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I_kwDOACgets5n2hMT
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Wrong typehint in `Structure.relax`
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"Thanks. I agree, but I am reluctant to add this because it will make ASE a core dependency for a type hint of a function that may or may not be used by most people.",
"Ah, that's a good point. We don't want to add ASE as a core dependency. @janosh, there isn't any trickery to get around the type hinting issue here? If the only way is to add ASE as a dependency, please feel free to close the issue.",
"We can hide the import behind\r\n\r\n```py\r\nif TYPE_CHECKING:\r\n from ase import Calculator\r\n```\r\n\r\n`TYPE_CHECKING==False` at runtime. Only `mypy` sets it to `True`."
] | 2023-06-05T18:36:39
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https://github.com/materialsproject/pymatgen/blob/f90929f75b27fe1d06faa4e2a5f44654009b98b0/pymatgen/core/structure.py#L3989
Should be type `str | Calculator` where `Calculator` is `from ase.calculators.calculator import Calculator`
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I_kwDOACgets5n2i_x
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Add a `Structure.calculate()` feature analagous to `Structure.relax`
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"That sounds great! Let me know if I can help with tests or reviewing.",
"I'll definitely be adding plenty of tests, but would love help with reviewing when I'm done! And probably fixing mypy issues...",
"Thanks. But my question is how different is it from a `AseAdaptor.get_atoms(structure).get_potential_energy()`?",
"In practice, the user might use a function like \r\n\r\n```python\r\nfrom pymatgen.io.ase import AseAtomsAdaptor\r\nfrom pymatgen.core import Structure, Molecule\r\n\r\n\r\ndef run_ase(s: Structure | Molecule, Calculator)\r\n atoms = AseAtomsAdaptor.get_atoms(s)\r\n atoms.calc = Calculator\r\n atoms.get_potential_energy() # note this can update the positions if using ISIF = 2, etc.\r\n if isinstance(s, Molecule):\r\n s_new = AseAtomsAdaptor.get_molecule(atoms)\r\n else:\r\n s_new = AseAtomsAdaptor.get_structure(atoms)\r\n \r\n # attach atoms.calc.results to the Structure or Molecule object. See Issue 2884.\r\n \r\n return s_new\r\n```\r\n\r\nHaving to do this (potentially with some additional logic baked in) to run a calculation is kind of annoying. The beauty of `Structure.relax` is that --- from a UX standpoint --- it's super simple. But if you want to use an internal optimizer (and not an ASE optimizer), you can't use it. Adding a `Structure.run` option would help reduce some boilerplate. There could be some other logic included, e.g. a boolean to raise an error if the calculation doesn't converge (as determined by ASE).\r\n\r\nI'll share a proof-of-concept. Yes, it's admittedly a pretty simple wrapper, but it's also a clear value-add in my mind because `Structure.relax` is relying on ASE constraints and optimizers that the user may not want."
] | 2023-06-05T18:40:42
| 2023-06-09T14:46:15
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2023-06-09T14:46:15Z
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Currently, there is a method to do `Structure.relax` which calls an ASE calculation with the ASE Optimizer class. There should be a similar method called `Structure.run` which calls ASE to run `atoms.get_potential_energy()`. This will allow for the use of the calculator's internal optimizers if the user wishes.
I can add this.
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PR_kwDOACgets5SPCaJ
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Add `(Structure|Molecule).calculate()` + `Molecule.relax()`, improve `Structure.relax()`
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"I suggest:\r\n1. We have a `run_calculation` method that replaces and extends most of the code in `relax` to be more flexible.\r\n2. We have `relax` call run_calculator with a specific set of parameters to do a relaxation.\r\n\r\n`Structure.run` as a naming sounds a bit strange to me.",
"Agreed. That'll clean things up and prevent duplication. And that's a much better name. That way it doesn't sound like the structure is running away...",
"@shyuep, @janosh: This is ready for either of you to review.\r\n\r\nA couple of notes:\r\n- I did not see any clean way of using `Structure.run_calculation` as the base logic for `Structure.relax`. They both do fairly different things, and the code between the two reflects that. Nonetheless, I did use `.run_calculation` instead of `run` as requested.\r\n- I can add in the analogous functions in `Molecule` once things look good for `Structure`. I imagine we should not use m3gnet as the default for `Molecule`, so I'm open to suggestions. This might also be a good spot to consider refactoring since we don't necessarily want to copy/paste things between `Structure` and `Molecule`. They'll be basically the same except for no options to relax the cell in the latter.\r\n- For some reason, m3gnet gives slightly different lattice constants on Mac/Windows than on Linux for one of the tests. I can modify the assertion, but I want to alert you of this odd behavior.\r\n- Instead of using the m3gnet custom `TrajectoryObserver`, I have switched to using ASE's native `Trajectory` object when `return_trajectory` is `True` in `Structure.relax`. The latter has all the desired properties (e.g. energies, forces, cells, stresses, etc.) without requiring the m3gnet dependency for all ASE calculations. \r\n- I will need a bit of help with the `mypy` test failures.",
"That was fast! Thanks @arosen93. Sorry for not bringing this up earlier but what do you think of `Structure.calc()` instead of `Structure.run_calculation()`?\r\n\r\n> For some reason, m3gnet gives slightly different lattice constants on Mac/Windows than on Linux for one of the tests. I can modify the assertion, but I want to alert you of this odd behavior.\r\n\r\nThat might be a TensorFlow quirk. I hope/expect the new matGL M3GNet built using DGL doesn't have that. So maybe not worth it to dig too deeply for now.",
"Thanks, @janosh! I'll address your comments.\n\nRegarding the naming, I actually assign the ASE calculator to `Structure.calc`, which is worth doing because this object contains all the calculation results and parameters (presumably highly desirable for the end user to be able to access).\n\nMaybe `Structure.calculate()` would be a better name for the function. Open to other ideas. ",
"calculate sounds good to me.",
"I would point out one thing - the Structure.relax / whatever are generally meant to be convenience methods for simple needs. It is for the user who just wants an answer without having to mess around with lots of differnet options. \r\n\r\nIf you are planning to properly use ASE calculators and/or M3Gnet etc., it is best to use the API in those packages instead.\r\n\r\nAlso, one more thing - matgl now has the M3Gnet universal potential implemented. We would probably need to replace the M3Gnet in this function shortly. ",
"> I would point out one thing - the Structure.relax / whatever are generally meant to be convenience methods for simple needs. It is for the user who just wants an answer without having to mess around with lots of differnet options.\r\n\r\nDefinitely understood. In case it's of interest, I will note that from speaking with folks who use both ASE and Pymatgen, there is a strong interest in building workflows centered around Pymatgen `Structure`/`Molecule` objects while still taking advantage of the convenience associated with ASE calculators. I also feel like many people are simply not aware of the `AseAtomsAdaptor` and so would not think to use it to construct similar functions on their own. With the `.relax` and `.calculate` methods, this should hopefully reduce the need for people to recreate the same boilerplate functions while still maximizing convenience. Of course, we shouldn't cover every edge case in Pymatgen, but I think the ability to pass objects like the `Calculator` or `Optimizer` class keeps things pretty general, especially with the defaults being something you can just \"set and forget.\"\r\n\r\nHopefully with this PR we'll hit a good middleground! Always open to suggestions.",
"@janosh: Okay, this is ready for review again! I'm \"done!\" :)\r\n\r\nSome examples you might consider trying:\r\n\r\n## Structure Relax with M3GNet\r\n\r\nThis is the default for `Strucuture.relax()`. It will tell you to install `m3gnet` if you run without it.\r\n\r\n```python\r\nfrom pymatgen.core import Structure\r\n\r\nstructure = Structure(\r\n lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],\r\n species=[\"Cu\", \"O\"],\r\n coords=[[0, 0, 0], [0.5, 0.5, 0.5]],\r\n)\r\nstructure.relax()\r\n```\r\n\r\n## Structure Relax with EMT\r\n\r\n```python\r\nfrom pymatgen.core import Structure\r\nfrom ase.calculators.emt import EMT\r\n\r\nstructure = Structure(\r\n lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],\r\n species=[\"Cu\", \"O\"],\r\n coords=[[0, 0, 0], [0.5, 0.5, 0.5]],\r\n)\r\nstructure.relax(calculator=EMT())\r\n```\r\n\r\n## Structure Static Calc with M3GNet\r\n\r\nThis is the default for `Structure.calculate()`. It will tell you to install `m3gnet` if you run without it.\r\n\r\n```python\r\nfrom pymatgen.core import Structure\r\n\r\nstructure = Structure(\r\n lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],\r\n species=[\"Cu\", \"O\"],\r\n coords=[[0, 0, 0], [0.5, 0.5, 0.5]],\r\n)\r\nstructure.calculate()\r\n```\r\n\r\n## Molecule Relax with GFN2-xTB\r\n\r\nThis is the default for `Molecule.relax()`. It will tell you to install `tblite[ase]` if you run without it.\r\n\r\n```python\r\nfrom pymatgen.core import Molecule\r\n\r\ncoords = [\r\n [0.000000, 0.000000, 0.000000],\r\n [0.000000, 0.000000, 1.089000],\r\n [1.026719, 0.000000, -0.363000],\r\n [-0.513360, -0.889165, -0.363000],\r\n [-0.513360, 0.889165, -0.363000],\r\n]\r\nmol = Molecule([\"C\", \"H\", \"H\", \"H\", \"H\"], coords)\r\nmol.relax()\r\n```\r\n\r\n## Molecule Relax with Lennard-Jones\r\n\r\n```python\r\nfrom pymatgen.core import Molecule\r\nfrom ase.calculators.lj import LennardJones\r\n\r\ncoords = [\r\n [0.000000, 0.000000, 0.000000],\r\n [0.000000, 0.000000, 1.089000],\r\n [1.026719, 0.000000, -0.363000],\r\n [-0.513360, -0.889165, -0.363000],\r\n [-0.513360, 0.889165, -0.363000],\r\n]\r\nmol = Molecule([\"C\", \"H\", \"H\", \"H\", \"H\"], coords)\r\nmol.relax(calculator=LennardJones())\r\n```\r\n\r\n## Molecule Static Calc with GFN2-xTB\r\n\r\nThis is the default for `Molecule.calculate()`. It will tell you to install `tblite[ase]` if you run without it.\r\n\r\n```python\r\nfrom pymatgen.core import Molecule\r\n\r\ncoords = [\r\n [0.000000, 0.000000, 0.000000],\r\n [0.000000, 0.000000, 1.089000],\r\n [1.026719, 0.000000, -0.363000],\r\n [-0.513360, -0.889165, -0.363000],\r\n [-0.513360, 0.889165, -0.363000],\r\n]\r\nmol = Molecule([\"C\", \"H\", \"H\", \"H\", \"H\"], coords)\r\nmol.calculate()\r\n```",
"@janosh --- ready for either re-review or merging. Some of the Mac tests died but seems to be a problem for everyone.",
"Thanks @arosen93! Took a few iterations but this was no small PR and I think it turned out really well! 😎 Thanks for the excellent test coverage! 🧪 "
] | 2023-06-05T20:02:29
| 2023-06-09T14:47:10
|
2023-06-09T14:46:13Z
|
MEMBER
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Closes #3042. Closes #3043. Closes #3047.
Links:
- #3042
- #3043
- #3047
In addition to the prior issues, I also increased the range of optimizers that can be passed to `Structure.relax` so the user doesn't have to rely solely on FIRE.
For molecules, I added a `Molecule.relax()` feature that defaults to GFN2-xTB and an analogous `Molecule.calculate()`.
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I_kwDOACgets5n4Xak
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Running pymatgen 2023.5.31 on Apple M1 MacOS yields incompatible architecture error
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[
"Could you try a clean re-install?\r\n\r\n```sh\r\npip uninstall -y pymatgen\r\npip cache purge\r\npip install pymatgen\r\n```\r\n\r\nIf that doesn't help, try outside a `conda` env.\r\n\r\n```sh\r\n# without a conda env active\r\npython -m venv debug\r\n. ./debug/bin/activate\r\npip install pymatgen\r\n```",
"Hi @janosh, I've tried both suggestions, none of them works (the error still persists).",
"Could you post the stack trace from the python `venv`, i.e. the error without `conda`?",
"```\r\nTraceback (most recent call last):\r\n File \"/Users/jw598/Rafael_project/codes/test.py\", line 9, in <module>\r\n from mp_api.client import MPRester\r\n File \"/Users/jw598/debug/lib/python3.9/site-packages/mp_api/client/__init__.py\", line 5, in <module>\r\n from .core import MPRestError\r\n File \"/Users/jw598/debug/lib/python3.9/site-packages/mp_api/client/core/__init__.py\", line 1, in <module>\r\n from .client import BaseRester, MPRestError\r\n File \"/Users/jw598/debug/lib/python3.9/site-packages/mp_api/client/core/client.py\", line 20, in <module>\r\n from emmet.core.utils import jsanitize\r\n File \"/Users/jw598/debug/lib/python3.9/site-packages/emmet/core/utils.py\", line 10, in <module>\r\n from pymatgen.analysis.graphs import MoleculeGraph\r\n File \"/Users/jw598/debug/lib/python3.9/site-packages/pymatgen/analysis/graphs.py\", line 26, in <module>\r\n from pymatgen.core import Lattice, Molecule, PeriodicSite, Structure\r\n File \"/Users/jw598/debug/lib/python3.9/site-packages/pymatgen/core/__init__.py\", line 14, in <module>\r\n from pymatgen.core.lattice import Lattice as Lattice\r\n File \"/Users/jw598/debug/lib/python3.9/site-packages/pymatgen/core/lattice.py\", line 21, in <module>\r\n from pymatgen.util.coord import pbc_shortest_vectors\r\n File \"/Users/jw598/debug/lib/python3.9/site-packages/pymatgen/util/coord.py\", line 16, in <module>\r\n from pymatgen.util import coord_cython as cuc\r\nImportError: dlopen(/Users/jw598/debug/lib/python3.9/site-packages/pymatgen/util/coord_cython.cpython-39-darwin.so, 0x0002): tried: '/Users/jw598/debug/lib/python3.9/site-packages/pymatgen/util/coord_cython.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/jw598/debug/lib/python3.9/site-packages/pymatgen/util/coord_cython.cpython-39-darwin.so' (no such file), '/Users/jw598/debug/lib/python3.9/site-packages/pymatgen/util/coord_cython.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))\r\n```",
"Could you try `ARCHFLAGS=\"-arch arm64\" pip install pymatgen --compile --no-cache-dir`?",
"It works with your command now!"
] | 2023-06-05T23:57:57
| 2023-06-15T06:33:11
|
2023-06-15T06:33:11Z
|
CONTRIBUTOR
|
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Running the following test code on Apple M1 MacOS:
```
from mp_api.client import MPRester
api_key = "*****"
with MPRester(api_key) as mpr:
struct = mpr.get_structure_by_material_id("mp-2534")
```
gives the following error:
```
Traceback (most recent call last):
File "/Users/jw598/Rafael_project/codes/test.py", line 9, in <module>
from mp_api.client import MPRester
File "/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/mp_api/client/__init__.py", line 5, in <module>
from .core import MPRestError
File "/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/mp_api/client/core/__init__.py", line 1, in <module>
from .client import BaseRester, MPRestError
File "/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/mp_api/client/core/client.py", line 20, in <module>
from emmet.core.utils import jsanitize
File "/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/emmet/core/utils.py", line 10, in <module>
from pymatgen.analysis.graphs import MoleculeGraph
File "/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/analysis/graphs.py", line 26, in <module>
from pymatgen.core import Lattice, Molecule, PeriodicSite, Structure
File "/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/core/__init__.py", line 14, in <module>
from pymatgen.core.lattice import Lattice as Lattice
File "/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/core/lattice.py", line 21, in <module>
from pymatgen.util.coord import pbc_shortest_vectors
File "/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/util/coord.py", line 16, in <module>
from pymatgen.util import coord_cython as cuc
ImportError: dlopen(/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/util/coord_cython.cpython-39-darwin.so, 0x0002): tried: '/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/util/coord_cython.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/util/coord_cython.cpython-39-darwin.so' (no such file), '/Users/jw598/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/util/coord_cython.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))
```
Operating system is Ventura 13.3.1, Python version is 3.9.16. The code above works with pymatgen 2023.5.10.
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PR_kwDOACgets5SQJ1y
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Better error message to clarify Structure.species only supported for ordered
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2023-06-06T00:42:36Z
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Closes #3033.
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https://github.com/materialsproject/pymatgen/issues/3047
| 1,742,915,409
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I_kwDOACgets5n4sdR
| 3,047
|
`Structure.relax` only works if m3gnet is installed even if it is not used
|
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[] | 2023-06-06T01:56:28
| 2023-06-09T14:46:15
|
2023-06-09T14:46:15Z
|
MEMBER
|
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Currently, if you want to use `Structure.relax` with an ASE `Calculator` object, you still need to install `m3gnet` even though it is not strictly needed for the relaxation procedure. The imports should be moved around to provide additional user flexibility.
|
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I_kwDOACgets5n53hY
| 3,048
|
`pip install -e .` not working on Windows
|
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[
"Naturally, installing Microsoft Visual C++ 14.0 resolves it. And I now see that's in the docs, so we're good."
] | 2023-06-06T07:04:48
| 2023-06-06T07:06:45
|
2023-06-06T07:06:44Z
|
MEMBER
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For 3ab085e9b4a7d1c4a0a88f252e5c11d010cd0497, I ran `pip install -e .` in a clean miniconda environment with Python 3.9 and got the following traceback:
```python
Building wheels for collected packages: pymatgen
Building editable for pymatgen (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building editable for pymatgen (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [93 lines of output]
C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\dist.py:519: InformationOnly: Normalizing '2023.05.31' to '2023.5.31'
self.metadata.version = self._normalize_version(
running editable_wheel
creating C:\Users\asros\AppData\Local\Temp\pip-wheel-rb27b0u5\.tmp-z3o89q05\pymatgen.egg-info
writing C:\Users\asros\AppData\Local\Temp\pip-wheel-rb27b0u5\.tmp-z3o89q05\pymatgen.egg-info\PKG-INFO
writing dependency_links to C:\Users\asros\AppData\Local\Temp\pip-wheel-rb27b0u5\.tmp-z3o89q05\pymatgen.egg-info\dependency_links.txt
writing entry points to C:\Users\asros\AppData\Local\Temp\pip-wheel-rb27b0u5\.tmp-z3o89q05\pymatgen.egg-info\entry_points.txt
writing requirements to C:\Users\asros\AppData\Local\Temp\pip-wheel-rb27b0u5\.tmp-z3o89q05\pymatgen.egg-info\requires.txt
writing top-level names to C:\Users\asros\AppData\Local\Temp\pip-wheel-rb27b0u5\.tmp-z3o89q05\pymatgen.egg-info\top_level.txt
writing manifest file 'C:\Users\asros\AppData\Local\Temp\pip-wheel-rb27b0u5\.tmp-z3o89q05\pymatgen.egg-info\SOURCES.txt'
reading manifest file 'C:\Users\asros\AppData\Local\Temp\pip-wheel-rb27b0u5\.tmp-z3o89q05\pymatgen.egg-info\SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'C:\Users\asros\AppData\Local\Temp\pip-wheel-rb27b0u5\.tmp-z3o89q05\pymatgen.egg-info\SOURCES.txt'
creating 'C:\Users\asros\AppData\Local\Temp\pip-wheel-rb27b0u5\.tmp-z3o89q05\pymatgen-2023.5.31.dist-info'
C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\normal\Lib\site-packages\wheel\bdist_wheel.py:100: RuntimeWarning: Config variable 'Py_DEBUG' is unset, Python ABI tag may be incorrect
if get_flag("Py_DEBUG", hasattr(sys, "gettotalrefcount"), warn=(impl == "cp")):
creating C:\Users\asros\AppData\Local\Temp\pip-wheel-rb27b0u5\.tmp-z3o89q05\pymatgen-2023.5.31.dist-info\WHEEL
running build_py
running build_ext
skipping 'pymatgen/optimization\linear_assignment.c' Cython extension (up-to-date)
skipping 'pymatgen/util\coord_cython.c' Cython extension (up-to-date)
cythoning pymatgen/optimization/neighbors.pyx to pymatgen/optimization\neighbors.c
building 'pymatgen.optimization.linear_assignment' extension
Traceback (most recent call last):
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\command\editable_wheel.py", line 155, in run
self._create_wheel_file(bdist_wheel)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\command\editable_wheel.py", line 344, in _create_wheel_file
files, mapping = self._run_build_commands(dist_name, unpacked, lib, tmp)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\command\editable_wheel.py", line 267, in _run_build_commands
self._run_build_subcommands()
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\command\editable_wheel.py", line 294, in _run_build_subcommands
self.run_command(name)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\dist.py", line 1244, in run_command
super().run_command(command)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 988, in run_command
cmd_obj.run()
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\command\build_ext.py", line 84, in run
_build_ext.run(self)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\Cython\Distutils\old_build_ext.py", line 186, in run
_build_ext.build_ext.run(self)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\_distutils\command\build_ext.py", line 345, in run
self.build_extensions()
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\Cython\Distutils\old_build_ext.py", line 195, in build_extensions
_build_ext.build_ext.build_extensions(self)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\_distutils\command\build_ext.py", line 467, in build_extensions
self._build_extensions_serial()
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\_distutils\command\build_ext.py", line 493, in _build_extensions_serial
self.build_extension(ext)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\command\build_ext.py", line 246, in build_extension
_build_ext.build_extension(self, ext)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\_distutils\command\build_ext.py", line 548, in build_extension
objects = self.compiler.compile(
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\_distutils\_msvccompiler.py", line 343, in compile
self.initialize()
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\_distutils\_msvccompiler.py", line 253, in initialize
vc_env = _get_vc_env(plat_spec)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\msvc.py", line 210, in msvc14_get_vc_env
return _msvc14_get_vc_env(plat_spec)
File "C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\msvc.py", line 164, in _msvc14_get_vc_env
raise distutils.errors.DistutilsPlatformError(
distutils.errors.DistutilsPlatformError: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
C:\Users\asros\AppData\Local\Temp\pip-build-env-3ofygtx0\overlay\Lib\site-packages\setuptools\_distutils\dist.py:988: _DebuggingTips: Problem in editable installation.
!!
********************************************************************************
An error happened while installing `pymatgen` in editable mode.
The following steps are recommended to help debug this problem:
- Try to install the project normally, without using the editable mode.
Does the error still persist?
(If it does, try fixing the problem before attempting the editable mode).
- If you are using binary extensions, make sure you have all OS-level
dependencies installed (e.g. compilers, toolchains, binary libraries, ...).
- Try the latest version of setuptools (maybe the error was already fixed).
- If you (or your project dependencies) are using any setuptools extension
or customization, make sure they support the editable mode.
After following the steps above, if the problem still persists and
you think this is related to how setuptools handles editable installations,
please submit a reproducible example
(see https://stackoverflow.com/help/minimal-reproducible-example) to:
https://github.com/pypa/setuptools/issues
See https://setuptools.pypa.io/en/latest/userguide/development_mode.html for details.
********************************************************************************
!!
cmd_obj.run()
error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building editable for pymatgen
Failed to build pymatgen
ERROR: Could not build wheels for pymatgen, which is required to install pyproject.toml-based projects
```
|
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| 1,743,417,854
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I_kwDOACgets5n6nH-
| 3,049
|
Generate random ordered structures from disordered structure
|
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[
"Could you share how this differs from `EnumerateStructureTransformation` backed by `enumlib`?",
"Also, thank you for the clearly described and illustrated issue.",
"Hi @mkhorton, thank you very much for your comment! I just found out about `EnumerateStructureTransformation`. Upon checking the documentation, it seems that this transformation requires `enumlib` and some other arguments (I'm not quite familiar with what these arguments do). It seems also that `EnumerateStructureTransformation` has some kind of ordering using either Ewald or M3GNet energy. These features are not present in `RandomStructureTransformation`, but it uses `random.shuffle` to randomly assign site elements. Does this answer your question somewhat?",
"hello, [exenGT](https://github.com/exenGT), I'm wondering how did you show the crystal strucuture in this Issue, please inform me, thank you very much !!!",
"Hi @HegemonyTao, sorry for my late reply. The crystal structures here are visualized with VESTA. Hope that helps!"
] | 2023-06-06T09:02:56
| 2023-07-18T21:08:37
|
CONTRIBUTOR
|
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#### Problem
For molecular dynamics simulation and machine learning data generation of random structures, one might desire to have a routine that transforms a given disordered structure $S$ to a set of randomly ordered structures $\\{S'_i\\}$, where each randomly ordered structure $S'_i$ has the same overall composition as the disordered structure $S$.
Currently for this purpose, there exists `OrderDisorderedStructureTransformation` in `transformations/standard_transformations.py`. However, this function over-complicates the problem by using the Ewald energy to rank the generated randomly ordered structures. When the structure in question is very large (e.g. >= thousands of atoms in a typical MD simulation), this approach simply won't work due to the combinatorially increasing search space. Instead, what we actually want is very simple: a set of randomly ordered structures. The energy ranking is not of concern here.
#### Proposed Solution
We have implemented a new standard transformation routine, named `RandomStructureTransformation`. Given a disordered `structure`, and a number `num_copies`, its method `apply_transformation` returns a set of `num_copies` copies of randomly ordered structures. This routine distinguishes between inequivalent sublattices of the crystal.
#### Additional Info
The following example shows the usage of this routine:
```py
from mp_api.client import MPRester
from pymatgen.transformations.standard_transformations \
import RandomStructureTransformation
# put your api_key here
api_key = "*****"
with MPRester(api_key) as mpr:
struct = mpr.get_structure_by_material_id("mp-2534", conventional_unit_cell=True) # GaAs
struct[0:4] = {"Ga": 0.5, "In": 0.5}
struct[4:] = {"P": 0.5, "As": 0.5}
struct.make_supercell([3, 3, 3])
# random structure transformation
trans = RandomStructureTransformation()
new_structs = trans.apply_transformation(structure = struct,
num_copies = 5)
# save structures to files
for i_struct, new_struct in enumerate(new_structs):
new_struct.to("random_structure_{}.cif".format(i_struct))
```
Below are the screenshots of the generated random structures:
<img width="310" alt="Screenshot 2023-06-06 at 1 37 52 AM" src="https://github.com/materialsproject/pymatgen/assets/13700125/35133031-3d5b-4959-8f91-93717dbedf09">
<img width="310" alt="Screenshot 2023-06-06 at 1 37 48 AM" src="https://github.com/materialsproject/pymatgen/assets/13700125/29ae578b-cbd8-4a65-889f-23a267218e83">
<img width="310" alt="Screenshot 2023-06-06 at 1 37 38 AM" src="https://github.com/materialsproject/pymatgen/assets/13700125/30216eaf-e1da-4ff4-a038-c869ea7e5c73">
<img width="310" alt="Screenshot 2023-06-06 at 1 37 34 AM" src="https://github.com/materialsproject/pymatgen/assets/13700125/17afb0c5-5e14-4184-904b-6245ba2eb7cb">
<img width="310" alt="Screenshot 2023-06-06 at 1 37 28 AM" src="https://github.com/materialsproject/pymatgen/assets/13700125/32da13c4-5959-404b-a538-30043a3f190b">
If this feature is desired, I can initiate a pull request.
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PR_kwDOACgets5STKzd
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Extend lobsterenv for coop/cobi
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[
"Hi @JaGeo , if you have any more suggestions / changes let me know ",
"@naik-aakash , very nice! I have added my tiny suggestion on the documentation and naming (which was initially, of couse, my fault ;))! ",
"Ready to be merged from my side! @naik-aakash \r\n\r\n@janosh , this is ready to be reviewed! :)",
"> Looking good overall. A few suggestions:\r\n> \r\n> * Best to remove the [WIP] from PR title when review-ready.\r\n> * Do we really need the new 90 KB `test_files/cohp/environments/ICOBILIST.lobster.mp_470.gz`? How does it differ from existing test files? Can `ICOBILIST.lobster.NaCl.gz` not be re-used?\r\n\r\nI included the `ICOBILIST.lobster.mp_470.gz` as it has a bit different structure type and just wanted to check if it works as intended. I hope this is fine. If not am happy to remove this file and associated tests.",
"Hi @janosh , I think this should be ready to be merged if all seems fine to you. \r\n\r\nAlso, it would be great, it the contributors list could be updated. I have filled out the form on the website several times, but so far it does not seem to work for me ",
"Sorry for the delay @naik-aakash, this seems to have gotten lost in my inbox.",
"> Sorry for the delay @naik-aakash, this seems to have gotten lost in my inbox.\r\n\r\nNo worries. I suspected this happened, as you are working constantly on so many tasks. It is totally fine and thanks again 😃 "
] | 2023-06-06T12:18:25
| 2024-01-10T12:23:31
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2023-07-24T14:43:22Z
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CONTRIBUTOR
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## Additions
- Extended lobsterenv.py module to work for ICOBILIST/ICOOPLIST
- Added test cases
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I_kwDOACgets5n99-_
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Replace `m3gnet` optional dependency with `matgl`
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[
"This is done (I hope)."
] | 2023-06-06T17:34:30
| 2023-06-09T20:02:55
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2023-06-09T20:02:55Z
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MEMBER
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This is just a tracker to keep tabs on it. It is my understanding that `matgl` is the new standard repo to use if you want a pre-trained m3gnet model.
~Note: From looking at the `matgl` `setup.py` file, there might be a file path or two that might cause issues on Windows. Also, the pinned versions in the `setup.py` probably aren't ideal. Might be better to propose a change such that `requirements.txt` has pinned versions but `setup.py` has minimal pins.~
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PR_kwDOACgets5SXW6s
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`IcohpValue.__str__` don't `return None`
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[
"CI failure caused by legacy `MPRester`, unrelated to PR."
] | 2023-06-07T03:51:14
| 2023-06-07T06:46:57
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2023-06-07T06:46:23Z
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MEMBER
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Also use modern f-string syntax.
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PR_kwDOACgets5SjFcJ
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`PourbaixDiagram` wrong composition bug fix
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[
"This is great, thanks @montoyjh! 👍 "
] | 2023-06-08T18:18:13
| 2023-06-09T05:48:15
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2023-06-09T05:48:12Z
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CONTRIBUTOR
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Closes #2943.
The Pourbaix diagram was generating multi-entries with the wrong composition because of Reaction coefficient handling. This fixes the issue by using the explicit list of reaction coefficients, rather than the hash retrieval, and adds a regression test that fails previously but passes now.
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PyPI trusted publishing for releases
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2023-06-09T08:27:43Z
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[PyPI's new trusted publishing](https://blog.pypi.org/posts/2023-04-20-introducing-trusted-publishers) has 1st party integration with GitHub Actions for easier and safer setup of automated releases. We should migrate the pymatgen release action to it.
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Migrate GHA release job to PyPI trusted publishing
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"@shyuep We could in principle remove the `TWINE_USERNAME` and `TWINE_PASSWORD` secrets from this repo after this is merged. But prob better to keep, esp. until the next release to make sure this actually works.\r\n"
] | 2023-06-09T05:42:03
| 2023-06-09T08:27:43
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2023-06-09T08:27:42Z
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Closes #3054.
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PR_kwDOACgets5SpTgE
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`AseAtomsAdaptor`: Ensure `Molecule.charge` and `Molecule.spin_multiplicity` aren't lost upon interconversion
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[] | 2023-06-09T18:04:30
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2023-06-18T13:09:53Z
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Thanks for spotting this, @samblau.
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Add `Structure.sublattices` and `class RandomStructureTransformation` to `standard_transformations.py`
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"Thanks @exenGT, I added a question to the associated issue.",
"@janosh All your suggestions have been addressed in my latest commits.",
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3057?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`86.36%`** and project coverage change: **`-0.57%`** :warning:\n> Comparison is base [(`5f369ec`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/5f369ec4c1205fd158e8030281a8b5a9585bc957?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.69% compared to head [(`b72f962`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3057?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.12%.\n> Report is 1 commits behind head on master.\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3057 +/- ##\n==========================================\n- Coverage 74.69% 74.12% -0.57% \n==========================================\n Files 230 230 \n Lines 69375 69419 +44 \n Branches 16154 16163 +9 \n==========================================\n- Hits 51818 51460 -358 \n- Misses 14490 14923 +433 \n+ Partials 3067 3036 -31 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3057?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [...matgen/transformations/standard\\_transformations.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3057?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vdHJhbnNmb3JtYXRpb25zL3N0YW5kYXJkX3RyYW5zZm9ybWF0aW9ucy5weQ==) | `86.04% <83.78%> (-0.22%)` | :arrow_down: |\n| [pymatgen/core/structure.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3057?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vY29yZS9zdHJ1Y3R1cmUucHk=) | `85.81% <100.00%> (+0.05%)` | :arrow_up: |\n\n... and [7 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3057/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3057?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n"
] | 2023-06-10T00:22:39
| 2024-08-03T19:01:57
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CONTRIBUTOR
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Closes #3049.
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I_kwDOACgets5oahar
| 3,058
|
The definition of the method used to identify symmetry of crystal structure
|
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[
"Hi @HegemonyTao, the symmetry finding algorithms come via a third-party library called \"spglib\". The best way to understand this library is to read their paper:\n\nhttps://arxiv.org/pdf/1808.01590.pdf\n\nI hope this helps!",
"> Hi @HegemonyTao, the symmetry finding algorithms come via a third-party library called \"spglib\". The best way to understand this library is to read their paper:\r\n> \r\n> https://arxiv.org/pdf/1808.01590.pdf\r\n> \r\n> I hope this helps!\r\n\r\nThanks a lot, it will be help!!!"
] | 2023-06-12T02:43:25
| 2023-06-12T04:05:41
|
NONE
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#### Description
Hi developers, I am very curious about the method of analyzing the space group of the given crystal structure you have achieved. But when I tried to read the source code, I found that you had already encapsulated it into a pyd file, which made it difficult for me to understand how the method was implemented.
Therefore, I would like to ask if it it possible to inform me of the specific method implementation and send it to my email address **18297420903@163.com**
#### Specific methods
First, I try to use the following code to obtain the Space group of the structure
`from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer`
`sp=SpacegroupAnalyzer(structure)`
Then I checked the specific implementation of SpacegroupAnalyzer step by step and found that in the end, I couldn't find the definition of the following method
`from . import _spglib as spg`
```
spg_ds = spg.dataset(
lattice, positions, numbers, hall_number, symprec, angle_tolerance)
```
The definition of **spg.dataset** is as follows
```
def dataset(*args, **kwargs): # real signature unknown
""" Dataset for crystal symmetry """
pass
```
Therefore, if you could inform me of the implementation method of **dataset**, I would greatly appreciate it
|
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I_kwDOACgets5of-wy
| 3,059
|
Error in Tensor symmetrization with certain monoclinic structures
|
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[
"Based on [`git blame` from 7 years ago](https://github.com/materialsproject/pymatgen/commit/48c9b1f5676241d02235bebe82aaab5cb2fd17f7), @montoyjh might know more.\r\n\r\n@matthewkuner Could you specify what the error is and post the output of `structure.to('material_id.json')` in HTML `<details>` (just start typing `/details` and let GH auto-complete).",
"@janosh the error I get is:\r\n\r\n> /global/home/users/matthewkuner/.conda/envs/atomate2/lib/python3.9/site-packages/pymatgen/core/tensors.py\\\", line 476, in get_ieee_rotation\\n c = [vec / mag for (mag, vec) in sorted(zip(lengths[n_umask], vecs[n_umask]))][0]\\nIndexError: list index out of range\\n\r\n\r\n<details><summary>Details</summary>\r\n<p>\r\n\r\n{\"@module\": \"pymatgen.core.structure\", \"@class\": \"Structure\", \"charge\": 0.0, \"lattice\": {\"matrix\": [[1.6330944037650026, 1.6330944037650026, 1.6330944037650026], [3.266188807530005, 0.0, -3.266188807530005], [-3.266188807530005, 6.53237761506001, -3.266188807530005]], \"pbc\": [true, true, true], \"a\": 2.828602480877387, \"b\": 4.61908850888014, \"c\": 8.000495982037968, \"alpha\": 90.0, \"beta\": 90.0, \"gamma\": 90.0, \"volume\": 104.53100201054758}, \"sites\": [{\"species\": [{\"element\": \"Ti\", \"occu\": 1}], \"abc\": [0.2614933717186148, 0.5, 0.1603201177754059], \"xyz\": [1.536501991440391, 1.4743149105751572, -1.7296868160896142], \"label\": \"Ti\", \"properties\": {\"velocities\": [0.0, 0.0, 0.0]}}, {\"species\": [{\"element\": \"Ti\", \"occu\": 1}], \"abc\": [0.5843327795853241, 0.0, 0.3311882512203042], \"xyz\": [-0.1274527670439516, 3.117717310919628, -0.1274527670439516], \"label\": \"Ti\", \"properties\": {\"velocities\": [0.0, 0.0, 0.0]}}, {\"species\": [{\"element\": \"Ti\", \"occu\": 1}], \"abc\": [0.0, 0.5, 0.5], \"xyz\": [0.0, 3.266188807530005, -3.266188807530005], \"label\": \"Ti\", \"properties\": {\"velocities\": [0.0, 0.0, 0.0]}}, {\"species\": [{\"element\": \"Ti\", \"occu\": 1}], \"abc\": [0.4156672204146759, 0.0, 0.6688117487796958], \"xyz\": [-1.5056416367210512, 5.047754707905385, -1.5056416367210512], \"label\": \"Ti\", \"properties\": {\"velocities\": [0.0, 0.0, 0.0]}}, {\"species\": [{\"element\": \"Ti\", \"occu\": 1}], \"abc\": [0.7385066282813852, 0.5, 0.8396798822245941], \"xyz\": [0.09659241232461158, 6.691157108249856, -3.1695963952053936], \"label\": \"Ti\", \"properties\": {\"velocities\": [0.0, 0.0, 0.0]}}, {\"species\": [{\"element\": \"Nb\", \"occu\": 1}], \"abc\": [0.0, 0.0, 0.0], \"xyz\": [0.0, 0.0, 0.0], \"label\": \"Nb\", \"properties\": {\"velocities\": [0.0, 0.0, 0.0]}}]}\r\n\r\n</p>\r\n</details> "
] | 2023-06-12T17:22:58
| 2023-06-13T21:57:49
|
CONTRIBUTOR
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https://github.com/materialsproject/pymatgen/blob/82f108a3cba5f12b88b95fecb4e3b775ca9de6c6/pymatgen/core/tensors.py#L460
For the structure below, an error occurs when attempting to create the IEEE rotation matrix. I believe it is due to this structure, which is identified as monoclinic by the SpaceGroupAnalyzer, having all 90 degree angles.
> Full Formula (Ti5 Nb1)
> Reduced Formula: Ti5Nb
> abc : 2.828602 4.619089 8.000496
> angles: 90.000000 90.000000 90.000000
> pbc : True True True
> Sites (6)
> \# SP a b c velocities
> \--- ---- -------- --- -------- ---------------
> 0 Ti. 0.261493 0.5 0.16032 [0.0, 0.0, 0.0]
> 1 Ti 0.584333 0 0.331188 [0.0, 0.0, 0.0]
> 2 Ti 0 0.5 0.5 [0.0, 0.0, 0.0]
> 3 Ti 0.415667 0 0.668812 [0.0, 0.0, 0.0]
> 4 Ti 0.738507 0.5 0.83968 [0.0, 0.0, 0.0]
> 5 Nb 0 0 0 [0.0, 0.0, 0.0]
Does anyone have any ideas how to fix this issue? Perhaps @mkhorton ?
|
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PR_kwDOACgets5SzzjU
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Skip `Molecule.relax()` tests
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[
"@janosh: I can confirm after running tests locally that everything works fine with `Molecule.calculate()` when `matgl` is not installed, but when you install `matgl` in the same environment as `tblite[ase]`, the GFN2-xTB calculations that `tblite` runs yield convergence errors and therefore fails the test suite.\r\n\r\n**The root cause is the `torch` dependency of `matgl`**: If you uninstall `torch`, everything works fine with `tblite`. Related error: https://github.com/tblite/tblite/issues/110. I tried not importing `matgl` anywhere but the issue only resolved if I uninstalled `torch`.\r\n\r\nHow should we best proceed? Should we split the tests up based on dependencies a bit until it's resolved upstream? `matgl` is not needed to run `Molecule.relax()`.\r\n\r\nNote that there was one import change I had to make in this PR regardless. I could use your help on this from a package management standpoint. What a frustrating bug.\r\n\r\nI've got to catch a flight so my hands are tied for a little bit.",
"Pinging @shyuep to let him know the (rather disappointing) cause.",
"I think the simple way to deal with this would be to have the tests in one single method, run the tblite first, and then import matgl and run the other tests? I agree this is a nutty bug. ",
"The alternative is to comment out the `tblite` tests first. I think that is less used than Structure.relax. ",
"Yup, that's exactly what I did here right now was comment them out. "
] | 2023-06-12T19:30:30
| 2023-06-13T14:30:33
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2023-06-13T14:30:33Z
|
MEMBER
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See below.
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I_kwDOACgets5og3Fk
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Ase in optional requirement vs. ase import in pymatgen.core.structure
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[
"@arosen93 Pls fix....",
"@shyuep: Will fix it ASAP right after this meeting. There's no need for it to be required. Something must have been missed.",
"Thanks, @janosh "
] | 2023-06-12T19:39:05
| 2023-06-22T18:55:37
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2023-06-13T10:03:07Z
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MEMBER
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#### Description
I installed pymatgen today and tried to use `pymatgen.io.structure.Structure`. It failed because of this import https://github.com/materialsproject/pymatgen/blob/82f108a3cba5f12b88b95fecb4e3b775ca9de6c6/pymatgen/core/structure.py#L27
`ase` is currently an optional requirement. After installing `ase`, everything was fine.
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PR_kwDOACgets5S0APu
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Don't require ASE as dependency
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[
"Thanks! ",
"No problem. Please let me know if this issue still arises anywhere else!",
"Just a heads up that this PR was merged empty and so #3061 isn't actually fixed yet. I'll re-open that issue and re-apply the fix."
] | 2023-06-12T20:04:03
| 2023-06-13T10:00:40
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2023-06-12T20:05:57Z
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Closes #3061. @JaGeo
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Update doc in periodic_table.py
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[
"Thank you! 👍 I remember wanting to clarify this myself at some point and then forgot. 😅 "
] | 2023-06-13T11:59:05
| 2023-06-13T12:12:54
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2023-06-13T12:12:40Z
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CONTRIBUTOR
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The description of `electronegativity` in periodic_table.py is not clear and a bit confusing as there are different types of `electronegativity` (see https://en.wikipedia.org/wiki/Electronegativity). Specified the `electronegativity` as `Pauling electronegativity`.
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Use self-documenting f-strings instead of hard-coding var names
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2023-06-13T14:45:12Z
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Also set `fail-fast: false` on `pytest` matrix jobs. This means we finish all tests even if one fails but still report the matrix as failed. This was originally intended when setting `continue-on-error: true` which also keeps going on test errors but doesn't report the matrix as failed. See 60757b8c50c4ba6fc774ade4b05a3afe6dd509c5.
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I_kwDOACgets5opvUr
| 3,065
|
Error in writing Structure to cif file, when site species have "spin" property
|
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[
"Be aware that disordered magnetic materials are possible. I've never been entirely satisfied with the distinction between Species.spin and the magmom site property, but the former does allow a disordered magnetic material to be defined, while the latter does not.",
"I would distinguish spin as an theoretical construct attached to a specie. Eg a low spin Co3+ in octahedral has a spin of 0. Magmom is an actual calculated property. Eg an actual Co3+ in LiCoO2 can have a non zero magmom. ",
"I remember this comment from you last time we discussed @shyuep :)\n\nI think the reason I find it unsatisfying is simply that the site properties are not typed, and the use of \"magmom\" is mostly by our own convention.",
"Is this technically a bug? Not sure if `pymatgen` guarantees CIF round-trip identity?\r\n\r\n@mkhorton Are you mostly concerned about not following a standard or site props being untyped? We could start typing by defining a `SiteProps` `TypedDict`:\r\n\r\n```py\r\nfrom typing import TypedDict\r\n\r\nclass SiteProps(TypedDict, total=true):\r\n magmom: list[float]\r\n charge: list[float]\r\n```\r\n\r\n`total=True` allows any key to be present in the dictionary, even if not specified in the type hint.\r\n\r\n@kamronald Could you post a minimal repro [similar to this](https://github.com/materialsproject/pymatgen/issues/3006#issuecomment-1563093693)?",
"Yes @janosh here is the repro. I have attached the CONTCAR and output structures below. \"enum_{i}.cif\" are structures with wrong atomic positions, and \"enum_mm_{i}.cif\" are structures with magnetic moment site properties that have the correct atomic positions. If you directly view the structures after running `MagneticStructureEnumerator` on Crystal Toolkit, they agree with the `enum_mm_{i}.cif` structures.\r\n\r\n<details><summary>Repro</summary>\r\n\r\n```\r\nfrom pymatgen.analysis.magnetism import MagneticStructureEnumerator\r\nfrom pymatgen.core import PeriodicSite, Structure\r\n\r\nstruc = Structure.from_file(\"CONTCAR\")\r\nmag_enum = MagneticStructureEnumerator(\r\n structure=struc,\r\n automatic=False,\r\n default_magmoms={\"Li\": 0.0, \"Mn\": 4.0, \"O\": 0.0},\r\n strategies=[\"ferromagnetic\", \"antiferromagnetic\"],\r\n)\r\nfor i, struc in enumerate(mag_enum.ordered_structures):\r\n struc.to(f\"enum_{i}.cif\")\r\n\r\n\r\ndef replace_spins_w_magmom(structure):\r\n sites = []\r\n for spec, site in zip(structure.species, structure.sites):\r\n spin = spec._properties.get(\"spin\", 0.0)\r\n new_site = PeriodicSite(\r\n species=spec.symbol,\r\n coords=site.frac_coords,\r\n lattice=site.lattice,\r\n properties={\"magmom\": spin},\r\n )\r\n sites.append(new_site)\r\n return Structure.from_sites(sites)\r\n\r\n\r\nfor i, struc in enumerate(mag_enum.ordered_structures):\r\n magmom_struc = replace_spins_w_magmom(struc)\r\n magmom_struc.to(f\"enum_mm_{i}.cif\")\r\n```\r\n[mag_debug_strucs.zip](https://github.com/materialsproject/pymatgen/files/11761255/mag_debug_strucs.zip)\r\n\r\n</details>",
"I have found the error: adding the site \"spin\" property causes certain columns of data in the cif file to be \"shifted\". Specifically, the site x coordinate column contains the site occupancies, y coordinate column actually contains the x coordinates, z coordinate column contains the y coordinate, and occupancy coordinate contains the site occupancies. \r\nI have attached a screenshot of this data from enum_1.cif (which has the wrong columns) and the original enumerated structure. The info about the species spin actually takes up a column in the incorrect cif file, which likely leads to the error.\r\n\r\nCorrect cif data:\r\n\r\nIncorrect \"shifted\" cif data\r\n\r\n",
"After changing a couple lines in CifWriter, the atomic locations in cif files are now correct, done in this commit: [([019dd8a](https://github.com/materialsproject/pymatgen/commit/019dd8a82e5bbbce6fbb15aaddc5fae772504dba))]\r\nBefore the CifWriter stores the whole Species string, which includes the spin property. Now I only store the element symbol, but this means the spin info would now be lost. Could we add a separate column to include this data?\r\n@shyuep @janosh @mkhorton @mattmcdermott",
"Actually, if the user wants to save magmom or spin info, they can do so by saving as MCIF. I just checked that this functionality works",
"More or less agree, but noting that during the mCIF specification discussions, it was an open question whether they would add a scalar magmom attribute; last I checked, mCIF is correctly more intended for vector moments (eg from a non-collinear calculation), so the current mCIF writer cheats a little by choosing an arbitrary axis. For regular CIF files, we could equally just write out spin or other site properties under our own prefix. We actually reserved the “_mp” prefix for our own usage: https://www.iucr.org/cgi-bin/cifreserve.pl"
] | 2023-06-13T23:06:07
| 2023-06-16T06:15:10
|
NONE
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Error arose when enumerating magnetic structures, related to #3006 . When saving the enumerated structures, cif files are very different from the actual Structure objects generated by MagneticStructureEnumerator.
Writing to cif is fixed when the structure is modified such that spins are not defined, but replaced by defining a "magmom" site property.
### Repro
```py
from pymatgen.analysis.magnetism import MagneticStructureEnumerator
from pymatgen.core import PeriodicSite, Structure
struc = Structure.from_file("CONTCAR")
mag_enum = MagneticStructureEnumerator(
structure=struc,
automatic=False,
default_magmoms={"Li": 0.0, "Mn": 4.0, "O": 0.0},
strategies=["ferromagnetic", "antiferromagnetic"],
)
for i, struc in enumerate(mag_enum.ordered_structures):
struc.to(f"enum_{i}.cif")
def replace_spins_w_magmom(structure):
sites = []
for spec, site in zip(structure.species, structure.sites):
spin = spec._properties.get("spin", 0.0)
new_site = PeriodicSite(
species=spec.symbol,
coords=site.frac_coords,
lattice=site.lattice,
properties={"magmom": spin},
)
sites.append(new_site)
return Structure.from_sites(sites)
for i, struc in enumerate(mag_enum.ordered_structures):
magmom_struc = replace_spins_w_magmom(struc)
magmom_struc.to(f"enum_mm_{i}.cif")
```
[mag_debug_strucs.zip](https://github.com/materialsproject/pymatgen/files/11761255/mag_debug_strucs.zip)
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PR_kwDOACgets5S82xs
| 3,066
|
Fix `ValueError: Unexpected atomic number Z=0`
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[] | 2023-06-14T05:21:04
| 2023-06-14T05:38:17
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2023-06-14T05:38:15Z
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MEMBER
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Caused by
```py
for idx, specie in enumerate(species):
sites.append(Site(specie, coords[idx], properties=prop))
```
where `species` is `dict`, not list so to get value, must be `species[idx]`, not `specie`.
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PR_kwDOACgets5S9CSO
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PymatgenTest add auto-used `tmp_path` fixture (replaces `ScratchDir`)
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[] | 2023-06-14T06:10:03
| 2023-06-14T11:14:42
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2023-06-14T11:14:41Z
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534af3078 `PymatgenTest` add `@pytest.fixture(autouse=True) def _tmp_dir(self, tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:`
a18903217 remove many no longer needed `monty.tempfile.ScratchDir(".")`
@shyuep It's a bit more magical since people who don't look at `PymatgenTest` won't know that their tests now run in a temporary directory by default due to [this new fixture](https://github.com/materialsproject/pymatgen/compare/PymatgenTest-autoused-tmp-path-fixture?expand=1#diff-e9cfd9b89de7ff172f8b6e26e92bb559f6f61ae34d0ee3c08c8b06954e1f69c1R48-R53). But the code is cleaner now imo and less chance of failing tests leaving behind undeleted files in the repo that litter `git status`.
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I_kwDOACgets5otuVX
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Reading and writing POTCAR files is broken
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"Just to confirm, the problem is `\"End of Dataset\"` not being on a new line?",
"Yes, exactly",
"Thanks for reporting this!\nI think the last fix on parsing fixed one white space problem and created another. I'm currently on family leave until the end of next week I can fix it when I come back.",
"I think the problem is in reading the POTCAR from file. The `.stip()` method is used when constructing the PotcarSingle objects when it should not be used.\r\n\r\nThis should work (in the Potcar class):\r\n~~~\r\n @staticmethod\r\n def from_file(filename: str):\r\n \"\"\"\r\n Reads Potcar from file.\r\n\r\n :param filename: Filename\r\n :return: Potcar\r\n \"\"\"\r\n with zopen(filename, \"rt\") as f:\r\n fdata = f.read()\r\n potcar = Potcar()\r\n\r\n functionals = []\r\n for p in fdata.split(\"End of Dataset\\n\"):\r\n if p.strip():\r\n single = PotcarSingle(p + \"End of Dataset\\n\")\r\n potcar.append(single)\r\n functionals.append(single.functional)\r\n if len(set(functionals)) != 1:\r\n raise ValueError(\"File contains incompatible functionals!\")\r\n potcar.functional = functionals[0]\r\n return potcar\r\n~~~\r\nIt is essentially what was there before commit 1e9119a07e0.\r\n\r\nRegarding the discussion in #2910, I understand that the hash system is a bit brittle and cumbersome. But I do not think commenting out tests is the way to go. If one needs to keep the hash checks, then one should try and add more unit tests precisely because it is a fickle thing. Otherwise, one should just get rid of it entirely.\r\n\r\nI want to stress that the issue @henriquemiranda describes does not only give a hash warning. The resulting POTCAR is not valid and will crash VASP. So this has not strictly to do with the hash system.\r\n",
"I think this can also work:\r\n```\r\n- single = PotcarSingle(p_strip + \"End of Dataset\\n\")\r\n+ single = PotcarSingle(p_strip + \"\\nEnd of Dataset\\n\")\r\n```\r\nI believe `p_strip` was used here to help make sure that the output POTCARs were more consistent with the hope that we implement some kind of more usable hashing in the future but that obviously backfired.\r\n\r\nI'm not actually able to pull the code since I'm in China (on family leave) until the end of next week and the VPN has been really slow.\r\nSo if this is an emergency someone else will have to patch and test this. Apologies.",
"This version does produce a valid POTCAR, but it still fails the implemented hash checks. I really do not see the point in reformatting POTCARs. No full file hash can work consistently for both POTCARs that are just taken from the library and maybe concatenated together, and ones that have been reformatted by pymatgen.\r\n\r\nI took me a lot of effort to repair the hashing system that was throwing warnings every time a POTCAR was used for a long time in #2762. I tried to make the hashing system more usable and future proof by using POTCAR internal hashes as well and not only the ones in the pymatgen hash tables. I am the first to admit that the solutions were not very easy to read because of all the regex statements, but at least it worked...",
"> I took me a lot of effort to repair the hashing system that was throwing warnings every time a POTCAR was used for a long time in https://github.com/materialsproject/pymatgen/pull/2762.\r\n\r\nApologies @MichaelWolloch. Certainly not our intent to waste anyone's time or undo work.\r\n\r\n> I really do not see the point in reformatting POTCARs.\r\n\r\nI think @jmmshn was having trouble parsing POTCAR headers which motivated the change in #2910:\r\n\r\n\r\n> > Without the fix:\r\n> > ```python\r\n> > pc = Potcar.from_file(\"./POTCAR\")\r\n> > {d.header for d in pc}\r\n> > ```\r\n> > Gives: \r\n> > ```\r\n> > {'PAW_PBE Ga_d 06Jul2010', ''}\r\n> > ```\r\n> > \r\n> > with the fix, you get:\r\n> > ```\r\n> > {'PAW_PBE Ga_d 06Jul2010', 'PAW_PBE N 08Apr2002'}\r\n> > ```\r\n\r\nMaybe there's a middle ground here...",
"No apologies needed @janosh , I realize of course that nobody is doing anything out of malice.\r\nMy only concern is that tests are being deleted and warnings ignored. Of course the header of each PotcarSingle should be accessible from the Potcar object.\r\n\r\nAnd I would also not be mad if the hashing checks are completely removed at some point. I personally think that they have value, and that POTCARs should never be modified (as is also the VASP companies policy), but one does not necessarily have to check for modification by hashes.\r\n\r\nThe code I posted above and also gives the right headers by the way (using @henriquemiranda's example):\r\n~~~\r\nfrom pymatgen.io.vasp import Potcar\r\n\r\npotcar = Potcar.from_file(\"POTCAR_old\")\r\npotcar.write_file(\"POTCAR\")\r\nprint({d.header for d in potcar})\r\n~~~\r\ngives (without a warning due to a failed hash):\r\n`{'PAW Sb 04Feb1998', 'PAW Te 03Oct2001'}`",
"Just remove all that ridiculous hashing stuff already. I see zero value in them, except to cause more headaches for maintainers.",
"Fine with me. Just be careful that the POTCARs are not modified in a way that breaks functionality as happened in #2910 in the future. I feel that hashing is a reasonable way to do this, even if it is not easy to maintain. But I am continuing to offer my help here.",
"Agreed there should have a basic POTCAR parsing/validation test. I'll make sure to add it when I get back.\r\n",
"Thanks @jmmshn , I am happy to take part in discussions on how this could look without using hashes or executing VASP to see if the POTCAR is valid.",
"@jmmshn just pinging you about the POTCAR parsing/validation test",
"I am on holiday until the 10th. I am happy to comment on any validation test that is proposed. However, I still think that the hashing is a pretty optimal way of doing the validation. If someone proposes something better I am happy to help with implementation and testing however, and I would also of course be willing to work on the hashing if we decide to keep it after all.",
"> I think the problem is in reading the POTCAR from file. The `.stip()` method is used when constructing the PotcarSingle objects when it should not be used.\r\n> \r\n> This should work (in the Potcar class):\r\n> \r\n> ```\r\n> @staticmethod\r\n> def from_file(filename: str):\r\n> \"\"\"\r\n> Reads Potcar from file.\r\n> \r\n> :param filename: Filename\r\n> :return: Potcar\r\n> \"\"\"\r\n> with zopen(filename, \"rt\") as f:\r\n> fdata = f.read()\r\n> potcar = Potcar()\r\n> \r\n> functionals = []\r\n> for p in fdata.split(\"End of Dataset\\n\"):\r\n> if p.strip():\r\n> single = PotcarSingle(p + \"End of Dataset\\n\")\r\n> potcar.append(single)\r\n> functionals.append(single.functional)\r\n> if len(set(functionals)) != 1:\r\n> raise ValueError(\"File contains incompatible functionals!\")\r\n> potcar.functional = functionals[0]\r\n> return potcar\r\n> ```\r\n> \r\n> It is essentially what was there before commit [1e9119a](https://github.com/materialsproject/pymatgen/commit/1e9119a07e0282bb89807a874583e66e57ea35f5).\r\n> \r\n> Regarding the discussion in #2910, I understand that the hash system is a bit brittle and cumbersome. But I do not think commenting out tests is the way to go. If one needs to keep the hash checks, then one should try and add more unit tests precisely because it is a fickle thing. Otherwise, one should just get rid of it entirely.\r\n> \r\n> I want to stress that the issue @henriquemiranda describes does not only give a hash warning. The resulting POTCAR is not valid and will crash VASP. So this has not strictly to do with the hash system.\r\n\r\nNote that I now discovered (see https://github.com/hackingmaterials/atomate/pull/778) that the original version of this code block was different than what I suggested. Before commit [1e9119a](https://github.com/materialsproject/pymatgen/commit/1e9119a07e0282bb89807a874583e66e57ea35f5) it did not include the newline after \"End of Dataset\" in the `split()` command. This resulted in the problems with `PotcarSingle.header` attributes being empty since the `PotcarSingles` started with a new line after the first one.\r\n~~~\r\nfunctionals = []\r\nfor p in fdata.split(\"End of Dataset\"):\r\n if p.strip():\r\n single = PotcarSingle(p + \"End of Dataset\\n\")\r\n~~~\r\n\r\nThe version of the `from_file` method I gave previously is correct however and will be part of a PR shortly.",
"BTW I did PR in the basic validation test a while ago in #3141 so we can close this if the atomate stuff all works.",
"@jmmshn , as you can see, I just made the PR that should fix issue we discovered in atomate. I think this can be closed, and if further discussion is needed, it can go there."
] | 2023-06-14T12:40:40
| 2023-08-15T16:26:38
|
2023-08-15T16:26:38Z
|
CONTRIBUTOR
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#### Description
Reading and writing POTCAR file with the Potcar class from pymatgen.io.vasp seems broken.
#### Repro
To reproduce the problem, I start with a file:
POTCAR
```
PAW Sb 04Feb1998
5.00000000000000
[...]
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
End of Dataset
PAW Te 03Oct2001
6.00000000000000
[...]
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
End of Dataset
```
I use the following script to copy the POTCAR:
```
from pymatgen.io.vasp import Potcar
potcar = Potcar.from_file('POTCAR')
potcar.write_file('POTCAR_NEW')
```
the resulting file becomes:
POTCAR_NEW
```
PAW Sb 04Feb1998
5.00000000000000
[...]
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00End of Dataset
PAW Te 03Oct2001
6.00000000000000
[...]
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00End of Dataset
```
#### Expected behavior
I would expect the files in POTCAR_NEW to be the same as the ones in POTCAR
#### Problem
The problem originated after #2910 was merged.
Perhaps @jmmshn and @janosh have some insight.
From the discussion, it looks like the relevant tests were broken by these changes and then deactivated.
I also mention @MichaelWolloch since he knows about the handling of the hashes of the POTCAR files.
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Remove assertEqual vestiges in tests
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Fix `MagOrderingTransformation` by enforcing implicit-zero magnetic moments in `SpaceGroupAnalyzer`
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[
"This PR has been open for a while and fixed some of the previous magnetic moment problems. I apologize for not adding tests yet to get it merged.\r\n\r\nHowever, with the recent changes in `Species` properties (related to spin), the`MagOrderingTransformation` code is again broken. I don't really understand what happened/changed, and now I am not sure I have the bandwidth to try fixing this again.\r\n\r\nDoes anyone with more knowledge of this situation able to address? @janosh @shyuep @mkhorton\r\n",
"Just for clarity, this PR still addresses a relevant bug and is just missing tests? Sounds like the `MagOrderingTransformation` breaking again is a different problem?",
"The original problem this PR addressed is still \"fixed\"(i.e., enforcing implicit-zero magnetic moments) but the implementation here will need to be reworked to account for the new defaults in how spin is handled.\r\n\r\nI am just somewhat confused about specifically why it's broken now and what is the right thing to do... I think @shyuep also expressed that sentiment: https://github.com/materialsproject/pymatgen/commit/9d0461f030f726f944a4d5f26002b6c997562f0f ",
">I am just somewhat confused about specifically why it's broken now and what is the right thing to do... I think @shyuep also expressed that sentiment: https://github.com/materialsproject/pymatgen/commit/9d0461f030f726f944a4d5f26002b6c997562f0f\r\n\r\nLol! 😄 \r\n\r\nWell, I'm happy to merge as is if this is at least a step towards improvement.",
"Well it certainly worked at some point! I think keeping this running in CI was tricky because of its dependence on `enumlib`, and since `enumlib` on `conda` was quite out of date (this is not to blame the issue on `enumlib`, simply for why this bug might have remained uncaught).",
"This fix actually works. I am merging.",
"I should add that my changes to Specie does not do anything backward incompatible. I was deliberate in making sure all existing code still works. @mattmcdermott 's solution works since it is based on existing ways of determining spin.",
"Also, no tests are necessary. There is an existing test in MagTransformation. The tests fail previously. Not sure why the Github actions is not detecting it. But I confirm the tests pass now.",
"Oh, that is great to hear! Glad you were able to pull this in, @shyuep. Thank you for investigating :) \r\n\r\nI should have spent some more time digging yesterday before I brought up that it was broken; it is actually a different section of code that is broken now -- specifically `CollinearMagneticStructureAnalyzer`. This seems only to be the case when a structure is provided that has a defined `spin` property but not defined `magmoms`. Seems to be something that is missed by our current tests.\r\n\r\nI just found a simple one-line fix for that, so I will open up a new PR :) thanks again everyone!"
] | 2023-06-15T22:56:00
| 2023-07-14T17:25:44
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2023-07-14T13:54:23Z
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This PR addresses the bugs described in #3006. To summarize: changes to default magnetic moments introduced in #2727 now mean that structures with only partially defined magnetic moments (e.g., on half the sites) cannot be successfully analyzed by `SpaceGroupAnalyzer`. This was encountered when performing magnetic ordering enumeration, as the previous default behavior for `MagOrderingTransformation` does not implicitly yield spins of 0 on the nonmagnetic sites. Altogether this has been fixed with two edits:
- Fix 1: Introduce logic in `SpaceGroupAnalyzer`. If any site in the structure has magnetic moments defined, then assume that any undefined ones are implicitly zero.
- Fix 2: Change the default behavior of `MagOrderingTransformation` to ensure that all the sites in the transformed structure have labeled spins (this means explicitly defining spin=0), per recommendation by @mkhorton
## Todos
- Still need to write tests!
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] All tests and linting pass.
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PR_kwDOACgets5TJAgg
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Bug fix: change CifWriter to save only the element symbol, and not the entire species string
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[
"@kamronald does this still handle species with oxidation state correctly?",
"@mkhorton good point, I just checked and it does not handle them properly, I'll fix that",
"@mkhorton oxidation states are now properly saved",
"Thanks @kamronald! 👍 \r\n\r\nIIUC @mkhorton in https://github.com/materialsproject/pymatgen/issues/3065#issuecomment-1593845643, he's suggesting we continue saving scalar magmoms to regular CIF using the local data name `mp` registered here https://www.iucr.org/cgi-bin/cifreserve.pl.\r\n\r\nAlso, would be great if you could refactor your repro https://github.com/materialsproject/pymatgen/issues/3065#issuecomment-1593523071 into a new test case.",
"@janosh @mkhorton Yes will work on that",
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3071?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`100.00%`** and project coverage change: **`-0.57%`** :warning:\n> Comparison is base [(`a1c19db`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/a1c19db7672a185e4f001494806bb19a115354fe?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.65% compared to head [(`324a675`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3071?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.09%.\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3071 +/- ##\n==========================================\n- Coverage 74.65% 74.09% -0.57% \n==========================================\n Files 230 230 \n Lines 69377 69382 +5 \n Branches 16154 16154 \n==========================================\n- Hits 51796 51410 -386 \n- Misses 14513 14937 +424 \n+ Partials 3068 3035 -33 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3071?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [pymatgen/io/cif.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3071?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vaW8vY2lmLnB5) | `92.21% <100.00%> (+0.04%)` | :arrow_up: |\n\n... and [6 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3071/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3071?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n"
] | 2023-06-15T23:25:21
| 2024-08-03T19:01:57
|
NONE
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Change the "atom site type symbol", such that the element symbol is saved instead of the full species string (which includes site properties). This fixes Issue #3065, allowing for accurate writing of structures containing species properties to CIF and MCIF files.
## Summary
Major updates:
Change the "atom site type symbol", such that the element symbol is saved instead of the full species string (which includes site properties).
## Todos
## Checklist
Ensure:
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] All tests and linting pass.
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PR_kwDOACgets5TNMDC
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More pytest.approx() refactoring
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Following https://github.com/materialsproject/pymatgen/commit/6af8a3d8b0e7e368e62daecc70173ab94594dc3e and https://github.com/materialsproject/pymatgen/commit/88b3738922cf3c05dce9fc39e7d7b3250d7e7881.
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Update test_kpath_lm.py, remove redundant test and simplify tests
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[
"Openbabel seems to be missing. Not sure why. Should be unrelated to this change. \r\n\r\nMany unrelated failing tests 🙈",
"Yeah I think that's caused by a the latest `mp-api` release. Thank for the cleanup!",
"Thanks!\r\n\r\n Maybe @munrojm could also shortly check if it should be an \"and\" rather than an \"or\" in the other lines and the one that I removed. I assume some of the tests should be related to the time-reversal symmetry for magnetic space groups. I also assume that the kpoint should be the same for every run and no \"or\" is necessary. "
] | 2023-06-17T06:41:24
| 2023-06-17T08:35:44
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2023-06-17T07:09:09Z
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MEMBER
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HI @janosh ,
I removed and simplified the tests. I am still not sure why there is an "or" for the other tests. In my opinion, the result should be always the same for one structure.
It's also redundant to test if g has a certain k-point and then later on tests if point g has the same kpoint or point xyz has a certain k-point.
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Single-line `None` assignment
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Breaking: change `Composition` bad key error type from `TypeError` to `KeyError`
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2023-06-18T14:54:44Z
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8011095ce single line None assignment
697dec8eb more precise error message testing
0f1256ca8 breaking: change Composition bad key error type from TypeError to KeyError
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Cosmetic fixes to `AseAtomsAdaptor` dictionary key ordering
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[
"Ready to go, @janosh! "
] | 2023-06-18T15:49:52
| 2023-06-18T18:29:25
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2023-06-18T18:10:45Z
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When interconverting between `Atoms` and `Structure`/`Molecule`, the key ordering in the `.todict()` representation changes. This PR fixes this trivial non-issue.
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Fix `ase` tests not running due to `pymatgen/io/ase.py` shadowing `ase` package
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[
"Thank you!! 🙏",
"If the user doesn't have ASE installed though, the test still skips right? On mobile so can't see what `ase_loaded` does. ",
"No, running _all_ tests now requires `ase` to be installed. I think that's fine. Running tests locally usually involves specifying a path to a test module so you only run the tests you care about in which case `ase` is not needed.",
"@janosh @arosen93 I think this is where the problem started.\r\n",
"Let's not do ugly hacks in main code for things like tests, linting, etc.! It is more important that features work properly. If tests or lintinig require hacks, they should be done in test code that don't affect deployed code.",
"Oops. Don't remember why I put this in `pymatgen/io/ase.py`. Definitely seems like a bad idea in retrospect. I think I meant to put this in `pymatgen/io/tests/test_ase.py` (presumably that didn't work, hence this bad alternative)."
] | 2023-06-18T16:54:04
| 2023-07-14T14:07:51
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Tests were set to skip if `ase` not importable (now removed so we catch this in the future).
@arosen93 `sys.path.insert(0, getsitepackages()[0])` is admittedly an ugly hack but, like you said, preferable over a breaking module rename.
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I_kwDOACgets5pC9wY
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test_fragmenter babel_PC_with_RO_depth fails
|
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[
"I'm having trouble installing `openbabel` on Mac so can't run this test myself. Is this value correct?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/47af172ac90ff5e23ce76bbaa5cb8b695d165a82/pymatgen/analysis/tests/test_fragmenter.py#L120\r\n\r\n I'm concerned these tests are apparently being skipped in CI. I was under the impression `openbabel` is installed in our Linux CI."
] | 2023-06-18T17:16:16
| 2023-06-22T23:02:58
|
2023-06-22T23:02:58Z
|
CONTRIBUTOR
|
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#### Description
Testing pymatgen 2023.05.31 on debian unstable, all tests pass except
test_babel_PC_with_RO_depth_0_vs_depth_10 from analysis/tests/test_fragmenter.py
#### Repro
Steps to reproduce the behavior:
1. Build from source, including pymatgen test-files
2. `pytest-3 -vv pymatgen/analysis/tests/test_fragmenter.py -k RO_depth`
3. See error
Short error:
```
_________________________________________________________________________ TestFragmentMolecule.test_babel_PC_with_RO_depth_0_vs_depth_10 __________________________________________________________________________
self = <test_fragmenter.TestFragmentMolecule testMethod=test_babel_PC_with_RO_depth_0_vs_depth_10>
def test_babel_PC_with_RO_depth_0_vs_depth_10(self):
pytest.importorskip("openbabel", reason="OpenBabel not installed")
fragmenter0 = Fragmenter(molecule=self.pc, depth=0, open_rings=True, opt_steps=1000)
> assert fragmenter0.total_unique_fragments == 509
E assert 411 == 509
E + where 411 = <pymatgen.analysis.fragmenter.Fragmenter object at 0x7f6e6e87bed0>.total_unique_fragments
test_fragmenter.py:118: AssertionError
```
Long error log:
```
/projects/pymatgen/pymatgen/analysis/tests$ PMG_TEST_FILES_DIR=/usr/share/doc/pymatgen-test-files/examples/test_files PYTHONPATH=/projects/pymatgen/.pybuild/cpython3_3.11_pymatgen/build/ pytest-3 -vv test_fragmenter.py -k RO_depth
=============================================================================================== test session starts ===============================================================================================
platform linux -- Python 3.11.4, pytest-7.3.2, pluggy-1.0.0+repack -- /usr/bin/python3
cachedir: .pytest_cache
hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/projects/pymatgen/pymatgen/analysis/tests/.hypothesis/examples')
rootdir: /projects/pymatgen
configfile: pyproject.toml
plugins: xvfb-2.0.0, remotedata-0.4.0, asyncio-0.20.3, arraydiff-0.5.0, filter-subpackage-0.1.2, flaky-3.7.0, cov-4.0.0, mpi-0.6, astropy-header-0.2.2, openfiles-0.5.0, hypothesis-6.73.0, mock-3.8.2, doctestplus-0.12.1, astropy-0.10.0
asyncio: mode=Mode.STRICT
collected 11 items / 10 deselected / 1 selected
test_fragmenter.py::TestFragmentMolecule::test_babel_PC_with_RO_depth_0_vs_depth_10 FAILED [100%]
==================================================================================================== FAILURES =====================================================================================================
_________________________________________________________________________ TestFragmentMolecule.test_babel_PC_with_RO_depth_0_vs_depth_10 __________________________________________________________________________
self = <test_fragmenter.TestFragmentMolecule testMethod=test_babel_PC_with_RO_depth_0_vs_depth_10>
def test_babel_PC_with_RO_depth_0_vs_depth_10(self):
pytest.importorskip("openbabel", reason="OpenBabel not installed")
fragmenter0 = Fragmenter(molecule=self.pc, depth=0, open_rings=True, opt_steps=1000)
> assert fragmenter0.total_unique_fragments == 509
E assert 411 == 509
E + where 411 = <pymatgen.analysis.fragmenter.Fragmenter object at 0x7f6e6e87bed0>.total_unique_fragments
test_fragmenter.py:118: AssertionError
---------------------------------------------------------------------------------------------- Captured stderr call -----------------------------------------------------------------------------------------------
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
============================================================================================== slowest 30 durations ===============================================================================================
10.02s call pymatgen/analysis/tests/test_fragmenter.py::TestFragmentMolecule::test_babel_PC_with_RO_depth_0_vs_depth_10
(2 durations < 0.005s hidden. Use -vv to show these durations.)
======================================================================================== 1 failed, 10 deselected in 13.08s ========================================================================================
```
#### Expected behavior
The test should pass.
#### Environment
- OS: Linux (debian unstable)
- pymatgen 2023.05.31
- openbabel 3.1.1
|
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PR_kwDOACgets5TTfET
| 3,079
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Improvements to the documentation of the Lobsterenv module
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[
"@janosh, I tried to add more type hinting but mypy was raising very weird errors. ",
"Where functions are returning a large tuple containing various types and lengths of data, it might be helpful to wrap them up as a NamedTuple. This would be backward-compatible as you still _can_ access the elements by index, but also allows:\r\n\r\n- clearer type-hinting than a dict would have, taking advantage of the immutability\r\n- named attribute access for more intelligible code and lower chance of accessing the wrong element by mistake\r\n- easier interactive exploration e.g. in a Jupyter notebook or IPython terminal; we get something a bit more self-describing than a bare list of tuple, but not a complicated new class that might have surprising behaviours\r\n\r\nBe aware that while a lot of the old docs and tutorials recommend to use the `namedtuple` function to produce them, we can now build them with `class` for clearer type-hinting. See examples at https://docs.python.org/3/library/typing.html#typing.NamedTuple\r\n\r\nSo we could do something like\r\n\r\n```python\r\nclass ICOHPNeighboursInfo(NamedTuple):\r\n total: float\r\n interaction_sums: List[float]\r\n n_bonds: int\r\n labels: List[str]\r\n atoms: List[SomeAtomTypeOrOther]\r\n central_isites: List[int]\r\n\r\nclass LobsterNeighbors(NearNeighbors):\r\n...\r\n def get_info_icohps_to_neighbors(\r\n self,\r\n isites: Optional[List[int]] = None,\r\n onlycation_isites: bool = True\r\n ) -> ICOHPNeighboursInfo:\r\n ...\r\n return ICOHPNeigboursInfo(summed_icohps, list_icohps, number_bonds, labels, atoms, final_isites)\r\n```\r\n",
"Thanks, @ajjackson , this is a great suggestion. I will implement it as it is much cleaner. ",
"@ajjackson , I implemented the named tuple"
] | 2023-06-19T06:34:11
| 2023-06-19T15:45:11
|
2023-06-19T15:45:09Z
|
MEMBER
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I improved the documentation of the LobsterEnv module which was triggered by our updates to LobsterPy (https://github.com/JaGeo/LobsterPy/pull/81) and suggestions by @ajjackson
@janosh : happy to hear additional thoughts from you.
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Add a cache to speed up get_el_sp
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[
"> One thing to keep in mind is that returned objects are not necessarily unique anymore, they could be returned again through the cache.\r\n\r\nThis sounds like a foot gun we should stay away from. Could you describe your motivation for this change? Maybe there's a safer way to go about this.",
"Closing this as stale for now. Feel free to report back and we can reopen/discuss further.",
"Element and Species are immutables. If this has a clear speed up, it should be fine. ",
"Species are immutable?\r\n\r\n```py\r\nfrom pymatgen.core import Species\r\n\r\nsp = Species(\"Fe2+\", properties={\"spin\": 5})\r\nsp.spin\r\n>>> 5\r\n\r\nsp.spin = 4\r\nsp.spin\r\n>>> 4\r\n```",
"They are *supposed* to be. That is the reason why this change has zero failures across pymatgen. If you really want to enforce strict immutability, then Species should be changed to a dataclass."
] | 2023-06-19T11:55:45
| 2023-06-27T20:18:51
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2023-06-27T20:01:11Z
|
CONTRIBUTOR
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Uses functools.cache to speed up the conversion of arbitrary objects into Element | Species | DummySpecies.
- One thing to keep in mind is that returned objects are not necessarily unique anymore, they could be returned again through the cache.
- Arguments to `get_el_sp` must be `Hashable`, luckily this seems to be the case
## Summary
Major updates:
- feature 1: massive speed up for get_el_sp
## Checklist
Ensure:
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [x] All tests and linting pass.
Tip: Install `pre-commit` hooks to auto-check before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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More precise error message tests and more informative errors in some cases
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[] | 2023-06-20T16:15:05
| 2023-06-20T17:18:02
|
2023-06-20T17:18:01Z
|
MEMBER
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| 1,765,841,477
|
PR_kwDOACgets5TdhhX
| 3,082
|
Add `test_apply_scissor_(insulator|spin_polarized)`
|
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[] | null |
[] | 2023-06-20T17:28:54
| 2023-06-20T17:56:39
|
2023-06-20T17:56:37Z
|
MEMBER
|
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Closes #1664.
|
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I_kwDOACgets5pSJ-6
| 3,084
|
Incorrect parsing of vasprun.xml for certain selective dynamics runs
|
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[] | null |
[] | 2023-06-20T23:59:17
| 2023-06-22T18:56:04
|
2023-06-22T17:40:50Z
|
CONTRIBUTOR
|
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|
#### Description
When selective dynamics is activated during a run but not all atomic sites are allowed to move (for instance, when calculating finite difference phonons at only a few sites with `IBRION = 5`), `Vasprun` in `pymatgen.io.vasp.outputs` erroneously sets the rank of the force constant matrix to be `(3 x 3)` for all atoms in the cell, instead of just those for which computations were made `len(hessian) // 3`.
In `pymatgen.io.vasp.outputs` on line `482`, change:
```python
natoms = len(self.atomic_symbols)
```
to:
```python
natoms = len(hessian) // 3
```
#### Steps to Reproduce
Follow these steps to reproduce the issue:
1. Attempt to create a `Vasprun` object with the attached VASP outputs, which perform a finite difference phonon calculation for just one lattice site.
* (This issue was identified because `custodian`'s `VasprunXMLValidator` failed, leading jobs to fizzle.) The following error should be returned:
```python
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<path_to_python_packages>/pymatgen/io/vasp/outputs.py", line 389, in __init__
self._parse(
File "<path_to_python_packages>/pymatgen/io/vasp/outputs.py", line 494, in _parse
self.force_constants[i, j] = hessian[i * 3 : (i + 1) * 3, j * 3 : (j + 1) * 3]
ValueError: could not broadcast input array from shape (3,0) into shape (3,3)
```
#### Expected Behavior
The expected outcome is the successful creation of a `Vasprun` object.
#### Environment
The issue was found in the following environments:
- Operating Systems: MacOS and Linux
- Version: 2023.3.10
#### Additional Context
The relevant file for reproduction is provided below:
[pymatgen_dyn_mat.tar.gz](https://github.com/materialsproject/pymatgen/files/11809337/pymatgen_dyn_mat.tar.gz)
|
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| 1,766,474,788
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PR_kwDOACgets5TfZbp
| 3,085
|
Immutable class defaults
|
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[] | 2023-06-21T01:03:46
| 2023-06-21T01:56:12
|
2023-06-21T01:56:11Z
|
MEMBER
|
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|
Mutable default values share state across all instances of the class, which most people aren't aware of. This can lead to bugs when the attributes are changed in one instance, as those changes will unexpectedly affect all other instances.
Fix is to change to immutable types like `tuple` or [`frozendict`](https://github.com/Marco-Sulla/python-frozendict) (new dependency) if class attr shouldn't change, else annotate with `typing.ClassVar` for clarity if mutability is intended/required.
### Example
**Bad**
```py
class SelfEnergy(AbivarAble):
"""
This object defines the parameters used for the computation of the self-energy.
"""
_SIGMA_TYPES = {
"gw": 0,
"hartree_fock": 5,
"sex": 6,
"cohsex": 7,
"model_gw_ppm": 8,
"model_gw_cd": 9,
}
```
**Good**
```py
from frozendict import frozendict
class SelfEnergy(AbivarAble):
"""
This object defines the parameters used for the computation of the self-energy.
"""
_SIGMA_TYPES = frozendict(
gw=0,
hartree_fock=5,
sex=6,
cohsex=7,
model_gw_ppm=8,
model_gw_cd=9
)
```
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PR_kwDOACgets5TftAN
| 3,086
|
Fix hill_formula Composition property
|
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[] | 2023-06-21T02:51:29
| 2023-06-21T19:24:11
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2023-06-21T19:24:10Z
|
CONTRIBUTOR
|
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## Summary
This PR fixes an error in the **hill_formula** property of the Composition object, which occurs in cases where C, H, and other element/s with symbol ordering alphabetically before H are present at the same time. In such a case, H should be placed directly after C, but this is not implemented nor tested in the current version.
- Fixed the property to match the description.
- Implemented additional tests.
Sidenote: @ml-evs This fix should help eliminate compatibility issues with the OPTIMADE _chemical_formula_hill_ field (except for the presence/lack of empty spaces).
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I_kwDOACgets5pUnn9
| 3,087
|
DosPlotterTest tests floating point values by equality
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[] | 2023-06-21T08:05:17
| 2023-06-21T21:17:53
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2023-06-21T21:17:53Z
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CONTRIBUTOR
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#### Description
test_plotting in electron_structures uses `==` equality to test floating point numbers. This inevitably fails, e.g. on i386 https://ci.debian.net/data/autopkgtest/testing/i386/p/pymatgen/34643142/log.gz
#### Repro
Steps to reproduce the behavior:
1. Go to 'pymatgen/electronic_structure/tests/' on an i386 system
2. `PMG_TEST_FILES_DIR=/usr/share/doc/pymatgen-test-files/examples/test_files pytest-3 test_plotting.py`
3. See error
#### Expected behavior
Test should pass.
#### Environment
Relevant versions and platform info:
- OS: Debian unstable
- pymatgen v2023.05.31
#### Additional context
Error reported at https://ci.debian.net/data/autopkgtest/testing/i386/p/pymatgen/34643142/log.gz is
```
=================================== FAILURES ===================================
_____________________ DosPlotterTest.test_get_plot_limits ______________________
self = <electronic_structure.tests.test_plotter.DosPlotterTest testMethod=test_get_plot_limits>
def test_get_plot_limits(self):
# Tests limit determination and if inverted_axes case
# reproduces the same energy and DOS axis limits
from matplotlib import rc
rc("text", usetex=False)
self.plotter.add_dos_dict(self.dos.get_element_dos(), key_sort_func=lambda x: x.X)
# Contains energy and DOS limits and expected results
with open(os.path.join(PymatgenTest.TEST_FILES_DIR, "complete_dos_limits.json")) as f:
limits_results = json.load(f)
for item in limits_results:
plt = self.plotter.get_plot(xlim=item["energy_limit"], ylim=item["DOS_limit"])
param_dict = self.get_plot_attributes(plt)
plt_invert = self.plotter.get_plot(invert_axes=True, xlim=item["DOS_limit"], ylim=item["energy_limit"])
param_dict_invert = self.get_plot_attributes(plt_invert)
assert item["energy_result"] == param_dict["xaxis_limits"]
assert item["energy_result"] == param_dict_invert["yaxis_limits"]
> assert item["DOS_result"] == param_dict["yaxis_limits"]
E assert [-7.398965958...0663693157038] == [-7.398965958...6636931570365]
E At index 1 diff: 7.020663693157038 != 7.0206636931570365
E Full diff:
E - [-7.398965958040221, 7.0206636931570365]
E ? ^^
E + [-7.398965958040221, 7.020663693157038]
E ? ^
runtests/pymatgen/electronic_structure/tests/test_plotter.py:89: AssertionError
```
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PR_kwDOACgets5TltZl
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|
Fix doc string punctuation
|
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[] | 2023-06-21T20:25:47
| 2023-06-21T20:44:36
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2023-06-21T20:44:35Z
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MEMBER
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PR_kwDOACgets5TlwXs
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|
Fix `DosPlotterTest.test_get_plot_limits()` assert floats equal not using `approx`
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[] | 2023-06-21T20:34:14
| 2023-06-21T21:17:53
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2023-06-21T21:17:51Z
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Closes #3087.
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I_kwDOACgets5pb6Gd
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Z-matrix representation
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[
"> I wonder if this wouldn't be a good convenience method for molecule.\r\n\r\nGood idea! Would you like to submit a PR that moves this method to the `Molecule` class and also adds a unit test for it?\r\n",
"Moving the method, yes. Just wondering if this is the best representation as you can use site number, elememt name with site number etc in the z matrix for input files. I just don't have the time to develop such a representation at the moment.\r\nAny ideas? Otherwise, I just move the method.",
"I'm probably not the right person to ask this since I don't work with molecules/z-matrices.",
"> I'm probably not the right person to ask this since I don't work with molecules/z-matrices.\r\n\r\nYeah, no worries. I usually don't use them as well but it's a typical part of the compchem curriculum to learn about z-matrices and use them in qc codes."
] | 2023-06-22T04:53:48
| 2023-06-24T05:56:18
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2023-06-23T13:31:45Z
|
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I am currently using some pymatgen parts that I hadn't used before. As far as I see, we currently have an option for a z-matrix representation as part of the Gaussian output generation: https://github.com/materialsproject/pymatgen/blob/f90929f75b27fe1d06faa4e2a5f44654009b98b0/pymatgen/io/gaussian.py#L383-L413
I wonder if this wouldn't be a good convenience method for molecule as this is also used in other quantum-chemical codes.
I am leaving this here as a suggestion for refactoring and in case pymatgen plans to support more molecular qm codes.
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PR_kwDOACgets5TqJ6k
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Check for expected error msg in `pytest.raises()`
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PR_kwDOACgets5TrecA
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Fix `ValueError` when parsing `vasprun.xml` with only some atom force constants
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Closes #3084.
Thanks @esoteric-ephemera for pointing out the fix. 👍
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Fix `test_babel_pc_with_ro_depth_0_vs_depth_10`
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[] | 2023-06-22T21:42:50
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Closes #3078.
Todo: Check why test failure was not caught in our CI. `openbabel` not installed correctly?
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Set `hashlib.md5(usedforsecurity=False)` when computing POTCAR hashes
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[] | 2023-06-22T23:01:34
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2023-06-23T02:35:35Z
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Closes #2804.
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PR_kwDOACgets5TuBv1
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Move `get_zmatrix` from `GaussianInput` to `Molecule`
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[
"@janosh I don't understand why this test would be failing. Hints are appreciated.",
"Ah, they have been failing already before. Okay. I was just confused that it was related to molecules."
] | 2023-06-23T06:53:14
| 2023-06-23T13:31:44
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2023-06-23T13:31:43Z
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MEMBER
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Closes #3090
I really just moved the method. It's not sophisticated yet but maybe someone can build on this implementation. I therefore left a todo.
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I_kwDOACgets5pjwBf
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BandStructureSymmLine from MP cannot be serialized
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[
"> I am not sure the issue is pymatgen related or emmet-related.\r\n\r\nNeither I think. I assume bandstructures should not be saved using `numpy` types, so just an issue with our db.\r\n\r\n@munrojm Would a re-parse fix this?\r\n\r\n@JaGeo Here's a temporary workaround:\r\n\r\n```py\r\njson.dump(band.as_dict(), f, default=lambda x: int(x) if isinstance(x, np.int64) else x)\r\n```"
] | 2023-06-23T07:40:05
| 2023-06-23T13:29:06
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@janosh @munrojm
I am not sure the issue is pymatgen related or emmet-related.
The following code fails as the BandstructureSymmline cannot be converted to a serializable json....
```Python
from mp_api.client import MPRester
import json
with MPRester("YOURKEY") as a:
band=a.get_bandstructure_by_material_id("mp-1219182")
with open("bandstructure.json",'w') as f:
json.dump(band.as_dict(),f)
```
I get `TypeError: Object of type int64 is not JSON serializable`. It works for other mpids such as "mp-406".
Plotting also works:
```Python
from mp_api.client import MPRester
import json
from pymatgen.electronic_structure.plotter import BSPlotter
with MPRester("YOURKEY") as a:
band=a.get_bandstructure_by_material_id("mp-1219182")
BSPlotter(band).get_plot().show()
```
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PR_kwDOACgets5TzCSI
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Add CHGNet to `structure.relax` and `structure.calculate`
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[
"@janosh: A small note. If you do \r\n```python\r\nfrom chgnet.model.dynamics import CHGNetCalculator\r\n```\r\n\r\nthen you have imported an ASE calculator. You can provide the calculator as a kwarg via `Structure.relax(calculator=CHGNetCalculator)` just like any other calculator. I'm not sure if this would reduce any redundancy in what you've written but just sharing that as well. It would still involve a few additional things like loading the model and setting the `stress_weight` appropriately, I think.",
"@janosh: Following up the conversation with @JaGeo, maybe we should remove `out.calc = preds` in addition to the block below:\r\n\r\n```python\r\n# Attach important ASE results\r\nsystem.calc = atoms.calc\r\nsystem.dynamics = dyn.todict()\r\n```\r\n\r\nEDIT: Ah, I know what I did the `.calc` assignment now. It was to enable data to be returned with `Structure.calculate()` or `Molecule.calculate()` since if the user is requesting to calculate something, they want the results. Hmm......",
"Thanks for the feedback. The discussion helped see things more clearly. I think we're in better shape now with the changes I just pushed.\r\n\r\nSeems to me that there's no need to return the structure or molecule when calling `calculate` on them. They don't change during the calculation so the user already has them. Instead, we now return the `ase` `Calculator` instance. Feels more natural to do this:\r\n\r\n```py\r\n\r\nfrom pymatgen.core import Lattice, Structure\r\n\r\nstruct = Structure(\r\n lattice=Lattice.cubic(3),\r\n species=(\"Fe\", \"Fe\"),\r\n coords=((0, 0, 0), (0.5, 0.5, 0.5)),\r\n)\r\nstruct.relax(calculator=\"chgnet\")\r\n\r\ncalculator = struct.calculate(calculator=\"chgnet\")\r\n\r\nprint(f\"\\n{[*calculator.__dict__]=}\\n\")\r\nprint(f\"{[*calculator.results]=}\\n\")\r\nprint(f\"{calculator.results['energy']=:.3} eV\\n\")\r\n```\r\n\r\nwhich prints\r\n\r\n```py\r\nCHGNet initialized with 400,438 parameters\r\nCHGNet will run on cpu\r\n\r\n[*calculator.__dict__]=['atoms', 'results', 'parameters', '_directory', 'prefix', 'name', 'get_spin_polarized', 'device', 'model', 'stress_weight']\r\n\r\n[*calculator.results]=['energy', 'forces', 'free_energy', 'magmoms', 'stress']\r\n\r\ncalculator.results['energy']=-16.5 eV\r\n```",
"@janosh: I agree that's more natural and likely preferred. Additionally, the calculator object already stores the `Atoms` object in it via `calc.atoms` (I think), so the user could still get the structure if they want (there are a few edge-cases where it can actually update, e.g. if you run a VASP calculation using its internal optimizers rather than ASE's). Thank you for cleaning that up. I greatly appreciate it!"
] | 2023-06-24T01:34:49
| 2023-06-25T22:56:43
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2023-06-25T22:56:42Z
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MEMBER
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Following hot (or not?) on the heels of #3044, this PR adds `calculator="chgnet"` as a recognized option to `Structure.relax()` and `Structure.calculate()` for running [CHGNet](https://github.com/CederGroupHub/chgnet)-powered structure relaxations and static calculations.
@BowenD-UCB This is a 1st draft. Will require further tweaks but would be good to get your feedback.
Also @arosen93 feel free to chime in if you feel inclined.
|
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Add `match=...` to all `pytest.raises()` in `io.vasp`
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PR_kwDOACgets5T0_mj
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No single letter vars: `s -> struct`
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PR_kwDOACgets5T2vOt
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fixed misspell in GB error message
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2023-06-25T22:40:18Z
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CONTRIBUTOR
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## Summary
Minor misspell fix in error message
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
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PR_kwDOACgets5T24zi
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ruff doc string auto fixes
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I_kwDOACgets5pu27s
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Add Atomate2 to the external tools page
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| 1,775,073,180
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PR_kwDOACgets5T77GO
| 3,104
|
Update `addons.rst`
|
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[
"I think it's ok to keep Quacc since it's likely of interest to some members of the `pymatgen` user base but I'm fine either way. Let me know if you want to merge as is.",
"Let's remove it for now :) Feel free to merge as-is."
] | 2023-06-26T15:39:11
| 2023-06-26T20:48:39
|
2023-06-26T20:48:39Z
|
MEMBER
|
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Closes #3102.
Changes:
- I added [Atomate2](https://github.com/materialsproject/atomate2), which seemed like a clear one to have included.
- I removed [`m3gnet`](https://github.com/materialsvirtuallab/m3gnet) in place of [`matgl`](https://github.com/materialsvirtuallab/matgl) since the former is archived and to be replaced with the latter
- I removed Quacc since it's not as dependent on Pymatgen as most of the other tools listed
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I_kwDOACgets5pzoN8
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"import openbabel" is deprecated, instead use "from openbabel import openbabel"
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[
"@drew-parsons Thanks for pointing this out! Note that this is not the only reason `MoleculeMatcherTest` isn't being run in CI. We're also not installing `openbabel`. IIRC we had serious installation issues in the past causing us to drop it. Just tried again on macOS and couldn't install. But happy to give it a try in Linux CI."
] | 2023-06-26T16:17:50
| 2023-06-27T02:27:15
|
2023-06-27T02:27:15Z
|
CONTRIBUTOR
|
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#### Description
[pymatgen/analysis/tests/test_molecule_matcher.py](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/tests/test_molecule_matcher.py) conditionally uses OBAlign from openbabel. openbabel is accessed by
```
import openbabel
```
and availability of OBAlign registered with
```
ob_align_missing = openbabel is None or "OBAlign" not in dir(openbabel)
```
But the special handling for OBAlign is redundant in this sense: openbabel has moved itself into its own submodule. The source for openbabel [`__init__.py`](https://github.com/openbabel/openbabel/blob/master/scripts/python/openbabel/__init__.py.in)
warns
```
"import openbabel" is deprecated, instead use "from openbabel import openbabel"
```
and the openbabel [documentation](https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonDoc.html) corroborates this usage. Indeed, with openbabel 3.1.1 this works, indicating that OBAlign is located at openbabel.openbabel.OBAlign, not openbabel.OBAlign
Hence MoleculeMatcherTest gets skipped unnecessarily, due to a missing `openbabel.OBAlign` when `openbabel.openbabel.OBAlign` is available.
So https://github.com/materialsproject/pymatgen/blob/6871dae21f245db8dafdf3767182ec7dc64f094a/pymatgen/analysis/tests/test_molecule_matcher.py#L24C21-L24C21 should be updated to replace
```
import openbabel
```
with
```
from openbabel import openbabel
```
A more complex variant with a double try block could be used if older versions of openbabel need to be supported. But probably best to just require a "recent" openbabel ("recent" means openbabel 3, since [March 2019](https://github.com/openbabel/openbabel/pull/1946))
#### Repro
Steps to reproduce the behavior:
1. Install openbabel 3
2. Go to pymatgen source
3. `pytest-3 -v -k MoleculeMatcherTest pymatgen/analysis/tests/test_molecule_matcher.py`
4. See if tests are skipped with `OBAlign is missing, Skipping`
#### Expected behavior
MoleculeMatcherTest (OBAlign) tests should be able to run on "modern" openbabel installations (as openbabel.openbabel.OBAlign)
#### Environment
Relevant versions and platform info:
- OS: Linux (debian unstable)
- pymatgen 2023.06.23
- openbabel 3.1.1
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I_kwDOACgets5p0V2r
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ValueError string does not match in test_connection (test_graph.py)
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[
"Good catch! Thanks for reporting! Fix incoming."
] | 2023-06-26T18:19:51
| 2023-06-27T02:30:06
|
2023-06-27T02:30:05Z
|
CONTRIBUTOR
|
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#### Description
The recent PR#3901 added pytest exception context to tests. In the case of test_construction in analysis/tests/test_graphs.py it [gave](https://github.com/materialsproject/pymatgen/blob/6871dae21f245db8dafdf3767182ec7dc64f094a/pymatgen/analysis/tests/test_graphs.py#L615)
```
with pytest.raises(ValueError, match="Strategy must be a LocalEnvStrategy"):
```
But the ValueError that is raised here in my tests is `"Chosen strategy is not designed for use with molecules! Please choose another strategy."` from https://github.com/materialsproject/pymatgen/blob/6871dae21f245db8dafdf3767182ec7dc64f094a/pymatgen/analysis/graphs.py#L1700
So the exception string does not match, and `pytest.raises` fails, emits `AssertionError: Regex pattern did not match`
#### Repro
Steps to reproduce the behavior:
1. Go to v2023.06.23 source
2. `pytest-3 -v -k test_construction pymatgen/analysis/tests/test_graphs.py`
3. See error
```
_____________________ MoleculeGraphTest.test_construction ______________________
self = <test_graphs.MoleculeGraphTest testMethod=test_construction>
def test_construction(self):
pytest.importorskip("openbabel")
edges_frag = {(e[0], e[1]): {"weight": 1.0} for e in self.pc_frag1_edges}
mol_graph = MoleculeGraph.with_edges(self.pc_frag1, edges_frag)
# dumpfn(mol_graph.as_dict(), os.path.join(module_dir,"pc_frag1_mg.json"))
ref_mol_graph = loadfn(os.path.join(module_dir, "pc_frag1_mg.json"))
assert mol_graph == ref_mol_graph
assert mol_graph.graph.adj == ref_mol_graph.graph.adj
for node in mol_graph.graph.nodes:
assert mol_graph.graph.nodes[node]["specie"] == ref_mol_graph.graph.nodes[node]["specie"]
for ii in range(3):
assert mol_graph.graph.nodes[node]["coords"][ii] == ref_mol_graph.graph.nodes[node]["coords"][ii]
edges_pc = {(e[0], e[1]): {"weight": 1.0} for e in self.pc_edges}
mol_graph = MoleculeGraph.with_edges(self.pc, edges_pc)
# dumpfn(mol_graph.as_dict(), os.path.join(module_dir,"pc_mg.json"))
ref_mol_graph = loadfn(os.path.join(module_dir, "pc_mg.json"))
assert mol_graph == ref_mol_graph
assert mol_graph.graph.adj == ref_mol_graph.graph.adj
for node in mol_graph.graph:
assert mol_graph.graph.nodes[node]["specie"] == ref_mol_graph.graph.nodes[node]["specie"]
for ii in range(3):
assert mol_graph.graph.nodes[node]["coords"][ii] == ref_mol_graph.graph.nodes[node]["coords"][ii]
mol_graph_edges = MoleculeGraph.with_edges(self.pc, edges=edges_pc)
mol_graph_strat = MoleculeGraph.with_local_env_strategy(self.pc, OpenBabelNN())
assert mol_graph_edges.isomorphic_to(mol_graph_strat)
# Check inappropriate strategy
with pytest.raises(ValueError, match="Strategy must be a LocalEnvStrategy"):
> MoleculeGraph.with_local_env_strategy(self.pc, VoronoiNN())
.pybuild/test_python3.11/pymatgen/analysis/tests/test_graphs.py:616:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
molecule = Molecule Summary
Site: O (-0.1537, -1.2376, -0.3760)
Site: O (-1.8072, -0.0351, -0.3321)
Site: O (-1.9413, -1.9132, -1... 1.6251, -0.2175)
Site: H (2.3955, -0.4128, -0.1005)
Site: H (1.9533, 1.1034, 0.6934)
Site: H (1.5552, 0.8495, -1.0151)
strategy = <pymatgen.analysis.local_env.VoronoiNN object at 0x7fb446f85d50>
@staticmethod
def with_local_env_strategy(molecule, strategy):
"""
Constructor for MoleculeGraph, using a strategy
from :class:`pymatgen.analysis.local_env`.
:param molecule: Molecule object
:param strategy: an instance of a
:class:`pymatgen.analysis.local_env.NearNeighbors` object
:return: mg, a MoleculeGraph
"""
if not strategy.molecules_allowed:
> raise ValueError("Chosen strategy is not designed for use with molecules! Please choose another strategy.")
E ValueError: Chosen strategy is not designed for use with molecules! Please choose another strategy.
.pybuild/test_python3.11/pymatgen/analysis/graphs.py:1718: ValueError
During handling of the above exception, another exception occurred:
self = <test_graphs.MoleculeGraphTest testMethod=test_construction>
def test_construction(self):
pytest.importorskip("openbabel")
edges_frag = {(e[0], e[1]): {"weight": 1.0} for e in self.pc_frag1_edges}
mol_graph = MoleculeGraph.with_edges(self.pc_frag1, edges_frag)
# dumpfn(mol_graph.as_dict(), os.path.join(module_dir,"pc_frag1_mg.json"))
ref_mol_graph = loadfn(os.path.join(module_dir, "pc_frag1_mg.json"))
assert mol_graph == ref_mol_graph
assert mol_graph.graph.adj == ref_mol_graph.graph.adj
for node in mol_graph.graph.nodes:
assert mol_graph.graph.nodes[node]["specie"] == ref_mol_graph.graph.nodes[node]["specie"]
for ii in range(3):
assert mol_graph.graph.nodes[node]["coords"][ii] == ref_mol_graph.graph.nodes[node]["coords"][ii]
edges_pc = {(e[0], e[1]): {"weight": 1.0} for e in self.pc_edges}
mol_graph = MoleculeGraph.with_edges(self.pc, edges_pc)
# dumpfn(mol_graph.as_dict(), os.path.join(module_dir,"pc_mg.json"))
ref_mol_graph = loadfn(os.path.join(module_dir, "pc_mg.json"))
assert mol_graph == ref_mol_graph
assert mol_graph.graph.adj == ref_mol_graph.graph.adj
for node in mol_graph.graph:
assert mol_graph.graph.nodes[node]["specie"] == ref_mol_graph.graph.nodes[node]["specie"]
for ii in range(3):
assert mol_graph.graph.nodes[node]["coords"][ii] == ref_mol_graph.graph.nodes[node]["coords"][ii]
mol_graph_edges = MoleculeGraph.with_edges(self.pc, edges=edges_pc)
mol_graph_strat = MoleculeGraph.with_local_env_strategy(self.pc, OpenBabelNN())
assert mol_graph_edges.isomorphic_to(mol_graph_strat)
# Check inappropriate strategy
> with pytest.raises(ValueError, match="Strategy must be a LocalEnvStrategy"):
E AssertionError: Regex pattern did not match.
E Regex: 'Strategy must be a LocalEnvStrategy'
E Input: 'Chosen strategy is not designed for use with molecules! Please choose another strategy.'
.pybuild/test_python3.11/pymatgen/analysis/tests/test_graphs.py:615: AssertionError
```
#### Expected behavior
Tests should pass.
#### Environment
Relevant versions and platform info:
- OS: Linux (Debian unstable)
- pymatgen 2023.06.23
- pytest 7.3.2
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PR_kwDOACgets5T9k67
| 3,107
|
Setup `duecredit` for machine-readable in-code citations
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[
"Yep, this looks perfect -- thanks @janosh.",
"Yay, took a bit longer than expected but I think I added `duecredit` decorators for all DOIs in doc strings. Have to admit my focus was wavering towards the end so might have missed a few. But we can always add more later.",
"Don't worry! Well done finding so many! ",
"I think this proves my point that the onus shouldn't be on Mp dev to do this. The contributor can do this themselves. Seriously why waste the time?",
"Anyway, if you want to ignore my advice in time management and prioritization, knock yourselves out doing unimportant stuff like this. It is not my time that is being wasted. This is something that can and should be crowd sourced to contributors. You are undertaking a centralized effort to do something that yields very little benefit. ",
"I have one concern about visibility of the references. Many users will find pymatgen functionality in the API docs (this is often the page returned by google searches rather than the GitHub source). Currently the paper references are included in the docstrings themselves, so you can immediately see the source for a certain feature. E.g. see the docstring for some of the [dimensionality functions](https://pymatgen.org/pymatgen.analysis.dimensionality.html#pymatgen.analysis.dimensionality.get_dimensionality_larsen).\r\n\r\nThese references are being removed in favour of duecredit decorators but is there a way to automatically include the references in the documentation built by sphinx?",
"Good point @utf, I guess the decorator could patch the `__doc__` string? Could be a nice way to standardise references in the docstring too.\r\n\r\nI also saw someone started something to collect them all in one place: https://github.com/duecredit/duecredit/pull/183/files\r\n\r\n",
"If it's helpful at all, I can provide a snippet:\r\n\r\n```\r\nfrom duecredit import Doi\r\ndef format_doi(self):\r\n \"\"\"\r\n Processes a DOI into a formatted reference via Crossref API.\r\n (Alternatively could cache these somewhere.)\r\n \r\n Returns a Sphinx-compatible string with URL, intended to be \r\n used with Sphinx documentation generation only.\r\n \"\"\"\r\n \r\n from habanero import cn\r\n # choose an appropriate style here, slice is to cut off newline\r\n ref = cn.content_negotiation(ids=self.doi, format=\"text\", style=\"apa\")[:-2]\r\n \r\n return f\"`{ref} <https://doi.org/{self.doi}>`_\"\r\nDoi.format_doi = format_doi\r\n```\r\n\r\nI imagine you can then wrap the original `cite`/`dcite` with functools.wrap, and modify the `__doc__` in place.",
"> These references are being removed in favour of duecredit decorators but is there a way to automatically include the references in the documentation built by sphinx?\r\n\r\n@utf That thought occurred to me as well after doing the first 3 or 4 at which point I decided to have both for now, i.e. I kept the doc string references and just added the `duecredit` decorators until we figure this out.",
"Just for clarity, if the references appeared twice both in the module doc string and the doc string of the main class defined in that file (e.g. `pymatgen/analysis/interface_reactions.py`), I removed the references from the module doc string, keeping only the class doc string references.",
"Lovely to see an old PR merged. Thanks again for picking it up @janosh ",
"> Anyway, if you want to ignore my advice in time management and prioritization, knock yourselves out doing unimportant stuff like this.\r\n\r\n@shyuep We're not going to town with this. My total time spent on this yesterday was ~2.5 hours incl. the MP update call where we discussed reviving this effort.\r\n\r\n> This is something that can and should be crowd sourced to contributors.\r\n\r\n@shyuep I disagree that external contributors should be asked to setup a systematic way for code citations. That's up to us to establish. Once we have that, we can ask contributors to follow our framework.\r\n\r\n> https://github.com/materialsproject/foundation/pull/7#issuecomment-1608837201\r\n> From Andrew: That said, how will users know about it and feel encouraged to use it? Presumably there will need to be something added to the docs in a visible way.\r\n\r\n@arosen93 I'll add a checkbox to the PR template asking contributors to consider whether citations are applicable",
"@janosh a systematic way involves writing in the contributor guidelines \"Feel free to add die credit decorators for your contributed code, as well as a reference in the doc.\" It does not involve spending time going through existing code to do it ourselves. \n\nAdding due credit for something like Ewald summation to the ewald code is not what this is meant for. Why not add duecredit to the VASP publication for the entire vasp package? Or for that matter, due credit to Kohn and Sham for everything DFT related? The Ewald class was written mostly by ME, with contributions from a few others over the years. If anything, I should be given due credit for that module. I just don't give enough of a shit about claiming credit for it. ",
"> If anything, I should be given due credit for that module.\r\n\r\nYou _are_ getting credit for that! It's all recorded in `git` history which I care more about than publications tbh when I want to know who did the actual work.\r\n\r\nAnyway, I take your point that setting up a citation system is not 1st priority and so shouldn't become a major time drain (which it wasn't)."
] | 2023-06-26T20:28:18
| 2023-06-27T19:29:29
|
2023-06-27T15:25:38Z
|
MEMBER
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Following this morning's MP Foundation meeting where I took this over from @mkhorton, this is a draft PR that adds `duecredit` class decorators and module citations to a dozen files to gather feedback before doing the rest.
@mkhorton Let me know if this is what you had in mind and I'll do the rest.
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BUG: force contiguous calling find_points_in_spheres
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[
"Quick qn: what is the purpose of this? Speed up?",
"Having the arrays contiguous makes it faster., which I had already added in the previous PR #3015.\r\n\r\nHowever, we noticed that when called internally by a structure where the lattice matrix or frac_coords had been changed in such a way (such as applying strain) that the arrays were not contiguous then the call to the cython function would raise errors.\r\n",
"@shyuep Just for context, this came up in https://github.com/CederGroupHub/chgnet/pull/39 where tests were failing with\r\n\r\n```py\r\nchgnet/graph/converter.py:142: in get_neighbors\r\n center_index, neighbor_index, image, distance = structure.get_neighbor_list(\r\n/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/pymatgen/core/structure.py:1533: in get_neighbor_list\r\n center_indices, points_indices, images, distances = find_points_in_spheres(\r\npymatgen/optimization/neighbors.pyx:49: in pymatgen.optimization.neighbors.find_points_in_spheres\r\n ???\r\nstringsource:660: in View.MemoryView.memoryview_cwrapper\r\n ???\r\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \r\n\r\n> ???\r\nE ValueError: ndarray is not C-contiguous\r\n```\r\n\r\n@lbluque Thanks for the really fast fix and unit test. 👍 Makes me sleep better every time we add a new test. 😄 ",
"Thanks."
] | 2023-06-26T23:20:09
| 2023-06-26T23:47:28
|
2023-06-26T23:47:24Z
|
CONTRIBUTOR
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## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
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_kwDOACgets5T-2rj
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Fix `openbabel` import to unskip `MoleculeMatcherTest`
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[
"@drew-parsons I fixed the `openbabel` import but I'm leaving out the openbabel install in CI which is also needed to get this test running again. Would you like to submit a PR for that?",
"I'm not sure how to patch the github CI. I'm working with the debian CI testing at https://ci.debian.net/packages/p/pymatgen/. But I've applied the import patch and it's running the OBAlign tests fine.\r\ne.g. https://ci.debian.net/data/autopkgtest/testing/amd64/p/pymatgen/34898502/log.gz shows\r\n```\r\nruntests/pymatgen/analysis/tests/test_molecule_matcher.py::MoleculeMatcherTest::test_cdi_23 PASSED [ 15%]\r\nruntests/pymatgen/analysis/tests/test_molecule_matcher.py::MoleculeMatcherTest::test_get_rmsd PASSED [ 15%]\r\nruntests/pymatgen/analysis/tests/test_molecule_matcher.py::MoleculeMatcherTest::test_group_molecules PASSED [ 15%]\r\nruntests/pymatgen/analysis/tests/test_molecule_matcher.py::MoleculeMatcherTest::test_strange_inchi PASSED [ 15%]\r\nruntests/pymatgen/analysis/tests/test_molecule_matcher.py::MoleculeMatcherTest::test_thiane PASSED [ 15%]\r\nruntests/pymatgen/analysis/tests/test_molecule_matcher.py::MoleculeMatcherTest::test_thiane_ethynyl PASSED [ 16%]\r\nruntests/pymatgen/analysis/tests/test_molecule_matcher.py::MoleculeMatcherTest::test_to_and_from_dict PASSED [ 16%]\r\n```\r\n\r\n(I configured it to skip `test_fit` since it was giving an error\r\n```\r\n> ob_atom.SetVector(*coords)\r\nE TypeError: in method 'OBAtom_SetVector', argument 2 of type 'double'\r\n\r\n/usr/lib/python3/dist-packages/pymatgen/io/babel.py:66: TypeError\r\n```\r\nI'm not yet confident enough on why it's doing that to file a separate bug)",
"[Based on this](https://gohom.win/2015/10/27/openbabel-py/), it looks like `ob_atom.SetVector` expects the first argument to be a vector.\r\n\r\n```py\r\nOBAtom.SetVector = new_instancemethod(_openbabel.OBAtom_SetVector, None, OBAtom)\r\n```\r\n\r\nIf you remove the unpacking operator, does the test still fail?\r\n\r\n```diff\r\n- ob_atom.SetVector(*coords)\r\n+ ob_atom.SetVector(coords)\r\n```",
"No, apparently not as simple as that. `ob_atom.SetVector(coords)` gets\r\n```\r\n> ob_atom.SetVector(coords)\r\nE TypeError: in method 'OBAtom_SetVector', argument 2 of type 'OpenBabel::vector3 const &'\r\n```\r\nI notice the openbabel source declares the vector with `const double` not `double`. Would the handover from python deal with `const` appropriately? ",
"Not sure but I assume so."
] | 2023-06-27T01:50:13
| 2023-06-27T21:34:09
|
2023-06-27T02:27:13Z
|
MEMBER
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Closes #3105.
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PR_kwDOACgets5T-6wL
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Fix unexpected error message in `MoleculeGraphTest.test_construction`
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Closes #3106.
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PR_kwDOACgets5T_xO3
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fix AttributeError in MoleculeGraph.draw_graph_to_file
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[
"Thanks @xjf729, I believe this change was the result of an API change in networkx, good catch!"
] | 2023-06-27T06:57:59
| 2023-06-27T14:03:43
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2023-06-27T14:03:43Z
|
CONTRIBUTOR
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In line 2602 and 2603, `g` is `MultiDiGraph` and has no attribute `node`.
## Summary
Major changes:
- fix 1: change g.node to g.nodes
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
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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`test_from_diff_fit` in `test_elastic.py` fails on `mips64el`
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[
"This test runs successfully in our Ubuntu, macOS and Windows CIs. Not sure how the huge differences in your logs might come about\r\n\r\n```logs\r\nMax absolute difference: 6.20711553e+09\r\nMax relative difference: 1.72207694e+23\r\n```\r\n\r\nThe last meaningful change to this test I could find is 72bd76c9d573f68f28ee0eec6de1558cab5c3411.\r\n\r\nwhere I changed\r\n\r\n```py\r\n @staticmethod\r\n def assertArrayAlmostEqual(actual, desired, decimal=7, err_msg=\"\", verbose=True):\r\n \"\"\"\r\n Tests if two arrays are almost equal to a tolerance. The CamelCase\r\n naming is so that it is consistent with standard unittest methods.\r\n \"\"\"\r\n return nptu.assert_almost_equal(actual, desired, decimal, err_msg, verbose)\r\n```\r\n\r\nto\r\n\r\n```py\r\n @staticmethod\r\n def assert_all_close(actual, desired, decimal=7, err_msg=\"\", verbose=True):\r\n \"\"\"\r\n Tests if two arrays are almost equal up to some relative or absolute tolerance.\r\n \"\"\"\r\n # TODO (janosh): replace the decimal kwarg with assert_allclose() atol and rtol kwargs\r\n return assert_allclose(actual, desired, atol=10**-decimal, err_msg=err_msg, verbose=verbose)\r\n```\r\n\r\nMaybe you could work the body of the old `assertArrayAlmostEqual` into the test function `NthOrderElasticTensorTest.test_from_diff_fit` and report whether the test still fails.",
"I skipped the test in the meantime to get the package built. I'll reopen if I can get more information"
] | 2023-06-28T11:01:05
| 2023-10-01T20:40:16
|
2023-10-01T19:39:43Z
|
CONTRIBUTOR
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#### Description
The NthOrderElasticTensorTest.test_from_diff_fit in test_elastic.py fails on mips64el fails during build-time tests on the mips64el architecture.
The error log reports
```
=================================== FAILURES ===================================
_________________ NthOrderElasticTensorTest.test_from_diff_fit _________________
self = <test_elastic.NthOrderElasticTensorTest testMethod=test_from_diff_fit>
def test_from_diff_fit(self):
c3 = NthOrderElasticTensor.from_diff_fit(
self.strains,
self.pk_stresses,
eq_stress=self.data_dict["eq_stress"],
order=3,
)
> self.assert_all_close(c3.voigt, self.data_dict["C3_raw"], decimal=2)
/<<PKGBUILDDIR>>/.pybuild/test_python3.11/pymatgen/analysis/elasticity/tests/test_elastic.py:376:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/<<PKGBUILDDIR>>/.pybuild/test_python3.11/pymatgen/util/testing.py:79: in assert_all_close
return assert_allclose(actual, desired, atol=10**-decimal, err_msg=err_msg, verbose=verbose)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_allclose.<locals>.compare at 0xffc5758220>, array([[[-9.98946829e+04, 1.01377485e+09, -2.41772239e+... [-2.90295942e+02, -2.91680089e+02, 1.73344536e+01,
9.43339561e-01, 3.57044033e-01, -1.79095915e+00]]]))
kwds = {'equal_nan': True, 'err_msg': '', 'header': 'Not equal to tolerance rtol=1e-07, atol=0.01', 'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
> return func(*args, **kwds)
E AssertionError:
E Not equal to tolerance rtol=1e-07, atol=0.01
E
E Mismatched elements: 216 / 216 (100%)
E Max absolute difference: 6.20711553e+09
E Max relative difference: 1.72207694e+23
E x: array([[[-9.989468e+04, 1.013775e+09, -2.417722e+09, 2.831976e+08,
E -1.330120e+09, 1.010315e+09],
E [ 1.013775e+09, -2.745317e+08, 5.983336e+08, 1.711881e+08,...
E y: array([[[-7.499064e+02, -4.256440e+02, -4.255552e+02, -1.420682e+00,
E -5.808052e-01, -6.920733e-01],
E [-4.256440e+02, -4.250986e+02, -7.928408e+01, -6.267099e-01,...
/usr/lib/python3.11/contextlib.py:81: AssertionError
```
Full log at https://buildd.debian.org/status/fetch.php?pkg=pymatgen&arch=mips64el&ver=2023.06.23%2Bdfsg1-1&stamp=1687855205&raw=0
#### Repro
Steps to reproduce the behavior:
1. Go to source on a mip64el system
1. Build pymatgen
1. `pytest-3 -v -k NthOrderElasticTensorTest pymatgen/analysis/elasticity/tests/test_elastic.py`
1. See error
#### Expected behavior
The test should pass.
#### Environment
Relevant versions and platform info:
- OS: Linux (debian unstable)
#### Additional context
pymatgen also failed on mip64el with v2023.05.31. v2023.2.22 was previously successful. Historical build logs available at https://buildd.debian.org/status/logs.php?pkg=pymatgen&arch=mips64el
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I_kwDOACgets5qCWDw
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|
Bug in processing entries of GGA/GGA+U/R2SCAN scheme
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[
"I can't repro this. Tried about 7 times. I get 638 entries every time.\r\n\r\n> which actually contains no energy adjustment related to the GGA/GGA+U/R2SCAN scheme\r\n\r\nI'm not very familiar with our r2SCAN/GGA mixing scheme but I think what might be happening here is that we place r2SCAN energies onto the GGA(+U) hull? If so, you wouldn't expect an adjustment on a GGA+U entry? Pinging @rkingsbury @munrojm to correct me in case I'm wrong.",
"> I'm not very familiar with our r2SCAN/GGA mixing scheme but I think what might be happening here is that we place r2SCAN energies onto the GGA(+U) hull? If so, you woudln't expect an adjustment on a GGA+U entry? Pinging @rkingsbury @munrojm to correct me in case I'm wrong here.\r\n\r\nThat's correct, some GGA/GGA+U entries will pass through the mixing scheme unmodified, if the hull is still being built with GGA/GGA+U entries. That would occur any time there are insufficient R2SCAN entries to build the hull. In such a high dimensional chemical system as this, I'm almost certain the hull would be built in GGA/GGA+U, so getting the entry back unmodified is exactly what should happen. Please refer to the mixing scheme publication for a more thorough explanation.\r\n\r\nAs for the non-reproducibility / I'm not sure. The mixing scheme does rely on structure matching, so perhaps due to some quirk in your computer system the matching occasionally fails to consider two structures \"the same\"? That's a stretch but it's the best thought I have.\r\n\r\nAlso, I note that you're using the old MPRester (`pymatgen.ext.matproj`). If you want to use r2SCAN data I think you would be better off using the rester from the `mp-api` package, but @munrojm would know better.\r\n",
"> Also, I note that you're using the old MPRester (`pymatgen.ext.matproj`). If you want to use r2SCAN data I think you would be better off using the rester from the `mp-api` package, but @munrojm would know better.\r\n\r\n@rkingsbury Oh, it is a typo here. Actually in my test codes, the MPRester method was imported by `from mp_api.client import MPRester`.\r\n\r\nI tested it on a different computer and network, but the inconsistency issue still happened. I will try to run them with a fresh environment in a container next.\r\n",
"The same issue happened, even though I ran the codes in a fresh set-up container of python3.10-alpine. I think this is a rare case (the chemical system and entry) that induces this issue whereas would not happen in other chemical systems, but the potential bug may still result in entry loss or excess, thereby possibly changing the shape of the convex hull.",
"Can you pinpoint the bug?",
"@janosh Yes, it is the the structure_matcher.group_structures() methods in mixing_scheme.py [564L](https://github.com/materialsproject/pymatgen/blob/b79f0dfc7bb62ea34fd1c22dda9069831a22d67c/pymatgen/entries/mixing_scheme.py#L564), that results in inconsistency when matching the structures of the entry `mp-1181411-GGA+U Fe4O13` with the entry `mp-1181334-GGA+U Fe4O13`. I found that the codes sometimes match the two entries together in one group, whereas sometimes divide them into two individual groups. In the latter case, there would be 638 processed entries, otherwise, there would be 637 entries.",
"> @janosh Yes, it is the the structure_matcher.group_structures() methods in mixing_scheme.py [564L](https://github.com/materialsproject/pymatgen/blob/b79f0dfc7bb62ea34fd1c22dda9069831a22d67c/pymatgen/entries/mixing_scheme.py#L564), that results in inconsistency when matching the structures of the entry `mp-1181411-GGA+U Fe4O13` with the entry `mp-1181334-GGA+U Fe4O13`. I found that the codes sometimes match the two entries together in one group, whereas sometimes divide them into two individual groups. In the latter case, there would be 638 processed entries, otherwise, there would be 637 entries.\r\n\r\n@peikai it sounds to me like you are running into an edge case related to the numerical tolerances of [`StructureMatcher`](https://pymatgen.org/pymatgen.analysis.structure_matcher.html#pymatgen.analysis.structure_matcher.StructureMatcher), where tiny numerical noise is causing those structures to sometimes match and sometimes not. I suggest 2 things:\r\n\r\n1. Can you reproduce the problem outside of the mixing scheme, by just running `StructureMatcher` on your list of input structures?\r\n2. If yes, then try adjusting the tolerance kwargs of `StructureMatcher`. If you slightly change the `ltol`, `stol`, or `angle_tol`, you can hopefully get reproducible results.",
"@rkingsbury, I tried with suggestion 1, the results are consistent that two entries are always distinguished to different groups.\n\nI can still reproduce the aforementioned issue with the up-to-date pymatgen and online database.",
"OK, so if `StructureMatcher` does not match the structures, then the mixing scheme will treat them as distinct materials. Can you try experimenting with the tolerances and other kwargs of `StructureMatcher` to see if you can get them to match more reliably?\n\nIf you can, those settings can be passed into the mixing scheme.",
"As a supplement, I tried to find a comparation from pre-computed phase diagram on this chemical system. The pre-computed phase diagram contains the entry `mp-1181334-GGA+U`. However, the entryList getting from the `MaterialsProjectDFTMixingScheme().process_entries()`, contain it in mostly cases whereas sometimes don't. I tend to believe it should be included into the processed entries, since the `StructureMatcher()` did not match them into the same group. In a high-throughput context, I think the adjustment of default parameters might create further consistency on other chemical systems. Moreover, it has not been clear that why the result from `process_entries()` is inconsistent with those of `StructureMatcher()`.\n\nAlthough, this is an issue that did not bother so much, I committed it in case there are potential bugs or possible improvements. I once attempted to migrate to using pre-computing phase diagrams to keep consistency, but I found that for certain chemical systems, pre-computing phase diagrams are not always available (missing) for entire thermo types. As a result, it is necessary to rely on the local processing methods.",
"I believe this is fixed in #4255 ",
"> I believe this is fixed in [#4255](https://github.com/materialsproject/pymatgen/pull/4255)\n\nIt fixed a new issue that r2SCAN entries are not included for the mixing correction.\n\nThe problem still exists that the entry `mp-1181334-GGA+U` can still appear or disappear in processed entries.\n\nI record the output messages accordingly.\n\n- mp-1181334-GGA+U is contained in processed entries.\n [output-appear.txt](https://github.com/user-attachments/files/18577490/output-appear.txt)\n\n- mp-1181334-GGA+U is not contained in processed entries.\n [output-disappear.txt](https://github.com/user-attachments/files/18577492/output-disappear.txt)\n\nI also noticed there is an unusual message in above two outputs:\n```\nspglib: ssm_get_exact_positions failed.\nspglib: get_bravais_exact_positions_and_lattice failed.\n```"
] | 2023-06-28T13:52:50
| 2025-01-28T18:13:51
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CONTRIBUTOR
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I found that the entry `mp-1181334-GGA+U` for `Cu-Fe-Li-O-Te` chemical system can disappear and reappear in the processed entries result occasionally, when the GGA/GGA+U/R2SCAN scheme correction was conducted multiple times. The inconsistency issue happened about every third run in my test -- although the codes below been tested in the latest `pymatgen` package.
```python
from pymatgen.ext.matproj import MPRester
from pymatgen.entries.mixing_scheme import MaterialsProjectDFTMixingScheme
with MPRester() as mpr:
entryList = mpr.get_entries_in_chemsys('Cu-Fe-Li-O-Te', additional_criteria={'thermo_types':['GGA_GGA+U', 'R2SCAN']})
entryList = MaterialsProjectDFTMixingScheme().process_entries(entryList, verbose=False)
print(len(entryList))
print('mp-1181334-GGA+U' in [e.entry_id for e in entryList])
```
There may be either 637 or 638 entries in the processed entryList. The latter case would contain an entry `mp-1181334-GGA+U`, which actually contains no energy adjustment related to the GGA/GGA+U/R2SCAN scheme, as shown in the exported JSON file below.
```
mp-1181334-GGA+U ComputedStructureEntry - Fe4 O13 (Fe4O13)
Energy (Uncorrected) = -92.6898 eV (-5.4523 eV/atom)
Correction = -11.1170 eV (-0.6539 eV/atom)
Energy (Final) = -103.8068 eV (-6.1063 eV/atom)
Energy Adjustments:
MP2020 anion correction (superoxide): -2.0930 eV (-0.1231 eV/atom)
MP2020 GGA/GGA+U mixing correction (Fe): -9.0240 eV (-0.5308 eV/atom)
Parameters:
potcar_spec = [{'titel': 'PAW_PBE Fe_pv 06Sep2000', 'hash': '5963411539032ec3298fa675a32c5e64'}, {'titel': 'PAW_PBE O 08Apr2002', 'hash': '7a25bc5b9a5393f46600a4939d357982'}]
is_hubbard = True
hubbards = {'Fe': 5.3, 'O': 0.0}
run_type = GGA+U
Data:
oxide_type = superoxide
aspherical = True
last_updated = 2021-02-05 09:26:25.316000
task_id = mp-1829691
material_id = mp-1181334
oxidation_states = {}
run_type = GGA+U
```
The potential bug needs to be found, as the reliability of local processing algorithms has become critical for the generation of GGA/GGA+U/R2SCAN phase diagrams[^note].
[^note]: https://docs.materialsproject.org/methodology/materials-methodology/thermodynamic-stability/phase-diagrams-pds#gga-gga+u-r2scan
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PR_kwDOACgets5UN_6e
| 3,114
|
Add citations for Lobster modules and tiny addition to DOSCAR processing
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[
"@janosh And another fix that adds more flexibility to the DOSCAR reading of Lobster files.",
"Linting is failing because IStructure and Structure do not agree with each other. Not sure how to fix it."
] | 2023-06-29T08:42:18
| 2023-06-29T15:39:58
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2023-06-29T15:39:57Z
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MEMBER
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@janosh, I have added the correct citations for the Lobster module. I wanted to do this for a very long time...
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Issue with Structure.from_spacegroup
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[
"your code does not even work because there is no arg called spacegroup in the from_spacegroup method. There is also no arg called symbols. While I definitely know how to fix this myself, I think it is generally a good practice to provide actual working code to minimize the load on developers when you are asking for help. Pls provide a proper working code and we will debug.",
"Sorry for the typos. Here is a working code. \r\n\r\n```py\r\nfrom pymatgen.core import Lattice, Structure\r\n\r\nlattice_params = [13.236, 13.236, 12.7, 90, 90, 90]\r\nlattice = Lattice.from_parameters(*lattice_params)\r\n\r\nstruct = Structure.from_spacegroup(\r\n sg=142,\r\n lattice=lattice,\r\n species=[\"Li\", \"La\", \"Zr\", \"La\", \"Li\", \"Li\", \"O\", \"O\", \"O\"],\r\n coords=[\r\n [1 / 2, 0, 3 / 4],\r\n [1 / 2, 0, 0],\r\n [3 / 4, 0.62737, 3 / 8],\r\n [3 / 4, 1 / 2, 5 / 8],\r\n [0.681211, 0.181211, 0],\r\n [0.337534, 0.080516, 0.319143],\r\n [0.805483, 0.465384, 0.471296],\r\n [0.102443, 0.054963, 0.590667],\r\n [0.776773, 0.650823, 0.178764],\r\n ],\r\n)\r\n```",
"This might be a `symprec` issue. You could try passing different `tol` values to `Structure.from_spacegroup()`.",
"Thanks for the suggestion. I tried `tol` values from `1e-1` to `1e-10` and still got 208 atoms. \r\n\r\nWhen I visualize just the La atoms, I get quite different structures between the Materials Project structure and the Pymatgen structure. It seems like the wychoff coordinate in Materials Project may not be correct, which is causing the incorrect symmetry reduction.\r\n\r\nPymatgen La structure\r\n\r\n\r\nMaterial Project La structure.\r\n\r\n",
"```py\r\nfrom pymatgen.ext.matproj import MPRester\r\n\r\nMPRester().summary.search(material_ids=[\"mp-942733\"])[0].symmetry\r\n>>> SymmetryData(crystal_system=<CrystalSystem.tet: 'Tetragonal'>, symbol='I4_1/acd', number=142, point_group='4/mmm', symprec=0.1, version='1.16.2')\r\n```\r\n\r\nYou might need to install `spglib==1.16.2`.",
"Thanks for the suggestion. I rolled back my `spglib` version to `1.16.2`, but am still getting the wrong symmetry operations even with `tol=0.1`.\r\n\r\nThe issue seems to be with identifying the symmetry of the state. If I just look at the La sublattice, I can find that the as created structure has all the atoms as the structure of materials project, but the 16 additional sites create linear patterns in the structure. It seems like it is mistakenly being assigned to a 32g Wychoff position instead of 16e. I've tried going through the source code but it doesn't seem to assign any atoms to a wychoff position. Instead all the symmetry operations are applied to the basis atoms using the symmetry operations of the spacegroup. I tried comparing the symmetry operations to an [online table ](https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list), but can't seem to understand where they come from besides that they are tabulated in `symm_ops.json`.\r\n\r\nThank you for helping me to figure this out. \r\n\r\nLa sublattice from pymatgen with 16e basis atom identified\r\n\r\n\r\nLa sublattice from Materials Project with 16e basis atom identified\r\n\r\n"
] | 2023-06-29T16:01:09
| 2023-06-30T23:13:07
|
NONE
|
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#### Description
I'm trying to reproduce the structure of [LLZO on materials project](https://next-gen.materialsproject.org/materials/mp-942733?chemsys=La-Li-O-Zr) using `pymatgen.core.Structure.from_spacegroup()` and it looks like the La wychoff coordinates give the incorrect multiplicity. I'm getting a structure with 208 atoms instead of 192, where the extra 16 atoms are La.
#### Repro
```py
struc = Structure.from_spacegroup(
spacegroup=142,
lattice={"a": 13.236, "c": 12.7},
symbols=["Li", "La", "Zr", "La", "Li", "Li", "O", "O", "O"],
basis=[
[1 / 2, 0, 3 / 4],
[1 / 2, 0, 0],
[3 / 4, 0.62737, 3 / 8],
[3 / 4, 1 / 2, 5 / 8],
[0.681211, 0.181211, 0],
[0.337534, 0.080516, 0.319143],
[0.805483, 0.465384, 0.471296],
[0.102443, 0.054963, 0.590667],
[0.776773, 0.650823, 0.178764],
],
)
```
Provide any example files that are needed to reproduce the error, especially if the bug pertains to parsing a file. If the file format is not supported by GitHub, zip it into an archive and upload that.
#### Expected behavior
Return a structure with 192 atoms
#### Environment
Relevant versions and platform info:
- OS: Linux
- Version: v2023.3.23
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| 1,783,849,991
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PR_kwDOACgets5UZvo_
| 3,116
|
Bump pypa/cibuildwheel from 2.12.3 to 2.13.1
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[
"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-07-01T12:07:22
| 2023-07-01T19:12:03
|
2023-07-01T19:11:54Z
|
CONTRIBUTOR
|
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Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.12.3 to 2.13.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p>
<blockquote>
<h2>v2.13.1</h2>
<ul>
<li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b2. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1516">#1516</a>)</li>
<li>🛠 Adds a moving <code>v<major>.<minor></code> tag for use in GitHub Actions workflow files. If you use this, you'll get the latest patch release within a minor version. Additionally, Dependabot won't send you PRs for patch releases. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1517">#1517</a>)</li>
</ul>
<h2>v2.13.0</h2>
<ul>
<li>
<p>✨ Adds CPython 3.12 support, under the prerelease flag <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#prerelease-pythons">CIBW_PRERELEASE_PYTHONS</a>. This version of cibuildwheel uses 3.12.0b1.</p>
<p>While CPython is in beta, the ABI can change, so your wheels might not be compatible with the final release. For this reason, we don't recommend distributing wheels until RC1, at which point 3.12 will be available in cibuildwheel without the flag. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1507">#1507</a>)</p>
</li>
<li>
<p>✨ Adds the ability to pass arguments to the container engine when the container is created, using the <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#container-engine">CIBW_CONTAINER_ENGINE</a> option. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1499">#1499</a>)</p>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md">pypa/cibuildwheel's changelog</a>.</em></p>
<blockquote>
<h3>v2.13.1</h3>
<p><em>10 June 2023</em></p>
<ul>
<li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b2. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1516">#1516</a>)</li>
<li>🛠 Adds a moving <code>v<major>.<minor></code> tag for use in GitHub Actions workflow files. If you use this, you'll get the latest patch release within a minor version. Additionally, Dependabot won't send you PRs for patch releases. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1517">#1517</a>)</li>
</ul>
<h3>v2.13.0</h3>
<p><em>28 May 2023</em></p>
<ul>
<li>
<p>✨ Adds CPython 3.12 support, under the prerelease flag <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#prerelease-pythons">CIBW_PRERELEASE_PYTHONS</a>. This version of cibuildwheel uses 3.12.0b1.</p>
<p>While CPython is in beta, the ABI can change, so your wheels might not be compatible with the final release. For this reason, we don't recommend distributing wheels until RC1, at which point 3.12 will be available in cibuildwheel without the flag. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1507">#1507</a>)</p>
</li>
<li>
<p>✨ Adds the ability to pass arguments to the container engine when the container is created, using the <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#container-engine">CIBW_CONTAINER_ENGINE</a> option. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1499">#1499</a>)</p>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/pypa/cibuildwheel/commit/0ecddd92b62987d7a2ae8911f4bb8ec9e2e4496a"><code>0ecddd9</code></a> Bump version: v2.13.1</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/f35d309173dfc5359b18ca3d2c9c422e4cf83abb"><code>f35d309</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1517">#1517</a> from pypa/major-dot-minor-tag</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/3160e8dbca733f3125ba9fcf5cf6b0007cdaca73"><code>3160e8d</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1516">#1516</a> from pypa/update-dependencies-pr</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/012ae48172b00cfbfad05e1a3fa6d0af04bc0d7b"><code>012ae48</code></a> Add workflow that updates a vX.Y tag on release</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/1c3b8e112e9ceccee1712627b5377213672ae155"><code>1c3b8e1</code></a> Update dependencies</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/ca7b0f75c61a9efc6dd42d7c0600f347df8ca5e0"><code>ca7b0f7</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1514">#1514</a> from pypa/fix-travis-windows</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/8d126bc281ea9d9e62e37ec7f604fcd2157044a0"><code>8d126bc</code></a> Try removing the offending line</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/2ca5ff2dcdd0bfc0d558906b2ae20e74b9c5cb51"><code>2ca5ff2</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1508">#1508</a> from pypa/update-dependencies-pr</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/7d45cf3dace7240123635298d7429bb99fad6b92"><code>7d45cf3</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1511">#1511</a> from ianthomas23/doc_fix_config_settings</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/f6edc817df1b26def09c0278a72f2d097df6da23"><code>f6edc81</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1512">#1512</a> from pypa/pre-commit-ci-update-config</li>
<li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.12.3...v2.13.1">compare view</a></li>
</ul>
</details>
<br />
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PR_kwDOACgets5UZ0Dr
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Bump pandas from 2.0.1 to 2.0.3
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-07-01T12:33:40
| 2023-07-01T19:11:55
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2023-07-01T19:11:45Z
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CONTRIBUTOR
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Bumps [pandas](https://github.com/pandas-dev/pandas) from 2.0.1 to 2.0.3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pandas-dev/pandas/releases">pandas's releases</a>.</em></p>
<blockquote>
<h2>Pandas 2.0.3</h2>
<p>This is a patch release in the 2.0.x series and includes some regression and bug fixes. We recommend that all users upgrade to this version.</p>
<p>See the <a href="https://pandas.pydata.org/pandas-docs/version/2.0.3/whatsnew/v2.0.3.html">full whatsnew</a> for a list of all the changes.</p>
<p>The release will be available on the defaults and conda-forge channels:</p>
<p>conda install pandas
Or via PyPI:</p>
<p>python3 -m pip install --upgrade pandas
Please report any issues with the release on the <a href="https://github.com/pandas-dev/pandas/issues">pandas issue tracker</a>.</p>
<p>Thanks to all the contributors who made this release possible.</p>
<h2>Pandas 2.0.2</h2>
<p>This is a patch release in the 2.0.x series and includes some regression and bug fixes. We recommend that all users upgrade to this version.</p>
<p>See the <a href="https://pandas.pydata.org/pandas-docs/version/2.0.2/whatsnew/v2.0.2.html">full whatsnew</a> for a list of all the changes.</p>
<p>The release will be available on the defaults and conda-forge channels:</p>
<pre><code>conda install pandas
</code></pre>
<p>Or via PyPI:</p>
<pre><code>python3 -m pip install --upgrade pandas
</code></pre>
<p>Please report any issues with the release on the <a href="https://github.com/pandas-dev/pandas/issues">pandas issue tracker</a>.</p>
<p>Thanks to all the contributors who made this release possible.</p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/pandas-dev/pandas/commit/0f437949513225922d851e9581723d82120684a6"><code>0f43794</code></a> RLS: 2.0.3</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/86036f226dd0d7e051c92388687c5d84282610ce"><code>86036f2</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53897">#53897</a>: DOC: Update release date for 2.0.3 (<a href="https://redirect.github.com/pandas-dev/pandas/issues/53913">#53913</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/0ef704cfc3ca94a966152babefdd636f6a65bdea"><code>0ef704c</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53888">#53888</a> on branch 2.0.x (CI: Fix pytest scripts and doc failure) (...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/b8f14c4a6815a66ac701ba755b607f7cefe34b2d"><code>b8f14c4</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53795">#53795</a> on branch 2.0.x (BUG: fixes weekday for dates before 1752)...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/7d8be444fabbace12bec7b55a850319be4f5a732"><code>7d8be44</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53855">#53855</a>: BUG: Fix string formatting (<a href="https://redirect.github.com/pandas-dev/pandas/issues/53860">#53860</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/000a42f595aa932bb5216e598065492b88f92948"><code>000a42f</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/52150">#52150</a> on branch 2.0.x (Fix/mpl37 compat) (<a href="https://redirect.github.com/pandas-dev/pandas/issues/53850">#53850</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/d273ee0ee00ed55104cf9a8b0a291284a63baec1"><code>d273ee0</code></a> CI: Backport changes to fix unreliable tests on ARM (<a href="https://redirect.github.com/pandas-dev/pandas/issues/53849">#53849</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/52990518baac8497e7af28f81f39b50f592a1efa"><code>5299051</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53819">#53819</a> on branch 2.0.x (TST/CI: Skipif test_complibs) (<a href="https://redirect.github.com/pandas-dev/pandas/issues/53823">#53823</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/dde820f84ff155e956fe81ae425c3e8f66fd174a"><code>dde820f</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53754">#53754</a> on branch 2.0.x (TST: Make test_complibs deterministic) (#...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/7839406da38638ccd1e3b183137b8cb0cd0619bb"><code>7839406</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53774">#53774</a> on branch 2.0.x (COMPAT: Remove np.compat) (<a href="https://redirect.github.com/pandas-dev/pandas/issues/53776">#53776</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/pandas-dev/pandas/compare/v2.0.1...v2.0.3">compare view</a></li>
</ul>
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PR_kwDOACgets5UZ0F4
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Bump cython from 0.29.32 to 0.29.35
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-07-01T12:33:47
| 2023-07-01T19:11:56
|
2023-07-01T19:11:46Z
|
CONTRIBUTOR
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Bumps [cython](https://github.com/cython/cython) from 0.29.32 to 0.29.35.
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/cython/cython/blob/master/CHANGES.rst">cython's changelog</a>.</em></p>
<blockquote>
<h1>0.29.35 (2023-05-24)</h1>
<h2>Bugs fixed</h2>
<ul>
<li>
<p>A garbage collection enabled subtype of a non-GC extension type could call into the
deallocation function of the super type with GC tracking enabled. This could lead
to crashes during deallocation if GC was triggered on the type at the same time.
(Github issue :issue:<code>5432</code>)</p>
</li>
<li>
<p>Some C compile failures and crashes in CPython 3.12 were resolved.</p>
</li>
<li>
<p><code>except + nogil</code> was syntactically not allowed.
<code>except +nogil</code> (i.e. defining a C++ exception handling function called <code>nogil</code>)
is now disallowed to prevent typos.
(Github issue :issue:<code>5430</code>)</p>
</li>
<li>
<p>A C compile failure in PyPy 3.10 was resolved.
Patch by Matti Picus. (Github issue :issue:<code>5408</code>)</p>
</li>
<li>
<p>Cython modules now use PEP-489 multi-phase init by default in PyPy 3.9 and later.
Original patch by Matti Picus. (Github issue :issue:<code>5413</code>)</p>
</li>
<li>
<p>API header files generated by different Cython versions can now be included in the
same C file.
(Github issue :issue:<code>5383</code>)</p>
</li>
<li>
<p>Function signatures containing a type like <code>tuple[()]</code> could not be printed.
Patch by Lisandro Dalcin. (Github issue :issue:<code>5355</code>)</p>
</li>
</ul>
<p>.. _0.29.34:</p>
<h1>0.29.34 (2023-04-02)</h1>
<h2>Bugs fixed</h2>
<ul>
<li>
<p>A refence leak of the for-loop list/tuple iterable was resolved if the for-loop's
<code>else:</code> branch executes a <code>break</code> for an outer loop.
(Github issue :issue:<code>5347</code>)</p>
</li>
<li>
<p>Some C compile failures in CPython 3.12 were resolved.</p>
</li>
<li>
<p>Some old usages of the deprecated Python <code>imp</code> module were replaced with <code>importlib</code>.
Patch by Matúš Valo. (Github issue :issue:<code>5300</code>)</p>
</li>
<li>
<p>Some issues with <code>depfile</code> generation were resolved.</p>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/cython/cython/commit/5cef4fa97285b32d1e7d78c57398c464106d14ab"><code>5cef4fa</code></a> Update changelog.</li>
<li><a href="https://github.com/cython/cython/commit/cca43b79d6e3c63ea71ef1230fdd8c7b21a79c77"><code>cca43b7</code></a> Prepare release of 0.29.35.</li>
<li><a href="https://github.com/cython/cython/commit/0673bb1d323948494a73f5391c8509c24873522e"><code>0673bb1</code></a> Work around doctest failures in Python 3.12.</li>
<li><a href="https://github.com/cython/cython/commit/fca96f8b03380e85ace18b95c55dd41f972ac1a7"><code>fca96f8</code></a> Work around the new Py3.12 error message suggestions in doctests by not print...</li>
<li><a href="https://github.com/cython/cython/commit/78688bdb57eb9a7d86dd9301e748bfbfdb4bdbb6"><code>78688bd</code></a> Update changelog.</li>
<li><a href="https://github.com/cython/cython/commit/fa9b2e92301ce9fc61a802ba11c6183d2688e20c"><code>fa9b2e9</code></a> Reject "except +nogil" in favour of "except + nogil" since the first is almos...</li>
<li><a href="https://github.com/cython/cython/commit/ba82c22200d6f72f6e05e2ebebc39727892c4f09"><code>ba82c22</code></a> Update the 0.29.x CI setup to Ubuntu 20.04 to make it work again, and copy so...</li>
<li><a href="https://github.com/cython/cython/commit/8af954f812f78d5258cb8440b13cc6944eccf940"><code>8af954f</code></a> Disable fast Py_SIZE(PyLong) check in Py3.12a7+ since it's no longer valid th...</li>
<li><a href="https://github.com/cython/cython/commit/38f6a5670c7004172502fee41d990519e2163666"><code>38f6a56</code></a> Prevent calling the dealloc slot of a non-GC base class with GC tracking enab...</li>
<li><a href="https://github.com/cython/cython/commit/a2db6deb18a64ca08da2f1298808fe5e1d460415"><code>a2db6de</code></a> enable passing datetime tests on PyPy (<a href="https://redirect.github.com/cython/cython/issues/5427">#5427</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/cython/cython/compare/0.29.32...0.29.35">compare view</a></li>
</ul>
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PR_kwDOACgets5UZ0Hh
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Bump plotly from 5.11.0 to 5.15.0
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-07-01T12:33:55
| 2023-07-01T19:11:56
|
2023-07-01T19:11:46Z
|
CONTRIBUTOR
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Bumps [plotly](https://github.com/plotly/plotly.py) from 5.11.0 to 5.15.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/releases">plotly's releases</a>.</em></p>
<blockquote>
<h2>v5.15.0</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.20.0 to version 2.24.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2241----2023-06-07">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add pattern to pie, funnelarea, sunburst, icicle and treemap traces [<a href="https://redirect.github.com/plotly/plotly.js/pull/6601">#6601</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6619">#6619</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6622">#6622</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6626">#6626</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6627">#6627</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6628">#6628</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6629">#6629</a>], with thanks to <a href="https://github.com/thierryVergult"><code>@thierryVergult</code></a> for the contribution!</li>
<li>Add <code>texttemplate</code> to shape.label for parametric shapes i.e. line, rect and circle [<a href="https://redirect.github.com/plotly/plotly.js/pull/6527">#6527</a>],
with thanks to the <a href="https://www.volkswagenag.com">Volkswagen</a> Center of Excellence for Battery Systems for sponsoring development!</li>
<li>Add strict option to custom bundle command [<a href="https://redirect.github.com/plotly/plotly.js/pull/6557">#6557</a>],
with thanks to <a href="https://github.com/CallumNZ"><code>@CallumNZ</code></a> for the contribution!</li>
<li>Add <code>legend</code> references to traces and <code>legend2</code>, <code>legend3</code>, etc. to layout,
also add <code>visible</code> to legend i.e. to allow positioning multiple legends on a graph [<a href="https://redirect.github.com/plotly/plotly.js/pull/6535">#6535</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
<li>Add <code>legend.xref</code> and <code>legend.yref</code> to enable container-referenced positioning of legends [<a href="https://redirect.github.com/plotly/plotly.js/pull/6589">#6589</a>], with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
<li>Add <code>colorbar.xref</code> and <code>colorbar.yref</code> to enable container-referenced positioning of colorbars [<a href="https://redirect.github.com/plotly/plotly.js/pull/6593">#6593</a>], with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
</ul>
</li>
<li><code>px</code> methods now accept data-frame-like objects that support a <code>to_pandas()</code> method, such as polars, cudf, vaex etc</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed another compatibility issue with Pandas 2.0, just affecting <code>px.*(line_close=True)</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4190">#4190</a>]</li>
<li>Empty pandas dataframe with facet row/column set no longer fails [<a href="https://redirect.github.com/plotly/plotly.py/pull/4038">#4038</a>]</li>
<li>Added some rounding to the <code>make_subplots</code> function to handle situations where the user-input specs cause the domain to exceed 1 by small amounts [<a href="https://redirect.github.com/plotly/plotly.py/pull/4153">#4153</a>]</li>
<li>Sanitize JSON output to prevent an XSS vector when graphs are inserted directly into HTML [<a href="https://redirect.github.com/plotly/plotly.py/pull/4196">#4196</a>]</li>
<li>Fixed issue with shapes and annotations plotting on the wrong y axis when supplied with a specific axis in the <code>yref</code> parameter [<a href="https://redirect.github.com/plotly/plotly.py/pull/4177">#4177</a>]</li>
<li>Remove <code>use_2to3</code> setuptools arg, which is invalid in the latest Python and setuptools versions [<a href="https://redirect.github.com/plotly/plotly.py/pull/4206">#4206</a>]</li>
<li>Fix <a href="https://redirect.github.com/plotly/plotly.py/issues/4066">#4066</a> JupyterLab v4 giving tiny default graph height [<a href="https://redirect.github.com/plotly/plotly.py/pull/4227">#4227</a>]</li>
<li>Fixed issue with <code>colors.n_colors</code> where generated RGB color values were not being constrained to stay between 0 and 255 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4110">#4110</a>]</li>
<li>Fix streamline figure factory with recent versions of Numpy</li>
<li>Fix issue with shapes and annotations not drawing on correct axis [<a href="https://redirect.github.com/plotly/plotly.py/pull/4177">#4177</a>]</li>
</ul>
<h2>v5.14.1</h2>
<h3>Fixed</h3>
<ul>
<li>Fixed compatibility issue with Pandas 2.0 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4103">#4103</a>]</li>
</ul>
<h2>v5.14.0</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.18.2 to version 2.20.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2200----2023-03-15">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>title.automargin</code> to enable automatic top and bottom margining for both container and paper referenced titles [<a href="https://redirect.github.com/plotly/plotly.js/pull/6428">#6428</a>],
with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
<li>Add <code>label</code> attribute to shapes [<a href="https://redirect.github.com/plotly/plotly.js/pull/6454">#6454</a>], with thanks to the <a href="https://www.volkswagenag.com">Volkswagen</a> Center of Excellence for Battery Systems for sponsoring development!</li>
<li>Add <code>labelalias</code> to various axes namely cartesian, gl3d, polar, smith, ternary, carpet,
indicator and colorbar [<a href="https://redirect.github.com/plotly/plotly.js/pull/6481">#6481</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
</ul>
</li>
<li>Key errors no longer precalculated when performing updates on plots [<a href="https://redirect.github.com/plotly/plotly.py/pull/4101">#4101</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed an issue with characters displaying incorrectly, by adding <code>charset="utf-8"</code> to scripts in <code>to_html</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4114">#4114</a>]</li>
<li>Added <code>packaging</code> to install requirements, fixing a <code>No module named 'packaging</code> error on Python 3.6 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4113">#4113</a>]</li>
</ul>
<h3>Added</h3>
<ul>
<li>Added option to allow passing a column name as a <code>str</code> in <code>hover_data</code> and <code>custom_data</code> in <code>plotly.express</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4083">4083</a>]</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/blob/master/CHANGELOG.md">plotly's changelog</a>.</em></p>
<blockquote>
<h2>[5.15.0] - 2023-06-08</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.20.0 to version 2.24.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2241----2023-06-07">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add pattern to pie, funnelarea, sunburst, icicle and treemap traces [<a href="https://redirect.github.com/plotly/plotly.js/pull/6601">#6601</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6619">#6619</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6622">#6622</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6626">#6626</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6627">#6627</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6628">#6628</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6629">#6629</a>], with thanks to <a href="https://github.com/thierryVergult"><code>@thierryVergult</code></a> for the contribution!</li>
<li>Add <code>texttemplate</code> to shape.label for parametric shapes i.e. line, rect and circle [<a href="https://redirect.github.com/plotly/plotly.js/pull/6527">#6527</a>],
with thanks to the <a href="https://www.volkswagenag.com">Volkswagen</a> Center of Excellence for Battery Systems for sponsoring development!</li>
<li>Add strict option to custom bundle command [<a href="https://redirect.github.com/plotly/plotly.js/pull/6557">#6557</a>],
with thanks to <a href="https://github.com/CallumNZ"><code>@CallumNZ</code></a> for the contribution!</li>
<li>Add <code>legend</code> references to traces and <code>legend2</code>, <code>legend3</code>, etc. to layout,
also add <code>visible</code> to legend i.e. to allow positioning multiple legends on a graph [<a href="https://redirect.github.com/plotly/plotly.js/pull/6535">#6535</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
<li>Add <code>legend.xref</code> and <code>legend.yref</code> to enable container-referenced positioning of legends [<a href="https://redirect.github.com/plotly/plotly.js/pull/6589">#6589</a>], with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
<li>Add <code>colorbar.xref</code> and <code>colorbar.yref</code> to enable container-referenced positioning of colorbars [<a href="https://redirect.github.com/plotly/plotly.js/pull/6593">#6593</a>], with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
</ul>
</li>
<li><code>px</code> methods now accept data-frame-like objects that support a <code>to_pandas()</code> method, such as polars, cudf, vaex etc</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed another compatibility issue with Pandas 2.0, just affecting <code>px.*(line_close=True)</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4190">#4190</a>]</li>
<li>Empty pandas dataframe with facet row/column set no longer fails [<a href="https://redirect.github.com/plotly/plotly.py/pull/4038">#4038</a>]</li>
<li>Added some rounding to the <code>make_subplots</code> function to handle situations where the user-input specs cause the domain to exceed 1 by small amounts [<a href="https://redirect.github.com/plotly/plotly.py/pull/4153">#4153</a>]</li>
<li>Sanitize JSON output to prevent an XSS vector when graphs are inserted directly into HTML [<a href="https://redirect.github.com/plotly/plotly.py/pull/4196">#4196</a>]</li>
<li>Fixed issue with shapes and annotations plotting on the wrong y axis when supplied with a specific axis in the <code>yref</code> parameter [<a href="https://redirect.github.com/plotly/plotly.py/pull/4177">#4177</a>]</li>
<li>Remove <code>use_2to3</code> setuptools arg, which is invalid in the latest Python and setuptools versions [<a href="https://redirect.github.com/plotly/plotly.py/pull/4206">#4206</a>]</li>
<li>Fix <a href="https://redirect.github.com/plotly/plotly.py/issues/4066">#4066</a> JupyterLab v4 giving tiny default graph height [<a href="https://redirect.github.com/plotly/plotly.py/pull/4227">#4227</a>]</li>
<li>Fixed issue with <code>colors.n_colors</code> where generated RGB color values were not being constrained to stay between 0 and 255 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4110">#4110</a>]</li>
<li>Fix streamline figure factory with recent versions of Numpy</li>
<li>Fix issue with shapes and annotations not drawing on correct axis [<a href="https://redirect.github.com/plotly/plotly.py/pull/4177">#4177</a>]</li>
</ul>
<h2>[5.14.1] - 2023-04-05</h2>
<h3>Fixed</h3>
<ul>
<li>Fixed compatibility issue with Pandas 2.0 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4103">#4103</a>]</li>
</ul>
<h2>[5.14.0] - 2023-03-29</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.18.2 to version 2.20.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2200----2023-03-15">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>title.automargin</code> to enable automatic top and bottom margining for both container and paper referenced titles [<a href="https://redirect.github.com/plotly/plotly.js/pull/6428">#6428</a>],
with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
<li>Add <code>label</code> attribute to shapes [<a href="https://redirect.github.com/plotly/plotly.js/pull/6454">#6454</a>], with thanks to the <a href="https://www.volkswagenag.com">Volkswagen</a> Center of Excellence for Battery Systems for sponsoring development!</li>
<li>Add <code>labelalias</code> to various axes namely cartesian, gl3d, polar, smith, ternary, carpet,
indicator and colorbar [<a href="https://redirect.github.com/plotly/plotly.js/pull/6481">#6481</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
</ul>
</li>
<li>Key errors no longer precalculated when performing updates on plots [<a href="https://redirect.github.com/plotly/plotly.py/pull/4101">#4101</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed an issue with characters displaying incorrectly, by adding <code>charset="utf-8"</code> to scripts in <code>to_html</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4114">#4114</a>]</li>
<li>Added <code>packaging</code> to install requirements, fixing a <code>No module named 'packaging</code> error on Python 3.6 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4113">#4113</a>]</li>
</ul>
<h3>Added</h3>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/plotly/plotly.py/commit/e42897d4be454be23004b3d1f8704386b57773dc"><code>e42897d</code></a> version changes for v5.15.0</li>
<li><a href="https://github.com/plotly/plotly.py/commit/69b4d3e0a099e80bbc8fe6fd5391c8280e3de117"><code>69b4d3e</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/3901">#3901</a> from plotly/px_to_pandas</li>
<li><a href="https://github.com/plotly/plotly.py/commit/0e0eaa80b2d3f95376c429100b55506cf166bca5"><code>0e0eaa8</code></a> Merge branch 'master' into px_to_pandas</li>
<li><a href="https://github.com/plotly/plotly.py/commit/c3b0fda15096638462f274237a0cdfbf64ba6d57"><code>c3b0fda</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/4233">#4233</a> from ArthurTlprt/master</li>
<li><a href="https://github.com/plotly/plotly.py/commit/6aae637a03eb856c395a6cbf1726598051398b0c"><code>6aae637</code></a> remove now-obsolete lines in streamline ff</li>
<li><a href="https://github.com/plotly/plotly.py/commit/2d055a439db4e80bee847ffa2deca3cad3ac8adf"><code>2d055a4</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/4210">#4210</a> from plotly/update-plotly-js</li>
<li><a href="https://github.com/plotly/plotly.py/commit/4367763af2ab22f78d9c638546d3ccf17df86047"><code>4367763</code></a> Update CHANGELOG.md</li>
<li><a href="https://github.com/plotly/plotly.py/commit/d1668b61c5244d656f25e90245c3fe162c73fa29"><code>d1668b6</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/3946">#3946</a> from jvdd/avoid_deepcopy</li>
<li><a href="https://github.com/plotly/plotly.py/commit/605ac4fc717b79ec679866a2106728ac3d07ac01"><code>605ac4f</code></a> Update packages/python/plotly/_plotly_utils/basevalidators.py</li>
<li><a href="https://github.com/plotly/plotly.py/commit/3dc764e67d78cd2dcd2a17b323afe26e5560ed04"><code>3dc764e</code></a> Update packages/python/plotly/_plotly_utils/basevalidators.py</li>
<li>Additional commits viewable in <a href="https://github.com/plotly/plotly.py/compare/v5.11.0...v5.15.0">compare view</a></li>
</ul>
</details>
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Bump sympy from 1.11.1 to 1.12
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-07-01T12:34:02
| 2023-07-01T19:11:57
|
2023-07-01T19:11:47Z
|
CONTRIBUTOR
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Bumps [sympy](https://github.com/sympy/sympy) from 1.11.1 to 1.12.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/sympy/sympy/releases">sympy's releases</a>.</em></p>
<blockquote>
<h2>SymPy 1.12</h2>
<p>See <a href="https://github.com/sympy/sympy/wiki/release-notes-for-1.12">https://github.com/sympy/sympy/wiki/release-notes-for-1.12</a> for the release notes.</p>
<!-- raw HTML omitted -->
<p><strong>Note</strong>: Do not download the <strong>Source code (zip)</strong> or the <strong>Source code (tar.gz)</strong>
files below.</p>
<h2>SymPy 1.12rc1</h2>
<p>See <a href="https://github.com/sympy/sympy/wiki/release-notes-for-1.12">https://github.com/sympy/sympy/wiki/release-notes-for-1.12</a> for the release notes.</p>
<!-- raw HTML omitted -->
<p><strong>Note</strong>: Do not download the <strong>Source code (zip)</strong> or the <strong>Source code (tar.gz)</strong>
files below.</p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/sympy/sympy/commit/8059df7394f648bf4be5a51752e6d343003c92e6"><code>8059df7</code></a> Merge pull request <a href="https://redirect.github.com/sympy/sympy/issues/25122">#25122</a> from oscarbenjamin/pr_bump_version_112</li>
<li><a href="https://github.com/sympy/sympy/commit/092a0e484cc7be2e7de9bc611157f16822dcbd43"><code>092a0e4</code></a> Add type: ignore</li>
<li><a href="https://github.com/sympy/sympy/commit/cb39cbfd310ae99e5383befd5c5fd2e46fba5483"><code>cb39cbf</code></a> ignore lint rules</li>
<li><a href="https://github.com/sympy/sympy/commit/43259d0517a87eb0a944e916948847ec4e9727c7"><code>43259d0</code></a> maint: bump version to 1.12</li>
<li><a href="https://github.com/sympy/sympy/commit/2c3de5f49f294b7f84b3d58fe15e90b49b9316dc"><code>2c3de5f</code></a> Merge pull request <a href="https://redirect.github.com/sympy/sympy/issues/25010">#25010</a> from oscarbenjamin/pr_xxe_112</li>
<li><a href="https://github.com/sympy/sympy/commit/3c8ffe3f9f7625265261e8c29c2ce5c7a33ff40f"><code>3c8ffe3</code></a> Use py file for more easier lookup</li>
<li><a href="https://github.com/sympy/sympy/commit/6ff75154de546cf4cc8323e18d09778104338d4e"><code>6ff7515</code></a> Add test_mathml to optional dependency tests and add .txt file to tarball</li>
<li><a href="https://github.com/sympy/sympy/commit/3a3e32f28cfad8f14ea7871c058698de86b07c9d"><code>3a3e32f</code></a> Fix XXE vulnerability for mathml parser</li>
<li><a href="https://github.com/sympy/sympy/commit/271ca9f68fb3c2b8a9e1341621dab1e2f3189249"><code>271ca9f</code></a> Merge pull request <a href="https://redirect.github.com/sympy/sympy/issues/24994">#24994</a> from asmeurer/jquery-fix-1.12</li>
<li><a href="https://github.com/sympy/sympy/commit/b5993ecb92521ce7cf94e05c0f8e1663627e47e1"><code>b5993ec</code></a> flake8: ignore C416</li>
<li>Additional commits viewable in <a href="https://github.com/sympy/sympy/compare/sympy-1.11.1...sympy-1.12">compare view</a></li>
</ul>
</details>
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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_kwDOACgets5UZ0Ii
| 3,121
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Bump numpy from 1.24.3 to 1.25.0
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-07-01T12:34:11
| 2023-07-01T19:11:58
|
2023-07-01T19:11:48Z
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CONTRIBUTOR
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Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.25.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/numpy/numpy/releases">numpy's releases</a>.</em></p>
<blockquote>
<h2>v1.25.0</h2>
<h1>NumPy 1.25.0 Release Notes</h1>
<p>The NumPy 1.25.0 release continues the ongoing work to improve the
handling and promotion of dtypes, increase the execution speed, and
clarify the documentation. There has also been work to prepare for the
future NumPy 2.0.0 release, resulting in a large number of new and
expired deprecation. Highlights are:</p>
<ul>
<li>Support for MUSL, there are now MUSL wheels.</li>
<li>Support the Fujitsu C/C++ compiler.</li>
<li>Object arrays are now supported in einsum</li>
<li>Support for inplace matrix multiplication (<code>@=</code>).</li>
</ul>
<p>We will be releasing a NumPy 1.26 when Python 3.12 comes out. That is
needed because distutils has been dropped by Python 3.12 and we will be
switching to using meson for future builds. The next mainline release
will be NumPy 2.0.0. We plan that the 2.0 series will still support
downstream projects built against earlier versions of NumPy.</p>
<p>The Python versions supported in this release are 3.9-3.11.</p>
<h2>Deprecations</h2>
<ul>
<li>
<p><code>np.core.MachAr</code> is deprecated. It is private API. In names defined
in <code>np.core</code> should generally be considered private.</p>
<p>(<a href="https://redirect.github.com/numpy/numpy/pull/22638">gh-22638</a>)</p>
</li>
<li>
<p><code>np.finfo(None)</code> is deprecated.</p>
<p>(<a href="https://redirect.github.com/numpy/numpy/pull/23011">gh-23011</a>)</p>
</li>
<li>
<p><code>np.round_</code> is deprecated. Use <code>np.round</code> instead.</p>
<p>(<a href="https://redirect.github.com/numpy/numpy/pull/23302">gh-23302</a>)</p>
</li>
<li>
<p><code>np.product</code> is deprecated. Use <code>np.prod</code> instead.</p>
<p>(<a href="https://redirect.github.com/numpy/numpy/pull/23314">gh-23314</a>)</p>
</li>
<li>
<p><code>np.cumproduct</code> is deprecated. Use <code>np.cumprod</code> instead.</p>
<p>(<a href="https://redirect.github.com/numpy/numpy/pull/23314">gh-23314</a>)</p>
</li>
<li>
<p><code>np.sometrue</code> is deprecated. Use <code>np.any</code> instead.</p>
<p>(<a href="https://redirect.github.com/numpy/numpy/pull/23314">gh-23314</a>)</p>
</li>
<li>
<p><code>np.alltrue</code> is deprecated. Use <code>np.all</code> instead.</p>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/numpy/numpy/commit/db4f43983cb938f12c311e1f5b7165e270c393b4"><code>db4f439</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/23966">#23966</a> from charris/prepare-1.25.0-release</li>
<li><a href="https://github.com/numpy/numpy/commit/8c6b0bca5d18405d4094d197b7815e25c5ac63fa"><code>8c6b0bc</code></a> REL: Prepare for the NumPy 1.25.0 release</li>
<li><a href="https://github.com/numpy/numpy/commit/d5f9d1a01a5574e64172fea6c59e13a127cc1523"><code>d5f9d1a</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/23963">#23963</a> from charris/backport-23962</li>
<li><a href="https://github.com/numpy/numpy/commit/9b19e19ab79eada8c415793a2c4e83a918c04d25"><code>9b19e19</code></a> TEST: change subprocess call to capture stderr too</li>
<li><a href="https://github.com/numpy/numpy/commit/78fa6fb9a3c9795b15fe5e06bb3ce3c7509e8f2b"><code>78fa6fb</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/23957">#23957</a> from charris/backport-23789</li>
<li><a href="https://github.com/numpy/numpy/commit/430fc83925706f3e815caa46d2837607cbb6cf2c"><code>430fc83</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/23956">#23956</a> from charris/backport-23953</li>
<li><a href="https://github.com/numpy/numpy/commit/42ef942edece1e25bb1d0577a2f8d8bd46272590"><code>42ef942</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/23955">#23955</a> from charris/backport-23881</li>
<li><a href="https://github.com/numpy/numpy/commit/fa62e8c86caa3440e4216d57ba73f4766186976a"><code>fa62e8c</code></a> delete 23789.new_feature.rst from this PR</li>
<li><a href="https://github.com/numpy/numpy/commit/350c0039ef6454f29ebb6b1c0049692576463771"><code>350c003</code></a> Shorten release note to single point</li>
<li><a href="https://github.com/numpy/numpy/commit/051d307b14a08e214567c8c008b05b85f74961ba"><code>051d307</code></a> release note</li>
<li>Additional commits viewable in <a href="https://github.com/numpy/numpy/compare/v1.24.3...v1.25.0">compare view</a></li>
</ul>
</details>
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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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You can trigger Dependabot actions by commenting on this PR:
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`SpaceGroup.__repr__`
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2023-07-01T19:03:04Z
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MEMBER
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Not sure why but `SpaceGroup` didn't have a `repr` yet.
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PR_kwDOACgets5UbDy2
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Deprecate `pymatgen.util.convergence`
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2023-07-01T21:10:15Z
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e511f9a14 rename single-letter var names i -> idx
66d546abb fix doc string issues
e907c315e deprecate pymatgen/util/convergence.py
|
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PR_kwDOACgets5UbTba
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Add `pymatgen.io.openmm` package to `addons.rst`
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[] | 2023-07-01T22:35:46
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2023-07-02T00:18:17Z
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CONTRIBUTOR
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The core functionality of [pymatgen.io.openmm](https://github.com/orionarcher/pymatgen-io-openmm) is in place so I thought I'd add it to the the add ons page.
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PR_kwDOACgets5UcjGh
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Migrate from `warnings.catch_warnings(record=True)` to `pytest.warns()`
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Reason: more concise + `pytest.warns(match='msg')` encourages testing warning message for added test precision.
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PR_kwDOACgets5UgV0T
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Fix for missing lattice matches in ZSLGenerator
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[
"Thanks for this fix and the analysis writeup in https://github.com/materialsproject/pymatgen/issues/2457!"
] | 2023-07-03T09:43:31
| 2023-07-03T15:18:34
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2023-07-03T15:18:33Z
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CONTRIBUTOR
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Closes https://github.com/materialsproject/pymatgen/issues/2457.
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PR_kwDOACgets5UjENb
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Bump `ruff` + fix `PERF402` violations
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2023-07-04T17:58:22Z
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bfaea2694 `pymatgen/core/__init__.py` add `MODULE_DIR` `PKG_DIR` `ROOT`
82d0a9869 refactor `SubstrateAnalyzerTest.test_init` to simple function
4e7841402 for site in (struct.sites -> struct)
bfd40e242 bump `ruff` + fix new `PERF402` violations
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pre-commit autoupdate
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2023-07-04T02:18:49Z
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CONTRIBUTOR
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<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.275 → v0.0.276](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.275...v0.0.276)
- [github.com/pre-commit/mirrors-mypy: v1.4.0 → v1.4.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.4.0...v1.4.1)
- [github.com/codespell-project/codespell: v2.2.4 → v2.2.5](https://github.com/codespell-project/codespell/compare/v2.2.4...v2.2.5)
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Test error messages
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[
"<details><summary>Per-file size reduction</summary>\r\n\r\n| File | Original Size (B) | Compressed Size (B) | Reduction (%) |\r\n|:------------------------------------------------------|--------------------:|----------------------:|----------------:|\r\n| Sn_def_stress.json | 3322 | 776 | 77 |\r\n| OUTCAR.LOPTICS | 228160 | 40633 | 82 |\r\n| Mn3Ge_IR2.mcif | 1929 | 783 | 59 |\r\n| PROCAR.new_format_5.4.4 | 728661 | 96013 | 87 |\r\n| InN_22205_bandstructure.json | 56206 | 14752 | 74 |\r\n| benzene.xyz | 592 | 151 | 74 |\r\n| UNK.std | 23108 | 22183 | 4 |\r\n| CHGCAR.Fe3O4_ref | 7.09241e+06 | 2.33461e+06 | 67 |\r\n| cube-gh-2817.xyz | 551 | 272 | 51 |\r\n| WAVECAR.N2.45210 | 24768 | 12857 | 48 |\r\n| LiFePO4.cif | 1935 | 677 | 65 |\r\n| La2CoO4.cif | 1379 | 533 | 61 |\r\n| OUTCAR.LaSnNO2.polar | 211497 | 33031 | 84 |\r\n| POSCAR.Al12O18 | 1056 | 280 | 73 |\r\n| MP2020Compatibility_alternate.yaml | 1561 | 597 | 62 |\r\n| Graphite.cif | 1806 | 846 | 53 |\r\n| POTCAR.Fe3O4 | 328045 | 120184 | 63 |\r\n| XDATCAR_6 | 1860 | 652 | 65 |\r\n| vasprun.xml.pbesol_vdw | 3.92586e+07 | 2.93181e+06 | 93 |\r\n| Cu2O_361_bandstructure.json | 1.71964e+06 | 198150 | 88 |\r\n| vasprun.xml.rscan | 3.42046e+06 | 306163 | 91 |\r\n| PF_sd_1615854.cif | 7893 | 2500 | 68 |\r\n| entries_thermo_type_GGA_GGA_U_R2SCAN.json | 18955 | 1824 | 90 |\r\n| NaCl_phonon_bandstructure.json | 281891 | 87438 | 69 |\r\n| dos_spin_polarization_mp-865805.json | 180897 | 14578 | 92 |\r\n| LiMn2O4.json | 3310 | 1123 | 66 |\r\n| INCAR | 197 | 175 | 11 |\r\n| vasprun.xml.random | 3.42142e+06 | 305221 | 91 |\r\n| rhomb_3478_conv.cif | 1206 | 474 | 61 |\r\n| PARAMETERS.2 | 299 | 176 | 41 |\r\n| vasprun.xml.scan_rvv10 | 3.72403e+06 | 177190 | 95 |\r\n| INCAR.lobster | 258 | 199 | 23 |\r\n| CaO_2605_structure.json | 735 | 387 | 47 |\r\n| POSCAR.lobster.spin_DOS | 174 | 136 | 22 |\r\n| vasprun.xml.opticaltransitions | 424788 | 62634 | 85 |\r\n| nosymm.cif | 7158 | 2765 | 61 |\r\n| OSZICAR | 1314 | 491 | 63 |\r\n| POTENTIALS | 335 | 148 | 56 |\r\n| magnetic.incommensurate.example.Cr.mcif | 4190 | 1462 | 65 |\r\n| OneLineSymmP1.cif | 704 | 356 | 49 |\r\n| structure_KF.json | 612 | 353 | 42 |\r\n| ATOMS | 42861 | 4356 | 90 |\r\n| WAVECAR.N2.malformed | 24768 | 12860 | 48 |\r\n| fit_symm_s2.vasp | 382 | 252 | 34 |\r\n| vasprun.xml.dielectric_5.4.4 | 1.13414e+06 | 148559 | 87 |\r\n| EDI.cssr | 1161 | 241 | 79 |\r\n| POTCAR.spec | 76 | 102 | -34 |\r\n| bad-unicode-gh-2947.mcif | 3946 | 1499 | 62 |\r\n| POSCAR.O2 | 1172 | 321 | 73 |\r\n| TiO2_super.json | 5656 | 1917 | 66 |\r\n| KPOINTS.explicit | 100 | 87 | 13 |\r\n| vasprun.xml.dfpt.ionic | 6.11821e+07 | 4.24164e+06 | 93 |\r\n| EDI_voro.xyz | 1942 | 575 | 70 |\r\n| MultiStructure.cif | 4924 | 1559 | 68 |\r\n| complete_dos_limits.json | 468 | 205 | 56 |\r\n| EnumerateTest.json | 2442 | 451 | 82 |\r\n| input_exciting2.xml | 1049 | 518 | 51 |\r\n| EDI_oxistate_decorated.cssr | 1191 | 265 | 78 |\r\n| Co8.cif | 1077 | 460 | 57 |\r\n| KPOINTS.cartesian | 89 | 93 | -4 |\r\n| INCAR.lobster3 | 246 | 193 | 22 |\r\n| monoc_1028.cif | 1863 | 768 | 59 |\r\n| garnet.cif | 4318 | 1523 | 65 |\r\n| CHGCAR.Fe3O4 | 1.36213e+07 | 4.34559e+06 | 68 |\r\n| OUTCAR.lepsilon | 3.34798e+06 | 470428 | 86 |\r\n| WAVECAR.N2 | 24768 | 12845 | 48 |\r\n| tric_684654.json | 1351 | 610 | 55 |\r\n| OUTCAR.dielectric | 261831 | 47037 | 82 |\r\n| OUTCAR | 274379 | 45882 | 83 |\r\n| POSCAR.symbols_natoms_multilines | 6388 | 1703 | 73 |\r\n| INCAR.lobster2 | 259 | 200 | 23 |\r\n| input_exciting1.xml | 2055 | 473 | 77 |\r\n| POSCAR.lobster.nonspin_DOS | 174 | 139 | 20 |\r\n| vasprun.xml.forcehybridlikecalc | 549307 | 46197 | 92 |\r\n| Na2Fe2PNO4Se4.json | 5887 | 1387 | 76 |\r\n| vasprun.xml | 8.66238e+06 | 679224 | 92 |\r\n| transformations.json | 10099 | 1904 | 81 |\r\n| vasprun.xml.dielectric_bad | 1.13418e+06 | 148563 | 87 |\r\n| Cu7Te5.cif | 5102 | 1516 | 70 |\r\n| OUTCAR.vasp.6.2.1.mpi | 514129 | 33533 | 93 |\r\n| CaO_2605_bandstructure.json | 28710 | 7659 | 73 |\r\n| vasprun.xml.dfpt.unconverged | 1.82309e+06 | 137870 | 92 |\r\n| C26H16BeN2O2S2.cif | 17528 | 6124 | 65 |\r\n| Si.cssr | 125 | 100 | 20 |\r\n| feff_radial_shell.xyz | 9657 | 2814 | 71 |\r\n| Li3GaPCO7.json | 5641 | 1697 | 70 |\r\n| site_type_symbol_test.cif | 3933 | 978 | 75 |\r\n| vasprun.xml.uniform | 927031 | 74983 | 92 |\r\n| WAVEDER.Si | 1.1552e+06 | 785670 | 32 |\r\n| C_48_bandstructure.json | 2.0541e+07 | 1.4866e+06 | 93 |\r\n| OUTCAR_merged_numbers2 | 282329 | 53447 | 81 |\r\n| ldos02.dat | 7286 | 2693 | 63 |\r\n| H6PbCI3N_mp-977013_symmetrized.cif | 1125 | 557 | 50 |\r\n| bs_ZnS_old.json | 535596 | 85230 | 84 |\r\n| rhomb_3478.cif | 841 | 399 | 53 |\r\n| pourbaix_test_data.json | 255471 | 14646 | 94 |\r\n| AgO_kpath_test.cif | 853 | 420 | 51 |\r\n| Traj_Combine_Test_XDATCAR_2 | 111001 | 42342 | 62 |\r\n| POSCAR.LiFePO4 | 948 | 422 | 55 |\r\n| CONTCAR.MD | 13279 | 4441 | 67 |\r\n| PF_sd_1811457.cif | 5458 | 1894 | 65 |\r\n| KPOINTS.band | 859 | 213 | 75 |\r\n| PROCAR.phase | 1.29688e+06 | 138446 | 89 |\r\n| KPOINTS_Si_bands | 855 | 234 | 73 |\r\n| POSCAR.CdS_HSE | 525 | 222 | 58 |\r\n| multicomp_pbx.json | 50099 | 4509 | 91 |\r\n| vasprun.xml.hse06 | 1.22541e+07 | 514952 | 96 |\r\n| Li.cif | 693 | 342 | 51 |\r\n| LiCoO2_batt.json | 103562 | 7995 | 92 |\r\n| P24Ru4H252C296S24N16.cif | 27563 | 7984 | 71 |\r\n| PF_sd_1928405.cif | 5352 | 1865 | 65 |\r\n| vasprun.xml.ml_md | 1.27264e+06 | 298152 | 77 |\r\n| Al3F9.json | 1368 | 633 | 54 |\r\n| TiO2_entries.json | 111943 | 15482 | 86 |\r\n| ldos01.dat | 7286 | 2687 | 63 |\r\n| hex_1170.cif | 1627 | 648 | 60 |\r\n| Li-Fe-P-O_entries.json | 455144 | 19132 | 96 |\r\n| vasprun.xml.sc_overflow | 1.26858e+07 | 1.07558e+06 | 92 |\r\n| ldos00.dat | 7286 | 2682 | 63 |\r\n| UNK.ncl | 46188 | 22342 | 52 |\r\n| KPOINTS.auto | 57 | 60 | -5 |\r\n| vasprun.xml.pbesol | 3.92586e+07 | 2.9318e+06 | 93 |\r\n| OUTCAR.Al | 229104 | 31818 | 86 |\r\n| magnetic_deformation.json | 1373 | 534 | 61 |\r\n| WAVECAR.N2.spin | 49536 | 24889 | 50 |\r\n| DOSCAR.lobster.spin | 2009 | 464 | 77 |\r\n| CHGCAR.nospin | 596890 | 180502 | 70 |\r\n| CaMoO2_batt.json | 24025 | 5491 | 77 |\r\n| IBZKPT.lobster | 8157 | 455 | 94 |\r\n| PF_sd_1002871.cif | 6374 | 2219 | 65 |\r\n| WAVECAR.H2_low_symm | 2304 | 1489 | 35 |\r\n| Li4Fe3Mn1(PO4)4.json | 6007 | 1696 | 72 |\r\n| Mn-O_entries.json | 43040 | 6013 | 86 |\r\n| feff_eels_powder.inp | 57334 | 10953 | 81 |\r\n| WAVEDER | 1.11987e+06 | 762533 | 32 |\r\n| example21.gout | 11933 | 2264 | 81 |\r\n| vasprun.lvel.Si2H.xml | 4.37613e+07 | 3.43978e+06 | 92 |\r\n| DYNMAT | 723 | 136 | 81 |\r\n| POSCAR.Fe3O4 | 543 | 248 | 54 |\r\n| LaMnO3_magnetic.mcif | 3082 | 1186 | 62 |\r\n| srycoo.cif | 2730 | 826 | 70 |\r\n| PROCAR.simple | 44712 | 4055 | 91 |\r\n| SrBa2Sn2O7.json | 61850 | 11703 | 81 |\r\n| OUTCAR.vasp.6.2.0 | 923841 | 122767 | 87 |\r\n| magnetic.example.NiO.mcif | 4508 | 1521 | 66 |\r\n| vasprun.xml.xe | 331920 | 26256 | 92 |\r\n| EDI.xr | 1772 | 423 | 76 |\r\n| Cu_30_bandstructure.json | 74405 | 21214 | 71 |\r\n| mp1048_raw_defect_energies.json | 1819 | 728 | 60 |\r\n| CuCl.cif | 1396 | 469 | 66 |\r\n| POSCAR | 1266 | 159 | 87 |\r\n| Na2Fe2PAsO4S4.json | 5875 | 1391 | 76 |\r\n| Traj_XDATCAR | 231007 | 88695 | 62 |\r\n| PF_sd_1622133.cif | 6312 | 2212 | 65 |\r\n| MgNiF6.cif | 1063 | 445 | 58 |\r\n| vasprun.xml.scan | 3.42141e+06 | 305203 | 91 |\r\n| OUTCAR_merged_numbers | 69415 | 13004 | 81 |\r\n| bad_occu.cif | 5480 | 2155 | 61 |\r\n| XDATCAR.MD | 15516 | 6431 | 59 |\r\n| Si_phonon_bandstructure.json | 189567 | 52985 | 72 |\r\n| V2O3.cif | 1825 | 938 | 49 |\r\n| vasprun.xml.nonlm | 3.72157e+07 | 2.07913e+06 | 94 |\r\n| CONTCAR.Li2O | 10859 | 480 | 96 |\r\n| Li8Fe2NiCoO8.cif | 2047 | 649 | 68 |\r\n| cif_finite_precision_frac_coord_error.cif | 1457 | 691 | 53 |\r\n| Fe2O3_exp.json | 12659 | 781 | 94 |\r\n| orcc_1003.cif | 2116 | 784 | 63 |\r\n| XDATCAR_5 | 756 | 156 | 79 |\r\n| test_toec_data.json | 44135 | 8361 | 81 |\r\n| WAVECAR.frac_encut | 4480 | 3173 | 29 |\r\n| POTCAR | 772006 | 278600 | 64 |\r\n| La4Fe4O12.cif | 1569 | 570 | 64 |\r\n| vasprun.xml.lobster.spin | 1.11239e+07 | 955374 | 91 |\r\n| Senegalite_implicit_hydrogen.cif | 1950 | 885 | 55 |\r\n| vasprun.xml.dielectric_6.0.8 | 1.46724e+06 | 165509 | 89 |\r\n| OUTCAR.lepsilon_old_born | 3.34791e+06 | 470433 | 86 |\r\n| CON_vesta.xyz | 7808 | 1897 | 76 |\r\n| LobsterCompleteDos_nonspin.json | 2381 | 694 | 71 |\r\n| ir_spectra_mp-991652_DDB.json | 4856 | 1358 | 72 |\r\n| vasprun.xml.wrong_sp | 331919 | 26264 | 92 |\r\n| LiTiO2_batt.json | 52933 | 4177 | 92 |\r\n| KPOINTS.forcehybridlikecalc | 99 | 95 | 4 |\r\n| MnO2_batt.json | 144133 | 31689 | 78 |\r\n| XDATCAR_4 | 652 | 123 | 81 |\r\n| lifepo4.xml | 1.54245e+07 | 914166 | 94 |\r\n| vasprun.xml.LiF | 337133 | 27383 | 92 |\r\n| feff.inp | 645 | 371 | 42 |\r\n| sio2.pw.in | 1158 | 549 | 53 |\r\n| OUTCAR_fc | 123727 | 20603 | 83 |\r\n| Al3F9_distorted.json | 2879 | 983 | 66 |\r\n| INCAR.3 | 284 | 262 | 8 |\r\n| Cod_4115344.cif | 13785 | 4556 | 67 |\r\n| vasprun.xml.unconverged | 3.79126e+06 | 244747 | 94 |\r\n| POSCAR_overlap | 381 | 138 | 64 |\r\n| xmu.dat | 8090 | 3074 | 62 |\r\n| KPOINTS.explicit_tet | 145 | 122 | 16 |\r\n| costdb_1.csv | 281 | 200 | 29 |\r\n| acetylene.xyz | 199 | 84 | 58 |\r\n| WAVECAR.H2.ncl | 4480 | 2861 | 36 |\r\n| WAVEDERF.Si | 9.09621e+06 | 1.50588e+06 | 83 |\r\n| vasprun.xml.r2scan | 3.42047e+06 | 305149 | 91 |\r\n| N2_12103_bandstructure.json | 3.5715e+06 | 293785 | 92 |\r\n| Li10GeP2S12.cif | 1834 | 576 | 69 |\r\n| POSCAR.Li2O | 4374 | 413 | 91 |\r\n| PARAMETERS | 207 | 175 | 15 |\r\n| LobsterCompleteDos_spin.json | 3083 | 773 | 75 |\r\n| multiple_frame_xyz.xyz | 996298 | 352069 | 65 |\r\n| vasprun.xml.Al | 336275 | 30848 | 91 |\r\n| bcc_1927.cif | 2245 | 747 | 67 |\r\n| NiO_19009_bandstructure.json | 81873 | 23240 | 72 |\r\n| UNK.N2.std | 248932 | 215495 | 13 |\r\n| costdb_2.csv | 411 | 209 | 49 |\r\n| Fe3O4.cif | 2206 | 809 | 63 |\r\n| INCAR.2 | 285 | 262 | 8 |\r\n| orci_1010.cif | 1751 | 698 | 60 |\r\n| PROCAR | 1.40534e+06 | 116612 | 92 |\r\n| PF_sd_1908491.cif | 5237 | 1851 | 65 |\r\n| OUTCAR.CL | 3.02906e+06 | 424317 | 86 |\r\n| Li4Fe3Mn1(PO4)4.cif | 2862 | 779 | 73 |\r\n| vasprun.bad_random_seed.xml | 3.14959e+06 | 566826 | 82 |\r\n| MgVO_batt.json | 15534 | 3623 | 77 |\r\n| UNK.H2.ncl | 77868 | 74515 | 4 |\r\n| WAVECAR.H2_low_symm.gamma | 1296 | 884 | 32 |\r\n| mp1048_defect_formation_energies.json | 4901 | 742 | 85 |\r\n| vasprun.xml.unknown | 3.42137e+06 | 305199 | 91 |\r\n| CsI3Pb.cif | 10878 | 3595 | 67 |\r\n| Traj_Combine_Test_XDATCAR_1 | 231007 | 88751 | 62 |\r\n| mp1487_raw_defect_energies.json | 1347 | 472 | 65 |\r\n| magnetic.ncl.example.GdB4.mcif | 3765 | 1392 | 63 |\r\n| POSCAR.tricky_symmetry | 4044 | 1194 | 70 |\r\n| FePO4a.cif | 2601 | 696 | 73 |\r\n| orac_632475.cif | 932 | 445 | 52 |\r\n| Si.pwscf.out | 12071 | 3572 | 70 |\r\n| LOCPOT | 596629 | 204686 | 66 |\r\n| cif_implicit_hydrogens_cod_1011130.cif | 4917 | 1724 | 65 |\r\n| vasprun.xml.dfpt.phonon | 2.96624e+06 | 169853 | 94 |\r\n| LobsterCompleteDos_MnO_nonspin.json | 3040 | 872 | 71 |\r\n| Traj_Combine_Test_XDATCAR_Full | 462007 | 176456 | 62 |\r\n| CsSnI3.cif | 1109 | 439 | 60 |\r\n| FeF3_batt.json | 32177 | 3035 | 91 |\r\n| structure_MnO.json | 634 | 368 | 42 |\r\n| ICSD59959.cif | 2628 | 1169 | 56 |\r\n| vasprun.xml.magmom_ldau | 5.10991e+06 | 417763 | 92 |\r\n| Mg_batt.json | 3441 | 1417 | 59 |\r\n| KPOINTS | 4211 | 777 | 82 |\r\n| vasprun.xml.vdw | 1.18038e+06 | 64975 | 94 |\r\n| vasprun_Si_bands.xml | 1.49116e+06 | 113424 | 92 |\r\n| OUTCAR.stopped | 7.03808e+06 | 1.0652e+06 | 85 |\r\n| PF_sd_1011081.cif | 4062 | 1465 | 64 |\r\n| log_fiesta | 39007 | 7154 | 82 |\r\n| DOSCAR.lobster.nonspin | 1349 | 419 | 69 |\r\n| bad_vasprun.xml | 36054 | 5966 | 83 |\r\n| rhomb_1170.cif | 1627 | 650 | 60 |\r\n| VBr2_971787_bandstructure.json | 80462 | 23525 | 71 |\r\n| OUTCAR.LOPTICS.vasp544 | 160873 | 28945 | 82 |\r\n| vasprun.xml.lobster.nonspin | 322805 | 27097 | 92 |\r\n| vasprun.GW0.xml | 410605 | 52013 | 87 |\r\n| Fe.cif | 3885 | 1386 | 64 |\r\n| PF_sd_1601634.cif | 5036 | 1915 | 62 |\r\n| KPOINTS_band.lobster | 26331 | 4629 | 82 |\r\n| LobsterCompleteDos_MnO.json | 4234 | 1096 | 74 |\r\n| CHGCAR.spin | 4.02636e+06 | 1.28304e+06 | 68 |\r\n| structure_CO2.json | 2433 | 482 | 80 |\r\n| Cod_2100513.cif | 28970 | 6311 | 78 |\r\n| assimilated.json | 128 | 135 | -5 |\r\n| vasprun.charged.xml | 353109 | 32904 | 91 |\r\n| magnetic.disordered.example.CuMnO2.mcif | 3846 | 1486 | 61 |\r\n| vasprun.xml.dielectric | 254683 | 28855 | 89 |\r\n| vasprun.xml.LiH_bad_efermi | 361527 | 27722 | 92 |\r\n| NaCl_complete_ph_dos.json | 13581 | 5677 | 58 |\r\n| SrTiO3_phonon_bandstructure.json | 5.87263e+06 | 1.87983e+06 | 68 |\r\n| OUTCAR.BaTiO3.polar | 232676 | 33174 | 86 |\r\n| fit_symm_s1.vasp | 382 | 246 | 36 |\r\n| complete_cohp_lobster.json | 43017 | 11793 | 73 |\r\n| LiFePO4.vasp | 1516 | 335 | 78 |\r\n| Li_no_projected.xml | 77687 | 8428 | 89 |\r\n| PF_sd_1704003.cif | 7601 | 2204 | 71 |\r\n| HEADER | 2900 | 1104 | 62 |\r\n| vasprun.split.charged.xml | 36522 | 6268 | 83 |\r\n| OUTCAR.icorelevel | 82352 | 14017 | 83 |\r\n| complete_dos.json | 2.38846e+06 | 117757 | 95 |\r\n| template_input_file.txt | 115 | 143 | -24 |\r\n| feff_eels_x.inp | 57340 | 10951 | 81 |\r\n| PF_sd_1500382.cif | 4932 | 1724 | 65 |\r\n| Li2O.cif | 5517 | 1792 | 68 |\r\n| btet_1915.cif | 1811 | 692 | 62 |\r\n| NaCl_ph_dos.json | 7542 | 3052 | 60 |\r\n| ieee_conversion_data.json | 132176 | 9982 | 92 |\r\n| vasprun.xml.dfpt | 3.00868e+06 | 209837 | 93 |\r\n| CoO19128.cif | 1751 | 702 | 60 |\r\n| PC_frag1.xyz | 162 | 123 | 24 |\r\n| TFSI.xyz | 461 | 262 | 43 |\r\n| EC.xyz | 563 | 266 | 53 |\r\n| PC.xyz | 419 | 207 | 51 |\r\n| water_cluster_K.xyz | 1546 | 763 | 51 |\r\n| water_cluster_Mg.xyz | 1345 | 679 | 50 |\r\n| LiEC.xyz | 455 | 223 | 51 |\r\n| phsh.xyz | 1459 | 607 | 58 |\r\n| POTCAR.Fe_pv | 187290 | 69962 | 63 |\r\n| WAVECAR | 0 | 28 | -inf |\r\n| test_lambda.json | 132 | 98 | 26 |\r\n| neb_analysis2.json | 57848 | 14243 | 75 |\r\n| CONTCAR | 4956 | 976 | 80 |\r\n| homo_lumo_nan_values.qcout | 123378 | 26480 | 79 |\r\n| so2_scan_opt.log | 522397 | 29425 | 94 |\r\n| killed.qcout | 45003 | 11854 | 74 |\r\n| H2O_gau_vib.out | 260386 | 39308 | 85 |\r\n| unable_to_determine_lambda_in_geom_opt.qcout | 153176 | 35782 | 77 |\r\n| quasirrho_gaufreq.log | 2.4876e+06 | 722042 | 71 |\r\n| partial_hessian.qcinp | 623 | 302 | 52 |\r\n| extra_scf_print.qcout | 1.4807e+06 | 443068 | 70 |\r\n| Ethane_e.pdb | 623 | 220 | 65 |\r\n| acene-n_gaussian09_opt.out | 424828 | 66941 | 84 |\r\n| aux_mpi_time_mol.qcout | 38641 | 10796 | 72 |\r\n| hf_opt_failed.qcout | 16002 | 4598 | 71 |\r\n| qchem43_batch_job.qcout | 29783 | 9725 | 67 |\r\n| so2_scan.log | 123745 | 9191 | 93 |\r\n| hf.qcout | 4852 | 2378 | 51 |\r\n| pt_dft_180.0.qcout | 113477 | 15101 | 87 |\r\n| ferrocenium_1pos.qcout | 455467 | 82200 | 82 |\r\n| ethane.mol | 786 | 213 | 73 |\r\n| ethane.gjf | 382 | 239 | 37 |\r\n| dh.xyz | 251 | 154 | 39 |\r\n| g305_hb.txt | 4780 | 1842 | 61 |\r\n| freq_seg_too_small.qcout | 18579 | 6862 | 63 |\r\n| CdBr2.qcout | 73121 | 11170 | 85 |\r\n| opt_fail_no_message.qcout | 77479 | 15985 | 79 |\r\n| quinoxaline_anion.qcout | 210587 | 31955 | 85 |\r\n| MgBF4_b_overalpped.qcout | 13043 | 4451 | 66 |\r\n| basis2_mixed.inp | 1005 | 375 | 63 |\r\n| pcm_solvent_deprecated.qcout | 14897 | 4611 | 69 |\r\n| time_nan_values.qcout | 35365 | 7366 | 79 |\r\n| scf_no_message_fail.qcout | 9064 | 3642 | 60 |\r\n| hirshfeld_population.qcout | 18548 | 5295 | 71 |\r\n| MethylPyrrolidine_drawn.gjf | 2819 | 811 | 71 |\r\n| c60.xyz | 3606 | 632 | 82 |\r\n| l-cysteine.out | 338165 | 57220 | 83 |\r\n| h2o_aimd.qcout | 65709 | 13202 | 80 |\r\n| l-cysteine.inp | 855 | 498 | 42 |\r\n| methane.log | 61774 | 11170 | 82 |\r\n| no_reading.qcout | 3405 | 1678 | 51 |\r\n| CH2O_CO2.log | 82538 | 15149 | 82 |\r\n| insufficient_memory.qcout | 24058 | 8730 | 64 |\r\n| H2O_scan_G16.out | 312107 | 21004 | 93 |\r\n| Carbon_Disulfide.xyz | 97 | 90 | 7 |\r\n| MgBF4_b_overalpped.qcinp | 375 | 222 | 41 |\r\n| negative_eigen.qcout | 23203 | 8316 | 64 |\r\n| crazy_scf_values.qcout | 319548 | 61577 | 81 |\r\n| not_enough_total_memory.qcout | 607326 | 163297 | 73 |\r\n| H2O_gau.out | 70123 | 11938 | 83 |\r\n| scf_opt_no_message_fail.qcout | 9065 | 3646 | 60 |\r\n| tfsi_nbo.qcout | 145606 | 32530 | 78 |\r\n| thiophene_wfs_5_carboxyl.qcout | 92384 | 18263 | 80 |\r\n| pcm_solvent_qc42_format.qcinp | 1366 | 509 | 63 |\r\n| gmd_scf.qcout | 60474 | 15689 | 74 |\r\n| ghost_atoms.qcout | 14034 | 5056 | 64 |\r\n| exit_code_134.qcout | 10617 | 4103 | 61 |\r\n| crowd_nbo_charges.qcout | 536675 | 106243 | 80 |\r\n| crowd_gradient_number.qcout | 73861 | 21195 | 71 |\r\n| b12h12.xyz | 1018 | 362 | 64 |\r\n| so2_td.log | 18266 | 5888 | 68 |\r\n| chelpg_charges.qcout | 20906 | 7280 | 65 |\r\n| bsse.qcout | 15612 | 5652 | 64 |\r\n| RhB18_adf.inp | 1490 | 592 | 60 |\r\n| adf.out | 135897 | 23225 | 83 |\r\n| logfile | 17037 | 2365 | 86 |\r\n| hf-rimp2.qcout | 11228 | 4066 | 64 |\r\n| hf_wb97xd_gen_scfman.qcout | 157541 | 28346 | 82 |\r\n| hf_b3lyp.qcout | 10186 | 3706 | 64 |\r\n| hf_tpssh.qcout | 10068 | 3699 | 63 |\r\n| hf_lxygjos.qcout | 11664 | 4246 | 64 |\r\n| hf_mp2.qcout | 9773 | 3652 | 63 |\r\n| hf_mosmp2.qcout | 11492 | 4130 | 64 |\r\n| hf_xygjos.qcout | 12389 | 4363 | 65 |\r\n| hf_xyg3.qcout | 10638 | 3872 | 64 |\r\n| hf_hf.qcout | 9349 | 3513 | 62 |\r\n| hf_riccsd(t).qcout | 17129 | 5063 | 70 |\r\n| hf_cosmo.qcout | 10313 | 3995 | 61 |\r\n| hf_pcm.qcout | 10174 | 3967 | 61 |\r\n| hf_ccsd(t).qcout | 16934 | 4965 | 71 |\r\n| hf_qcisd(t).qcout | 21281 | 6472 | 70 |\r\n| NucVeloc.velocities | 957794 | 277126 | 71 |\r\n| mg2dig_nvt_langevin.inp | 5111 | 1939 | 62 |\r\n| molecule_read_error.qout | 4919 | 2631 | 47 |\r\n| nbo5_1.qout | 184524 | 36190 | 80 |\r\n| pt_n2_gs_rimp2_pvqz_90.0.qcout | 50298 | 11311 | 78 |\r\n| 1570.qout | 1.89119e+06 | 73974 | 96 |\r\n| lebdevpts.qout | 16742 | 5365 | 68 |\r\n| isosvp_water_single.qcout | 15174 | 6173 | 59 |\r\n| nbo7_1.qout | 1.19831e+06 | 308320 | 74 |\r\n| pes_scan_single_variable.qout | 4.62519e+06 | 642735 | 86 |\r\n| os_gap.qout | 1.37001e+07 | 3.83074e+06 | 72 |\r\n| roothaan_diis_gdm.qout | 1.47793e+06 | 133754 | 91 |\r\n| cmirs_dielst10_single.qcout | 16225 | 6481 | 60 |\r\n| basis_not_supported.qout | 6498 | 3246 | 50 |\r\n| 1746.qout | 1.91565e+06 | 92920 | 95 |\r\n| isosvp_dielst10.qcout | 27791 | 7111 | 74 |\r\n| nbo7_inf.qout | 2.71445e+07 | 7.33644e+06 | 73 |\r\n| 1570_2.qout | 325841 | 47703 | 85 |\r\n| Optimization_no_equal.qout | 133162 | 20158 | 85 |\r\n| VCLi_solv_eps10.qcout | 246600 | 41002 | 83 |\r\n| gdm.qout | 26612 | 9437 | 65 |\r\n| almo.out | 22551 | 7427 | 67 |\r\n| fodft.out | 17072 | 5429 | 68 |\r\n| VC_solv_eps10.qcout | 248270 | 54407 | 78 |\r\n| mpi_error.qout | 173 | 148 | 14 |\r\n| fodft_2.out | 17225 | 5425 | 69 |\r\n| ts.out | 111104 | 25620 | 77 |\r\n| nbo.qout | 424727 | 77846 | 82 |\r\n| fodft_3.out | 17273 | 5434 | 69 |\r\n| custom_gdm_gdmqls_opt.qout | 546371 | 149666 | 73 |\r\n| cdft_simple.qout | 17600 | 6458 | 63 |\r\n| 2068.qout | 1.88662e+06 | 204100 | 89 |\r\n| VCGenSCFMan.qcout | 25067 | 7725 | 69 |\r\n| 2620.qout | 2.32865e+06 | 256673 | 89 |\r\n| custom_smd.qin | 1389 | 564 | 59 |\r\n| N2.qcout | 16958 | 5615 | 67 |\r\n| MECLi_solv_eps10.qcout | 1.00749e+06 | 146050 | 86 |\r\n| pod1.out | 15438 | 5995 | 61 |\r\n| pod2_gs.out | 15482 | 6012 | 61 |\r\n| pes_scan_double_variable.qout | 1.17202e+07 | 1.86861e+06 | 84 |\r\n| switch_to_cartesian.qout | 2.90757e+06 | 933121 | 68 |\r\n| e2pert.qin | 95462 | 17922 | 81 |\r\n| DinfH.qout | 82255 | 12677 | 85 |\r\n| Frequency_no_equal.qout | 103092 | 27298 | 74 |\r\n| pt_n2_n_wb_180.0.qcout | 77007 | 15359 | 80 |\r\n| pes_scan.qin | 991 | 537 | 46 |\r\n| isosvp_water.qcout | 27794 | 7089 | 74 |\r\n| gap.qout | 21626 | 8774 | 59 |\r\n| cmirs_benzene_single.qcout | 16173 | 6480 | 60 |\r\n| unexpected_ts.out | 531391 | 100769 | 81 |\r\n| 3C.qout | 2.23995e+07 | 6.31089e+06 | 72 |\r\n| nbo7.qin | 510 | 300 | 41 |\r\n| svd_failed.qout | 210842 | 62965 | 70 |\r\n| cdft_dc.qout | 60001 | 10650 | 82 |\r\n| pcm.qin | 857 | 480 | 44 |\r\n| pt_n2_trip_wb_90.0.qcout | 346602 | 55070 | 84 |\r\n| nbo7_2.qout | 2.83281e+06 | 775073 | 73 |\r\n| cmirs_water_single.qcout | 16302 | 6536 | 60 |\r\n| cmirs_benzene.qcout | 28424 | 7269 | 74 |\r\n| single_point.qout | 20237 | 7616 | 62 |\r\n| hyper.qout | 2.71445e+07 | 7.33644e+06 | 73 |\r\n| ccsdt.qout | 24319 | 8327 | 66 |\r\n| isosvp_dielst10_single.qcout | 15171 | 6163 | 59 |\r\n| VC_solv_eps10.2.qcout | 34961 | 11481 | 67 |\r\n| v6_old_driver.out | 162457 | 31169 | 81 |\r\n| nbo7_3.qout | 767247 | 190492 | 75 |\r\n| ccsd.qout | 36112 | 10823 | 70 |\r\n| unable.qout | 3.6297e+06 | 1.16186e+06 | 68 |\r\n| cmirs_dielst10.qcout | 28474 | 7271 | 74 |\r\n| frag_1.xyz | 199 | 105 | 47 |\r\n| frag_2.xyz | 199 | 114 | 43 |\r\n| HESS | 1933 | 915 | 53 |\r\n| 132.0 | 1152 | 802 | 30 |\r\n| Si_cluster_2.xyz | 496 | 289 | 42 |\r\n| thiane2.sdf | 1549 | 374 | 76 |\r\n| cyclohexane2.xyz | 886 | 281 | 68 |\r\n| k2.sdf | 1860 | 458 | 75 |\r\n| oxygen2.xyz | 39 | 54 | -38 |\r\n| ethene2.xyz | 297 | 143 | 52 |\r\n| t5.xyz | 1768 | 574 | 68 |\r\n| t4.xyz | 1768 | 574 | 68 |\r\n| grouped_mol_list.txt | 274 | 141 | 49 |\r\n| cyclohexane1.xyz | 886 | 283 | 68 |\r\n| thiane1.sdf | 1549 | 377 | 76 |\r\n| k1.sdf | 1851 | 448 | 76 |\r\n| ethene1.xyz | 297 | 141 | 53 |\r\n| oxygen1.xyz | 35 | 50 | -43 |\r\n| Si2O_cluster_perturbed.xyz | 186 | 161 | 13 |\r\n| t1.xyz | 1278 | 404 | 68 |\r\n| t3.xyz | 1278 | 409 | 68 |\r\n| Si_cluster_rotated.xyz | 495 | 287 | 42 |\r\n| t2.xyz | 1278 | 405 | 68 |\r\n| j2.xyz | 1768 | 567 | 68 |\r\n| thiane_ethynyl2.sdf | 1733 | 421 | 76 |\r\n| j1.xyz | 1768 | 565 | 68 |\r\n| mol_list.txt | 197 | 115 | 42 |\r\n| thiane_ethynyl1.sdf | 1759 | 437 | 75 |\r\n| Si_cluster_permuted.xyz | 489 | 170 | 65 |\r\n| Si_cluster.xyz | 489 | 140 | 71 |\r\n| cdi_23_2.xyz | 4905 | 1246 | 75 |\r\n| Si2O_cluster.xyz | 186 | 133 | 28 |\r\n| cdi_23_1.xyz | 4905 | 1417 | 71 |\r\n| Si_cluster_perturbed.xyz | 492 | 291 | 41 |\r\n| toluene2.xyz | 739 | 264 | 64 |\r\n| toluene1.xyz | 739 | 264 | 64 |\r\n| Si2O_cluster_2.xyz | 186 | 149 | 20 |\r\n| Si2O_cluster_rotated.xyz | 186 | 158 | 15 |\r\n| Si2O_cluster_permuted.xyz | 186 | 143 | 23 |\r\n| c1.xyz | 1768 | 567 | 68 |\r\n| benzene1.xyz | 592 | 218 | 63 |\r\n| c2.xyz | 1768 | 564 | 68 |\r\n| benzene2.xyz | 592 | 214 | 64 |\r\n| MgBH42.xyz | 552 | 217 | 61 |\r\n| thiophene2.xyz | 627 | 273 | 56 |\r\n| thiophene1.xyz | 606 | 227 | 63 |\r\n| mol_1_3_bond.qcout | 194729 | 32472 | 83 |\r\n| molecule_with_halogen_bonds_2.xyz | 1042 | 379 | 64 |\r\n| molecule_with_halogen_bonds_1.xyz | 1243 | 364 | 71 |\r\n| coc-115925-9326-14.res | 1600 | 907 | 43 |\r\n| spins-in-last-col.res | 2956 | 917 | 69 |\r\n| CuO.json | 3566 | 813 | 77 |\r\n| mag_orderings_test_cases.json | 230324 | 28513 | 88 |\r\n| Cr2FeS4.json | 34445 | 1552 | 95 |\r\n| Cr2NiO4.json | 5425 | 934 | 83 |\r\n| LiMnPO4.json | 75396 | 4085 | 95 |\r\n| Ta2CoO6.json | 24715 | 1754 | 93 |\r\n| Ca3Co2O6.json | 10027 | 1779 | 82 |\r\n| Ni(SbO3)2.json | 12542 | 2288 | 82 |\r\n| Cr2WO6.json | 3435 | 649 | 81 |\r\n| MnNi2Sn.json | 15055 | 1609 | 89 |\r\n| MnSi.json | 11969 | 1133 | 91 |\r\n| CoS2.json | 16345 | 1568 | 90 |\r\n| Mn3Al.json | 15224 | 1578 | 90 |\r\n| LaMnO3.json | 4000 | 860 | 78 |\r\n| NbFe2.json | 8640 | 953 | 89 |\r\n| vasp_inputs_for_grid_check.json | 8.6504e+06 | 944476 | 89 |\r\n| NaCl_partial_dos.dat | 12280 | 3872 | 68 |\r\n| POSCAR-NaCl | 743 | 138 | 81 |\r\n| POSCAR-unitcell | 2222 | 551 | 75 |\r\n| FORCE_CONSTANTS | 860165 | 19492 | 98 |\r\n| NaCl_band.yaml | 485041 | 72115 | 85 |\r\n| NaCl_phonopy.yaml | 11868 | 954 | 92 |\r\n| NaCl_total_dos.dat | 8260 | 2702 | 67 |\r\n| shared_ops.pkl | 57712 | 791 | 99 |\r\n| point_ops.pkl | 8999 | 405 | 95 |\r\n| CONTROL-CSLD_Si | 555 | 274 | 51 |\r\n| func_group_test_no_h.mol | 910 | 277 | 70 |\r\n| func_group_test.mol | 1554 | 388 | 75 |\r\n| CH4.nwout | 239127 | 38155 | 84 |\r\n| ch4.nw | 849 | 261 | 69 |\r\n| H4C3O3_1.nwout | 689937 | 120528 | 83 |\r\n| CH3CH2O.nwout | 802979 | 142393 | 82 |\r\n| N2O4.nwout | 806943 | 125344 | 84 |\r\n| anthrachinon_wfs_15_carboxyl.nwout | 1.93835e+06 | 367560 | 81 |\r\n| anthrachinon_wfs_16_ethyl.nwout | 3.48915e+06 | 645188 | 82 |\r\n| C1N1Cl1_1.nwout | 4448 | 1451 | 67 |\r\n| phen_tddft.log | 117272 | 21304 | 82 |\r\n| CONTCAR_bulk | 7343 | 348 | 95 |\r\n| thermal_displacement_matrices.yaml | 107270 | 15674 | 85 |\r\n| csentries_o_ads.json | 12805 | 2074 | 84 |\r\n| ZnO-wz.cif | 1995 | 934 | 53 |\r\n| Au_slab_init.cif | 1201 | 512 | 57 |\r\n| La_fcc_entries.txt | 46578 | 11299 | 76 |\r\n| ucell_entries.txt | 11422 | 1956 | 83 |\r\n| MgO_slab_entries.txt | 8340 | 1025 | 88 |\r\n| La_hcp_entries.txt | 60827 | 14831 | 76 |\r\n| isolated_O_entry.txt | 805 | 470 | 42 |\r\n| Cu_slab_init.cif | 1225 | 518 | 58 |\r\n| icsd_LiCoO2.cif | 2104 | 734 | 65 |\r\n| Cu_slab_fin.cif | 1225 | 589 | 52 |\r\n| icsd_TeI.cif | 2518 | 1140 | 55 |\r\n| icsd_batio3.cif | 2627 | 1122 | 57 |\r\n| Cu_entries.txt | 96336 | 14711 | 85 |\r\n| csentries_slabs.json | 4798 | 1210 | 75 |\r\n| Ni_fcc_111_adatom_bridge_1x1.cif | 1298 | 502 | 61 |\r\n| Fe_bcc_100_zigzag_rt2xrt2.cif | 2333 | 596 | 74 |\r\n| Ni_fcc_111_adatom_ht_1x1.cif | 1298 | 502 | 61 |\r\n| Ni_fcc_111_adatom_ft_1x1.cif | 1297 | 499 | 62 |\r\n| Si_diamond_100_2x1.cif | 2147 | 605 | 72 |\r\n| Ni_fcc_100_missing_row_1x1.cif | 1671 | 507 | 70 |\r\n| Ni_fcc_111_adatom_t_1x1.cif | 1297 | 489 | 62 |\r\n| Si_diamond_110_1x1.cif | 1957 | 574 | 71 |\r\n| Ni_fcc_111_adatom_h_1x1.cif | 1298 | 497 | 62 |\r\n| Si_diamond_111_1x2.cif | 2715 | 739 | 73 |\r\n| Ni_fcc_111_missing_row_1x2.cif | 1672 | 544 | 67 |\r\n| Ni_fcc_110_missing_row_1x2.cif | 2423 | 571 | 76 |\r\n| CP2K-GTENSOR-1_0.data | 1263 | 292 | 77 |\r\n| include.inc | 87 | 105 | -21 |\r\n| Static-ALPHA_k1-1.pdos | 705 | 250 | 65 |\r\n| CP2K-CHI-1_0.data | 939 | 300 | 68 |\r\n| cp2k.inp | 3728 | 1260 | 66 |\r\n| CP2K-HYPERFINE-1_0.eprhyp | 929 | 247 | 73 |\r\n| Si | 3652 | 1005 | 72 |\r\n| CP2K-1.dos | 259 | 153 | 41 |\r\n| cp2k.out | 78876 | 11745 | 85 |\r\n| BAND.bs | 47493 | 1887 | 96 |\r\n| ldos.inp | 256 | 162 | 37 |\r\n| ldos03.dat | 7286 | 2692 | 63 |\r\n| pot.inp | 1396 | 509 | 64 |\r\n| ICSD_170.cif | 5997 | 1808 | 70 |\r\n| mgb2_nscf.abo | 109088 | 22801 | 79 |\r\n| O.GGA_PBE-JTH-paw.xml | 570592 | 219821 | 61 |\r\n| si.cif | 1579 | 593 | 62 |\r\n| Si2_GSR.nc | 7072 | 1663 | 76 |\r\n| ge.oncvpsp | 590 | 299 | 49 |\r\n| mgb2_nscf.log | 47719 | 9041 | 81 |\r\n| H-wdr.oncvpsp | 57451 | 14016 | 76 |\r\n| 14-Si.LDA.fhi | 135868 | 53420 | 61 |\r\n| Pb-d-3_r.psp8 | 569 | 327 | 43 |\r\n| mgb2_scf.log | 69562 | 11297 | 84 |\r\n| 14si.pspnc | 305169 | 119803 | 61 |\r\n| mgb2_scf.abo | 81064 | 15474 | 81 |\r\n| 14si.4.hgh | 811 | 324 | 60 |\r\n| sic_relax.abo | 49268 | 12020 | 76 |\r\n| gan.cif | 903 | 399 | 56 |\r\n| badyaml.log | 10148 | 2710 | 73 |\r\n| LFP_POSCAR_s | 1558 | 374 | 76 |\r\n| LFP_POSCAR_e | 1558 | 376 | 76 |\r\n| pztfcm.npy | 7328 | 1610 | 78 |\r\n| becops.pkl | 2645 | 455 | 83 |\r\n| sharedops.npy | 74979 | 9685 | 87 |\r\n| istops.npy | 1095 | 553 | 49 |\r\n| pointops.npy | 11245 | 1935 | 83 |\r\n| fcmops.pkl | 3772 | 688 | 82 |\r\n| pztist.npy | 2240 | 631 | 72 |\r\n| pb2tizro6.json | 1690 | 498 | 71 |\r\n| pztborn.npy | 848 | 416 | 51 |\r\n| pt_n2_wb97mv_0.0.in | 1736 | 636 | 63 |\r\n| pt_test_mol.xyz | 788 | 285 | 64 |\r\n| detailed_voronoi_container_coordination_numbers_1.png | 28122 | 23428 | 17 |\r\n| test_A--2_SO2_icsd_24645.json | 2727 | 604 | 78 |\r\n| test_TS--3_ClF3_icsd_203121.json | 7465 | 1459 | 80 |\r\n| test_T--4_CCl4_icsd_246796.json | 37730 | 5405 | 86 |\r\n| test_TT_1--9_RbTh3F13_icsd_9915.json | 7535 | 1228 | 84 |\r\n| test_PB--7_PaCl5_icsd_15391.json | 5546 | 1092 | 80 |\r\n| test_SS--4_XeO2F2_icsd_10203.json | 4586 | 821 | 82 |\r\n| test_SBT--8_PuBr3_icsd_31588.json | 3493 | 644 | 82 |\r\n| test_T--4_SiO2_icsd_34927.json | 3158 | 778 | 75 |\r\n| test_T--5_cod_YMn0.63In0.37O3_4105420.json | 8999 | 1565 | 83 |\r\n| test_TL--3_BF3_icsd_20904.json | 7778 | 1927 | 75 |\r\n| test_S--4_BaCuSi4O10_icsd_71865.json | 14709 | 1595 | 89 |\r\n| test_TY--3_K2SO3_icsd_60762.json | 2977 | 707 | 76 |\r\n| test_TL--3_CaCO3_icsd_32100.json | 4876 | 988 | 80 |\r\n| test_O--6_NaCl_icsd_61662.json | 840 | 438 | 48 |\r\n| test_S--4_BaCrSi4O10_icsd_83463.json | 14808 | 1684 | 89 |\r\n| test_S--5_V2O5_icsd_41030.json | 3501 | 802 | 77 |\r\n| test_C--8_CsCl_icsd_622367.json | 768 | 391 | 49 |\r\n| test_T--4_LiNdP4O12_icsd_14.json | 9117 | 1801 | 80 |\r\n| test_SS--4_SeF4_icsd_85451.json | 4723 | 1069 | 77 |\r\n| test_L--2_CO2_icsd_16428.json | 2814 | 583 | 79 |\r\n| test_TL--3_CaCO3_icsd_40107.json | 2559 | 670 | 74 |\r\n| test_L--2_Cu2O_icsd_52043.json | 1574 | 491 | 69 |\r\n| test_A--2_KNO2_icsd_36202.json | 1285 | 535 | 58 |\r\n| test_S--5_BrF5_icsd_31690.json | 5496 | 957 | 83 |\r\n| test_T--4_ZrSiO4_icsd_69643.json | 3250 | 828 | 75 |\r\n| test_T--4_FePO4_icsd_4266.json | 4566 | 1069 | 77 |\r\n| test_S--1_ClF_icsd_406442.json | 2260 | 707 | 69 |\r\n| test_T--6_MoS2_icsd_38401.json | 972 | 451 | 54 |\r\n| test_O--6_Sr3Fe2O7_icsd_2648.json | 9646 | 1022 | 89 |\r\n| test_T--4_CrPO4_icsd_60836.json | 9255 | 1500 | 84 |\r\n| test_TY--3_NH3_icsd_29321.json | 3791 | 737 | 81 |\r\n| test_S--1_CO_icsd_26962.json | 2052 | 557 | 73 |\r\n| test_O--6_LaFeO3_icsd_93611.json | 4644 | 903 | 81 |\r\n| test_T--5_PF5_icsd_62554.json | 3113 | 693 | 78 |\r\n| test_I--12_Mg3Cr2Al18_icsd_606797.json | 12104 | 1514 | 87 |\r\n| test_SA--8_ThMo2O8_icsd_37236.json | 19679 | 2497 | 87 |\r\n| test_S--4_BaFeSi4O10_icsd_6256.json | 14132 | 1634 | 88 |\r\n| test_ST--7_K2TaF7_icsd_46005.json | 9215 | 1701 | 82 |\r\n| test_L--2_HgCl2_icsd_23277.json | 2926 | 726 | 75 |\r\n| test_L--2_XeF2_icsd_260950.json | 985 | 454 | 54 |\r\n| test_S--4_Pd2P2O7_icsd_415239.json | 5720 | 1260 | 78 |\r\n| test_S--4_XeF4_icsd_26626.json | 2558 | 779 | 70 |\r\n| test_SA--8_ThTi2O6_icsd_27017.json | 4772 | 1088 | 77 |\r\n| test_S--4_PdSO4_icsd_79559.json | 5814 | 1175 | 80 |\r\n| test_T--4_SiO2_icsd_174.json | 2494 | 738 | 70 |\r\n| se_mp-5020.json | 124900 | 20114 | 84 |\r\n| se_mp-7000.json | 186870 | 19964 | 89 |\r\n| se_mp-743972.json | 1.06697e+07 | 1.26468e+06 | 88 |\r\n| LiTFSi.xyz | 788 | 288 | 63 |\r\n| EMC.xyz | 739 | 199 | 73 |\r\n| PbTe_bandstructure.json | 25688 | 7893 | 69 |\r\n| N2_bandstructure.json | 649512 | 66278 | 90 |\r\n| vasprun_spin.xml | 1.80474e+06 | 123792 | 93 |\r\n| EC-12.qout | 49244 | 15808 | 68 |\r\n| PC01.qout | 63007 | 19322 | 69 |\r\n| CHGCAR | 26 | 51 | -96 |\r\n| gruneisen_band_Si.yaml | 307899 | 50555 | 84 |\r\n| gruneisen_mesh_InP.yaml | 1.24275e+06 | 220020 | 82 |\r\n| gruneisen_eq_plus_minus_InP.yaml | 319505 | 52142 | 84 |\r\n| gruneisen_mesh_only_one_q_InP.yaml | 1199 | 427 | 64 |\r\n| gruneisen_mesh_InP_without_struct.yaml | 1.24208e+06 | 219789 | 82 |\r\n| gruneisen_mesh_Si.yaml | 1.24275e+06 | 228080 | 82 |\r\n| POSCAR_Si | 512 | 118 | 77 |\r\n| POSCAR_InP | 495 | 129 | 74 |\r\n| structure_mp-12103.json | 607 | 337 | 44 |\r\n| dft_bs_sym_line.json | 46711 | 12126 | 74 |\r\n| boltztrap.outputtrans | 4441 | 1418 | 68 |\r\n| boltztrap.proj_0_dx2 | 53467 | 846 | 98 |\r\n| boltztrap.proj_0_dxy | 53467 | 846 | 98 |\r\n| boltztrap.proj_0_s | 53467 | 3534 | 93 |\r\n| boltztrap.proj_1_dxy | 53467 | 846 | 98 |\r\n| boltztrap.sigxxx | 690420 | 111504 | 84 |\r\n| boltztrap.proj_1_dx2 | 53467 | 846 | 98 |\r\n| boltztrap.energyso | 11889 | 1590 | 87 |\r\n| boltztrap.proj_1_pz.transdos | 316397 | 38654 | 88 |\r\n| boltztrap_BZ.cube | 0 | 38 | -inf |\r\n| boltztrap.proj_0_py | 53467 | 4077 | 92 |\r\n| boltztrap.proj_0_dx2.transdos | 316397 | 29920 | 91 |\r\n| boltztrap.proj_0_py.transdos | 316397 | 38481 | 88 |\r\n| boltztrap.proj_0_px.transdos | 316397 | 38404 | 88 |\r\n| boltztrap.proj_0_px | 53467 | 4307 | 92 |\r\n| boltztrap.proj_1_dxy.transdos | 316397 | 29920 | 91 |\r\n| boltztrap.proj_0_s.transdos | 316397 | 38699 | 88 |\r\n| boltztrap.proj_1_px | 53467 | 4272 | 92 |\r\n| boltztrap.proj_1_dyz | 53467 | 846 | 98 |\r\n| boltztrap.proj_1_dx2.transdos | 316397 | 29920 | 91 |\r\n| boltztrap.proj_0_dyz | 53467 | 846 | 98 |\r\n| boltztrap.engre | 673388 | 597140 | 11 |\r\n| boltztrap.proj_1_py | 53467 | 4060 | 92 |\r\n| boltztrap.proj_0_dxy.transdos | 316397 | 29920 | 91 |\r\n| boltztrap.sigxx | 242580 | 34559 | 86 |\r\n| boltztrap.proj_0_dyz.transdos | 316397 | 29920 | 91 |\r\n| boltztrap.halltens | 4.31862e+06 | 1.42599e+06 | 67 |\r\n| boltztrap.proj_1_dxz | 53467 | 846 | 98 |\r\n| boltztrap.proj_0_dxz | 53467 | 846 | 98 |\r\n| boltztrap.struct | 286 | 131 | 54 |\r\n| boltztrap.proj_1_dyz.transdos | 316397 | 29920 | 91 |\r\n| boltztrap.condtens | 4.31889e+06 | 1.28029e+06 | 70 |\r\n| boltztrap.proj_0_dz2.transdos | 316397 | 29920 | 91 |\r\n| boltztrap.proj_0_dxz.transdos | 316397 | 29920 | 91 |\r\n| boltztrap.proj_0_pz | 53467 | 3639 | 93 |\r\n| boltztrap.intrans | 736 | 433 | 41 |\r\n| fort.152 | 272636 | 58894 | 78 |\r\n| fort.45 | 298764 | 9498 | 97 |\r\n| boltztrap.transdos | 68506 | 11999 | 82 |\r\n| boltztrap.proj_1_s | 53467 | 3526 | 93 |\r\n| boltztrap.proj_1_dxz.transdos | 316397 | 29920 | 91 |\r\n| boltztrap.proj_1_dz2.transdos | 316397 | 29920 | 91 |\r\n| boltztrap.trace | 1.37213e+06 | 429692 | 69 |\r\n| boltztrap.proj_1_px.transdos | 316397 | 38454 | 88 |\r\n| boltztrap.proj_1_py.transdos | 316397 | 38486 | 88 |\r\n| BoltzTraP.def | 831 | 223 | 73 |\r\n| boltztrap.proj_0_dz2 | 53467 | 846 | 98 |\r\n| boltztrap.proj_1_dz2 | 53467 | 846 | 98 |\r\n| boltztrap.proj_1_pz | 53467 | 3659 | 93 |\r\n| boltztrap.proj_1_s.transdos | 316397 | 38668 | 88 |\r\n| boltztrap.proj_0_pz.transdos | 316397 | 38798 | 88 |\r\n| boltztrap_band.gpl | 0 | 39 | -inf |\r\n| boltztrap_deriv.dat | 402696 | 87555 | 78 |\r\n| boltztrap_mass.dat | 1.1923e+06 | 260332 | 78 |\r\n| boltztrap_band.dat | 521136 | 82766 | 84 |\r\n| fort.25 | 15033 | 5172 | 66 |\r\n| boltztrap.condtens_fixdoping | 45370 | 14437 | 68 |\r\n| boltztrap.banddat | 0 | 38 | -inf |\r\n| boltztrap.energy | 257426 | 52794 | 79 |\r\n| fort.26 | 45370 | 14416 | 68 |\r\n| fort.27 | 45098 | 16464 | 63 |\r\n| boltztrap.halltens_fixdoping | 45098 | 16485 | 63 |\r\n| CHGCAR.CoO2 | 9.0676e+06 | 2.70493e+06 | 70 |\r\n| LiCoO2.cif | 1206 | 472 | 61 |\r\n| CHGCAR.FePO4 | 2.62755e+06 | 625888 | 76 |\r\n| Fe_gb_init.cif | 1774 | 537 | 70 |\r\n| Zn_gb_init.cif | 5917 | 1015 | 83 |\r\n| Cu_mp-30_primitive.cif | 690 | 347 | 50 |\r\n| Mo_gb_init.cif | 1781 | 547 | 69 |\r\n| Cu_mp-30_conventional_standard.cif | 828 | 382 | 54 |\r\n| Pa_mp-62_conventional_standard.cif | 736 | 375 | 49 |\r\n| Be_gb_fin.cif | 5916 | 1461 | 75 |\r\n| Bi_mp-23152_primitive.cif | 736 | 371 | 50 |\r\n| Br_mp-23154_conventional_standard.cif | 1012 | 451 | 55 |\r\n| Be_mp-87_conventional_standard.cif | 737 | 393 | 47 |\r\n| Be_gb_init.cif | 5916 | 1016 | 83 |\r\n| Fe_gb_fin.cif | 1765 | 606 | 66 |\r\n| site2_k_xanes.json | 5779 | 1704 | 71 |\r\n| LiCoO2_k_xanes.json | 3270 | 1361 | 58 |\r\n| ZnO_l2_xanes.json | 3435 | 1290 | 62 |\r\n| site1_k_xanes.json | 5766 | 1704 | 70 |\r\n| ZnO_l3_xanes.json | 3440 | 1309 | 62 |\r\n| LiCoO2_k_exafs.json | 9167 | 3806 | 58 |\r\n| MoS2_critic2_stdout.txt | 20088 | 5807 | 71 |\r\n| MoS2.cif | 789 | 394 | 50 |\r\n| MoS2_critic2_stdout_new_format.txt | 20980 | 6276 | 70 |\r\n| crest_in.xyz | 435 | 234 | 46 |\r\n| coord | 1104 | 348 | 68 |\r\n| coord.original | 976 | 480 | 51 |\r\n| FW.json | 27898 | 2340 | 92 |\r\n| cregen_0.tmp | 3092 | 832 | 73 |\r\n| crest_best.xyz | 936 | 327 | 65 |\r\n| lr6_job-28275610.error | 0 | 43 | -inf |\r\n| cregen_1.tmp | 3093 | 832 | 73 |\r\n| crest_out.out | 25803 | 4466 | 83 |\r\n| crest_rotamers_1.xyz | 228967 | 82277 | 64 |\r\n| crest_rotamers_0.xyz | 48295 | 12919 | 73 |\r\n| crest_rotamers_2.xyz | 235301 | 83792 | 64 |\r\n| FW_submit.script | 591 | 387 | 35 |\r\n| crest_rotamers_3.xyz | 51526 | 16497 | 68 |\r\n| wbo | 637 | 189 | 70 |\r\n| crest_rotamers_6.xyz | 24118 | 6352 | 74 |\r\n| crest_rotamers_4.xyz | 24118 | 6542 | 73 |\r\n| crest_conformers.xyz | 1872 | 630 | 66 |\r\n| crest_rotamers_5.xyz | 28492 | 9630 | 66 |\r\n| lr6_job-28275610.out | 2115 | 690 | 67 |\r\n| c1_r12.xyz | 437 | 238 | 46 |\r\n| c1_r13.xyz | 437 | 234 | 46 |\r\n| c1_r11.xyz | 435 | 234 | 46 |\r\n| c1_r8.xyz | 435 | 235 | 46 |\r\n| c1_r9.xyz | 435 | 232 | 47 |\r\n| c1_r10.xyz | 437 | 233 | 47 |\r\n| c1_r14.xyz | 437 | 233 | 47 |\r\n| c1_r15.xyz | 437 | 242 | 45 |\r\n| c1_r17.xyz | 437 | 236 | 46 |\r\n| c1_r16.xyz | 435 | 235 | 46 |\r\n| expected_constrains.txt | 104 | 134 | -29 |\r\n| c0_r0.xyz | 436 | 190 | 56 |\r\n| c0_r1.xyz | 437 | 220 | 50 |\r\n| c0_r3.xyz | 437 | 225 | 49 |\r\n| c0_r2.xyz | 437 | 219 | 50 |\r\n| c0_r6.xyz | 435 | 220 | 49 |\r\n| c0_r7.xyz | 436 | 226 | 48 |\r\n| c0_r5.xyz | 437 | 224 | 49 |\r\n| c0_r4.xyz | 437 | 223 | 49 |\r\n| expected_crest_best.xyz | 936 | 336 | 64 |\r\n| c0_r8.xyz | 436 | 228 | 48 |\r\n| c1_r2.xyz | 435 | 238 | 45 |\r\n| c1_r3.xyz | 437 | 233 | 47 |\r\n| c1_r1.xyz | 437 | 236 | 46 |\r\n| c1_r0.xyz | 437 | 232 | 47 |\r\n| c1_r4.xyz | 435 | 237 | 46 |\r\n| c1_r5.xyz | 435 | 231 | 47 |\r\n| c1_r7.xyz | 437 | 233 | 47 |\r\n| c1_r6.xyz | 435 | 236 | 46 |\r\n| ethylene.xyz | 297 | 150 | 49 |\r\n| cyclohexene.xyz | 788 | 285 | 64 |\r\n| butadiene.xyz | 494 | 199 | 60 |\r\n| li_ec_2.xyz | 621 | 242 | 61 |\r\n| ff_ethane.yaml | 1357 | 491 | 64 |\r\n| cocktail.xyz | 1667 | 791 | 53 |\r\n| ethane.data | 3849 | 1010 | 74 |\r\n| dump.rdx_wc.25 | 889 | 438 | 51 |\r\n| lgps.in | 831 | 482 | 42 |\r\n| li_minimal.data | 231 | 168 | 27 |\r\n| dump.tatb | 15848 | 5240 | 67 |\r\n| data.quartz | 684 | 311 | 55 |\r\n| in.peptide | 935 | 495 | 47 |\r\n| li_2.xyz | 20 | 41 | -105 |\r\n| dump.rdx_wc.75 | 893 | 439 | 51 |\r\n| crambin.data | 109843 | 32948 | 70 |\r\n| tatb.data | 69268 | 28698 | 59 |\r\n| dump.rdx_wc.100 | 894 | 438 | 51 |\r\n| dump.rdx_wc.0 | 894 | 441 | 51 |\r\n| peo_head.xyz | 216 | 159 | 26 |\r\n| peo_bulk.xyz | 195 | 150 | 23 |\r\n| dump.rdx_wc.50 | 895 | 446 | 50 |\r\n| peo_tail.xyz | 215 | 159 | 26 |\r\n| li_ec.xyz | 621 | 242 | 61 |\r\n| lgps.cif | 3262 | 803 | 75 |\r\n| li.data | 404 | 228 | 44 |\r\n| kappa.txt | 1635 | 729 | 55 |\r\n| virus.data | 15869 | 7359 | 54 |\r\n| data.peptide | 298623 | 82045 | 73 |\r\n| VASP_DDEC_analysis.output | 21922 | 4556 | 79 |\r\n| DDEC_atomic_Rfourth_moments.xyz | 428 | 208 | 51 |\r\n| DDEC_atomic_Rsquared_moments.xyz | 428 | 207 | 52 |\r\n| DDEC6_even_tempered_bond_orders.xyz | 2152 | 507 | 76 |\r\n| DDEC_atomic_Rcubed_moments.xyz | 428 | 206 | 52 |\r\n| overlap_populations.xyz | 2187 | 368 | 83 |\r\n| DDEC6_even_tempered_net_atomic_charges.xyz | 3837 | 1248 | 67 |\r\n| DDEC6_even_tempered_atomic_spin_moments.xyz | 765 | 419 | 45 |\r\n| vasprun.xml.chemical_shift.scstep | 996265 | 73222 | 93 |\r\n| core.diff.chemical.shifts.OUTCAR | 1.07254e+06 | 105442 | 90 |\r\n| POTCAR.Fe_pv_with_hash | 238654 | 86487 | 64 |\r\n| bandOverlaps.lobster.1 | 901114 | 265640 | 71 |\r\n| cobi.json | 16998 | 3435 | 80 |\r\n| ICOHPLIST.lobster.BiSe | 901 | 289 | 68 |\r\n| POTCAR.GaAs | 486101 | 173770 | 64 |\r\n| complete_cohp_lmto.json | 133522 | 37075 | 72 |\r\n| lobsterout.normal | 1717 | 956 | 44 |\r\n| lobsterout.fatband_grosspop_densityofenergy | 2030 | 1062 | 48 |\r\n| lobsterout.twospins | 1834 | 983 | 46 |\r\n| ICOOPLIST.lobster.KF | 524 | 188 | 64 |\r\n| POSCAR.W | 312 | 160 | 49 |\r\n| CHARGE.lobster.MnO | 276 | 171 | 38 |\r\n| bandOverlaps.lobster.new.2 | 158105 | 47423 | 70 |\r\n| POSCAR.Na2UO4 | 1695 | 307 | 82 |\r\n| lobsterout.onethread | 2011 | 1054 | 48 |\r\n| ICOBILIST.lobster.spinpolarized.additional_case | 853 | 225 | 74 |\r\n| CTRL | 3164 | 1387 | 56 |\r\n| MadelungEnergies.lobster.perovskite | 268 | 221 | 18 |\r\n| ICOOPLIST.lobster.BiSe | 901 | 279 | 69 |\r\n| POSCAR.perovskite | 876 | 195 | 78 |\r\n| ICOHPLIST.lobster.back | 901 | 299 | 67 |\r\n| lobsterout.GaAs | 1353 | 750 | 45 |\r\n| CTRL.BiSe | 12027 | 3552 | 70 |\r\n| complete_cohp_forb.json | 661736 | 56747 | 91 |\r\n| lobsterout_cobi_madelung | 2130 | 1050 | 51 |\r\n| lobsterin.1 | 214 | 175 | 18 |\r\n| IBZKPT_2_2_2_Li | 657 | 133 | 80 |\r\n| POSCAR.SiO2 | 1293 | 346 | 73 |\r\n| SitePotentials.lobster.perovskite | 529 | 310 | 41 |\r\n| lobsterout.skipping_all | 1903 | 986 | 48 |\r\n| cohp.str | 13110 | 4526 | 65 |\r\n| POSCAR.COBI | 876 | 189 | 78 |\r\n| POSCAR.GaAs | 180 | 104 | 42 |\r\n| bandOverlaps.lobster.2 | 31370 | 11168 | 64 |\r\n| POSCAR.BiSe | 1033 | 407 | 61 |\r\n| ICOBILIST.lobster.withoutorbitals | 262 | 166 | 37 |\r\n| POSCAR.Li | 143 | 86 | 40 |\r\n| ICOHPLIST.lobster.KF_nospin | 524 | 202 | 61 |\r\n| ICOBILIST.lobster.additional_case | 426 | 198 | 54 |\r\n| ICOBILIST.lobster.spinpolarized | 12508 | 607 | 95 |\r\n| coop.json | 13072 | 3305 | 75 |\r\n| bandOverlaps.lobster.new.1 | 316191 | 93414 | 70 |\r\n| COPL | 344034 | 50083 | 85 |\r\n| cohp.json | 35917 | 6049 | 83 |\r\n| lobsterout_doscar_lso | 1685 | 836 | 50 |\r\n| complete_coop_lobster.json | 68077 | 14310 | 79 |\r\n| COPL.BiSe | 156559 | 34867 | 78 |\r\n| ICOBILIST.lobster | 6254 | 535 | 91 |\r\n| POSCAR.orbitalwise | 423 | 194 | 54 |\r\n| lobsterin.2 | 286 | 211 | 26 |\r\n| GROSSPOP.lobster | 2956 | 306 | 90 |\r\n| coop.str | 6089 | 2447 | 60 |\r\n| lobsterout.saveprojection | 1950 | 1010 | 48 |\r\n| complete_cohp_orbitalwise.json | 134185 | 22066 | 84 |\r\n| ICOHPLIST.lobster | 470 | 187 | 60 |\r\n| IBZKPT_3_3_3_Li | 1107 | 161 | 85 |\r\n| ICOOPLIST.lobster | 470 | 185 | 61 |\r\n| lobsterout_from_projection | 829 | 517 | 38 |\r\n| lobsterout.skip_cobi_madelung | 2339 | 1068 | 54 |\r\n| lobsterin.3 | 149 | 144 | 3 |\r\n| FATBAND_o8_2p_z.lobster | 100056 | 14175 | 86 |\r\n| FATBAND_o4_2p_y.lobster | 100056 | 14300 | 86 |\r\n| FATBAND_o7_2s.lobster | 195346 | 15306 | 92 |\r\n| FATBAND_si2_3s.lobster | 195347 | 15196 | 92 |\r\n| FATBAND_si1_3p_y.lobster | 100057 | 14374 | 86 |\r\n| FATBAND_o5_2p_x.lobster | 100056 | 14390 | 86 |\r\n| FATBAND_si1_3p_x.lobster | 100057 | 14345 | 86 |\r\n| FATBAND_o9_2p_z.lobster | 100056 | 14303 | 86 |\r\n| FATBAND_o5_2p_y.lobster | 100056 | 14152 | 86 |\r\n| FATBAND_o4_2p_x.lobster | 100056 | 14403 | 86 |\r\n| FATBAND_o5_2s.lobster | 195346 | 15296 | 92 |\r\n| FATBAND_si1_3p_z.lobster | 100057 | 14086 | 86 |\r\n| FATBAND_o9_2p_x.lobster | 100056 | 14345 | 86 |\r\n| FATBAND_o4_2p_z.lobster | 100056 | 14296 | 86 |\r\n| FATBAND_o8_2s.lobster | 195346 | 15171 | 92 |\r\n| FATBAND_o8_2p_y.lobster | 100056 | 14280 | 86 |\r\n| FATBAND_o8_2p_x.lobster | 100056 | 14246 | 86 |\r\n| FATBAND_o5_2p_z.lobster | 100056 | 14462 | 86 |\r\n| FATBAND_o9_2p_y.lobster | 100056 | 14114 | 86 |\r\n| FATBAND_si2_3p_z.lobster | 100057 | 14264 | 86 |\r\n| FATBAND_o7_2p_z.lobster | 100056 | 14453 | 86 |\r\n| FATBAND_si3_3p_z.lobster | 100057 | 14253 | 86 |\r\n| FATBAND_o6_2s.lobster | 195346 | 15177 | 92 |\r\n| FATBAND_si3_3s.lobster | 195347 | 15185 | 92 |\r\n| FATBAND_o6_2p_z.lobster | 100056 | 14161 | 86 |\r\n| FATBAND_si3_3p_x.lobster | 100057 | 14314 | 86 |\r\n| FATBAND_o7_2p_y.lobster | 100056 | 14411 | 86 |\r\n| FATBAND_o6_2p_x.lobster | 100056 | 14286 | 86 |\r\n| FATBAND_si2_3p_y.lobster | 100057 | 14428 | 86 |\r\n| FATBAND_o6_2p_y.lobster | 100056 | 14234 | 86 |\r\n| FATBAND_o4_2s.lobster | 195346 | 15270 | 92 |\r\n| FATBAND_si1_3s.lobster | 195347 | 14856 | 92 |\r\n| FATBAND_si2_3p_x.lobster | 100057 | 14315 | 86 |\r\n| FATBAND_o9_2s.lobster | 195346 | 15267 | 92 |\r\n| FATBAND_si3_3p_y.lobster | 100057 | 14274 | 86 |\r\n| FATBAND_o7_2p_x.lobster | 100056 | 14377 | 86 |\r\n| FATBAND_o8_2p.lobster | 195346 | 16136 | 92 |\r\n| FATBAND_o5_2p.lobster | 195346 | 16221 | 92 |\r\n| FATBAND_si2_3p.lobster | 195347 | 16325 | 92 |\r\n| FATBAND_o7_2p.lobster | 195346 | 16199 | 92 |\r\n| FATBAND_o9_2p.lobster | 195346 | 16217 | 92 |\r\n| lobster_band_structure_spin.json | 1.64827e+06 | 119333 | 93 |\r\n| FATBAND_si1_3p.lobster | 195347 | 16362 | 92 |\r\n| FATBAND_o4_2p.lobster | 195346 | 16192 | 92 |\r\n| lobster_band_structure.json | 826842 | 60998 | 93 |\r\n| FATBAND_si3_3p.lobster | 195347 | 16317 | 92 |\r\n| FATBAND_o6_2p.lobster | 195346 | 16141 | 92 |\r\n| pztstructs2.json | 11949 | 1110 | 91 |\r\n| bestsqs_nacl.out | 1171 | 222 | 81 |\r\n| bestsqs_pzt.cif | 894 | 363 | 59 |\r\n| pztstructs.json | 14588 | 884 | 94 |\r\n| bestsqs_pzt.out | 805 | 224 | 72 |\r\n| bestsqs_nacl.cif | 1269 | 366 | 71 |\r\n| perfect_match_zzn_rs.json | 1042 | 401 | 62 |\r\n\r\n</details> \r\n\r\n<small>negative numbers mean file size increased during compression</small>",
"@JaGeo @rkingsbury @arosen93 If anybody feels like chipping away at the above-mentioned issues, feel free to checkout the `compress-test-files` branch and open a PR to that same branch.",
"> @JaGeo @rkingsbury @arosen93 If anybody feels like chipping away at the above-mentioned issues, feel free to checkout the `compress-test-files` branch and open a PR to that same branch.\r\n\r\nThanks for the initiative @janosh ! I'll try to help out over the next few weeks. I'm honestly amazed at how much potential size reduction we can get this way."
] | 2023-07-05T00:11:43
| 2024-08-03T19:01:57
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #2994.
Here's a 1st swing at compressing all test files. Takes the total size of the `test_files` from ~900 MB to 243 MB (73 % reduction) using simple Gzip compression as implemented in the Python standard library.
<details><summary>Migration script <code>compress_test_files.py</code></summary>
```py
import gzip
import os
import re
import shutil
from pathlib import Path
import pandas as pd
from tqdm import tqdm
from pymatgen.core import ROOT
__author__ = "Janosh Riebesell"
__date__ = "2023-07-04"
# %% Gzip compress all test files in ./test_files/
source_dir = f"{ROOT}/test_files/"
# Dictionary to store compressed files
compressed_files: dict[str, str] = {}
# Dataframe to store file names and sizes
cols = ["Original Size (B)", "Compressed Size (B)", "Reduction (%)"]
orig_size_col, comp_size_col, change_col = cols
df = pd.DataFrame(columns=cols)
df.index.name = "File"
for root, _dir, files in tqdm(list(os.walk(source_dir)), desc="Compressing files"):
for file in files:
# check if file is already compressed, ignore hidden OS files
compressed_exts = (".gz", ".gzip", ".z", ".bz2", ".bzip2", ".xz", ".lzma", ".lz")
if file.casefold().endswith(compressed_exts) or file.startswith("."):
continue
original_file = os.path.join(root, file)
gz_file = original_file + ".gz"
# Store the original file size
original_size = os.path.getsize(original_file)
# Create a gzip compressed file
with open(original_file, "rb") as f_in, gzip.open(gz_file, "wb") as f_out:
shutil.copyfileobj(f_in, f_out)
# Store the compressed file size
compressed_size = os.path.getsize(gz_file)
percent_change = f"{((compressed_size - original_size) / original_size):.2%}"
# Remove the original file
os.remove(original_file)
# Add to the dictionary of compressed files
compressed_files[file] = gz_file
df.loc[file] = dict(zip(cols, [original_size, compressed_size, percent_change]))
df.to_csv("compressed_files_report.csv", index=False)
print(df.to_markdown())
# %% update test file paths to use compressed version
target_dir = f"{ROOT}/pymatgen/"
for root, _dir, files in tqdm(list(os.walk(target_dir)), desc="Replacing file names"):
for file in files:
if file.endswith(".py") and not file.startswith(".") and root.endswith("tests"):
file_path = Path(root) / file
# Read in the file
with open(file_path) as file:
file_data = file.read()
# Replace the target string
for original_file, gz_file in compressed_files.items():
gz_file_basename = os.path.basename(gz_file)
pattern = re.compile(f"([(\"']){re.escape(original_file)}([)\"'])")
replacement = r"\g<1>" + gz_file_basename + r"\g<2>"
file_data = pattern.sub(replacement, file_data)
# Write the file out again
with open(file_path, "w") as file:
file.write(file_data)
```
</details>
This PR will require a lot of tweaking, I'm sure, since the automated file path migration is naive and will invariably encounter both false positives and negatives. Also, not all tests support loading compressed files. We'll have to refactor those or revert to uncompressed.
|
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| 1,790,305,374
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PR_kwDOACgets5UvpC4
| 3,133
|
Enable `ruff` `PT011`
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[] | 2023-07-05T20:58:06
| 2023-07-05T23:26:01
|
2023-07-05T23:25:59Z
|
MEMBER
|
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Also fix remaining violations.
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| 1,790,677,452
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I_kwDOACgets5qu5HM
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|
Release 2023.6.28 on PyPI is incomplete
|
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[] | null |
[
"There's a [newer release out now that's sound](https://pypi.org/project/pymatgen/2023.7.11/#files). I guess we could delete the old partial release but not sure if that creates more problems than it solves. Usually you deprecate a broken release rather than delete but looks like PyPI doesn't have a deprecation feature.\r\n\r\nEither way would have to be done by @shyuep.",
"I yanked the 2023.6.28 version. This should be now solved.",
"Thank you, @shyuep!"
] | 2023-07-06T02:27:12
| 2023-07-12T03:36:12
|
2023-07-11T15:21:37Z
|
NONE
|
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|
#### Description
There is only one wheel file available for v2023.6.28 on PyPI (`pymatgen-2023.6.28-cp39-cp39-macosx_11_0_arm64.whl`). All other versions are missing: the wheels for Linux, macOS, and Windows (Python 3.8-3.11) at https://pypi.org/project/pymatgen/2023.6.28/#files:
#### Repro
Go to https://pypi.org/project/pymatgen/2023.6.28/#files, and check the list of wheel files.
#### Expected behavior
Same set of wheel files for various platforms as at https://pypi.org/project/pymatgen/2023.6.23/#files:
#### Environment
Relevant versions and platform info:
- PyPI, v2023.6.28
|
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I_kwDOACgets5qwl2O
| 3,135
|
Get site labels from cif file
|
{
"login": "stefsmeets",
"id": 873520,
"node_id": "MDQ6VXNlcjg3MzUyMA==",
"avatar_url": "https://avatars.githubusercontent.com/u/873520?v=4",
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"url": "https://api.github.com/users/stefsmeets",
"html_url": "https://github.com/stefsmeets",
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[] | 2023-07-06T09:01:30
| 2023-07-06T18:26:05
|
2023-07-06T18:26:05Z
|
CONTRIBUTOR
|
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#### Problem
I'm interested in having access to the site labels in a cif file when reading a structure ("_atom_site_label"). I need this to classify different groups of sites with the same symbol.
#### Proposed Solution
I think these data can be made available via `Structure.site_properties`.
In [`pymatgen.io.cif:CifBlock._get_structure`](https://github.com/materialsproject/pymatgen/blob/a5596534548abc1f29cb1d5e9cd9e995e185a4eb/pymatgen/io/cif.py#L874) the site label is already being used [to identify the sites](https://github.com/materialsproject/pymatgen/blob/a5596534548abc1f29cb1d5e9cd9e995e185a4eb/pymatgen/io/cif.py#L911).
I think it would be quite straightforward to store the label in `site_properties`. This will expand with the symmetry.
This solution would be good for my use case, without too much impact on the rest of the code base.
#### Alternatives
I think the ideal solution is if the site label would be accessible attribute under `PeriodicSite`, i.e. `PeriodicSite.label`. This would require far more significant changes to the code.
|
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"id": 30958850,
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"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
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PR_kwDOACgets5Uy43W
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|
Read site labels from cif file
|
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"login": "stefsmeets",
"id": 873520,
"node_id": "MDQ6VXNlcjg3MzUyMA==",
"avatar_url": "https://avatars.githubusercontent.com/u/873520?v=4",
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[] | null |
[
"Thanks @stefsmeets! 👍 ",
"Sorry, was a bit trigger happy on the merge. Tests didn't run on account of this change [1975b921f](https://github.com/materialsproject/pymatgen/commit/1975b921f038dbc523a8800c2c3ad4598a6f73d5#diff-faff1af3d8ff408964a57b2e475f69a6b7c7b71c9978cccc8f471798caac2c88R26) I just reverted. Could you do me a favor and take a look at the failing tests?\r\n\r\n- https://github.com/materialsproject/pymatgen/actions/runs/5478881416/jobs/9979959523#step:6:47\r\n- https://github.com/materialsproject/pymatgen/actions/runs/5478881416/jobs/9979960142#step:6:43",
"I reverted fc6cfaf and ef0d5a5\r\n in https://github.com/materialsproject/pymatgen/commit/5cdc9d30c2f6bd13267e23b8defea1eefce28374 for now. Sorry about the inconvenience. Feel free to open another PR as tests will run correctly this time."
] | 2023-07-06T10:20:26
| 2023-07-07T19:22:42
|
2023-07-06T18:26:04Z
|
CONTRIBUTOR
|
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## Summary
Major changes:
- feature 1: Read site labels from cif file and store these under `Structure.site_properties`.
Closes #3135
## 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_kwDOACgets5VFReL
| 3,137
|
Read site labels from cif file (2)
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[
"Thanks for the feedback! I added a bunch of tests for the new code. Let me know if there is anything else."
] | 2023-07-10T12:37:00
| 2023-07-14T07:28:45
|
2023-07-13T23:13:09Z
|
CONTRIBUTOR
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## Summary
This PR follows up from #3136 which was reverted because of CI test failures, see https://github.com/materialsproject/pymatgen/pull/3136#issuecomment-1624198814 . This PR addresses these issues.
Major changes:
- feature 1: Read site labels from cif file and store these under `Structure.site_properties`.
Closes #3135
## 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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I_kwDOACgets5rH2o5
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returning matplotlib.pyplot module in plotting methods
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[
"I don't think this was a design choice per se. The general idea was to return an object that would allow `show` to be called and for some basic testing of the plot generation code. I have no problems with changing it to returning a Figure object.\r\n\r\nThe plotly backend came much later and so is a bit more coherent in design.",
"Agreed that this behavior is generally counter-intuitive for new users (and myself whenever I revisit the phase diagram plotter...).",
"I think then returning the figure object might be reasonable since it also has a `show` method. \r\n\r\n@shyuep if you are on board (and/or anyone else appropriate), I can draft up a PR changing the return values from `plt` to `Figure` throughout pymatgen.",
"Yes pls go ahead. ",
"> I can draft up a PR changing the return values from `plt` to `Figure` throughout pymatgen.\r\n\r\nThat would be great! I think that makes much more sense. It's how [`pymatviz`](https://github.com/janosh/pymatviz) does it as well.\r\n\r\nWould be a breaking change though so should be highlighted in the change log and release notes.",
"> > I can draft up a PR changing the return values from `plt` to `Figure` throughout pymatgen.\r\n> \r\n> That would be great! I think that makes much more sense. It's how [`pymatviz`](https://github.com/janosh/pymatviz) does it as well.\r\n> \r\n> Would be a breaking change though so should be highlighted in the change log and release notes.\r\n\r\n@janosh thanks for pointing me to `pymatviz`! I noticed you return `Axes` in the matplotlib functions there, instead of `Figure`. Maybe that makes more sense because the`Axes` object is what actually has the plot attributes (lines, legend, labels, etc). One can always get the `Figure` from the `Axes`, but the reverse can be ambiguous if the Figure has multiple axes.\r\n\r\nAny thoughts? I like the design of pymatviz functions with the optional Axes argument and always returning the Axes where the plot was drawn.\r\n\r\nIn all cases, it will likely be a breaking change but one that is \"easy\" to adjust to, but perhaps with noticeable effects on projects using `pymatgen` plotting functions.",
"It would potentially break 100s of projects, scripts. (😬) Mine included. ",
"@JaGeo Why would it break any scripts? I am assuming most people call show() after getting the plt. ",
"@shyuep switching to `Figure` is completely fine, agreed. ",
"@lbluque I think returning the `axes` object is even better from an API design standpoint (for the reasons you mentioned, `Axes` is what actually changes and what you interact most with when making plots) but it would break more existing code. `figure` and the `plt` module share at least some of their interface (e.g. `.show()` as @shyuep mentioned). But even that is not backwards compatible in every way.\r\n\r\n@shyuep Re breakage, people might call\r\n\r\n```py\r\nfrom pymatgen import SomePlotter\r\n\r\nplt = SomePlotter().get_plot()\r\nplt.ylabel(\"some custom ylabel\")\r\n```\r\n\r\nthis no longer works if we return `fig` instead of `plt`.\r\n\r\n@JaGeo We might be able to write a script that you point at some directory and that at least adds a `TODO` comment to every line of code that might have been broken by this change. I still think this is enough of an API improvement to warrant the effort.\r\n\r\n",
"Thanks so much for getting this done @janosh !",
"> It would potentially break 100s of projects, scripts. (😬) Mine included.\r\n\r\nSorry to open this issue again. In our project updated to latest pymatgen, we encounter unexpected errors in various scripts customizing the window title and size after using get_plot(). After updating all the scripts according to the above breaking changes, we still get the following error: \r\n\r\nTraceback (most recent call last):\r\n\r\n.../pymatgen/electronic_structure/plotter.py\", line 711, in fix_layout\r\n ax.gcf().tight_layout()\r\n ^^^^^^\r\nAttributeError: 'Axes' object has no attribute 'gcf'\r\n\r\nThis error seems to be due to Line 711/712 in pymatgen/electronic_structure/plotter.py:\r\n\r\n def fix_layout(event):\r\n if (event.name == \"key_press_event\" and event.key == \"t\") or event.name == \"resize_event\":\r\n ax.gcf().tight_layout()\r\n ax.gcf().canvas.draw()\r\n\r\nsince ax is now an Axes object, not a pyplot object. ",
"Sorry to bother again. The BSPlotter.plot_brillouin() seems to not work after the breaking changes. I wonder what the reason of this problem is. The following is the script and result. Thanks. \r\n\r\npython\r\n>>> from pymatgen.ext.matproj import MPRester\r\n>>> mpr = MPRester(\"32-digit key\")\r\n>>> bs = mpr.get_bandstructure_by_material_id(\"mp-3748\")\r\nRetrieving ElectronicStructureDoc documents: 100%|███████████████████████████████████████████████| 1/1 [00:00<?, ?it/s]\r\n>>> from pymatgen.electronic_structure.plotter import BSPlotter\r\n>>> plotter = BSPlotter(bs)\r\n>>> plotter.plot_brillouin()\r\n\r\nResult: an empty window comes out."
] | 2023-07-10T17:35:21
| 2023-09-15T10:09:06
|
2023-08-17T22:35:34Z
|
CONTRIBUTOR
|
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#### Description
This may be more a clarification than a bug necessarily.
I have noticed that many of the plotting methods using the `matplotlib` backend return the `matplotlib.pyplot` module.
For example in the [phase diagram plotter](https://github.com/materialsproject/pymatgen/blob/9f0c7c28fee6681058dadbaafd2b2b52a0f9e251/pymatgen/analysis/phase_diagram.py#L3719) or this general [pretty_plot](https://github.com/materialsproject/pymatgen/blob/9f0c7c28fee6681058dadbaafd2b2b52a0f9e251/pymatgen/util/plotting.py#L63) function.
#### Expected behavior
I am confused by this design choice since it is not particularly helpful to return the `plt` module.
Would it be more appropriate to to return the `Figure` object? Though users can access get it by using `plt.gca` it makes more sense to me, and seems to parallel the `go.Figure` object returned when using the `plotly` backend in plotting methods.
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PR_kwDOACgets5VHW93
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Refactor `analysis/graphs.py` using `dict.pop()`
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[] | 2023-07-10T18:33:54
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2023-07-10T18:54:54Z
|
MEMBER
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```py
if key in dict:
val = dict[key]
del dict[key]
```
to
```py
val = dict.pop(key, None)
```
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PR_kwDOACgets5VHjyk
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Breaking: Rename `[SomeCode]ParserError` to `[SomeCode]ParseError` and inherit from `SyntaxError`
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[] | 2023-07-10T19:11:12
| 2023-07-10T20:18:23
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2023-07-10T20:18:22Z
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MEMBER
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By making all `ParseError` classes inherit from the new `pymatgen.io.core.ParseError` (used to be generic `Exception`) which subclasses `SyntaxError`, `ParseErrors` can now add line numbers and filenames to errors:
```py
class SyntaxError(Exception):
msg: str
lineno: int | None
offset: int | None
text: str | None
filename: str | None
if sys.version_info >= (3, 10):
end_lineno: int | None
end_offset: int | None
```
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PR_kwDOACgets5VI3_H
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explicit test POTCAR
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[] | 2023-07-10T23:13:35
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2023-07-11T01:44:50Z
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CONTRIBUTOR
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## Explicit test for POTCAR writing
Added basic test to make sure that the written POTCAR file is readable by VASP.
in response to Issue #3068
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I_kwDOACgets5rKnVX
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`MaterialsProjectDFTMixingScheme.process_entries()` should have a kwarg to avoid POTCAR checks
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[
"I would go one step further - why not have a global setting that disables all POTCAR checks? This can be in the pmgrc. ",
"I would personally appreciate an option to avoid all POTCAR-related checks because then I don't have to do extra work just to have Pymatgen tell me I know what I'm doing. Although, finding where every POTCAR check is done in Pymatgen (to ensure the setting works as expected) might be a bit difficult/time-consuming, especially because they are not all done in the same way or in the same context. Here, at least, it's a check based on the symbols and not the hash (by default) otherwise it'd be more severe.\r\n\r\nFull disclaimer: While I'm reporting this issue, I don't have time to address it (at least right now).",
"Closing as a duplicate of #2499 because I forgot I opened a similar issue a year ago.",
"Very much agreed that POTCAR checks in `MaterialsProjectDFTMixingScheme` should have a flag to disable.\r\n\r\nAnother related issue is #2952 by @BowenD-UCB (and in fact was linked in #2499).",
"Ah, thanks for linking these together. Seems like it's all very similar, even if they touch on slightly different functions."
] | 2023-07-11T02:15:43
| 2023-07-11T04:10:08
|
2023-07-11T03:27:40Z
|
MEMBER
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When using `MaterialsProjectDFTMixingScheme.process_entries()`, if the user does not provide `ComputedStructureEntry` objects with POTCAR symbols in `.parameters`, the mixing scheme will crash. While it's understandable to do a validity check by default, there should be a kwarg to disable this.
If a user is trying to use the `MaterialsProjectDFTMixingScheme` on calculations they ran manually (i.e. without Atomate), the procedure is something like:
- Run VASP calculation with MP-compatible settings
- Make a `Structure` and get the energy from the outputs
- From that, make a `ComputedStructureEntry`
- Run the `ComputedStructureEntry` objects through `MaterialsProjectDFTMixingScheme` alongside `ComputedStructureEntry` objects pulled from MP for that chemical system.
By default, this `ComputedStructureEntry` does not have (nor does it require) any information about the POTCARs used. When passing these `ComputedStructureEntry` objects to `MaterialsProjectDFTMixingScheme`, one would naively expect the mixing scheme to "just work," but instead it raises an error because the `ComputedStructureEntry` doesn't have the properties needed for a validity check. Pymatgen shouldn't expect the user to know to parse the POTCAR hash from the `vasprun.xml` or `POTCAR` and add it to the `properties` of the `ComputedStructureEntry`, especially when it's only needed for a validity check. Alternatively, there should be clearer documentation at the least.
On a related note, there should be some additional documentation that the user should be specifying `.parameters["run_type"]` and the related Hubbard parameters when constructing their `ComputedStructureEntry` objects. The way the mixing scheme currently works, it kind of assumes the user is familiar with the Atomate/MP entry format. This is very closely tied to #2500.
Edit: I realized this is basically the same issue as #2499 from a while ago. I'll keep this one open since it has a bit more context.
----------------------------------------------------------------------------
```python
1 scheme = MaterialsProjectDFTMixingScheme()
----> 2 corrected_entries = scheme.process_entries(entries)
3 rosen_corrected_entries = [
4 entry for entry in corrected_entries if "rosen" in entry.entry_id
5 ]
File [c:\Users\asros\miniconda3\envs\cms\lib\site-packages\pymatgen\entries\mixing_scheme.py:178](file:///C:/Users/asros/miniconda3/envs/cms/lib/site-packages/pymatgen/entries/mixing_scheme.py:178), in MaterialsProjectDFTMixingScheme.process_entries(self, entries, clean, verbose, inplace, mixing_state_data)
175 for ea in entry.energy_adjustments:
176 entry.energy_adjustments.remove(ea)
--> 178 entries_type_1, entries_type_2 = self._filter_and_sort_entries(entries, verbose=verbose)
180 if mixing_state_data is None:
181 if verbose:
File [c:\Users\asros\miniconda3\envs\cms\lib\site-packages\pymatgen\entries\mixing_scheme.py:628](file:///C:/Users/asros/miniconda3/envs/cms/lib/site-packages/pymatgen/entries/mixing_scheme.py:628), in MaterialsProjectDFTMixingScheme._filter_and_sort_entries(self, entries, verbose)
625 # preprocess entries with any corrections
626 # make an EntrySet to enable some useful methods like .chemsys and .is_ground_state
627 if self.compat_1:
--> 628 entries_type_1 = self.compat_1.process_entries(entries_type_1)
629 if verbose:
630 print(
631 f" Processed {len(entries_type_1)} compatible {self.run_type_1} entries with "
632 f"{type(self.compat_1).__name__}"
633 )
File [c:\Users\asros\miniconda3\envs\cms\lib\site-packages\pymatgen\entries\compatibility.py:587](file:///C:/Users/asros/miniconda3/envs/cms/lib/site-packages/pymatgen/entries/compatibility.py:587), in Compatibility.process_entries(self, entries, clean, verbose, inplace)
584 entry.energy_adjustments = []
586 try: # get the energy adjustments
--> 587 adjustments = self.get_adjustments(entry)
588 except CompatibilityError:
589 continue
File [c:\Users\asros\miniconda3\envs\cms\lib\site-packages\pymatgen\entries\compatibility.py:941](file:///C:/Users/asros/miniconda3/envs/cms/lib/site-packages/pymatgen/entries/compatibility.py:941), in MaterialsProject2020Compatibility.get_adjustments(self, entry)
939 if entry.parameters.get("software", "vasp") == "vasp":
940 pc = PotcarCorrection(MPRelaxSet, check_hash=self.check_potcar_hash)
--> 941 pc.get_correction(entry)
943 # apply energy adjustments
944 adjustments: list[CompositionEnergyAdjustment] = []
File [c:\Users\asros\miniconda3\envs\cms\lib\site-packages\pymatgen\entries\compatibility.py:162](file:///C:/Users/asros/miniconda3/envs/cms/lib/site-packages/pymatgen/entries/compatibility.py:162), in PotcarCorrection.get_correction(self, entry)
160 psp_settings = {d.get("titel").split()[1] for d in entry.parameters["potcar_spec"] if d}
161 else:
--> 162 psp_settings = {sym.split()[1] for sym in entry.parameters["potcar_symbols"] if sym}
164 if {self.valid_potcars.get(str(el)) for el in entry.composition.elements} != psp_settings:
165 raise CompatibilityError("Incompatible potcar")
KeyError: 'potcar_symbols'
```
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PR_kwDOACgets5VJ9-6
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|
Add `check_potcar: bool = True` to `MaterialsProject2020Compatibility`, `MaterialsProjectDFTMixingScheme` and `PotcarCorrection`
|
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[
"You are the hero we don't deserve.",
"Closes #2952 as well?",
"Pls do not merge this. I have a different fix.",
"@arosen93 Re #2952 not 100% sure since there was talk of a `ComputedEntry.from_settings` method in that issue. Not sure if anyone still wants that if you can set `MaterialsProject2020Compatibility(check_potcar=False)`.",
"I just pushed a fix. A global .pmgrc.yaml setting called DISABLE_POTCAR_CHECKS would skip all potcar checking in compatibility.",
"I don't think this needs to be closed. Having the option to disable `check_potcar` on a case-by-case basis is still useful. Plus not every user knows about `.pmgrc.yaml`.",
"Thanks a lot for implementing this!",
"I agree that there is still value for a kwarg (although the global setting is nice too).",
"@shyuep Forgot to mention this morning I think it'd be better to call the `.pmgrc` flag `POTCAR_CHECKS: true | false` rather than `DISABLE_POTCAR_CHECKS: false | true`. Easier to read:\r\n\r\n```diff\r\n- if SETTINGS.get(\"DISABLE_POTCAR_CHECKS\", False):\r\n+ if not SETTINGS.get(\"POTCAR_CHECKS\"):\r\n return ufloat(0.0, 0.0)",
"Sure. Go ahead and make the change, including the new documentation on global config variables that I added this morning. I don't have a strong opinion on this.",
"Will do. Just added tests for `check_potcar` in `MaterialsProjectDFTMixingScheme` and `MaterialsProjectCompatibility2020`. I think this is ready to go.",
"@shyuep One more thing (bringing this up just to make sure I'm not missing something). It seems you can't actually set booleans (or any type other than `str` like `floats`, `ints`, `None` for that matter) using the `pmg` CLI atm.\r\n\r\n```sh\r\npmg config --add PMG_POTCAR_CHECKS False\r\n```\r\n\r\nwill be stored as\r\n\r\n```\r\nPMG_POTCAR_CHECKS: 'False'\r\n```\r\n\r\nwhich is truthy and so the opposite of expected behavior."
] | 2023-07-11T04:18:06
| 2023-07-12T23:48:39
|
2023-07-12T23:03:15Z
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Closes #2499, closes #2952 (and #3142).
07f9730c2 add check_potcar: bool = True to PotcarCorrection
c0087761e add check_potcar: bool = True to MaterialsProject2020Compatibility
19f88c07e add check_potcar: bool = True to MaterialsProjectDFTMixingScheme
0209a5ab1 fix broken test due to modified error msg
|
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Design type system for `site_properties`
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[
"This can be closed. The strategy going forward is to add new `Site` properties directly as 1st-level instance attributes rather than as keys in the `Site.properties` dict. See #3137 for an example which added `Site.label`."
] | 2023-07-11T14:39:07
| 2023-07-14T02:42:33
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2023-07-14T02:42:33Z
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`site_properties` not being typed causes downstream problems (see e.g. #3137).
Imagine we had explicit types for possible site properties: `ScalarProperty`, `PolarVectorProperty`, `AxialVectorProperty`, etc, `Categorical`, `Comment`. Something physical like `Magmom` could be handled under this system, and also something like a label could be a `Comment` type, which could then be gracefully excluded from equality comparisons.
_Originally posted by @mkhorton in https://github.com/materialsproject/pymatgen/pull/3137#discussion_r1259824241_
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Fix/test files
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[] | 2023-07-11T21:07:30
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2023-07-11T21:09:58Z
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NONE
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## Summary
Major changes:
Fixes tests in `pymatgen/entries` after compressing and renaming files.
|
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