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I_kwDOACgets6Sis6M
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Incompatability with numpy <2 on Windows for `Lattice.find_points_in_spheres`
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[
"Thanks a lot for reporting. The [unit test for `chgnet` is failing for the same reason](https://github.com/CederGroupHub/chgnet/actions/runs/10312892054/job/28565439869?pr=184), following our recent migration of build system to NumPy 2 #3894, as in NumPy 2 [the default int type has been changed from `int32` to `int64` in Windows 64-bit system](https://numpy.org/doc/stable/numpy_2_0_migration_guide.html).\r\n\r\nI would look into this ASAP.",
"@Andrew-S-Rosen I believe you just saved the world :) It turns out there're way more uncaught errors https://github.com/materialsproject/pymatgen/actions/runs/10330245550/job/28599007337"
] | 2024-08-09T19:47:46
| 2024-08-24T08:54:11
|
2024-08-24T08:54:11Z
|
MEMBER
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### Python version
3.11
### Pymatgen version
2024.8.9
### Operating system version
Windows
### Current behavior
As of pyamtgen 2024.8.8, there is an incompatibility with `Lattice.get_points_in_sphere` on Windows when using numpy < 2. Everything seems to run fine on numpy 2.0.1 and/or non-Windows machines.
```
pip install pymatgen==2024.8.9 numpy==1.26.4
```
```python
from pymatgen.core import Structure
structure = Structure(
lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
species=["Mg", "O"],
coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
)
structure.lattice.get_points_in_sphere(structure.frac_coords,(0,0,0),1)
```
Traceback:
```python
----> 1 structure.lattice.get_points_in_sphere(structure.frac_coords,(0,0,0),1)
File ~\miniconda\envs\test\Lib\site-packages\pymatgen\core\lattice.py:1387, in Lattice.get_points_in_sph)
1384 pbc = np.ascontiguousarray(self.pbc, dtype=int)
1385 center_coords = np.ascontiguousarray([center], dtype=float)
-> 1387 _, indices, images, distances = find_points_in_spheres(
1388 all_coords=cart_coords, center_coords=center_coords, r=float(r), pbc=pbc, lattice=latt_matrix, tol=1e-8
1389 )
1390 if len(indices) < 1:
1391 # Return empty np.array (not list or tuple) to ensure consistent return type
1392 # whether sphere contains points or not
1393 return np.array([]) if zip_results else tuple(np.array([]) for _ in range(4))
File src\\pymatgen\\optimization\\neighbors.pyx:48, in pymatgen.optimization.neighbors.find_points_in_sp)
ValueError: Buffer dtype mismatch, expected 'const int64_t' but got 'long'
```
This influences many other functions in Pymatgen, such as the example below:
```python
from pymatgen.core.surface import generate_all_slabs
structure = Structure(
lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
species=["Mg", "O"],
coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
)
generate_all_slabs(structure,1,10,10)
```
Traceback:
```python
File ~\miniconda\envs\test\Lib\site-packages\pymatgen\core\surface.py:1650, in generate_all_slabs(structure, max_index, min_slab_size, min_vacuum_size, bonds, tol, ftol, max_broken_bonds, lll_reduce, center_slab, primitive, max_normal_search, symmetrize, repair, include_reconstructions, in_unit_planes)
1638 for miller in get_symmetrically_distinct_miller_indices(structure, max_index):
1639 gen = SlabGenerator(
1640 structure,
1641 miller,
(...)
1648 in_unit_planes=in_unit_planes,
1649 )
-> 1650 slabs = gen.get_slabs(
1651 bonds=bonds,
1652 tol=tol,
1653 ftol=ftol,
1654 symmetrize=symmetrize,
1655 max_broken_bonds=max_broken_bonds,
1656 repair=repair,
1657 )
1659 if len(slabs) > 0:
1660 logger.debug(f"{miller} has {len(slabs)} slabs... ")
File ~\miniconda\envs\test\Lib\site-packages\pymatgen\core\surface.py:1348, in SlabGenerator.get_slabs(self, bonds, ftol, tol, max_broken_bonds, symmetrize, repair, ztol)
1345 matcher = StructureMatcher(ltol=tol, stol=tol, primitive_cell=False, scale=False)
1347 final_slabs: list[Slab] = []
-> 1348 for group in matcher.group_structures(slabs):
1349 # For each unique slab, symmetrize the
1350 # surfaces by removing sites from the bottom
1351 if symmetrize:
1352 sym_slabs = self.nonstoichiometric_symmetrized_slab(group[0])
File ~\miniconda\envs\test\Lib\site-packages\pymatgen\analysis\structure_matcher.py:795, in StructureMatcher.group_structures(self, s_list, anonymous)
793 s_list = self._process_species(s_list)
794 # Prepare reduced structures beforehand
--> 795 s_list = [self._get_reduced_structure(s, self._primitive_cell, niggli=True) for s in s_list]
797 # Use structure hash to pre-group structures
798 if anonymous:
File ~\miniconda\envs\test\Lib\site-packages\pymatgen\analysis\structure_matcher.py:795, in <listcomp>(.0)
793 s_list = self._process_species(s_list)
794 # Prepare reduced structures beforehand
--> 795 s_list = [self._get_reduced_structure(s, self._primitive_cell, niggli=True) for s in s_list]
797 # Use structure hash to pre-group structures
798 if anonymous:
File ~\miniconda\envs\test\Lib\site-packages\pymatgen\analysis\structure_matcher.py:947, in StructureMatcher._get_reduced_structure(cls, struct, primitive_cell, niggli)
945 reduced = struct.copy()
946 if niggli:
--> 947 reduced = reduced.get_reduced_structure(reduction_algo="niggli")
948 if primitive_cell:
949 reduced = reduced.get_primitive_structure()
File ~\miniconda\envs\test\Lib\site-packages\pymatgen\core\structure.py:2252, in IStructure.get_reduced_structure(self, reduction_algo)
2242 """Get a reduced structure.
2243
2244 Args:
(...)
2249 Structure: Niggli- or LLL-reduced structure.
2250 """
2251 if reduction_algo == "niggli":
-> 2252 reduced_latt = self._lattice.get_niggli_reduced_lattice()
2253 elif reduction_algo == "LLL":
2254 reduced_latt = self._lattice.get_lll_reduced_lattice()
File ~\miniconda\envs\test\Lib\site-packages\pymatgen\core\lattice.py:1227, in Lattice.get_niggli_reduced_lattice(self, tol)
1224 gamma = math.acos(Y / 2 / a / b) / math.pi * 180
1225 lattice = type(self).from_parameters(a, b, c, alpha, beta, gamma)
-> 1227 mapped = self.find_mapping(lattice, e, skip_rotation_matrix=True)
1228 if mapped is not None:
1229 if np.linalg.det(mapped[0].matrix) > 0:
File ~\miniconda\envs\test\Lib\site-packages\pymatgen\core\lattice.py:1010, in Lattice.find_mapping(self, other_lattice, ltol, atol, skip_rotation_matrix)
974 def find_mapping(
975 self,
976 other_lattice: Self,
(...)
979 skip_rotation_matrix: bool = False,
980 ) -> tuple[Lattice, np.ndarray | None, np.ndarray] | None:
981 """Find a mapping between current lattice and another lattice. There
982 are an infinite number of choices of basis vectors for two entirely
983 equivalent lattices. This method returns a mapping that maps
(...)
1008 None is returned if no matches are found.
1009 """
-> 1010 return next(self.find_all_mappings(other_lattice, ltol, atol, skip_rotation_matrix), None)
File ~\miniconda\envs\test\Lib\site-packages\pymatgen\core\lattice.py:947, in Lattice.find_all_mappings(self, other_lattice, ltol, atol, skip_rotation_matrix)
944 lengths = other_lattice.lengths
945 alpha, beta, gamma = other_lattice.angles
--> 947 frac, dist, _, _ = self.get_points_in_sphere(
948 [[0, 0, 0]], [0, 0, 0], max(lengths) * (1 + ltol), zip_results=False
949 )
950 cart = self.get_cartesian_coords(frac)
951 # This can't be broadcast because they're different lengths
File ~\miniconda\envs\test\Lib\site-packages\pymatgen\core\lattice.py:1387, in Lattice.get_points_in_sphere(self, frac_points, center, r, zip_results)
1384 pbc = np.ascontiguousarray(self.pbc, dtype=int)
1385 center_coords = np.ascontiguousarray([center], dtype=float)
-> 1387 _, indices, images, distances = find_points_in_spheres(
1388 all_coords=cart_coords, center_coords=center_coords, r=float(r), pbc=pbc, lattice=latt_matrix, tol=1e-8
1389 )
1390 if len(indices) < 1:
1391 # Return empty np.array (not list or tuple) to ensure consistent return type
1392 # whether sphere contains points or not
1393 return np.array([]) if zip_results else tuple(np.array([]) for _ in range(4))
File src\\pymatgen\\optimization\\neighbors.pyx:48, in pymatgen.optimization.neighbors.find_points_in_spheres()
ValueError: Buffer dtype mismatch, expected 'const int64_t' but got 'long
```
|
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PR_kwDOACgets53_Mnv
| 3,991
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Ion: fix CO2- and I3- parsing errors; enhance tests
|
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[
"@janosh I request a quick merge and release on this one so that it doesn't adversely affect anyone doing aqueous work (e.g. Pourbaix diagrams) that involve `I[-1]`. Sorry I didn't catch this in the original PR!"
] | 2024-08-09T21:02:25
| 2024-10-10T01:54:19
|
2024-08-11T19:52:16Z
|
CONTRIBUTOR
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## Summary
My recent PR #3942 contained two bugs that were revealed by testing in downstream code (see [pyEQL PR](https://github.com/KingsburyLab/pyEQL/pull/169#issuecomment-2278396689)). This PR fixes those and expands the unit tests to catch them.
```
>>> Ion.from_formula('CO2-').reduced_formula
'C2O4[-0.5]'
>>> Ion.from_formula('CO2--').reduced_formula
'C2O4[-1]'
```
```
>>> Ion.from_formula('I3-').get_reduced_formula_and_factor()
('I3', 1.0)
>>> Ion.from_formula('I-').get_reduced_formula_and_factor()
('I3', 0.3333333333333333)
```
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[
"@njzjz Perhaps you could give me some advice or comment here because I'm not a cython expert? Thanks a ton in advance.\r\n\r\nLooks like quite some code is broken when running on Windows system with NumPy < 2, because with 862c454bfd2e0428b27fdafe9e0a7d81654005b9 integer is explicitly declared as `int64` independent of the platform, however on Windows with NumPy < 2 arrays might still be `int32` (`long`) by default.\r\n\r\nIt looks like we should update all cython-related code to internally cast type as `int64`. But would this `long` -> `int64` replacement cause unexpected downstream breakage if downstream cython code don't explicitly cast to `int64`? Is this necessary or recommended by NumPy?\r\n\r\n",
"Fused types may help: http://docs.cython.org/en/stable/src/userguide/fusedtypes.html\nhttps://stackoverflow.com/a/28112966/9567349",
"Also, it may be useful to run tests against both numpy 1.x and 2.x.",
"\r\n\r\n> Also, it may be useful to run tests against both numpy 1.x and 2.x.\r\n\r\nAgreed! [NumPy is recommending the same](https://numpy.org/devdocs/dev/depending_on_numpy.html#build-time-dependency):\r\n> We recommend that you have at least one CI job which builds/installs via a wheel, and then runs tests against the oldest numpy version that the package supports. ",
"@njzjz I decide perhaps still explicitly use `int64` to ensure consistency (not sure if that's the best solution, free feel to correct me). Would appreciate it if you have any comment. Thanks a ton!\r\n\r\n@janosh I'm not a cython expert (important 😅 ) so please review all changes very carefully :) \r\n\r\nAdded a `NumPy 1` workflow for windows as [recommended by NumPy doc](https://numpy.org/devdocs/dev/depending_on_numpy.html#build-time-dependency), but still not sure if it's worth it because I'm not expecting no new issues to pop up once we fixes these.\r\n> We recommend that you have at least one CI job which builds/installs via a wheel, and then runs tests against the oldest numpy version that the package supports.\r\n\r\n",
"> it sounds like the potential for platform inconsistency is specific to cython code?\r\n\r\nSorry perhaps I should tweak the title, current one might be misleading. After NumPy 2.x, the default NumPy int type for 64-bit windows system [changed from `int32` to `int64`](https://numpy.org/doc/stable/release/2.0.0-notes.html) (not just cython, sorry).\r\n\r\n> The default integer type on Windows is now int64 rather than int32, matching the behavior on other platforms\r\n\r\nMeaning if we pass a numpy array as `np.array(data, dtype=int)` into a cython function, the latter now would explicitly expect `int64`, and the dtype could be `int32` for the former in Numpy 1.x windows machines (therefore those CI failures). So I don't think just changing just the types in cython code suffice.\r\n\r\nMeanwhile I think this is better than a fused type of `int32` and `int64`, because if we explicitly use `int64`, we then could be confident our code would generate consistent results independent of OS? Because personally I think `int64` might be the \"mainstream\" way to go (any NP2 system or Linux system)?\r\n",
"No problem. Also appreciate the input from @njzjz \r\n\r\nPerhaps we should add a note in next release informing downstream packages of such potentially breaking change (`chgnet` for example)?",
"sure thing! would you like to draft a note?",
"Sure, and feel free to polish it as you like.\r\n\r\n### [Breaking] Default NumPy/Cython integer type changed to `int64` on Windows \r\n\r\n**Change**: With NumPy 2.x, [the default integer type changed to `int64` on Windows 64-bit system](https://numpy.org/doc/stable/release/2.0.0-notes.html). Consequently, `pymatgen` now explicitly uses `np.int64` for all NumPy and Cython code instead of the platform-dependent `int` type.\r\n\r\n**Recommendation**: Please explicitly declare `dtype=np.int64` when initializing a NumPy array if possible. You might also need to [test NumPy 1.x on Windows in CI pipelines](https://numpy.org/devdocs/dev/depending_on_numpy.html#build-time-dependency).\r\n\r\n\r\n"
] | 2024-08-10T08:20:33
| 2024-10-10T06:44:09
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2024-08-24T08:54:10Z
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CONTRIBUTOR
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### Summary
- Explicitly use `int64` in cython code to avoid OS inconsistency ([default int type changed in Windows](https://numpy.org/doc/stable/numpy_2_0_migration_guide.html)) as follow up PR of #3894, to fix #3990
- [x] Run unit test on Windows with `NumPy < 2`
- [x] Revert NumPy<2 pin after tests pass
### Cython code need attention
- `src/pymatgen/optimization/linear_assignment.pyx`
- `src/pymatgen/optimization/neighbors.pyx`
- `src/pymatgen/util/coord_cython.pyx`
### Pin some threads from `NumPy` for reference:
- https://github.com/numpy/numpy/pull/24224
- [NumPy roadmap- Change default int on windows to int64](https://github.com/orgs/numpy/projects/9/views/1?pane=issue&itemId=23800241)
- https://github.com/numpy/numpy/issues/9464
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Kpoints Sampling Saved as Float When Writing Kpoints file
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[
"Hi thanks for reporting and diagnosing and sorry for the trouble caused. I could confirm the issue and would fix ASAP."
] | 2024-08-11T15:52:56
| 2024-09-06T22:41:27
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2024-08-20T10:13:20Z
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### Python version
Python 3.10.14
### Pymatgen version
Version: 2024.7.18
### Operating system version
Red Hat Enterprise Linux Ver 8.6
### Current behavior
When using the `Kpoints` class from `pymatgen.io.vasp.inputs` to read a Gamma-centered KPOINTS file and then write it back, the fourth line of the KPOINTS file is converted to a float string. This causes VASP5.4.4 calculations to fail when using this file. Specifically, in the `from_str` method of the Kpoints class, the fourth line of the KPOINTS file is cast to `kpts` as `Sequence[tuple[float, float, float]]`. The `kpts` attribute is then handled as a sequence of floats throughout the process, and it is written back as floats.
### Expected Behavior
When writting a Gamma-centered KPOINTS file, the number of K-point divisions should be cast to a int, or it should be explicitly cast to an integer when writing the file if the style is Gamma-centered or Monkhorst-Pack.
Initially, the `kpts` attribute of the Kpoints class was handled as `list[int]` in `from_str` method, but it was changed to `Sequence[tuple[float, float, float]]` in #3758. While this change itself is not problematic, it would be more convenient if `kpts` were an integer sequence for Gamma-centered or Monkhorst-Pack.
### Minimal example
```Python
#The following source code is a simplified code that reproduces this problem.
#The fourth line of the KPOINTS file resulting from the output of this code is `3.0 3.0 3.0`.
from pymatgen.io.vasp.inputs import Kpoints
Kpoints_str = """\
An example
0
Gamma
3 3 3
0.0 0.0 0.0"""
kpoints = Kpoints.from_str(Kpoints_str)
kpoints.write_file("KPOINTS")
```
### Relevant files to reproduce this bug
_No response_
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Set `kpoints` in `from_str` method as integer in auto Gamma and Monkhorst modes
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[
"It turns out typing `Kpoint` as a sequence of `float` is giving us quite some headache and confusion: https://github.com/materialsproject/pymatgen/blob/b28c9371d684b8a605830cd13060bef9accf68cf/src/pymatgen/util/typing.py#L63\r\n\r\nIt was originally done this way for compatibility with line-mode and explicit kpoint mode (when typing, `float` acts as a Union type of `int | float` instead of just `float`). Is there any other cases where `Kpoint` could be `float` that I forgot to mention?\r\n\r\n**Inputs and comments are hugely appreciated.**",
"@janosh Could you please comment and review this PR? \r\n\r\nCurrently the type of Kpoint is a bit confusing (mainly around the existing of `tuple[float, float, float]` for line mode and explicit kpoint mode) and I tried to clarify as much as I could in this PR. Also is there any other cases where Kpoint could be a sequence of floats that I left out?",
"Thanks @janosh "
] | 2024-08-12T02:28:23
| 2024-08-20T10:31:02
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2024-08-20T10:13:19Z
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CONTRIBUTOR
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### Summary
- Set kpoints in `Kpoints.from_str` method as integer in auto Gamma-centered and Monkhorst-Pack modes, to fix #3993
It turns out typing `Kpoint` as a sequence of `float` is giving us quite some headache and confusion: https://github.com/materialsproject/pymatgen/blob/b28c9371d684b8a605830cd13060bef9accf68cf/src/pymatgen/util/typing.py#L63
It was originally done this way for compatibility with line-mode and explicit kpoint mode (when typing, `float` acts as `Union[int, float]` instead of just `float`). Is there any other cases where `Kpoint` could be `float` that I forgot to mention?
**Inputs and comments are hugely appreciated.**
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Add additional metadata to default CIF comment string
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[PR in draft, needs tests.]
Should a bug be found in either pymatgen's CIFWriter or spglib, a key package depended upon by pymatgen, this updated comment string will make it easier to find affected CIF files.
|
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Docstring tweaks for `io.vasp.inputs` and format tweaks for some other parts
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[] | 2024-08-12T05:57:32
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2024-08-14T15:41:34Z
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CONTRIBUTOR
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### Summary
Separated from #3994 to avoid PR pollution
- Docstring and format tweaks for `io.vasp.inputs`
- Get rid of some `mypy` errors by putting property `getter` and `setter` together, https://github.com/python/mypy/issues/1465
- Fix `use-named-expression` with `sourcery`, and some other tweaks
- Remove a lot of unused `logger`
- Make module level variable ALL CAPS
### TODOs:
- [x] Look closer into (https://github.com/python/mypy/issues/16816): https://github.com/materialsproject/pymatgen/blob/b28c9371d684b8a605830cd13060bef9accf68cf/src/pymatgen/io/vasp/sets.py#L373-L376
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PR_kwDOACgets54KU2R
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Re-organizing VASP I/O code
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[
"Here are my comments:\r\n1. Axiom 1: No. of lines is not a good metric of whether a module should be broken up. In even the most basic IDEs, there are tools to show the class structure, not to mention keyboard shortcuts to jump to any class/method name/line. I can't recall when the last time I had to use mouse scrolling for any file was. Note that the code files in vasp io are hardly the largest ones in pymatgen. \r\n2. Given Axiom 1, the only reason to break up a module into separate pieces is if there is a **logical** consistency to the subparts. While I can get onboard with breaking up sets.py (which has many classes), inputs.py and outputs.py should stay as they are. There is no good reason to split them up. Inputs only has 5 classes and they all pertain to vasp inputs.\r\n3. Even when breaking up sets.py, there is a certain inconsistency to the current choice. Why should input sets be split based on who wrote them, i.e., MP, MIT, MVL? Why not based on type of calculation (relaxation, static, electronic structure, NEB, etc.)? Do people select input sets based on organization? Isn't it more logical that they select an input set based on what they want to do?\r\n4. In so far as module subdivision is merely a developer-related detail (which it seems you are suggesting it is, since the primary justification was \"ease of maintenance\") and not a user API detail, the modules should all be private, i.e., with a \"_\" prefix. This gives the flexibility to completely reorganize when needed without some user seeing his code `from pymatgen.vasp.io.sets.mp import MPRelaxSet` suffer from backwards incompatible breakages. I do not want to see anyone using that line - it must be `from pymatgen.vasp.io.sets import MPRelaxSet`, even if the sets reside in separate files.\r\n\r\nI refer you to the scikit-learn module and class organization. Please use that as a guide on how to organize. Finally, I would point out that many of sklearn's module files are about the same length as sets.py (2800-3200 lines). They do not break up a module for maintenance - they break it up when there is a logic to the organization.",
"The sklearn comparison is illustrative: even where there are large LOC, often there is only a single class per file, and they are quite readable. This is not the case for these specific files in pymatgen. I am not making axiomatic statements; I agree that a high number of LOC is not in itself an error.\r\n\r\nLong-time pymatgen developers (we are in good company) might know exactly where in the file to go to make an edit, but before you can get there, one has to read and understand the structure of the code. It is nice to know what classes are available, for example, without needing to read the entire file first.\r\n\r\nPoint 3 I concur; perhaps it is better to split up the input sets according to functionality instead.",
"Re 3, i think the most common use case is to have consistent settings across whatever mixture of workflows you run (relax, band gap, EOS, phonon, etc.). so after having run some number of relaxations, a user is unlikely to care about half a dozen other band gap workflows with inconsistent VASP settings to their relaxations. more likely, the only thing they want to know is if a band gap workflow from the same lineage (say MP) exists. hence splitting input sets by lineage makes sense imo.\r\n\r\ni guess it doesn't have to be one or the other. if you look at [`atomate2/vasp/jobs`](https://github.com/materialsproject/atomate2/tree/409679b73085ce4c3326aad834bc449e89cf3fa7/src/atomate2/vasp/jobs), it has a mixture of splits by lineage (`mp.py`, `matpes.py`, `lobster.py`, `amset.py`) and by workflow type (`md.py`, `elastic.py`, `phonon.py`, ...)",
"If splitting by source is preferred, I am ok with that. Note that I don't really think atomate2's organizational structure should be the reference here. In any case, if the module split is a private implementation, then it really doesn't matter since we can always reorganize as needed without breaking downstream codes."
] | 2024-08-12T22:29:52
| 2024-08-21T19:07:26
|
MEMBER
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## Summary
Re-opening changes initially introduced by @janosh in #3865 and later reverted by @shyuep (see [thread](https://github.com/materialsproject/pymatgen/issues/3988)).
**I will be taking responsibility for this PR.** This PR will require approval from both @janosh and @shyuep before merging.
Specifically,
- [ ] For each module changed, I will manually inspect `__dir__()` to make sure *all* imports remain unaffected and that there are no backwards-incompatible changes.
- [ ] Also split `pymatgen.io.vasp.inputs` and `pymatgen.io.vasp.outputs` into separate files.
This change is well-motivated to improve maintainability.
I hope we can get this PR merged without too much difficulty. Thank you again to @janosh for starting this PR, to @Andrew-S-Rosen for the bug report due to the errors caused, and to @shyuep for implementing a rapid fix.
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The Error `MAGMOM` Format in `INCAR` for R2SCAN Structure Optimization.
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[
"I believe that's correctly formatted and intended. On the website it's not an INCAR file which you could use directly as a VASP input file, but a dict representation instead. To convert to a VASP INCAR file, you might need the `Incar.from_dict` method and `write_file` if you wish to write out.\r\n\r\nExample INCAR file:\r\n```\r\nMAGMOM = 0.6 0.6\r\n```\r\n\r\nWith script:\r\n```python\r\nfrom pymatgen.io.vasp.inputs import Incar\r\n\r\n\r\nincar = Incar.from_file(\"INCAR\")\r\n\r\nincar_dict = incar.as_dict()\r\n\r\nprint(incar_dict)\r\n>>> {'MAGMOM': [0.6, 0.6], '@module': 'pymatgen.io.vasp.inputs', '@class': 'Incar'}\r\n\r\nprint(incar.from_dict(incar_dict))\r\n>>> MAGMOM = 2*0.6\r\n```\r\n\r\n\r\n",
"You are right, and I also figured out the following method:\r\n```python\r\n # Write INCAR file\r\n try:\r\n incar = task.orig_inputs.incar\r\n incar_path = f\"{task_id}/INCAR\"\r\n with open(incar_path, \"w\") as f:\r\n f.write(str(incar))\r\n```",
"Yes that would work as `write_file` is just a wrapper method: https://github.com/materialsproject/pymatgen/blob/b28c9371d684b8a605830cd13060bef9accf68cf/src/pymatgen/io/vasp/inputs.py#L819-L826",
"Beautiful, enjoy and happy coding!"
] | 2024-08-13T03:02:09
| 2024-08-13T05:10:55
|
2024-08-13T03:59:12Z
|
CONTRIBUTOR
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[Here](https://next-gen.materialsproject.org/materials/mp-149/tasks/mp-1947498) gives the error `MAGMOM` format:
> [MAGMOM](https://www.vasp.at/wiki/index.php/MAGMOM) [0.6, 0.6]
It should be written as: `MAGMOM = 0.6 0.6`.
Regards,
Zhao
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VaspInputSet.write_input: Improve error message
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[
"Pls fix the ruff errors. Thanks.",
"Done. (I am not sure why local pre-commit did not identify problems)",
"Thanks!"
] | 2024-08-14T12:48:15
| 2024-09-10T13:16:20
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2024-08-15T16:52:02Z
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CONTRIBUTOR
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## Summary
This is a small patch improving error message when writing VASP input without VASP installation.
The original message thrown by Potcar constructor is very generic and sounds like VASP _must_ be installed:
pymatgen.io.vasp.inputs.PMG_VASP_PSP_DIR_Error: No POTCAR for H with functional='PBE' found. Please set the PMG_VASP_PSP_DIR in .pmgrc.yaml.
The new message highlights the existance of `potcar_spec` argument:
ValueError: PMG_VASP_PSP_DIR is not set. Please set the PMG_VASP_PSP_DIR in .pmgrc.yaml or use potcar_spec=True argument.
## Checklist
(used pre-commit hook)
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
- [X] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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Enable formatting customization for `PWInput`
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[] | 2024-08-14T18:50:24
| 2024-09-10T13:15:44
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2024-08-15T16:44:58Z
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CONTRIBUTOR
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### Feature Requested
Right now, when `PWInput` instance is written into a file, the underlying structure's coordinate information is restricted to 6 decimal digits. This causes issues when we need a higher precision, especially for the lattice matrix values (the `CELL_PARAMETERS` card), for PWscf to run without raising `lone vector` error (see [here](https://pw-forum.pwscf.narkive.com/R4HBmxKk/error-in-routine-sym-rho-init-shell-lone-vector-with-fixed-fft-dimension)).
A feature to be able to increase decimal precision on the structure information (atomic positions and lattice vectors), therefore, is requested.
### Proposed Solution
To maintain backwards compatibility, instead of uniformly increasing precision to another fixed number of decimal digits (say, 9 or 12 digits), we can add a keyword argument to `PWInput` constructor where users can specify arbitrary # of decimal digits to best fit their use cases. To maximize flexibility to future changes, we can let the new keyword argument to also allow formatting customization in other ways, e.g., # of indentation spaces, # of decimal digits for other values where a less precision is sufficient (e.g., atomic mass).
### Relevant Information
Here is a `.zip` file with an example of PWscf input file (`scf.in` produced by `PWInput.write_file()` method that reproduces a crash using QE PWscf v7.3. The stdout is captured in `scf.out` and also included in the zipfile. The new input file with higher precision (`scf-new.in`) with the corresponding stdout capture (`scf-new.out`) is also included.
[files.zip](https://github.com/user-attachments/files/16617646/files.zip)
The pseudopotential file can be downloaded and extracted from: http://www.pseudo-dojo.org/pseudos/nc-sr-04_pbe_standard/C.upf.gz
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[
"Great. Thanks."
] | 2024-08-14T19:00:43
| 2024-09-10T13:15:50
|
2024-08-15T16:44:57Z
|
CONTRIBUTOR
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## Summary
Add optional keyword argument `format_options` of type `dict`, which specifies
- `indent`: # of spaces for indentation (defaults to 2)
- `kpoints_crystal_b_indent` # of spaces for indentation in `K_POINTS` card with `crystal_b` option (defaults to 1)
- `coord_decimals`: # of decimal digits for structure information (atomic position coordinates, lattice vector coordinates; defaults to 6)
- `atomic_mass_decimals`: # of decimal digits for atomic mass under `ATOMIC_SPECIES` card (defaults to 4)
- `kpoints_grid_decimals`: # of decimal digits for k-point reciprocal lattice coordinate values in `K_POINTS` card with `crystal_b` option (defaults to 4)
as keys. The default values are chosen to maintain the same output format as before the change.
This PR aims to close #4000
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Fix failing ruff `PT001` on master
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[
"@janosh Perhaps you could review this `ruff` fix on master branch? Thanks!",
"Thanks!"
] | 2024-08-16T07:39:21
| 2024-08-16T10:52:18
|
2024-08-16T09:34:18Z
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CONTRIBUTOR
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### Summary
- Fix failing ruff `PT001` on master
- Bump `ruff` version in pre-commit
@shyuep please review this, thanks!
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[Question] Why do we set SIGMA in INCAR for MPRelaxSet when ISMEAR is -5?
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[
"Because it doesn't matter whether it was set if ISMEAR=-5? And if we set SIGMA to 0, then 0.05 is the default value we use.",
"Thanks for the reply! \r\n\r\n> Because it doesn't matter whether it was set if ISMEAR=-5?\r\n\r\nSounds like it might be better to exclude SIGMA for tetrahedron method and include it later when required to avoid confusion. But anyway, we get the same results."
] | 2024-08-19T10:11:04
| 2024-08-22T02:28:32
|
2024-08-21T18:51:46Z
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CONTRIBUTOR
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### Summary
Why do we set SIGMA in INCAR for MPRelaxSet when ISMEAR is -5 ([SIGMA would be ignored in this case](https://www.vasp.at/wiki/index.php/ISMEAR))? Is it going to be corrected by #3322?
> Mind: [SIGMA](https://www.vasp.at/wiki/index.php/SIGMA) is ignored for the tetrahedron method.
https://github.com/materialsproject/pymatgen/blob/6427b556ea82f364ff4b619dfbcdf7fd7169cce7/src/pymatgen/io/vasp/MPRelaxSet.yaml#L11
https://github.com/materialsproject/pymatgen/blob/6427b556ea82f364ff4b619dfbcdf7fd7169cce7/src/pymatgen/io/vasp/MPRelaxSet.yaml#L80
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[CI] Unit test for `command_line.vampire` is failing
|
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[] | 2024-08-20T05:25:12
| 2024-08-20T05:25:49
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CONTRIBUTOR
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Singled out from #3985 for visibility, the only unit test for `command_line.vampire` seems to be failing now: https://github.com/materialsproject/pymatgen/blob/3fee7d58fdc963b8fb8faf76ce92b68f7ccd0bf9/tests/command_line/test_vampire_caller.py#L35-L47
Where `vc.output.critical_temp` is now `500` instead of expected `400`.
Help needed as I have zero knowledge about `vampire`.
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[CI] Unit test `test_all` for `io.qchem.outputs` is failing
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CONTRIBUTOR
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Singled out from #3985 for visibility.
The following unit test for `io.qchem.outputs` is failing, **need help**: https://github.com/materialsproject/pymatgen/blob/3fee7d58fdc963b8fb8faf76ce92b68f7ccd0bf9/tests/io/qchem/test_outputs.py#L304-L316
It appears the dimension from `out_data` and `SINGLE_JOB_DICT` mismatch, with the former having one extra dimension for some reason (i.e. `[[a, b, c], ]` vs `[a, b, c]`).
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[CI] Multiple unit tests failing for `openbabel` related functions on Windows
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[
"See https://github.com/materialsproject/pymatgen/pull/3967#issuecomment-2264473437 for a similar problem.",
"Hi @hongyi-zhao thanks for the comment. However I don't think that's related to this issue, [currently matgl doesn't support torch>2.2.1](https://github.com/materialsproject/pymatgen/pull/3958#issuecomment-2265326754). Those tests have been skipped until `matgl` resolve that. You should [see those CI failures gone once master is merged](https://github.com/materialsproject/pymatgen/pull/3967/checks).",
"@DanielYang59 Thank you for pointing this out."
] | 2024-08-20T05:44:32
| 2024-11-30T08:19:40
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CONTRIBUTOR
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Singled out from #3985 for visibility.
~~[See the full CI log](https://github.com/materialsproject/pymatgen/actions/runs/10465243127)~~, multiple unit tests failing for `openbabel` related functions on Windows (skipped in f3dc772c25cc06b26b0702af37f1d278da8b6169 and f1393af2acfb098fe2e34c0bed193910e6f444e6).
Update: The CI log expired after 90 days (if I remember correctly), so please check above commits for what tests are skipped.
**Help needed.**
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|
Generating unique displacements with EnumLibAdaptor
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[] | 2024-08-20T15:03:30
| 2024-08-20T15:03:30
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NONE
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### Feature Requested
From this paper (https://www.sciencedirect.com/science/article/pii/S0927025617302069?via%3Dihub), it looks like enumlib should be able to enumerate unique displacements as well. Can this be implemented in pymatgen?
### Proposed Solution
Implement this feature in the class EnumlibAdaptor.
### Relevant Information
https://www.sciencedirect.com/science/article/pii/S0927025617302069?via%3Dihub
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Drop Python 3.9 support
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[
"Thanks @janosh @shyuep ",
"Hey 👋🏻 \r\n\r\nI know it's just a minor thing, but I guess this [](https://python.org/downloads) should also be adjusted to [](https://python.org/downloads) in the README file then?",
"@QuantumChemist Thanks a ton for catching this! I missed this one."
] | 2024-08-21T02:07:02
| 2024-08-28T01:05:04
|
2024-08-21T18:55:07Z
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CONTRIBUTOR
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### Summary
- Drop Python 3.9 support, following NumPy https://github.com/numpy/numpy/issues/24932
- Remove a few outdated TODOs
### TODOs
- [x] Implement https://github.com/materialsproject/pymatgen/pull/3958#issuecomment-2259644593
### Future PR
- Looks like Python 3.13 rc1 is not supported by micromamba (perhaps I did it incorrectly), let's wait until [the stable release Oct 2024](https://peps.python.org/pep-0719/#schedule)?
- Fix ignore of `RUF017` rules
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Use `strict=True` with `zip` to ensure length equality
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[
"\r\n> did you notice any cases where `strict=True` stood out as potentially problematic? \r\n\r\nSorry I didn't really go through each of these replacements (just a batch replace and fixed those CI failures in 89dc24775a9926f335ba271f477dd58890aae35d and b149ebb52918a35151a127cd99b555c809473e90). Perhaps I should mark it as draft now and fully go through all changes later.\r\n\r\n> i assume there are cases where `strict=True` wouldn't raise a CI warning \r\n\r\nWith `strict=True` [a `ValueError` would be raised](https://github.com/materialsproject/pymatgen/actions/runs/10503059600/job/29095707287) directly instead of warning. So it would be a good thing (reveal untested code) and a bad thing (might lead to many breakages from untested code).\r\n",
"> With strict=True [a ValueError would be raised](https://github.com/materialsproject/pymatgen/actions/runs/10503059600/job/29095707287) directly instead of warning\r\n\r\nsorry, i meant error, not warning\r\n\r\n> So it would be a good thing (reveal untested code) and a bad thing (might lead to many breakages from untested code).\r\n\r\nagreed\r\n\r\n> Perhaps I should mark it as draft now and fully go through all changes later.\r\n\r\nnot strictly necessary imo. these issues are very hard to spot by just looking at the code. overall less time spent reporting and fixing errors as they occur",
"\r\n> not strictly necessary imo. these issues are very hard to spot by just looking at the code. overall less time spent reporting and fixing errors as they occur\r\n\r\nYes that's what I thought... Though sounds a bit irresponsible, but it's quite hard just by eyeballing\r\n\r\n",
"No problem. Thanks for reviewing. Fingers crossed that this PR wouldn't be pinged a hundred times :) "
] | 2024-08-22T06:33:31
| 2024-08-22T09:21:15
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2024-08-22T09:19:08Z
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CONTRIBUTOR
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### Summary
- Use `strict=True` when `zip` to ensure length equality @janosh, to finish https://github.com/materialsproject/pymatgen/pull/4009#discussion_r1724511180
### TODOs
- [x] Let's see how many tests are failing
- [x] Make sure `strict` keyword is for `zip` not other function
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Fix ruff PD901 and prefer `sum` over `len`+`if`
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minor fix in `src/pymatgen/io/cp2k/outputs.py` `parse_energy_file`
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Bump rexml from 3.3.3 to 3.3.6 in /docs
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[] | 2024-08-22T20:57:20
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2024-08-23T15:53:22Z
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Bumps [rexml](https://github.com/ruby/rexml) from 3.3.3 to 3.3.6.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/ruby/rexml/releases">rexml's releases</a>.</em></p>
<blockquote>
<h2>REXML 3.3.6 - 2024-08-22</h2>
<h3>Improvements</h3>
<ul>
<li>
<p>Removed duplicated entity expansions for performance.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/194">GH-194</a></li>
<li>Patch by Viktor Ivarsson.</li>
</ul>
</li>
<li>
<p>Improved namespace conflicted attribute check performance. It was
too slow for deep elements.</p>
<ul>
<li>Reported by l33thaxor.</li>
</ul>
</li>
</ul>
<h3>Fixes</h3>
<ul>
<li>
<p>Fixed a bug that default entity expansions are counted for
security check. Default entity expansions should not be counted
because they don't have a security risk.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/198">GH-198</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/199">GH-199</a></li>
<li>Patch Viktor Ivarsson</li>
</ul>
</li>
<li>
<p>Fixed a parser bug that parameter entity references in internal
subsets are expanded. It's not allowed in the XML specification.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/191">GH-191</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
<li>
<p>Fixed a stream parser bug that user-defined entity references in
text aren't expanded.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/200">GH-200</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>
<p>Viktor Ivarsson</p>
</li>
<li>
<p>NAITOH Jun</p>
</li>
<li>
<p>l33thaxor</p>
</li>
</ul>
<h2>REXML 3.3.5 - 2024-08-12</h2>
<h3>Fixes</h3>
<ul>
<li>Fixed a bug that <code>REXML::Security.entity_expansion_text_limit</code>
check has wrong text size calculation in SAX and pull parsers.
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/193">GH-193</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/195">GH-195</a></li>
<li>Reported by Viktor Ivarsson.</li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/ruby/rexml/blob/master/NEWS.md">rexml's changelog</a>.</em></p>
<blockquote>
<h2>3.3.6 - 2024-08-22 {#version-3-3-6}</h2>
<h3>Improvements</h3>
<ul>
<li>
<p>Removed duplicated entity expansions for performance.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/194">GH-194</a></li>
<li>Patch by Viktor Ivarsson.</li>
</ul>
</li>
<li>
<p>Improved namespace conflicted attribute check performance. It was
too slow for deep elements.</p>
<ul>
<li>Reported by l33thaxor.</li>
</ul>
</li>
</ul>
<h3>Fixes</h3>
<ul>
<li>
<p>Fixed a bug that default entity expansions are counted for
security check. Default entity expansions should not be counted
because they don't have a security risk.</p>
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/198">GH-198</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/199">GH-199</a></li>
<li>Patch Viktor Ivarsson</li>
</ul>
</li>
<li>
<p>Fixed a parser bug that parameter entity references in internal
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<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/191">GH-191</a></li>
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</ul>
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<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/200">GH-200</a></li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<h3>Thanks</h3>
<ul>
<li>
<p>Viktor Ivarsson</p>
</li>
<li>
<p>NAITOH Jun</p>
</li>
<li>
<p>l33thaxor</p>
</li>
</ul>
<h2>3.3.5 - 2024-08-12 {#version-3-3-5}</h2>
<h3>Fixes</h3>
<ul>
<li>Fixed a bug that <code>REXML::Security.entity_expansion_text_limit</code>
check has wrong text size calculation in SAX and pull parsers.
<ul>
<li><a href="https://redirect.github.com/ruby/rexml/issues/193">GH-193</a></li>
<li><a href="https://redirect.github.com/ruby/rexml/issues/195">GH-195</a></li>
<li>Reported by Viktor Ivarsson.</li>
<li>Patch by NAITOH Jun.</li>
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/ruby/rexml/commit/95871f399eda642a022b03550479b7994895c742"><code>95871f3</code></a> Add 3.3.6 entry</li>
<li><a href="https://github.com/ruby/rexml/commit/7cb5eaeb221c322b9912f724183294d8ce96bae3"><code>7cb5eae</code></a> parser tree: improve namespace conflicted attribute check performance</li>
<li><a href="https://github.com/ruby/rexml/commit/6109e0183cecf4f8b587d76209716cb1bbcd6bd5"><code>6109e01</code></a> Fix a bug that Stream parser doesn't expand the user-defined entity reference...</li>
<li><a href="https://github.com/ruby/rexml/commit/cb158582f18cebb3bf7b3f21f230e2fb17d435aa"><code>cb15858</code></a> parser: keep the current namespaces instead of stack of Set</li>
<li><a href="https://github.com/ruby/rexml/commit/2b47b161db19c38c5e45e36c2008c045543e976e"><code>2b47b16</code></a> parser: move duplicated end tag check to BaseParser</li>
<li><a href="https://github.com/ruby/rexml/commit/35e1681a179c28d5b6ec97d4ab1c110e5ac00303"><code>35e1681</code></a> test tree-parser: move common method to base class</li>
<li><a href="https://github.com/ruby/rexml/commit/6e00a14daf2f901df535eafe96cc94d43a957ffe"><code>6e00a14</code></a> test: fix indent</li>
<li><a href="https://github.com/ruby/rexml/commit/df3a0cc83013f3cde7b7c2044e3ce00bcad321cb"><code>df3a0cc</code></a> test: fix indent</li>
<li><a href="https://github.com/ruby/rexml/commit/fdbffe744b38811be8b1cf6a9eec3eea4d71c412"><code>fdbffe7</code></a> Use loop instead of recursive call for Element#namespace</li>
<li><a href="https://github.com/ruby/rexml/commit/6422fa34494fd4145d7bc68fbbe9525d42becf62"><code>6422fa3</code></a> Use loop instead of recursive call for Element#root</li>
<li>Additional commits viewable in <a href="https://github.com/ruby/rexml/compare/v3.3.3...v3.3.6">compare view</a></li>
</ul>
</details>
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Remove the `skip` mark for `test_delta_func`
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"All windows tests have passed.",
"Thanks for keeping an eye on this, perhaps we should bump `scipy` version also (to `>=1.14.1`)?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/41e4c69911f2b724734e0917c436ee5a1de63091/pyproject.toml#L68",
"> perhaps we should bump `scipy` version also (to `>=1.14.1`)?\r\n\r\nI bump it for Windows only."
] | 2024-08-23T16:14:29
| 2024-08-30T06:12:43
|
2024-08-29T20:10:27Z
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CONTRIBUTOR
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## Summary
https://github.com/scipy/scipy/issues/21052 has been fixed and released in scipy 1.14.1. This PR removes the skip mark.
## Todos
If this is work in progress, what else needs to be done?
- feature 2: ...
- fix 2:
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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Fix fixable `ruff` rules
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[
"No problem, thanks for reviewing!"
] | 2024-08-25T08:17:52
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2024-08-28T10:27:56Z
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CONTRIBUTOR
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### Summary
Fix fixable `ruff` rules
### TODOs
- [x] Unit test of `io.aims` doesn't follow name convention, and has test files inside it.
- [x] Fix NPY201 https://github.com/materialsproject/pymatgen/blob/41e4c69911f2b724734e0917c436ee5a1de63091/pyproject.toml#L209
- [x] Fix PD011 (there might be a few false-positive for example in `io.abinit.pseudo` and io.cp2k keywords, https://github.com/astral-sh/ruff/issues/6432)
- [x] [**Need help**] Use of relative import in test cf24f12ccd5adf5c34a9c32899f87b2f790effe0
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[Dev] Remove `mysql` dependency from `ext.cod` and fix S608
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"> * Resolve following `mysql` dependency issue:\r\n\r\ni think `mysql` can be replaced with https://pypi.org/project/mysqlclient (based on [the advice here](https://pypi.org/project/mysql/))",
"Why bother? This is a small feature within pymatgen and we probably can count on a few fingers the number of people who use it. Those who use it can install mysql. In fact, the onus should be on COD to offer a REST API rather than an SQL one. Pls focus efforts on more impactful changes.",
"> This is a small feature within pymatgen and we probably can count on a few fingers the number of people who use it. Those who use it can install mysql.\r\n\r\nThat's true, I posted this in case someone who need to use SQL might be interested to take over and fix this?\r\n\r\n> Pls focus efforts on more impactful changes.\r\n\r\nThat's the reason I opened this instead of fixing it myself. Can we reopen this? This looks like a good first issue if anyone is interested in getting involved in open source.\r\n\r\n\r\n"
] | 2024-08-26T02:36:09
| 2024-09-10T01:40:49
|
2024-09-09T21:09:43Z
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CONTRIBUTOR
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- Resolve following `mysql` dependency issue: https://github.com/materialsproject/pymatgen/blob/41e4c69911f2b724734e0917c436ee5a1de63091/src/pymatgen/ext/cod.py#L70
- Also need to fix two `S608` violations (SQL injection): https://github.com/materialsproject/pymatgen/blob/41e4c69911f2b724734e0917c436ee5a1de63091/src/pymatgen/ext/cod.py#L73
https://github.com/materialsproject/pymatgen/blob/41e4c69911f2b724734e0917c436ee5a1de63091/src/pymatgen/ext/cod.py#L109
Help needed.
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Fix `S101`, replace all `assert` in code base (except for tests)
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"> thanks a lot for all this work @DanielYang59! 🙏\r\n\r\nNo problem. Thanks for reviewing!\r\n\r\n> to make the messages more informative, i think it would be great to include the offending value/type in all `(Value|Type)Errors` (see [135f69e](https://github.com/materialsproject/pymatgen/commit/135f69ef7db4b1318c0882fd46e08d31204f4b86) for a fe examples)\r\n\r\nThat's a very sensible suggestion, I would implement this later :)\r\n",
"Manually trace this link https://github.com/materialsproject/pymatgen/commit/135f69ef7db4b1318c0882fd46e08d31204f4b86 to the discussion on f-string (sometimes comment doesn't show up in the PR for reasons I don't know 😄 ), in case I want to get back to this thread."
] | 2024-08-26T03:16:39
| 2024-08-31T06:02:29
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2024-08-31T06:01:58Z
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CONTRIBUTOR
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### Summary
- Fix `S101`, replace all `assert` in code base
- [x] Use offending value in error message
**Please review all changes carefully to make sure the assert condition is correctly reversed** (there're just too many changes and I tried not to make mistakes).
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Remove explicit declare of package-data
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[
"**UPDATE: ignore the following**, it turns out I didn't understand \"package-data\" correctly before. In \"package-data\", we declare files to be included into the source distribution, and after that, with `include-package-data = true` we include them into the wheels.\r\n\r\n@janosh Would appreciate it if you could give me a hand on this :)\r\n\r\n\r\n",
"> @janosh Would appreciate it if you could give me a hand on this :)\r\n\r\nhappy to help. what's the problem exactly? that some cython files aren't included in the wheel?",
"Thanks for your reply @janosh :)\r\n\r\nI originally opened this PR because I thought declaring all files was a bit inefficient (also prone to error if someone add a new file but forgot to update `pyproject.toml`), and I would expect all files included inside the `src` to be packed (really?).\r\n\r\n**The main cause of my headache is**: the sdist need to include `*.pyx` but not `*.so` (the latter should not exist with `python -m build --sdist` so not a big issue), but the wheels should include `*.so` but not `*.pyx` (not sure if this is possible because with `include-package-data = true` everything from sdist would be copied to the wheel?).\r\n\r\nBut I didn't manage to find a more elegant yet safe way to handle file inclusion/exclusion at this moment (I hope I'm wrong).\r\n\r\nAs of my knowledge, [to declare package data](https://github.com/pypa/setuptools/issues/4638#issuecomment-2335123635):\r\n1. (Current method) Explicitly declare all non-`.py/pyx` files.\r\n2. Add a `MANIFEST.in` file to declare package data file, but I don't think it's offering much benefit over current method.\r\n3. Use the following to include everything inside the `src` directory, but this would also include `*.c` and `*.pyx` files inside the wheels.\r\n ```\r\n [tool.setuptools.package-data]\r\n \"*\" = [\"*\", ]\r\n ```\r\n4. Use [`setuptools-scm`](https://setuptools.pypa.io/en/latest/userguide/datafiles.html#include-package-data) to include everything tracked by Git, but this would include `tests` as well.\r\n\r\nI sneaked a peek at Jinzhe's DeepMD-kit and [it looks like he's using a custom backend altogether](https://github.com/deepmodeling/deepmd-kit/blob/6dafa5076ec88557dbc1bbf68e46cbc91d1ae86c/pyproject.toml#L9).\r\n\r\n",
"> but this would also include `*.c` and `*.pyx` files inside the wheels.\r\n\r\ncould you explain what the downsides of this are? is it a problem/bad practice to have those files in a wheel? seems like it could help with debugging to have the source files around if compiled code is ever causing issues. and the files are small so wouldn't noticeably increase wheel size.",
"I have a feeling that making `test_egg_sources_txt_is_complete` optional is not a good idea, we should setup the test such that it would always run in unit test, otherwise we may or may not be checking the contents at all:\r\nhttps://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/tests/test_pkg.py#L11-L15\r\n\r\nI would update `test_pkg` to cover bdist/sdist build\r\n\r\n\r\n\r\n",
"I am closing this PR. I prefer to be explicit about what package data is being included, rather than taking an exclusionary approach. ",
"Ok thanks for the comment"
] | 2024-08-26T06:28:54
| 2025-04-15T16:35:06
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2025-04-15T16:21:01Z
|
CONTRIBUTOR
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### Summary
- Remove explicit declare of package data, [sse Git plugin instead](https://setuptools.pypa.io/en/latest/userguide/datafiles.html): https://pypi.org/project/setuptools-scm/, also see https://github.com/pypa/setuptools-scm/issues/199
This would include "everything" tracked by Git, including "docs", "tests", ...
[Unwanted files have to be excluded by `MANIFEST.in`](https://github.com/pypa/setuptools-scm?tab=readme-ov-file), I would prefer not to add an additional file but currently it looks like it's our only option:
> Unwanted files must be excluded via MANIFEST.in or [configuring Git archive](https://setuptools-scm.readthedocs.io/en/stable/usage/#builtin-mechanisms-for-obtaining-version-numbers).
- [x] Really make sure the `setuptools-scm` plugin would NOT change the versioning of pymatgen
- [x] Test install from source distribution, 2c50c00b6556d3c373401893c768628369c66ee5 https://github.com/materialsproject/pymatgen/pull/4018/checks?check_run_id=32982665662
---
#### Fix `py.typed` usage for namespace packages migrated to #4199
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Support for LOBSTER 5.1.0 outputs parsing
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"This is partially closed by #4065 "
] | 2024-08-26T10:39:27
| 2024-10-20T07:26:27
|
CONTRIBUTOR
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### Feature Requested
Support for LOBSTER 5.1.0 outputs file parsing.
Once added, downstream lobsterpy package and LOBSTER workflow in atomate2 can also be used.
### Proposed Solution
The LOBSTER output file parsers will be adapted to be able to tackle these new output files and tests will be added
### Relevant Information
_No response_
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[
"I’m on vacation right now but I’ll get to this once I’m back Monday!\r\n\r\nOn Wed, Aug 28, 2024 at 3:21 AM Janosh Riebesell ***@***.***>\r\nwrote:\r\n\r\n> ***@***.**** commented on this pull request.\r\n> ------------------------------\r\n>\r\n> In tests/io/vasp/test_help.py\r\n> <https://github.com/materialsproject/pymatgen/pull/4020#discussion_r1734399836>\r\n> :\r\n>\r\n> > + with patch(\"sys.stdout\", new=io.StringIO()) as fake_stdout:\r\n> + vasp_doc.print_help(tag)\r\n> + output = fake_stdout.getvalue()\r\n> +\r\n> + assert tag in output\r\n> +\r\n> + @pytest.mark.parametrize(\"tag\", [\"ISYM\"])\r\n> + def test_get_help(self, tag):\r\n> + vasp_doc = VaspDoc()\r\n> + docstr = vasp_doc.get_help(tag)\r\n> +\r\n> + assert tag in docstr\r\n> +\r\n> + def test_get_incar_tags(self):\r\n> + incar_tags = VaspDoc.get_incar_tags()\r\n> + assert incar_tags\r\n>\r\n> i assume the VASP docs cover both the latest and earlier versions. if the\r\n> tags are no longer documented, they may have been deprecated a while ago.\r\n> still probably makes sense for incar_parameters.json to be permissive,\r\n> i.e. allow older tags that have been deprecated (though ideally with a\r\n> warning to the user when deprecated tags are validated). maybe\r\n> @esoteric-ephemera <https://github.com/esoteric-ephemera> knows more\r\n>\r\n> —\r\n> Reply to this email directly, view it on GitHub\r\n> <https://github.com/materialsproject/pymatgen/pull/4020#discussion_r1734399836>,\r\n> or unsubscribe\r\n> <https://github.com/notifications/unsubscribe-auth/AH6VV6FHGIUEI77PKZFVJFLZTWQCHAVCNFSM6AAAAABNF5ENGOVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDENRVHAYTCNJRHE>\r\n> .\r\n> You are receiving this because you were mentioned.Message ID:\r\n> ***@***.***>\r\n>\r\n",
"@DanielYang59 for updating VASP defaults, you can take a look at [the `pymatgen-io-validation` add-on](https://github.com/materialsproject/pymatgen-io-validation/blob/main/pymatgen/io/validation/vasp_defaults.yaml) from @matthewkuner and myself. I think we got most of the relevant defaults there, otherwise you'll need to scrape them from the site\r\n\r\nThere are also undocumented tags which we can safely ignore. There are a set of \"joke\" VASP settings (like `LMUSIC` and `IDIOT`), and also developmental/debugging tags\r\n\r\nThe last category is VASP add-ons which can be compiled as external libraries to VASP, and add INCAR tags that VASP would not document. Some of these add-ons (like BEEF, DFTD4, and VTST) are common enough that it maybe warrants documenting a few in pymatgen",
"Hi @esoteric-ephemera great to see your response as always. Thanks a lot for the reply :)\r\n\r\n> for updating VASP defaults, you can take a look at [the pymatgen-io-validation add-on](https://github.com/materialsproject/pymatgen-io-validation/blob/main/pymatgen/io/validation/vasp_defaults.yaml) from @matthewkuner and myself. I think we got most of the relevant defaults there\r\n\r\nPerhaps there's some misunderstanding here, but I was intended to test/update the `io/vasp/incar_parameters.json` file which contains the known **types** for INCAR tags (not really default values).\r\n\r\n> There are also undocumented tags which we can safely ignore. There are a set of \"joke\" VASP settings (like LMUSIC and IDIOT), and also developmental/debugging tags\r\n\r\nI didn't see those \"joke\" tags in VASP wiki so perhaps we could safely ignore them for now.\r\n\r\n> The last category is VASP add-ons which can be compiled as external libraries to VASP, and add INCAR tags that VASP would not document.\r\n\r\nGreat to know that. In this regard I agree with Janosh that we'd better be more permissive to include those tags in the json file which are not listed in VASP wiki for any reason.\r\n",
"@janosh Perhaps let's just test `io.vasp.help` for now? Sound like there's more discussion needed to check and update `incar_parameters.json` file (too many INCAR tags are absent from the json file).",
"always love to see new tests! thanks @DanielYang59 👍 ",
"No problem, thanks for reviewing and everyone for the helpful discussion :)"
] | 2024-08-27T11:24:25
| 2024-09-04T14:08:17
|
2024-09-04T14:07:12Z
|
CONTRIBUTOR
|
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### Summary
- Add unit test for `io.vasp.help`
- Bump python requirement to 3.10+ in README, thanks @QuantumChemist for pointing out (re pattern: `py(?:thon)?\s?3\.?9`)
- Reduce timeout for `requests` to 60 seconds, 600 seconds might be too impractical
### Not planned (for this PR?)
- [x] `test_get_incar_tags` also check `incar_parameters.json` file
- [ ] Update `incar_parameters.json`file
|
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PR_kwDOACgets55tYkd
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Replace HTTP URLs with HTTPS, avoid `from pytest import raises/mark`
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[
"@janosh Please review this. Looks like we might need to regenerate docs, thanks!\r\n\r\nI reverted the rebuild doc commit because it makes it impossible to review. Would let you do this, appreciate that!",
"Currently on my phone. Could you apply the docs commit again?",
"> ideally, we should have a link checker CI [similar to pymativz](https://github.com/janosh/pymatviz/blob/1de350a146b53ae03f343ff9a78454ba7c976186/.github/workflows/link-check.yml) to make sure all the new (and old links) are actually still alive. but i'm happy to leave that to a future PR. maybe something to open an issue for so it's not forgotton\r\n\r\nWonderful. Added to my TODO list (which is not very long at this moment :) ). I would need some investigation on that because [markdown-link-check](https://github.com/tcort/markdown-link-check) seemingly just check markdown files.\r\n\r\nCan you regenerate documents after reviewing? Thanks!",
"@DanielYang59 do you want to reapply the docs update commit before i merge?",
"@janosh certainly, got two warnings at the start, not sure if we should worry about that or not (it seems `favicon.ico` and `html_static_path = [\"assets\"]` don't exist?):\r\n```\r\n>>> invoke make-doc\r\nrm: pymatgen.*.rst: No such file or directory\r\nRunning Sphinx v7.4.7\r\nloading translations [en]... done\r\nmaking output directory... done\r\nWARNING: html_static_path entry 'assets' does not exist\r\nWARNING: favicon file 'favicon.ico' does not exist\r\nConverting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.\r\nbuilding [mo]: targets for 0 po files that are out of date\r\nwriting output... \r\nbuilding [html]: targets for 49 source files that are out of date\r\nupdating environment: [new config] 49 added, 0 changed, 0 removed\r\n```",
"> @janosh certainly, got two warnings at the start, not sure if we should worry about that or not (it seems favicon.ico and html_static_path = [\"assets\"] don't exist?):\r\n\r\nsafe to ignore for now. the docs need some more work at some point but that would be a bigger project",
"Great to know! Thanks."
] | 2024-08-28T13:17:33
| 2024-08-30T06:54:25
|
2024-08-30T06:01:32Z
|
CONTRIBUTOR
|
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### Summary
- Replace HTTP URLs with HTTPS
- Replace some expired URLs
- Avoid `from pytest import raises/mark` (a bit unsure about `MonkeyPatch` so just use `pytest.MonkeyPatch` if `pytest` is already imported)
- [ ] Regenerate documents
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PR_kwDOACgets55yJvY
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Fix PT013: incorrect import of `pytest`
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[
"I might close this one because `approx` is heavily used and `pytest.approx` is way too verbose, [pytest doc also use `from pytest import approx`](https://docs.pytest.org/en/stable/reference/reference.html#pytest.approx) so perhaps we should not say it's \"incorrect import\".\r\n\r\nI might fix `from pytest import other_than_approx` in #4021"
] | 2024-08-29T05:58:18
| 2024-08-30T03:46:45
|
2024-08-29T06:18:53Z
|
CONTRIBUTOR
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### Summary
- Fix [PT013: incorrect import of `pytest`](https://docs.astral.sh/ruff/rules/pytest-incorrect-pytest-import/)
> For consistency, pytest should be imported as import pytest and its members should be accessed in the form of pytest.xxx.yyy for consistency
Admittedly, `approx` is less verbose than `pytest.approx` (sad we cannot set an exception for `approx`), not sure if we want to fix this
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Bug in inverse of MagSymmOp
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[] | 2024-08-29T17:16:16
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2024-10-21T20:54:57Z
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NONE
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### Python version
Python 3.11.7
### Pymatgen version
2023.7.18
### Operating system version
_No response_
### Current behavior
When the `inverse` of `MagSymmOp` is called, an error, `TypeError: MagSymmOp.__init__() missing 1 required positional argument: 'time_reversal'`, happens. This is probably because, in the definition in `class SymmOp`,
```py
@property
def inverse(self) -> Self:
"""Inverse of transformation."""
inverse = np.linalg.inv(self.affine_matrix)
return type(self)(inverse)
```
`type(self)` does not take a `time_reversal` argument.
### Expected Behavior
returns a `MagSymmOp` instance whose `affine_matrix` is inversed.
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
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I_kwDOACgets6UzArC
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[Dev/CI] Check for accessibility of hyperlinks in CI
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[] | 2024-08-30T06:56:45
| 2024-11-30T13:11:44
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CONTRIBUTOR
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Repost from https://github.com/materialsproject/pymatgen/pull/4021#pullrequestreview-2271225895, it might be good to check in CI workflow for the accessibility of hyperlinks to make sure they're still alive.
Something like [markdown-link-check](https://github.com/tcort/markdown-link-check) might be useful, but this just check markdown files.
- [ ] ignore `CHANGES.md` as it contains a lot of links to PRs
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I_kwDOACgets6U0R_3
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GAMMA in xticks, how to fix it to Greek alphabet style
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[] | null |
[
"problem solved by changing \"GAMMA\" to \"\\Gamma\" in KPOINTS"
] | 2024-08-30T09:38:20
| 2024-08-30T10:28:05
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2024-08-30T10:26:54Z
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NONE
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### Discussed in https://github.com/materialsproject/pymatgen/discussions/4025
<div type='discussions-op-text'>
<sup>Originally posted by **1lifetime1** August 30, 2024</sup>
</div>
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PR_kwDOACgets56HiSk
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Recover commented out code in tests and mark with `pytest.mark.skip` instead
|
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[] | null |
[
"Looks like there isn't more commented out code in tests (searched with `#\\s+def ` and `#\\s+class `, using `\\s+` in case multiple spaces are inserted).\r\n\r\nAlso we only have 104 lines of code commented in tests (might include a few false positive), should be possible to enable `ERA` for tests at some point.",
"Thanks!"
] | 2024-09-02T06:30:56
| 2024-09-02T09:11:02
|
2024-09-02T08:47:47Z
|
CONTRIBUTOR
|
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### Summary
- Recover commented out code in tests and mark with `pytest.mark.skip` instead (with `TODO: need someone to fix this` message for easy search), though currently [`ERA`](https://docs.astral.sh/ruff/rules/commented-out-code/) is ignored: https://github.com/materialsproject/pymatgen/blob/c06abf1a3c8d1507d9b128a91b51babbca650ab9/pyproject.toml#L192
### Rationale
Commented out code ages badly if not covered by any linter, perhaps we should mark them with `pytest.mark.skip` instead until someone come and fix them (hopefully).
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I_kwDOACgets6VEHyz
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CifParser taking forever without throwing an error
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[
"Hey @anyangml this works fine with `primitive = False` and then calling `get_primitive_structure` on the structure:\r\n```\r\nfrom pymatgen.io.cif import CifParser\r\n\r\ndef read_file(fpth: str):\r\n cif = CifParser(fpth)\r\n structures = [\r\n s.get_primitive_structure() for s in cif.parse_structures()\r\n ]\r\n if any(cif.check(structure) is not None for structure in structures):\r\n raise ValueError(\"CIF file is not valid.\")\r\n \r\n return structures\r\n```",
"I might assign myself for further investigation on this because ideally the code should never hung forever, but throw a proper exception in such scenario, but still deeply appreciate @esoteric-ephemera's workaround :)",
"I think it's related to the box shape and periodic boundary conditions. If one side of the box is extremely short, and the box is somewhat flat. It might cause issues in calculating neighbor atoms, and it is probably implemented in c++. I find a way to add timer to the function using subprocess.",
"Thanks for sharing your thoughts! I cannot say for sure as I haven't got time to trace this yet. \r\n",
"@anyangml Hi sorry for the lack of response and thanks again for reporting.\r\n\r\nUpon further investigation, I believe you are correct:\r\n> the box is somewhat flat. It might cause issues in calculating neighbor atoms\r\n\r\nIn your case, the generated structure is \"2D-like/flat\" leading to many allowed repetitions when `find_points_in_spheres`, more specifically the following:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/2541b9f7e04478ae14a7f000d557fc232246820f/src/pymatgen/optimization/neighbors.pyx#L160\r\n\r\nIn your case the max repetition `maxr` is on the ~10<sup>8</sup> range, and leading to the following image generation code into an \"infinite\" loop (strictly speaking not infinite, but practically taking forever owing to ~10<sup>24</sup> combinations): https://github.com/materialsproject/pymatgen/blob/2541b9f7e04478ae14a7f000d557fc232246820f/src/pymatgen/optimization/neighbors.pyx#L170-L179\r\n\r\nIdeally, pymatgen is not designed to handle \"unphysical\" structures, but I agree that it should gracefully rejected rather than entering an infinite loop. As generative methods become more widely used, I could see this be practical. I’ll add a pre-filter for clean termination.\r\n\r\n---\r\n\r\n> I even tried to add a timer to raise TimeoutError using the sigal package [like this](https://stackoverflow.com/questions/492519/timeout-on-a-function-call), but it won't exit the function call.\r\n\r\nThe reason your method didn't work out is related to the global interpreter lock (GIL) in the cython (`neighbors.pyx`) code used to `find_points_in_spheres`, where the GIL in held (unless you use something like `nogil`) and interruptions could not be caught (unlike python functions where GIL is usually released) (you might also noticed keyboard interrupt doesn't work either)\r\n\r\n\r\n\r\n"
] | 2024-09-02T12:43:47
| 2024-10-25T12:34:59
|
2024-10-17T02:50:36Z
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NONE
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### Python version
python 3.11.5
### Pymatgen version
2024.7.18
### Operating system version
_No response_
### Current behavior
I have some cif files generated by diffusion models, and they are likely to be invalid. I am trying to use CifParser (default setting) to read those files, and save the structure if the structure turns out to be valid. For some of the files, it takes forever for CifParser to read the file without throwing an error. Below is an example
```
# generated using pymatgen
data_V23Ni
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 1.49244463
_cell_length_b 3.79421616
_cell_length_c 30.42398643
_cell_angle_alpha 20.62129211
_cell_angle_beta 83.61568451
_cell_angle_gamma 62.99439240
_symmetry_Int_Tables_number 1
_chemical_formula_structural V23Ni
_chemical_formula_sum 'V23 Ni1'
_cell_volume 0.00000000
_cell_formula_units_Z 1
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
V V0 1 0.67231035 0.73907024 0.30680549 1
V V1 1 0.34705946 0.37159106 0.52686268 1
V V2 1 0.36653438 0.38854167 0.52153718 1
V V3 1 0.00921166 0.93152356 0.19919881 1
V V4 1 0.95677882 0.91787136 0.49960217 1
Ni Ni5 1 0.51781291 0.50244284 0.32125005 1
V V6 1 0.09629190 0.08547926 0.87447387 1
V V7 1 0.49141514 0.52637476 0.74801213 1
V V8 1 0.78377295 0.75774127 0.46150076 1
V V9 1 0.86805952 0.95672750 0.67616075 1
V V10 1 0.17673326 0.06560791 0.04854067 1
V V11 1 0.09662235 0.06218648 0.66348130 1
V V12 1 0.35039228 0.35385907 0.34141171 1
V V13 1 0.78324890 0.72533828 0.17591193 1
V V14 1 0.96514380 0.07838918 0.98198533 1
V V15 1 0.95602196 0.05976810 0.88894337 1
V V16 1 0.19058158 0.27560839 0.92930967 1
V V17 1 0.64331728 0.62581986 0.41340443 1
V V18 1 0.29390040 0.31569031 0.45524845 1
V V19 1 0.18374869 0.24463138 0.70731211 1
V V20 1 0.02409820 0.10269854 0.72434735 1
V V21 1 0.45413128 0.44173402 0.29142430 1
V V22 1 0.91658413 0.93522346 0.09281332 1
V V23 1 0.02599846 0.12289974 0.88971388 1
```
below is the function I used to read the file:
```
def read_file(fpth: str):
cif = CifParser(fpth)
structure = cif.parse_structures(primitive=True)[0]
if cif.check(structure) is not None:
raise ValueError("CIF file is not valid.")
return structure
```
I even tried to add a timer to raise TimeoutError using the `sigal` package [like this](https://stackoverflow.com/questions/492519/timeout-on-a-function-call), but it won't exit the function call.
### Expected Behavior
if the structure is invalid, I would expect an error of some kind.
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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[] | 2024-09-02T20:28:25
| 2024-09-03T08:52:52
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2024-09-03T08:52:49Z
|
CONTRIBUTOR
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<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.0 → v0.6.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.0...v0.6.3)
- [github.com/pre-commit/mirrors-mypy: v1.11.1 → v1.11.2](https://github.com/pre-commit/mirrors-mypy/compare/v1.11.1...v1.11.2)
- [github.com/RobertCraigie/pyright-python: v1.1.376 → v1.1.378](https://github.com/RobertCraigie/pyright-python/compare/v1.1.376...v1.1.378)
<!--pre-commit.ci end-->
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[DOCS] Links to source in each function returns a 404 error
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[
"Thanks for reporting @tawe141. I could confirm this and would fix soon."
] | 2024-09-03T05:16:48
| 2024-09-03T08:41:30
|
2024-09-03T08:41:30Z
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CONTRIBUTOR
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The main pymatgen code now falls under a src parent directory, but in the documentation (as of 2024.8.9 at least), this change caused all of the hyperlinks for each function pointing to the code in Github to fail. Pretty easy fix, just need to add "src" in the link to point to the right files.
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I_kwDOACgets6VIRSM
| 4,031
|
noncollinear attribute of Outcar class has wrong value for VASP calculations with LNONCOLLINEAR=.TRUE.
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[] | null |
[
"could you share the `OUTCAR` file so we can repro?",
"> ```python\r\n> ```python\r\n> print(outcar.noncollinear) # 'True' for LNONCOLLINEAR=.TRUE.\r\n> ```\r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> ```\r\n\r\nYes. Please check the attached file (Please remove the suffix .txt).\r\n[OUTCAR.txt](https://github.com/user-attachments/files/16846108/OUTCAR.txt) ",
"Thanks. I was able to reproduce this with the OUTCAR attached. Looks like the pattern match failed:\r\nhttps://github.com/materialsproject/pymatgen/blob/edcd4654cc5048d7f0f00417d82755d98b03b739/src/pymatgen/io/vasp/outputs.py#L2114-L2118\r\n\r\nI haven't looked through this part of source code before, wondering why was this `re` pattern compiled like this (number of spaces hard coded?",
"> Thanks. I was able to reproduce this with the OUTCAR attached. Looks like the pattern match failed:\r\n> \r\n> https://github.com/materialsproject/pymatgen/blob/edcd4654cc5048d7f0f00417d82755d98b03b739/src/pymatgen/io/vasp/outputs.py#L2114-L2118\r\n> \r\n> I haven't looked through this part of source code before, wondering why was this `re` pattern compiled like this (number of spaces hard coded?\r\n\r\nThough the number of white spaces are hard-coded, this should work. The problem lies at line 2118. Here is the correct code. \r\n```\r\n self.read_pattern({\"noncollinear\": r\"LNONCOLLINEAR\\s*=\\s*T\"})\r\n if self.data.get(\"noncollinear\", []):\r\n self.noncollinear = True # !!!\r\n```",
"Yep the logic should be reversed. would fix this. Thanks!"
] | 2024-09-03T05:49:39
| 2024-09-04T16:39:14
|
2024-09-04T16:39:14Z
|
NONE
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### Python version
Python 3.11.0
### Pymatgen version
2024.7.18
### Operating system version
Ubuntu 22.04 LTS
### Current behavior
I expect that `outcar.noncollinear` is `True` for noncollinear calculations. But I got `False`.
### Expected Behavior
I expect that `outcar.noncollinear` is `True` for noncollinear calculations.
### Minimal example
```Python
from pymatgen.io.vasp.outputs import Outcar
outcar = Outcar(filename='OUTCAR')
print(outcar.noncollinear) # 'True' for LNONCOLLINEAR=.TRUE.
```
```
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets56OwU0
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|
Fix missing `/src` in doc links to source code
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[
"No problem. Thanks for the better title :)",
"Looks like there might be a off-by-one error with the URL generator, need a closer look:\r\n<img width=\"833\" alt=\"image\" src=\"https://github.com/user-attachments/assets/c112fe52-ce68-4a72-8cd8-ffef37b79385\">\r\n\r\nThis only happens for some classes, in https://pymatgen.org/pymatgen.alchemy.html, line indexes for `AbstractStructureFilter` is correct, but `ChargeBalanceFilter` is off-by-one\r\n"
] | 2024-09-03T08:30:17
| 2024-09-04T07:37:59
|
2024-09-03T08:41:30Z
|
CONTRIBUTOR
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closes #4030
- Fix missing `src` in hyperlinks to source code in docs
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I_kwDOACgets6VJzWH
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Outcar class returns empty magnetization attribute when parsing OUTCAR file on Windows operating system
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[
"Thanks for providing the OUTCAR and code snippet, it's super helpful. I could confirm this.\r\n\r\nIt's owing to difference in `reverse_readfile` from `monty` (different line endings for Windows `\\r\\n` and Linux`\\n`): https://github.com/materialsproject/pymatgen/blob/edcd4654cc5048d7f0f00417d82755d98b03b739/src/pymatgen/io/vasp/outputs.py#L1941\r\n\r\nIn a [previous bug fix](https://github.com/materialsvirtuallab/monty/pull/700), I replaced the hard-coded line separator `\\n` with an OS-independent `os.linesep`, which leads to failure to identify `i` in [the following code](https://github.com/materialsvirtuallab/monty/blob/1270c7b230b43cdbc4f5f184ac645ece31d49b61/src/monty/io.py#L76-L81) for the case of OUTCAR, where the file was generated in Linux but parsed on Windows (which is a common use case):\r\n\r\n```python\r\nfilemap = mmap.mmap(file.fileno(), 0, access=mmap.ACCESS_READ)\r\nn = len(filemap)\r\nwhile n > 0:\r\n i = filemap.rfind(os.linesep.encode(), 0, n)\r\n yield filemap[i + 1 : n].decode(\"utf-8\").rstrip(os.linesep)\r\n n = i\r\n```\r\n\r\nI would fix this soon."
] | 2024-09-03T09:28:29
| 2025-03-26T20:32:22
|
2025-03-26T20:32:22Z
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NONE
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### Python version
Python 3.11.5
### Pymatgen version
2024.7.18
### Operating system version
Windows 11, 24H2
### Current behavior
When using the Outcar class to parse an OUTCAR file from VASP on Windows 11, the magnetization attribute returns an empty tuple (). However, this issue does not occur on Ubuntu 22.04 LTS, where the attribute works as expected.
```
# Windows 11
from pymatgen.io.vasp.outputs import Outcar
outcar = Outcar(filename='OUTCAR')
print(outcar.magnetization) # ==> ()
```
I hope the attched file helps to reproduce this issue (Please remove the suffix .txt of `OUTCAR.txt`).
[OUTCAR.txt](https://github.com/user-attachments/files/16846408/OUTCAR.txt)
### Expected Behavior
I expect the `outcar.magnetization` output on Windows to be identical to the one on Ubuntu 22.04 LTS.
```
# Ubuntu 22.04 LST
from pprint import pprint # prety print
from pymatgen.io.vasp.outputs import Outcar
outcar = Outcar(filename='OUTCAR')
pprint(outcar.magnetization)
({'d': Magnetic moment [ 0. -0. 4.474],
'p': Magnetic moment [-0. 0. 0.029],
's': Magnetic moment [-0. -0. 0.036],
'tot': Magnetic moment [-0. -0. 4.539]},
{'d': Magnetic moment [ 0. 0. -4.474],
'p': Magnetic moment [-0. -0. -0.029],
's': Magnetic moment [-0. -0. -0.036],
'tot': Magnetic moment [-0. 0. -4.539]},
{'d': Magnetic moment [0. 0. 0.],
'p': Magnetic moment [-0. 0.001 0. ],
's': Magnetic moment [ 0. -0. 0.],
'tot': Magnetic moment [-0. 0. 0.]},
{'d': Magnetic moment [0. 0. 0.],
'p': Magnetic moment [-0. -0.001 0. ],
's': Magnetic moment [-0. 0. 0.],
'tot': Magnetic moment [-0. -0. 0.]},
{'d': Magnetic moment [-0. -0. -0.],
'p': Magnetic moment [-0. -0. 0.],
's': Magnetic moment [0. 0. 0.],
'tot': Magnetic moment [ 0. -0. 0.]},
{'d': Magnetic moment [-0. -0. -0.],
'p': Magnetic moment [-0. -0. -0.],
's': Magnetic moment [0. 0. 0.],
'tot': Magnetic moment [ 0. -0. -0.]},
{'d': Magnetic moment [ 0. -0. -0.],
'p': Magnetic moment [ 0. -0. 0.],
's': Magnetic moment [-0. 0. -0.],
'tot': Magnetic moment [-0. -0. 0.]},
{'d': Magnetic moment [ 0. 0. -0.],
'p': Magnetic moment [0. 0. 0.],
's': Magnetic moment [-0. -0. 0.],
'tot': Magnetic moment [-0. 0. 0.]},
{'d': Magnetic moment [-0. 0. -0.],
'p': Magnetic moment [-0. 0. 0.],
's': Magnetic moment [ 0. -0. -0.],
'tot': Magnetic moment [0. 0. 0.]},
{'d': Magnetic moment [ 0. 0. -0.],
'p': Magnetic moment [ 0. 0. -0.],
's': Magnetic moment [-0. -0. -0.],
'tot': Magnetic moment [-0. 0. -0.]})
```
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets56QXFj
| 4,034
|
Fix `LNONCOLLINEAR` match in `Outcar` parser
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[
"Thanks @KylinGuo for reporting this and providing the test OUTCAR. Can I have your permission to include your OUTCAR as a test file for `pymatgen`?",
"> Thanks @KylinGuo for reporting this and providing the test OUTCAR. Can I have your permission to include your OUTCAR as a test file for `pymatgen`?\r\n\r\nIt's my pleasure! Yes, please. ",
"Thanks a lot. All credit goes to you :)",
"thanks for the lightning-fast fix @DanielYang59! 👍 ",
"No problem. Thanks for questioning the usage of `terminate_on_match`, might look closer later :)"
] | 2024-09-03T12:13:13
| 2024-09-05T01:17:15
|
2024-09-04T16:39:13Z
|
CONTRIBUTOR
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### Summary
- Fix `LNONCOLLINEAR` match in `Outcar` parser, to fix #4031
- [x] Add unit test
- Avoid hard coding number of spaces in `re` pattern
### For a future PR
- [**Reverted**] Turn on `terminate_on_match` to early exit upon match, I wish I didn't misunderstand the usage, but early exit should speed up the search?
|
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PR_kwDOACgets56S4Y1
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Fix `ruff` PLC0206 and PLR6104
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[] | 2024-09-03T18:01:45
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2024-09-08T20:37:47Z
|
MEMBER
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- [PLR6104](https://docs.astral.sh/ruff/rules/non-augmented-assignment)
- [PLC0206](https://docs.astral.sh/ruff/rules/dict-index-missing-items/)
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add LRU cache to structure matcher
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"Beautiful! That's an impressive performance gain! \r\n\r\nI guess we should also be aware of the potential [memory leakage issue for `lru_cache` when applied on methods](https://docs.astral.sh/ruff/rules/cached-instance-method/) (I believe a reference to the `cls` would also be held in the case of class methods, **but I could be wrong here**):\r\n\r\n> Using the functools.lru_cache and functools.cache decorators on methods can lead to memory leaks, as the global cache will retain a reference to the instance, preventing it from being garbage collected.\r\n\r\nAlso here is a [more detailed explanation](https://youtu.be/sVjtp6tGo0g?si=8EbBIZDkgIo6nSmM) from [Anthony Sottile](https://github.com/asottile) .\r\n\r\nI guess we could just make it a `staticmethod` to avoid this unless there's some reason to make it `classmethod` that I'm not aware of?",
"I would move the method out of the class and just make it a method. This will resolve the memory leak issue (though I don't think it is a significant problem in our case).",
"I would be very wary of the current hash function. That looks like an extremely expensive hash function. Furthermore, depending on transformations, this hash violates some basic rules on hashes. I would argue it is better to use the formula as a hash.",
"@shyuep, it could be expensive but my concern about using the formula is uniqueness - thinking about polymorphs, displacements, different magnetic configs\r\n\r\nFor transformations, shouldn't the hash change to reflect that the underlying object has changed? Maybe this is my misunderstanding of how hashes should apply to mutables\r\n\r\nMy thinking is: if I run a transformation on a structure to displace a site, the original hash should no longer apply to the transformed structure, right?",
"@esoteric-ephemera The rule for hashes is that they do not have to be unique. Ultimately, the `__eq__` function is what must be unique for different objects. A valid but bad hash function would be `return 42`. This is a common implementation in simple \"Hello World\" type tutorials for many languages.\r\n\r\nSee https://www.geeksforgeeks.org/what-are-hash-functions-and-how-to-choose-a-good-hash-function\r\n\r\nEfficiency and minimizing collisions is the key. But collisions need not be 0 (that is what `__eq__` is for). For a structure, the formula is a pretty good hash function - equal structures definitely have the same formula, and formula is cheap to compute. There will be collisions but they should be relatively minimal (polymorphs basically).",
"@shyuep @esoteric-ephemera An alternative to adding a hash function to Structure that would work for this use case is to create an IStructure copy in the class method and call the new cached function with that copy. It would be something like this:\r\n\r\nchanging the class method to\r\n```py\r\n@classmethod\r\ndef _get_reduced_structure(cls, struct: Structure, primitive_cell: bool = True, niggli: bool = True) -> Structure:\r\n immutable_struct = IStructure.from_dict(struct.as_dict())\r\n return _get_reduced_structure(immutable_struct, primitive_cell, niggli)\r\n```\r\n\r\nand the new function to\r\n\r\n```py\r\n@lru_cache(maxsize=LRU_CACHE_SIZE)\r\ndef _get_reduced_structure(\r\n struct: IStructure, primitive_cell: bool, niggli: bool\r\n) -> Structure:\r\n \"\"\"Helper method to find a reduced structure.\"\"\"\r\n if niggli:\r\n struct = struct.get_reduced_structure(reduction_algo=\"niggli\")\r\n if primitive_cell:\r\n struct = struct.get_primitive_structure()\r\n return Structure.from_dict(struct.as_dict())\r\n```",
"I think we have a good solution now that doesn't require hashing `Structure`, and the failing ruff stuff is unrelated to this PR -should be ready for review",
"Merged. Thanks.",
"Could we push a release relatively soon (or a release candidate)? Would help with builder development on our side"
] | 2024-09-03T21:48:13
| 2024-09-10T13:19:27
|
2024-09-06T15:56:52Z
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CONTRIBUTOR
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## Summary
This adds an LRU cache to the structure matcher, specifically to the StructureMatcher._get_reduced_structure function.
This suggested improvement is motivated by the performance of the AflowPrototypeMatcher._match_prototype function (and in turn the robocrys builder that uses it). We believe this will speed up that calculation by ~288x since the sometimes expensive calculation in StructureMatcher._get_reduced_structure will only need to be performed once per structure rather than the 288 times it is performed now.
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Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows
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[
"[this broke the release workflow](https://github.com/materialsproject/pymatgen/actions/runs/10794178560/job/29939315099)\r\n\r\n> Error: Unable to download artifact(s): Artifact not found for name: artifact\r\n Please ensure that your artifact is not expired and the artifact was uploaded using a compatible version of toolkit/upload-artifact.\r\n\r\nit's also only a partial version bump which should not have been merged. there are 3 uses of `actions/upload-artifact@v3` in `.github/workflows/release.yml` and this PR only updated 1 of them\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/48e7c984e7c981b395af43734b43d2b544ece43d/.github/workflows/release.yml#L39\r\nhttps://github.com/materialsproject/pymatgen/blob/48e7c984e7c981b395af43734b43d2b544ece43d/.github/workflows/release.yml#L60"
] | 2024-09-03T22:40:22
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2024-09-06T15:56:38Z
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Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.1.7.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/actions/download-artifact/releases">actions/download-artifact's releases</a>.</em></p>
<blockquote>
<h2>v4.1.7</h2>
<h2>What's Changed</h2>
<ul>
<li>Update <code>@actions/artifact</code> dependency by <a href="https://github.com/bethanyj28"><code>@bethanyj28</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/325">actions/download-artifact#325</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/actions/download-artifact/compare/v4.1.6...v4.1.7">https://github.com/actions/download-artifact/compare/v4.1.6...v4.1.7</a></p>
<h2>v4.1.6</h2>
<h2>What's Changed</h2>
<ul>
<li>updating <code>@actions/artifact</code> dependency to v2.1.6 by <a href="https://github.com/eggyhead"><code>@eggyhead</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/324">actions/download-artifact#324</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/actions/download-artifact/compare/v4.1.5...v4.1.6">https://github.com/actions/download-artifact/compare/v4.1.5...v4.1.6</a></p>
<h2>v4.1.5</h2>
<h2>What's Changed</h2>
<ul>
<li>Update readme with v3/v2/v1 deprecation notice by <a href="https://github.com/robherley"><code>@robherley</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/322">actions/download-artifact#322</a></li>
<li>Update dependencies <code>@actions/core</code> to v1.10.1 and <code>@actions/artifact</code> to v2.1.5</li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/actions/download-artifact/compare/v4.1.4...v4.1.5">https://github.com/actions/download-artifact/compare/v4.1.4...v4.1.5</a></p>
<h2>v4.1.4</h2>
<h2>What's Changed</h2>
<ul>
<li>Update <code>@actions/artifact</code> by <a href="https://github.com/bethanyj28"><code>@bethanyj28</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/307">actions/download-artifact#307</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/actions/download-artifact/compare/v4...v4.1.4">https://github.com/actions/download-artifact/compare/v4...v4.1.4</a></p>
<h2>v4.1.3</h2>
<h2>What's Changed</h2>
<ul>
<li>Update release-new-action-version.yml by <a href="https://github.com/konradpabjan"><code>@konradpabjan</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/292">actions/download-artifact#292</a></li>
<li>Update toolkit dependency with updated unzip logic by <a href="https://github.com/bethanyj28"><code>@bethanyj28</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/299">actions/download-artifact#299</a></li>
<li>Update <code>@actions/artifact</code> by <a href="https://github.com/bethanyj28"><code>@bethanyj28</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/303">actions/download-artifact#303</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/bethanyj28"><code>@bethanyj28</code></a> made their first contribution in <a href="https://redirect.github.com/actions/download-artifact/pull/299">actions/download-artifact#299</a></li>
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<p><strong>Full Changelog</strong>: <a href="https://github.com/actions/download-artifact/compare/v4...v4.1.3">https://github.com/actions/download-artifact/compare/v4...v4.1.3</a></p>
<h2>v4.1.2</h2>
<ul>
<li>Bump <code>@actions/artifacts</code> to latest version to include <a href="https://redirect.github.com/actions/toolkit/pull/1648">updated GHES host check</a></li>
</ul>
<h2>v4.1.1</h2>
<ul>
<li>Fix transient request timeouts <a href="https://redirect.github.com/actions/download-artifact/issues/249">actions/download-artifact#249</a></li>
<li>Bump <code>@actions/artifacts</code> to latest version</li>
</ul>
<h2>v4.1.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Some cleanup by <a href="https://github.com/robherley"><code>@robherley</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/247">actions/download-artifact#247</a></li>
<li>Fix default for run-id by <a href="https://github.com/stchr"><code>@stchr</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/252">actions/download-artifact#252</a></li>
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<!-- raw HTML omitted -->
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<li><a href="https://github.com/actions/download-artifact/commit/65a9edc5881444af0b9093a5e628f2fe47ea3b2e"><code>65a9edc</code></a> Merge pull request <a href="https://redirect.github.com/actions/download-artifact/issues/325">#325</a> from bethanyj28/main</li>
<li><a href="https://github.com/actions/download-artifact/commit/fdd1595981c1a29187d3de99c28c28a166bc38f7"><code>fdd1595</code></a> licensed</li>
<li><a href="https://github.com/actions/download-artifact/commit/c13dba102f4bb92b3f679fa086db9e2973960ca7"><code>c13dba1</code></a> update <code>@actions/artifact</code> dependency</li>
<li><a href="https://github.com/actions/download-artifact/commit/0daa75ebeac4617faeb127496dbd716b8bcce26e"><code>0daa75e</code></a> Merge pull request <a href="https://redirect.github.com/actions/download-artifact/issues/324">#324</a> from actions/eggyhead/use-artifact-v2.1.6</li>
<li><a href="https://github.com/actions/download-artifact/commit/9c19ed7fe5d278cd354c7dfd5d3b88589c7e2395"><code>9c19ed7</code></a> Merge branch 'main' into eggyhead/use-artifact-v2.1.6</li>
<li><a href="https://github.com/actions/download-artifact/commit/3d3ea8741ef44e86f7392b41e391bde3c36219bd"><code>3d3ea87</code></a> updating license</li>
<li><a href="https://github.com/actions/download-artifact/commit/89af5db8211998d3ca691103a86b0b9362a94286"><code>89af5db</code></a> updating artifact package v2.1.6</li>
<li><a href="https://github.com/actions/download-artifact/commit/b4aefff88e83a2676a730654e1ce3dce61880379"><code>b4aefff</code></a> Merge pull request <a href="https://redirect.github.com/actions/download-artifact/issues/323">#323</a> from actions/eggyhead/update-artifact-v215</li>
<li><a href="https://github.com/actions/download-artifact/commit/8caf195ad4b1dee92908e23f56eeb0696f1dd42d"><code>8caf195</code></a> package lock update</li>
<li><a href="https://github.com/actions/download-artifact/commit/d7a2ec411d177e8ca679ac5969b70be59c322700"><code>d7a2ec4</code></a> updating package version</li>
<li>Additional commits viewable in <a href="https://github.com/actions/download-artifact/compare/v3...v4.1.7">compare view</a></li>
</ul>
</details>
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[Doc/Dev] Inconsistent line numbers in documentation `source` owing to editable install of `pymatgen`
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[
"I'm currently looking into this. I believe this `linkcode_resolve` is working correctly, and the issue should be related to the source code locating mechanism. \r\n\r\nThe final URL is reported on a specific version (the correct behaviour): https://github.com/materialsproject/pymatgen/blob/54046154d3f97d1227b2bfc0f29d0e13ef5bde43/docs/apidoc/conf.py#L365\r\n\r\nHowever the source code locating is done on `sys.modules`, meaning it would depend on what version of `pymatgen` is installed on the person what called `linkcode_resolve`, and as developers tend to install `pymatgen` in editable mode, the page number in editable package and the published static version might be inconsistent.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/54046154d3f97d1227b2bfc0f29d0e13ef5bde43/docs/apidoc/conf.py#L345\r\n\r\nI believe this would be resolved by #4056, i.e. automate the docs building process and install corresponding static version of pymatgen.\r\n\r\n\r\n\r\n"
] | 2024-09-04T07:41:42
| 2025-02-25T09:24:09
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CONTRIBUTOR
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The source code line numbers generated from: https://github.com/materialsproject/pymatgen/blob/edcd4654cc5048d7f0f00417d82755d98b03b739/docs/apidoc/conf.py#L360
Seems to have off-by-one errors for some classes, but not all.
For example in https://pymatgen.org/pymatgen.alchemy.html, pointer to `AbstractStructureFilter` is correct, but off-by-one for `ChargeBalanceFilter`
<img width="833" alt="image" src="https://github.com/user-attachments/assets/725df18c-4821-4d4d-be04-911252a7e890">
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PR_kwDOACgets56WuxS
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Fix incorrect attribute name in `Lobster.outputs.Cohpcar` docstring
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[
"I will merge this as it only changes the doc string. Thanks @DanielYang59 !",
"Thanks for reviewing!"
] | 2024-09-04T08:00:08
| 2024-09-10T13:18:57
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2024-09-06T14:51:29Z
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CONTRIBUTOR
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### Summary
- Fix incorrect attribute name in `Lobster.outputs.Cohpcar` docstring, `orb_cohp` -> `orb_res_cohp`
https://github.com/materialsproject/pymatgen/blob/edcd4654cc5048d7f0f00417d82755d98b03b739/src/pymatgen/io/lobster/outputs.py#L261
```python
from pymatgen.io.lobster.outputs import Cohpcar
cohp = Cohpcar(filename="COHPCAR.lobster")
print(dir(cohp))
```
```['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__getstate__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', '_get_bond_data', 'are_cobis', 'are_coops', 'are_multi_center_cobis', 'cohp_data', 'efermi', 'energies', 'is_spin_polarized', 'orb_res_cohp']```
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I_kwDOACgets6VaCU6
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[CI] Unit test of `boltztrap2` generate files inplace
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| 2024-10-26T02:03:23
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2024-10-25T21:25:48Z
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CONTRIBUTOR
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Should use temporary scratch directory such that unit test wouldn't generate files inplace.
Test of `boltztrap2` generate files locally:
- [x] `TestBztTransportProperties` generate `bztTranspoPros.json.gz`
- [x] `TestBztInterpolator` generates `bztinterp.json.gz`
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I_kwDOACgets6VaDmP
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[Enhancement] Enable `terminate_on_match` for `Outcar` parser
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[
"Another related proposal, perhaps we should consider:\r\n- Write a lazy version of `read_pattern`, to get a collection of all patterns and walk through the file once\r\nAND/OR\r\n- State machine\r\n- Refactor `read_pattern` to process in memory"
] | 2024-09-05T02:27:48
| 2024-11-25T07:26:07
|
CONTRIBUTOR
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Re-post from https://github.com/materialsproject/pymatgen/pull/4034#discussion_r1743594451, need investigation of implications of turning on `terminate_on_match` of `read_pattern` for `io.vasp.outputs.Outcar` parser (at least for those "global" tags that is consistent across the entire run). Sounds like this would speed up initialization by early exit upon hit.
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[Enhancement] Update `incar_parameters.json` file under `io.vasp`
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[] | 2024-09-05T02:47:11
| 2024-09-05T10:34:46
|
CONTRIBUTOR
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Post from https://github.com/materialsproject/pymatgen/pull/4020#discussion_r1734263672, there are quite some INCAR tags missing from `incar_parameters.json` (the type recording file), perhaps we should update it.
We also want to [make this json file more permissive](https://github.com/materialsproject/pymatgen/pull/4020#discussion_r1734399836), i.e. don't remove those tags absent (deprecated) from VASP wiki.
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I_kwDOACgets6VgnZn
| 4,043
|
Free energy correction
|
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[] | 2024-09-05T17:26:17
| 2024-09-05T17:26:18
|
MEMBER
|
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### Feature Requested
With the advent of universal machine learning potentials (MLPs), we now have the capability of generating free energy corrections such as vibrational entropy at specific temperatures. This allows the generation of finite temperature phase diagrams.
### Proposed Solution
I propose to implement a `FreeEnergyCorrection` in `pymatgen.entries`. Given this serves a different purpose from the current corrections, it should be in a different module (e.g., `pymatgen.entries.thermodynamics`. These FreeEnergyCorrections can be applied to a set of ComputedEntries and then used to generate the finite T phase diagram without any other code changes.
@rul048 will implement.
### Relevant Information
See https://github.com/materialsvirtuallab/matcalc on how to obtain phonon corrections with MLPs.
|
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I_kwDOACgets6VhgYV
| 4,044
|
Use `astral-sh/setup-uv` in CI
|
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[
"Thanks! I would have a look at this later. \r\n\r\nI'm not hoping `enable-cache: true` would work for our test workflow because I believe [GitHub-hosted runner is disposed of after each run](https://docs.github.com/en/actions/writing-workflows/choosing-where-your-workflow-runs/choosing-the-runner-for-a-job).\r\n> Cache the installed version of uv to speed up consecutive runs on self-hosted runners\r\n\r\n> If you use a GitHub-hosted runner, each job runs in a fresh instance of a runner image specified by runs-on."
] | 2024-09-05T19:45:34
| 2024-09-13T10:58:14
|
2024-09-13T10:58:14Z
|
MEMBER
|
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`uv` now has 1st-party GitHub Action support with built-in caching which could speedup our `test.yml` workflow. not sure if it clashes with our `mamba` setup
https://github.com/materialsproject/pymatgen/blob/1404220105d4dc1e421ac603b1cb83daf6b085c5/.github/workflows/test.yml#L64-L72
but if not, would be good to adopt this. should only require adding a new step:
```yml
- name: Set up uv
uses: astral-sh/setup-uv@v2
with:
enable-cache: true
```
|
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I_kwDOACgets6Vkzx4
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[BUG] Entire `BoltztrapPlotter` is broken
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[] | 2024-09-06T03:51:06
| 2024-09-06T11:20:33
|
CONTRIBUTOR
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After [installing `BoltzTraP` in CI](https://github.com/materialsproject/pymatgen/pull/3985), turns out the `BoltztrapPlotter` is completely broken after #3237, see [the CI log](https://github.com/materialsproject/pymatgen/actions/runs/10731988727/job/29762940665?pr=3985).
The entire `TestBoltztrapPlotter` has been skipped for now.
Note: we need to [examine the generated plot](https://github.com/materialsproject/pymatgen/pull/3985#discussion_r1726850254) to really determine whether it's "fixed", cannot just rely on CI passes for plotters.
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I_kwDOACgets6Vq02E
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`ValueErrors` in the `CoherentInterfaceBuilder`
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[] | null |
[
"Hi @nightroxide thanks for reporting this. This is a duplicate of #3990 and has been fixed by #3992. "
] | 2024-09-06T18:59:45
| 2024-09-08T20:03:08
|
2024-09-07T10:31:53Z
|
NONE
|
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### Python version
Python 3.12.5
### Pymatgen version
2024.8.9
### Operating system version
Windows 11
### Current behavior
Value error when trying to make interfaces
### Expected Behavior
A list of possible homojunction structures
### Minimal example
```Python
from pymatgen.analysis.interfaces import CoherentInterfaceBuilder
from pymatgen.core.structure import Structure
from mp_api.client import MPRester
id = "mp-13"
mpapi_key="key here"
with MPRester(mpapi_key, mute_progress_bars=True) as mpr:
# get substrate data
summary = mpr.materials.summary.search(material_ids=id)[0]
s = substrate_summary.structure
# make a simple homojunction
cib=CoherentInterfaceBuilder(s,s,(1,0,0),(1,1,1))
homojunctions=cib.get_interfaces(cib.terminations[0],film_thickness=8,substrate_thickness=8)
```
### Relevant files to reproduce this bug
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[7], line 12
9 summary = mpr.materials.summary.search(material_ids=id)[0]
10 s = substrate_summary.structure
---> 12 cib=CoherentInterfaceBuilder(s,s,(1,0,0),(1,1,1))
13 homojunctions=cib.get_interfaces(cib.terminations[0],film_thickness=8,substrate_thickness=8)
File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\analysis\interfaces\coherent_interfaces.py:53, in CoherentInterfaceBuilder.__init__(self, substrate_structure, film_structure, film_miller, substrate_miller, zslgen)
50 self.substrate_miller = substrate_miller
51 self.zslgen = zslgen or ZSLGenerator(bidirectional=True)
---> 53 self._find_matches()
54 self._find_terminations()
File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\analysis\interfaces\coherent_interfaces.py:82, in CoherentInterfaceBuilder._find_matches(self)
60 film_sg = SlabGenerator(
61 self.film_structure,
62 self.film_miller,
(...)
68 reorient_lattice=False, # This is necessary to not screw up the lattice
69 )
71 sub_sg = SlabGenerator(
72 self.substrate_structure,
73 self.substrate_miller,
(...)
79 reorient_lattice=False, # This is necessary to not screw up the lattice
80 )
---> 82 film_slab = film_sg.get_slab(shift=0)
83 sub_slab = sub_sg.get_slab(shift=0)
85 film_vectors = film_slab.lattice.matrix
File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\core\surface.py:1147, in SlabGenerator.get_slab(self, shift, tol, energy)
1145 # Center the slab layer around the vacuum
1146 if self.center_slab:
-> 1147 struct = center_slab(struct)
1149 # Reduce to primitive cell
1150 if self.primitive:
File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\core\surface.py:762, in center_slab(slab)
759 all_indices = list(range(len(slab)))
761 # Get a reasonable cutoff radius to sample neighbors
--> 762 bond_dists = sorted(nn[1] for nn in slab.get_neighbors(slab[0], 10) if nn[1] > 0)
763 # TODO (@DanielYang59): magic number for cutoff radius (would 3 be too large?)
764 cutoff_radius = bond_dists[0] * 3
File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\core\structure.py:1662, in IStructure.get_neighbors(self, site, r, include_index, include_image)
1641 def get_neighbors(
1642 self,
1643 site: PeriodicSite,
(...)
1646 include_image: bool = False,
1647 ) -> list[PeriodicNeighbor]:
1648 """Get all neighbors to a site within a sphere of radius r. Excludes the
1649 site itself.
1650
(...)
1660 PeriodicNeighbor
1661 """
-> 1662 return self.get_all_neighbors(r, include_index=include_index, include_image=include_image, sites=[site])[0]
File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\core\structure.py:1997, in IStructure.get_all_neighbors(self, r, include_index, include_image, sites, numerical_tol)
1995 if sites is None:
1996 sites = self.sites
-> 1997 center_indices, points_indices, images, distances = self.get_neighbor_list(
1998 r=r, sites=sites, numerical_tol=numerical_tol
1999 )
2000 if len(points_indices) < 1:
2001 return [[]] * len(sites)
File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\core\structure.py:1782, in IStructure.get_neighbor_list(self, r, sites, numerical_tol, exclude_self)
1780 lattice_matrix = np.ascontiguousarray(self.lattice.matrix, dtype=float)
1781 pbc = np.ascontiguousarray(self.pbc, dtype=int)
-> 1782 center_indices, points_indices, images, distances = find_points_in_spheres(
1783 cart_coords,
1784 site_coords,
1785 r=r,
1786 pbc=pbc,
1787 lattice=lattice_matrix,
1788 tol=numerical_tol,
1789 )
1790 cond = np.array([True] * len(center_indices))
1791 if exclude_self:
File src\\pymatgen\\optimization\\neighbors.pyx:48, in pymatgen.optimization.neighbors.find_points_in_spheres()
ValueError: Buffer dtype mismatch, expected 'const int64_t' but got 'long'
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| 2,511,273,800
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PR_kwDOACgets56tixd
| 4,048
|
Pascal-case `PMG_VASP_PSP_DIR_Error`
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[] | 2024-09-06T22:28:02
| 2024-09-06T22:39:04
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2024-09-06T22:39:03Z
|
MEMBER
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`PMG_VASP_PSP_DIR_Error` is a class and hence should use PascalCase.
no downstream effects expected from this (strictly speaking) breaking change.
`PMG_VASP_PSP_DIR_Error` was only added 3 weeks ago in https://github.com/materialsproject/pymatgen/pull/3999 and [the last release](https://github.com/materialsproject/pymatgen/releases/tag/v2024.8.9) was a month ago.
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I_kwDOACgets6VtTFT
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|
BUG: INCAR Updates not working
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[
"Tagging @esoteric-ephemera and @janosh as this is likely due to the move from atomate2 to pymatgen inputs. ",
"[`incar` is a `VaspInput` property](https://github.com/materialsproject/pymatgen/blob/15dc137c9325b58e7ce6b14bc14bd434e5f907f3/src/pymatgen/io/vasp/inputs.py#L2910) which returns a new `Incar` every time it's called if `VaspInput['incar']` is a `dict`. the new `Incar` is modified in place `vis.incar.update({\"NPAR\": 4})` but then immediately discarded since it's not connected to `vis` in any way. this pitfall could be avoided by converting `incar` `dicts` to `Incar` in `__init__` and then always return `self[\"INCAR\"]`\r\n```diff\r\n @property\r\n def incar(self) -> Incar:\r\n \"\"\"INCAR object.\"\"\"\r\n- return Incar(self[\"INCAR\"]) if isinstance(self[\"INCAR\"], dict) else self[\"INCAR\"]\r\n+ return self[\"INCAR\"]\r\n```\r\n",
"@janosh I am happy with any solution that works. Should we make a change in pymatgen then?",
"Thanks for finding / correcting this!"
] | 2024-09-07T07:38:29
| 2024-09-09T16:57:19
|
2024-09-07T14:38:10Z
|
MEMBER
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Currently, this line https://github.com/materialsproject/atomate2/blob/f14586c7b29a7d5cbf7eabfe399728ab6362e0e7/src/atomate2/vasp/files.py#L195 does not have the intended effect of updating the INCAR.
This reproduces the error:
```py
from atomate2.vasp.sets.base import VaspInputGenerator
from mp_api.client import MPRester
mpr = MPRester()
structure = mpr.get_structure_by_material_id("mp-84")
vis = VaspInputGenerator().get_input_set(
structure=structure, potcar_spec=True
)
print(vis.incar)
vis.incar.update({"NPAR": 4})
print(vis.incar)
```
(pymatgen version: 2024.8.9)
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I_kwDOACgets6Vsxue
| 4,049
|
pymatgen no "_init_.py" file
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[
"this is not enough information to understand your problem. please paste a code snippet and error message and what you're trying to accomplish",
"I guess he refers to the fact that [we don't have a `__init__.py` file for the first level `pymatgen` package](https://github.com/materialsproject/pymatgen/tree/master/src/pymatgen) (is it intended?), which would make `pymatgen` a namespace package. And I didn't notice this before.\r\n\r\nWhich effectively means we cannot access subpackages directly via `pymatgen` namespace:\r\n```py\r\nimport pymatgen\r\n\r\nprint(dir(pymatgen)) # >>> ['__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__']\r\n\r\nprint(dir(pymatgen.io.vasp.Outcar)) # >>> AttributeError: module 'pymatgen' has no attribute 'io'\r\n```\r\n\r\nUntil we import subpackages into the `pymatgen` namespace:\r\n```py\r\nimport pymatgen\r\nfrom pymatgen.io.vasp import Outcar\r\n\r\nprint(dir(pymatgen)) # >>> ['__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', 'core', 'electronic_structure', 'entries', 'io', 'symmetry', 'util']\r\n\r\nprint(dir(pymatgen.io.vasp.Outcar)) # >>> no error this time\r\n```\r\n\r\nI also noticed the following code demo from our docs, which looks super weird (thought `pmg` would be a shorthand for `pymatgen`, not `pymatgen.core`):\r\nhttps://github.com/materialsproject/pymatgen/blob/15dc137c9325b58e7ce6b14bc14bd434e5f907f3/docs/index.md?plain=1#L181\r\n\r\n\r\nAnd the following funny usage (there're some other cases):\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/15dc137c9325b58e7ce6b14bc14bd434e5f907f3/src/pymatgen/io/openff.py#L10-L13\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/15dc137c9325b58e7ce6b14bc14bd434e5f907f3/src/pymatgen/io/openff.py#L164\r\n\r\n\r\n",
"> I guess he refers to the fact that [we don't have a __init__.py file for the first level pymatgen package](https://github.com/materialsproject/pymatgen/tree/master/src/pymatgen) (is it intended?),\r\n\r\nyes, i remember that was a deliberate change to `pymatgen` before i started getting involved. i believe the motivation was to make pymatgen more modular and facilitate external addon packages like [pymatgen-io-validation](https://github.com/materialsproject/pymatgen-io-validation), [pymatgen-analysis-diffusion](https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion), etc. though i don't actually understand why it was necessary or how it helps. see the relevant commit https://github.com/materialsproject/pymatgen/commit/f462d35cab98d15f6abbbb9d3eec4d0ec53e49a8 from @shyup in Mar 2021",
"It was deliberate. As for why, note the existence of pymatgen-analysis-defects, pymatgen-io-validation, etc. ",
"> As for why, note the existence of pymatgen-analysis-defects, pymatgen-io-validation, etc.\r\n\r\nhow does having a central `__init__.py` clash with pymatgen-analysis-defects, pymatgen-io-validation, ...?",
"There may be instances where we want to create a pymatgen/ml namespace. Also, namespaces are hierarchical. "
] | 2024-09-07T08:35:03
| 2024-09-07T15:30:34
|
2024-09-07T14:22:31Z
|
NONE
|
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### Python version
Python3.9.19
### Pymatgen version
2024.8.9
### Operating system version
Linux: miniconda
### Current behavior
In the conda env, pip install pymatgen, no "_init_.py" file
### Expected Behavior
_init_.py" file
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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I_kwDOACgets6Vsx4j
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pymatgen no "_init_.py" file
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[
"closing as duplicate of #4049."
] | 2024-09-07T08:36:58
| 2024-09-07T10:57:55
|
2024-09-07T10:57:42Z
|
NONE
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### Python version
Python3.9.19
### Pymatgen version
2024.8.9
### Operating system version
Linux: miniconda
### Current behavior
In conda env, pip install, no "_init_py" file
### Expected Behavior
"_init_py" file
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets56u3mx
| 4,052
|
Fix in-place `VaspInput.incar` updates having no effect if `incar` is dict (not `Incar` instance)
|
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[
"Thanks @janosh ! "
] | 2024-09-07T14:27:58
| 2024-09-07T15:27:28
|
2024-09-07T14:38:09Z
|
MEMBER
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closes #4051
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PR_kwDOACgets56wgno
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Avoid importing namespace package `pymatgen` directly
|
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[
"> [Question] Should we recommend the following alias (I thought pmg would be a shorthand of pymatgen instead of pymatgen.core):\r\n\r\nno strong opinion but leaning towards not proliferating that usage",
"> > [Question] Should we recommend the following alias (I thought pmg would be a shorthand of pymatgen instead of pymatgen.core):\r\n> \r\n> no strong opinion but leaning towards not proliferating that usage\r\n\r\nOkay thanks for your reply, we might just `from pymatgen.core import xxx` (not the wild card `*`) then. And we might need to rebuild docs again (perhaps add rebuilding docs as an automate workflow as well?).",
"> perhaps add rebuilding docs as an automate workflow as well?\r\n\r\nyes, that should have been done a long time ago. in particular, there's no reason to keep the generated HTML for docs under version control. it's a major history pollutant",
"> > perhaps add rebuilding docs as an automate workflow as well?\r\n> \r\n> yes, that should have been done a long time ago.\r\n\r\nOkay I would have a look at this if you don't have much time ATM :)\r\n\r\n\r\n> in particular, there's no reason to keep the generated HTML for docs under version control. it's a major history pollutant\r\n\r\nYes!"
] | 2024-09-08T02:06:50
| 2024-09-09T02:12:38
|
2024-09-08T15:49:35Z
|
CONTRIBUTOR
|
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### Summary
- Avoid importing namespace package `pymatgen` directly
- [**Question**] Should we recommend the following alias (I thought `pmg` would be a shorthand of `pymatgen` instead of `pymatgen.core`): https://github.com/materialsproject/pymatgen/blob/15dc137c9325b58e7ce6b14bc14bd434e5f907f3/docs/index.md?plain=1#L181
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PR_kwDOACgets56wmYo
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|
Make AimsSpeciesFile a dataclass
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[] | 2024-09-08T04:13:55
| 2024-09-08T14:23:49
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2024-09-08T14:23:49Z
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CONTRIBUTOR
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As recommended by @janosh in #3878
## Summary
Major changes:
- Make AimsSpeciesFile a dataclass
## Todos
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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PR_kwDOACgets56xyyD
| 4,055
|
Fix typo in `Cp2kOutput.parse_hirshfeld` `add_site_property("hirshf[i->'']eld")`
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[] | 2024-09-08T21:14:15
| 2024-09-08T21:37:54
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2024-09-08T21:37:53Z
|
MEMBER
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only important change in this PR in the title, rest is linting/refactoring
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I_kwDOACgets6VxW9z
| 4,056
|
[Docs] Automate docs generation and exclude HTML from main branch
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[] | 2024-09-09T02:10:28
| 2025-01-28T17:39:24
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CONTRIBUTOR
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Post from https://github.com/materialsproject/pymatgen/pull/4053#issuecomment-2336725417:
- [ ] Add docs builder as an automatic workflow, I think we already have one `jekyll-gh-pages.yml` but it doesn't seem to be used
- [ ] Exclude generated HTMLs from main branch, we would need a dedicated branch just to host docs
This would also resolve:
- https://github.com/materialsproject/pymatgen/issues/4038
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PR_kwDOACgets564gkK
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|
Fix `apply_operation(fractional=True)`
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[
"This fixed implementation is tested and shown to be working in the attached notebook as well",
"Done!\r\nAlso checked that this test fails with the old code (for `fractional=True`), but works all fine with the new code."
] | 2024-09-09T17:39:59
| 2024-09-09T22:01:15
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2024-09-09T22:01:15Z
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CONTRIBUTOR
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## Summary
`Structure.apply_operation()` fails when using the `fractional=True` operation.
The issue is that the ``SymmOp`` is applied to the site frac coords (in the original lattice), but then these new frac coords (in the old basis) are used directly with the new (transformed) lattice, giving a 'doubled' transformation and messing with the output.
Fix added here, matching the implementation in [`doped`](https://github.com/SMTG-Bham/doped/blob/develop/doped/utils/symmetry.py#L211) (which also has a couple more options and a cleaner implementation).
MWE:
<img width="728" alt="image" src="https://github.com/user-attachments/assets/96246dc4-1f92-4dc3-969d-cc36ce2c171a">
<img width="701" alt="image" src="https://github.com/user-attachments/assets/b5090429-09bf-4ea9-807b-d65da6ba0aa8">
(Notebook and structure being used attached too as always 😉 , with more examples)
[Pymatgen_SymmOp_Fix_PR.zip](https://github.com/user-attachments/files/16934325/Pymatgen_SymmOp_Fix_PR.zip)
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PR_kwDOACgets56_fUG
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Use distinct names for artifacts
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[
"@janosh The [release just failed](https://github.com/materialsproject/pymatgen/actions/runs/10794178560) and I think this should solve it.",
"thanks @ab5424! 👍 could you also bump the `sdist` `upload-artifacts`?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/48e7c984e7c981b395af43734b43d2b544ece43d/.github/workflows/release.yml#L39",
"@janosh Sorry I missed that one, done 👍"
] | 2024-09-10T14:18:36
| 2024-09-13T14:10:09
|
2024-09-10T17:50:28Z
|
CONTRIBUTOR
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## Summary
Major changes:
- `upload-artifacts` was recently bumped to `v4` (see #4037). I think that this breaks the release workflow because from `v4` upwards they are not allowed to have the same name anymore (see https://github.com/actions/upload-artifact/issues/478). This PR should fix it, according to [this suggestion](https://github.com/actions/upload-artifact/issues/478#issuecomment-1885470013)
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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I_kwDOACgets6WGoiW
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get_band_structure_from_vasp_multiple_branches
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[
"Hi @Nokimann thanks for reporting this. I could confirm this issue introduced by #3690, would fix ASAP.\r\n\r\nMeanwhile is it possible to share your files such that we could enhance unit test (this function is not covered by unit test)? Thanks a lot!\r\n\r\n\r\n"
] | 2024-09-11T02:35:44
| 2024-09-11T05:15:29
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NONE
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### Python version
PYthon 3.12.5
### Pymatgen version
2024.8.9
### Operating system version
CentOS 7.6
### Current behavior
in pymatgen/io/vasp/output.py
`get_band_structure_from_vasp_multiple_branches`
`if os.path.isfile(f"{dir_name}/branch_0"):`
### Expected Behavior
`get_band_structure_from_vasp_multiple_branches`
the line `if os.path.isfile(f"{dir_name}/branch_0"):`
check the `filename` for the `dirname`
So, it return `None` always.
I don't know why the newest version changed.
### Minimal example
```Python
from pymatgen.io.vasp.outputs import get_band_structure_from_vasp_multiple_branches
bs = get_band_structure_from_vasp_multiple_branches('./bs')
print(bs == None)
```
### Relevant files to reproduce this bug
_No response_
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Fix branch directory check in `io.vasp.outputs.get_band_structure_from_vasp_multiple_branches`
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[
"@shyuep Perhaps you could review this as well? \r\n\r\nI tried to add a unit test but I don't have any real test file for \"VASP multi-branch bandstructure calculation\" and had to create a dummy one instead, so I guess this is as far as I could get :)\r\n",
"@shyuep Can you review this please? I guess this has been lost :)"
] | 2024-09-11T05:26:08
| 2025-05-01T21:34:20
|
CONTRIBUTOR
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### Summary
- Fix branch directory check in `io.vasp.outputs.get_band_structure_from_vasp_multiple_branches`, to fix #4060
- [ ] Improve unit test (waiting for data, I don't have experience with "VASP multi-branch bandstructure calculation")
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(Not) Use `setup-uv` in CI tests workflow
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[
"@janosh Turns out there isn't much speed advantage for `setup-uv` over `pip install uv`, the first time running `setup-uv` is even slower. Perhaps we just keep things simple (also easy to maintain) and still use `pip install uv` for now.",
"> Turns out there isn't much speed advantage for `setup-uv` over `pip install uv`, the first time running `setup-uv` is even slower.\r\n\r\ngood to know. i wasn't expecting it to be faster on a cold cache though. mainly hoping `setup-uv` would have good caching and be faster on subsequent runs",
"> i wasn't expecting it to be faster on a cold cache though. mainly hoping `setup-uv` would have good caching and be faster on subsequent runs\r\n\r\nTests on second runs (`native mamba + native uv (second run)`) didn't show obvious advantage. Probably because [our installation stage](https://github.com/materialsproject/pymatgen/actions/runs/10842026588/job/30086994748?pr=4063) is not bottlenecked by dependency download, see extracted debug info below:\r\n\r\n<img width=\"699\" alt=\"image\" src=\"https://github.com/user-attachments/assets/47cdc67b-8137-4b50-88b0-0ac933417f0a\">\r\n\r\n---\r\n\r\n`pip install torch` (**70% of the total time**):\r\n```\r\n2024-09-13 02:33:35.316 torch install starts (`Collecting torch==2.2.1 ...`)\r\n2024-09-13 02:34:05.962 All downloading finished (`Installing collected packages: ...`)\r\n2024-09-13 02:34:42.070 Install finished (`Successfully installed ...`)\r\n```\r\n\r\n`uv pip install -e .[extras]`:\r\n```\r\n2024-09-13 02:34:42.691 pymatgen dependency install starts (`DEBUG Found static `pyproject.toml` for: pymatgen`)\r\n2024-09-13 02:34:52.577 DEBUG Building: pymatgen @ file:///home/runner/work/pymatgen/pymatgen\r\n2024-09-13 02:35:10.553 DEBUG Finished building: pymatgen @ file:///home/runner/work/pymatgen/pymatgen\r\n```\r\n",
"thanks so much for your benchmarking! ❤️ that's super useful for the decision at hand _and_ later reference. i agree seems there's not much point in adopting `setup-uv`.\r\n\r\nmerging now. thanks for cleaning up the needless build-time deps install",
"> that's super useful for the decision at hand and later reference\r\n\r\nNo problem! That's what I was hoping too. Looks like `torch` is the huge bottleneck, hoping #3826 could have a solution soon :)"
] | 2024-09-12T04:14:27
| 2024-09-13T11:01:30
|
2024-09-13T10:58:13Z
|
CONTRIBUTOR
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### Summary
- [Use `setup-uv` in CI tests workflow](https://docs.astral.sh/uv/guides/integration/github/), to close #4044
## Performance benchmark
The following word "native" refers to package installed by native github action setups: `setup-Python/micromamba/uv`
**NOTE**: `setup-uv` installer might provide caching function, so the run time might be slower for the first run
### Dependency installation time
Time (in seconds) is reported on the `Install pymatgen and dependencies` stage for "split 1", excluding conda and optional Ubuntu dependencies
| | Ubuntu 22.04 | Windows 11 | MacOS |
|---------------------------|--------------|------------|-------|
| native mamba + pip | 88 | 235 | 26 |
| native mamba + uv | 85 | 150 | 28 |
| native mamba + native uv (first run) | 93 | 254 | 24 |
| native mamba + native uv (second run) | 97 | 141 | 23 |
**Conclusion**: not much difference between `setup-uv` and `pip install uv`, and [the M1 MacOS runner](https://docs.github.com/en/actions/using-github-hosted-runners/using-github-hosted-runners/about-github-hosted-runners) is just another level.
### Pytest running time
Time (in seconds) is reported for "split 1"
| | Ubuntu 22.04 | Windows 11 | MacOS |
|---------------------------|--------------|------------|-------|
| native mamba + pip | 187 | 262 | 101 |
| native mamba + uv | 181 | 249 | 114 |
| native mamba + native uv (first run) | 183 | 258 | 100 |
| native mamba + native uv (second run) | 186 | 249 | 100 |
**Conclusion**: Actual test running time is largely not influenced (as expected).
### Link to above workflow runs
| | Link |
|---------------------------|------|
| native mamba + pip | https://github.com/materialsproject/pymatgen/actions/runs/10824932738 |
| native mamba + uv | https://github.com/materialsproject/pymatgen/actions/runs/10824062208 |
| native mamba + native uv (first run) | https://github.com/materialsproject/pymatgen/actions/runs/10824811886 |
| native mamba + native uv (second run) | https://github.com/materialsproject/pymatgen/actions/runs/10824892797 |
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I_kwDOACgets6Wao6J
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Fix `ruff` PERF401
|
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would be good to refactor or individually ignore the 144 violations of [PERF401](https://docs.astral.sh/ruff/rules/manual-list-comprehension) in the code base so we can enable that rule for future PRs
https://github.com/materialsproject/pymatgen/blob/6bb293896945106476d6676cb2b65550d791edb5/pyproject.toml#L218
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Add support to LOBSTER >=5.0
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"@naik-aakash thanks! I was about to start doing it myself 🙈",
"I think we also don't have a parser for the polarization file 😅. But maybe, this can be done in a subsequent pull request ",
"@naik-aakash should we maybe get a part of this merged as a bug fix and do the other things later?",
"> @naik-aakash should we maybe get a part of this merged as a bug fix and do the other things later?\r\n\r\nI was in contact with the LOBSTER developers and they will release a hotfix this week for a bug that prevents the LCFO anaylsis currently. I would suggest to wait with merging until then. ",
"> @naik-aakash should we maybe get a part of this merged as a bug fix and do the other things later?\r\n\r\nHi @JaGeo , we can do this. I can add test for this updates in next 1 or 2 days. \r\n\r\nAlso, a bug was found in the new MOFE feature. Thus, I could not generate test files or write parsers for outputs for that specific analysis. In anycase a new version for LOBSTER is expected soon. ",
"Hi @JaGeo, this PR can now be reviewed. I am happy to address any issues that are spotted or needs some change. ",
"Hi @JaGeo, I have now addressed all the review comments where possible. For the `Cohpcar `and `Doscar` parsers, I do not see any other way to extract file types from the data within the file itself, so I have left them as they are, and it seems to work for now.",
"So far, we mostly let users choose the filetype (eg Icohps, Icoops). I would do the same here.",
"> So far, we mostly let users choose the filetype (eg Icohps, Icoops). I would do the same here.\r\n\r\nOh, okay. This way sounds much simpler. I have now added the `is_lcfo` arg to the relevant parsers with the docstrings. ",
"Hi @shyuep , now all tests also pass after last merge. If there are no specific comments on the changes, PR is ready to be merged.",
"Great. Thanks!"
] | 2024-09-13T07:47:16
| 2024-10-17T16:32:45
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2024-10-17T16:32:39Z
|
CONTRIBUTOR
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## Summary
This PR aims to update the `lobster.io.inputs` and `lobster.io.outputs` modules to support LOBSTER v5. There are some changes in v5.1, mainly with the format of output files. Also, new output files are generated from fragment orbital analysis. A few new keywords have also been added.
# Todos
- [x] add new keywords from lobster >= v5 to the inputs module
- [x] update ICOHPLIST parser
- [x] update GROSSPOP parser
- [x] update Lobsterout parser
- [x] Add parser for POLARIZATION.lobster lobster file (LOBSTER >=5.0 generates this)
- [x] Add parser for BWDF.lobster lobster file
- [x] Add support for `COXXCAR.LCFO.lobster, ICOXXLIST.LCFO.lobster, GROSSPOP.LCFO.lobster` file parsing
- [x] Add support for `DOSCAR.LCFO.lobster, CHARGE.LCFO.lobster` file parsing
- [x] Add attributes to lobsterout parser for MOFE generated files
- [x] Add tests
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Fix all `ruff` DOC202
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fix a dozen functions/methods that document return values but didn't actually return anything
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Fix `monty` imports, enhance test for `Outcar` parser to cover uncompressed format
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[
"@shyuep I guess this PR has been forgotten, can you please review this? Thanks!",
"Thanks!"
] | 2024-09-15T04:09:58
| 2025-03-26T20:58:33
|
2025-03-26T20:32:21Z
|
CONTRIBUTOR
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### Summary
- Test `monty` fix for reverse readline, close #4033 and close #4237
- Replace `reverse_readline` with faster `reverse_readfile`
- Fix incorrect `monty` imports
- [x] Enhance unit test for reported Outcar parser (need to test **unzipped format**)
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Update addons.md
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[] | 2024-09-15T19:56:30
| 2024-09-18T01:13:01
|
2024-09-18T01:13:01Z
|
CONTRIBUTOR
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Added DebyeCalculator as an external tool
## Summary
Major changes:
- feature 1: ...
- fix 1: ...
## Todos
If this is work in progress, what else needs to be done?
- feature 2: ...
- fix 2:
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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fix phase diagram break from 41e6d99
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[
"Sigh... why does this have to happen again?!\r\n",
"I have released an emergency version. Thanks for tracking this down.",
"@yang-ruoxi thanks for finding and fixing! 👍 \r\n\r\n\r\n> Sigh... why does this have to happen again?!\r\n\r\n@shyuep you should have asked for a unit test to prevent future regressions.",
"Thanks for that helpful suggestion. \n\nThis is a plotting code. I don't expect @yang-ruoxi to implement a unittest to check annotation positions. Also, I did ask that we avoid unnecessary cosmetic changes. Not like it did any good what I asked. Switching dict.update to the assignment syntax falls under that category and I am not even sure it is an improvement in code aesthetics even. ",
"@shyuep thanks for the speedy release. \r\n@janosh while unit test may help, I don't think pymatgen users are expected, or able to, write tests for all possible scenarios of every class they consume. There should be scrutiny over multi-file changes that involve hundreds of lines of code. ",
"@yang-ruoxi i disagree. 100% coverage should absolutely be the goal even if we never get there. But a bug fix PR is an obvious place to inch towards it, since code breaking is a strong signal that it needs a test.\n\n@shyuep shorter code is generally preferred",
"@janosh While unittests are always preferred, I will state again that I do not expect @yang-ruoxi to implement a unittest to check annotations - which is what this bug fix is about. Also, a proper response would have been to apologize for making the mistake (which I did not see anywhere in the responses) rather than just delivering these comebacks that suggest the onus is on others. ",
"> Also, a proper response would have been to apologize for making the mistake\r\n\r\nlet's not pretend you care about apologies. mistakes happen, esp. in a code base as large and with as much suboptimal code as pymatgen. i regret that it did. but the important thing is to have guard rails in place that allow you to code with confidence. that requires adding unit tests whenever something breaks which you could have asked me to write given i introduced the bug instead of merging immediately\r\n\r\n> I will state again that I do not expect @yang-ruoxi to implement a unittest to check annotations\r\n\r\nno need to repeat yourself, i still disagree the 2nd time",
"@janosh The apology wasn't meant for me. And it does matter. Since you are not interested in giving it, we have nothing left to talk about. Go ahead and occupy yourself with other concerns. ",
"As a maintainer of this repo, I have to remind that we expect all discussions to be civil and polite.\r\n\r\nFor example, this is not an appropriate comment because I would consider this a personal attack:\r\n\r\n> let's not pretend you care about apologies.\r\n\r\nI would like to offer an apology to @yang-ruoxi for the discourse in this thread, and say thank you again for reporting the bug.\r\n\r\nI take all comments in good faith because I know we all share the motivation to have code that is accurate, reliable and well-tested. I would like to make sure that we keep things friendly and welcoming while we pursue this goal. Thanks everyone.",
"> For example, this is not an appropriate comment because I would consider this a personal attack:\r\n\r\n@mkhorton in good faith, i'm too familiar with the characters involved to take @shyuep's request at face value:\r\n\r\n>> Also, a proper response would have been to apologize for making the mistake\r\n\r\nthat was an obvious attempt at forcing submission rather than a genuine effort to steer towards a healthier community. asking for apologies should go hand in hand with acknowledging them when others make them unprompted and making some yourself. i've yet to see @shyuep do either",
"To avoid further off-topic whining about my intentions, I am locking this thread. I will not bother censoring any comments since they paint a clear picture."
] | 2024-09-16T23:31:55
| 2024-09-19T03:35:55
|
2024-09-17T03:09:13Z
|
MEMBER
|
off-topic
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## Summary
This PR fixed the break of phase diagram plot caused by commit 41e6d99 which made changes not only to syntax but also plotting logic without careful review. This is a small fix but did require human hour to track down the issue, and caused downstream breakage on MP website and for pymatgen users who plot phase diagrams.
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|
Fix: fixed electronic step check with algo = exact and nelm = 1
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[
"Tagging @utf for awareness.",
"Thanks,"
] | 2024-09-17T11:59:55
| 2024-09-18T01:12:33
|
2024-09-18T01:12:28Z
|
CONTRIBUTOR
|
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## Summary
Major changes:
This PR fixes the bug when parsing non-self-consistent calculation done with `ALGO=Exact` and `NELM=1`. In such senario, the electronic step of the calculation will never truly converge. However, this is what we expect in non-self-consistent calculations, as we only have one electronic step. In this PR, I hacked the `converged_electronic` method of the `Vasprun` class, which will return `True` in this senario.
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fix chempot_diagram
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[
"Can you try reverting the entire commit doing the in place assignment change and see if it solves the problem on your machine?",
"reverting this particular line solved the issue. Would you prefer reverting the entire commit for this PR? ",
"OK, if it already fixes it. I will merge now. Thanks for the fix.",
"thank you! "
] | 2024-09-17T21:59:59
| 2024-09-18T17:16:17
|
2024-09-18T01:08:36Z
|
MEMBER
|
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|
## Summary
A strange behavior was caught for chemical potential diagram where the planes were crossed.
Using the in-place [assignment expression](https://github.com/materialsproject/pymatgen/blob/150f816c55be80dd146cb20ebbf5f930633c8aeb/src/pymatgen/analysis/chempot_diagram.py#L649), the plot shows below:
<img width="817" alt="Screenshot 2024-09-17 at 2 38 07 PM" src="https://github.com/user-attachments/assets/5dc7a153-e968-42ab-9dd9-8e08d74343dd">
It it not obvious how it could cause the breakage. I spent sometime debugging but with no luck, it could be something much deeper. For now I suggest we revert it to the original form till we have a real solution. Would much appreciate a quick release due to breakage for MP...
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PR_kwDOACgets576qsy
| 4,073
|
Use binary distribution (wheels) to install pymatgen in test suite
|
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[] | 2024-09-18T15:09:48
| 2024-11-30T12:46:45
|
2024-11-13T17:50:03Z
|
CONTRIBUTOR
|
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### Summary
- Use binary distribution (wheels) to install `pymatgen` in test suite, currently neither source distribution nor binary distribution is tested against test suite, might lead to breakage if we miss anything from them (heard this happened before). The reason to use binary distribution over source distribution is [the former is what at the end of day being installed on a user's machine](https://github.com/pypa/setuptools/pull/4643#discussion_r1756510320):
<img width="1115" alt="image" src="https://github.com/user-attachments/assets/16262941-9bb0-47ad-b0fd-41121683b952">
- [x] Intentionally exclude some core file from source dist and see if test fails, 0dba0284903f640da953ab70e50ff5eef6562f7d, [issue indeed captured by CI](https://github.com/materialsproject/pymatgen/actions/runs/11311495423/job/31457797228)
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PR_kwDOACgets58MTf1
| 4,074
|
return `bool` instead of `np.bool_`
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[
"Beautiful! I believe I have seen issues related to this at some point. \r\n\r\nI just did a global search (re pattern `return np\\..* [><=]`) and there are a few more cases that perhaps you could fix as well? Thanks!\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/ea7c3390e2db99a35f3eee242073ffc2830bbd4c/src/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py#L716-L727\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/ea7c3390e2db99a35f3eee242073ffc2830bbd4c/src/pymatgen/core/surface.py#L308-L321\r\n\r\nThe following might return `[True]` or `[False]` as a single element array if I understand correctly?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/ea7c3390e2db99a35f3eee242073ffc2830bbd4c/src/pymatgen/analysis/interfaces/zsl.py#L317-L330",
"I did some messy `inspect` voodoo and got this list:\r\n\r\n```\r\nFunction '_normalization_factor' in 'pymatgen.analysis.phase_diagram' returned a NumPy generic object\r\nFunction 'matches' in 'pymatgen.core.structure' returned a NumPy generic object\r\nFunction 'get' in 'pymatgen.core.composition' returned a NumPy generic object\r\nFunction 'get_n_moment' in 'pymatgen.electronic_structure.dos' returned a NumPy generic object\r\nFunction 'is_symmetric' in 'pymatgen.core.tensors' returned a NumPy generic object\r\nFunction 'get_coeff' in 'pymatgen.analysis.reaction_calculator' returned a NumPy generic object\r\nFunction 'r2_score' in 'pymatgen.phonon.dos' returned a NumPy generic object\r\nFunction 'mae' in 'pymatgen.phonon.dos' returned a NumPy generic object\r\nFunction 'best_case' in 'pymatgen.analysis.ewald' returned a NumPy generic object\r\nFunction '__getitem__' in 'pymatgen.core.structure' returned a NumPy generic object\r\nFunction 'get_d' in 'pymatgen.core.surface' returned a NumPy generic object\r\nFunction 'get_specific_energy' in 'pymatgen.apps.battery.conversion_battery' returned a NumPy generic object\r\nFunction '__getitem__' in 'pymatgen.core.composition' returned a NumPy generic object\r\nFunction 'get_interpolated_value' in 'pymatgen.core.spectrum' returned a NumPy generic object\r\nFunction 'get_linear_interpolated_value' in 'pymatgen.util.coord' returned a NumPy generic object\r\nFunction 'get_band_width' in 'pymatgen.electronic_structure.dos' returned a NumPy generic object\r\nFunction 'get_average_voltage' in 'pymatgen.apps.battery.conversion_battery' returned a NumPy generic object\r\nFunction 'cv' in 'pymatgen.phonon.dos' returned a NumPy generic object\r\nFunction 'project' in 'pymatgen.core.tensors' returned a NumPy generic object\r\nFunction 'get_el_amount' in 'pymatgen.analysis.reaction_calculator' returned a NumPy generic object\r\nFunction 'is_polar' in 'pymatgen.core.surface' returned a NumPy generic object\r\nFunction 'get_e_above_hull' in 'pymatgen.analysis.phase_diagram' returned a NumPy generic object\r\nFunction 'einsum_sequence' in 'pymatgen.core.tensors' returned a NumPy generic object\r\nFunction 'get_band_skewness' in 'pymatgen.electronic_structure.dos' returned a NumPy generic object\r\nFunction 'get_capacity_vol' in 'pymatgen.apps.battery.conversion_battery' returned a NumPy generic object\r\nFunction 'helmholtz_free_energy' in 'pymatgen.phonon.dos' returned a NumPy generic object\r\nFunction '_get_item_index' in 'pymatgen.core.tensors' returned a NumPy generic object\r\nFunction 'get_band_kurtosis' in 'pymatgen.electronic_structure.dos' returned a NumPy generic object\r\nFunction 'd_hkl' in 'pymatgen.core.lattice' returned a NumPy generic object\r\nFunction 'distance' in 'pymatgen.core.sites' returned a NumPy generic object\r\nFunction 'value_at' in 'pymatgen.io.vasp.outputs' returned a NumPy generic object\r\nFunction 'get_reference_energy' in 'pymatgen.analysis.phase_diagram' returned a NumPy generic object\r\nFunction 'internal_energy' in 'pymatgen.phonon.dos' returned a NumPy generic object\r\nFunction 'get_fermi_interextrapolated' in 'pymatgen.electronic_structure.dos' returned a NumPy generic object\r\nFunction '__array_wrap__' in 'pymatgen.core.tensors' returned a NumPy generic object\r\nFunction 'get_gap' in 'pymatgen.electronic_structure.dos' returned a NumPy generic object\r\nFunction '__abs__' in 'pymatgen.electronic_structure.core' returned a NumPy generic object\r\nFunction 'get_fermi' in 'pymatgen.electronic_structure.dos' returned a NumPy generic object\r\nFunction 'average_over_unit_sphere' in 'pymatgen.core.tensors' returned a NumPy generic object\r\nFunction 'get_band_filling' in 'pymatgen.electronic_structure.dos' returned a NumPy generic object\r\nFunction 'entropy' in 'pymatgen.phonon.dos' returned a NumPy generic object\r\nFunction 'width' in 'pymatgen.phonon.bandstructure' returned a NumPy generic object\r\nFunction 'get_last_peak' in 'pymatgen.phonon.dos' returned a NumPy generic object\r\nFunction 'get_doping' in 'pymatgen.electronic_structure.dos' returned a NumPy generic object\r\nFunction 'get_equilibrium_reaction_energy' in 'pymatgen.analysis.phase_diagram' returned a NumPy generic object\r\nFunction 'selling_dist' in 'pymatgen.core.lattice' returned a NumPy generic object\r\nFunction 'get_distance' in 'pymatgen.core.structure' returned a NumPy generic object\r\nFunction 'debye_temp_phonopy' in 'pymatgen.phonon.gruneisen' returned a NumPy generic object\r\nFunction 'in_simplex' in 'pymatgen.util.coord' returned a NumPy generic object\r\nFunction 'get_site_energy' in 'pymatgen.analysis.ewald' returned a NumPy generic object\r\nFunction 'get_hull_energy_per_atom' in 'pymatgen.analysis.phase_diagram' returned a NumPy generic object\r\nFunction 'is_fit_to_structure' in 'pymatgen.core.tensors' returned a NumPy generic object\r\nFunction 'get_interpolated_value' in 'pymatgen.phonon.dos' returned a NumPy generic object\r\nFunction 'compute_partial_energy' in 'pymatgen.analysis.ewald' returned a NumPy generic object\r\nFunction 'get_energy_density' in 'pymatgen.apps.battery.conversion_battery' returned a NumPy generic object\r\nFunction 'zero_point_energy' in 'pymatgen.phonon.dos' returned a NumPy generic object\r\nFunction 'is_rotation' in 'pymatgen.core.tensors' returned a NumPy generic object\r\nFunction 'get_direct_band_gap' in 'pymatgen.electronic_structure.bandstructure' returned a NumPy generic object\r\nFunction 'thermal_conductivity_slack' in 'pymatgen.phonon.gruneisen' returned a NumPy generic object\r\nFunction 'get_hull_energy' in 'pymatgen.analysis.phase_diagram' returned a NumPy generic object\r\nFunction 'get_form_energy' in 'pymatgen.analysis.phase_diagram' returned a NumPy generic object\r\nFunction 'get_phase_separation_energy' in 'pymatgen.analysis.phase_diagram' returned a NumPy generic object\r\nFunction 'has_imaginary_freq' in 'pymatgen.phonon.bandstructure' returned a NumPy generic object\r\nFunction 'calculate_energy' in 'pymatgen.analysis.reaction_calculator' returned a NumPy generic object\r\nFunction 'average_gruneisen' in 'pymatgen.phonon.gruneisen' returned a NumPy generic object\r\nFunction 'get_capacity_grav' in 'pymatgen.apps.battery.conversion_battery' returned a NumPy generic object\r\nFunction 'fit' in 'pymatgen.analysis.structure_matcher' returned a NumPy generic object\r\nFunction 'get_band_center' in 'pymatgen.electronic_structure.dos' returned a NumPy generic object\r\nFunction '__getitem__' in 'pymatgen.electronic_structure.core' returned a NumPy generic object\r\nFunction '__lt__' in 'pymatgen.electronic_structure.core' returned a NumPy generic object\r\nFunction '__array_wrap__' in 'pymatgen.analysis.elasticity.strain' returned a NumPy generic object\r\nFunction 'get_upper_band_edge' in 'pymatgen.electronic_structure.dos' returned a NumPy generic object\r\nFunction 'get_atomic_fraction' in 'pymatgen.core.composition' returned a NumPy generic object\r\nFunction 'formula_double_format' in 'pymatgen.util.string' returned a NumPy generic object\r\n```\r\n\r\nThe `@njit` wrapper might have messed with the `inspect` voodoo.\r\nI'll patch these next week.\r\n\r\nSlightly updated list:\r\n```\r\nFunction 'best_case' in 'pymatgen.analysis.ewald.EwaldMinimizer' returned a NumPy generic object\r\nFunction 'get_coeff' in 'pymatgen.analysis.reaction_calculator.BalancedReaction' returned a NumPy generic object\r\nFunction 'get_n_moment' in 'pymatgen.electronic_structure.dos.CompleteDos' returned a NumPy generic object\r\nFunction 'get_upper_band_edge' in 'pymatgen.electronic_structure.dos.CompleteDos' returned a NumPy generic object\r\nFunction 'get_capacity_grav' in 'pymatgen.apps.battery.conversion_battery.ConversionElectrode' returned a NumPy generic object\r\nFunction 'is_rotation' in 'pymatgen.core.tensors.SquareTensor' returned a NumPy generic object\r\nFunction 'get_energy_density' in 'pymatgen.apps.battery.conversion_battery.ConversionElectrode' returned a NumPy generic object\r\nFunction 'formula_double_format' in 'pymatgen.util.string' returned a NumPy generic object\r\nFunction 'get_site_energy' in 'pymatgen.analysis.ewald.EwaldSummation' returned a NumPy generic object\r\nFunction 'get_e_above_hull' in 'pymatgen.analysis.phase_diagram.PhaseDiagram' returned a NumPy generic object\r\nFunction 'has_imaginary_freq' in 'pymatgen.phonon.bandstructure.PhononBandStructureSymmLine' returned a NumPy generic object\r\nFunction 'thermal_conductivity_slack' in 'pymatgen.phonon.gruneisen.GruneisenParameter' returned a NumPy generic object\r\nFunction 'get_gap' in 'pymatgen.electronic_structure.dos.Dos' returned a NumPy generic object\r\nFunction 'get_band_center' in 'pymatgen.electronic_structure.dos.CompleteDos' returned a NumPy generic object\r\nFunction 'entropy' in 'pymatgen.phonon.dos.CompletePhononDos' returned a NumPy generic object\r\nFunction '_normalization_factor' in 'pymatgen.analysis.phase_diagram.PDEntry' returned a NumPy generic object\r\nFunction 'calculate_energy' in 'pymatgen.analysis.reaction_calculator.ComputedReaction' returned a NumPy generic object\r\nFunction '__array_wrap__' in 'pymatgen.core.tensors.SquareTensor' returned a NumPy generic object\r\nFunction 'get_band_filling' in 'pymatgen.electronic_structure.dos.CompleteDos' returned a NumPy generic object\r\nFunction 'get_interpolated_value' in 'pymatgen.phonon.dos.PhononDos' returned a NumPy generic object\r\nFunction 'get_band_skewness' in 'pymatgen.electronic_structure.dos.CompleteDos' returned a NumPy generic object\r\nFunction 'cv' in 'pymatgen.phonon.dos.PhononDos' returned a NumPy generic object\r\nFunction 'is_symmetric' in 'pymatgen.core.tensors.SquareTensor' returned a NumPy generic object\r\nFunction 'get_gap' in 'pymatgen.electronic_structure.dos.DOS' returned a NumPy generic object\r\nFunction 'get_gap' in 'pymatgen.electronic_structure.dos.FermiDos' returned a NumPy generic object\r\nFunction 'width' in 'pymatgen.phonon.bandstructure.PhononBandStructureSymmLine' returned a NumPy generic object\r\nFunction 'selling_dist' in 'pymatgen.core.lattice.Lattice' returned a NumPy generic object\r\nFunction 'cv' in 'pymatgen.phonon.dos.CompletePhononDos' returned a NumPy generic object\r\nFunction '__getitem__' in 'pymatgen.core.composition.Composition' returned a NumPy generic object\r\nFunction 'get_fermi' in 'pymatgen.electronic_structure.dos.FermiDos' returned a NumPy generic object\r\nFunction '__array_wrap__' in 'pymatgen.analysis.elasticity.strain.Deformation' returned a NumPy generic object\r\nFunction 'get_capacity_vol' in 'pymatgen.apps.battery.conversion_battery.ConversionElectrode' returned a NumPy generic object\r\nFunction 'einsum_sequence' in 'pymatgen.core.tensors.Tensor' returned a NumPy generic object\r\nFunction 'get_hull_energy' in 'pymatgen.analysis.phase_diagram.PhaseDiagram' returned a NumPy generic object\r\nFunction 'get_interpolated_value' in 'pymatgen.core.spectrum.Spectrum' returned a NumPy generic object\r\nFunction 'get_atomic_fraction' in 'pymatgen.core.composition.Composition' returned a NumPy generic object\r\nFunction 'compute_partial_energy' in 'pymatgen.analysis.ewald.EwaldSummation' returned a NumPy generic object\r\nFunction 'get_average_voltage' in 'pymatgen.apps.battery.conversion_battery.ConversionElectrode' returned a NumPy generic object\r\nFunction 'average_over_unit_sphere' in 'pymatgen.core.tensors.Tensor' returned a NumPy generic object\r\nFunction 'in_simplex' in 'pymatgen.util.coord.Simplex' returned a NumPy generic object\r\nFunction 'get_equilibrium_reaction_energy' in 'pymatgen.analysis.phase_diagram.PhaseDiagram' returned a NumPy generic object\r\nFunction 'matches' in 'pymatgen.core.structure.Structure' returned a NumPy generic object\r\nFunction 'get_el_amount' in 'pymatgen.analysis.reaction_calculator.BalancedReaction' returned a NumPy generic object\r\nFunction '__getitem__' in 'pymatgen.electronic_structure.core.Magmom' returned a NumPy generic object\r\nFunction 'helmholtz_free_energy' in 'pymatgen.phonon.dos.CompletePhononDos' returned a NumPy generic object\r\nFunction 'get_phase_separation_energy' in 'pymatgen.analysis.phase_diagram.PhaseDiagram' returned a NumPy generic object\r\nFunction 'is_polar' in 'pymatgen.core.surface.Slab' returned a NumPy generic object\r\nFunction 'd_hkl' in 'pymatgen.core.lattice.Lattice' returned a NumPy generic object\r\nFunction 'internal_energy' in 'pymatgen.phonon.dos.PhononDos' returned a NumPy generic object\r\nFunction '__abs__' in 'pymatgen.electronic_structure.core.Magmom' returned a NumPy generic object\r\nFunction 'get_direct_band_gap' in 'pymatgen.electronic_structure.bandstructure.LobsterBandStructureSymmLine' returned a NumPy generic object\r\nFunction 'get_band_width' in 'pymatgen.electronic_structure.dos.CompleteDos' returned a NumPy generic object\r\nFunction 'helmholtz_free_energy' in 'pymatgen.phonon.dos.PhononDos' returned a NumPy generic object\r\nFunction '__array_wrap__' in 'pymatgen.core.tensors.Tensor' returned a NumPy generic object\r\nFunction 'get_reference_energy' in 'pymatgen.analysis.phase_diagram.PhaseDiagram' returned a NumPy generic object\r\nFunction 'get_last_peak' in 'pymatgen.phonon.dos.PhononDos' returned a NumPy generic object\r\nFunction 'get_band_kurtosis' in 'pymatgen.electronic_structure.dos.CompleteDos' returned a NumPy generic object\r\nFunction 'zero_point_energy' in 'pymatgen.phonon.dos.PhononDos' returned a NumPy generic object\r\nFunction 'r2_score' in 'pymatgen.phonon.dos.PhononDos' returned a NumPy generic object\r\nFunction 'debye_temp_phonopy' in 'pymatgen.phonon.gruneisen.GruneisenParameter' returned a NumPy generic object\r\nFunction '__lt__' in 'pymatgen.electronic_structure.core.Magmom' returned a NumPy generic object\r\nFunction 'fit' in 'pymatgen.analysis.structure_matcher.StructureMatcher' returned a NumPy generic object\r\nFunction 'mae' in 'pymatgen.phonon.dos.PhononDos' returned a NumPy generic object\r\nFunction 'get_linear_interpolated_value' in 'pymatgen.util.coord' returned a NumPy generic object\r\nFunction 'internal_energy' in 'pymatgen.phonon.dos.CompletePhononDos' returned a NumPy generic object\r\nFunction 'get_doping' in 'pymatgen.electronic_structure.dos.FermiDos' returned a NumPy generic object\r\nFunction 'average_gruneisen' in 'pymatgen.phonon.gruneisen.GruneisenParameter' returned a NumPy generic object\r\nFunction 'get_specific_energy' in 'pymatgen.apps.battery.conversion_battery.ConversionElectrode' returned a NumPy generic object\r\nFunction 'get_d' in 'pymatgen.core.surface' returned a NumPy generic object\r\nFunction 'get_distance' in 'pymatgen.core.structure.Structure' returned a NumPy generic object\r\nFunction 'get_direct_band_gap' in 'pymatgen.electronic_structure.bandstructure.BandStructureSymmLine' returned a NumPy generic object\r\nFunction 'is_symmetric' in 'pymatgen.core.tensors.Tensor' returned a NumPy generic object\r\nFunction 'value_at' in 'pymatgen.io.vasp.outputs.VolumetricData' returned a NumPy generic object\r\nFunction 'distance' in 'pymatgen.core.sites.PeriodicSite' returned a NumPy generic object\r\nFunction 'get_gap' in 'pymatgen.electronic_structure.dos.CompleteDos' returned a NumPy generic object\r\nFunction 'get_hull_energy_per_atom' in 'pymatgen.analysis.phase_diagram.PhaseDiagram' returned a NumPy generic object\r\nFunction 'get' in 'pymatgen.core.composition.Composition' returned a NumPy generic object\r\nFunction 'project' in 'pymatgen.core.tensors.Tensor' returned a NumPy generic object\r\nFunction 'get_fermi_interextrapolated' in 'pymatgen.electronic_structure.dos.FermiDos' returned a NumPy generic object\r\nFunction 'is_fit_to_structure' in 'pymatgen.core.tensors.Tensor' returned a NumPy generic object\r\nFunction 'calculate_energy' in 'pymatgen.analysis.reaction_calculator.BalancedReaction' returned a NumPy generic object\r\nFunction '__getitem__' in 'pymatgen.core.structure.PeriodicNeighbor' returned a NumPy generic object\r\nFunction 'get_form_energy' in 'pymatgen.analysis.phase_diagram.PhaseDiagram' returned a NumPy generic object\r\nFunction '_get_item_index' in 'pymatgen.core.tensors.TensorMapping' returned a NumPy generic object\r\nFunction 'entropy' in 'pymatgen.phonon.dos.PhononDos' returned a NumPy generic object\r\n```\r\n\r\n",
"I think this script can be adapted later to handle a more thorough check of serialization bugs caused by custom `as_dicts`.\r\n\r\n```python\r\nimport pytest\r\nimport inspect\r\nimport pkgutil\r\nimport importlib\r\nimport pymatgen\r\nimport numpy as np\r\n\r\ntriggered = set()\r\n\r\ndef log_numpy_return(func, path_name, name):\r\n def wrapper(*args_, **kwargs_):\r\n result = func(*args_, **kwargs_)\r\n if isinstance(result, np.generic):\r\n # print(f\"Function '{name}' in '{path_name}' returned a NumPy generic object\")\r\n triggered.add(f\"Function '{name}' in '{path_name}' returned a NumPy generic object\")\r\n return result\r\n return wrapper\r\n\r\ndef wrap_func(path, name, func, path_name):\r\n setattr(path, name, log_numpy_return(func, path_name, name))\r\n\r\ndef get_all_functions(package):\r\n \"\"\"\r\n Get all functions and methods from a package and its submodules.\r\n \"\"\"\r\n functions = dict()\r\n for module_info in pkgutil.walk_packages(package.__path__, prefix=f\"{package.__name__}.\"):\r\n try:\r\n # Dynamically import the module\r\n module = importlib.import_module(module_info.name)\r\n # Get all functions in the module\r\n for name, func_ in inspect.getmembers(module, inspect.isfunction):\r\n source_module = func_.__module__\r\n if package.__name__ not in source_module: continue\r\n functions[f\"{module.__name__}.{name}\"] = (module, name, func_, source_module)\r\n # Get all the methods in the module\r\n for class_name, obj in inspect.getmembers(module, inspect.isclass):\r\n source_module = obj.__module__\r\n if package.__name__ not in source_module: continue\r\n for name2, method_ in inspect.getmembers(obj, inspect.isfunction):\r\n functions[f\"{module.__name__}.{class_name}.{name2}\"] = (obj, name2, method_, f\"{source_module}.{class_name}\")\r\n except Exception as e:\r\n # Handle modules that cannot be imported or have issues\r\n print(f\"Failed to inspect {module_info.name}: {e}\")\r\n return functions\r\n\r\nfuncs = get_all_functions(pymatgen)\r\nfor v in funcs.values():\r\n wrap_func(*v)\r\n\r\n# Run pytest\r\npytest.main(['-v', '-s'])\r\nprint(\"Triggered:\")\r\nprint(triggered)\r\n# write triggerd to file\r\nwith open(\"triggered.txt\", \"w\") as f:\r\n f.write(\"\\n\".join(triggered))\r\n```\r\n\r\n",
"Ok I went through the list and found ones where a user will plausibly serialize into a DB.\r\nFor most of them the return type was already annotated with `bool` so this is just something that the linters should have caught\r\nhttps://github.com/python/mypy/issues/10385\r\n\r\n\r\n",
"Wow, that's way more thorough than mine :)\r\n\r\n> For most of them the return type was already annotated with bool so this is just something that the linters should have caught\r\n\r\nI thought `mypy` should be able to catch such mismatch but for some reason it didn't. Do you have any idea?\r\n\r\n```python\r\nimport numpy as np\r\n\r\n\r\ndef foo() -> bool:\r\n return np.bool_(True) >>> Incompatible return value type (got \"numpy.bool\", expected \"builtins.bool\") [return-value]\r\n```\r\n\r\nI'm not seeing `return-value` being suppressed or something: https://github.com/materialsproject/pymatgen/blob/ea7c3390e2db99a35f3eee242073ffc2830bbd4c/pyproject.toml#L282-L287\r\n",
"Yeah `mypy` should work for this. So not sure why this these got ignored.",
"Will go ahead and merge this, thanks both"
] | 2024-09-20T17:04:47
| 2024-10-12T23:47:24
|
2024-09-24T22:14:12Z
|
CONTRIBUTOR
|
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## Summary
The return signature of this function is currently `np.bool_` which can cause serialization problems with older atomate1 workflows.
Changed to `bool` instead.
|
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More Flexible `Vasprun` Parsing
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[] | 2024-09-20T19:47:53
| 2024-09-21T01:33:50
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CONTRIBUTOR
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### Feature Requested
Currently the `Vasprun` parser crashes (with `ParseError`) if the file is not complete. If one sets `exception_on_bad_xml=False` this can be avoided, but then most of the information is not parsed (even though it is still present in the file). This can occur fairly often when large VASP calculations complete the SCF cycles, but then crash at the last moment when writing long eigenvalue outputs or wavefunctions, due to memory or filespace issues etc.
It would be very useful if this information was still able to be pulled from the vasprun file, particularly in the case of large calculations where re-running the whole calculation just to get a properly-formatted output can be quite inefficient (e.g. hybrid+SOC singleshots on a large supercell which crashed at the last moment, with no wavefunction output).
### Proposed Solution
This functionality should be achievable relatively easily, by smartly handling the XML elements which aren't fully complete.
As a rough demonstration of one possible approach, this code can be used to determine the current tag stack:
```python
from xml.etree.ElementTree import iterparse
def validate_tags(file_path):
tag_stack = []
try:
with open(file_path, 'r') as file:
for event, elem in iterparse(file, events=("start", "end")):
if event == "start":
tag_stack.append(elem.tag)
elif event == "end":
if tag_stack and tag_stack[-1] == elem.tag:
tag_stack.pop()
else:
print(f"Mismatched tag found: {elem.tag}")
break
except ET.ParseError as e:
print(f"Parse error: {e}. Missing closing tag for {tag_stack[-1]} if stack is not empty.")
if tag_stack:
print(f"Current tag stack: {tag_stack}")
```
which in the example partially-complete `vasprun.xml` I've provided gives:
```
Parse error: no element found: line 9455, column 0. Missing closing tag for set if stack is not empty.
Current tag stack: ['modeling', 'calculation', 'eigenvalues', 'array', 'set', 'set', 'set']
```
If I then append these tags to a copy of the loaded `file` object, parsing can proceed without issue, loading all the information available in the (incomplete) `vasprun.xml`:
```python
# open file and append closing tags for any missing ones:
# current tag stack: ['modeling', 'calculation', 'eigenvalues', 'array', 'set', 'set', 'set']
file_path = "vasprun.xml"
ionic_steps = []
with open(file_path, 'a+') as file:
# TODO: This should be a temp file copy, so as not to modify file on system
# append closing tags for any missing ones:
file.writelines([
"</set>\n</set>\n</set>\n</array>\n</eigenvalues>\n</calculation>\n</modeling>"
])
file.seek(0) # move the file pointer back to the beginning to read content
for event, elem in ET.iterparse(file, events=["start", "end"]):
tag = elem.tag
if tag == "calculation":
parsed_header = True
ionic_steps.append(_parse_ionic_step(vr, elem))
...
```
There are presumably far smarter ways of doing this, this is just a rough example showing how it could be achieved.
This could be implemented only when the user uses the `exception_on_bad_xml=False` option, which already throws a warning if indeed the `vasprun.xml` is incomplete.
Example `vasprun.xml` where this is desirable:
[vasprun.xml.gz](https://github.com/user-attachments/files/17080194/vasprun.xml.gz)
### Relevant Information
Often this truncated output can result in truncated array outputs (e.g. of the eigenvalues/DOS), so it might require a quick check that all arrays are of the expected size, and if not they are dropped?
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PR_kwDOACgets58VxnM
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Install `BoltzTraP2` directly through `uv`
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[
"I tried but still cannot figure out why build for `BoltzTrap2` fails for Windows runners. But in any case, this wouldn't worsen our tests as it was installed for Ubuntu-only before."
] | 2024-09-23T09:38:06
| 2024-10-03T01:52:50
|
2024-10-02T20:12:42Z
|
CONTRIBUTOR
|
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### Summary
- Install `BoltzTraP2` directly through `uv` as `BoltzTraP2` now support PEP-517 with build isolation
- [ ] ~~Look into why install failed for Windows~~
|
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pymatgen fails to load MPRester
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"Pls state whether you are using MPRester basic or the mp-api version. If it is the mp-api version, then you will have to post this in that repo. If it is basic, then let us know.",
"It happens with both, but it's really a problem with pymatgen rather than mp-api. If numpy>2.0 is installed, the following two commands both fail:\r\n\r\n>> from pymatgen.ext.matproj import MPRester\r\n>> from mp_api.client import MPRester\r\n\r\nHowever, the problem in general is not a problem for mp-api since there is a requirement there to install numpy<2.0. Thus if both mp-api and pymatgen are pip installed, both work, since mp-api will downgrade numpy to <2.0, and pymatgen does not require numpy>2.0. If only pymatgen is installed in a clean environment, numpy does not have the <2.0 requirement and MPRester fails. \r\n",
"> If only pymatgen is installed in a clean environment, numpy does not have the <2.0 requirement and MPRester fails.\r\n\r\n@jjkas I cannot reproduce this issue. Can you please confirm your `pymatgen` version? I would expect version [v2024.9.10](https://github.com/materialsproject/pymatgen/releases/tag/v2024.9.10) and afterwards to fully support numpy 2.\r\n\r\n```python\r\nimport numpy as np\r\nfrom pymatgen.ext.matproj import MPRester\r\nimport pkg_resources\r\n\r\n\r\nprint(\"NumPy version:\", np.__version__) # >>> NumPy version: 2.1.1\r\nprint(\"pymatgen version:\", pkg_resources.get_distribution(\"pymatgen\").version) # >>> pymatgen version: 2024.9.17.1\r\nprint(dir(MPRester)) \r\n```",
"Windows 10 64 bit\r\nAs my environment is now, MPRester loads just fine.\r\n\r\n>Python 3.12.5 | packaged by Anaconda, Inc. | (main, Sep 12 2024, 18:18:29) [MSC v.1929 64 bit (AMD64)] on win32\r\n>Type \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>\\>>> import numpy as np\r\n>\\>>> from pymatgen.ext.matproj import MPRester\r\n>\\>>> import pkg_resources\r\n>\\<stdin>:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/>\\pkg_resources.html\r\n>\\>>>\r\n>\\>>>\r\n>\\>>> print(\"NumPy version:\", np.__version__) # >>> NumPy version: 2.1.1\r\n>\\NumPy version: 1.26.4\r\n>\\>>> print(\"pymatgen version:\", pkg_resources.get_distribution(\"pymatgen\").version) # >>> pymatgen version: 2024.9.17.1\r\n>\\pymatgen version: 2024.9.17.1\r\n>\\>>> print(dir(MPRester))\r\n>\\['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__getstate__', '__gt__', >\\'__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', >\\'__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__']\r\n\r\n\r\n",
"I'm now having trouble reproducing the problem myself. I'll see if I can get it to occur again.",
"Cool, let me know if you found anything.\r\n\r\n> NumPy version: 1.26.4\r\n\r\nNote you appear to be running numpy 1.26 while the original issue was reported on numpy 2.x, so please make sure you have the correct version of numpy installed.\r\n\r\nI tried to run both numpy 1.26 and numpy 2.1 on my Windows machine and cannot reproduce this.\r\n"
] | 2024-09-23T22:45:41
| 2024-09-26T07:17:54
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### Python version
Python 3.12.5
### Pymatgen version
2024.9.17
### Operating system version
Linux Mint V22, windows10 64 bit,
### Current behavior
>>> from pymatgen.ext.matproj import MPRester
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "<stdin>", line 1, in <module>
File "/home/jjkas/miniconda3/envs/Corvus/lib/python3.12/site-packages/pymatgen/ext/matproj.py", line 25, in <module>
from pymatgen.core import SETTINGS
File "/home/jjkas/miniconda3/envs/Corvus/lib/python3.12/site-packages/pymatgen/core/__init__.py", line 13, in <module>
from pymatgen.core.lattice import Lattice
File "/home/jjkas/miniconda3/envs/Corvus/lib/python3.12/site-packages/pymatgen/core/lattice.py", line 19, in <module>
from pymatgen.util.coord import pbc_shortest_vectors
File "/home/jjkas/miniconda3/envs/Corvus/lib/python3.12/site-packages/pymatgen/util/coord.py", line 15, in <module>
from pymatgen.util import coord_cython
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/jjkas/miniconda3/envs/Corvus/lib/python3.12/site-packages/pymatgen/ext/matproj.py", line 25, in <module>
from pymatgen.core import SETTINGS
File "/home/jjkas/miniconda3/envs/Corvus/lib/python3.12/site-packages/pymatgen/core/__init__.py", line 13, in <module>
from pymatgen.core.lattice import Lattice
File "/home/jjkas/miniconda3/envs/Corvus/lib/python3.12/site-packages/pymatgen/core/lattice.py", line 19, in <module>
from pymatgen.util.coord import pbc_shortest_vectors
File "/home/jjkas/miniconda3/envs/Corvus/lib/python3.12/site-packages/pymatgen/util/coord.py", line 15, in <module>
from pymatgen.util import coord_cython
File "pymatgen/util/coord_cython.pyx", line 1, in init pymatgen.util.coord_cython
ImportError: numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use '<void>numpy._import_array' to disable if you are certain you don't need it).
### Expected Behavior
Since pymatgen change log states explicit fixes for version v2024.9.10, I would expect its requirements also to work with numpy >2.0. Not sure if this is a bug, but perhaps changing installation via pypi to require numpy<2.0 would be a good idea?
Notes:
1. Seems to be due to requirement of emmet-core of numpy<2.0.
2. Works on mac m2 with the same versions of python/pymatgen.
3. Works on windows 11 running as a virtual machine on the same mac m2.
### Minimal example
```Python
>> from pymatgen.ext.matproj import MPRester
fails with numpy 2.1.1
works with numpy 1.26.
```
### Relevant files to reproduce this bug
_No response_
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JDFTx IO module
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[
"Thanks @benrich37, I will review this",
"> Thanks @benrich37, I will review this\r\n\r\n@mkhorton Sorry didn't see your comment, will pause on new commits until you're finished. Thank you!\r\n\r\nEdit: Also, it looks like there are some typos baked into how JDFTx creates out files, which is causing pre-commit to fail on codespell for the example out files I've added. Would it be possible to add 'tests/files/io/jdftx/example_files/*out' to the exclude hook for codespell in .pre-commit-config.yaml? Unless there is a cleaner way to exclude those files",
"@benrich37 thanks for this PR and for your patience! Is the current branch up-to-date, and are there are specific areas of concern?",
"> @benrich37 thanks for this PR and for your patience! Is the current branch up-to-date, and are there are specific areas of concern?\r\n\r\nHey! Thank you for your comments! Sorry I hadn't checked this PR in a few days. My main concern for this PR is its readability - I wrote the JDFTx output's data structure to be object oriented to help develop faster, but I can understand how the hierarchy of objects can make it difficult to understand what's going on. I feel confident with functionality itself though (aside from edge cases for JDFTx outputs that keep popping up)",
"From my side, can you explain the changes to periodic_table.py? Since it's a core class the changes should ideally be separated out from new functionality.",
"There is a failing test that I am pretty sure is related to the changes to periodic table.",
"> There is a failing test that I am pretty sure is related to the changes to periodic table.\r\n\r\nHi @shyuep ! Sorry yes - I thought it would be cleaner to have the Species valence(s) property defer to the Element valence(s) property, but I'm seeing now these need to be defined separately so that Species can incorporate oxidation state. Fixing right now.\r\n\r\nAlso @computron - that makes to me, I wasn't sure if it would be better to have internal redundancy to the periodic_table module in this PR or to update alongside this IO module. @mkhorton - would it be okay to go back to using the ad-hoc method in the io.jdftx.data module for the time being? \r\n\r\nEdit: @computron sorry misread your comment - part of the JDFTx output parsing requires a method which can fetch the number of valence electrons for each element in a Structure. The original method that did this was redundant to data that could be fetched by periodic_table, but the valence property needed to do this would throw errors for mixed valence species. I'm okay with either a) Species and Element updated to include a valences property, or b) have my own method (for now) to get the number of valence electrons that works for mixed valence species. As long as there is consensus, I can roll back changes to periodic_table and re-introduce them in a new PR after this one is accepted.",
"Quick update: some of the dataclasses are having issues calling attributes that used to work. Should be fixed soon.\r\n\r\nEdit: Fixed now.",
"> I wasn't sure if it would be better to have internal redundancy to the periodic_table module in this PR or to update alongside this IO module.\r\n\r\nDefinitely let's try to minimize internal redundancy. That kind of thing can get out of control quickly and lead us towards a messy codebase.\r\n\r\nI'll take another look at this soon, but if you want to arrange a quick call (~1hr) to review this PR I'm also open to that. I do not expect big issues but it might make it easier/quicker for us to get through it together.",
"@mkhorton - all modules are ready to review!",
"@DanielYang59 previous weird edits I made to some of the existing code in periodic_table.py has been reverted - now I just need to figure out what's wrong with my laptop's execution of pre-commit! Thank you again for taking the time to review!",
"> Hey Daniel! Thank you for your review!\r\n\r\nNo problem, I'm not a maintainer, but I'm hoping my comments would be helpful.\r\n\r\n> Running pre-commit with the line as elif isinstance(val, list | dict) raises the error within the mypy hook error: Unsupported left operand type for | (\"type[dict[Any, Any]]\") [operator]\r\n\r\nThis exactly suggests that the `pre-commit` is installed on a python <= 3.9 interpreter (`|` is not supported).\r\n\r\nI fully understand this Python module thing could be very confusing, here is how to resolve it.\r\n\r\n---\r\n\r\n### First of all, why this happened (my best guess): \r\nAs I don't have access to your env of course, my best guess is, you have multiple python interpreters install on your system (say one Python from the system package manager, for example `apt` for Ubuntu), and you installed `pre-commit` on your base interpreter. Then you create a virtual environment but didn't install `pre-commit`. If you run `pre-commit` at this point, it would come from your base Python interpreter, something like:\r\n\r\n```bash\r\n>>> which python3 \r\n/usr/bin/python3 # the system installed base interpreter\r\n\r\n# assume you haven't activated venv so far\r\n>>> python3 -m pip install pre-commit # pre-commit installed to your base interepreter\r\n\r\n>>> source venv/bin/activate \r\n\r\n>>> which pre-commit\r\n~/.local/bin/pre-commit # pre-commit but from your base interpreter\r\n```\r\n\r\n### How to resolve this?\r\n1. Install `pre-commit` on your activated venv as it would take higher priority than the system one (in general you might want to keep your base env clean BTW)\r\n ```bash\r\n # Continue previous demo\r\n >>> python3.12 -m pip install pre-commit # install pre-commit for your venv\r\n \r\n >>> which pre-commit\r\n ~/test/venv/bin/pre-commit # now from venv\r\n \r\n ```\r\n2. Use module run with explicit interpreter path like `python3 -m pre_commit run --all-files`, do note for the package name on PyPI use Kebab case like `pre-commit` (dash) and use snake case for module name `pre_commit` (underscore)\r\n3. Use explicit path, something like `venv/bin/pre-commit run --all-files` to make sure `pre-commit` comes from that particular venv\r\n\r\nHope this helps :)\r\n",
"> No problem, I'm not a maintainer, but I'm hoping my comments would be helpful.\r\n\r\nThey certainly are helpful! Really appreciate you stepping in here @DanielYang59 :) ",
"Note - I noticed from a merge conflict that some codespell exceptions were replaced by skipping certain files instead. To follow suit I'm replacing the exceptions I previously had in there with telling codespell to skip the out files in the test files for JDFTx IO",
"> Note - I noticed from a merge conflict that some codespell exceptions were replaced by skipping certain files instead. To follow suit I'm replacing the exceptions I previously had in there with telling codespell to skip the out files in the test files for JDFTx IO\r\n\r\nPerhaps it makes sense to skip all **test files** (not tests scripts) from `codespell` altogether? \r\n\r\n@benrich37 May I link to my previous comment again https://github.com/materialsproject/pymatgen/pull/4078#discussion_r1841594048? As far as I'm concerned:\r\n- We might need to format docstring to Google Style \r\n- Currently all interfaces seem public, but I believe a portion of them should be private?\r\n\r\n\r\n\r\n\r\n",
"Closing this PR until planned changes to integrate inputs and outputs submodules are fully developed"
] | 2024-09-24T20:05:48
| 2025-01-24T18:29:51
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2025-01-24T18:29:51Z
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## Summary
This PR has been divided into the following 3 PR's
- 1: (#4187) (Code change) Addition of `valences` property to ElementBase and Species
- 2: (#4189) (Code addition) Addition of `inputs.py` module to `pymatgen.io.jdftx` and helper modules for representing and parsing JDFTx inputs
- 3: (#4190) (Code addition) Addition of `outputs.py`module to `pymatgen.io.jdftx` and helper modules for representing and parsing JDFTx outputs
This PR can be ignored until those PR's are approved
## Todos
- Add methods which interface between input and output objects (namely creating input objects from output objects)
- Write broader inputs and outputs class to house JDFTXInfile and JDFTXOutfile along with additional inputs/outputs information
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Parsing cp2k output fails after v2024.8.9 release.
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"Hi @msiron-entalpic thanks for reporting this, I could confirm this issue.\r\n\r\nThe reason being we added `strict=True` to ensure the two iterators (`mols` and `lattices`) to unpack are of the same length: https://github.com/materialsproject/pymatgen/blob/e9ea813107ea223d5ce693bdf5e4f74fe29f76db/src/pymatgen/io/cp2k/outputs.py#L300\r\n\r\n---\r\n\r\nI'm not a `CP2K` user, so I would need your help to confirm this (also ping the original author @nwinner ):\r\n- Looks like in our case the length of `mols` (`CP2K-pos-1.xyz`) is longer than `lattices` by 1 (`CP2K-1.cell`), can I know the reason for this? Is it because the initial structure is recorded while lattice only starts after the run begins? \r\n- If so should we skip the first structure during unpacking (`zip(mols[1:], lattices, strict=True)`) to make the structure and lattice match? \r\n\r\n---\r\n\r\nAlso the `total_energy` entry is longer than `structures` by 1 (SCF run at the start I assume?):\r\nhttps://github.com/materialsproject/pymatgen/blob/e9ea813107ea223d5ce693bdf5e4f74fe29f76db/src/pymatgen/io/cp2k/outputs.py#L523\r\n\r\nIf so, should we skip the first energy to make the energy-structure match each other (`zip(self.structures, self.data.get(\"total_energy\")[1:], strict=True)`)?\r\n\r\n---\r\n\r\nIs it possible for you to provide a **unsuccessful** run such that we could enhance the unit test for unsuccessful runs as well?\r\n"
] | 2024-09-25T12:20:38
| 2024-10-02T19:41:01
|
2024-10-02T19:41:01Z
|
NONE
|
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### Python version
3.12.5
### Pymatgen version
v2024.9.17.1
### Operating system version
MacOSX
### Current behavior
When parsing cp2k output using
```
from pymatgen.io.cp2k.outputs import Cp2kOutput
o = Cp2kOutput('cp2k.out', auto_load=True)
```
With any version of Pymatgen after v2024.8.9 stacktrace:
```
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[2], line 1
----> 1 o = Cp2kOutput('cp2k.out', auto_load=True)
File [~/dev/pymatgen/src/pymatgen/io/cp2k/outputs.py:78](http://localhost:8888/lab/tree/job_2024-09-25-08-56-39-543707-66393/~/dev/pymatgen/src/pymatgen/io/cp2k/outputs.py#line=77), in Cp2kOutput.__init__(self, filename, verbose, auto_load)
75 self.ran_successfully()
76 self.convergence()
---> 78 self.parse_structures()
79 self.parse_energies()
80 self.parse_forces()
File [~/dev/pymatgen/src/pymatgen/io/cp2k/outputs.py:300](http://localhost:8888/lab/tree/job_2024-09-25-08-56-39-543707-66393/~/dev/pymatgen/src/pymatgen/io/cp2k/outputs.py#line=299), in Cp2kOutput.parse_structures(self, trajectory_file, lattice_file)
298 gs = self.initial_structure.site_properties.get("ghost")
299 if not self.is_molecule:
--> 300 for mol, latt in zip(mols, lattices, strict=True):
301 self.structures.append(
302 Structure(
303 lattice=latt,
(...)
309 )
310 )
311 else:
ValueError: zip() argument 2 is shorter than argument 1
```
After testing the lattices variable has one less entry than the mols variable. Adding one more entry to lat or removing first entry from mols leads to errors downstream.
### Expected Behavior
Expect to be able to parse output without errors with auto_load as in v2024.8.9
### Minimal example
```Python
from pymatgen.io.cp2k.outputs import Cp2kOutput
o = Cp2kOutput('cp2k.out', auto_load=True)
```
### Relevant files to reproduce this bug
[Archive 2.zip](https://github.com/user-attachments/files/17130777/Archive.2.zip)
|
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| 2,551,457,094
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PR_kwDOACgets581_uy
| 4,081
|
Allow more than 20 terminal groups in CompoundPhaseDiagram
|
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[] | null |
[
"There are merge conflicts. Pls fix them first. Thanks.",
"Resolved, thanks."
] | 2024-09-26T20:15:44
| 2024-10-21T21:00:09
|
2024-10-21T21:00:09Z
|
CONTRIBUTOR
|
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## Summary
Major changes:
- fix 1: CompoundPhaseDiagram can now have more than 20 terminal groups
|
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PR_kwDOACgets582pGd
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SLME Bug Fixes
|
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[] | null |
[
"Thanks @kavanase! Will merge. \r\n\r\n@knc6, notifying yourself too as a courtesy since I think you originally contributed this functionality, just in case the bug has affected you.",
"Realised we should have asked for a test modification here too, but the fix seems clear enough to me."
] | 2024-09-26T22:41:53
| 2024-09-27T02:18:34
|
2024-09-27T02:17:34Z
|
CONTRIBUTOR
|
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This fixes some bugs in the `slme` code:
- Avoids overwriting the input data, which was leading to SLME results changing every time the function was (repeatedly) called.
- Removes some hard-coded settings for the plot and adds some labels
|
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PR_kwDOACgets589Se7
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|
Fix bug with species defaults
|
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[] | 2024-09-27T19:19:16
| 2024-10-02T19:39:47
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2024-10-02T19:39:47Z
|
CONTRIBUTOR
|
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Need to specify the default value properly
## Summary
Major changes:
- fix 1: Species Defaults need to be read from SETTINGS object
## 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_kwDOACgets59A8kt
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Fix usage of `strict=True` for `zip` in `cp2k.outputs`
|
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[] | null |
[
"Given that no one has commented, I will merge. People can complain if they run into problems.",
"Thanks, anyone with experience in CP2K please feel free to comment.",
"@shyuep @janosh @mkhorton Could a new version of pymatgen be released? We see Cp2k output related failures showing up in atomate2 ",
"Done",
"@shyuep Thank you very much for the fast reaction!"
] | 2024-09-29T03:53:44
| 2024-10-03T17:30:10
|
2024-10-02T19:41:00Z
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CONTRIBUTOR
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### Summary
- Fix usage of `strict=True` during `zip` in `cp2k.outputs`, to fix #4079
- [ ] Add unit tests? (**need input**)
- Rename and clean up some tests
I have to revert to `strict=False` for now, but **it's better if we could know the reason for such mismatch**. Anyone experienced with CP2K please feel free to comment.
|
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I_kwDOACgets6YSx2G
| 4,085
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`pymatgen.analysis.structure_matcher.StructureMatcher.fit()` does not work properly on structures with `selective_dynamics` property
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[
"Thanks for the detailed diagnosis, I could recreate this "
] | 2024-09-29T18:19:40
| 2024-10-02T19:41:23
|
2024-10-02T19:41:23Z
|
NONE
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### Python version
Python 3.10.14
### Pymatgen version
Version: 2024.9.17
### Operating system version
Red Hat Enterprise Linux Ver 8.6
### Current behavior
A `Poscar` object created from a POSCAR string with Selective Dynamics stores `selective_dynamics` as a NumPy array of booleans. However, these arrays cannot be directly compared using the `==` operator.
This error can be easily demonstrated with the following code:
```
import numpy as np
site_prop_1 = {"selective_dynamics": np.array([True, True, False])}
site_prop_2 = {"selective_dynamics": np.array([True, True, False])}
print(site_prop_1 == site_prop_2)
# -> ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
```
This error can cause issues during the `pymatgen.analysis.structure_matcher.StructureMatcher.fit()` process. A simple example using `StructureMatcher.fit()` will be provided later.
Just to be clear, I'm using NumPy ver. 1.26.0.
### Expected Behavior
It is desirable that the structure variable of a Poscar object created by Poscar.from_str can be directly compared using StructureMatcher.fit() without any additional processing such as casting to a list.
### Minimal example
```Python
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.io.vasp.inputs import Poscar
poscar_string = """\
H
1.0
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
H
1
Selective dynamics
direct
0.000 0.000 0.000 F F T H
"""
poscar1 = Poscar.from_str(poscar_string)
poscar2 = Poscar.from_str(poscar_string)
structure1 = poscar1.structure
structure2 = poscar2.structure
sm = StructureMatcher()
sm.fit(struct1=structure1, struct2=structure2)
```
### Relevant files to reproduce this bug
_No response_
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PR_kwDOACgets59FCWN
| 4,086
|
Fix dict equality check with numpy array
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[] | null |
[
"Thanks.",
"I realized I didn't really test other data types other than string, list and np.array (all are sequences of some sort). **Would `np.array_equal` fail for any dtype?** From the source code, looks like it would return `False` directly for any dtype that cannot be converted to an array: https://github.com/numpy/numpy/blob/2f7fe64b8b6d7591dd208942f1cc74473d5db4cb/numpy/_core/numeric.py#L2550-L2553\r\n\r\nOr do we want to play safe, loop through each value, `try` to compare with `==`, `except` any exception, use `np.array_equal` as a fallback option? \r\n- [ ] need speed benchmark\r\n"
] | 2024-09-30T08:20:27
| 2024-10-03T03:19:15
|
2024-10-02T19:41:22Z
|
CONTRIBUTOR
|
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### Summary
- Fix dict equality check with numpy array, to fix #4085
- Added a helper function to compare two dicts because I have a feeling some other parts of the code might need it as well
- [x] Add unit tests
- [x] Add unit tests for new util function
### Efficiency
Turns out `np.testing.assert_equal` is much slower than `np.array_equal` for each value. See the following benchmark:
<details>
<summary>Script (by GPT)</summary>
```python
import numpy as np
import time
# 1. Comparison using `np.testing.assert_equal()`
def dicts_equal_np_test_assert(d1, d2):
"""Compare two dictionaries using np.testing.assert_equal."""
try:
np.testing.assert_equal(d1, d2)
return True
except AssertionError:
return False
# 2. Comparison by using array_equal
def dicts_equal_array_equal(d1, d2):
"""Compare two dictionaries by using np.array_equal."""
if d1.keys() != d2.keys():
return False
for key in d1:
if not np.array_equal(d1[key], d2[key]):
return False
return True
# Helper function to average the time over 10 runs
def average_time(func, d1, d2, num_runs=10):
total_time = 0
for _ in range(num_runs):
start = time.time()
func(d1, d2)
total_time += time.time() - start
return total_time / num_runs
# 4. Running comparisons across array sizes
def run_comparisons(array_size):
"""Generate test dictionaries and run comparison methods."""
# Create two identical dictionaries with numpy arrays
arr1 = np.random.random(array_size)
arr2 = np.copy(arr1) # Create an identical array for comparison
d1 = {"array": arr1}
d2 = {"array": arr2}
print(f"\nComparing dictionaries with array size: {array_size}")
# 4.1. Using np.testing.assert_equal (averaged over 10 runs)
avg_time_np_assert = average_time(dicts_equal_np_test_assert, d1, d2)
print(f"np.testing.assert_equal: Average Time = {avg_time_np_assert * 1E6:.4f} microseconds")
# 4.2. Using np.array_equal (averaged over 10 runs)
avg_time_list_cast = average_time(dicts_equal_array_equal, d1, d2)
print(f"np.array_equal: Average Time = {avg_time_list_cast * 1E6:.4f} microseconds")
if __name__ == "__main__":
# Test with different array sizes
for size in [1, 10, 100, 1000, 10_000]:
run_comparisons(size)
```
</details>
```
Comparing dictionaries with array size: 1
np.testing.assert_equal: Average Time = 2419.4241 microseconds
np.array_equal: Average Time = 2.5749 microseconds
Comparing dictionaries with array size: 10
np.testing.assert_equal: Average Time = 19.1927 microseconds
np.array_equal: Average Time = 1.4067 microseconds
Comparing dictionaries with array size: 100
np.testing.assert_equal: Average Time = 19.1450 microseconds
np.array_equal: Average Time = 1.2159 microseconds
Comparing dictionaries with array size: 1000
np.testing.assert_equal: Average Time = 21.8868 microseconds
np.array_equal: Average Time = 1.5020 microseconds
Comparing dictionaries with array size: 10000
np.testing.assert_equal: Average Time = 43.8929 microseconds
np.array_equal: Average Time = 4.3869 microseconds
```
|
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PR_kwDOACgets59JujH
| 4,087
|
Enable parsing of "SCF energy" and "Total energy" from `QCOutput` for Q-chem 6.1.1+
|
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[
"Thank you @Jaebeom-P ! Tagging @Andrew-S-Rosen and @samblau as well.\r\n\r\nThis looks clean and straightforward to me. We will need to make sure all the existing tests pass too (i.e., this doesn't break any of the previous versions), but I don't think it should. Because this is your first contribution to pymatgen, I think @shyuep has to approve the PR before the automatic tests will run.",
"Great. Thanks for the contribution."
] | 2024-09-30T17:39:05
| 2024-10-02T19:39:14
|
2024-10-02T19:39:01Z
|
CONTRIBUTOR
|
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## Summary
Additional parser update for #3578, similar to #3580, for Q-chem 6.1.1+. This PR addresses errors in the `QCOutput._read_optimization_data()` and `QCOutput._read_frequency_data()` functions, which are essential for FFOpt (Frequency Flattening Optimization) functionality from `custodian` and `atomate2` package.
CC: @rkingsbury
## 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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| Metric | Average | Median | 90th percentile |
| --- | --- | --- | ---: |
| Time to first response | 5:21:58 | 3:12:13 | 13:24:19 |
| Time to close | 1 day, 12:01:00 | 6:59:41 | 3 days, 22:10:49 |
| Time to answer | None | None | None |
| Metric | Count |
| --- | ---: |
| Number of items that remain open | 15 |
| Number of items closed | 7 |
| Number of most active mentors | 0 |
| Total number of items created | 22 |
| Title | URL | Author | Time to first response | Time to close | Time to answer |
| --- | --- | --- | --- | --- | --- |
| `pymatgen.analysis.structure_matcher.StructureMatcher.fit()` does not work properly on structures with `selective_dynamics` property | https://www.github.com/materialsproject/pymatgen/issues/4085 | [yutoml](https://github.com/yutoml) | 13:58:41 | None | None |
| Parsing cp2k output fails after v2024.8.9 release. | https://www.github.com/materialsproject/pymatgen/issues/4079 | [msiron-entalpic](https://github.com/msiron-entalpic) | 14:02:02 | None | None |
| pymatgen fails to load MPRester | https://www.github.com/materialsproject/pymatgen/issues/4077 | [jjkas](https://github.com/jjkas) | 0:13:40 | None | None |
| More Flexible `Vasprun` Parsing | https://www.github.com/materialsproject/pymatgen/issues/4075 | [kavanase](https://github.com/kavanase) | None | None | None |
| Fix `ruff` PERF401 | https://www.github.com/materialsproject/pymatgen/issues/4064 | [janosh](https://github.com/janosh) | None | None | None |
| get_band_structure_from_vasp_multiple_branches | https://www.github.com/materialsproject/pymatgen/issues/4060 | [Nokimann](https://github.com/Nokimann) | 2:39:44 | None | None |
| [Dev/Docs] Automate docs generation and exclude HTML from VCS | https://www.github.com/materialsproject/pymatgen/issues/4056 | [DanielYang59](https://github.com/DanielYang59) | None | None | None |
| pymatgen no "_init_.py" file | https://www.github.com/materialsproject/pymatgen/issues/4050 | [YXT996](https://github.com/YXT996) | 2:20:44 | 2:20:44 | None |
| pymatgen no "_init_.py" file | https://www.github.com/materialsproject/pymatgen/issues/4049 | [YXT996](https://github.com/YXT996) | 2:21:25 | 5:47:28 | None |
| BUG: INCAR Updates not working | https://www.github.com/materialsproject/pymatgen/issues/4051 | [JaGeo](https://github.com/JaGeo) | 3:12:49 | 6:59:41 | None |
| `ValueErrors` in the `CoherentInterfaceBuilder` | https://www.github.com/materialsproject/pymatgen/issues/4047 | [nightroxide](https://github.com/nightroxide) | 6:56:28 | 15:32:08 | None |
| [BUG] Entire `BoltztrapPlotter` is broken | https://www.github.com/materialsproject/pymatgen/issues/4045 | [DanielYang59](https://github.com/DanielYang59) | None | None | None |
| Use `astral-sh/setup-uv` in CI | https://www.github.com/materialsproject/pymatgen/issues/4044 | [janosh](https://github.com/janosh) | 8:15:04 | 7 days, 15:12:40 | None |
| Free energy correction | https://www.github.com/materialsproject/pymatgen/issues/4043 | [shyuep](https://github.com/shyuep) | None | None | None |
| [Enhancement] Update `incar_parameters.json` file under `io.vasp` | https://www.github.com/materialsproject/pymatgen/issues/4042 | [DanielYang59](https://github.com/DanielYang59) | None | None | None |
| [Enhancement] Enable `terminate_on_match` for `Outcar` parser | https://www.github.com/materialsproject/pymatgen/issues/4041 | [DanielYang59](https://github.com/DanielYang59) | None | None | None |
| [CI] Unit test of `boltztrap2` generate files inplace | https://www.github.com/materialsproject/pymatgen/issues/4040 | [DanielYang59](https://github.com/DanielYang59) | None | None | None |
| [Doc/Dev] Off-by-one errors for line numbers in documentation `source` | https://www.github.com/materialsproject/pymatgen/issues/4038 | [DanielYang59](https://github.com/DanielYang59) | None | None | None |
| Outcar class returns empty magnetization attribute when parsing OUTCAR file on Windows operating system | https://www.github.com/materialsproject/pymatgen/issues/4033 | [KylinGuo](https://github.com/KylinGuo) | 4:02:23 | None | None |
| noncollinear attribute of Outcar class has wrong value for VASP calculations with LNONCOLLINEAR=.TRUE. | https://www.github.com/materialsproject/pymatgen/issues/4031 | [KylinGuo](https://github.com/KylinGuo) | 3:09:02 | 1 day, 10:49:35 | None |
| [DOCS] Links to source in each function returns a 404 error | https://www.github.com/materialsproject/pymatgen/issues/4030 | [tawe141](https://github.com/tawe141) | 3:11:37 | 3:24:42 | None |
| CifParser taking forever without throwing an error | https://www.github.com/materialsproject/pymatgen/issues/4028 | [anyangml](https://github.com/anyangml) | None | None | None |
_This report was generated with the [Issue Metrics Action](https://github.com/github/issue-metrics)_
Search query used to find these items: `repo:materialsproject/pymatgen is:issue created:2024-09-01..2024-09-30 -reason:"not planned"`
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I_kwDOACgets6YlLkl
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Glob logic with `bader_analysis_from_path` is error-prone
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[] | 2024-10-01T18:06:41
| 2024-10-01T20:30:52
|
MEMBER
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### Python version
3.11.9
### Pymatgen version
2024.9.17.1
### Operating system version
Linux
### Current behavior
When calling `bader_analysis_from_path`, I get an indexing error due to poor glob logic.
### Expected Behavior
No indexing error
### Minimal example
The following files are taken directly from MP.
```Python
from monty.serialization import loadfn
from pymatgen.command_line.bader_caller import bader_analysis_from_path
chgcar = loadfn('CHGCAR.json.gz')['data']
aeccar0 = loadfn('AECCAR0.json.gz')['data']
aeccar2 = loadfn('AECCAR2.json.gz')['data']
chgcar.write_file('CHGCAR')
aeccar0.write_file('AECCAR0')
aeccar2.write_file('AECCAR2')
bader_analysis_from_path('.')
```
Traceback:
```python
File /scratch/gpfs/asrosen/software/miniconda/envs/quacc/lib/python3.11/site-packages/pymatgen/command_line/bader_caller.py:537, in bader_analysis_from_path(path, suffix)
535 if not aeccar0_path:
536 warnings.warn("Could not find AECCAR0, interpret Bader results with severe caution!")
--> 537 aeccar0 = Chgcar.from_file(aeccar0_path) if aeccar0_path else None
539 aeccar2_path = _get_filepath("AECCAR2")
540 if not aeccar2_path:
File /scratch/gpfs/asrosen/software/miniconda/envs/quacc/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:3711, in Chgcar.from_file(cls, filename)
3701 @classmethod
3702 def from_file(cls, filename: str) -> Self:
3703 """Read a CHGCAR file.
3704
3705 Args:
(...)
3709 Chgcar
3710 """
-> 3711 poscar, data, data_aug = VolumetricData.parse_file(filename)
3712 return cls(poscar, data, data_aug=data_aug)
File /scratch/gpfs/asrosen/software/miniconda/envs/quacc/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:3562, in VolumetricData.parse_file(filename)
3557 data_aug = {
3558 "total": all_dataset_aug.get(0),
3559 "diff": all_dataset_aug.get(1),
3560 }
3561 else:
-> 3562 data = {"total": all_dataset[0]}
3563 data_aug = {"total": all_dataset_aug.get(0)}
3564 return poscar, data, data_aug
IndexError: list index out of range
```
This is because of the following code, which is looking for the `.json.gz` files instead of the newly written out files:
https://github.com/materialsproject/pymatgen/blob/fa62ff460762f431014177e63a695c013c984391/src/pymatgen/command_line/bader_caller.py#L515-L527
### Relevant files to reproduce this bug
[CHGCAR.json.gz](https://github.com/user-attachments/files/17214097/CHGCAR.json.gz)
[AECCAR0.json.gz](https://github.com/user-attachments/files/17214098/AECCAR0.json.gz)
[AECCAR2.json.gz](https://github.com/user-attachments/files/17214099/AECCAR2.json.gz)
CC @aryannsaha
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Bump webrick from 1.8.1 to 1.8.2 in /docs
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[] | 2024-10-02T20:14:35
| 2024-10-21T20:59:37
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2024-10-21T20:59:35Z
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CONTRIBUTOR
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Bumps [webrick](https://github.com/ruby/webrick) from 1.8.1 to 1.8.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/ruby/webrick/releases">webrick's releases</a>.</em></p>
<blockquote>
<h2>v1.8.2</h2>
<h2>What's Changed</h2>
<ul>
<li>Drop commented-out line by <a href="https://github.com/olleolleolle"><code>@olleolleolle</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/108">ruby/webrick#108</a></li>
<li>Add Ruby 3.1 & 3.2 to CI matrix by <a href="https://github.com/tricknotes"><code>@tricknotes</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/109">ruby/webrick#109</a></li>
<li>Fix/redos by <a href="https://github.com/ooooooo-q"><code>@ooooooo-q</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/114">ruby/webrick#114</a></li>
<li>Raise HTTPStatus::BadRequest for requests with invalid/duplicate content-length headers by <a href="https://github.com/jeremyevans"><code>@jeremyevans</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/120">ruby/webrick#120</a></li>
<li>Bump actions/checkout from 3 to 4 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/121">ruby/webrick#121</a></li>
<li>Improve CI by <a href="https://github.com/hsbt"><code>@hsbt</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/123">ruby/webrick#123</a></li>
<li>Fix WEBrick::TestFileHandler#test_short_filename test not working on mswin by <a href="https://github.com/KJTsanaktsidis"><code>@KJTsanaktsidis</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/128">ruby/webrick#128</a></li>
<li>Fix bug chunk extension detection by <a href="https://github.com/jeremyevans"><code>@jeremyevans</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/125">ruby/webrick#125</a></li>
<li>Fix CI. by <a href="https://github.com/ioquatix"><code>@ioquatix</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/131">ruby/webrick#131</a></li>
<li>Merge multiple cookie headers, preserving semantic correctness. by <a href="https://github.com/ioquatix"><code>@ioquatix</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/130">ruby/webrick#130</a></li>
<li>Test on macos-latest by <a href="https://github.com/byroot"><code>@byroot</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/132">ruby/webrick#132</a></li>
<li>Require CRLF line endings in request line and headers by <a href="https://github.com/jeremyevans"><code>@jeremyevans</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/138">ruby/webrick#138</a></li>
<li>Prefer squigly heredocs. by <a href="https://github.com/ioquatix"><code>@ioquatix</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/143">ruby/webrick#143</a></li>
<li>Only strip space and horizontal tab in headers by <a href="https://github.com/jeremyevans"><code>@jeremyevans</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/141">ruby/webrick#141</a></li>
<li>Treat missing CRLF separator after headers as an EOFError by <a href="https://github.com/jeremyevans"><code>@jeremyevans</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/142">ruby/webrick#142</a></li>
<li>Return 400 response for chunked requests with unexpected data after chunk by <a href="https://github.com/jeremyevans"><code>@jeremyevans</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/136">ruby/webrick#136</a></li>
<li>Fix reference to URI::REGEXP::PATTERN::HOST by <a href="https://github.com/casperisfine"><code>@casperisfine</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/144">ruby/webrick#144</a></li>
<li>Prevent request smuggling by <a href="https://github.com/jeremyevans"><code>@jeremyevans</code></a> in <a href="https://redirect.github.com/ruby/webrick/pull/146">ruby/webrick#146</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/tricknotes"><code>@tricknotes</code></a> made their first contribution in <a href="https://redirect.github.com/ruby/webrick/pull/109">ruby/webrick#109</a></li>
<li><a href="https://github.com/ooooooo-q"><code>@ooooooo-q</code></a> made their first contribution in <a href="https://redirect.github.com/ruby/webrick/pull/114">ruby/webrick#114</a></li>
<li><a href="https://github.com/KJTsanaktsidis"><code>@KJTsanaktsidis</code></a> made their first contribution in <a href="https://redirect.github.com/ruby/webrick/pull/128">ruby/webrick#128</a></li>
<li><a href="https://github.com/byroot"><code>@byroot</code></a> made their first contribution in <a href="https://redirect.github.com/ruby/webrick/pull/132">ruby/webrick#132</a></li>
<li><a href="https://github.com/casperisfine"><code>@casperisfine</code></a> made their first contribution in <a href="https://redirect.github.com/ruby/webrick/pull/144">ruby/webrick#144</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/ruby/webrick/compare/v1.8.1...v1.8.2">https://github.com/ruby/webrick/compare/v1.8.1...v1.8.2</a></p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/ruby/webrick/commit/0fb9de6788a3ba5fe903e63d778a0fb8c1dce786"><code>0fb9de6</code></a> Bump up v1.8.2</li>
<li><a href="https://github.com/ruby/webrick/commit/b9a4c81ea94dec02a750c6b34092c55234519bf1"><code>b9a4c81</code></a> Removed trailing spaces</li>
<li><a href="https://github.com/ruby/webrick/commit/f5faca9222541591e1a7c3c97552ebb0c92733c7"><code>f5faca9</code></a> Prevent request smuggling</li>
<li><a href="https://github.com/ruby/webrick/commit/0c600e169bd4ae267cb5eeb6197277c848323bbe"><code>0c600e1</code></a> Fix reference to URI::REGEXP::PATTERN::HOST</li>
<li><a href="https://github.com/ruby/webrick/commit/15a93914782789520837c334e0c302702aec34e2"><code>15a9391</code></a> Return 400 response for chunked requests with unexpected data after chunk</li>
<li><a href="https://github.com/ruby/webrick/commit/2b38d5614e876d313fe981e87c4e35b91556d226"><code>2b38d56</code></a> Treat missing CRLF separator after headers as an EOFError</li>
<li><a href="https://github.com/ruby/webrick/commit/e4efb4a2300540f14f93c09c06bf0357ac1597dc"><code>e4efb4a</code></a> Remove unnecessary gsub calls in test_httprequest.rb</li>
<li><a href="https://github.com/ruby/webrick/commit/426e214532bb0be5e4ab8b3c9cef328432012d0d"><code>426e214</code></a> Only strip space and horizontal tab in headers</li>
<li><a href="https://github.com/ruby/webrick/commit/e72cb697836e2ff201a4a74c108fdca9d3d2d0ed"><code>e72cb69</code></a> Prefer squigly heredocs. (<a href="https://redirect.github.com/ruby/webrick/issues/143">#143</a>)</li>
<li><a href="https://github.com/ruby/webrick/commit/ee60354bcb84ec33b9245e1d1aa6e1f7e8132101"><code>ee60354</code></a> Require CRLF line endings in request line and headers</li>
<li>Additional commits viewable in <a href="https://github.com/ruby/webrick/compare/v1.8.1...v1.8.2">compare view</a></li>
</ul>
</details>
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PR_kwDOACgets59b17P
| 4,091
|
Review edits
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[
"Wrong fork"
] | 2024-10-02T23:09:33
| 2024-10-02T23:10:52
|
2024-10-02T23:10:02Z
|
CONTRIBUTOR
|
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Merging edits from shyuep's review comments into master
## Summary
Major changes:
- valence electron dictionary replaced with references to Element class
- get_atom_valence_electrons method created within data.py to circumvent current error raised on the "valence" property of an Element
- missing __init__.py added
- moved README text into __init__.py docustring, removed README.md
- improved clarity of docustring language for jeiter module to distinguish from jeiters module
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PR_kwDOACgets59cncJ
| 4,092
|
Enhance test for util function `is_np_dict_equal`
|
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[
"The experimental implementation (with try-except) is slightly slower than using `np.array_equal`:\r\n```\r\nArray size: 10\r\nis_np_dict_equal: 3.38 µs\r\nis_np_dict_equal_try_except: 2.03 µs\r\n--------------------------------------------------\r\nArray size: 100\r\nis_np_dict_equal: 1.64 µs\r\nis_np_dict_equal_try_except: 1.77 µs\r\n--------------------------------------------------\r\nArray size: 1000\r\nis_np_dict_equal: 1.86 µs\r\nis_np_dict_equal_try_except: 2.29 µs\r\n--------------------------------------------------\r\nArray size: 10000\r\nis_np_dict_equal: 4.20 µs\r\nis_np_dict_equal_try_except: 7.01 µs\r\n--------------------------------------------------\r\nArray size: 100000\r\nis_np_dict_equal: 25.15 µs\r\nis_np_dict_equal_try_except: 43.69 µs\r\n--------------------------------------------------\r\nArray size: 1000000\r\nis_np_dict_equal: 330.77 µs\r\nis_np_dict_equal_try_except: 424.17 µs\r\n--------------------------------------------------\r\n```\r\n\r\nStill not sure what dtype would cause `np.array_equal` to fail. **Input would be hugely appreciated.**\r\n\r\n<details>\r\n\r\n<summary> Benchmark script (GPT) </summary>\r\n\r\n```python\r\nimport timeit\r\nimport numpy as np\r\nfrom pymatgen.util.misc import is_np_dict_equal, is_np_dict_equal_try_except\r\n\r\n\r\n# Function to run the benchmarks\r\ndef benchmark(func, dict1, dict2, runs=10):\r\n timings = timeit.repeat(lambda: func(dict1, dict2), repeat=runs, number=1)\r\n avg_time = (sum(timings) / runs) * 1e6 # Convert to microseconds\r\n return avg_time\r\n\r\n# Function to generate dictionaries with np arrays of different sizes\r\ndef generate_dict(size):\r\n arr = np.random.rand(size)\r\n dict1 = {\"a\": arr}\r\n dict2 = {\"a\": arr.copy()} # Ensure they are equal but independent\r\n return dict1, dict2\r\n\r\n# Sizes to test\r\nsizes = [10, 100, 1000, 10_000, 100_000, 1_000_000]\r\n\r\n# Benchmark each size\r\nfor size in sizes:\r\n dict1, dict2 = generate_dict(size)\r\n\r\n # Benchmark is_np_dict_equal\r\n avg_time_equal = benchmark(is_np_dict_equal, dict1, dict2)\r\n\r\n # Benchmark is_np_dict_equal_try_except\r\n avg_time_equal_try_except = benchmark(is_np_dict_equal_try_except, dict1, dict2)\r\n\r\n print(f\"Array size: {size}\")\r\n print(f\"is_np_dict_equal: {avg_time_equal:.2f} µs\")\r\n print(f\"is_np_dict_equal_try_except: {avg_time_equal_try_except:.2f} µs\")\r\n print(\"-\" * 50)\r\n```\r\n\r\n</details>"
] | 2024-10-03T03:19:04
| 2024-10-22T02:05:46
|
2024-10-21T20:59:52Z
|
CONTRIBUTOR
|
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### Summary
- Enhance test for `is_np_dict_equal` with different data types, follow up #4086
|
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PR_kwDOACgets59i_hv
| 4,093
|
Correctly compute rotational symmetry number for D*h point group
|
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[
"Thanks."
] | 2024-10-03T20:01:47
| 2024-10-22T02:43:26
|
2024-10-22T02:43:20Z
|
CONTRIBUTOR
|
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Correct value is 2.
Example is H2. Also see See, for example, Table 10.1 and Appendix B of C. Cramer “Essentials of Computational Chemistry”, 2nd Ed.
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PR_kwDOACgets59kHD0
| 4,094
|
added ramannoodle external package to addons.md
|
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[
"Thanks. Looks like a useful package!"
] | 2024-10-04T01:26:12
| 2024-10-04T01:49:33
|
2024-10-04T01:49:10Z
|
CONTRIBUTOR
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## Summary
I'm the maintainer of [ramannoodle](https://github.com/wolearyc/ramannoodle), an new API for calculating off-resonance Raman spectra from first principles calculations. The API includes an interface with pymatgen, and I wish to add it to pymatgen's list of external packages.
Cheers,
Willis
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|
Prevent unit test of `boltztrap2` from modifying files in place
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[] | 2024-10-04T03:16:45
| 2024-10-26T02:03:02
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2024-10-25T21:25:47Z
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CONTRIBUTOR
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### Summary
- Prevent unit test of `boltztrap2` from modifying files in place, to close #4040
- [x] relocate tests from `setUp` method
> [!CAUTION]
> [NEED CONFIRM] replace very general `BoltztrapError` with more semantic exception type, cec569fef7d63dd70dd220c12d6389d4f4bb346d
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[] | 2024-10-07T21:46:29
| 2024-10-21T20:59:22
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2024-10-21T20:59:20Z
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CONTRIBUTOR
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<!--pre-commit.ci start-->
updates:
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- [github.com/RobertCraigie/pyright-python: v1.1.379 → v1.1.383](https://github.com/RobertCraigie/pyright-python/compare/v1.1.379...v1.1.383)
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PR_kwDOACgets5-AYcj
| 4,097
|
Fix `selective_dyn` handling issue in `python>=3.12`
|
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[
"Thanks."
] | 2024-10-08T22:52:52
| 2024-10-23T01:28:52
|
2024-10-23T01:28:49Z
|
CONTRIBUTOR
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Hi,
I noticed I was getting some deprecation warnings like these, when parsing `vasprun.xml` files with `python=3.12`:
```
[DeprecationWarning("Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead."), DeprecationWarning("Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.")]
```
I traced this down to this line (https://github.com/materialsproject/pymatgen/blob/master/src/pymatgen/io/vasp/outputs.py#L1465).
With this small update, it fixes `selective_dyn` handling (as mentioned in the warning, this would always be set to `True` with future versions) and avoids these deprecation warnings.
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