the way `ionic_radii` are stored. The data themselves are taken from the NIST ASD database listed in the docstrings of the respective methods.
- I removed the word `"(tentative")` from the electron config of `Lr (0)` because the one listed is shown in the NIST database (presumably last time the .json file was updated, `Lr` was not as well understood as it is now).
- Update `electronic_structure` in `Element` to accommodate the new data format
- Implement `electronic_structure`, `full_electronic_structure`, and `valence` methods for `Species`
- Added unit tests, including a comprehensive test covering all `Element` and `common_oxidation_states` which ensures the total number of electrons between the `Element` and `Species` (based on the `full_electronic_structure` is consistent with the oxidation state.
- Updated docstrings with references and slightly more explanatory text for all methods.
## Note
the NIST database only contains electronic structures of **cations**. I was unable to find a similar resource for **anions**, however all of the negative "common oxidation states" could be achieved by filling p orbitals of the corresponding ground state element (e.g., ground state is p2, -4 anion is p6). I took this approach for all negative oxidation states (which are relatively few in comparison to the positive ones) because I feel confident it is correct. However, I welcome suggestions if anyone knows where to find hard data to confirm this.
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<!--pre-commit.ci start-->
updates:
- [github.com/pre-commit/mirrors-mypy: v1.10.0 → v1.10.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.10.0...v1.10.1)
- [github.com/adamchainz/blacken-docs: 1.16.0 → 1.18.0](https://github.com/adamchainz/blacken-docs/compare/1.16.0...1.18.0)
- [github.com/RobertCraigie/pyright-python: v1.1.366 → v1.1.369](https://github.com/RobertCraigie/pyright-python/compare/v1.1.366...v1.1.369)
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I_kwDOACgets6OJxja
| 3,905
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Why assume trajectory lattice does not change by default?
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[] | 2024-07-01T23:51:28
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https://github.com/materialsproject/pymatgen/blob/d77f77697c7298fd0596e3aa55689709445bdf0e/src/pymatgen/core/trajectory.py#L51
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I_kwDOACgets6OPt4a
| 3,906
|
Build up customized pourbaix entries
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[
"I realize the relevant entries are available in mp_api repo. However, is there a way to let user to customize the ion entries? Especially when new ion data is found?"
] | 2024-07-02T14:54:33
| 2024-07-02T15:24:37
|
NONE
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### Feature Requested
I am not sure if such feature is already existing. Can someone create a new entry for ions for building pourbaix diagram? According to https://journals.aps.org/prb/pdf/10.1103/PhysRevB.85.235438, one just need to define the correction of E(exp-DFT). However, I did not find any function in pymatgen that computes such energy difference.
### Proposed Solution
Prepare a datafile that document the correction and then define a class/function to do the correction on the fly? It seems that the ion entries are downloaded directly from MP database.
### Relevant Information
_No response_
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I_kwDOACgets6OUeoB
| 3,907
|
VASP Convergence Testing
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[] | 2024-07-03T05:52:49
| 2024-08-30T10:14:00
|
CONTRIBUTOR
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### Feature Requested
So far, there is no systematic method for doing VASP Convergence Testing. So, it would be nice to add this feature to pymatgen.
### Proposed Solution
Maybe something adapted from the following implementatoin:
https://github.com/kavanase/vaspup2.0
### Relevant Information
See https://doped.readthedocs.io/en/latest/GGA_workflow_tutorial.html#convergence-of-encut-and-kpoints-for-epsilon-ionic for the related example.
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PR_kwDOACgets50Ub1X
| 3,908
|
add option to color phonon bands as per gruneisen parameter value
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[
"Hi @shyuep, @janosh, @mkhorton and @JaGeo, I have added this new functionality to the Grüneisen parameter BS plotter. Happy to address review comments if there are any, or else it can be merged 😄 ",
"Great thanks. "
] | 2024-07-03T12:21:44
| 2024-07-03T13:27:30
|
2024-07-03T13:27:20Z
|
CONTRIBUTOR
|
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# Note
This new functionality was initially implemented as part of ongoing workflow development for computing the Grüneisen parameter in atomate2, see https://github.com/materialsproject/atomate2/pull/752
As it mainly relies on the pymatgen code with minor additions, I think it would be appropriate if the code resides here.
## Changes
1. Added an option to get phonon bandstructure colored based on Grüneisen parameter values along the K-path in `GruneisenPhononBSPlotter`.
2. Added `plot_ph_bs_with_gruneisen` arg to `save_plot_gs `and `get_plot_gs` methods
3. Added tests to ensure the functionality works as expected
## Example output for Si with new functionality
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PR_kwDOACgets50kz3n
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Added Note about StructureGraph and lattice translations
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[] | 2024-07-06T01:30:51
| 2024-07-08T12:11:14
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2024-07-08T12:11:13Z
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CONTRIBUTOR
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Added more documentation in response to #3888
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PR_kwDOACgets50k9L1
| 3,911
|
Support `PBE_64` functional in `MPScanRelaxSet`.
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[
"Unittests need to be added for the new parameters.",
"Noting this is a partial duplicate of #3899, let's merge #3899. Thanks @hongyi-zhao "
] | 2024-07-06T02:29:00
| 2024-07-23T10:43:15
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2024-07-23T10:43:15Z
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CONTRIBUTOR
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Support `PBE_64` functional in `MPScanRelaxSet`:
- Added `PBE_64` to the list of valid POTCARs.
- Updated documentation to include `PBE_64`.
|
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PR_kwDOACgets50k9b1
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Bump certifi from 2024.6.2 to 2024.7.4
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[] | 2024-07-06T02:30:00
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2024-07-15T04:56:35Z
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CONTRIBUTOR
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Bumps [certifi](https://github.com/certifi/python-certifi) from 2024.6.2 to 2024.7.4.
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/certifi/python-certifi/commit/bd8153872e9c6fc98f4023df9c2deaffea2fa463"><code>bd81538</code></a> 2024.07.04 (<a href="https://redirect.github.com/certifi/python-certifi/issues/295">#295</a>)</li>
<li><a href="https://github.com/certifi/python-certifi/commit/06a2cbf21f345563dde6c28b60e29d57e9b210b3"><code>06a2cbf</code></a> Bump peter-evans/create-pull-request from 6.0.5 to 6.1.0 (<a href="https://redirect.github.com/certifi/python-certifi/issues/294">#294</a>)</li>
<li><a href="https://github.com/certifi/python-certifi/commit/13bba02b72bac97c432c277158bc04b4d2a6bc23"><code>13bba02</code></a> Bump actions/checkout from 4.1.6 to 4.1.7 (<a href="https://redirect.github.com/certifi/python-certifi/issues/293">#293</a>)</li>
<li><a href="https://github.com/certifi/python-certifi/commit/e8abcd0e62b334c164b95d49fcabdc9ecbca0554"><code>e8abcd0</code></a> Bump pypa/gh-action-pypi-publish from 1.8.14 to 1.9.0 (<a href="https://redirect.github.com/certifi/python-certifi/issues/292">#292</a>)</li>
<li>See full diff in <a href="https://github.com/certifi/python-certifi/compare/2024.06.02...2024.07.04">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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PR_kwDOACgets50mz8i
| 3,914
|
Add HSE-specific vdW parameters for dftd3 and dftd3-bj to MPHSERelaxSet.
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[
"This PR may not be a good way. Another way I can think of is to modify [vdw_parameters.yaml](https://github.com/materialsproject/pymatgen/blob/master/src/pymatgen/io/vasp/vdW_parameters.yaml) as follows:\r\n\r\n```yaml\r\ndiff --git a/src/pymatgen/io/vasp/vdW_parameters.yaml b/src/pymatgen/io/vasp/vdW_parameters.yaml\r\nindex 6708fbd1e..8adcda275 100644\r\n--- a/src/pymatgen/io/vasp/vdW_parameters.yaml\r\n+++ b/src/pymatgen/io/vasp/vdW_parameters.yaml\r\n@@ -3,8 +3,15 @@ dftd2:\r\n IVDW: 1\r\n dftd3:\r\n IVDW: 11\r\n+ hse:\r\n+ VDW_SR: 1.129\r\n+ VDW_S8: 0.109 \r\n dftd3-bj:\r\n IVDW: 12\r\n+ hse:\r\n+ VDW_A1: 0.383\r\n+ VDW_S8: 2.310\r\n+ VDW_A2: 5.685 \r\n dftd4:\r\n IVDW: 13\r\n ts:\r\n```\r\nHowever, I could not effectively implement the corresponding code adjustments in other parts of pymatgen for this alternative method.",
"Also see [here](https://www.vasp.at/forum/viewtopic.php?t=19658) for the related discussion.",
"Pls add tests for the new parameters. @mkhorton What needs to be done about the hashes? I still maintain the hashes are creating more headache than they solve.",
"@shyuep What do you mean by saying **the hashes** here?",
"The failing tests are due to a hash check whenever input set yaml files are modified. ",
"> The failing tests are due to a hash check whenever input set yaml files are modified.\r\n\r\n1. I should always create a PR branch based on [materialsproject:master](https://github.com/materialsproject/pymatgen/tree/master) of pymatgen instead of my local master branch which includes other unmerged PRs I have made, which triggered this issue.\r\n2. Using additional hash checks over these input sets of YAML files is unnecessary and troublesome, because they are all simple text files, and git itself already can trace them perfectly and is designed for such a job."
] | 2024-07-07T06:50:34
| 2024-07-27T04:01:04
|
2024-07-23T10:43:15Z
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CONTRIBUTOR
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Add HSE-specific vdW parameters for dftd3 and dftd3-bj to MPHSERelaxSet. For the related discussion and information, see below:
https://www.vasp.at/forum/viewtopic.php?t=19551
https://github.com/dftd3/simple-dftd3/blob/3a50cbdf8566b3caa8760499ae21746ec9a5e535/assets/parameters.toml#L80-L82
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PR_kwDOACgets507Zkj
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Fix chemical system method for different oxidation states
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[
"Thanks for reporting and fixing @danielzuegner, this seems like a clear bug. We should get this merged :) "
] | 2024-07-10T07:54:29
| 2024-08-09T00:07:27
|
2024-07-26T15:07:07Z
|
CONTRIBUTOR
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## Summary
Currently, when the same element occurs in multiple oxidation states in a structure (e.g., `Composition({"Na+": 1, "Na2+": 1, "Cl-": 1})`), `structure.composition.chemical_system` yields that element repeated, e.g., `Composition({"Na+": 1, "Na2+": 1, "Cl-": 1})`), `structure.composition.chemical_system == "Cl-Na-Na"`. My hypothesis is that this was introduced by the fix to this issue: https://github.com/materialsproject/pymatgen/issues/2248.
This PR fixes the bug by using the newly introduced `chemical_system_set` property of `Composition`, and adds the line
```python
assert Composition({"Na+": 1, "Na2+": 1, "Cl-": 1}).chemical_system == "Cl-Na"
```
to `test_composition.py`.
## 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_kwDOACgets50_pCY
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|
Add new MP input sets / concurrently update MatPES POTCARs
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[
"@esoteric-ephemera is this PR ready for merging?",
"@matthewkuner debugging some potential issues with the Ba pseudo (updated to the GW one) - hope to have an update soon",
"Copying a suggestion here:\r\n\r\n> @esoteric-ephemera a late suggestion, but can we set GGA_COMPAT to False? See [here](https://www.vasp.at/wiki/index.php/GGA_COMPAT) for discussion.",
"@mkhorton: Sorry I forgot to answer! Yes shouldn't be an issue to add this, makes sense to me. Been running the recompute with this tag added\r\n\r\n@shyuep: Should be ready for review"
] | 2024-07-10T16:53:13
| 2025-02-23T17:45:06
|
2025-01-09T16:37:48Z
|
CONTRIBUTOR
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This PR adds new MP input sets that resulted from a benchmarking effort over the past year. For the benchmarks, refer to:
- https://github.com/materialsproject/foundation/pull/26
- [Reference living document](https://drive.google.com/file/d/1fUUx0wrrtMRcSss5yv3NiQuC7J5IiEKL/view)
Critical updates include:
- POTCARs
- `KSPACING` adjustment by bandgap
- `LREAL = False`
- `LMAXMIX = 6`
The updated KSPACING function is slightly different from what was discussed with the MP foundation initially. This is to ensure that calculations with the highest $k$-point density (KSPACING = 0.22) would not be deprecated by this PR. Previously I recommended that the minimum KSPACING = 0.2, but this is effectively the same as 0.22.
~Leaving this up as a WIP pending further community discussion and writing tests~
**`MatPESStaticSet` Users:** please note that the recommended POTCARs for MatPES (PBE64 generally) have updated. These updates are consistent with the data generation for MatPES, please use the 12 recommended updated POTCARs
|
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PR_kwDOACgets51AF8P
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|
added cp2k_output cube to pymatgen volume parser
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[
"@DanielYang59 any chance you can help me with this ",
"Sorry I have never used CP2K... But I could probably answer some general questions. So is there anything I could help with?\r\n\r\n@JaGeo Any chance you know who is maintaining the CP2K module? Thanks! @nwinner maybe (from the `__author__`)?\r\n\r\n",
"@DanielYang59 at least, @nwinner wrote a cp2k workflow for atomate2 😀",
"I originally wrote the cp2k module and the cube parser. Yes, I also included an atomate2 workflow.\r\n\r\nHere is the constructor for cube parsing into VolumetricData.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/27d90b777cedc80593d93b6e8b66dee04c167460/src/pymatgen/io/common.py#L356\r\n\r\nIs there a reason to implement a separate parser now in the cp2k module?\r\n\r\nAny other questions you have for me?\r\n"
] | 2024-07-10T18:11:38
| 2024-07-19T12:00:05
|
2024-07-19T12:00:05Z
|
NONE
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## Summary
added a function parse_cube() in pymatgen.io.cp2k.output
slight change in parse_initial_structure() ... cp2k output different ...i used cp2k/cp2k-git-feb-2022 to generate outputs....
I have benchmarked the planar average using pymatgen against cubecruncher(https://www.cp2k.org/tools:cubecruncher)...
These results are in shown in "https://github.com/Sudo-Raheel/cp2k_to_pymatgen/tree/main/cube_file"
Few more points
1) the documentation should mention that print level should be at least medium in cp2k ..else it wont be able to parse the structure from cp2k.out
2) allow using the phrase "poisson_periodicity" to find whether is_molecule() works only when default poisson solver in cp2k is used .
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I_kwDOACgets6PWPd7
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Cannot get element projected data
|
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[] | 2024-07-12T07:48:31
| 2024-07-12T07:48:31
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NONE
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### Python version
Python.3.12.4
### Pymatgen version
2024.6.10
### Operating system version
_No response_
### Current behavior
banddos_fig = BSDOSPlotter(bs_projection='elements', dos_projection='elements', vb_energy_range=2, cb_energy_range=2, font='Times New Roman', axis_fontsize=20)
Results: UserWarning: Cannot get element projected data; either the projection data doesn't exist, or you don't have a compound with exactly 2 or 3 or 4 unique elements.
### Expected Behavior
I have five types of atoms in my POSCAR. Actually, I want to show three projections for different atoms with specific orbitals,like this figure
, can I use get_projection_on_elements to realise this?
### Minimal example
```Python
import matplotlib.pyplot as plt
import matplotlib.pyplot as plt
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import BSDOSPlotter,\
BSPlotter,BSPlotterProjected,DosPlotter
# read vasprun.xml，get band and dos information
bs_vasprun = Vasprun("./vasprun.xml",parse_projected_eigen=True)
bs_data = bs_vasprun.get_band_structure(line_mode=True)
dos_vasprun=Vasprun("./vasprun.xml")
dos_data=dos_vasprun.complete_dos
# set figure parameters, draw figure
banddos_fig = BSDOSPlotter(bs_projection='elements', dos_projection='elements', vb_energy_range=2, cb_energy_range=2, font='Times New Roman', axis_fontsize=20)
banddos_fig.get_plot(bs=bs_data, dos=dos_data)
plt.savefig('./banddos_fig.png')
```
### Relevant files to reproduce this bug
_No response_
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I_kwDOACgets6Pbwre
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|
More robust parsing of (electronic) piezoelectric tensor from OUTCAR
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[] | 2024-07-12T22:18:27
| 2024-07-12T22:18:27
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NONE
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### Feature Requested
Using VASP v6.3.2:
1. Running a calculation with LEPSILON=.TRUE. and LRPA=.FALSE. produces the following OUTCAR line: `PIEZOELECTRIC TENSOR (including local field effects) for field in x, y, z (C/m^2)`. This line does not match the search string in `pymatgen > io > vasp > outputs.py` line 2909, resulting in an improperly parsed `piezo_tensor`
2. It would be useful to define a `read_lcalceps()` method, equivalent to `read_lepsilon()`, to extract the piezoelectric tensor from calculations using LCALCEPS=.TRUE. since it is sometimes beneficial to use the finite differences approach
### Proposed Solution
1. Modify the search string to look for the relevant elements of the output string, i.e. "PIEZOELECTRIC TENSOR" && "for field in x, y, z (C/m^2)" as opposed to the whole string. This would accommodate variations in the output related to VASP versions.
2. Add a check for `lcalceps` and create a duel of the `read_lepsilon()`
### Relevant Information
These changes would allow for
1. greater compatibility with different VASP versions, which seem to use different output strings in the OUTCAR.
2. ability to parse the piezolectric tensor from LCALCEPS calculations
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PR_kwDOACgets51SZxf
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Format aflow_prototypes.json and exclude it from codespell check in pre-commit
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[] | 2024-07-13T09:57:18
| 2024-07-20T03:07:36
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2024-07-15T04:57:45Z
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CONTRIBUTOR
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### Summary
- Similar to #3901, format `aflow_prototypes.json`
- Ignore this file from codespell check in pre-commit, otherwise it would always fail
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I_kwDOACgets6PdubY
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[Ext] The link to `boltztrap` is not valid anymore
|
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[] | 2024-07-13T13:37:42
| 2024-07-24T11:09:05
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2024-07-24T11:09:05Z
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CONTRIBUTOR
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I was trying to enable `boltztrap` in CI test, and found the URL is not valid anymore it appears: https://github.com/materialsproject/pymatgen/blob/35b1f448c5842b9b13c0ace0f3fe811bbcb5ffd1/src/pymatgen/electronic_structure/boltztrap.py#L1-L17
Also the same one in the `requires` decorator: https://github.com/materialsproject/pymatgen/blob/35b1f448c5842b9b13c0ace0f3fe811bbcb5ffd1/src/pymatgen/electronic_structure/boltztrap.py#L62-L72
However [this mirror from TU Wien](https://www.tuwien.at/en/tch/tc/theoretical-materials-chemistry/boltztrap) seems to be working, and I could get the "latest" v1.2.5 (released around 2017).
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Adapt pymatgen.symmetry.analyzer to new spglib (>=2.5.0) output data format
|
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[
"I'm happy to implement this change :)",
"Thanks @DanielYang59 !! 😀"
] | 2024-07-16T08:13:34
| 2024-07-16T13:33:06
|
2024-07-16T13:33:06Z
|
CONTRIBUTOR
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### Feature Requested
The recent spglib release v2.5.0 changed the output data types from dict to new classes like SpglibDataset.
https://spglib.readthedocs.io/en/stable/releases.html#v2-5-0-9-jul-2024
The dict-like interface is planned to be removed, so it will be necessary to adapt the pymatgen interface in the near future.
### Proposed Solution
For now, modifiying the version of spglib to <2.5.0 in pyproject.toml might be best - @DanielYang59 already confirmed that this fixes the failing `test_get_crystal_system` in tests/symmetry/test_analyzer.py (https://github.com/materialsproject/pymatgen/pull/3859#issuecomment-2228279612), so that test can be re-included @shyuep
### Relevant Information
_No response_
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Migrate `spglib` to new `SpglibDataset` format with version 2.5.0
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[
"@kaueltzen Is everything looking good to you?",
"Thanks for reviewing. @janosh For some reason [all tests in windows are failing](https://github.com/materialsproject/pymatgen/actions/runs/9957894146/job/27510952746)? Doesn't looks like owing to this PR and still need to find out why I guess "
] | 2024-07-16T08:42:28
| 2024-07-16T13:42:41
|
2024-07-16T13:33:05Z
|
CONTRIBUTOR
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### Summary
- Migrate `spglib` to new data format as pointed out by @kaueltzen, to fix #3922
- Add types for `SpacegroupAnalyzer` and `PointGroupAnalyzer`
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Add multiwfn QTAIM parsing capabilities
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"Hey @shyuep @janosh @mkhorton, can I get someone's eyes on this? Everything is working as expected, and I don't anticipate adding more major features at this point.",
"Yo, pinging this again @shyuep @janosh @mkhorton. Can anyone take a look and help me get this merged?",
"Thanks for this PR @espottesmith, apologies it sat in the queue for so long!"
] | 2024-07-16T14:34:01
| 2024-08-09T00:08:01
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2024-07-30T19:51:33Z
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CONTRIBUTOR
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## Summary
This PR adds parsing capabilities for Mulitwfn. Currently, the functionality is limited to parsing quantum theory of atoms in molecules (QTAIM) information.
Shout-out to @santi921. A lot of this code is his, and I've mostly cleaned it up, simplified it, and added tests.
## 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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Fix `lll_reduce` for slab generation
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"@DanielYang59 Sorry, it seems that my changes have conflicts with the recent updates, I remake another pull request using the recent version",
"I understand merge conflicts could be confusing but don't worry. Merge conflicts are common things that would happen when you and another person try to make changes to the same line of code. When such things happen, you just need to choose whatever [conflict resolver that works best for you](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/addressing-merge-conflicts/resolving-a-merge-conflict-using-the-command-line) (GUI/CLI), and decide what the final conflicted line should end up by yourself.\r\n\r\nIn most cases, reopen a PR is not necessary, perhaps you could try to resolve them next time when such things happen.\r\n\r\nI would ping @janosh for review as I'm not a maintainer and therefore don't have write access to the repo. Can I ask for your patience as he has been quite busy recently? Thank you for your effort towards correcting and improving the code.",
"Many thanks for the suggestion... I have another issue here. I found that installing the package and by `pip install pymatgen` by `pip install .` at the forked folder have different effects. For me, I cannot successfully import the modules like pymatgen.core, pymatgen.analysis etc... by installing the recently released version on 2024.6.10 I forked to local folder. May I have some comments on this issue?\r\n\r\n",
"> I found that installing the package and by `pip install pymatgen` by `pip install .` at the forked folder have different effects. \r\n\r\nThat's exactly right observation. By `pip install pymatgen`, you are installing `pymatgen` from PyPI, and by running `pip install .`, you are instead installing from a local project, refer to [this](https://pip.pypa.io/en/stable/cli/pip_install/) for more details if you are interested.\r\n\r\nMeanwhile, if you were trying to contribute to the code, you might want to use `pip install --editable .` or `pip install -e .` for short in [editable mode](https://pip.pypa.io/en/stable/cli/pip_install/), such that your changes to the code could be tested in real time. \r\n\r\n> For me, I cannot successfully import the modules like pymatgen.core, pymatgen.analysis etc... by installing the recently released version on 2024.6.10 I forked to local folder. \r\n\r\n I didn't manage to recreate this issue from my side. Perhaps you should double check if you have a file called `pymatgen.py` locally which might have shadowed the real `pymaygen` you are trying to import?\r\n\r\n",
"Thank you for the explanation but I found the that the reason might be the package is not fully installed, this is the pymatgen folder installed using conda environment... As you can see most of the modules were not successfully installed\r\n\r\n",
"It's weird, but it's hard to give any advice without seeing the log. Can you show me the log from `pip install -e .`? Meanwhile I guess it's more readable for me, and easier for you to just copy and paste the terminal outputs. You could also use [markdown grammars](https://www.markdownguide.org/cheat-sheet/) like triple \\``` in both sides of the code to highlight it,or [add a collapsible section](https://gist.github.com/pierrejoubert73/902cc94d79424356a8d20be2b382e1ab) if the log is too long.",
"> ```\r\n> (3.11) jason@YaoshuXiedeMacBook-Pro pymatgen % pip install -e . \r\n> Obtaining file:///Users/jason/Documents/GitHub/pymatgen\r\n> Installing build dependencies ... done\r\n> Checking if build backend supports build_editable ... done\r\n> Getting requirements to build editable ... done\r\n> Preparing editable metadata (pyproject.toml) ... done\r\n> Requirement already satisfied: matplotlib>=3.8 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (3.9.1)\r\n> Requirement already satisfied: monty>=2024.5.24 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (2024.7.12)\r\n> Requirement already satisfied: networkx>=2.2 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (3.3)\r\n> Requirement already satisfied: palettable>=3.1.1 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (3.3.3)\r\n> Requirement already satisfied: pandas>=2 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (2.2.2)\r\n> Requirement already satisfied: plotly>=4.5.0 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (5.22.0)\r\n> Requirement already satisfied: pybtex>=0.24.0 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (0.24.0)\r\n> Requirement already satisfied: requests>=2.32 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (2.32.3)\r\n> Requirement already satisfied: ruamel.yaml>=0.17.0 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (0.18.6)\r\n> Requirement already satisfied: scipy>=1.13.0 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (1.14.0)\r\n> Requirement already satisfied: spglib>=2.5.0 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (2.5.0)\r\n> Requirement already satisfied: sympy>=1.2 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (1.13.0)\r\n> Requirement already satisfied: tabulate>=0.9 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (0.9.0)\r\n> Requirement already satisfied: tqdm>=4.60 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (4.66.4)\r\n> Requirement already satisfied: uncertainties>=3.1.4 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (3.2.2)\r\n> Requirement already satisfied: joblib>=1 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (1.4.2)\r\n> Requirement already satisfied: numpy>=1.25.0 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pymatgen==2024.6.10) (1.26.4)\r\n> Requirement already satisfied: contourpy>=1.0.1 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (1.2.1)\r\n> Requirement already satisfied: cycler>=0.10 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (0.12.1)\r\n> Requirement already satisfied: fonttools>=4.22.0 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (4.53.1)\r\n> Requirement already satisfied: kiwisolver>=1.3.1 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (1.4.5)\r\n> Requirement already satisfied: packaging>=20.0 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (24.1)\r\n> Requirement already satisfied: pillow>=8 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (10.4.0)\r\n> Requirement already satisfied: pyparsing>=2.3.1 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (3.1.2)\r\n> Requirement already satisfied: python-dateutil>=2.7 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (2.9.0.post0)\r\n> Requirement already satisfied: pytz>=2020.1 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pandas>=2->pymatgen==2024.6.10) (2024.1)\r\n> Requirement already satisfied: tzdata>=2022.7 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pandas>=2->pymatgen==2024.6.10) (2024.1)\r\n> Requirement already satisfied: tenacity>=6.2.0 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from plotly>=4.5.0->pymatgen==2024.6.10) (8.5.0)\r\n> Requirement already satisfied: PyYAML>=3.01 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pybtex>=0.24.0->pymatgen==2024.6.10) (6.0.1)\r\n> Requirement already satisfied: latexcodec>=1.0.4 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pybtex>=0.24.0->pymatgen==2024.6.10) (3.0.0)\r\n> Requirement already satisfied: six in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from pybtex>=0.24.0->pymatgen==2024.6.10) (1.16.0)\r\n> Requirement already satisfied: charset-normalizer<4,>=2 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from requests>=2.32->pymatgen==2024.6.10) (3.3.2)\r\n> Requirement already satisfied: idna<4,>=2.5 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from requests>=2.32->pymatgen==2024.6.10) (3.7)\r\n> Requirement already satisfied: urllib3<3,>=1.21.1 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from requests>=2.32->pymatgen==2024.6.10) (2.2.2)\r\n> Requirement already satisfied: certifi>=2017.4.17 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from requests>=2.32->pymatgen==2024.6.10) (2024.7.4)\r\n> Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from ruamel.yaml>=0.17.0->pymatgen==2024.6.10) (0.2.8)\r\n> Requirement already satisfied: mpmath<1.4,>=1.1.0 in /opt/anaconda3/envs/3.11/lib/python3.11/site-packages (from sympy>=1.2->pymatgen==2024.6.10) (1.3.0)\r\n> Building wheels for collected packages: pymatgen\r\n> Building editable for pymatgen (pyproject.toml) ... done\r\n> Created wheel for pymatgen: filename=pymatgen-2024.6.10-0.editable-cp311-cp311-macosx_11_0_arm64.whl size=7492 sha256=2548cfbf6576818aa421af52eb35c4419af329a6ddc25491aefea55384cdd940\r\n> Stored in directory: /private/var/folders/km/tznxn_d162bgzpqpzp9wcjn00000gn/T/pip-ephem-wheel-cache-w9pptfr8/wheels/86/ad/75/5dd22e6df08f3c8b6e3dfe775999afd0464ff20204e3661ff7\r\n> Successfully built pymatgen\r\n> Installing collected packages: pymatgen\r\n> ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.\r\n> emmet-core 0.84.1 requires pymatgen==2024.4.13, but you have pymatgen 2024.6.10 which is incompatible.\r\n> Successfully installed pymatgen-2024.6.10```\r\n> ```\r\n\r\nIndeed there is an issue of the emmet-core dependency problem but it finally says successfully installed...",
"`emmet-core` explicitly required `pymatgen==2024.4.13` https://github.com/materialsproject/emmet/issues/1020. My suggestion would be creating a separate Python env for developing `pymatgen` (or any other dedicated task) to avoid such version conflicts.\r\n\r\nI believe it's better not to trust an incompletely resolved package dependency?",
"yes, I found the problem. I am using mp-api which requires emmet-core, and emmet-core requires lower version of pymatgen... In this way I can only use the old version pymatgen now... Many thanks for your help there",
"> @jinlhr542 thanks for these improvements! could you add unit tests for the keywords you added?\r\n\r\nCould you please try this test?\r\n```python\r\nimport unittest\r\nfrom pymatgen.core.structure import Structure\r\nfrom pymatgen.core.lattice import Lattice\r\nfrom pymatgen.analysis.interfaces import CoherentInterfaceBuilder, SubstrateAnalyzer\r\n\r\nclass TestCoherentInterfaceBuilder(unittest.TestCase):\r\n\r\n def setUp(self):\r\n #build substrate & film structure\r\n basis = [[0, 0, 0], [0.25, 0.25, 0.25]]\r\n self.substrate = Structure(\r\n Lattice.cubic(a=5.431),\r\n [\"Si\", \"Si\"],\r\n basis)\r\n self.film = substrate = Structure(\r\n Lattice.cubic(a=5.658),\r\n [\"Ge\", \"Ge\"],\r\n basis)\r\n\r\n def test_termination_searching(self):\r\n sub_analyzer = SubstrateAnalyzer()\r\n matches = list(sub_analyzer.calculate(substrate = self.substrate, film = self.film))\r\n cib = CoherentInterfaceBuilder(film_structure = self.film,\r\n substrate_structure=self.substrate,\r\n film_miller=matches[0].film_miller,\r\n substrate_miller=matches[0].substrate_miller,\r\n zslgen=sub_analyzer,termination_ftol=1e-4,label_index=True,\\\r\n filting_out_sym_slabs=False)\r\n self.assertTrue(cib.terminations == [('1_Ge_P4/mmm_1', '1_Si_P4/mmm_1'),\\\r\n ('1_Ge_P4/mmm_1', '2_Si_P4/mmm_1'),\\\r\n ('2_Ge_P4/mmm_1', '1_Si_P4/mmm_1'),\\\r\n ('2_Ge_P4/mmm_1', '2_Si_P4/mmm_1')], \\\r\n\"\"\"\r\ntermination results wrong; the correct list should be:\r\n[('1_Ge_P4/mmm_1', '1_Si_P4/mmm_1'),\r\n('1_Ge_P4/mmm_1', '2_Si_P4/mmm_1'),\r\n('2_Ge_P4/mmm_1', '1_Si_P4/mmm_1'),\r\n('2_Ge_P4/mmm_1', '2_Si_P4/mmm_1')].\r\n\"\"\")\r\n\r\nif __name__ == \"__main__\":\r\n unittest.main()\r\n```",
"Can you please insert that new test into `pymatgen/tests/analysis/interfaces/test_coherent_interface.py` ([usually the location of the unit tests follow the same structure of the module/package you wish to test](https://docs.pytest.org/en/stable/explanation/goodpractices.html)) and commit it? Such that it would be run automatically in the future.\r\n\r\nCan you also do me a favor and rename the following unit test to `TestMillerIndexFinder`? Thanks:\r\nhttps://github.com/materialsproject/pymatgen/blob/252efa7839e337c78b8633d32a3961aea949f58a/tests/core/test_surface.py#L693 \r\n",
"> TestMillerIndexFinder\r\n\r\nDone",
"> @jinlhr542 thanks for these improvements! could you add unit tests for the keywords you added?\r\n\r\nDear Janosh\r\n\r\nCould you please check the commited tests? It will be appreciated if this pull request can be accepted soon.",
"> minor variable rename suggestions\r\n\r\nModified accordingly, please review again.",
"@jinlhr542 Great work!"
] | 2024-07-17T05:25:54
| 2024-09-12T08:54:03
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2024-09-11T12:52:48Z
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CONTRIBUTOR
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By making the termination identification process for interface generation more robust.
1. fixing problem for the lll_reduce process when making slabs, doing mapping before updating the structure
2. allow to set ftol of the termination distances for hierarchical cluster so that some non-identical terminations close to each other can be identified
3. allow to add index for terminations so that terminations with the same space group can be distinguished
4. allow to not filter symmetic film and substrate slabs when finding terminations
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[
"I'm guessing you might have a `pymatgen.py` file shadowing the real `pymatgen` package, let me know if it's not the case :)",
"Same issue here. Python 3.12, Pymatgen version 2024.6.10, CentOS Linux 7. Trying to run\r\n\r\n```\r\nfrom pymatgen.io.pwscf import PWInput\r\n```\r\n\r\nafter installing my forked pymatgen gives\r\n\r\n```\r\nTraceback (most recent call last):\r\n File \"<stdin>\", line 1, in <module>\r\nModuleNotFoundError: No module named 'pymatgen.io'\r\n```\r\n\r\nTried using both `pip install .` in the top directory and `pip install -U git+https://github.com/jsukpark/pymatgen` (the latter per the instructions in https://github.com/materialsproject/pymatgen?tab=readme-ov-file#installation adapted for my fork) for installing my forked pymatgen, same issue happens in both.\r\n\r\nAnd I don't have `pymatgen.py` file floating around anywhere.",
"Hi @jsukpark thanks for providing the information. I just tried to clone your fork and things seem to work fine on my side. \r\n\r\nCan you post the output of ~`pip install .`~ `pip install -e .` so that I could have a closer look?",
"```\r\n(torch-v2) login2.frontera(1027)$ pip install .\r\nProcessing /work2/08542/epark/frontera/pymatgen\r\n Installing build dependencies ... done\r\n Getting requirements to build wheel ... done\r\n Preparing metadata (pyproject.toml) ... done\r\nRequirement already satisfied: matplotlib>=3.8 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (3.9.0)\r\nRequirement already satisfied: monty>=2024.5.24 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (2024.7.12)\r\nRequirement already satisfied: networkx>=2.2 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (3.3)\r\nRequirement already satisfied: palettable>=3.1.1 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (3.3.3)\r\nRequirement already satisfied: pandas>=2 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (2.2.2)\r\nRequirement already satisfied: plotly>=4.5.0 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (5.22.0)\r\nRequirement already satisfied: pybtex>=0.24.0 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (0.24.0)\r\nRequirement already satisfied: requests>=2.32 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (2.32.2)\r\nRequirement already satisfied: ruamel.yaml>=0.17.0 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (0.18.6)\r\nRequirement already satisfied: scipy>=1.13.0 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (1.13.0)\r\nRequirement already satisfied: spglib>=2.5.0 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (2.5.0)\r\nRequirement already satisfied: sympy>=1.2 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (1.12)\r\nRequirement already satisfied: tabulate>=0.9 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (0.9.0)\r\nRequirement already satisfied: tqdm>=4.60 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (4.66.4)\r\nRequirement already satisfied: uncertainties>=3.1.4 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (3.1.7)\r\nRequirement already satisfied: joblib>=1 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (1.4.2)\r\nRequirement already satisfied: numpy>=1.25.0 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pymatgen==2024.6.10) (1.26.4)\r\nRequirement already satisfied: contourpy>=1.0.1 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (1.2.1)\r\nRequirement already satisfied: cycler>=0.10 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (0.12.1)\r\nRequirement already satisfied: fonttools>=4.22.0 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (4.51.0)\r\nRequirement already satisfied: kiwisolver>=1.3.1 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (1.4.5)\r\nRequirement already satisfied: packaging>=20.0 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (24.0)\r\nRequirement already satisfied: pillow>=8 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (10.3.0)\r\nRequirement already satisfied: pyparsing>=2.3.1 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (3.1.2)\r\nRequirement already satisfied: python-dateutil>=2.7 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from matplotlib>=3.8->pymatgen==2024.6.10) (2.9.0.post0)\r\nRequirement already satisfied: pytz>=2020.1 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pandas>=2->pymatgen==2024.6.10) (2024.1)\r\nRequirement already satisfied: tzdata>=2022.7 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pandas>=2->pymatgen==2024.6.10) (2024.1)\r\nRequirement already satisfied: tenacity>=6.2.0 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from plotly>=4.5.0->pymatgen==2024.6.10) (8.3.0)\r\nRequirement already satisfied: PyYAML>=3.01 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pybtex>=0.24.0->pymatgen==2024.6.10) (6.0.1)\r\nRequirement already satisfied: latexcodec>=1.0.4 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pybtex>=0.24.0->pymatgen==2024.6.10) (3.0.0)\r\nRequirement already satisfied: six in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from pybtex>=0.24.0->pymatgen==2024.6.10) (1.16.0)\r\nRequirement already satisfied: charset-normalizer<4,>=2 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from requests>=2.32->pymatgen==2024.6.10) (3.3.2)\r\nRequirement already satisfied: idna<4,>=2.5 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from requests>=2.32->pymatgen==2024.6.10) (3.7)\r\nRequirement already satisfied: urllib3<3,>=1.21.1 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from requests>=2.32->pymatgen==2024.6.10) (2.2.1)\r\nRequirement already satisfied: certifi>=2017.4.17 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from requests>=2.32->pymatgen==2024.6.10) (2024.2.2)\r\nRequirement already satisfied: ruamel.yaml.clib>=0.2.7 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from ruamel.yaml>=0.17.0->pymatgen==2024.6.10) (0.2.8)\r\nRequirement already satisfied: mpmath>=0.19 in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from sympy>=1.2->pymatgen==2024.6.10) (1.3.0)\r\nRequirement already satisfied: future in /work2/08542/epark/frontera/miniconda3/envs/torch-v2/lib/python3.12/site-packages (from uncertainties>=3.1.4->pymatgen==2024.6.10) (1.0.0)\r\nBuilding wheels for collected packages: pymatgen\r\n Building wheel for pymatgen (pyproject.toml) ... done\r\n Created wheel for pymatgen: filename=pymatgen-2024.6.10-cp312-cp312-linux_x86_64.whl size=337779 sha256=7d284a9afa36dc9b5efab55eb2491005147c89c38d83bfdf16c1ce10134c3109\r\n Stored in directory: /tmp/pip-ephem-wheel-cache-wepbrq2c/wheels/f8/0d/31/8029a58ece5c6f8f5e5e16824abde28f5dd1efc7d9d479d03a\r\nSuccessfully built pymatgen\r\nInstalling collected packages: pymatgen\r\nSuccessfully installed pymatgen-2024.6.10\r\n(torch-v2) login2.frontera(1028)$ python3\r\nPython 3.12.3 | packaged by Anaconda, Inc. | (main, May 6 2024, 19:46:43) [GCC 11.2.0] on linux\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> from pymatgen.io.pwscf import PWInput\r\nTraceback (most recent call last):\r\n File \"<stdin>\", line 1, in <module>\r\nModuleNotFoundError: No module named 'pymatgen.io'\r\n>>> \r\n```",
"My guess would be that the pip and the python are two different envs. Please create a *fresh* virtual env and try again.",
"I was able to reproduce this issue from the master branch, it appears after moving to the src layout, the wheel is built with incomplete package content, I'm trying to fix this.\r\n```\r\n> python3 -m build --wheel\r\n......\r\ncreating '/Users/yang/temporary/pymatgen/dist/.tmp-z71e47nv/pymatgen-2024.6.10-cp312-cp312-macosx_11_0_arm64.whl' and adding 'build/bdist.macosx-11.1-arm64/wheel' to it\r\nadding 'pymatgen/dao.py'\r\nadding 'pymatgen/py.typed'\r\nadding 'pymatgen/optimization/linear_assignment.cpython-312-darwin.so'\r\nadding 'pymatgen/optimization/linear_assignment.pyx'\r\nadding 'pymatgen/optimization/neighbors.cpython-312-darwin.so'\r\nadding 'pymatgen/optimization/neighbors.pyx'\r\nadding 'pymatgen/util/coord_cython.cpython-312-darwin.so'\r\nadding 'pymatgen/util/coord_cython.pyx'\r\nadding 'pymatgen-2024.6.10.dist-info/LICENSE'\r\nadding 'pymatgen-2024.6.10.dist-info/METADATA'\r\nadding 'pymatgen-2024.6.10.dist-info/WHEEL'\r\nadding 'pymatgen-2024.6.10.dist-info/entry_points.txt'\r\nadding 'pymatgen-2024.6.10.dist-info/top_level.txt'\r\nadding 'pymatgen-2024.6.10.dist-info/RECORD'\r\nremoving build/bdist.macosx-11.1-arm64/wheel\r\nSuccessfully built pymatgen-2024.6.10-cp312-cp312-macosx_11_0_arm64.whl\r\n```",
"I just confirmed that after pulling Daniel's hotfix to my fork, things are working fine on my end as well! Thanks for addressing this!",
"@jsukpark Thanks for confirming! Happy coding!\r\n\r\nMeanwhile, if you were to \"develop\" the code, you might need `pip install -e .` to install it in [\"editable\" mode](https://setuptools.pypa.io/en/latest/userguide/development_mode.html) instead of `pip install .`",
"@janosh Sorry I forgot to include a \"to fix\" (or similar) keyword in the PR, but we can close this now."
] | 2024-07-17T06:53:33
| 2024-07-23T12:39:27
|
2024-07-23T12:39:27Z
|
CONTRIBUTOR
|
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### Python version
3.11
### Pymatgen version
2024.06.10
### Operating system version
Mac
### Current behavior
I am trying to contribute to pymatgen but as you can see when I install my forked pymatgen by 'pip install .' The packages are not installed
### Expected Behavior
\
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets51m-_g
| 3,929
|
Replace expired BoltzTraP link
|
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[
"@janosh Would appreciate it if you could review this as well, thanks!",
"Thanks for reviewing!"
] | 2024-07-17T08:28:08
| 2024-07-24T11:21:33
|
2024-07-24T11:09:04Z
|
CONTRIBUTOR
|
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### Summary
- Replace expired BoltzTraP link, to close #3921
- Some nitpicking docstring tweaks
- Remove unused `.gitignore` items
|
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I_kwDOACgets6P5Fx1
| 3,930
|
Bugs in `io.pwscf.PWInput.from_str()` method
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[] | 2024-07-17T17:04:15
| 2024-08-06T14:36:37
|
2024-08-06T14:36:37Z
|
CONTRIBUTOR
|
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|
### Python version
3.12.4
### Pymatgen version
2024.6.10
### Operating system version
Ubuntu 22.04.4 LTS
### Current behavior
1. Some namelist options (e.g., `calculation`, `pseudo_dir`, `ecutwfc`) are not parsed in correctly when their values end with a trailing comma. This becomes an issue when we try to read in a file written using `PWInput.write_file()` method, which appends comma after every namelist option pair.
2. The `ATOMIC_SPECIES` and `ATOMIC_POSITIONS` cards of `PWInput` for structures with oxidation states are not parsed in at all.
### Expected Behavior
Given a PWscf input file written using the `PWInput.write_file()` method, I expected an identical output if I try to read in the file using the `PWInput.from_file()` and then write again using the `PWInput.write_file()` method.
### Minimal example
```Python
import numpy as np
from pymatgen.core import Structure
from pymatgen.io.pwscf import PWInput
struct = Structure(
np.array([
[2.917389, 0.097894, 1.520005],
[0.964634, 2.755036, 1.520005],
[0.133206, 0.097894, 3.286918],
]),
['O2-', 'Li+', 'Li+'],
np.array([
[0.000000, 0.000000, 0.000000],
[0.750178, 0.750178, 0.750178],
[0.249822, 0.249822, 0.249822],
]),
)
pw1 = PWInput(
struct,
pseudo={
"Li+": "Li.pbe-n-kjpaw_psl.0.1.UPF",
"O2-": "O.pbe-n-kjpaw_psl.0.1.UPF",
},
control={"calculation": "scf", "pseudo_dir": "./"},
system={"ecutwfc": 50},
)
pw1.write_file("scf-expected.in")
pw2 = PWInput.from_file("scf-expected.in")
pw2.write_file("scf-observed.in")
```
### Relevant files to reproduce this bug
Contents of `scf-expected.in` from above:
```
&CONTROL
calculation = 'scf',
pseudo_dir = './',
/
&SYSTEM
ecutwfc = 50,
ibrav = 0,
nat = 3,
ntyp = 2,
/
&ELECTRONS
/
&IONS
/
&CELL
/
ATOMIC_SPECIES
Li+ 6.9410 Li.pbe-n-kjpaw_psl.0.1.UPF
O2- 15.9994 O.pbe-n-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS crystal
O2- 0.000000 0.000000 0.000000
Li+ 0.750178 0.750178 0.750178
Li+ 0.249822 0.249822 0.249822
K_POINTS automatic
1 1 1 0 0 0
CELL_PARAMETERS angstrom
2.917389 0.097894 1.520005
0.964634 2.755036 1.520005
0.133206 0.097894 3.286918
```
Contents of `scf-observed.in` from above:
```
&CONTROL
calculation = None,
pseudo_dir = None,
/
&SYSTEM
ecutwfc = None,
ibrav = 0,
nat = 3,
ntyp = 2,
/
&ELECTRONS
/
&IONS
/
&CELL
/
ATOMIC_SPECIES
ATOMIC_POSITIONS crystal
K_POINTS automatic
1 1 1 0 0 0
CELL_PARAMETERS angstrom
2.917389 0.097894 1.520005
0.964634 2.755036 1.520005
0.133206 0.097894 3.286918
```
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| 2,414,133,149
|
PR_kwDOACgets51q6T_
| 3,931
|
Bugfix: `io.pwscf.PWInput.from_str()`
|
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[] | 2024-07-17T17:16:31
| 2024-08-06T14:36:36
|
2024-08-06T14:36:36Z
|
CONTRIBUTOR
|
{
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|
## Summary
Fix wrong parsing in `io.pwscf.PWInput.from_str()` of
- Namelist options ending with comma (`,`), and
- `ATOMIC_SPECIES` and `ATOMIC_POSITIONS` cards for structures with oxidation states,
to close https://github.com/materialsproject/pymatgen/issues/3930
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PR_kwDOACgets51rylu
| 3,932
|
Fix d2k function
|
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[] | null |
[
"Any updates on if this can get merged in?",
"Test added via static-no-kgrid-si test. \r\n\r\nUnit test can also be added if you prefer that too"
] | 2024-07-17T19:30:27
| 2024-08-06T15:53:23
|
2024-08-06T15:53:23Z
|
CONTRIBUTOR
|
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Need to use the transpose of the inverse matrix for recipmatrix
## Summary
Major changes:
- fix 1: FHI-aims k-grid sizes from a density
## 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))
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_kwDOACgets51r-qt
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Parallel Joblib Process Entries
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[
"Thanks @CompRhys for the PR. Wondering if we should add `n_workers` to the pymatgen config yaml? If pymatgen is doing processing in parallel in different aspects of the code, might be good to be able to set the correct parallelization centrally",
"Regarding default for n_workers i'm not opposed but I would always want to have it be controllable at the function call and it would be best to make that update in a separate PR imo. \r\n\r\nRe test failures I have been using this method and works very great for me on 3.12. I don't see these pickle errors when running local tests so not sure which object is responsible. I will try take a look at the weekend. ",
"Cannot replicate the error locally even building a py39 venv.\r\n```python\r\nTraceback (most recent call last):\r\n File \"/home/runner/micromamba/envs/pmg/lib/python3.12/site-packages/joblib/externals/loky/process_executor.py\", line 426, in _process_worker\r\n call_item = call_queue.get(block=True, timeout=timeout)\r\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n File \"/home/runner/micromamba/envs/pmg/lib/python3.12/multiprocessing/queues.py\", line 122, in get\r\n return _ForkingPickler.loads(res)\r\n ^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n File \"/home/runner/micromamba/envs/pmg/lib/python3.12/site-packages/monty/design_patterns.py\", line 84, in __new__\r\n inst = klass(*args, **kwargs)\r\n ^^^^^^^^^^^^^^^^^^^^^^\r\nTypeError: GasCorrection.__init__() missing 1 required positional argument: 'config_file'\r\n``` \r\n\r\n"
] | 2024-07-17T20:02:03
| 2024-08-09T00:11:35
|
2024-08-02T22:34:59Z
|
CONTRIBUTOR
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## Summary
Adds the option to use joblib to apply corrections in parallel, this depended on https://github.com/materialsvirtuallab/monty/pull/691 which was linked to https://github.com/materialsproject/pymatgen/issues/3898. Opening this PR incase maintainers think it's a useful addition to the code.
## 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))
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PR_kwDOACgets51uqWl
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[Hot Fix] Fix `setuptools` for pymatgen packaging
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[
"@shyuep @janosh @mkhorton Can you please review this hot fix? Thanks!"
] | 2024-07-18T05:54:47
| 2024-09-10T01:55:05
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2024-07-18T11:41:17Z
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CONTRIBUTOR
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### Summary
- A hot fix for #3928, where the `setuptools` in not configured to include the complete `pymatgen` package (all subpackages are missing) after moving to the src layout.
- (description is incorrect, see #4018) ~~Turn off `include-package-data`, which [is `true` by default](https://setuptools.pypa.io/en/latest/userguide/datafiles.html), meaning `package-data` is not having any effect and all data files would be included into the package.~~
- Remove resolved skip tag: https://github.com/materialsproject/pymatgen/blob/02341828b94a001b4f3cbdae6b24eaeeb0df7d7d/tests/core/test_structure.py#L1771
#### Site note
To reliably recreate this issue, one might need to [completely clear build cache](https://setuptools.pypa.io/en/latest/userguide/miscellaneous.html#caching-and-troubleshooting) (removing `build/`, `dist/` and `*.egg-info`), otherwise you might find yourself (~me for example~) modifying the `pyproject.toml` file but find the wheel remains unchanged.
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PR_kwDOACgets51vyFA
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Raise `DeprecationWarning` as errors
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[] | 2024-07-18T08:43:41
| 2024-08-06T15:28:14
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2024-07-24T11:27:56Z
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CONTRIBUTOR
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### Summary
- Raise `DeprecationWarning` as errors, which might help us [adapt earlier for deprecation](https://numpy.org/devdocs/dev/depending_on_numpy.html#runtime-dependency-version-ranges)
> Furthermore, we recommend to raise errors on warnings in CI for this job, either all warnings or otherwise at least DeprecationWarning and FutureWarning. This gives you an early warning about changes in NumPy to adapt your code.
- [ ] `Pybtex` would need a new release to fully fix this https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
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Adding Abinit magmoms from netCDF files to Structure.site_properties
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[
"This is ready to be reviewed. I don't know why ruff is failing, I did not make changes in io.vasp, io.aims and analysis. ",
"Hi @janosh, @shyuep, @mkhorton, whenever you have some time, this is ready to be reviewed. It would be great for us if these changes could be included in the next release, to facilitate developments in abipy (since this PR is fixing breaking changes). Thanks!"
] | 2024-07-18T09:19:24
| 2024-07-26T15:10:26
|
2024-07-26T15:07:21Z
|
CONTRIBUTOR
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## Summary
In recent developments in Abinit, the variables `intgden` and `ratsph` have been added in the netCDF output files. These correspond to the computed integrated density around atoms and the integration radii. The former can be interpreted as the local magnetic moment on each atom. Since this is a useful quantity for, e.g., CHGNet model training, I have added them as `site_properties` of the `Structure` that is extracted from the netCDF file. If `intgden` is not found in the .nc file, nothing is added.
While testing with abipy, I also found that recent commits in io.abinit.pseudos were backward incompatible for PAW pseudopotentials. I reverted the changes and added a test.
Tagging @gmatteo to check this.
|
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I_kwDOACgets6QCsBC
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Group-subgroup relationship bugs in `SpaceGroup` and `PointGroup` class
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[] | 2024-07-18T14:43:29
| 2024-11-13T17:53:20
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2024-11-13T17:53:20Z
|
CONTRIBUTOR
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### Python version
3.10
### Pymatgen version
master
### Operating system version
_No response_
### Current behavior
Hey, two remarks regarding the `is_subgroup` method of `SpaceGroup`:
First, the current implementation does not allow isomorphic group-subgroup relationships (same space group type) because of
https://github.com/materialsproject/pymatgen/blob/02341828b94a001b4f3cbdae6b24eaeeb0df7d7d/src/pymatgen/symmetry/groups.py#L537
For example, I would expect the following code to not raise an error:
`assert SpaceGroup("P3").is_subgroup(SpaceGroup("P3"))`
The `if j not in all_groups` needs to be removed in the first iteration.
Second, the current implementation disregards klassengleiche group-supergroup relationships where the overall translational symmetry is increased, but not through centering. For example, I would expect this to not raise an error:
`assert SpaceGroup("Fm-3m").is_subgroup(SpaceGroup("Pm-3m"))`
However, because of https://github.com/materialsproject/pymatgen/blob/02341828b94a001b4f3cbdae6b24eaeeb0df7d7d/src/pymatgen/symmetry/groups.py#L528 this returns False. I assume it is to save resources? I would either remove it completely (safest) or restrict it to certain cases, if possible(?).
-------------------
Also, I had a look at the uncommented `PointGroup` subgroup test:
https://github.com/materialsproject/pymatgen/blob/02341828b94a001b4f3cbdae6b24eaeeb0df7d7d/tests/symmetry/test_groups.py#L59
This test is failing because the -3 is defined along (111) in m-3m, but along (001) in -3m (therefore, the matrices are different). Generally, this affects all group-subgroup relationships if the groups are in crystal systems with different crystallographic directions / blickrichtungen. For example, this is also failing,
`assert PointGroup("2").is_subgroup(PointGroup("4"))`
because the rotation axis is along *c* in the tetragonal, but is notated along *b* in the monoclinic system (in this database).
I would specify this in the warning https://github.com/materialsproject/pymatgen/blob/02341828b94a001b4f3cbdae6b24eaeeb0df7d7d/src/pymatgen/symmetry/groups.py#L79
In the future, it would probably be best to have a database similar to the maximal subgroup database of space group types.
---------------------
If you agree, I can implement and test the SpaceGroup changes.
### Expected Behavior
I would expect my code snippets from above to not raise an error.
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets514vYp
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Extend `CubicSupercell` transformation to also be able to look for orthorhombic cells
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[
"The failing linting does not stem from our changes.\r\n",
"Once the other tests pass, this is ready for review ",
"@shyuep @mkhorton @janosh this pull request is ready for review. The linting issues show up in different parts of the code.",
"There are many mysteries in the world of linters, including why they jump up on untouched parts of the code out of the blue 🤣 .\r\n\r\nI tried to push a PR to your branch but for some reason your branch wouldn't show up?\r\n\r\n**src/pymatgen/analysis/local_env.py:3051:32:**\r\n```diff\r\n- if (m != j) and (m != k) and (not flag_xaxis):\r\n+ if m not in {j, k} and (not flag_xaxis):\r\n```\r\n\r\n**src/pymatgen/io/aims/parsers.py:333:12:**\r\n```diff\r\n- if (line_start == LINE_NOT_FOUND) or (line_end == LINE_NOT_FOUND) or (line_end - line_start != n_kpts):\r\n+ if LINE_NOT_FOUND in {line_start, line_end} or (line_end - line_start != n_kpts):\r\n```\r\n\r\n**src/pymatgen/io/vasp/outputs.py:1707:25:**\r\n```diff\r\n- if (\r\n- tag == \"eigenvalues_kpoints_opt\"\r\n- or tag == \"projected_kpoints_opt\"\r\n- or (tag == \"dos\" and elem.attrib.get(\"comment\") == \"kpoints_opt\")\r\n- ):\r\n+ if tag in {\"eigenvalues_kpoints_opt\", \"projected_kpoints_opt\"} or (\r\n+ tag == \"dos\" and elem.attrib.get(\"comment\") == \"kpoints_opt\"\r\n+ ):\r\n```",
"@DanielYang59 can you try again? You should now be allowed to do this",
"Beautiful! Thanks for granting the access. Actually I was not looking for writing access to your fork, but to open a PR where your fork is the base repo, but I cannot find yours as the target repo for some reason.\r\n",
"@DanielYang59 i am very confused. You mean this branch https://github.com/JaGeo/pymatgen/tree/orthorhombic_supercell ?",
"Sorry for the confusion. For some reason I can see your fork now (wasn't showing up before):\r\n<img width=\"1369\" alt=\"image\" src=\"https://github.com/user-attachments/assets/936a7ff5-44ca-4c63-a065-3ab2821ea0d1\">\r\n\r\nEverything is working fine now! Thanks!",
"@DanielYang59 thank you 😀.\r\n\r\nI hope someone will then merge our backward compatible code soon!",
"No problem!",
"> Beautiful! Thanks for granting the access. Actually I was not looking for writing access to your fork, but to open a PR where your fork is the base repo, but I cannot find yours as the target repo for some reason.\r\n\r\nI had the same problem yesterday btw. I worked around it by starting the PR in the JaGeo repo. But good everything worked in the end.",
"Merged. Sometimes lint errors come up on other parts due to update of the linting software versions. ",
"Thank you @shyuep "
] | 2024-07-19T11:30:05
| 2024-08-09T00:06:25
|
2024-07-23T21:25:07Z
|
MEMBER
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## Summary
Added code to also allow to search for orthorhombic supercells. Here, I also introduce the option to check for a `maximum_length` of the cells
@QuantumChemist will now take over and write the tests for this class and fix the linting etc. :)
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I_kwDOACgets6QLb8K
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Calling PhaseDiagram.as_dict() breaks the link between different Entries
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[] | 2024-07-19T13:24:40
| 2024-07-19T13:30:31
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CONTRIBUTOR
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### Feature Requested
When saving the `PhaseDiagram` it could reduce the memory footprint if to keep track of the ids of entries rather than just save multiple copies of entries in the separate lists.
### Proposed Solution
Refactor the PhaseDiagram class to use `@property` to return the different lists of entries that are kept track of based on lists of ids as opposed to making references that result in duplication when serializing.
### Relevant Information
This isn't a priority and would only be worth merging if the differences in speed are negligible. Posting this issue because it may be a good first issue for someone to tackle if I can't get round to it in the near term.
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PR_kwDOACgets516MVu
| 3,941
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`is_subgroup()` modifications in `SpaceGroup` and `PointGroup`
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[
"Hey @shyuep @mkhorton @janosh this is ready to be reviewed."
] | 2024-07-19T14:44:27
| 2024-11-13T17:53:19
|
2024-11-13T17:53:19Z
|
CONTRIBUTOR
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## Summary
Resolves #3937 .
### SpaceGroup
- enabled isomorphic group subgroup relationships, added test
- Constrained https://github.com/materialsproject/pymatgen/blob/02341828b94a001b4f3cbdae6b24eaeeb0df7d7d/src/pymatgen/symmetry/groups.py#L528 to non-klassengleiche group subgroup relationships so cases like `assert SpaceGroup("Fm-3m").is_subgroup(SpaceGroup("Pm-3m"))` pass, added test
- fixed bug introduced by me in #3859 (Apologies!) of wrong short Hermann Mauguin symbol computation for multiple trigonal groups
- modified `point_group` entries of `symm_data.json` to be possible `symbol` attributes of `PointGroup` (also see comment below)
### PointGroup
- added `crystal_system` attribute to `PointGroup`
- enabled `init` from other settings than in database and from full symbol, added test
- added notes in docs that axes of `PointGroup` object may differ from given `int_symbol` in `init` / given space group symbol in `from_space_group` as currently only one setting per point group is available
- added crystallographic direction issue check for `is_subgroup` of `PointGroup` -> a `NotImplementedError` is now raised if the blickrichtungen / crystallographic directions of the crystal systems of the two groups differ
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PR_kwDOACgets51_Ph8
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Fix Ion formula parsing bug; add more special formulas
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[
"I don't understand why the `lint` action is looking at files that didn't change in this PR. Please advise if I need to take action somehow to fix.\r\n\r\n```\r\n src/pymatgen/analysis/local_env.py:3051:32: PLR1714 Consider merging multiple comparisons: `m not in (j, k)`. Use a `set` if the elements are hashable.\r\n |\r\n3050 | for m in range(n_neighbors):\r\n3051 | if (m != j) and (m != k) and (not flag_xaxis):\r\n | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ PLR1714\r\n3052 | tmp = max(-1.0, min(np.inner(zaxis, rij_norm[m]), 1.0))\r\n3053 | thetam = math.acos(tmp)\r\n |\r\n = help: Merge multiple comparisons\r\n\r\nsrc/pymatgen/io/aims/parsers.py:333:12: PLR1714 Consider merging multiple comparisons: `LINE_NOT_FOUND in (line_start, line_end)`. Use a `set` if the elements are hashable.\r\n |\r\n331 | line_start = self.reverse_search_for([\"| K-points in task\"])\r\n332 | line_end = self.reverse_search_for([\"| k-point:\"])\r\n333 | if (line_start == LINE_NOT_FOUND) or (line_end == LINE_NOT_FOUND) or (line_end - line_start != n_kpts):\r\n | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ PLR1714\r\n334 | self._cache.update(\r\n335 | {\r\n |\r\n = help: Merge multiple comparisons\r\n\r\nsrc/pymatgen/io/vasp/outputs.py:1707:25: PLR1714 Consider merging multiple comparisons. Use a `set` if the elements are hashable.\r\n |\r\n1705 | # The start event tells us when we have entered blocks\r\n1706 | if (\r\n1707 | tag == \"eigenvalues_kpoints_opt\"\r\n | _________________________^\r\n1708 | | or tag == \"projected_kpoints_opt\"\r\n1709 | | or (tag == \"dos\" and elem.attrib.get(\"comment\") == \"kpoints_opt\")\r\n | |_________________________________________________________________________________________^ PLR1714\r\n1710 | ):\r\n1711 | in_kpoints_opt = True\r\n |\r\n = help: Merge multiple comparisons\r\n\r\nFound 3 errors.\r\nNo fixes available (3 hidden fixes can be enabled with the `--unsafe-fixes` option).\r\nError: Process completed with exit code 1.\r\n```\r\n",
"@DanielYang59 already fixed this for our PR #3938 . If this PR gets merged, this should vanish",
"Will close this since #3938 was merged, but thank you for reporting and suggesting fix @rkingsbury, greatly appreciated!",
"Apologies, re-opening because I don't see how this was fixed in #3938. Is this the correct PR @JaGeo ?",
"Sorry for the confusion. I believe @JaGeo was referring to the linter issue alone :)",
"@mkhorton no, the issue is not fixed. Just the linting issue was similar in both pull requests",
"> @mkhorton no, the issue is not fixed. Just the linting issue was similar in both pull requests\r\n\r\n@shyuep @mkhorton @janosh , sending a friendly ping to request a review of these changes. Just to clarify and reiterate Janine's comment - she was referring to a linting issue that is not related to the substance of this PR, so until this is merged, the ion formula parsing bug will persist."
] | 2024-07-20T13:37:55
| 2024-07-31T15:56:22
|
2024-07-31T15:56:21Z
|
CONTRIBUTOR
|
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## Summary
Major changes:
1. Fixes a serious bug in `Ion.get_reduced_formula_and_factor` introduced by [this commit](https://github.com/materialsproject/pymatgen/commit/b4a70eef7666743459a6e242a0efc18762ff3b49). The bug could cause certain formulas to be parsed incorrectly, resulting in a different stoichiometry of `O` and `H` than what was input. For example:
```
>>> from pymatgen.core.ion import Ion
>>> Ion.from_formula('H2PO4-').get_reduced_formula_and_factor()
('P(OH2)2', 1)
```
Notice how the parsed formula has 4 H and 2 O, whereas he input formula has 2 H and 4 O
2. Adds recognition for a number of additional special formulas to ensure that they are represented in the way that is most common in aqueous solution literature. These inclue:
- Ammonia (previously `H4N[+1]`, now `NH4[+1]`)
- Ammonium
- Methane
- formate ion
- oxalate ion
- phosphoric acid system
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I_kwDOACgets6QUIUX
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|
Mix GGA/GGAU/RSCAN not available as compatibility?
|
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[
"Hi @Jeff-oakley, this is implemented in `pymatgen.entries.mixing_scheme` as `MaterialsProjectDFTMixingScheme`"
] | 2024-07-21T03:42:18
| 2024-07-23T17:20:07
|
NONE
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### Feature Requested
It seems that mix GGA/GGAU/R2SCAN is not available as a compatibility option? I did not see that class in pymatgen.entries.compatibility. However in the paper below, it has been indicated that this workflow is already implemented.
https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.6.013801
Maybe I missunderstand something here? Any instructions will be greatly appreciated.
This is also important as now the phase diagram from mprester are different from the one in materials project website.
### Proposed Solution
Implement it. I suppose it should already be existing somewhere given that paper is already published.
### Relevant Information
_No response_
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PR_kwDOACgets52BbMk
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`Element`/`Species`: order `full_electron_structure` by energy
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[] | 2024-07-21T19:43:51
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2024-07-23T21:22:54Z
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CONTRIBUTOR
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## Summary
This is a follow up to #3902 to address an inconsistent behavior I encountered. The major change in this PR is that `full_electronic_structure` is now always returned as a sorted list according to the Madelung rule, so that the final element is always the valence shell. Prior to this PR, this was sometimes but not always the case, as I elaborate below.
Major changes:
- `Element` and `Species.full_electronic_structure` are now sorted by increasing energy level according to the Madelung rule
- Updated and expanded unit tests to ensure `valence` and `full_electronic_structure` both work as expected
- Minor changes to crystal field methods and associated unit tests to accommodate the sorting.
- (indirectly related): added a `n_electrons` property to `Species` and `Element`
## Background
As we discussed in #3902, `electronic_structure` should not be sorted by energy level, because this is how NIST and many other sources report it (e.g., for `Ce(0)` we have `'[Xe].4f1.5d1.6s2'`).
`full_electronic_structure` parses `electronic_structure` into a list but did not make any attempt to sort it. In theory, given the above convention, one might expect this to mean that `full_electronic_structure` always gives orbitals in order of increasing quantum numbers (e.g. 1s, 2s ... 3d, 4s, 4p, 4d, 4f, 5s...), but that was not always the case. For example, it worked for `Fe(0)` which gave
```
[(1, 's', 2),
(2, 's', 2),
(2, 'p', 6),
(3, 's', 2),
(3, 'p', 6),
(3, 'd', 6),
(4, 's', 2)]
```
but for `Ce(0)` we get
```
[(1, 's', 2),
(2, 's', 2),
(2, 'p', 6),
(3, 's', 2),
(3, 'p', 6),
(3, 'd', 10),
(4, 's', 2),
(4, 'p', 6),
(4, 'd', 10),
(5, 's', 2),
(5, 'p', 6),
(4, 'f', 1),
(5, 'd', 1),
(6, 's', 2)]
```
Ultimately, this is caused by the fact that when `electronic_structure` is written in shorthand (for example, Ce is `[Xe].4f1.5d1.6s2`), `full_electronic_structure` just takes that structure of the atom (`[Xe]`) and appends the new orbitals to it. This can result in unpredictable ordering of the orbitals as shown above.
`valence` DOES make an attempt to sort the orbitals, but because of the issues raised above, it will fail to find the correct valence for some `Species`.
The changes in this PR remedy all of the above problems and ensure that `full_electronic_structure` has a consistent meaning for all `Element` and `Species`.
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PR_kwDOACgets52DQ81
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Correct method `get_projection_on_elements` docstring under `Procar` class
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[
"@janosh Please review this at your convenience, thanks!",
"Thanks for reviewing!"
] | 2024-07-22T07:11:58
| 2024-07-24T11:23:11
|
2024-07-24T11:16:29Z
|
CONTRIBUTOR
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### Summary
- Correct method `get_projection_on_elements` docstring of `Procar` class, where the band index and kpoint index is reversed.
https://github.com/materialsproject/pymatgen/blob/27d90b777cedc80593d93b6e8b66dee04c167460/src/pymatgen/io/vasp/outputs.py#L3915-L3916
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PR_kwDOACgets52GtvS
| 3,946
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DOS Fingerprints enhancements
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[] | null |
[
"Hi @shyuep , @janosh , @mkhorton and @JaGeo , this PR is ready for review.",
"Thanks @janosh for the feedback. I will try to address the comments next week :smile: ",
"Hi @JaGeo and @janosh , I have now addressed review comments now and could be merged if there are no further comments.\r\n\r\nPS: Regarding creating a separate module for fingerprints, I had another detailed look at the code and concluded it would overcomplicate the code logic with minimal advantage of reducing few lines of code. So better to keep it in current place I feel as of now.",
"thanks @naik-aakash! 👍 "
] | 2024-07-22T15:10:11
| 2024-08-16T09:20:24
|
2024-08-16T09:20:01Z
|
CONTRIBUTOR
|
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# Summary
1. Add possibility to compare phonon dos , implementation is similar to electronic dos as implemented in https://github.com/materialsproject/pymatgen/pull/2772
2. Add `Wasserstein `distance as metric besides existing Tanimoto index
# Todo's
- [x] Add methods to compute fingerprints and compare phonon dos
- [x] Move methods to compute fingerprints and compare phonon dos to `PhononDos ` class from `CompletePhononDos` class (Phonon workflow returns `PhononDos` objects in the taskdoc)
- [x] Update doc-strings where needed
- [x] Add tests for phonon dos comparisons
- [x] Adapt electronic dos fingerprint comparison to include Wasserstein metric
- [x] Add tests for updated electronic dos comparisons
- [x] Address review comments
|
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Add atomic concentrations to hovertext on ternary graphs
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[] | 2024-07-22T18:02:27
| 2024-08-05T23:53:51
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2024-07-22T21:16:25Z
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CONTRIBUTOR
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## Summary
- The atomic concentrations of each material in the ternary graph are added to the 2D and 3D ternary graphs for readability.
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Updating Ternary and Quaternary Plots
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[
"Thanks for this PR @JoshuaNgXY! Since it deals with plotting can you add some screenshots?",
"Sure, here are the before and after for the ternary and quaternary plots.\r\n\r\n## Ternary Plot Update:\r\n### Old\r\n\r\n\r\n### New\r\n\r\n\r\n## Quaternary Plot Update:\r\n### Old\r\n\r\n\r\n### New\r\n\r\n",
"@JoshuaNgXY is working with MP to update the PD plotting functionality. If you think it's good to go then we can then update the dependencies. Thank you @mkhorton @janosh ! ",
"Battery Voltage Graph has added labels to the hovertext to display the x location and the corresponding x-axis title. \r\nBefore:\r\n\r\n\r\nAfter:\r\n\r\n"
] | 2024-07-22T21:19:51
| 2024-08-09T13:22:17
|
2024-08-09T13:22:17Z
|
CONTRIBUTOR
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## Summary
The atomic concentrations of each material in the ternary graph are added to the 2D and 3D ternary graphs for readability. A toggle is added to the quaternary graph hull surfaces.
Extra labels added to hovertext of the Voltage graph for readability.
## Adding atomic concentrations:
- Atomic concentrations are added to the hovertext of the stable and unstable markers within the `get_marker_props()` for both the ternary and quaternary graphs.
## Adding Toggle to Quaternary Graph Hull Surfaces:
- 3D Mesh objects for the hull surfaces are added to a legend group named `facets`. The first 3D Mesh object is used to display the whole group in the legend, and is renamed to `Hull Surfaces (toggle to access points easier)`.
- This fixes a bug where datapoints encased within the hull surface could not be accessed by toggling the surfaces.
- Added text before the formation energy and energy above hull values to make it more clear what was being shown.
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PR_kwDOACgets52X6Sr
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Allow custom `.pmgrc.yaml` location via new `PMG_CONFIG_FILE` env var
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[] | 2024-07-24T18:06:07
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2024-07-24T21:17:22Z
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MEMBER
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the hard-coded settings path in the user's home directory poses a problem when running on compute nodes that only have access to the scratch file system, not the `/home` fs. this PR provides an escape hatch for such cases
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PR_kwDOACgets52i_0D
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Fix MPRester tests and access phonon properties from the new API without having `mp-api` installed.
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[
"Many thanks for this contribution. "
] | 2024-07-26T07:23:19
| 2024-08-09T00:07:02
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2024-07-26T09:05:21Z
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CONTRIBUTOR
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## Summary
Major changes:
* Add functions to get phonon properties (phonon band structures and phonon DOS) to `_MPResterBasic`, so that a non-power user can retrieve this properties without using `mp-api` making `_MPResterBasic` closer in line with `_MPResterLegacy` in terms of the properties that can be retrieved.
* Fix `get_summary_by_material_id`
* Fixes issue in `test_matproj.py` where tests are always skipped because `requests.get("https://materialsproject.org", timeout=600).status_code` always returns 403 and instead either checks the status the relevant Materials Project site depending on whether a legacy or next-gen API KEY is supplied
* Fix issue in `test_matproj.py` where `TestMPResterNewBasic` was failing because it didn't inherit from the `PymatgenTest` class and the `setUp` method was in the incorrect case.
* Uncomment phonon tests for for `TestMPResterNewBasic`
* Import the `MPRestError` from `pymatgen.ext.matproj_legacy` instead of `pymatgen.ext.matproj`
## Todos
* A future PR will incorporate accessing electronic structure data, but this will require more time due to issues I've found in the new API. Not needed to be done for this particular PR.
## 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_kwDOACgets6Q_DLT
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When reading in a POTCAR file with pymatgen.io.vasp.inputs.Potcar, the object can't distinguish between PBE_54 and PBE.
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[
"I think this is intended: https://github.com/materialsproject/pymatgen/blob/5256fce19f7366d33fd5b062bd41cc5cb713505f/src/pymatgen/io/vasp/inputs.py#L1776-L1788\r\n\r\n**Probably** because POTCAR itself doesn't carry a one-to-one mapping to VASP version (but compatible functionals) itself with its `LEXCH` tag. I could be wrong here, so let's see if @esoteric-ephemera has any corrections.\r\n\r\nI think the reason versioned functional tags exist in `pymatgen` is to help locate the corresponding POTCAR directories from local file system: https://github.com/materialsproject/pymatgen/blob/5256fce19f7366d33fd5b062bd41cc5cb713505f/src/pymatgen/io/vasp/inputs.py#L1757-L1763\r\n",
"Hi @DanielYang59. Thank you for the reply. \r\n\r\nAt the moment, I am storing my results on my personal MongoDB database. When I read in a POTCAR file that I used with PBE_54, I would just like it to say PBE_54 to reflect the actual 54 version that I use instead of the old PBE. \r\n\r\nI am wondering if there is any way around this. If not, that is ok. ",
"No problem at all. \r\n\r\nI wish I could be more helpful on this, but I don't have much experience with the functionality you were looking for. **Hopefully others would have smarter solutions.**\r\n\r\nThe `functional` property of `PotcarSingle` is not writable, however that of `Potcar` (a collection of `PotcarSingle`) is writable, therefore you could overwrite it directly:\r\n```python\r\nfrom pymatgen.io.vasp.inputs import Potcar\r\n\r\n\r\npotcar = Potcar.from_file(\"POTCAR\")\r\npotcar.functional = \"PBE_54\"\r\n\r\nprint(potcar.functional) # >>> \"PBE_54\"\r\n```\r\n\r\nBut you have to double check if such modification breaks any downstream operations (i.e. OPs that require `functional` to be exactly `PBE`).\r\n\r\nIf you just want to \"tag\" the `Potcar`, perhaps you could add a separate attribute:\r\n```\r\npotcar = Potcar.from_file(\"POTCAR\")\r\npotcar.functional_versioned = \"PBE_54\"\r\n\r\nprint(potcar.functional_versioned) # >>> \"PBE_54\"\r\n```\r\n\r\nHope this helps.\r\n",
"@DanielYang59 Thanks again for your help. I've opted for the first option (overwrite directly) for now. \r\n\r\nCheers.",
"All good, and do let me know if you (or any other) come up with smarter options :)",
"This has also confused me in the past but I don't know that it's a bug. The `PotcarSingle` class assumes instantiation from a string (or file), but has an optional `from_symbol_and_functional` instantiation method\r\n\r\nConversely, the `Potcar` class (a list of `PotcarSingle`'s) assumes instantiation from symbols and a functional, with an optional `from_file` instantiation\r\n\r\nIt would probably make sense to have these be consistent in terms of what the `default` construction method is, but there's not enough reason to change this now and incur obvious breaking changes\r\n\r\nSo as @DanielYang59 said, the `functional` attr of any `PotcarSingle` reflects the DFT functional used to generate it (PBE or LDA)"
] | 2024-07-26T15:12:07
| 2024-07-31T02:48:43
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### Python version
3.12.4
### Pymatgen version
2024.6.10
### Operating system version
Ubuntu-22.04
### Current behavior
I have a POTCAR file written with PBE_54. When I read it into a Potcar object, potcar.functional will equal PBE instead of PBE_54.
### Expected Behavior
I would expect it to be PBE_54 to reflect the actual POTCAR file being read.
### Minimal example
```Python
from pymatgen.io.vasp.inputs import Potcar
path = "path_to_POTCAR_file"
potcar = Potcar.from_file(path)
print(potcar.functional)
```
### Relevant files to reproduce this bug
Try any PBE_54 POTCAR file.
|
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`pre-commit run --files` will trigger errors.
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[
"This doesn't look like an issue related to `pymatgen`:\r\n> ERROR: Could not install packages due to an OSError: Missing dependencies for SOCKS support.\r\n\r\nLooks like your SOCKS support is missing, maybe try `pip install pysocks` before `pre-commit`?",
"I've installed `pysocks` before creating this issue, but it doesn't fix the problem:\r\n\r\n```\r\n(datasci) werner@x13dai-t:~/Desktop/add-hse-vdw-parameters$ uv pip list|grep -i pysocks\r\npysocks 1.7.1\r\n```\r\n\r\n",
"I think `pre-commit` was using a different and temporary venv other than your currently activated one for hook installation process.\r\n\r\nCan you perhaps run the following to install `pysocks` for that particular venv?\r\n`/home/werner/.cache/pre-commit/repod_9xb5e9/py_env-python3.11/bin/python -m pip install pysocks`\r\n\r\nA less hacky way might be to modify the `.pre-commit-config.yaml` file as such:\r\n```diff\r\n - repo: https://github.com/astral-sh/ruff-pre-commit\r\n rev: v0.5.4\r\n hooks:\r\n - id: ruff\r\n args: [ --fix, --unsafe-fixes ]\r\n+ additional_dependencies: [pysocks]\r\n - id: ruff-format\r\n+ additional_dependencies: [pysocks]\r\n```\r\n",
"> Can you perhaps run the following to install `pysocks` for that particular venv?\r\n> `/home/werner/.cache/pre-commit/repod_9xb5e9/py_env-python3.11/bin/python -m pip install pysocks`\r\n\r\n\r\n```shell\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ pre-commit run --files src/pymatgen/io/vasp/sets.py tests/io/vasp/test_sets.py\r\n[INFO] Installing environment for https://github.com/astral-sh/ruff-pre-commit.\r\n[INFO] Once installed this environment will be reused.\r\n[INFO] This may take a few minutes...\r\nAn unexpected error has occurred: CalledProcessError: command: ('/home/werner/.cache/pre-commit/repo54jli8fc/py_env-python3.11/bin/python', '-mpip', 'install', '.')\r\nreturn code: 1\r\nstdout:\r\n Processing /home/werner/.cache/pre-commit/repo54jli8fc\r\n Installing build dependencies: started\r\n Installing build dependencies: finished with status 'error'\r\nstderr:\r\n error: subprocess-exited-with-error\r\n \r\n × pip subprocess to install build dependencies did not run successfully.\r\n │ exit code: 1\r\n ╰─> [2 lines of output]\r\n ERROR: Could not install packages due to an OSError: Missing dependencies for SOCKS support.\r\n \r\n [end of output]\r\n \r\n note: This error originates from a subprocess, and is likely not a problem with pip.\r\n error: subprocess-exited-with-error\r\n \r\n × pip subprocess to install build dependencies did not run successfully.\r\n │ exit code: 1\r\n ╰─> See above for output.\r\n \r\n note: This error originates from a subprocess, and is likely not a problem with pip.\r\nCheck the log at /home/werner/.cache/pre-commit/pre-commit.log\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ /home/werner/.cache/pre-commit/repo54jli8fc/py_env-python3.11/bin/python -mpip install pysocks\r\nbash: /home/werner/.cache/pre-commit/repo54jli8fc/py_env-python3.11/bin/python: No such file or directory\r\n```\r\n\r\n> A less hacky way might be to modify the `.pre-commit-config.yaml` file as such:\r\n\r\nStill failed:\r\n\r\n```\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ git diff .pre-commit-config.yaml\r\ndiff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml\r\nindex 23276773f..358150d10 100644\r\n--- a/.pre-commit-config.yaml\r\n+++ b/.pre-commit-config.yaml\r\n@@ -12,7 +12,9 @@ repos:\r\n hooks:\r\n - id: ruff\r\n args: [ --fix, --unsafe-fixes ]\r\n+ additional_dependencies: [pysocks]\r\n - id: ruff-format\r\n+ additional_dependencies: [pysocks]\r\n \r\n - repo: https://github.com/pre-commit/pre-commit-hooks\r\n rev: v4.6.0\r\n\r\n\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ pre-commit run --files src/pymatgen/io/vasp/sets.py tests/io/vasp/test_sets.py\r\n[INFO] Installing environment for https://github.com/astral-sh/ruff-pre-commit.\r\n[INFO] Once installed this environment will be reused.\r\n[INFO] This may take a few minutes...\r\nAn unexpected error has occurred: CalledProcessError: command: ('/home/werner/.cache/pre-commit/repo5dklgkp0/py_env-python3.11/bin/python', '-mpip', 'install', '.', 'pysocks')\r\nreturn code: 1\r\nstdout:\r\n Processing /home/werner/.cache/pre-commit/repo5dklgkp0\r\n Installing build dependencies: started\r\n Installing build dependencies: finished with status 'error'\r\nstderr:\r\n error: subprocess-exited-with-error\r\n \r\n × pip subprocess to install build dependencies did not run successfully.\r\n │ exit code: 1\r\n ╰─> [2 lines of output]\r\n ERROR: Could not install packages due to an OSError: Missing dependencies for SOCKS support.\r\n \r\n [end of output]\r\n \r\n note: This error originates from a subprocess, and is likely not a problem with pip.\r\n error: subprocess-exited-with-error\r\n \r\n × pip subprocess to install build dependencies did not run successfully.\r\n │ exit code: 1\r\n ╰─> See above for output.\r\n \r\n note: This error originates from a subprocess, and is likely not a problem with pip.\r\nCheck the log at /home/werner/.cache/pre-commit/pre-commit.log\r\n```",
"Anyway, I have done the checks manually as follows:\r\n\r\n```python\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ pytest -v tests/io/vasp/test_sets.py::TestMPHSERelaxSet\r\n======================================================================== test session starts =========================================================================\r\nplatform linux -- Python 3.11.1, pytest-8.2.2, pluggy-1.5.0\r\nrootdir: /home/werner/Public/repo/github.com/materialsproject/pymatgen.git\r\nconfigfile: pyproject.toml\r\nplugins: split-0.9.0, cov-5.0.0, dash-2.16.1, anyio-4.4.0\r\ncollected 6 items \r\n\r\ntests/io/vasp/test_sets.py ...... [100%]\r\n\r\n======================================================================== slowest 30 durations ========================================================================\r\n0.11s call tests/io/vasp/test_sets.py::TestMPHSERelaxSet::test_from_prev_calc\r\n0.09s call tests/io/vasp/test_sets.py::TestMPHSERelaxSet::test_override_from_prev_calc\r\n0.01s call tests/io/vasp/test_sets.py::TestMPHSERelaxSet::test_user_incar_settings\r\n0.01s call tests/io/vasp/test_sets.py::TestMPHSERelaxSet::test_vdw_and_lasph_dftd3\r\n0.01s call tests/io/vasp/test_sets.py::TestMPHSERelaxSet::test_vdw_and_lasph_dftd3_bj\r\n\r\n(13 durations < 0.005s hidden. Use -vv to show these durations.)\r\n========================================================================= 6 passed in 3.82s ==========================================================================\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ ruff check src/pymatgen/io/vasp/sets.py tests/io/vasp/test_sets.py\r\nAll checks passed!\r\n```\r\n\r\nThe new PR is located here: https://github.com/materialsproject/pymatgen/pull/3955.",
"That beats me, looks like the first method failed because the `python` is not in your nominated path:\r\n> (datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ /home/werner/.cache/pre-commit/repo54jli8fc/py_env-python3.11/bin/python -mpip install pysocks\r\nbash: /home/werner/.cache/pre-commit/repo54jli8fc/py_env-python3.11/bin/python: No such file or directory\r\n\r\nCan you double check if `python` really is there?\r\n\r\nIn any case, this issue has nothing to be with `pymatgen`, but all to do with `pre-commit` and your local proxy settings (did you try to [unset proxy](https://superuser.com/a/196180) if possible, at least for your current SSH session). \r\n\r\nIf everything failed, perhaps you should [open an issue there](https://github.com/pre-commit/pre-commit)?\r\n",
"> Can you double check if `python` really is there?\r\n\r\n```shell\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ ls /home/werner/.cache/pre-commit/repo54jli8fc/py_env-python3.11/bin/python\r\nls: cannot access '/home/werner/.cache/pre-commit/repo54jli8fc/py_env-python3.11/bin/python': No such file or directory\r\n``` \r\n\r\n> In any case, this issue has nothing to be with `pymatgen`, but all to do with `pre-commit` and your local proxy settings (did you try to [unset proxy](https://superuser.com/a/196180) if possible, at least for your current SSH session).\r\n\r\n```python\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ pre-commit install\r\npre-commit installed at .git/hooks/pre-commit\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ unset HTTP_PROXY\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ pre-commit run --files src/pymatgen/io/vasp/sets.py tests/io/vasp/test_sets.py\r\n[INFO] Installing environment for https://github.com/astral-sh/ruff-pre-commit.\r\n[INFO] Once installed this environment will be reused.\r\n[INFO] This may take a few minutes...\r\nAn unexpected error has occurred: CalledProcessError: command: ('/home/werner/.cache/pre-commit/repo54jli8fc/py_env-python3.11/bin/python', '-mpip', 'install', '.')\r\nreturn code: 1\r\nstdout:\r\n Processing /home/werner/.cache/pre-commit/repo54jli8fc\r\n Installing build dependencies: started\r\n Installing build dependencies: finished with status 'error'\r\nstderr:\r\n error: subprocess-exited-with-error\r\n \r\n × pip subprocess to install build dependencies did not run successfully.\r\n │ exit code: 1\r\n ╰─> [2 lines of output]\r\n ERROR: Could not install packages due to an OSError: Missing dependencies for SOCKS support.\r\n \r\n [end of output]\r\n \r\n note: This error originates from a subprocess, and is likely not a problem with pip.\r\n error: subprocess-exited-with-error\r\n \r\n × pip subprocess to install build dependencies did not run successfully.\r\n │ exit code: 1\r\n ╰─> See above for output.\r\n \r\n note: This error originates from a subprocess, and is likely not a problem with pip.\r\nCheck the log at /home/werner/.cache/pre-commit/pre-commit.log\r\n```\r\n\r\n[pre-commit.log.zip](https://github.com/user-attachments/files/16398318/pre-commit.log.zip)\r\n\r\n \r\n> If everything failed, perhaps you should [open an issue there](https://github.com/pre-commit/pre-commit)?\r\n\r\nThank you for your advice.",
"Looks like python is indeed not in the path nominated, and I'm not sure why. I cannot reproduce this on my machine (I could access the venv managed by `pre-commit` just fine). **You should definitely double check the path to your python executable**.\r\n\r\n**Not sure if this would help or not at all**, but if you have sudo privilege perhaps you could try (assuming you are running Ubuntu, not sure what distro you're running either) `sudo apt install python3-socks`.\r\n\r\nSorry I might not be able to assist further. But certainly let me know how you resolve this if you do (I believe you will), and happy coding! \r\n",
"I understand. Several reasons caused my problem:\r\n\r\n1. More precisely, this is a [chicken-and-egg problem](https://github.com/pre-commit/pre-commit/pull/1697#issue-743656776), so I first changed the proxy used by pip to the following in `~/.pip/pip.conf`: \r\n```conf\r\n#proxy = socks5h://127.0.0.1:16668\r\n#proxy = socks5://127.0.0.1:16668\r\nproxy = http://127.0.0.1:8080\r\n```\r\n2. The node version is not up-to-date, so I updated it according the guidance [here](https://nodejs.org/en/download/package-manager/current) using [nvm](https://github.com/nvm-sh/nvm).\r\n3. The pre-commit environment itself will install many packages from GitHub, so a proxy is needed in my case, an HTTP or socks5 proxy will do the trick.\r\n\r\nFinally, the command executed successfully as follows:\r\n\r\n```shell\r\n$ pyenv shell datasci\r\n$ cd ~/Public/repo/github.com/materialsproject/pymatgen.git\r\n#https://pymatgen.org/contributing.html\r\n$ proxychains-ng-socks5 uv pip install -e '.[ci,optional]' --config-settings editable_mode=compat\r\n$ pre-commit gc\r\n$ pre-commit install\r\n\r\n# In this case, proxychains-ng is used for the first time to download dependent packages,\r\n# and the subsequent use of the pre-commit command does not need it.\r\n\r\n# https://pymatgen.org/contributing.html#coding-guidelines\r\n\r\n# Both proxychains-ng-http and proxychains-ng-socks5 are all OK:\r\n$ proxychains-ng-http pre-commit run --files src/pymatgen/io/vasp/sets.py tests/io/vasp/test_sets.py\r\nruff.....................................................................Passed\r\nruff-format..............................................................Passed\r\ncheck yaml...........................................(no files to check)Skipped\r\nfix end of files.........................................................Passed\r\ntrim trailing whitespace.................................................Passed\r\nmypy.....................................................................Passed\r\ncodespell................................................................Passed\r\ncython-lint..........................................(no files to check)Skipped\r\ndouble-quote Cython strings..........................(no files to check)Skipped\r\nblacken-docs.............................................................Passed\r\nmarkdownlint.........................................(no files to check)Skipped\r\nnbstripout...........................................(no files to check)Skipped\r\npyright..................................................................Passed\r\n```",
"Great to know that. I don't have much experience with proxy per se, but great to know you worked out a solution."
] | 2024-07-26T15:27:22
| 2024-07-28T02:03:34
|
2024-07-27T08:35:15Z
|
CONTRIBUTOR
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I want to reimplement https://github.com/materialsproject/pymatgen/pull/3914, but the `pre-commit` command suggested [here](https://pymatgen.org/contributing.html#coding-guidelines) failed as stated below:
The revised file:
```
(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ git diff
diff --git a/src/pymatgen/io/vasp/sets.py b/src/pymatgen/io/vasp/sets.py
index 5bc09f6d4..ed7ac86e6 100644
--- a/src/pymatgen/io/vasp/sets.py
+++ b/src/pymatgen/io/vasp/sets.py
@@ -1348,9 +1348,25 @@ class MPMetalRelaxSet(VaspInputSet):
@dataclass
class MPHSERelaxSet(VaspInputSet):
- """Same as the MPRelaxSet, but with HSE parameters."""
+ """Same as the MPRelaxSet, but with HSE parameters and vdW corrections."""
CONFIG = _load_yaml_config("MPHSERelaxSet")
+ vdw: Literal["dftd3", "dftd3-bj"] | None = None
+
+ @property
+ def incar_updates(self) -> dict[str, Any]:
+ """Updates to the INCAR config for this calculation type."""
+ updates: dict[str, Any] = {}
+
+ if self.vdw:
+ hse_vdw_par = {
+ "dftd3": {"VDW_SR": 1.129, "VDW_S8": 0.109},
+ "dftd3-bj": {"VDW_A1": 0.383, "VDW_S8": 2.310, "VDW_A2": 5.685},
+ }
+ if vdw_param := hse_vdw_par.get(self.vdw):
+ updates.update(vdw_param)
+
+ return updates
@dataclass
```
The `ruff check` passed:
```
(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ ruff check src/pymatgen/io/vasp/sets.py
All checks passed!
```
The failed `pre-commit run` command:
```
(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ env -u HTTP_PROXY -u HTTPS_PROXY -u SOCKS_PROXY pre-commit run --files src/pymatgen/io/vasp/sets.py
[INFO] Installing environment for https://github.com/astral-sh/ruff-pre-commit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('/home/werner/.cache/pre-commit/repod_9xb5e9/py_env-python3.11/bin/python', '-mpip', 'install', '.')
return code: 1
stdout:
Processing /home/werner/.cache/pre-commit/repod_9xb5e9
Installing build dependencies: started
Installing build dependencies: finished with status 'error'
stderr:
error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> [2 lines of output]
ERROR: Could not install packages due to an OSError: Missing dependencies for SOCKS support.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
Check the log at /home/werner/.cache/pre-commit/pre-commit.log
```
Any hints/comments for this problem?
Regards,
Zhao
|
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ValueError: numpy.dtype size changed
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"The issue here seems to be that the build specifies,\r\nhttps://github.com/materialsproject/pymatgen/blob/98c57888cc4f17ef4d8692d777ad0d1806ee7ae9/pyproject.toml#L5\r\n\r\nWhich wont work with numpy>=2.0. \r\n\r\nTo fix quickly, downgrade numpy.\r\n\r\nTo actually support numpy>=2.0, looks like the build system has to use numpy>=2, which should be backward compatible. See:\r\nhttps://numpy.org/devdocs/dev/depending_on_numpy.html#numpy-2-0-specific-advice ",
"Hi @ftherrien thanks for reporting this. I believe this issue has been resolved by #3894. Can you have another try?",
"Works now. Thanks!"
] | 2024-07-26T17:48:30
| 2024-09-02T17:22:35
|
2024-09-02T17:22:35Z
|
CONTRIBUTOR
|
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### Python version
Python 3.10.12
### Pymatgen version
pymatgen-2024.7.18
### Operating system version
Ubuntu 22.04.4 LTS
### Current behavior
```
>>> from pymatgen.core import Lattice
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/felixtherrien/envs/ocpenv/lib/python3.10/site-packages/pymatgen/core/__init__.py", line 11, in <module>
from pymatgen.core.lattice import Lattice
File "/home/felixtherrien/envs/ocpenv/lib/python3.10/site-packages/pymatgen/core/lattice.py", line 19, in <module>
from pymatgen.util.coord import pbc_shortest_vectors
File "/home/felixtherrien/envs/ocpenv/lib/python3.10/site-packages/pymatgen/util/coord.py", line 14, in <module>
from pymatgen.util import coord_cython
File "src/pymatgen/util/coord_cython.pyx", line 1, in init pymatgen.util.coord_cython
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
```
This happens in a fresh environment where I only installed pymatgen
`pip install pymatgen `
In that environment the version of numpy is *2.0.1*
### Expected Behavior
If I install numpy version *1.26.4*, the error disapears
### Minimal example
```Python
from pymatgen.core import Lattice
```
### Relevant files to reproduce this bug
_No response_
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PR_kwDOACgets52m0bf
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Fix coordination number bug
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[
"Ah, so there was a dual bug, an error in the test too? Thanks for fixing.",
"> Ah, so there was a dual bug, an error in the test too? Thanks for fixing.\r\n\r\nYeah, I'm 99% sure the test is wrong."
] | 2024-07-26T17:56:56
| 2024-07-26T22:00:01
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2024-07-26T21:48:49Z
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CONTRIBUTOR
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# `StructureGraph.get_coordination_of_site` gives wrong number for small unit cells
Refer to #3888
The `StructureGraph` object assumes that periodic images of the edges will added twice in the graph so the coordination number algorithm assumes that all self-connections are double-counted.
However, we have updated the definition of the graph such that periodic images of the same edge will only appear once (ie. if `SiteA[0,0,0]--SiteA[0,0,1]` is an edge, we should not see another edge from `SiteA[0,0,0]--SiteA[0,0,-1]`)
I have also removed the double counting from MoleculeGraph under the assumption that self-connection should never show up in a molecule.
## Modified test assertion value
The two of the edges added here are redundant:
https://github.com/materialsproject/pymatgen/blob/98c57888cc4f17ef4d8692d777ad0d1806ee7ae9/tests/analysis/test_graphs.py#L53-L56
But the coordination number should still be `4` since we have a square lattice.
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PR_kwDOACgets52oji2
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Add HSE-specific vdW parameters for dftd3 and dftd3-bj to MPHSERelaxSet.
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[
"Thanks."
] | 2024-07-27T04:40:22
| 2024-09-10T13:16:38
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2024-08-21T18:55:37Z
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CONTRIBUTOR
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This is the reimplementation of https://github.com/materialsproject/pymatgen/pull/3914, and the test has been added.
For the related discussion and information, see below:
https://www.vasp.at/forum/viewtopic.php?t=19551
https://www.vasp.at/forum/viewtopic.php?t=19658
https://github.com/dftd3/simple-dftd3/blob/3a50cbdf8566b3caa8760499ae21746ec9a5e535/assets/parameters.toml#L80-L82
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Adding PBE_64 support: Clarification on hash types used in POTCAR hash files.
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"Hi @hongyi-zhao, the hash-based identification is deprecated right now, those files (vasp_potcar_pymatgen_hashes.json and vasp_potcar_file_hashes.json) are maintained for backwards compatibility. Only the summary stats should be updated moving forward. \r\n\r\nSupport for `PBE_64` pseudopotentials was added to pymatgen in [#3370](https://github.com/materialsproject/pymatgen/pull/3370). Are there `PBE_64` pseudopotentials missing support?\r\n",
"> Are there `PBE_64` pseudopotentials missing support?\r\n\r\nI checked [this file](https://github.com/esoteric-ephemera/pymatgen/raw/4a84723374f6428cd00b4a530505c8361a1981b7/pymatgen/io/vasp/potcar_summary_stats.json.gz) as follows:\r\n\r\n```\r\n$ jq '.PBE_64 | with_entries(select(.key | startswith(\"PAW_PBE\")))' potcar_summary_stats.json |grep -Po 'PAW_PBE\\K[^\"]+' | wc -l\r\n342\r\n```\r\nThis is **1** less than the number of files in my local **POT_PAW_PBE_64** directory\r\n```\r\nwerner@x13dai-t:~/Public/hpc/vasp/pot/pmg_potcar/POT_PAW_PBE_64$ ls |wc -l\r\n343\r\n```\r\n\r\nA further quick and dirty check gives the following result:\r\n```\r\nwerner@x13dai-t:~/Downloads$ diff <(jq '.PBE_64 | with_entries(select(.key | startswith(\"PAW_PBE\")))' potcar_summary_stats.json |grep -Po 'PAW_PBE\\K[^\"]+' | sort -u) <( ls $HOME/Public/hpc/vasp/pot/pmg_potcar/POT_PAW_PBE_64 | xargs -P0 -I{} bash -c 'zcat \"$HOME/Public/hpc/vasp/pot/pmg_potcar/POT_PAW_PBE_64/{}\" | head -1' | awk '{print $2$3}' | sort -u )\r\n129a130\r\n> H_AE28Mar2008\r\n135c136\r\n< Hf_sv10Jan2008GWsuitable\r\n---\r\n> Hf_sv10Jan2008\r\n```",
"I would suggest simply disabling the hash altogether. "
] | 2024-07-30T10:48:56
| 2024-09-18T01:09:07
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CONTRIBUTOR
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Hi there,
I'm working on adding support for PBE_64 potentials in pymatgen. This requires updating two JSON files containing POTCAR hash information:
1. [vasp_potcar_pymatgen_hashes.json](https://github.com/materialsproject/pymatgen/blob/master/src/pymatgen/io/vasp/vasp_potcar_pymatgen_hashes.json)
2. [vasp_potcar_file_hashes.json](https://github.com/materialsproject/pymatgen/blob/master/src/pymatgen/io/vasp/vasp_potcar_file_hashes.json)
I've noticed different hash values are used for the same potcar file in the above two files.
Another file that should also be updated is [potcar-summary-stats.json.bz2](https://github.com/materialsproject/pymatgen/blob/master/src/pymatgen/io/vasp/potcar-summary-stats.json.bz2).
Questions:
1. What's the recommended process for generating these hash info and summary stats data for the new PBE_64 potentials to update these files?
5. Is there any additional documentation or code that needs to be updated alongside these JSON files?
Understanding the above questions will help ensure I implement the PBE_64 support correctly. Any insights would be greatly appreciated. Thank you!
Regards,
Zhao
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I_kwDOACgets6RWW6v
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Vasp Incar check_params() can't handle Union types
|
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[
"Ah ok I see why this was not caught. In tests.io.vasp.inputs, the only test for Incar.check_params() is\r\n\r\n```python \r\n def test_check_params(self):\r\n # Triggers warnings when running into invalid parameters\r\n with pytest.warns(BadIncarWarning) as record:\r\n incar = Incar(\r\n {\r\n \"ADDGRID\": True,\r\n \"ALGO\": \"Normal\",\r\n \"AMIN\": 0.01,\r\n \"ICHARG\": 1,\r\n \"MAGMOM\": [1, 2, 4, 5],\r\n \"NBAND\": 250, # typo in tag\r\n \"METAGGA\": \"SCAM\", # typo in value\r\n \"EDIFF\": 5 + 1j, # value should be a float\r\n \"ISIF\": 9, # value out of range\r\n \"LASPH\": 5, # value should be bool\r\n \"PHON_TLIST\": \"is_a_str\", # value should be a list\r\n }\r\n )\r\n incar.check_params()\r\n```\r\n\r\nWhich means that no matter the incar input, it will catch a warning and pass. \r\n",
"Hi @wladerer thanks for reporting. Can you please double check your `pymatgen` version? As the following code has been updated four months ago from:\r\n```python \r\nif param_type is not None and not isinstance(val, eval(param_type)):\r\n``` \r\n\r\nTo: https://github.com/materialsproject/pymatgen/blob/720fdf86539236c737f12250ae71d68e3872c616/src/pymatgen/io/vasp/inputs.py#L1032\r\n\r\nWith the intention to avoid using `eval` (perhaps I overreacted there as `param_type` would not come from any untrusted source, and therefore should not introduce security concerns).\r\n\r\nEven with the latest version, it looks like there is indeed an issue with type checking of `LREAL` here alone: https://github.com/materialsproject/pymatgen/blob/720fdf86539236c737f12250ae71d68e3872c616/src/pymatgen/io/vasp/incar_parameters.json#L652-L661\r\n\r\nI just had another complete check of `incar_parameters.json` and it seems `LREAL` is the only INCAR tag that requires a Union type here, and I must have missed it, apologies.\r\n\r\nI would fix this ASAP.\r\n\r\n> Which means that no matter the incar input, it will catch a warning and pass.\r\n\r\nThe checking mechanism are those following: https://github.com/materialsproject/pymatgen/blob/720fdf86539236c737f12250ae71d68e3872c616/tests/io/vasp/test_inputs.py#L786-L791\r\n",
"Hi I very unfortunately had a python environment disaster when trying to install a different package. I pulled that version I reported using the command line command recommended in the environment where I was developing in. I'm sorry that I am unable to double check :(\r\n\r\nI will try and see if I have any way of tracing it back and recreating the env and will report back. \r\n\r\nAnd I see now that this test is sufficient since it only catches warnings rather than errors. Sorry for the confusion. \r\n\r\nThanks!\r\n",
"No need to apologize at all. This is indeed an issue and I'm trying to fix it now. Thanks for reporting!"
] | 2024-07-30T19:45:19
| 2024-08-02T21:59:54
|
2024-08-02T21:59:54Z
|
CONTRIBUTOR
|
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### Python version
3.11.9
### Pymatgen version
2024.6.10
### Operating system version
Ubuntu 22.04.4 LTS
### Current behavior
Error Message:
```
Traceback (most recent call last):
File "/home/wladerer/github/abvio/tests/test_incar.py", line 356, in test_valid_model
incar.check_params()
File "/home/wladerer/.venv/base/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py", line 979, in check_params
if param_type is not None and not isinstance(val, eval(param_type)):
^^^^^^^^^^^^^^^^
File "<string>", line 1, in <module>
NameError: name 'Union' is not defined
----------------------------------------------------------------------
Ran 1 test in 0.002s
FAILED (errors=1)
Finished running tests!
```
Incar.check_params() does not seem to handle Union types
Something strange is happening here where `isinstance(eval(param_type))`
```python
# Check value and its type
param_type = incar_params[tag].get("type")
allowed_values = incar_params[tag].get("values")
if param_type is not None and not isinstance(val, eval(param_type)):
warnings.warn(f"{tag}: {val} is not a {param_type}", BadIncarWarning, stacklevel=2)
```
Is unaware of the typing module Union type. I can see that it is not imported, so when I update the imports
```python
from typing import TYPE_CHECKING, Any, Literal, Union
```
the error goes away.
```
test_valid_model (test_incar.TestIncarModel.test_valid_model) ... EDIFF tag type: <class 'str'> tag value <class 'float'>
ISMEAR tag type: <class 'str'> tag value <class 'int'>
LREAL tag type: <class 'str'> tag value <class 'bool'>
EDIFFG tag type: <class 'str'> tag value <class 'float'>
LWAVE tag type: <class 'str'> tag value <class 'bool'>
MAGMOM tag type: <class 'str'> tag value <class 'list'>
ok
----------------------------------------------------------------------
Ran 1 test in 0.001s
OK
Finished running tests!
```
### Expected Behavior
No output
### Minimal example
```Python
import unittest
from pymatgen.io.vasp import Incar
class TestCheckIncarParams(unittest.TestCase):
def test_dict_with_magmoms(self):
incar_dict = {
"SYSTEM": "Test",
"ENCUT": 400,
"ISMEAR": 0,
"SIGMA": 0.1,
"IBRION": 2,
"NSW": 0,
"LCHARG": False,
"LWAVE": False,
"LORBIT": 11,
"LREAL": "Auto",
"ISYM": 0,
"MAGMOM": [0.6, 0.6, 0.2],
}
incar = Incar.from_dict(incar_dict)
incar.check_params()
```
### Relevant files to reproduce this bug
Can be run using the minimal example
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PR_kwDOACgets528H_q
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|
Fix `Incar` `check_params` for `Union` type
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[
"This might be a silly question, but is changing the \"type\" parameter in the json file possible? The following evaluates to typing.Union\r\n \r\n```python\r\ntype(eval('bool | str'))\r\n```\r\nExample:\r\n\r\n```\r\n>>> isinstance(True, eval('bool | str'))\r\nTrue\r\n>>> isinstance(\"string thing\", eval('bool | str'))\r\nTrue\r\n>>> isinstance(55, eval('bool | str'))\r\nFalse\r\n```",
"That's actually an ingenious solution IMO, now that using of `eval` is not risky in this scenario. \r\n\r\nHowever the only pitfall being that the [alias of `Union[x, y]` as `x | y` is introduced in Python 3.10](https://peps.python.org/pep-0604/), and as the min supported version for `pymatgen` is 3.9 at this moment, we still cannot implement that change. But still I think it's a cleaner solution than mine, perhaps we could import `Union` for now until we move to Python 3.10+.",
"Not sure why some errors (seemingly unrelated to this PR) popped up, fixed some but still get one left:\r\n> src/pymatgen/util/provenance.py:49: in is_valid_bibtex\r\n parser = bibtex.Parser()\r\nE AttributeError: 'NoneType' object has no attribute 'Parser'\r\n\r\nPerhaps owing to the import error: https://github.com/materialsproject/pymatgen/blob/720fdf86539236c737f12250ae71d68e3872c616/src/pymatgen/util/provenance.py#L15-L19\r\n\r\nBut it seems `pytex` has been correctly installed in CI:\r\n> + pybtex==0.24.0",
"@janosh Can you please review this? Thanks. I believe the CI failing is unrelated to this PR.",
"> I believe the CI failing is unrelated to this PR.\r\n\r\ni think the issue is due to installing the latest `torch` in `test.yml` while `matGL` requires `torch=2.2.1` or older\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/633e7bd7700fc96b407d882cce2b473a38a97c67/.github/workflows/test.yml#L80\r\n\r\ncan you try pinning to torch `2.2.1` in CI with a TODO to remove pin later?",
"Yes sure. Let me have a try.",
"Looks like `matgl` has removed the `torch` version limitation, but still we need to wait for a new release. https://github.com/materialsvirtuallab/matgl/commit/d0bf202ad4316d058e8e64a08f5c4fccb53aa0d9",
"afaik `dgl` isn't compatible with `torch==2.3` yet, let alone 2.4 so don't think the `matgl` up pin should have been removed. i was advocating for a down pin in another thread. either way, let's revert the temp `torch==2.2.1` pin here and just skip the matGL tests for now to keep things moving",
"Sure! Thanks for the input, and I know nothing about `matgl` :)",
"Thanks for reviewing!"
] | 2024-07-31T03:08:32
| 2024-08-09T00:11:03
|
2024-08-02T21:59:53Z
|
CONTRIBUTOR
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### Summary
- Fix Incar `check_params` for `Union` type, to fix #3957, changed `incar_parameters.json` of Union type to use `isinstance` syntax directly. Otherwise Python 3.9 Windows don't support type checking with `isinstance(data, Union[str, float])`.
**Would appreciate it if anyone has smarted way to resolve this!**
- Bump `palettable` version to remove dependency of `setuptools` https://github.com/jiffyclub/palettable/pull/46
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I_kwDOACgets6RbKNs
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Wrong sign in NMR convention?
|
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[
"Thank you for reporting this. I am personally not an expert for this module. \r\n\r\n@shyuep, do you by chance have some insights here? This comment has been added more than 8 years ago. "
] | 2024-07-31T11:28:38
| 2024-07-31T11:34:26
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NONE
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I've just been going through the NMR analysis module and noticed the comment about the sign inconsistency across the two papers referenced. I'm not sure there _is_ a sign inconsistency between the papers, and the sign chosen in the code appears to be incorrect (I may be wrong, so double-check!)
In equation 20 from Magn. Resonance Chem. 2008, 46, 582-598 they give the sign as $\sigma_{iso}$ - $\sigma_{22}$ and in Solid State Nucl. Magn. Resonance 1993, 2, 285-288 they give the same way round for _shieldings_. However, if talking about _shifts_ ($\delta$) instead of _shieldings_ ($\sigma$) then the sign should be reversed (i.e. $\delta_{22}$ - $\delta_{iso}$) as it is in the last line of skew definition in the 1993 paper.
https://github.com/materialsproject/pymatgen/blob/720fdf86539236c737f12250ae71d68e3872c616/src/pymatgen/analysis/nmr.py#L113
In general there might be other places where NMR conventions are given in terms of the experimentally measured chemical shifts but VASP/CASTEP etc deal only in absolute magnetic shieldings so the conventions should sometimes be reversed.
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# Issue Metrics
| Metric | Average | Median | 90th percentile |
| --- | --- | --- | ---: |
| Time to first response | 11:43:21 | 4:06:58 | 1 day, 3:01:09 |
| Time to close | 4 days, 12:26:10 | 3 days, 11:26:54 | 9 days, 11:59:44 |
| Time to answer | None | None | None |
| Metric | Count |
| --- | ---: |
| Number of items that remain open | 14 |
| Number of items closed | 4 |
| Number of most active mentors | 0 |
| Total number of items created | 18 |
| Title | URL | Author | Time to first response | Time to close | Time to answer |
| --- | --- | --- | --- | --- | --- |
| Wrong sign in NMR convention? | https://github.com/materialsproject/pymatgen/issues/3959 | [jkshenton](https://github.com/jkshenton) | 0:05:47 | None | None |
| Vasp Incar check_params() can't handle Union types | https://github.com/materialsproject/pymatgen/issues/3957 | [wladerer](https://github.com/wladerer) | 6:58:55 | None | None |
| Adding PBE_64 support: Clarification on hash types used in POTCAR hash files. | https://github.com/materialsproject/pymatgen/issues/3956 | [hongyi-zhao](https://github.com/hongyi-zhao) | None | None | None |
| ValueError: numpy.dtype size changed | https://github.com/materialsproject/pymatgen/issues/3953 | [ftherrien](https://github.com/ftherrien) | 1:02:35 | None | None |
| `pre-commit run --files` will trigger errors. | https://github.com/materialsproject/pymatgen/issues/3952 | [hongyi-zhao](https://github.com/hongyi-zhao) | 10:27:50 | 17:07:53 | None |
| When reading in a POTCAR file with pymatgen.io.vasp.inputs.Potcar, the object can't distinguish between PBE_54 and PBE. | https://github.com/materialsproject/pymatgen/issues/3951 | [nhew1994](https://github.com/nhew1994) | 12:11:10 | None | None |
| Mix GGA/GGAU/RSCAN not available as compatibility? | https://github.com/materialsproject/pymatgen/issues/3943 | [Jeff-oakley](https://github.com/Jeff-oakley) | 2 days, 13:37:48 | None | None |
| Calling PhaseDiagram.as_dict() breaks the link between different Entries | https://github.com/materialsproject/pymatgen/issues/3940 | [CompRhys](https://github.com/CompRhys) | None | None | None |
| Group-subgroup relationship bugs in `SpaceGroup` and `PointGroup` class | https://github.com/materialsproject/pymatgen/issues/3937 | [kaueltzen](https://github.com/kaueltzen) | None | None | None |
| Bugs in `io.pwscf.PWInput.from_str()` method | https://github.com/materialsproject/pymatgen/issues/3930 | [jsukpark](https://github.com/jsukpark) | None | None | None |
| Installation failed using self-forked version | https://github.com/materialsproject/pymatgen/issues/3928 | [jinlhr542](https://github.com/jinlhr542) | 1:15:00 | 6 days, 5:45:54 | None |
| Adapt pymatgen.symmetry.analyzer to new spglib (>=2.5.0) output data format | https://github.com/materialsproject/pymatgen/issues/3922 | [kaueltzen](https://github.com/kaueltzen) | 0:07:42 | 5:19:32 | None |
| [Ext] The link to `boltztrap` is not valid anymore | https://github.com/materialsproject/pymatgen/issues/3921 | [DanielYang59](https://github.com/DanielYang59) | None | 10 days, 21:31:23 | None |
| More robust parsing of (electronic) piezoelectric tensor from OUTCAR | https://github.com/materialsproject/pymatgen/issues/3919 | [knoori](https://github.com/knoori) | None | None | None |
| Cannot get element projected data | https://github.com/materialsproject/pymatgen/issues/3918 | [Nick12-hub](https://github.com/Nick12-hub) | None | None | None |
| VASP Convergence Testing | https://github.com/materialsproject/pymatgen/issues/3907 | [hongyi-zhao](https://github.com/hongyi-zhao) | None | None | None |
| Build up customized pourbaix entries | https://github.com/materialsproject/pymatgen/issues/3906 | [Jeff-oakley](https://github.com/Jeff-oakley) | None | None | None |
| Why assume trajectory lattice does not change by default? | https://github.com/materialsproject/pymatgen/issues/3905 | [matthewkuner](https://github.com/matthewkuner) | None | None | None |
_This report was generated with the [Issue Metrics Action](https://github.com/github/issue-metrics)_
Search query used to find these items: `repo:materialsproject/pymatgen is:issue created:2024-07-01..2024-07-31 -reason:"not planned"`
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Site property indexing in `SymmetrizedStructure`
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[
"excellent catch!\r\n\r\n> Therefore, it may not make a lot of sense to give site properties here at all or at least a warning\r\n\r\nthanks for pointing that out. i'm leaning towards not trying to translate site properties from `Structure` to `SymmetrizedStructure` at all in order to not mislead users. a warning might be missed and doesn't sound like a great user experience anyway. but i defer to @mkhorton if he wants to weigh in"
] | 2024-08-01T09:01:07
| 2024-08-01T11:04:06
|
CONTRIBUTOR
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### Python version
3.10
### Pymatgen version
master or 2024.7.18
### Operating system version
Debian GNU/Linux 11
### Current behavior
The current implementation of `__str__` of `SymmetrizedStructure` appends site properties as per the index of `self.equivalent_sites`, not of the actual site index.
https://github.com/materialsproject/pymatgen/blob/660ba7a584fae5b5d8bb1095614f0104c9d89049/src/pymatgen/symmetry/structure.py#L120
This means that a structure with the species string as a test property
```
Full Formula (La4 Mn4 O12)
Reduced Formula: LaMnO3
abc : 5.746100 7.663700 5.533300
angles: 90.000000 90.000000 90.000000
pbc : True True True
Sites (20)
# SP a b c test_property
--- ---- ------- ------ ------ ---------------
0 La 0.0513 0.25 0.9905 La
1 La 0.9487 0.75 0.0095 La
2 La 0.5513 0.25 0.5095 La
3 La 0.4487 0.75 0.4905 La
4 Mn 0 0 0.5 Mn
5 Mn 0 0.5 0.5 Mn
6 Mn 0.5 0.5 0 Mn
7 Mn 0.5 0 0 Mn
8 O 0.48493 0.25 0.0777 O
9 O 0.51507 0.75 0.9223 O
10 O 0.98493 0.25 0.4223 O
11 O 0.01507 0.75 0.5777 O
12 O 0.3085 0.0408 0.7227 O
13 O 0.6915 0.5408 0.2773 O
14 O 0.6915 0.9592 0.2773 O
15 O 0.3085 0.4592 0.7227 O
16 O 0.8085 0.4592 0.7773 O
17 O 0.1915 0.9592 0.2227 O
18 O 0.1915 0.5408 0.2227 O
19 O 0.8085 0.0408 0.7773 O
```
will give the following `SymmetrizedStructure` string:
```
SymmetrizedStructure
Full Formula (La4 Mn4 O12)
Reduced Formula: LaMnO3
Spacegroup: Pnma (62)
abc : 5.746100 7.663700 5.533300
angles: 90.000000 90.000000 90.000000
Sites (20)
# SP a b c Wyckoff test_property
--- ---- ------- ------ ------ --------- ---------------
0 La 0.0513 0.25 0.9905 4c La
1 Mn 0 0 0.5 4b La
2 O 0.48493 0.25 0.0777 4c La
3 O 0.3085 0.0408 0.7227 8d La
```
This can be corrected by replacing the respective line with `row.append(site.properties[key])` and I can raise a PR with that.
However, the whole approach does not ensure that the site property has the same symmetry as the site itself as only the atomic coordinates and numbers are mapped onto each other. Therefore, it may not make a lot of sense to give site properties here at all or at least a warning should be raised that the symmetry of the property was not taken into account in the symmetry search.
### Expected Behavior
A symmetrized structure like
```
SymmetrizedStructure
Full Formula (La4 Mn4 O12)
Reduced Formula: LaMnO3
Spacegroup: Pnma (62)
abc : 5.746100 7.663700 5.533300
angles: 90.000000 90.000000 90.000000
Sites (20)
# SP a b c Wyckoff test_property
--- ---- ------- ------ ------ --------- ---------------
0 La 0.0513 0.25 0.9905 4c La
1 Mn 0 0 0.5 4b Mn
2 O 0.48493 0.25 0.0777 4c O
3 O 0.3085 0.0408 0.7227 8d O
```
or preferably without site properties (see above).
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
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Don't run `issue-metrics` on forks
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[
"No idea why the test are failing...",
"likely caused by the recent [`torch==2.4.0`](https://pypi.org/project/torch/2.4.0/) release\r\n\r\nunrelated issue but just noticed [`matgl` is not setting a minimum `torch` version](https://github.com/materialsvirtuallab/matgl/blob/main/pyproject.toml#L56) @kenko911"
] | 2024-08-01T16:18:55
| 2024-08-21T12:17:54
|
2024-08-02T21:58:38Z
|
CONTRIBUTOR
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## Summary
Major changes:
- `issue-metrics` should not be run on forks because it can't create a new issue on the fork anyway.
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wrong number of atoms generated from cif file.
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"Just to aid in diagnosing this, the relevant output is the following\r\n```\r\n/home/wladerer/.venv/base/lib/python3.10/site-packages/pymatgen/io/cif.py:1285: UserWarning: Issues encountered while parsing CIF: 3 fractional coordinates rounded to ideal values to avoid issues with finite precision.\r\nSkipping relative stoichiometry check because CIF does not contain formula keys.\r\n warnings.warn(\"Issues encountered while parsing CIF: \" + \"\\n\".join(self.warnings))\r\nFull Formula (Si36 O76)\r\nReduced Formula: Si9O19\r\n```\r\n\r\nAnd the file contents don't pass a first check of the following section of the cif file\r\n\r\n```\r\nloop_\r\n_atom_site_label\r\n_atom_site_type_symbol\r\n_atom_site_fract_x\r\n_atom_site_fract_y\r\n_atom_site_fract_z\r\n O1 O 0.6667 0.1347 0.8333\r\n O2 O 0.5760 0.0000 0.0000\r\n O3 O 0.5544 0.1089 0.1382\r\n O4 O 0.6667 0.1006 0.3333\r\n T1 Si 0.6160 0.0861 0.0763\r\n```\r\n\r\nSaid check:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/633e7bd7700fc96b407d882cce2b473a38a97c67/src/pymatgen/io/cif.py#L1423-L1428\r\n\r\n# Update:\r\n\r\nIt seems to be a precision issue. If you use the space group analyzer with the default precision, you will get the following error \r\n\r\n```\r\nTraceback (most recent call last):\r\n File \"/home/wladerer/Downloads/atotest/pmgtest.py\", line 11, in <module>\r\n orginal_sg = SpacegroupAnalyzer(original).get_space_group_number()\r\n File \"/home/wladerer/.venv/base/lib/python3.10/site-packages/pymatgen/symmetry/analyzer.py\", line 142, in __init__\r\n self._space_group_data = _get_symmetry_dataset(self._cell, symprec, angle_tolerance)\r\n File \"/home/wladerer/.venv/base/lib/python3.10/site-packages/pymatgen/symmetry/analyzer.py\", line 70, in _get_symmetry_dataset\r\n raise SymmetryUndetermined\r\npymatgen.symmetry.analyzer.SymmetryUndetermined\r\n```\r\n\r\nSo if you go from\r\n\r\n```python\r\nSpacegroupAnalyzer(original).get_space_group_number()\r\n```\r\n\r\nto \r\n\r\n```python\r\nSpacegroupAnalyzer(original, 0.0001).get_space_group_number()\r\n```\r\nYou get space group 1. If you use ASE to find the space group, it gets space group 146 (R 3). Neither of these are correct according to the header of the file, saying that it is R -3 m / 166. It is still interesting that ASE gets the correct stoichiometry but incorrect space group.\r\n\r\n \r\n\r\n ",
"Hi, it seems to be a precision issue of site O3. If you parse the structure with default settings and have a look at the distance matrix, you can see that there are 4 pairs of very close oxygen sites:\r\n\r\n```\r\ndist_matrix = cif_struct.distance_matrix\r\ndists = list(dist_matrix.flatten())\r\nsorted_dists = sorted(dists)\r\nc = Counter(dists)\r\nprint({k: c[k] for k in sorted_dists if k < 1.5})\r\n\r\nclose_ids = set()\r\nfor row_id, row in enumerate(dist_matrix):\r\n for col_id, cell in enumerate(row):\r\n if 0.0 < cell < 0.003:\r\n print(row_id, col_id, cell, cif_struct.sites[row_id].frac_coords, cif_struct.sites[col_id].frac_coords)\r\n```\r\n\r\ngives the following output:\r\n\r\n```\r\n{0.0: 112, 0.002091399999999175: 2, 0.00209140000000036: 2, 0.002091400000002075: 2, 0.002091400000002283: 2}\r\n\r\n77 81 0.002091400000002283 [0.22443333 0.11216667 0.80486667] [0.22443333 0.11226667 0.80486667]\r\n80 82 0.002091399999999175 [0.88783333 0.11226667 0.80486667] [0.88773333 0.11216667 0.80486667]\r\n81 77 0.002091400000002283 [0.22443333 0.11226667 0.80486667] [0.22443333 0.11216667 0.80486667]\r\n82 80 0.002091399999999175 [0.88773333 0.11216667 0.80486667] [0.88783333 0.11226667 0.80486667]\r\n84 92 0.002091400000002075 [0.11226667 0.22443333 0.19513333] [0.11216667 0.22443333 0.19513333]\r\n90 93 0.00209140000000036 [0.11216667 0.88773333 0.19513333] [0.11226667 0.88783333 0.19513333]\r\n92 84 0.002091400000002075 [0.11216667 0.22443333 0.19513333] [0.11226667 0.22443333 0.19513333]\r\n93 90 0.00209140000000036 [0.11226667 0.88783333 0.19513333] [0.11216667 0.88773333 0.19513333]\r\n```\r\n\r\nThis can be circumvented by changing the `site_tolerance` parameter of `CifParser` to count two close sites as one. E.g., the following structure\r\n```\r\ncif_struct = CifParser(\"ATO.cif\", site_tolerance=1e-3).parse_structures()[0]\r\n```\r\nwill have the correct formula Si36 O72.\r\n\r\nThe equivalent functionality in ase seems to have a higher tolerance parameter (`symprec`) to count two sites as one (https://gitlab.com/ase/ase/-/blob/master/ase/spacegroup/spacegroup.py?ref_type=heads#L378), this is why the correct stochiometry is found with the default settings @wladerer .",
"Thank you @kaueltzen !\r\n\r\nIs this answer sufficient for you, @JPBergsma ? I would close the issue then. ",
"Thank you for looking into this issue more deeply on such short notice.\r\n\r\nThe main thing I am still wondering about is whether such a structure as I encountered here could be handled more elegantly in the future.\r\n\r\nAssuming that the site occupancy is 1, there is a minimum distance two sites could have in any realistic structure. Let's assume that this distance is 0.5 angstrom. Then any inter site distance of less than 0.25 Angstrom probably means that two sites should overlap and only one atom should be added to the structure. I guess the best atomic position would be the average of the two positions in that case. \r\n\r\nDo you think that this is reasonable and that this could be added to how structures are handled?",
"@JPBergsma I am not sure. I personally wouldn't want any code to handle this automatically for me as I would fear unexpected side effects.\r\n\r\nAre there Maintainer opinions? @shyuep @mkhorton @janosh ?",
"See https://github.com/spglib/spglib/discussions/514 for the related discussion."
] | 2024-08-01T17:01:45
| 2024-08-08T01:48:14
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NONE
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### Python version
python 3.12.4
### Pymatgen version
2024.7.18
### Operating system version
Linux Mint 21.3
### Current behavior
the wrong number of Oxygen and Silicon atoms is generated from the Cif file.
### Expected Behavior
The correct number of Oxygen and Silicon atoms. 72 Oxygen atoms and 36 silicon atoms
The file is read correctly by Ovito.
### Minimal example
```Python
from pymatgen.core import Structure
structure = Structure.from_file("ATO.cif")
print(structure.formula)
```
### Relevant files to reproduce this bug
https://europe.iza-structure.org/IZA-SC/download_cif.php?ID=42
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switch to attr access interface for transformation matrix
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[] | 2024-08-01T20:26:44
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2024-08-01T20:36:08Z
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CONTRIBUTOR
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an attr access interface change was missed in Tensor when spglib was upgraded to >=2.5.0 (#3923)
spglib throws the following deprecation warning currently:
`DeprecationWarning: dict interface (SpglibDataset['transformation_matrix']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead`
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Bump rexml from 3.2.8 to 3.3.3 in /docs
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CONTRIBUTOR
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Bumps [rexml](https://github.com/ruby/rexml) from 3.2.8 to 3.3.3.
<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 3.3.3 - 2024-08-01</h2>
<h3>Improvements</h3>
<ul>
<li>
<p>Added support for detecting invalid XML that has unsupported
content before root element</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/184">GH-184</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Added support for <code>REXML::Security.entity_expansion_limit=</code> and
<code>REXML::Security.entity_expansion_text_limit=</code> in SAX2 and pull
parsers</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/187">GH-187</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Added more tests for invalid XMLs.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/183">GH-183</a></li>
<li>Patch by Watson.</li>
</ul>
</li>
<li>
<p>Added more performance tests.</p>
<ul>
<li>Patch by Watson.</li>
</ul>
</li>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/186">GH-186</a></li>
<li>Patch by tomoya ishida.</li>
</ul>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>
<p>NAITOH Jun</p>
</li>
<li>
<p>Watson</p>
</li>
<li>
<p>tomoya ishida</p>
</li>
</ul>
<h2>REXML 3.3.2 - 2024-07-16</h2>
<h3>Improvements</h3>
<ul>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/160">GH-160</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/169">GH-169</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/170">GH-170</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/171">GH-171</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/172">GH-172</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/173">GH-173</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/174">GH-174</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/175">GH-175</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/176">GH-176</a></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>3.3.3 - 2024-08-01 {#version-3-3-3}</h2>
<h3>Improvements</h3>
<ul>
<li>
<p>Added support for detecting invalid XML that has unsupported
content before root element</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/184">GH-184</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Added support for <code>REXML::Security.entity_expansion_limit=</code> and
<code>REXML::Security.entity_expansion_text_limit=</code> in SAX2 and pull
parsers</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/187">GH-187</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Added more tests for invalid XMLs.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/183">GH-183</a></li>
<li>Patch by Watson.</li>
</ul>
</li>
<li>
<p>Added more performance tests.</p>
<ul>
<li>Patch by Watson.</li>
</ul>
</li>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/186">GH-186</a></li>
<li>Patch by tomoya ishida.</li>
</ul>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>
<p>NAITOH Jun</p>
</li>
<li>
<p>Watson</p>
</li>
<li>
<p>tomoya ishida</p>
</li>
</ul>
<h2>3.3.2 - 2024-07-16 {#version-3-3-2}</h2>
<h3>Improvements</h3>
<ul>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/160">GH-160</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Improved parse performance.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/169">GH-169</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/170">GH-170</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/171">GH-171</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/172">GH-172</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/173">GH-173</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/174">GH-174</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/175">GH-175</a></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/e4a067e11235a2ec7a00616d41350485e384ec05"><code>e4a067e</code></a> Add 3.3.3 entry</li>
<li><a href="https://github.com/ruby/rexml/commit/17ff3e78745b31db4e841357e8eed2f6669bea7b"><code>17ff3e7</code></a> test: add a performance test for attribute list declaration</li>
<li><a href="https://github.com/ruby/rexml/commit/be86b3de0aca8394534b715a83a63bf51c5195f5"><code>be86b3d</code></a> test: fix wrong test name</li>
<li><a href="https://github.com/ruby/rexml/commit/b93d790b36c065a3f7f3e0c3f5b2b71254a4d96d"><code>b93d790</code></a> test: use double quote for string literal</li>
<li><a href="https://github.com/ruby/rexml/commit/0fbe7d5a0eac8cfaffa6c3b27f3b9a90061a0fbc"><code>0fbe7d5</code></a> test: don't use abbreviated name</li>
<li><a href="https://github.com/ruby/rexml/commit/1599e8785f2d7734169aeb37a0b5d94f8212356d"><code>1599e87</code></a> test: add a performance test for PI with many tabs</li>
<li><a href="https://github.com/ruby/rexml/commit/e2546e6ecade16b04c9ee528e5be8509fe16c2d6"><code>e2546e6</code></a> parse pi: improve invalid case detection</li>
<li><a href="https://github.com/ruby/rexml/commit/73661ef281f5a829f7fec4ea673d42436c533ded"><code>73661ef</code></a> test: fix a typo</li>
<li><a href="https://github.com/ruby/rexml/commit/850488abf20f9327ebc00094cd3bb64eea400a59"><code>850488a</code></a> test: use double quote for string literal</li>
<li><a href="https://github.com/ruby/rexml/commit/46c6397d5c647a700fb1817d0093471621d92a27"><code>46c6397</code></a> test: add performance tests for entity declaration</li>
<li>Additional commits viewable in <a href="https://github.com/ruby/rexml/compare/v3.2.8...v3.3.3">compare view</a></li>
</ul>
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I_kwDOACgets6Rqm0f
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More up to date Critic2 JSON parser
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[] | 2024-08-02T02:29:28
| 2024-08-02T06:17:50
|
CONTRIBUTOR
|
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### Feature Requested
This is either a bug or feature request, I am unsure which.
I was wondering which version of critic2 is compatible with the Critic2Analysis class? I see that it is looking for some properties that are formatted differently than in my cpreport json file.
For reference, this is the input file I used
```bash
#use core density file for crystal structure
crystal AECCAR0
# and valence densities
load AECCAR0
load AECCAR2
load as "$1+$2" id rhoae smoothrho
reference rhoae
auto
auto discard "$1 < 1e-5"
cpreport VERYLONG cpreport.json
YT JSON yt.json
end
```
And here is one of the nonequiv. critical points
```
"nonequivalent_cps": [
{
"id": 1,
"name": "K",
"fractional_coordinates": [
0.81593899999999997E+0,
0.81593899999999997E+0,
0.27805999999999997E+0
],
"cartesian_coordinates": [
0.26019124853424746E+2,
0.0E+0,
0.43464039668231935E+1
],
"multiplicity": 2,
"point_group": "Cs",
"rank": 3,
"signature": -3,
"field": 0.50927265092358703E+4,
"field_valence": 0.50927265092358703E+4,
"gradient": [
0.0E+0,
0.0E+0,
0.0E+0
],
"hessian": [
-0.57792119105068703E+10,
-0.85445783604125997E-1,
0.11811907822821733E+3,
-0.85445783604125997E-1,
-0.57792118885804806E+10,
-0.27167020562287797E+0,
0.11811907822821733E+3,
-0.27167020562287797E+0,
-0.57792119676928844E+10
],
"gradient_norm": 0.0E+0,
"gradient_norm_valence": 0.0E+0,
"laplacian": -0.17337635766780235E+11,
"laplacian_valence": -0.17337635766780235E+11,
"hessian_eigenvalues": [
-0.57792120606305885E+10,
-0.5779211888581109E+10,
-0.57792118175685415E+10
],
"number_of_pointprops": 0,
"is_nucleus": true
}
```
You can see that the Hessian is a 1D vector rather than a 3x3 matrix. This is fine, but it seems like the parser doesn't enjoy this very much when I tried to run
```python
from pymatgen.command_line.critic2_caller import Critic2Analysis, Critic2Caller
from pymatgen.core import Structure
import json
with open('testfiles/cpreport.json') as f:
cpreport = json.load(f)
with open('testfiles/yt.json') as f:
integrated = json.load(f)
with open('testfiles/stdout.txt') as f:
stdout = f.read()
structure = Structure.from_file('testfiles/CONTCAR')
analyzer = Critic2Analysis(structure, cpreport=cpreport)
graph = analyzer.structure_graph()
```
Which produces the following error
```
Traceback (most recent call last):
File "/home/wladerer/github/crit/analysis.py", line 18, in <module>
graph = analyzer.structure_graph()
File "/home/wladerer/.venv/base/lib/python3.10/site-packages/pymatgen/command_line/critic2_caller.py", line 523, in structure_graph
"ellipticity": cp.ellipticity,
File "/home/wladerer/.venv/base/lib/python3.10/site-packages/pymatgen/command_line/critic2_caller.py", line 411, in ellipticity
eig, _ = np.linalg.eig(self.field_hessian)
File "/home/wladerer/.venv/base/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 1327, in eig
_assert_stacked_2d(a)
File "/home/wladerer/.venv/base/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 206, in _assert_stacked_2d
raise LinAlgError('%d-dimensional array given. Array must be '
numpy.linalg.LinAlgError: 1-dimensional array given. Array must be at least two-dimensional
```
And I think this could be fixed pretty quickly with `np.reshape((3, 3)` on
https://github.com/materialsproject/pymatgen/blob/633e7bd7700fc96b407d882cce2b473a38a97c67/src/pymatgen/command_line/critic2_caller.py#L660
Or just before it is being passed to the linear algebra routine.
I know this is a problem with the parser because parsing stdout seems to not throw an error when I get the graph.
## Issue 2
Another issue is that "charge_idx" is never found because it is looking for a key `$chg_int` that is not present in the JSON file. This leads to the following function never being able to update `charge_idx` for being None and then being handed off as an invalid index to a dictionary.
https://github.com/materialsproject/pymatgen/blob/633e7bd7700fc96b407d882cce2b473a38a97c67/src/pymatgen/command_line/critic2_caller.py#L711-L737
```
RROR:pymatgen.command_line.critic2_caller:Volume property: {'id': 1, 'label': 'Volume', 'field_name': 'Volume'}
ERROR:pymatgen.command_line.critic2_caller:Nonequiv idx: 1
ERROR:pymatgen.command_line.critic2_caller:Attractor: {'id': 1, 'cell_cp': '1', 'nonequivalent_cp': '1', 'name': 'K', 'atomic_number': '19', 'fractional_coordinates': [0.815939, 0.815939, 0.27806], 'integrals': [141.9672447299829, 17.726198335010356, -7.43067100813538]}
Traceback (most recent call last):
File "/home/wladerer/github/crit/analysis.py", line 17, in <module>
analyzer = Critic2Analysis(structure, cpreport=cpreport, yt=integrated)
File "/home/wladerer/.venv/base/lib/python3.10/site-packages/pymatgen/command_line/critic2_caller.py", line 486, in __init__
self.structure = self._annotate_structure_with_yt(yt, structure, zpsp)
File "/home/wladerer/.venv/base/lib/python3.10/site-packages/pymatgen/command_line/critic2_caller.py", line 745, in _annotate_structure_with_yt
volume, charge = get_volume_and_charge(site["nonequivalent_id"])
File "/home/wladerer/.venv/base/lib/python3.10/site-packages/pymatgen/command_line/critic2_caller.py", line 733, in get_volume_and_charge
attractor["integrals"][charge_idx],
TypeError: list indices must be integers or slices, not NoneType
```
I am some what sure that the new value is simply "Pop" instead of $chg_int but I will double check. The only reason why I am not certain is that if I replace this value with "Pop", then the I get an error that the sites in the structure and the sites in the json file do not match. I am unsure if they are related, but will do further testing.
### Proposed Solution
# Issue 1
Turn
https://github.com/materialsproject/pymatgen/blob/633e7bd7700fc96b407d882cce2b473a38a97c67/src/pymatgen/command_line/critic2_caller.py#L660
into
```python
field_hessian=np.array(p["hessian"]).reshape(3,3)
```
This works and gives valid output.
# Issue 2
Change
https://github.com/materialsproject/pymatgen/blob/633e7bd7700fc96b407d882cce2b473a38a97c67/src/pymatgen/command_line/critic2_caller.py#L718
to
```python
elif prop["label"] == "Pop":
```
I can test if these changes produce the same output as the stdout parser.
Thanks!
### Relevant Information
I haven't been able to find any tests for the JSON file parser, actually. I can run one of the calculations to produce the json file and have it cross reference the results in the other unit tests for both new and old stdout processing.
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PR_kwDOACgets53Mwrl
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Add VASP setting for the dftd4 vdW functional and extend PBE_64 support.
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[
"I've installed the dev and optional dependencies per the guidance [here](https://pymatgen.org/contributing.html). There were no problems with my local pre-commit and pytest checks. So, I don't know why the PR failed to pass some of the tests.",
"And, @hongyi-zhao , thank you!",
"There seems to be some conflicts that need to be resolved first.",
"@shyuep Done."
] | 2024-08-02T03:11:34
| 2024-08-24T08:18:49
|
2024-08-24T08:18:48Z
|
CONTRIBUTOR
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This is an enhancement and re-implementation of https://github.com/materialsproject/pymatgen/pull/3899 and the PRs suggested to include in it.
Add VASP setting for the dftd4 vdW functional and extend `PBE_64` support:
- Add `IVDW: 13` for dftd4 in `vdW_parameters.yaml`
- Support `PBE_64` functional in `MPScanRelaxSet`, `MVLRelax52Set`, `MVLScanRelaxSet`, and `LobsterSet`
- Update documentation and error messages to include `PBE_64`
- Add warning for `LobsterSet` when using `PBE_52` and `PBE_64` POTCARs with `PBE_54` basis functions
- Update relevant test cases to accommodate `PBE_64` support
|
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PR_kwDOACgets53TYUj
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Fix import sorting
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[] | 2024-08-02T21:55:10
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2024-08-02T21:57:38Z
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MEMBER
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fix the import sorting issue [affecting many PRs](https://github.com/materialsproject/pymatgen/pull/3876#issuecomment-2248527074) after 9100860d7d didn't ensure [`pymatgen` is recognized as a first-party package](https://docs.astral.sh/ruff/settings/#lint_isort_known-first-party)
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I_kwDOACgets6RyImU
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TestStructureGraph.test_draw TypeError: unhashable type: 'list'
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[
"Thanks for reporting this. I might help fix this, but more importantly I should push #3786 a bit :)",
"I think it might need to be replaced with\r\n```\r\npdfs = {path.split(\"/\")[-1] for path in glob(f\"{self.tmp_path}/*.pdf\")}\r\n```\r\ncontrolling handling of the split output",
"Please open a PR if you would like to, and I would try to keep up and enable CI test with `pygraphviz` :)",
"I've created PR #3972 for it."
] | 2024-08-02T22:29:45
| 2024-08-05T11:18:45
|
2024-08-05T11:18:45Z
|
CONTRIBUTOR
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There is an error in python3.12 in the analysis test_graph at
https://github.com/materialsproject/pymatgen/blob/940eb60cbc2848530b2560f75d56298a3c3f714c/tests/analysis/test_graphs.py#L376C9-L376C76
Output running tests is
```py
_________________________ TestStructureGraph.test_draw _________________________
self = <tests.analysis.test_graphs.TestStructureGraph testMethod=test_draw>
@pytest.mark.skipif(
pygraphviz is None or not (which("neato") and which("fdp")),
reason="graphviz executables not present",
)
def test_draw(self):
# draw MoS2 graph
self.mos2_sg.draw_graph_to_file(f"{self.tmp_path}/MoS2_single.pdf", image_labels=True, hide_image_edges=False)
mos2_sg = self.mos2_sg * (9, 9, 1)
mos2_sg.draw_graph_to_file(f"{self.tmp_path}/MoS2.pdf", algo="neato")
# draw MoS2 graph that's been successively multiplied
mos2_sg_2 = self.mos2_sg * (3, 3, 1)
mos2_sg_2 = mos2_sg_2 * (3, 3, 1)
mos2_sg_2.draw_graph_to_file(f"{self.tmp_path}/MoS2_twice_mul.pdf", algo="neato", hide_image_edges=True)
# draw MoS2 graph that's generated from a pre-multiplied Structure
mos2_sg_premul = StructureGraph.from_local_env_strategy(self.structure * (3, 3, 1), MinimumDistanceNN())
mos2_sg_premul.draw_graph_to_file(f"{self.tmp_path}/MoS2_premul.pdf", algo="neato", hide_image_edges=True)
# draw graph for a square lattice
self.square_sg.draw_graph_to_file(f"{self.tmp_path}/square_single.pdf", hide_image_edges=False)
square_sg = self.square_sg * (5, 5, 1)
square_sg.draw_graph_to_file(f"{self.tmp_path}/square.pdf", algo="neato", image_labels=True, node_labels=False)
# draw graph for a body-centered square lattice
self.bc_square_sg.draw_graph_to_file(f"{self.tmp_path}/bc_square_single.pdf", hide_image_edges=False)
bc_square_sg = self.bc_square_sg * (9, 9, 1)
bc_square_sg.draw_graph_to_file(f"{self.tmp_path}/bc_square.pdf", algo="neato", image_labels=False)
# draw graph for a body-centered square lattice defined in an alternative way
self.bc_square_sg_r.draw_graph_to_file(f"{self.tmp_path}/bc_square_r_single.pdf", hide_image_edges=False)
bc_square_sg_r = self.bc_square_sg_r * (9, 9, 1)
bc_square_sg_r.draw_graph_to_file(f"{self.tmp_path}/bc_square_r.pdf", algo="neato", image_labels=False)
# ensure PDF files were created
> pdfs = {path.split("/") for path in glob(f"{self.tmp_path}/*.pdf")}
E TypeError: unhashable type: 'list'
/build/pymatgen/.pybuild/test_python3.12/tests/analysis/test_graphs.py:376: TypeError
```
But the error is trivial to reproduce (if there are pdf files in the directory):
```py
$ touch 1.pdf 2.pdf
$ python3 -c 'from glob import glob; pdfs = {path.split("/") for path in glob("./*.pdf")}; print(pdfs)'
Traceback (most recent call last):
File "<string>", line 1, in <module>
TypeError: unhashable type: 'list'
```
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PR_kwDOACgets53U-xg
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|
Dedup `numpy`dependency in `pyproject`
|
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[
"All good! Can you leave this to me? :) https://github.com/materialsproject/pymatgen/blob/380a81bada34f3e38636f5edf9cdc19154633e99/pyproject.toml#L218",
"And no pressure of course, just a gentle reminder that there are still a few typing PRs (starting from #3873, the others are branched from this) that is waiting for review :) Sorry there are all pretty big PRs, so if you prefer to have some rest during the weekend that's totally alright. Thanks!",
"> starting from https://github.com/materialsproject/pymatgen/pull/3873\r\n\r\nsorry for the wait, those PRs had dropped off my radar"
] | 2024-08-03T11:08:11
| 2024-08-03T13:47:24
|
2024-08-03T11:19:36Z
|
MEMBER
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thanks @DanielYang59 👍
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Problem parsing some cif files?
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[
"Not so much a bug as providing misinformation or unnecessary warning. Sorry about the mislabeling.",
"@cajfisher Thank you for reporting this. Could you check a newer version of pymatgen and see if this problem still persists? (We had this pull request recently: https://github.com/materialsproject/pymatgen/pull/3628)",
"Pull request #3628 appears to have dealt with this issue already. The latest version gives the following warning:\r\nio\\cif.py:1285: UserWarning: Issues encountered while parsing CIF: Skipping relative stoichiometry check because CIF does not contain formula keys.\r\n warnings.warn(\"Issues encountered while parsing CIF: \" + \"\\n\".join(self.warnings))\r\n\r\nThis makes more sense.\r\nSorry for the repetition. I'll make sure to run tests on the most up-to-date version next time.",
"@cajfisher I will close this then"
] | 2024-08-04T05:41:18
| 2024-08-05T13:04:51
|
2024-08-05T13:04:51Z
|
CONTRIBUTOR
|
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### Python version
Python 3.11.5
### Pymatgen version
2024.2.8
### Operating system version
Windows 11
### Current behavior
The cif file below produces a "non-stoichiometric" error:
io/cif.py:1134: UserWarning: Incorrect stoichiometry:
CIF={'O': 5.0, 'Si': 2.0}
PMG={'Si': 12.0, 'O': 24.0}
ratios={'Si': 6.0, 'O': 4.8}
warnings.warn(cif_failure_reason)
### Expected Behavior
Different Wyckoff sites can have different multiplicities, so I don't think simply taking the ratio between number of total sites and number of Wyckoff sites is a good indicator of stoichiometry. Please correct me if I am wrong.
### Minimal example
```Python
parser = CifParser('MVY.cif', occupancy_tolerance=1.0, site_tolerance=0.00005)
```
### Relevant files to reproduce this bug
data_MVY
_cell_length_a 5.0210(0)
_cell_length_b 8.1510(0)
_cell_length_c 13.9770(0)
_cell_angle_alpha 90.0000(0)
_cell_angle_beta 90.0000(0)
_cell_angle_gamma 90.0000(0)
_symmetry_space_group_name_H-M 'P n n m'
_symmetry_Int_Tables_number 58
_symmetry_cell_setting orthorhombic
loop_
_symmetry_equiv_pos_as_xyz
'+x,+y,+z'
'-x,-y,+z'
'1/2-x,1/2+y,1/2-z'
'1/2+x,1/2-y,1/2-z'
'-x,-y,-z'
'+x,+y,-z'
'1/2+x,1/2-y,1/2+z'
'1/2-x,1/2+y,1/2+z'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
O1 O 0.1370 0.2998 0.2713
O2 O 0.2777 0.2676 0.0952
O3 O 0.5000 0.5000 0.1981
O4 O 0.0000 0.0000 0.5000
O5 O 0.5000 0.0000 0.5000
T1 Si 0.3882 0.3151 0.2000
T3 Si 0.2501 0.8772 0.5000
|
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PR_kwDOACgets53aUlj
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test_graph: add filename only to pdf list
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[
"Thanks for the fix. I'm still looking into the issue, as I just installed `pygraphviz` in CI and I was having a different error for that particular test for some reason (both in CI and locally) https://github.com/materialsproject/pymatgen/actions/runs/10246364887/job/28343300325?pr=3786.\r\n\r\n**Update**: Issued fixed in c67abbc6678ebeee6a324440570aa38cc0c66adb and your reported issue recreated successfully. Also I believe your proposed fix is correct. Thanks!"
] | 2024-08-05T08:10:14
| 2024-08-05T11:18:44
|
2024-08-05T11:18:44Z
|
CONTRIBUTOR
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The pdfs list must be constructed from filenames only without other path components, i.e. use last entry from split()
## Summary
Major changes:
- fix: fix list of pdf files in test_draw (test_graph)
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [x ] Tests added for new features/fixes (test already present).
Closes: #3969
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I_kwDOACgets6R6RNV
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Function _semicircle_integral in class CrystalNN gives unwanted results
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[
"thanks @nisse3000 for the detailed issue and for your PR! 👍 not my area of expertise but i'll review the code and wait for @mkhorton to weigh on the discrepancy between quadrant and semicircle functions",
"Hi all,\r\n\r\nThanks for your work in this PR. Do we have a sense for whether the new function (which is now the default with no option to change to the old function as far as I can tell) gives *better* results than the old function? At the end of the day, users will just want to use the scheme that provides more accurate results, especially sine the scheme is more or less just invented without much theoretical basis. Since I believe we benchmarked the coordination scheme using the old (and \"incorrect\") function, I fear that users may actually be less satisfied with the more correct function.\r\n\r\n@nisse3000 do you have a sense for how the \"reasonableness\" of the coordination numbers produced by CrystalNN change with this update?"
] | 2024-08-05T08:44:53
| 2024-09-10T19:55:01
|
CONTRIBUTOR
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### Python version
Python 3.11.5
### Pymatgen version
2024.7.18
### Operating system version
_No response_
### Current behavior
Thanks to Dr. Wagner from MPI for Chemical Physics of Solids in Dresden I became aware of the issue that the function _semicircle_integral in class CrystalNN does not correctly calculate the normalized areas of circular segments of a unit quadrant. Dr. Wagner discovered the issue by trying to reproduce results for coordination probabilities of BCC sites that were published in Reference 1. Therefore, such sites will be used in the following to illustrate the problem.
As described in References 1 und 2, CrystalNN determines coordination probabilities by projecting weights from Voronoi neighbor finding (normalized solid angles) onto a unit quadrant in descending order. The probability of coordination number CN is then determined as the area of the quadrant segment between the weight of CN and the weight of the next larger CN in the set. For BCC, this means, for example, that the probability of a coordination number of eight (nearest neighbors) is determined as the segment between the weight of CN=8 and the weight associated with CN=14 (next-nearest neighbors). Finally, the resulting area is normalized by the area of the unit quadrant (pi/4).
The current _semicircle_integral yields a probability of p(CN=8)=0.55, whereas it should be 0.76 using the Voronoi weights of 1 for nearest neighbors and 0.36 for next-nearest neighbors. The normalized weight of the next-nearest neighbors was already published by O'Keeffe in Acta Cryst., 1979, and agrees with VoronoiNN results from pymatgen.
Using the formula from https://en.wikipedia.org/wiki/Circular_segment for the area of a circular segment, rearranging the expression under the square root to "2Rh - h**2", and then dividing the entire expression by two to account for the fact that we are aiming for a quadrant I obtain the value of 0.76 (see Figure below), which Dr. Wagner also indicated.
When I systematically compare the results for two sets of neighbors (nearest and next-nearest neighbors) with varying weight for the next-nearest neighbors (the weight of nearest neighbors is always 1), I get the curves displayed in the Figure above. The currently implemented method thus gives consistently lower coordination probabilities than results with the quadrant area function that should be mathematically correct.
---
References
[1] Local structure order parameters and site fingerprints for quantification of coordination environment and crystal structure similarity; Zimmermann, Jain, RSC Advances, 10, 6063-6081, 2020
[2] Benchmarking coordination number prediction algorithms on inorganic crystal structures; Pan, Ganose, Horton, Aykol, Persson, Zimmermann, Jain, Inorganic Chemistry, 60, 1590-1603, 2021
### Expected Behavior
I expected the semicircle function to calculate circular segments of a unit quadrant, which it apparently did not do correctly.
### Minimal example
```Python
import math
def semicircle_integral(dist_bins, idx):
radius = 1
x1 = dist_bins[idx]
x2 = dist_bins[idx + 1]
if dist_bins[idx] == 1:
area1 = 0.25 * math.pi * radius**2
else:
area1 = 0.5 * (
(x1 * math.sqrt(radius**2 - x1**2)) + (radius**2 * math.atan(x1 / math.sqrt(radius**2 - x1**2)))
)
area2 = 0.5 * ((x2 * math.sqrt(radius**2 - x2**2)) + (radius**2 * math.atan(x2 / math.sqrt(radius**2 - x2**2))))
return (area1 - area2) / (0.25 * math.pi * radius**2)
def quadrant_integral(dist_bins, idx):
radius = 1
x1 = dist_bins[idx]
x2 = dist_bins[idx + 1]
areaquarter = 0.25 * math.pi * radius**2
area1 = areaquarter - 0.5 * (radius**2 * math.acos(1.0 - x1 / radius) - (radius - x1) * math.sqrt(2.0 * radius * x1 - x1**2))
area2 = areaquarter - 0.5 * (radius**2 * math.acos(1.0 - x2 / radius) - (radius - x2) * math.sqrt(2.0 * radius * x2 - x2**2))
return (area2 - area1) / areaquarter
for i in range(1, 500):
x = 1.0 - float(i) / 500.0
print(i, x, quadrant_integral([1, x], 0), semicircle_integral([1, x], 0))
```
### Relevant files to reproduce this bug
_No response_
|
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Added _quadrant_integral function in CrystalNN
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[] | 2024-08-05T08:46:06
| 2025-04-15T16:22:14
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CONTRIBUTOR
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Addresses [Issue #3973](https://github.com/materialsproject/pymatgen/issues/3973)
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Bug in NearNeighbors Class
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[
"This is not how you use NearestNeighbor. You are supposed to use one of the other analysis tools to get a NearestNeighbor object. This is not a bug. Please refer to the documentation and python tutorial on how such classes work."
] | 2024-08-05T23:20:54
| 2024-08-05T23:27:51
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2024-08-05T23:27:51Z
|
NONE
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### Python version
3.11.2
### Pymatgen version
2024.4.13
### Operating system version
MacOS Ventura 13.5.1 (22G90)
### Current behavior
When using the NearNeighbors class functions like get_nn_info(), get_all_nn_info(), and get_nn_shell_info(), the function is unable to read all the input parameters.
For example, when using _NearNeighbors.get_nn_shell_info(mystructure, 0, 1)_, error reports that "NearNeighbors.get_nn_shell_info() missing 1 required positional argument: 'shell'".
A similar error occurs for other functions, instead of not being able to receive the argument for "shell", they cannot receive the argument for an integer n, which is the last argument.
### Expected Behavior
get_nn_shell_info() should return a list of dictionaries. Each entry in the list is information about a certain neighbor in the structure.
### Minimal example
```Python
from pymatgen.core import Lattice, Structure, Element
from pymatgen.analysis.local_env import NearNeighbors
# Define the lattice parameters for NaCl (a = 5.64 Å)
a = 5.64
lattice = Lattice.cubic(a)
# Define the atomic positions for NaCl
# Na at (0, 0, 0), Cl at (0.5, 0.5, 0.5) in fractional coordinates
structure = Structure(
lattice,
["Na", "Cl"], # Species
[[0, 0, 0], [0.5, 0.5, 0.5]] # Fractional coordinates
)
print(structure)
#use argument 0 for the index site: the Na site, argument 1 for the first neighbor shell
NearNeighbors.get_nn_shell_info(structure,0,1)
```
### Relevant files to reproduce this bug
<img width="307" alt="Screenshot 2024-08-05 at 4 19 59 PM" src="https://github.com/user-attachments/assets/46a3fcf8-ddce-431c-a96c-f2b62b94aceb">
<img width="677" alt="Screenshot 2024-08-05 at 4 19 44 PM" src="https://github.com/user-attachments/assets/cb074a84-58ad-4a2a-bb4e-b7bbb27d587e">
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I_kwDOACgets6SW3Cn
| 3,976
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Some type annotations errors when trying to merge master into my local development branch.
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[
"I could probably give a hand on this, but it's really hard for me to say anything useful just from those code pieces. Can you perhaps provide the link to the branch in question?",
"i see the same errors by running `pre-commit run --all-files` on the `master` branch. you might have to set `entry: env MYPYPATH=src mypy` on the `mypy` hook for it to work at all",
"I could confirm I'm seeing (even more) `mypy` errors on the master branch, I would fix them now.\r\n```\r\nmypy.....................................................................Failed\r\n- hook id: mypy\r\n- exit code: 1\r\n\r\nsrc/pymatgen/symmetry/analyzer.py:1543: error: Incompatible types in assignment (expression has type \"Collection[Any]\", variable has type \"Molecule\") [assignment]\r\nsrc/pymatgen/entries/compatibility.py:558: error: Incompatible types in assignment (expression has type \"ComputedEntry | None\", variable has type \"ComputedEntry\") [assignment]\r\nsrc/pymatgen/entries/compatibility.py:614: error: Incompatible return value type (got \"tuple[ComputedEntry | ComputedStructureEntry, bool]\", expected \"ComputedEntry | None\") [return-value]\r\nsrc/pymatgen/entries/compatibility.py:1536: error: List item 0 has incompatible type \"Any | list[ComputedEntry | ComputedStructureEntry]\"; expected \"ComputedEntry\" [list-item]\r\nsrc/pymatgen/io/packmol.py:216: error: Item \"None\" of \"Molecule | None\" has no attribute \"to\" [union-attr]\r\nsrc/pymatgen/analysis/structure_prediction/substitution_probability.py:106: error: Invalid index type \"Element | Species\" for \"dict[Species, float]\"; expected type \"Species\" [index]\r\nsrc/pymatgen/io/cp2k/inputs.py:2045: error: Argument \"mesh\" to \"get_ir_reciprocal_mesh\" of \"SpacegroupAnalyzer\" has incompatible type \"Sequence[tuple[float, float, float] | tuple[int]]\"; expected \"tuple[int, int, int]\" [arg-type]\r\nsrc/pymatgen/io/cp2k/inputs.py:2045: note: Error code \"arg-type\" not covered by \"type: ignore\" comment\r\nsrc/pymatgen/entries/mixing_scheme.py:117: error: Signature of \"process_entries\" incompatible with supertype \"Compatibility\" [override]\r\nsrc/pymatgen/entries/mixing_scheme.py:117: note: Superclass:\r\nsrc/pymatgen/entries/mixing_scheme.py:117: note: def process_entries(self, entries: ComputedEntry | ComputedStructureEntry | list[ComputedEntry | ComputedStructureEntry], clean: bool = ..., verbose: bool = ..., inplace: bool = ..., n_workers: int = ..., on_error: Literal['ignore', 'warn', 'raise'] = ...) -> list[ComputedEntry | ComputedStructureEntry]\r\nsrc/pymatgen/entries/mixing_scheme.py:117: note: Subclass:\r\nsrc/pymatgen/entries/mixing_scheme.py:117: note: def process_entries(self, entries: ComputedEntry | ComputedStructureEntry | list[ComputedEntry | ComputedStructureEntry], clean: bool = ..., verbose: bool = ..., inplace: bool = ..., mixing_state_data: Any = ...) -> list[ComputedEntry | ComputedStructureEntry]\r\nsrc/pymatgen/transformations/site_transformations.py:319: error: Argument 1 to \"are_symmetrically_equivalent\" of \"SpacegroupOperations\" has incompatible type \"list[PeriodicSite]\"; expected \"set[PeriodicSite]\" [arg-type]\r\nsrc/pymatgen/transformations/site_transformations.py:319: error: Argument 2 to \"are_symmetrically_equivalent\" of \"SpacegroupOperations\" has incompatible type \"list[PeriodicSite]\"; expected \"set[PeriodicSite]\" [arg-type]\r\nFound 10 errors in 7 files (checked 560 source files)\r\n```\r\n\r\n@janosh There're only 6 errors on your side?",
"1. I'm on my local development branch and trying to merge the upstream master branch.\r\n2. `entry: env MYPYPATH=src mypy` has already been on the mypy hook:\r\n\r\n```yaml\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ grep -A1 -B4 env .pre-commit-config.yaml \r\n - repo: https://github.com/pre-commit/mirrors-mypy\r\n rev: v1.11.1\r\n hooks:\r\n - id: mypy\r\n entry: env MYPYPATH=src mypy\r\n```\r\n3. Now, I check out to the pymatgen official master branch, and retest as follows:\r\n\r\n```shell\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ git rev-parse --abbrev-ref `git status | head -1 | awk '{print $NF}'`@{upstream}\r\nupstream/master\r\n\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ git remote get-url upstream\r\nhttps://github.com/materialsproject/pymatgen.git\r\n\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ pre-commit run --all-files\r\nruff.....................................................................Passed\r\nruff-format..............................................................Passed\r\ncheck yaml...............................................................Passed\r\nfix end of files.........................................................Passed\r\ntrim trailing whitespace.................................................Passed\r\nmypy.....................................................................Failed\r\n- hook id: mypy\r\n- exit code: 1\r\n\r\nsrc/pymatgen/symmetry/analyzer.py:1543: error: Incompatible types in assignment (expression has type \"Collection[Any]\", variable has type \"Molecule\") [assignment]\r\nsrc/pymatgen/entries/compatibility.py:558: error: Incompatible types in assignment (expression has type \"ComputedEntry | None\", variable has type \"ComputedEntry\") [assignment]\r\nsrc/pymatgen/entries/compatibility.py:614: error: Incompatible return value type (got \"tuple[ComputedEntry | ComputedStructureEntry, bool]\", expected \"ComputedEntry | None\") [return-value]\r\nsrc/pymatgen/entries/compatibility.py:1536: error: List item 0 has incompatible type \"Any | list[ComputedEntry | ComputedStructureEntry]\"; expected \"ComputedEntry\" [list-item]\r\nsrc/pymatgen/io/packmol.py:216: error: Item \"None\" of \"Molecule | None\" has no attribute \"to\" [union-attr]\r\nsrc/pymatgen/analysis/structure_prediction/substitution_probability.py:106: error: Invalid index type \"Element | Species\" for \"dict[Species, float]\"; expected type \"Species\" [index]\r\nsrc/pymatgen/io/cp2k/inputs.py:2045: error: Argument \"mesh\" to \"get_ir_reciprocal_mesh\" of \"SpacegroupAnalyzer\" has incompatible type \"Sequence[tuple[float, float, float] | tuple[int]]\"; expected \"tuple[int, int, int]\" [arg-type]\r\nsrc/pymatgen/io/cp2k/inputs.py:2045: note: Error code \"arg-type\" not covered by \"type: ignore\" comment\r\nsrc/pymatgen/entries/mixing_scheme.py:117: error: Signature of \"process_entries\" incompatible with supertype \"Compatibility\" [override]\r\nsrc/pymatgen/entries/mixing_scheme.py:117: note: Superclass:\r\nsrc/pymatgen/entries/mixing_scheme.py:117: note: def process_entries(self, entries: ComputedEntry | ComputedStructureEntry | list[ComputedEntry | ComputedStructureEntry], clean: bool = ..., verbose: bool = ..., inplace: bool = ..., n_workers: int = ..., on_error: Literal['ignore', 'warn', 'raise'] = ...) -> list[ComputedEntry | ComputedStructureEntry]\r\nsrc/pymatgen/entries/mixing_scheme.py:117: note: Subclass:\r\nsrc/pymatgen/entries/mixing_scheme.py:117: note: def process_entries(self, entries: ComputedEntry | ComputedStructureEntry | list[ComputedEntry | ComputedStructureEntry], clean: bool = ..., verbose: bool = ..., inplace: bool = ..., mixing_state_data: Any = ...) -> list[ComputedEntry | ComputedStructureEntry]\r\nsrc/pymatgen/transformations/site_transformations.py:319: error: Argument 1 to \"are_symmetrically_equivalent\" of \"SpacegroupOperations\" has incompatible type \"list[PeriodicSite]\"; expected \"set[PeriodicSite]\" [arg-type]\r\nsrc/pymatgen/transformations/site_transformations.py:319: error: Argument 2 to \"are_symmetrically_equivalent\" of \"SpacegroupOperations\" has incompatible type \"list[PeriodicSite]\"; expected \"set[PeriodicSite]\" [arg-type]\r\nFound 10 errors in 7 files (checked 560 source files)\r\n\r\ncodespell................................................................Passed\r\ncython-lint..............................................................Passed\r\ndouble-quote Cython strings..............................................Passed\r\nblacken-docs.............................................................Passed\r\nmarkdownlint.............................................................Passed\r\nnbstripout...............................................................Passed\r\npyright..................................................................Passed\r\n```",
"Looks like we're getting the same errors, and thanks a lot for reporting. I would fix them soon.",
"There are still the following errors:\r\n\r\n```shell\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ git log -1\r\ncommit 45b9facc0ea124691c08bf51d99c45fced367719 (HEAD -> upstream-master, tag: v2024.8.8, upstream/master)\r\nAuthor: Janosh Riebesell <janosh.riebesell@gmail.com>\r\nDate: Thu Aug 8 20:14:41 2024 -0400\r\n\r\n v2024.8.8\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ PIP_PROXY='' proxychains-ng-country-control pre-commit run --all-files\r\nruff.....................................................................Passed\r\nruff-format..............................................................Passed\r\ncheck yaml...............................................................Passed\r\nfix end of files.........................................................Passed\r\ntrim trailing whitespace.................................................Passed\r\nmypy.....................................................................Failed\r\n- hook id: mypy\r\n- exit code: 1\r\n\r\nsrc/pymatgen/io/cp2k/inputs.py:2045: error: Argument \"mesh\" to \"get_ir_reciprocal_mesh\" of \"SpacegroupAnalyzer\" has incompatible type \"Sequence[tuple[float, float, float] | tuple[int]]\"; expected \"tuple[int, int, int]\" [arg-type]\r\nsrc/pymatgen/io/cp2k/inputs.py:2045: note: Error code \"arg-type\" not covered by \"type: ignore\" comment\r\nsrc/pymatgen/transformations/advanced_transformations.py:806: error: Signature of \"apply_transformation\" incompatible with supertype \"AbstractTransformation\" [override]\r\nsrc/pymatgen/transformations/advanced_transformations.py:806: note: Superclass:\r\nsrc/pymatgen/transformations/advanced_transformations.py:806: note: def apply_transformation(self, structure: Structure) -> Structure | list[dict[str, Any]]\r\nsrc/pymatgen/transformations/advanced_transformations.py:806: note: Subclass:\r\nsrc/pymatgen/transformations/advanced_transformations.py:806: note: def apply_transformation(self, structure: Structure, return_ranked_list: bool | int = ...) -> Structure | list[Structure]\r\nFound 2 errors in 2 files (checked 560 source files)\r\n\r\ncodespell................................................................Passed\r\ncython-lint..............................................................Passed\r\ndouble-quote Cython strings..............................................Passed\r\nblacken-docs.............................................................Passed\r\nmarkdownlint.............................................................Passed\r\nnbstripout...............................................................Passed\r\npyright..................................................................Passed\r\n```",
"Yes indeed, I haven't got a chance to fix this yet :) Would do that now. Thanks!",
"Up to https://github.com/materialsproject/pymatgen/commit/1bfd330dcdc93c733fcb6d3ec7542dbc8f310bac, I confirm that the issue has been resolved now:\r\n\r\n```shell\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ git log -1\r\ncommit 1bfd330dcdc93c733fcb6d3ec7542dbc8f310bac (HEAD -> upstream-master, upstream/master)\r\nAuthor: Shyue Ping Ong <shyuep@gmail.com>\r\nDate: Fri Aug 9 10:24:10 2024 -0700\r\n\r\n Update tasks.py formatting of desc.\r\n\r\n(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ pre-commit run --all-files\r\nruff.....................................................................Passed\r\nruff-format..............................................................Passed\r\ncheck yaml...............................................................Passed\r\nfix end of files.........................................................Passed\r\ntrim trailing whitespace.................................................Passed\r\nmypy.....................................................................Passed\r\ncodespell................................................................Passed\r\ncython-lint..............................................................Passed\r\ndouble-quote Cython strings..............................................Passed\r\nblacken-docs.............................................................Passed\r\nmarkdownlint.............................................................Passed\r\nnbstripout...............................................................Passed\r\npyright..................................................................Passed\r\n```",
"Thanks a lot for the conformation and for reporting! Happy coding! @hongyi-zhao "
] | 2024-08-08T10:40:08
| 2024-08-10T01:16:29
|
2024-08-09T00:07:55Z
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CONTRIBUTOR
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Today, I tried to merge pymatgen master into my local development branch, but met the following type annotations errors:
```shell
(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ git commit -am 'merge master'
[INFO] Checking merge-conflict files only.
ruff.....................................................................Passed
ruff-format..............................................................Passed
check yaml...........................................(no files to check)Skipped
fix end of files.........................................................Passed
trim trailing whitespace.................................................Passed
mypy.....................................................................Failed
- hook id: mypy
- exit code: 1
src/pymatgen/symmetry/analyzer.py:1543: error: Incompatible types in assignment (expression has type "Collection[Any]", variable has type "Molecule") [assignment]
src/pymatgen/io/vasp/sets.py:833: error: Argument 1 to "get_ir_reciprocal_mesh" of "SpacegroupAnalyzer" has incompatible type "tuple[float, float, float] | tuple[int]"; expected "tuple[int, int, int]" [arg-type]
src/pymatgen/io/vasp/sets.py:867: error: Argument 1 to "get_ir_reciprocal_mesh" of "SpacegroupAnalyzer" has incompatible type "tuple[float, float, float] | tuple[int]"; expected "tuple[int, int, int]" [arg-type]
src/pymatgen/entries/compatibility.py:558: error: Incompatible types in assignment (expression has type "ComputedEntry | None", variable has type "ComputedEntry") [assignment]
src/pymatgen/entries/compatibility.py:614: error: Incompatible return value type (got "tuple[ComputedEntry | ComputedStructureEntry, bool]", expected "ComputedEntry | None") [return-value]
src/pymatgen/entries/compatibility.py:1536: error: List item 0 has incompatible type "Any | list[ComputedEntry | ComputedStructureEntry]"; expected "ComputedEntry" [list-item]
Found 6 errors in 3 files (checked 2 source files)
codespell................................................................Passed
cython-lint..........................................(no files to check)Skipped
double-quote Cython strings..........................(no files to check)Skipped
blacken-docs.............................................................Passed
markdownlint.........................................(no files to check)Skipped
nbstripout...........................................(no files to check)Skipped
pyright..................................................................Passed
```
The corresponding problematic code lines are shown below:
```python
werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ sed -n '1543p' src/pymatgen/symmetry/analyzer.py
new = eq["sym_mol"]
werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ sed -n '833p;867p' src/pymatgen/io/vasp/sets.py
mesh = sga.get_ir_reciprocal_mesh(base_kpoints.kpts[0])
mesh = sga.get_ir_reciprocal_mesh(zero_weighted_kpoints.kpts[0])
werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ sed -n '558p;614p;1536p' src/pymatgen/entries/compatibility.py
entry = self._process_entry_inplace(entry, **kwargs)
return entry, ignore_entry
return [entries]
```
I tried some possible modifications, but none of them could pass the pre-commit check. I would be very grateful if you have any suggestions for fixes.
Regards,
Zhao
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| 2,455,614,855
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PR_kwDOACgets53094Q
| 3,977
|
Fix `mypy` errors on master branch
|
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[
"Thanks for reviewing. There was one type error for `io.cp2k` I haven't got to fix, isn't it failing on your side?"
] | 2024-08-08T11:59:11
| 2024-08-09T21:11:29
|
2024-08-09T00:07:54Z
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CONTRIBUTOR
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### Summary
- Fix `mypy` errors on master branch, to fix #3976
- Docstring tweaks
|
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PR_kwDOACgets532T3H
| 3,978
|
Check Inputs to Trajectory.
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[] | 2024-08-08T14:46:46
| 2024-08-08T15:33:57
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2024-08-08T15:30:24Z
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CONTRIBUTOR
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## Summary
Checks the inputs to Trajectory following an issue encountered where `get_positions()` method can return more positions than sites depending on filters.
## 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))
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PR_kwDOACgets532u5_
| 3,979
|
Assign frame properties to molecule/structure when indexing trajectory
|
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[] | 2024-08-08T15:43:32
| 2024-08-08T23:33:32
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2024-08-08T23:33:17Z
|
CONTRIBUTOR
|
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## Summary
When indexing a trajectory the site properties would be assigned to the structure/molecule but the frame properties would not be propagated down to the structure/molecule in question.
## 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))
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I_kwDOACgets6SZsMx
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|
Cannot reproduce Materials Project energy for ZnCu (mp-987)
|
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[] | 2024-08-08T16:32:44
| 2024-08-09T00:00:29
|
2024-08-09T00:00:29Z
|
NONE
|
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Hi there!
During calculations on a ZnCu structure from the Materials Project (mp-987), I noticed that I cannot reproduce the energies provided on their website, despite using parameters from MPRelaxSet in pymatgen. The energies obtained from VASP relaxations lie approx. 500 meV (i.e. ~250 meV/atom) above the reported entries in Materials Project.
For the calculations, I used the ZnCu structure directly downloaded from MP (see POSCAR). Then, I prepared the other input files using MPRelaxSet from pymatgen.io.vasp, see INCAR, KPOINTS, POTCAR, and create_vasp_input.py files attached. (This step has been tested with pymatgen versions 2022.9.8 and 2024.4.13 and yields identical files.) Finally, I obtain a VASP energy of -5.025 eV (i.e. -2.513 eV/atom), see OUTCAR or vasprun.xml attached, whereas MP reports -5.54 eV (i.e. -2.77 eV/atom).
I have asked several colleagues to reproduce this result and all calculations end up at around the same values ranging from -5.00 eV to -5.05 eV, even with varying k-point grids, different initial magnetic moments, different VASP versions, or even different pseudopotentials. Furthermore, I confirmed that I used exactly the same POTCAR versions as in the original Materials Project relaxation (PAW_PBE Zn from 06Sep2000 & PAW_PBE Cu_pv from 06Sep2000).
Could you please validate these observations or point me towards potential sources of error in this workflow?
Thanks in advance for your help and feel free to reach out, should you require more details!
Greetings,
Konstantin
[ZnCu_MP.tar.gz](https://github.com/user-attachments/files/16550883/ZnCu_MP.tar.gz)
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PR_kwDOACgets535BSG
| 3,981
|
Fix 98 cases of `ruff` `PLR6104`
|
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[
"closing as even more breaking auto-\"fixes\" than expected 😅 "
] | 2024-08-08T23:21:00
| 2024-09-08T21:17:48
|
2024-08-08T23:30:30Z
|
MEMBER
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`ruff check --preview --fix --select PLR6104 --unsafe-fixes`
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I_kwDOACgets6Scmp6
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|
Bug in pymatgen.analysis.reaction_calculator.ComputedReaction
|
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[] | 2024-08-09T02:28:28
| 2024-08-09T02:28:28
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NONE
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### Python version
Python 3.10.6
### Pymatgen version
2024.8.8
### Operating system version
Windows
### Current behavior
```
rxn: 12 LiCuS -> Cu + Cu7S4 + 4 Li3CuS2
rxn_e: 0.003
reactants: ['H2O', 'LiCuS']
products: ['H2S', 'Cu', 'Cu7S4', 'Li3CuS2']
--------------after normalization to H2O---------------
rxn: 6e+15 LiCuS + 1.489 H2S -> H2O + 5e+14 Cu + 5e+14 Cu7S4 + 2e+15 Li3CuS2
rxn_e: 1499976386498.000
reactants: ['H2O', 'LiCuS']
products: ['H2S', 'Cu', 'Cu7S4', 'Li3CuS2']
version of pymatgen: 2024.8.8
```
When I take Cu, Cu7S4, and Li3CuS2 as the products of the hydrolysis reaction of LiCuS, it reports a decomposition from LiCuS to Cu, Cu7S4, and Li3CuS2. However, the H2O and H2S are also listed in reactant and product entries, respectively. Moreover, when I normalize the decomposition to H2O or H2S, it reports a wrong hydrolysis reaction with strange stoichiometric numbers.
### Expected Behavior
The reaction with imbalanced reactant and product entries is expected to be reported as None. And I wonder why the error normalization occured.
### Minimal example
```Python
from pymatgen.analysis.reaction_calculator import ComputedReaction
from pymatgen.entries.computed_entries import ComputedEntry
from pymatgen.core import Composition
from pymatgen import core
entry_h2o = ComputedEntry(Composition("H2O"), -3.440)
entry_h2s = ComputedEntry(Composition("H2S"), -1.049)
entry_licus = ComputedEntry(Composition("LiCuS"), -2.592)
entry_cu = ComputedEntry(Composition("Cu"), 0.0)
entry_cu7s4 = ComputedEntry(Composition("Cu7S4"), -2.541)
entry_li3cus2 = ComputedEntry(Composition("Li3CuS2"), -7.14)
reactants = [entry_h2o, entry_licus]
products = [entry_h2s, entry_cu, entry_cu7s4, entry_li3cus2]
rxn = ComputedReaction(reactants, products)
print(f"rxn: {rxn}")
print(f"rxn_e: {rxn.calculated_reaction_energy:.3f}")
print(f"reactants: {[e.name for e in rxn._reactant_entries]}")
print(f"products: {[e.name for e in rxn._product_entries]}")
print("--------------after normalization to H2O---------------")
rxn.normalize_to(entry_h2o.composition, 1.0)
print(f"rxn: {rxn}")
print(f"rxn_e: {rxn.calculated_reaction_energy:.3f}")
print(f"reactants: {[e.name for e in rxn._reactant_entries]}")
print(f"products: {[e.name for e in rxn._product_entries]}")
print()
print(f"version of pymatgen: {core.__version__}")
```
### Relevant files to reproduce this bug
_No response_
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PR_kwDOACgets535mqe
| 3,984
|
Fix mypy errors for `io.cp2k`
|
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[] | 2024-08-09T03:05:49
| 2024-08-09T13:23:53
|
2024-08-09T13:20:12Z
|
CONTRIBUTOR
|
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### Summary
- Fix mypy errors for `io.cp2k`
- `mypy` now ignore `override` error globally, rationale: it's common practice and intended to write methods that have different signatures with parent class
|
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| 2,457,111,914
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PR_kwDOACgets53590Q
| 3,985
|
Install optional boltztrap, vampire and openbabel in CI
|
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[] | null |
[
"Looks like `fdint` is needed by unit test as well: https://github.com/materialsproject/pymatgen/blob/9703a1c3a364f87d43692172d30010813f2a9159/tests/electronic_structure/test_boltztrap.py#L22\r\n\r\nNever mind, just found https://github.com/materialsproject/pymatgen/pull/2714",
"@janosh Please review this at your convenience (and perhaps help me verify the \"fix\" for electronic_structure plotters in https://github.com/materialsproject/pymatgen/pull/3985#discussion_r1711375519). Perhaps it's best to check those plots but I never use `boltztrap`.\r\n\r\nI singled out those newly discovered CI failures as separate issues for visibility (would appreciate it if you could tag them as `help wanted`).",
"@janosh I decide to separate the `BoltztrapPlotter` issue (it's not broken by this PR), and all changed made on `BoltztrapPlotter` in this PR has been reverted. It would take some effort to manually inspect the generated plot, instead of relying on passing of unit test.",
"Thanks for reviewing!"
] | 2024-08-09T05:07:52
| 2024-09-06T13:04:49
|
2024-09-06T12:53:04Z
|
CONTRIBUTOR
|
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### Summary
- Install more optional dependencies in CI, follow up #3786 (originally #3684)
### Installed
- [x] `x_trans`: https://www.tuwien.at/en/tch/tc/theoretical-materials-chemistry/boltztrap
- [x] `vampire`: https://vampire.york.ac.uk/download/ Ubuntu test split 3
- [x] `OBAlign`: Use the [`openbabel-wheel` unofficial prebuilt wheels](https://github.com/njzjz/openbabel-wheel) instead
> [!CAUTION]
> [**Need help**] Broken unit tests revealed
> - [ ] `electronic_structure.plotter`: https://github.com/materialsproject/pymatgen/pull/3985#discussion_r1711375519
> - [ ] `command_line.vampire_caller`: https://github.com/materialsproject/pymatgen/pull/3985#discussion_r1716550575
> - [ ] `io.qchem.outputs`: https://github.com/materialsproject/pymatgen/pull/3985#discussion_r1719578743
> - [ ] A dozen tests for `openbabel` are failing for Windows
### Future PR
- `critic2`: https://aoterodelaroza.github.io/critic2/installation/
- `zeo/pyzeo`: http://www.zeoplusplus.org/download.html (last update 2017)
- Properly test no ASE (mock ASE not installed): https://github.com/materialsproject/pymatgen/blob/cadcae4f3bda1706c197f97cf48f77724961e137/tests/io/test_ase.py#L356-L357
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PR_kwDOACgets537mt8
| 3,986
|
Minor change for step_size in CubicSupercellTransformation.apply_transformation
|
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[
"@shyuep @mkhorton @janosh could you have a look at this PR please? Thank you! 😄 ",
" I will merge this as this is a very minor change in a method that I recently implemented and all tests are passing (everything is backward compatible anyway)",
"> I will merge this as this is a very minor change in a method that I recently implemented and all tests are passing (everything is backward compatible anyway)\r\n\r\nThank you 😄 ",
"@QuantumChemist I overlooked something. I will revert this. Could you check again in more detail where to adapt the step size? Thanks!",
"If this change is breaking the backwards compatibility, I will find another solution for my problem. I overlooked that I can simply use the **common_kwds kwargs in get_supercell_size in atomate2 for the same purpose. Sorry.",
"@QuantumChemist I am happy to discuss this further."
] | 2024-08-09T10:15:57
| 2024-08-09T12:04:43
|
2024-08-09T10:41:15Z
|
CONTRIBUTOR
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Recently, @JaGeo and I had made some changes to the CubicSupercellTransformation.apply_transformation function in https://github.com/materialsproject/pymatgen/pull/3938.
I would like to set the step_size more coarse for the "cubic" supercells without the force_90_degree constraints as the previous step_size has led to unreasonable long run times for me.
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PR_kwDOACgets5374qS
| 3,987
|
Revert "Minor change for step_size in CubicSupercellTransformation.apply_transformation "
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[
"Cannot revert at the moment, as the connection to COD is failing. Will do this, as soon as possible."
] | 2024-08-09T11:03:39
| 2024-08-09T13:18:43
|
2024-08-09T13:18:42Z
|
MEMBER
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Reverts materialsproject/pymatgen#3986
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I_kwDOACgets6Shh3g
| 3,988
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Breaking behavior: Removal of `pymatgen.io.vasp.sets.get_vasprun_outcar` without warning
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[
"This has been fixed with the 2024.8.9 emergency release.",
"Thank you!",
"@shyuep please unrevert my #3865 PR. just add back the \r\n`get_vasprun_outcar` function that was accidentally dropped during merge conflict resolution which I might add was unnecessarily confusing because you moved everything to a `src` layout after i opened #3865. the reason it wasn't already merged before you [pointlessly moved all those files](https://github.com/materialsproject/pymatgen/issues/3874#issue-2344184349) (for which btw you never asked my or @mkhorton's approval either) is because [you asked](https://github.com/materialsproject/pymatgen/pull/3835#issuecomment-2118103809) that i do it after https://github.com/materialsproject/pymatgen/pull/3835 which was sensible so i did.\r\n\r\nthe split of several-thousand-line files is an obvious improvement. you're throwing away my time by undoing that work\r\n\r\nin https://github.com/materialsproject/pymatgen/pull/3989 [you write](https://github.com/materialsproject/pymatgen/pull/3989#issue-2458280210)\r\n\r\n> I did not agree to this.\r\n\r\nwhat's that supposed to mean? there are hundreds of PRs that you don't agree to. if every one of those required your explicit approval, pymatgen development would grind to a standstill",
"I think we should re-open #3865 and more comprehensively test.\r\n\r\nIt's a good idea to split these files up for maintainability. This can be done without backwards-incompatible changes; it seems like `get_vasprun_outcar` was an oversight.\r\n\r\nHowever, I would go further than #3865. The `pymatgen.io.vasp.outputs` and `pymatgen.io.vasp.inputs` could also be split up into new folders without introducing backwards incompatibility, and just to improve ease-of-navigation. This would mean, e.g. `pymatgen.io.vasp.inputs.potcar` etc. Like the `/src` change, this sort of change does not need to introduce any breakage.\r\n\r\nTo be specific `pymatgen.io.vasp.inputs` is currently 2932 LOC, `.outputs` is 5363 LOC and `.sets` is 3205 LOC. While having long files is not in itself an error, it does makes things more difficult than necessary."
] | 2024-08-09T16:20:27
| 2024-08-12T04:24:31
|
2024-08-09T17:25:00Z
|
MEMBER
|
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### Python version
3.11
### Pymatgen version
pymatgen 2024.8.8
### Operating system version
_No response_
### Current behavior
```python
from pymatgen.io.vasp.sets import get_vasprun_outcar
```
The above used to work on pymatgen < 2024.8.8 but does not exist any longer in pymatgen >= 2024.8.8. I don't believe there was a deprecation warning, so it may break other people's codes as-is.
### Expected Behavior
A deprecation warning before removal.
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets53958A
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|
Revert "Split VASP input sets into submodules"
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[] | 2024-08-09T16:31:36
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|
2024-08-09T16:31:43Z
|
MEMBER
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Reverts materialsproject/pymatgen#3865.
1. I did not agree to this.
2. It clearly broke something. See #3988
|
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