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https://api.github.com/repos/materialsproject/pymatgen/issues/2404
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Finding Symmetrically Equivalent Bonds (Neighbors) in Structure
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[
"Thanks. I would suggest you go ahead and implement the PeriodicBond or Bond first. It shouldn't be a subclass of PeriodicNeighbor, but rather is a container of the starting site and the PeriodicNeighbor.",
"\n[](https://coveralls.io/builds/48680679)\n\nCoverage decreased (-0.7%) to 83.297% when pulling **7437cc64fc8a850d4820ce5043c896a89bd0019a on nheinsdorf:master** into **834dc9c507f0ceb735887be2db358be37c52a4d7 on materialsproject:master**.\n",
"Thanks for this PR @nheinsdorf!\r\n\r\nAnother place to put this may even be `pymatgen.analysis.graphs.StructureGraph`. That way the method can be more agnostic to _how_ the bond is determined, e.g. a neighbor list is not necessarily equal to a list of bonds.",
"Hey @mkhorton, \r\nyeah I know that you gave the incentive back then on the FAQ to use pymatgen's graph functionality. I agree that due to the different environments it is more flexible, and also that you are free to define some properties of a node. Here, I wanted to start with the simplest example of just considering connections between points with no intrinsic properties that might also transform under the symmetry. E.g. it would be nice if one could put orbitals on a site and then the algorithm could also check whether some symmetry is able to map the orbitals on top of each other (same with spin or some magnetic configurations). ",
"Just made sure that always the first instance of a bond of a certain symmetry index in the output is the one that is assigned the identity matrix as a symmetry operation. That's more convenient when constructing models with the neighbor list that are generated by the symmetries that connect the bonds. ",
"Hey @mkhorton, so I added some extra functionality to the two functions I implemented. I did this because I noticed I run into problems with the previous implementations. Let me illustrate: \r\nI used the new 'get_symmetric_neighbor_list' to build a physical model. Each neighbor (which I will call bond from now on) was given some exchange vector D that also has to obey the symmetries of the model. In the previous version, get_symmetric_neighbor_list essentially gave every bond twice. From i to j along R and from j to i along -R. Usually, if a physical model is built, only one of these bond is considered, since the inverted direction just corresponds to the hermitian conjugate. This is why I implemented the option 'unique'. If True, the code will output each bond once. \r\n\r\nThen I ran into the problem that 'are_symmetrically_related_bond' does not check for the direction of the bond, since from i to j along R is equivalent to j to i along -R. I added a bool to the method's output that allows the user to trace whether a bond has been inverted or not. 'get_symmetric_neighbor_list' makes use of that. If unique is set to True, it always gives the bond in the output that has NOT been inverted. Now it is ensured that applying the symmetry operation associated with given bond to the first bond with the same symmetry_index, yields the actual bond and not its inverted counterpart. \r\n\r\nIf I now associate the vector D to a given bond, applying the symmetry operations from the output of 'get_symmetric_neighbor_list' to D generates the right vector (pointing in the right direction) for each bond. \r\n\r\nI can gladly provide a code example where this is used to conveniently build a magnetic low-energy model with DM exchange. ",
"Thanks for the added context @nheinsdorf. Indeed, some of the issues you mention, namely bond \"directionality\" and equivalency, are handled by the StructureGraph class which encodes a bond as a directed edge and ensures that duplicate bonds cannot be added. However, that code is not symmetry-aware, so definitely inferior in that sense to the code suggested in this PR. The advantage of the StructureGraph is simply that it acts a container for this kind of bond information, providing a unified interface and allowing it to be easily serialized and deserialized alongside the corresponding Structure, though at the cost of efficiency in terms of instantiating the class.\r\n\r\nThis PR looks to be high quality, so I would be glad to merge it in some form.\r\n\r\nFor code review, I have two questions:\r\n\r\n(1) what is the purpose of the commented-out test block, should this be retained?\r\n\r\n(2) The docstring for `get_symmetric_neighbor_list` is excellent, but the code itself is a little difficult to follow, some comments throughout would be welcome.\r\n\r\nIf you were happy to share the code example to test, that would definitely be useful. I believe you can attach files to a Github comment.",
"Hey @mkhorton , \r\nThank you very much for your feedback. Concerning your points\r\n1) You mean the block above `test_get_symmetric_neighbor_list`? I did not add it. It was contained in the repo I cloned. \r\n2) I can add comments! Browsing through the source code it felt like that most of the commenting is done in the docstring, but not in the actual code. But I can add some comments in between steps, no problem!\r\n\r\nWhen I have some time, I'll put to together an example script with maybe some images to show the intended use of the code!",
"As promised:\r\n\r\nAn example script that uses the new functionality to generate generate spin exchanges for a toy model. The following code generates the figure that is given below: \r\n\r\n```\r\nfrom pymatgen.core.structure import Structure\r\n\r\nimport numpy as np\r\nimport matplotlib.pyplot as plt\r\nfrom mpl_toolkits.mplot3d import Axes3D\r\nfrom matplotlib.lines import Line2D\r\n\r\nclass SpinModelExample(object):\r\n \"\"\"\r\n Example for using the 'get_symmetric_neighbor_list'-method.\r\n We use it to first find the all the next-nearest neighbors in \r\n a localized magnetic moment model with space group 198. We use\r\n the method's functionality to first distinguish two symmetrically\r\n inequivalent hoppings to assign different exchanges. Next, we assign\r\n an antisymmetric exchange (Dzyalioshinskii-Moriya) to the bonds and \r\n use the method to rotate the exchange vector in accordance with the\r\n space groups symmetry. \r\n \r\n \"\"\"\r\n\r\n def __init__(self):\r\n\r\n # Lattice parameters\r\n a = 8.908\r\n self.SG = 198\r\n lattice = [[a, 0, 0], [0, a, 0], [0, 0, a]]\r\n\r\n # Initialize structure\r\n self.struc = Structure.from_spacegroup(self.SG, lattice, ['Cu'], [[0, 0, 0]])\r\n\r\n self.bonds = None\r\n self.Js = None\r\n self.Ds = None\r\n\r\n def examplify_symmetry_indices(self, J1=-1, J2=-1.5):\r\n \"\"\"\r\n Use 'get_symmetric_neighbor_list' to find all next-nearest neigbhors.\r\n Note that we provide the space group to the method. If that is not \r\n done, the method will try to determine the space group based on the \r\n Structure, which in our case has higher symmetry than space group 198, because\r\n we only provided the atoms that have a finite, localized magnetic moment.\r\n Further, we set unique to True, because we only want to consider each \r\n bond once (not back and forth).\r\n \"\"\"\r\n\r\n self.bonds = self.struc.get_symmetric_neighbor_list(7, sg=self.SG, unique=True)\r\n\r\n # All nearest neighbors have the same distance.\r\n print(f'Unique distances: {np.unique(self.bonds[3])}\\n')\r\n\r\n # Naively, we would consider all of these equivalent. However, checking\r\n # the symmetry indices assigned by the methods, we see that there are \r\n # actually two groups of symmetrically inequvialent nearest neighbors.\r\n print(f'Symmetrically inequivalent neighbors {int(np.max(self.bonds[4]) + 1)}\\n')\r\n\r\n # Let us use this information to assign two hopping parameters to the \r\n # symmetrically distinct nearest neighbors\r\n sym_idcs = self.bonds[4]\r\n self.Js = np.zeros(sym_idcs.shape)\r\n self.Js[np.where(sym_idcs == 0)] = J1\r\n self.Js[np.where(sym_idcs == 1)] = J2\r\n\r\n print('#\\tSymmetry\\tExchange\\n')\r\n for _, (sym_idx, J) in enumerate(zip(sym_idcs, self.Js)):\r\n print(f'{_}\\t{int(sym_idx)}\\t{J}')\r\n print('\\n')\r\n\r\n def examplify_symmetry_ops(self, D1=[0, 0, 0.1], D2=[0, 0, -0.2]):\r\n \"\"\"\r\n Use 'get_symmetric_neighbor_list' to assign vector quantities to \r\n symmetrically equivalent bonds and make sure they transform according\r\n to the symmetry of the provided space group.\r\n \"\"\"\r\n\r\n # Again, we start by constructing all the nearest neighbors\r\n self.bonds = self.struc.get_symmetric_neighbor_list(7, sg=self.SG, unique=True)\r\n sym_idcs = self.bonds[4]\r\n sym_ops = self.bonds[5]\r\n self.Ds = np.zeros((sym_idcs.shape[0], 3))\r\n for _, (sym_idx, sym_op) in enumerate(zip(sym_idcs, sym_ops)):\r\n if sym_idx == 0:\r\n self.Ds[_] = sym_op.apply_rotation_only(D1)\r\n if sym_idx == 1:\r\n self.Ds[_] = sym_op.apply_rotation_only(D2)\r\n\r\n print('#\\tSymmetry\\tExchange\\n')\r\n for _, (sym_idx, D) in enumerate(zip(sym_idcs, self.Ds)):\r\n print(f'{_}\\t{int(sym_idx)}\\t{D}')\r\n print('\\n')\r\n\r\n def plot(self, Js, Ds):\r\n \"\"\"\r\n We plot the structure to illustrate the neighbors that\r\n we found in the two examples above\r\n \"\"\"\r\n\r\n fig = plt.figure()\r\n ax = fig.add_subplot(111, projection='3d')\r\n # plot the conventional (cubic) unit cell\r\n lines = [[(0, 1), (0, 0), (0, 0)],\r\n [(0, 0), (0, 1), (0, 0)],\r\n [(0, 0), (0, 0), (0, 1)],\r\n [(1, 0), (1, 1), (1, 1)],\r\n [(1, 1), (1, 0), (1, 1)],\r\n [(1, 1), (1, 1), (1, 0)],\r\n [(1, 1), (0, 0), (0, 1)],\r\n [(1, 1), (0, 1), (0, 0)],\r\n [(0, 0), (0, 1), (1, 1)],\r\n [(0, 0), (1, 1), (0, 1)],\r\n [(0, 1), (1, 1), (0, 0)],\r\n [(0, 1), (0, 0), (1, 1)]]\r\n for line in lines:\r\n ax.plot(line[0], line[1], line[2], c='black')\r\n\r\n # plot the 4 (magnetic) sites\r\n # and its periodic images in the 1x1x1 cube\r\n images = [(1, 0, 0), (0, 1, 0), (0, 0, 1),\r\n (1, 1, 0), (1, 0, 1), (0, 1, 1),\r\n (1, 1, 1), (0.5, 0.5, 1), (0.5, 1, 0.5),\r\n (1, 0.5, 0.5)]\r\n size = 100\r\n for site in self.struc:\r\n ax.scatter(*site.frac_coords, s=size, c='blue')\r\n for image in images:\r\n ax.scatter(*image, s=size, c='blue')\r\n\r\n # plot the bonds and the DM vectors\r\n tol = 0.01\r\n for (i, j, R, d, sym_idx, sym_op, D) in zip(*self.bonds, self.Ds):\r\n ri = self.struc[i].frac_coords\r\n rj = self.struc[j].frac_coords + R\r\n m = rj < (0 - tol)\r\n if sym_idx == 0:\r\n c='red'\r\n else:\r\n c='green'\r\n ax.plot(*zip(ri + m, rj + m), c=c)\r\n ar = (rj + m - (ri + m)) / 2 + (ri + m)\r\n ax.quiver(*ar, *D, length=0.1, normalize=True)\r\n\r\n ax.set_xticks([])\r\n ax.set_yticks([])\r\n ax.set_zticks([])\r\n ax.set_axis_off()\r\n legend = [Line2D([0], [0], color='red', lw=2),\r\n Line2D([0], [0], color='green', lw=2),\r\n Line2D([0], [0], color='lightblue', lw=2)]\r\n ax.legend(legend, ['J1', 'J2', 'DM'])\r\n fig.tight_layout()\r\n\r\n plt.show()\r\n\r\nif __name__ == '__main__':\r\n\r\n example = SpinModelExample()\r\n example.examplify_symmetry_indices()\r\n example.examplify_symmetry_ops()\r\n example.plot(example.Js, example.Ds)\r\n```\r\n\r\n\r\n\r\n\r\n",
"Thanks for the comprehensive example @nheinsdorf, I'll try and review this shortly, and thanks for your patience as well.",
"Hey @mkhorton, \r\njust changed a small thing (litterally just added a '~' in front of a mask) and now all the tests fail. However, the test on my system (in a new venv) runs smoothly :thinking: \r\nDid you guys change anything major, or am I just stupid? :thinking: \r\nBest, \r\nNiclas ",
"Okay, so apparently the problem is that now the 'symmetry_ops' class method of a symmetry.groups.SpaceGroup-instance returns a set rather than a list. Fixed the problem! Should work fine now! Looking forward seeing the PR merged. \r\n\r\nIf you need anything else, let me know. \r\n\r\nNext, I might tackle implementing it in a way that returns neighbors in an own class as suggested above.",
"Apologies @nheinsdorf for the extreme delay here -- we don't usually let PRs sit for so long, especially ones that are so detailed + pass tests (and from a first time contributor like yourself), so my apologies, I can only say I've been busy recently.\r\n\r\nI've gone ahead and run your example and explored it a bit, and it runs beautifully.\r\n\r\nI have the following comments:\r\n\r\n* Would prefer lowercase `R_a`, `R_b`, etc. for PEP8 compliance, I appreciate this is mathematically less ideal\r\n* I still think, to avoid confusion with existing functionality that is specifically *for* bonds, the `are_symmetrically_related_bond` function should be renamed `are_symmetrically_related_vectors` -- this makes it sufficiently clear that it's a general function.\r\n* I noticed a commented-out test, could this be restored?\r\n\r\nOtherwise, I am very happy to merge! The functionality itself is great.\r\n\r\n> Next, I might tackle implementing it in a way that returns neighbors in an own class as suggested above.\r\n\r\nThis would be good, but please familiarize yourself with `NearNeighbor` and `StructureGraph` classes first, so that we may integrate any additions cleanly.",
"Hey @mkhorton, \r\ndon't worry! \r\nI don't mind changing R_a, and R_b to lowercase and renaming the function. Will you take care of this when merging, or you want me to edit and update the PR? \r\n\r\nConcerning your third remark, this commented-out block was not written by me. It was contained in the repo when I cloned it. Do with it as you please. \r\n\r\nHappy I could help! ",
"> Will you take care of this when merging, or you want me to edit and update the PR?\r\n\r\nIf it's straight forward for you to do, it'd be appreciated if you could this (along with the function rename to `vector`).\r\n\r\n> Concerning your third remark, this commented-out block was not written by me. It was contained in the repo when I cloned it. Do with it as you please.\r\n\r\nUnderstood! It showed up in the diff, I guess mistakenly.",
"Done! But changed it 'vectors' as suggested in your first comment and not to 'vector'. Hope that both is fine. I guess the plural is implied anyway in 'are_symmetrically_related' since it compares two sites?! \r\nWell anyway, looking forward to see it merged!",
"Merged!"
] | 2022-01-31T16:35:03
| 2022-04-28T21:19:32
|
2022-04-28T21:19:29Z
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CONTRIBUTOR
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## Summary
Added a method that gets all the neighbors up a maximum distance for a Structure, and groups these 'bonds' according to their symmetry. This is useful when building a physical model to see which bonds should have the same attributes by symmetry (like a tight-binding hopping amplitude). Furthermore, for each bond, a symmetry operation is given that connects it to the first bond of this symmetry group. This is useful if a directional attribute (like a Dzyaloshinskii-Moriya (DM) interaction in a spin model) is associated with a given bond. The operations can then be used to rotate a given DM vector obeying the symmetry of the crystal. For a set of bonds with the same symmetry, these operations basically constitute what is known as the orbit for a Wyckoff position.
This was written in response to the discussion on the pymatgen forum:
https://matsci.org/t/finding-symmetry-equivalent-bonds-neighbors/38171/3
* Added the 'are_symmetrically_related_bond'-method to SymmOp-class to check if the operation relates two bonds.
* Added the 'get_symmetric_neighbor_list'-method to Structure that gives a similar output as 'get_neighbor_list' but groups the bonds according to symmetry.
## TODO
Similar to the method 'get_all_neighbors', it would be nice to have similar method that does not return the output as a tuple of lists, but returns a list of 'PeriodicBond' instances (that could inherit from PeriodicNeighbor). In addition to the properties of PeriodicNeighbor, this class would also store its own 'index' (as opposed to the index of the neighbor), as well as the space group of the structure. Then, the '==' operator of that class can be overloaded to see whether they are symmetrically related.
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PR_kwDOACgets4x2d7x
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Remove more deprecated stuff
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[
"The get_neighbors old should not be removed. It is a debugging code that is very useful. Basically it is a brute force version of the get_neighbors that is very slow but guaranteed to be correct because of the very simple logic. ",
"@shyuep Yeah wasn't sure about whether that one should go. Put it back in.",
"\n[](https://coveralls.io/builds/46103092)\n\nCoverage decreased (-0.6%) to 83.432% when pulling **e8f828d1b5b374017c2f2741cd3aaf7cd5d7fc8f on janosh:more-deprecation-drops** into **eeb2a9111d6d68ff9b2ec42f2afe59d1181e8af8 on materialsproject:master**.\n",
"Thanks for this @janosh. If removing old code (even if marked as deprecated), please also add a note to https://github.com/materialsproject/pymatgen/blob/master/docs_rst/compatibility.rst in the PR.",
"@mkhorton Ah cool, wasn't even aware of that file (even though I'd made auto-changes to it 😅). Good thing it exists! Though it appears to be a bit out of date. The file says pmg still supports py3.7. Will bring it up to date.",
"I placed the removed functions under a new heading \"Unreleased\". Whoever publishes the next version should fill in the right version number.",
"\r\n",
"Thanks @janosh!"
] | 2022-01-31T17:01:06
| 2022-01-31T22:08:06
|
2022-01-31T21:36:10Z
|
MEMBER
|
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Follow up to #2397 and #2401.
Deletes some more code [@shyuep said is very old](https://github.com/materialsproject/pymatgen/pull/2397#issuecomment-1025976675).
|
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| 1,119,846,254
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I_kwDOACgets5Cv39u
| 2,406
|
Add mirroring of slabs to CoherentInterfaceBuilder
|
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[
"Yes this would be a helpful feature! But if you mirror, wouldn't that create a twin boundary?",
"Hmm I'm not sure that would happen. What the _CoherentInterfaceBuilder_ module does now is to take two specified slabs and make an interface out of them. If both slabs are symmetric, there is no issue with the orientation of each. However, if the surfaces are non-symmetric there is a number of combinations between the distinct surface terminations. So far the module does not take that into account and simply aligns whatever is the top of the substrate with the bottom of the film (oriented along the non periodic direction). "
] | 2022-01-31T19:29:07
| 2022-02-09T16:25:05
|
NONE
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The _CoherentInterfaceBuilder_ works rather nicely when creating interfaces between various lattices. However, it seems like it currently doesn't consider mirroring non-symmetric slabs, which then leaves quite a few possible structures unexplored.
Not sure whether this would be easier to implement at this step or in the _Surface_ module?
(If that feature is already present and I missed it, let me know!)
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PR_kwDOACgets4x3k-5
| 2,407
|
Improve parsing of coupled-cluster calculations in Q-Chem
|
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[
"\n[](https://coveralls.io/builds/46106512)\n\nCoverage decreased (-0.6%) to 83.439% when pulling **0632be938dae90de301a0c93f68fb1ca53f879d7 on espottesmith:qchem_cc** into **6dbdeec119491f21da88f3bdb7f4c33ee5fe7ff7 on materialsproject:master**.\n",
"Thanks!"
] | 2022-01-31T23:01:06
| 2022-02-01T18:47:34
|
2022-02-01T17:40:15Z
|
CONTRIBUTOR
|
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## Summary
Currently, QCOutput will parse CCSD and CCSD(T) calculations, but will only grab the final energy, not the components (HF SCF, MP2, CCSD correlation, (T) correlation, etc.). This PR makes small changes to the QCOutput class to improve parsing of CC calculations.
An additional small change is made to how PES Scan calculations are parsed, to check if the connectivity of the molecule has changed from the beginning to the end of the scan.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [X] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [N/A] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [N/A] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [X] Tests have been added for any new functionality or bug fixes.
- [] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
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I_kwDOACgets5C2ay2
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|
Vasprun().complete_dos.spin_polarization yields a KeyError for ISPIN=1
|
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[] | 2022-02-02T06:30:52
| 2022-02-03T18:39:20
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2022-02-03T18:39:20Z
|
MEMBER
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For the a ISPIN=1 calculation with VASP, the `complete_dos` from the `Vasprun` parser yields a `KeyError`. The `spin_polarization` property is not applicable for ISPIN=1, but we should make it clearer for the user rather than throwing a `KeyError`.
There are also no tests for this property.
```python
from pymatgen.io.vasp.outputs import Vasprun
v = Vasprun('vasprun.xml.gz')
v.complete_dos.spin_polarization
```
```python
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-23-84089bcd748d> in <module>
----> 1 v.complete_dos.spin_polarization
~/software/miniconda/envs/rosen/lib/python3.8/site-packages/pymatgen/electronic_structure/dos.py in spin_polarization(self)
800
801 n_F_up = n_F[Spin.up]
--> 802 n_F_down = n_F[Spin.down]
803
804 if (n_F_up + n_F_down) == 0:
KeyError: <Spin.down: -1>
```
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PR_kwDOACgets4x8t8q
| 2,409
|
Return None for complete_dos.spin_polarization if ISPIN=1
|
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[
"Thanks."
] | 2022-02-02T06:49:43
| 2022-02-03T17:39:19
|
2022-02-03T17:26:53Z
|
MEMBER
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Addresses #2408.
If a VASP calculation is carried out with ISPIN=1, the `Vasprun('vasprun.xml').complete_dos.spin_polarization` property throws a `KeyError`. This PR makes it so that `None` is returned instead.
The `.spin_polarization` property also had no tests. I added them.
|
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PR_kwDOACgets4x9DAz
| 2,410
|
Allow for float ENCUTs in Wavecar class
|
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[
"Many thanks for addressing this issue @arosen93, this looks good.\r\n\r\nOn a technical note, I don't think this can be classed as a cosmetic change -- the return type is changing, this will have downstream consequences for anyone using the pymatgen parser (eg to store results in a database). However, I can't anticipate a case where this would cause issues so happy to merge.",
"@mkhorton, apologies! I wasn't clear in my original response. I meant the change to the test file I made is a cosmetic change (ie 25 == 25.0 and so it doesn't matter which I used in the test).\n\nYou're right about the change in return behavior. ",
"Actually, the one test case that may be useful is a test case that reproduces @RyanNKHall's original bug report, so we can confirm it's fixed",
"Sure, I can run a quick calculation on H2 with an encut of like 25.5. I want to keep the filesize small. ",
"Thanks, I appreciate the concern about filesize. We do have a few wavecar in the test_files dir, so not unprecedented, but definitely good to keep to minimum.",
"Thanks @arosen93 for the mention here. I'm surprised and pleased to see someone else encountering the same issue within the same period of time. Let me know if you need/require any of my original files to replicate and/or test the bug and associated fix. I believe, however, that everything I provided in the original bug report should suffice.",
"@RyanNKHall, I opened this PR because of your issue! :) I wanted to make sure it got fixed in future versions of pymatgen. Of course, if you want to do the PR, you can by all means do so! Otherwise, I'll finish this up in the next day or two. Thanks for reporting!",
"@arosen93 I'm more than happy for you to make the PR :) Thanks for your help.",
"I managed to make a 5 kb WAVECAR file. A teeny-tiny one! Not sure what `pip install` is complaining about though.\r\n\r\nEdit: Looks like pre-commit is getting a bit too excited here. Seems like the same `black` issue as in #2411.",
"Sorry, I was battling the pre-commit CI there for a little bit as it was wreaking havoc on this otherwise simple PR.\r\n\r\nAll done!",
"\n[](https://coveralls.io/builds/46272754)\n\nCoverage decreased (-0.6%) to 83.449% when pulling **a66ab854bac8eb71272d35de2c489197b3e7dd1c on arosen93:rosen-gvec** into **0edacc7ee9c640202b12782315facb0967d12822 on materialsproject:master**.\n",
"@mkhorton, just a reminder that this one is done.",
"Thanks @arosen93 :)"
] | 2022-02-02T09:09:13
| 2022-02-28T07:45:44
|
2022-02-23T17:57:27Z
|
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Addresses #2361.
As noted by @RyanNKHall, the `Wavecar` class requires that ENCUT be an `int` when strictly speaking, this is not necessary within VASP. This PR implements the change suggested by @RyanNKHall to read ENCUT as a `float`.
If a test is requested, I can run a super cheap H2 calc, although I'm not sure it's necessary for this one. The change I made to the test is only a cosmetic change for the reader.
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PR_kwDOACgets4x_3nA
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More string format tidying
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[
"Thanks for fixing my `EnvironmentError`'s too. I just looked it up in response and it does not mean what I thought it meant.",
"There is a version difference for black between `.pre-commit-config.yaml` (21.12b0) and in requirements-dev.txt (22.1.0). Its also quite confusing that there is both a `.pre-commit-config.yaml` and a `pre-commit` script that do different things.\r\n\r\nIt could be better to only use `.pre-commit-config.yaml` and then call pre-commit in the linting GH action. E.g., [I do that in atomate2](https://github.com/materialsproject/atomate2/blob/8d75d850fb3c95c6662fd1833183fe8e6951d5c7/.github/workflows/testing.yml#L29) with a line like:\r\n\r\n```\r\n - name: Lint\r\n run: pre-commit run --all-files --show-diff-on-failure\r\n```\r\n\r\nAnd you could always run `pylint` after pre-commit in the GH action if it takes too long to run as part of `.pre-commit-config.yaml`\r\n",
"I fixed the pre-commit black version. This is the first time we are using it. I will make it consistent in future.",
"\n[](https://coveralls.io/builds/46237735)\n\nCoverage decreased (-0.6%) to 83.438% when pulling **6a02653635daea5c7df6d50776102d07ed69c7c1 on utf:str-fixes** into **479ea52f78644618e2eb7a1107e3f8a69296b14d on materialsproject:master**.\n",
"There still seems to be an issue with the different pre-commit configurations?\r\n\r\nAlso, windows tests are failing for an unrelated reason.",
"As I said, I pinned the correct black version in the precommit. Pls pull the latest master into your fork.",
"Thanks."
] | 2022-02-03T00:42:57
| 2022-02-04T16:12:24
|
2022-02-04T16:12:19Z
|
MEMBER
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Continuing on from #2379
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I_kwDOACgets5C8OX5
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"infinite" loop when importing pymatgen.core and MPRester
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[
"I can't reproduce this. Can you try renaming your .pmgrc.yaml file to sometjing else (e.g., .pmgrc.yaml.bak) and see if this still recurs. You can also try downgrading ruamel.yaml and see if that helps.",
"Thank you so much, renaming pmgrc.yaml worked! Why though?\r\n",
"Probably means your .pmgrc.yaml was corrupted in some way and caused the parser to trip up. You will need to reconfigure it though if you plan to use psuedopotentials or the MPRester. ",
"I tried launching a query with MPRester and it appears to work. It automatically generated a new pmgrc.yaml. The older one has a crazy volume of 3.9 Gb, is it something expected?",
"No. That is a config yaml file. It should a less than 1kb. Pls delete that old corrupted file. "
] | 2022-02-03T13:25:02
| 2022-02-03T16:35:54
|
2022-02-03T16:35:54Z
|
NONE
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## Bug description
The commands `import pymatgen.core` and `from pymatgen.ext.matproj import MPRester` are not completed, but result in a loop between two lines. Here follows the traceback after I interrupt the run with ctrl+c:
```
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\anton\anaconda3\envs\pymat\lib\site-packages\pymatgen\core\__init__.py", line 54, in <module>
SETTINGS = _load_pmg_settings()
File "C:\Users\anton\anaconda3\envs\pymat\lib\site-packages\pymatgen\core\__init__.py", line 43, in _load_pmg_settings
d_yml = yaml.load(f)
File "C:\Users\anton\anaconda3\envs\pymat\lib\site-packages\ruamel\yaml\main.py", line 343, in load
return constructor.get_single_data()
File "C:\Users\anton\anaconda3\envs\pymat\lib\site-packages\ruamel\yaml\constructor.py", line 111, in get_single_data
node = self.composer.get_single_node()
File "C:\Users\anton\anaconda3\envs\pymat\lib\site-packages\ruamel\yaml\composer.py", line 78, in get_single_node
document = self.compose_document()
File "C:\Users\anton\anaconda3\envs\pymat\lib\site-packages\ruamel\yaml\composer.py", line 101, in compose_document
node = self.compose_node(None, None)
File "C:\Users\anton\anaconda3\envs\pymat\lib\site-packages\ruamel\yaml\composer.py", line 138, in compose_node
node = self.compose_mapping_node(anchor)
File "C:\Users\anton\anaconda3\envs\pymat\lib\site-packages\ruamel\yaml\composer.py", line 218, in compose_mapping_node
```
where the last two lines (138 and 218) are repeated for a number of times, until run interruption by ctrl+c.
## To Reproduce
The error appeared in the following cases:
1) fresh installation of miniconda3
1.1) new virtual environment where I run `conda install -c anaconda ipykernel` followed by `conda install --channel conda-forge pymatgen`
1.2) new virtual environment where I run `conda install -c anaconda ipykernel` followed by c`onda install --yes numpy scipy matplotlib` and `pip install pymatgen`
1.2.1) same happens if I `conda update ruamel.yaml`, which appears to be the problematic package (see the traceback above).
2) Same on anaconda3.
I tried python 3.9.7 and 3.10.2
## Expected behavior
Just import pymatgen's modules
## Operating system
OS Name Microsoft Windows 10 Pro
Version 10.0.19043 Build 19043
System Type x64-based PC
Any help would be very welcome!
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PR_kwDOACgets4yEl6I
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Update minimal basis
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[
"Not sure what is going on with the tests as I did not change anything on the code :).",
"\n[](https://coveralls.io/builds/46236468)\n\nCoverage decreased (-0.6%) to 83.439% when pulling **338aa705ce794fe21aa2949dfde9ddca4e471025 on JaGeo:master** into **e45234a881379b6b2785d3a72e861e68d0587af6 on materialsproject:master**.\n",
"One other thing: the coverage always seems to be reduced by -0.6% independent of what we are doing. Here, I haven't changed anything on the code.",
"Don't worry about the coverage. I made it an optional check. This is more for our information rather than a strict check.",
"Thank you very much."
] | 2022-02-04T09:16:54
| 2022-02-04T15:13:29
|
2022-02-04T14:49:09Z
|
MEMBER
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This is a very small change of the configuration files for the Lobster basis. We removed the 2p orbitals for Be as they led to problems in our computations and probably should be optional during the projection.
This should hopefully not affect any of the tests.
Best,
JG
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pre-commit.ci readme badge
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[
"@shyuep Better to leave the `flake8`, `autoflake` and `mypy` hooks in place so that users running `pre-commit` locally can still check new code they write against these hooks and only disable them in CI. As errors are fixed slowly over time, they can be re-enabled.",
"\n[](https://coveralls.io/builds/46238068)\n\nCoverage decreased (-0.6%) to 83.44% when pulling **d70d096ae805a4c030c5f8ade6fda8b588e6973c on janosh:pre-commit-ci-badge** into **479ea52f78644618e2eb7a1107e3f8a69296b14d on materialsproject:master**.\n",
"How do you disable them in CI? As far as I can see, mypy and flake8 does not do autofix but only checks. This is unlike black where changes are made automatically,.",
"> mypy and flake8 does not do autofix but only checks. This is unlike black where changes are made automatically\r\n\r\nThat's correct.\r\n\r\nI already made the change that disables these hooks in CI only: d70d096\r\n\r\nHere are the config docs: https://pre-commit.ci/#configuration-skip",
"Ok thanks.",
"There's 1 more file that offends the `check-yaml` hook:\r\n\r\n```\r\ncheck yaml...............................................................Failed\r\n- hook id: check-yaml\r\n- exit code: 1\r\n\r\ncould not determine a constructor for the tag 'tag:yaml.org,2002:python/tuple'\r\n in \"pymatgen/analysis/vesta_cutoffs.yaml\", line 1, column 3\r\n```",
"Yeah, I am not sure that one is solvable. There is no \"tuple\" in yaml per se. For this particular use case, we need it to be a hashable tuple as it is a dict key. We can just disable the yaml check. YAML is only used as a data file in most cases and if the yaml is not right, the parser won't even load it. So this check is kind of redundant.",
"If a yaml file fails to parse, you only encounter an error at run time. So I do think it's valuable to keep the yaml checker in place to catch such cases before deployment.\r\n\r\nIt is possible to exclude specific files for specific hooks. Maybe that's the better solution here.\r\n\r\n```yaml\r\n - repo: https://github.com/pre-commit/pre-commit-hooks\r\n rev: v4.1.0\r\n hooks:\r\n - id: check-yaml\r\n+ exclude: pymatgen/analysis/vesta_cutoffs.yaml\r\n```\r\n\r\n",
"That is fine. Yes a yaml failure occurs at run time. But when someone includes a yaml config file in pymatgen, it is typically actually USED somewhere. The tests will catch these yaml failures. I am not sure we want to wring ourselves into knots creating file exceptions. Ultimately, this is a python code base and the yamls are not the key component."
] | 2022-02-04T15:21:45
| 2022-02-04T16:36:40
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2022-02-04T16:17:17Z
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MEMBER
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Nice to see you adopted pre-commit.ci!
Normally it auto-updates the hooks in `.pre-commit-config.yaml` weekly. Set it to monthly to keep down the noise.
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isort
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"\n[](https://coveralls.io/builds/46241233)\n\nCoverage decreased (-0.6%) to 83.438% when pulling **ed995811800d6cd1f8fab9aebdde0c1b3679a2b3 on janosh:isort** into **df6515c1a55835aaee3c530c182e78cd651530a2 on materialsproject:master**.\n"
] | 2022-02-04T16:38:42
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2022-02-04T18:12:23Z
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Add `isort` pre-commit hook and apply auto-fixes across code base.
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Update docs to say min python is 3.8
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] | 2022-02-04T17:15:35
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2022-02-04T17:17:03Z
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Update readme and docs in all places stating `pymatgen` still supports py37.
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PR_kwDOACgets4yGqDs
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Remove last remaining star imports
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[
"\n[](https://coveralls.io/builds/46255716)\n\nCoverage decreased (-0.6%) to 83.438% when pulling **07fa7114872fcdb0e46907bfe7cc267a57e223c3 on janosh:no-more-star-imports** into **0edacc7ee9c640202b12782315facb0967d12822 on materialsproject:master**.\n",
"Interesting. I didn't know that they introduced `which` in Python 3.3. I coded that `which` command back in Python 2.7+."
] | 2022-02-04T20:55:48
| 2024-09-09T11:12:52
|
2022-02-05T16:45:05Z
|
MEMBER
|
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`flake8` complains about star imports (for good reason imo, they make code harder to understand and debug).
One step closer to enabling `flake8` in CI.
I noticed one odd thing,
```
pymatgen/io/abinit/netcdf.py
pymatgen/io/abinit/pseudos.py
```
both define `class AbinitHeader(dict)`. The 2nd starred import was overwriting the class from the first file in `pymatgen/io/abinit/__init__.py` so I imported that one for backwards compat.
|
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I_kwDOACgets5DEOsp
| 2,418
|
Parsing `vasprun.xml` with `RANDOM_SEED` tag
|
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[] | 2022-02-06T11:53:02
| 2022-02-06T17:49:34
|
2022-02-06T17:49:34Z
|
CONTRIBUTOR
|
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**Describe the bug**
I consider this issue more of a `VASP` bug rather than `pyamtgen` bug. However, I think it would be good to have a mechanism in place within the `Vasprun` class to mitigate this issue and warn user too.
If user wants to use `RANDOM_SEED` tag in `VASP` and chooses numbers greater than `999999`, it will be reported in `vasprun.xml` as `<v type="int" name="RANDOM_SEED">****** 0 0</v>`. Then, once trying to parse it using `Vasprun`, we will get the following expection:
```
ValueError Traceback (most recent call last)
File ~/.local/software/miniforge3/envs/general/lib/python3.8/site-packages/pymatgen/io/vasp/outputs.py:91, in _parse_v_parameters(val_type, val, filename, param_name)
90 try:
---> 91 val = [int(i) for i in val.split()]
92 except ValueError:
93 # Fix for stupid error in vasprun sometimes which displays
94 # LDAUL/J as 2****
File ~/.local/software/miniforge3/envs/general/lib/python3.8/site-packages/pymatgen/io/vasp/outputs.py:91, in <listcomp>(.0)
90 try:
---> 91 val = [int(i) for i in val.split()]
92 except ValueError:
93 # Fix for stupid error in vasprun sometimes which displays
94 # LDAUL/J as 2****
ValueError: invalid literal for int() with base 10: '******'
```
**To Reproduce**
I attached a [vasprun.tar.gz](https://github.com/materialsproject/pymatgen/files/8010090/vasprun.tar.gz) that has two `vasprun.xml` files:
1. `vasprun.OK.xml`: has a `RANDOM_SEED` value of `999999` and will be parsed without problem.
2. `vasprun.FAILED.xml`: has a seven figure `RANDOM_SEED` value of `1000000` and will throw the exception mentioned above.
**Expected behavior**
Unfortunately, I do not see a clean way to mitigate this issue.
Couple of things that come to my mind:
1. Preventing user to use numbers greater than `999999` when the `INCAR` file is generated (until this issue would be resolved on `VASP` side)
2. I think `Vasprun` class would required a specific rule when `RANDOM_SEED` tag exists. So, if it exists and does carry the `*****`, it would not be parsed.
3. Also, if such event occurs, parser can look for `INCAR` file within the same directory and catch the correct `RANDOM_SEED` to include in the outputs if it finds the `INCAR`.
**Desktop (please complete the following information):**
- OS: macOS Monterey 12.2
- Version: 2022.1.9
|
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| 1,125,320,688
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I_kwDOACgets5DEwfw
| 2,419
|
SpacegroupAnalyzer.get_crystal_system() does not raise on negative space group, returns 'monoclinic'
|
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[] | 2022-02-06T21:19:31
| 2022-02-07T03:41:06
|
2022-02-07T03:41:06Z
|
MEMBER
|
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Current implementation of `SpacegroupAnalyzer.get_crystal_system()` is meant to raise on invalid space groups but doesn't:
https://github.com/materialsproject/pymatgen/blob/03112486486c8203991b14dafeb3314a3f3c1ba7/pymatgen/symmetry/analyzer.py#L142-L167
Example
```py
from pymatgen.core import Lattice, Structure
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = Lattice.from_parameters(a=3.84, b=3.84, c=3.84, alpha=120, beta=90, gamma=60)
struct = Structure(lattice, ["Si", "Si"], coords)
sga._space_group_data['number'] = 0
sga.get_crystal_system()
>>> 'monoclinic'
```
|
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PR_kwDOACgets4yIwxK
| 2,420
|
Ensure SpacegroupAnalyzer.get_crystal_system() raises ValueError on neg space groups
|
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[
"\n[](https://coveralls.io/builds/46269991)\n\nCoverage decreased (-0.6%) to 83.45% when pulling **8ede104926f5cfa46f5772de1332d65577975325 on janosh:fix-get-crys-sys** into **03112486486c8203991b14dafeb3314a3f3c1ba7 on materialsproject:master**.\n"
] | 2022-02-06T21:21:09
| 2022-02-07T06:49:38
|
2022-02-07T03:41:06Z
|
MEMBER
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Closes #2419.
|
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I_kwDOACgets5DGrsv
| 2,421
|
Variables in `.pmgrc.yaml` file are no longer acessible since new update to pymatgen==2022.2.1
|
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[
"I just want to add that I have the same problem as @naik-aakash. The .pmgrc.yaml gets overwritten while connecting to the Materials Project database. ",
"I had the same problem 2 weeks ago but I thought it was already fixed... @shyuep [said so](https://github.com/materialsproject/pymatgen/issues/2377#issuecomment-1021268224) and I haven't encountered the issue since. So maybe it's a different one given your using latest version. Can you post the contents of your `.pmgrc.yaml` after the error occurs? Is it full of `ruamel.yaml` garbage?",
"@janosh : here is the small snipet as requested of `.pmgrc.yaml` after the error occurs.\r\n```\r\n!!python/object/apply:ruamel.yaml.comments.CommentedMap\r\ndictitems:\r\n MAPI_DB_VERSION:\r\n LAST_ACCESSED: '2020_09_08'\r\n LOG: {'2020_09_08': 1}\r\n dictitems: !!python/object/apply:ruamel.yaml.comments.CommentedMap\r\n dictitems:\r\n MAPI_DB_VERSION: !!python/object/apply:ruamel.yaml.comments.CommentedMap\r\n dictitems:\r\n LAST_ACCESSED: '2020_09_08'\r\n LOG: !!python/object/apply:ruamel.yaml.comments.CommentedMap\r\n dictitems: {'2020_09_08': 1}\r\n state:\r\n _yaml_format: !!python/object/new:ruamel.yaml.comments.Format\r\n state: !!python/tuple\r\n - null\r\n - {_flow_style: true}\r\n _yaml_line_col: !!python/object:ruamel.yaml.comments.LineCol\r\n col: 9\r\n data:\r\n '2020_09_08': [4, 10, 4, 24]\r\n line: 4\r\n state:\r\n _yaml_format: !!python/object/new:ruamel.yaml.comments.Format\r\n state: !!python/tuple\r\n - null\r\n - {_flow_style: false}\r\n _yaml_line_col: !!python/object:ruamel.yaml.comments.LineCol\r\n col: 4\r\n data:\r\n LAST_ACCESSED: [3, 4, 3, 19]\r\n LOG: [4, 4, 4, 9]\r\n line: 3\r\n PMG_DEFAULT_FUNCTIONAL: PBE_54\r\n PMG_MAPI_KEY: mympapi\r\n PMG_VASP_PSP_DIR: /pathto/POTCAR\r\n state:\r\n _yaml_format: !!python/object/new:ruamel.yaml.comments.Format\r\n state: !!python/tuple\r\n - null\r\n - {_flow_style: false}\r\n _yaml_line_col: !!python/object:ruamel.yaml.comments.LineCol\r\n col: 2\r\n data:\r\n MAPI_DB_VERSION: [2, 2, 3, 4]\r\n PMG_DEFAULT_FUNCTIONAL: [5, 2, 5, 26]\r\n PMG_MAPI_KEY: [6, 2, 6, 16]\r\n PMG_VASP_PSP_DIR: [7, 2, 7, 20]\r\n line: 2\r\n state: !!python/object/apply:ruamel.yaml.comments.CommentedMap\r\n dictitems:\r\n _yaml_format: !!python/object/apply:ruamel.yaml.comments.CommentedMap\r\n dictitems:\r\n state: !!python/object/new:ruamel.yaml.comments.CommentedSeq\r\n listitems:\r\n - null\r\n - !!python/object/apply:ruamel.yaml.comments.CommentedMap\r\n dictitems: {_flow_style: false}\r\n state:\r\n _yaml_format: !!python/object/new:ruamel.yaml.comments.Format\r\n state: !!python/tuple\r\n - null\r\n - {_flow_style: true}\r\n _yaml_line_col: !!python/object:ruamel.yaml.comments.LineCol\r\n col: 6\r\n data:\r\n _flow_style: [12, 7, 12, 20]\r\n line: 12\r\n state:\r\n _yaml_format: !!python/object/new:ruamel.yaml.comments.Format\r\n state: !!python/tuple\r\n - null\r\n - {_flow_style: false}\r\n _yaml_line_col: !!python/object:ruamel.yaml.comments.LineCol {col: 11,\r\n data: null, line: 10}\r\n _yaml_tag: !!python/object/new:ruamel.yaml.comments.Tag\r\n state: !!python/tuple\r\n - null\r\n - {value: '!!python/tuple'}\r\n```",
"We will also investigate this further. Maybe really some leftover from an old version of pymatgen?! We will check with a completely new environment.",
"@naik-aakash Yeah that looks exactly like mine.\r\n\r\n@JaGeo Prob not necessary to try a clean install, I think. Seems pretty clear there's still a problem in the code base.",
"That's odd. I don't seem to have an issue with importing variables. Let me suggest the following:\r\n1. Rename your `.pmgrc.yaml` to `.pmgrc.yaml.bak`\r\n2. Add your PMG_MAPI_KEY again via `pmg config`.\r\n\r\nTry to do the query again.\r\nIf the above doesn't work, try upgrading your ruamel.yaml.",
"I think my last commit should fix it. I think the problem is that the MPREster apparently writes the database version to the .pmgrc.yaml. I wasn't aware that it did that. But I have made everything consistent via using ruamel.yaml directly.",
"> @naik-aakash Yeah that looks exactly like mine.\r\n> \r\n> @JaGeo Prob not necessary to try a clean install, I think. Seems pretty clear there's still a problem in the code base.\r\n\r\nFresh install does not seem to have this issue. Also when I tried force-reinstall tag . this issue does not occur. I saw when I uninstalled pymatgen, there are some leftover files in site-packages directory and maybe that causes the problem when upgrading.",
"@shyuep : Thanks! I tested with new release, it is resolved with your fix.",
"Sorry I'm late to this issue -- I noticed this too with a student, the conclusion seemed to be that the version of `ruamel.yaml` caused the `.pmgrc.yaml` to be parsed as an ordered dict and then written back out as an ordered dict in the unusual syntax showing above, causing all kinds of issues.\r\n\r\nCoercing the parsed `.pmgrc.yml` dictionary to be type `dict` fixed it (noting that this is now a nested dictionary, so there were multiple conversions necessary). However, it seemed like this issue might affect the usage of `monty.serialization.loadfn/dumpfn` in many other places too, so that perhaps a broader fix would be necessary in `monty`.\r\n\r\nGlad it's now been fixed, thanks @shyuep. Sharing above context in case it re-occurs in some manner."
] | 2022-02-07T10:56:26
| 2022-02-14T23:28:43
|
2022-02-07T15:07:32Z
|
CONTRIBUTOR
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**The bug**
Since the latest update the variables defined in `.pmgrc.yaml` file are no longer acessible after first usage of MPRester.
Consider the vairables defined for eg in the `~/.pmgrc.yaml` file are as follows :
```
PMG_DEFAULT_FUNCTIONAL: PBE_54
PMG_VASP_PSP_DIR: /pathtopotcars/POTCAR
PMG_MAPI_KEY: yourkeyfrommp
```
**To Reproduce**
Steps to reproduce the behavior:
1. IMPORT the MPRester module in Jupyternotebook/Any other python IDE
`from pymatgen.ext.matproj import MPRester`
2. Get a structure from the Materials Project after initializing MPRester
```
m = MPRester()
struct = m.get_structure_by_material_id('mp-xxxx')
```
3. Now restart the Jupyter Notebook kernel
4. Run first two code blocks again
5. You see following error
`MPRestError: REST query returned with error status code 403. Content: b'{"valid_response": false, "error": "API_KEY is not supplied.", "version": {"db": "2020_09_08", "pymatgen": "2022.0.8", "rest": "2.0"}, "created_at": "2022-02-07T02:43:53.161480"}'`
**Expected behavior**
This normally should not happen because, once the variables are defined it were accessible in earlier versions of pymatgen. And currently to use pymatgen I need to always recreate the `~/.pmgrc.yaml` file
**Screenshots**
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[
"The verison info is not longer in the root level. you should use `print(pymatgen.core.__version__)`. In any case, it is generally better to find out the version info using pkgutil.",
"how to import pymatgen.core?\n\nOn Mon, Feb 7, 2022 at 8:38 PM Shyue Ping Ong ***@***.***>\nwrote:\n\n> The verison info is not longer in the root level. you should use\n> print(pymatgen.core.__version__). In any case, it is generally better to\n> find out the version info using pkgutil.\n>\n> —\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/2422#issuecomment-1031569997>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AXUZ2FSYX4FXXM27LPSAGYLUZ7OAXANCNFSM5NXWOVJA>\n> .\n> Triage notifications on the go with GitHub Mobile for iOS\n> <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>\n> or Android\n> <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.\n>\n> You are receiving this because you authored the thread.Message ID:\n> ***@***.***>\n>\n\n\n-- \nWith Regards,\nNisha Kumari\n",
"ValueError Traceback (most recent call\nlast)/var/folders/75/_7mxz6mx3v92wzt64xtzbtx40000gn/T/ipykernel_2224/1591616909.py\nin <module>----> 1 import pymatgen\n~/anaconda3/lib/python3.9/site-packages/pymatgen/__init__.py in\n<module> 18 # Note that these have to come after the SETTINGS have\nbeen loaded. Otherwise, import does not work. 19 ---> 20 from\n.core import SETTINGS, SETTINGS_FILE # noqa 21 from\n.core.composition import Composition # noqa 22 from .core.lattice\nimport Lattice # noqa\n~/anaconda3/lib/python3.9/site-packages/pymatgen/core/__init__.py in\n<module> 19 20 from .composition import Composition #\nnoqa---> 21 from .lattice import Lattice # noqa 22 from\n.operations import SymmOp # noqa 23 from .periodic_table import\nDummySpecies, Element, Species # noqa\n~/anaconda3/lib/python3.9/site-packages/pymatgen/core/lattice.py in\n<module> 21 from numpy.linalg import inv 22 ---> 23 from\npymatgen.util.coord import pbc_shortest_vectors 24 from\npymatgen.util.num import abs_cap 25 from pymatgen.util.typing\nimport ArrayLike\n~/anaconda3/lib/python3.9/site-packages/pymatgen/util/coord.py in\n<module> 15 import numpy as np 16 ---> 17 from . import\ncoord_cython as cuc 18 19 # array size threshold for looping\ninstead of broadcasting\npymatgen/util/coord_cython.pyx in init pymatgen.util.coord_cython()\nValueError: numpy.ndarray size changed, may indicate binary\nincompatibility. Expected 96 from C header, got 88 from PyObject\n\n\nOn Tue, Feb 8, 2022 at 3:12 PM nisha kumari ***@***.***> wrote:\n\n> how to import pymatgen.core?\n>\n> On Mon, Feb 7, 2022 at 8:38 PM Shyue Ping Ong ***@***.***>\n> wrote:\n>\n>> The verison info is not longer in the root level. you should use\n>> print(pymatgen.core.__version__). In any case, it is generally better to\n>> find out the version info using pkgutil.\n>>\n>> —\n>> Reply to this email directly, view it on GitHub\n>> <https://github.com/materialsproject/pymatgen/issues/2422#issuecomment-1031569997>,\n>> or unsubscribe\n>> <https://github.com/notifications/unsubscribe-auth/AXUZ2FSYX4FXXM27LPSAGYLUZ7OAXANCNFSM5NXWOVJA>\n>> .\n>> Triage notifications on the go with GitHub Mobile for iOS\n>> <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>\n>> or Android\n>> <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.\n>>\n>> You are receiving this because you authored the thread.Message ID:\n>> ***@***.***>\n>>\n>\n>\n> --\n> With Regards,\n> Nisha Kumari\n>\n>\n>\n\n-- \nWith Regards,\nNisha Kumari\n",
"Do a pip install pymatgen. It seems that the C compilation of the package was not properly done.",
"when i'm doing pip install pymatgen ? then if m trying to import\npymatgen same error is showing. What to do??\n\n\nRequirement already satisfied: pymatgen in\n./anaconda3/lib/python3.9/site-packages (2021.3.9)\nRequirement already satisfied: palettable>=3.1.1 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (3.3.0)\nRequirement already satisfied: requests in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (2.26.0)\nRequirement already satisfied: spglib>=1.9.9.44 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (1.16.3)\nRequirement already satisfied: monty>=3.0.2 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (2021.12.1)\nRequirement already satisfied: matplotlib>=1.5 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (3.4.3)\nRequirement already satisfied: sympy in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (1.9)\nRequirement already satisfied: pandas in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (1.3.4)\nRequirement already satisfied: numpy>=1.20.1 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (1.20.3)\nRequirement already satisfied: plotly>=4.5.0 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (5.5.0)\nRequirement already satisfied: uncertainties>=3.1.4 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (3.1.6)\nRequirement already satisfied: scipy>=1.5.0 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (1.7.1)\nRequirement already satisfied: networkx>=2.2 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (2.6.3)\nRequirement already satisfied: tabulate in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (0.8.9)\nRequirement already satisfied: ruamel.yaml>=0.15.6 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (0.17.20)\nRequirement already satisfied: cycler>=0.10 in\n./anaconda3/lib/python3.9/site-packages (from\nmatplotlib>=1.5->pymatgen) (0.10.0)\nRequirement already satisfied: pillow>=6.2.0 in\n./anaconda3/lib/python3.9/site-packages (from\nmatplotlib>=1.5->pymatgen) (8.4.0)\nRequirement already satisfied: pyparsing>=2.2.1 in\n./anaconda3/lib/python3.9/site-packages (from\nmatplotlib>=1.5->pymatgen) (3.0.4)\nRequirement already satisfied: kiwisolver>=1.0.1 in\n./anaconda3/lib/python3.9/site-packages (from\nmatplotlib>=1.5->pymatgen) (1.3.1)\nRequirement already satisfied: python-dateutil>=2.7 in\n./anaconda3/lib/python3.9/site-packages (from\nmatplotlib>=1.5->pymatgen) (2.8.2)\nRequirement already satisfied: six in\n./anaconda3/lib/python3.9/site-packages (from\ncycler>=0.10->matplotlib>=1.5->pymatgen) (1.16.0)\nRequirement already satisfied: tenacity>=6.2.0 in\n./anaconda3/lib/python3.9/site-packages (from plotly>=4.5.0->pymatgen)\n(8.0.1)\nRequirement already satisfied: ruamel.yaml.clib>=0.2.6 in\n./anaconda3/lib/python3.9/site-packages (from\nruamel.yaml>=0.15.6->pymatgen) (0.2.6)\nRequirement already satisfied: future in\n./anaconda3/lib/python3.9/site-packages (from\nuncertainties>=3.1.4->pymatgen) (0.18.2)\nRequirement already satisfied: pytz>=2017.3 in\n./anaconda3/lib/python3.9/site-packages (from pandas->pymatgen)\n(2021.3)\nRequirement already satisfied: urllib3<1.27,>=1.21.1 in\n./anaconda3/lib/python3.9/site-packages (from requests->pymatgen)\n(1.26.7)\nRequirement already satisfied: idna<4,>=2.5 in\n./anaconda3/lib/python3.9/site-packages (from requests->pymatgen)\n(3.2)\nRequirement already satisfied: charset-normalizer~=2.0.0 in\n./anaconda3/lib/python3.9/site-packages (from requests->pymatgen)\n(2.0.4)\nRequirement already satisfied: certifi>=2017.4.17 in\n./anaconda3/lib/python3.9/site-packages (from requests->pymatgen)\n(2021.10.8)\nRequirement already satisfied: mpmath>=0.19 in\n./anaconda3/lib/python3.9/site-packages (from sympy->pymatgen) (1.2.1)\nNote: you may need to restart the kernel to use updated packages.\n\n\nOn Tue, Feb 8, 2022 at 4:23 PM nisha kumari ***@***.***> wrote:\n\n> ValueError Traceback (most recent call last)/var/folders/75/_7mxz6mx3v92wzt64xtzbtx40000gn/T/ipykernel_2224/1591616909.py in <module>----> 1 import pymatgen\n> ~/anaconda3/lib/python3.9/site-packages/pymatgen/__init__.py in <module> 18 # Note that these have to come after the SETTINGS have been loaded. Otherwise, import does not work. 19 ---> 20 from .core import SETTINGS, SETTINGS_FILE # noqa 21 from .core.composition import Composition # noqa 22 from .core.lattice import Lattice # noqa\n> ~/anaconda3/lib/python3.9/site-packages/pymatgen/core/__init__.py in <module> 19 20 from .composition import Composition # noqa---> 21 from .lattice import Lattice # noqa 22 from .operations import SymmOp # noqa 23 from .periodic_table import DummySpecies, Element, Species # noqa\n> ~/anaconda3/lib/python3.9/site-packages/pymatgen/core/lattice.py in <module> 21 from numpy.linalg import inv 22 ---> 23 from pymatgen.util.coord import pbc_shortest_vectors 24 from pymatgen.util.num import abs_cap 25 from pymatgen.util.typing import ArrayLike\n> ~/anaconda3/lib/python3.9/site-packages/pymatgen/util/coord.py in <module> 15 import numpy as np 16 ---> 17 from . import coord_cython as cuc 18 19 # array size threshold for looping instead of broadcasting\n> pymatgen/util/coord_cython.pyx in init pymatgen.util.coord_cython()\n> ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject\n>\n>\n> On Tue, Feb 8, 2022 at 3:12 PM nisha kumari ***@***.***> wrote:\n>\n>> how to import pymatgen.core?\n>>\n>> On Mon, Feb 7, 2022 at 8:38 PM Shyue Ping Ong ***@***.***>\n>> wrote:\n>>\n>>> The verison info is not longer in the root level. you should use\n>>> print(pymatgen.core.__version__). In any case, it is generally better\n>>> to find out the version info using pkgutil.\n>>>\n>>> —\n>>> Reply to this email directly, view it on GitHub\n>>> <https://github.com/materialsproject/pymatgen/issues/2422#issuecomment-1031569997>,\n>>> or unsubscribe\n>>> <https://github.com/notifications/unsubscribe-auth/AXUZ2FSYX4FXXM27LPSAGYLUZ7OAXANCNFSM5NXWOVJA>\n>>> .\n>>> Triage notifications on the go with GitHub Mobile for iOS\n>>> <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>\n>>> or Android\n>>> <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.\n>>>\n>>> You are receiving this because you authored the thread.Message ID:\n>>> ***@***.***>\n>>>\n>>\n>>\n>> --\n>> With Regards,\n>> Nisha Kumari\n>>\n>>\n>>\n>\n> --\n> With Regards,\n> Nisha Kumari\n>\n>\n>\n\n-- \nWith Regards,\nNisha Kumari\n",
"when doin pip install pymatgen\n\nRequirement already satisfied: pymatgen in\n./anaconda3/lib/python3.9/site-packages (2021.3.9)\nRequirement already satisfied: palettable>=3.1.1 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (3.3.0)\nRequirement already satisfied: requests in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (2.26.0)\nRequirement already satisfied: spglib>=1.9.9.44 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (1.16.3)\nRequirement already satisfied: monty>=3.0.2 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (2021.12.1)\nRequirement already satisfied: matplotlib>=1.5 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (3.4.3)\nRequirement already satisfied: sympy in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (1.9)\nRequirement already satisfied: pandas in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (1.3.4)\nRequirement already satisfied: numpy>=1.20.1 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (1.20.3)\nRequirement already satisfied: plotly>=4.5.0 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (5.5.0)\nRequirement already satisfied: uncertainties>=3.1.4 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (3.1.6)\nRequirement already satisfied: scipy>=1.5.0 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (1.7.1)\nRequirement already satisfied: networkx>=2.2 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (2.6.3)\nRequirement already satisfied: tabulate in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (0.8.9)\nRequirement already satisfied: ruamel.yaml>=0.15.6 in\n./anaconda3/lib/python3.9/site-packages (from pymatgen) (0.17.20)\nRequirement already satisfied: cycler>=0.10 in\n./anaconda3/lib/python3.9/site-packages (from\nmatplotlib>=1.5->pymatgen) (0.10.0)\nRequirement already satisfied: pillow>=6.2.0 in\n./anaconda3/lib/python3.9/site-packages (from\nmatplotlib>=1.5->pymatgen) (8.4.0)\nRequirement already satisfied: pyparsing>=2.2.1 in\n./anaconda3/lib/python3.9/site-packages (from\nmatplotlib>=1.5->pymatgen) (3.0.4)\nRequirement already satisfied: kiwisolver>=1.0.1 in\n./anaconda3/lib/python3.9/site-packages (from\nmatplotlib>=1.5->pymatgen) (1.3.1)\nRequirement already satisfied: python-dateutil>=2.7 in\n./anaconda3/lib/python3.9/site-packages (from\nmatplotlib>=1.5->pymatgen) (2.8.2)\nRequirement already satisfied: six in\n./anaconda3/lib/python3.9/site-packages (from\ncycler>=0.10->matplotlib>=1.5->pymatgen) (1.16.0)\nRequirement already satisfied: tenacity>=6.2.0 in\n./anaconda3/lib/python3.9/site-packages (from plotly>=4.5.0->pymatgen)\n(8.0.1)\nRequirement already satisfied: ruamel.yaml.clib>=0.2.6 in\n./anaconda3/lib/python3.9/site-packages (from\nruamel.yaml>=0.15.6->pymatgen) (0.2.6)\nRequirement already satisfied: future in\n./anaconda3/lib/python3.9/site-packages (from\nuncertainties>=3.1.4->pymatgen) (0.18.2)\nRequirement already satisfied: pytz>=2017.3 in\n./anaconda3/lib/python3.9/site-packages (from pandas->pymatgen)\n(2021.3)\nRequirement already satisfied: urllib3<1.27,>=1.21.1 in\n./anaconda3/lib/python3.9/site-packages (from requests->pymatgen)\n(1.26.7)\nRequirement already satisfied: idna<4,>=2.5 in\n./anaconda3/lib/python3.9/site-packages (from requests->pymatgen)\n(3.2)\nRequirement already satisfied: charset-normalizer~=2.0.0 in\n./anaconda3/lib/python3.9/site-packages (from requests->pymatgen)\n(2.0.4)\nRequirement already satisfied: certifi>=2017.4.17 in\n./anaconda3/lib/python3.9/site-packages (from requests->pymatgen)\n(2021.10.8)\nRequirement already satisfied: mpmath>=0.19 in\n./anaconda3/lib/python3.9/site-packages (from sympy->pymatgen) (1.2.1)\nNote: you may need to restart the kernel to use updated packages.\n\n\nand then if m trying to import pymatgen showing error\n\nn*umpy.ndarray size changed, may indicate binary incompatibility.\nExpected 96 from C header, got 88 from PyObject.*\n\n\n\n\nOn Tue, Feb 8, 2022 at 8:10 PM Shyue Ping Ong ***@***.***>\nwrote:\n\n> Do a pip install pymatgen. It seems that the C compilation of the package\n> was not properly done.\n>\n> —\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/2422#issuecomment-1032682194>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AXUZ2FSEU7TQN3YOZLRAIADU2ETNTANCNFSM5NXWOVJA>\n> .\n> Triage notifications on the go with GitHub Mobile for iOS\n> <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>\n> or Android\n> <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.\n>\n> You are receiving this because you authored the thread.Message ID:\n> ***@***.***>\n>\n\n\n-- \nWith Regards,\nNisha Kumari\n",
"Please do `pip install numpy --upgrade`. This is likely your numpy installation issue."
] | 2022-02-07T15:03:30
| 2022-02-09T16:15:46
|
2022-02-07T15:08:49Z
|
NONE
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i have successfully installed pymatgen by import pymatgen but when want to print(pymatgen.__version__) getting error module 'pymatgen' has no attribute '__version___'. Not able to import pymatgen.core. pls help
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https://github.com/materialsproject/pymatgen/pull/2423
| 1,126,148,977
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PR_kwDOACgets4yLeEV
| 2,423
|
Add --backup flag to pmg config
|
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[
"\n[](https://coveralls.io/builds/46305647)\n\nCoverage decreased (-0.6%) to 83.449% when pulling **045954cebceb2464f734a76624b0423b5e034e96 on janosh:pmg-config-backup-flag** into **c1335efbe8fe68f20427a5131dad4a0dc41e59ea on materialsproject:master**.\n"
] | 2022-02-07T15:31:59
| 2022-02-07T20:11:34
|
2022-02-07T19:54:59Z
|
MEMBER
|
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Mostly to allow _not_ creating a backup file when modifying `.pmgrc.yaml`.
|
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PR_kwDOACgets4yMOgK
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[pre-commit.ci] pre-commit autoupdate
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"\n[](https://coveralls.io/builds/46304522)\n\nCoverage decreased (-0.001%) to 84.086% when pulling **cb8b05f484040dfea3d61d416272aac8e74007ef on pre-commit-ci-update-config** into **c1335efbe8fe68f20427a5131dad4a0dc41e59ea on master**.\n"
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| 2022-02-09T16:46:47
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2022-02-09T16:46:47Z
|
CONTRIBUTOR
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<!--pre-commit.ci start-->
updates:
- [github.com/pre-commit/mirrors-mypy: v0.930 → v0.931](https://github.com/pre-commit/mirrors-mypy/compare/v0.930...v0.931)
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I_kwDOACgets5DJ6XA
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install without internet connection
|
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[
"There are a lot of dependency packages. Sorry, but we do expect an internet connection when installing packages.",
"export CC=gcc before installing fixed the issue.\r\n\r\nThe issue I'm having now is that I don't have a pmgrc.yaml file; how to I get/create the file or specifically get a PMG_MAPI_KEY?",
"got it from materialsproject.org"
] | 2022-02-08T01:04:11
| 2022-02-08T15:27:27
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2022-02-08T14:40:47Z
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NONE
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Hi,
I'm having issues installing/running on a computer without internet connection so I can't just pip install. I believe I have installed all required dependencies. I can build and install "python setup.py build" and "python setup.py install"; I can even do "pip install pymatgen" (all: Requirement already satisfied). So it seems like I have installed it (pymatgen 2022.2.7 is listed in "pip list"); however, if I try to simply import "import pymatgen.core" I get
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/projects/pymatgen-master/pymatgen/core/__init__.py", line 15, in <module>
from .lattice import Lattice
File "/projects/pymatgen-master/pymatgen/core/lattice.py", line 22, in <module>
from pymatgen.util.coord import pbc_shortest_vectors
File "/projects/pymatgen-master/pymatgen/util/coord.py", line 16, in <module>
from . import coord_cython as cuc
ImportError: cannot import name 'coord_cython' from 'pymatgen.util' (/projects/pymatgen-master/pymatgen/util/__init__.py)
Within python I can "import pymatgen" then use autofill and see pymatgen.ext and pymatgen.util but that is it.
Thanks for any help
|
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| 1,129,515,377
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I_kwDOACgets5DUwlx
| 2,426
|
sdist doesn't include `.c` files
|
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[
"Nevermind, was missing cython :)"
] | 2022-02-10T06:25:04
| 2022-02-10T06:26:48
|
2022-02-10T06:26:48Z
|
CONTRIBUTOR
|
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**Describe the bug**
Trying to build from sdist
**To Reproduce**
```
pip install --no-binary --user https://files.pythonhosted.org/packages/00/eb/fc120e9c0d006788015cff8a6e8650bce18e23c5f24811f7a71f1ffab01b/pymatgen-2022.2.7.tar.gz
```
**Expected behavior**
Builds with C toolchain and other dependencies.
**Desktop (please complete the following information):**
- OS: Linux
- Version 2022.2.7
**Additional context**
```
> running build_ext
> building 'pymatgen.optimization.linear_assignment' extension
> creating build/temp.linux-x86_64-3.9
> creating build/temp.linux-x86_64-3.9/pymatgen
> creating build/temp.linux-x86_64-3.9/pymatgen/optimization
> gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/nix/store/hzi6fdch87l6hx9yyb6c3c2qbapczpg0-python3.9-numpy-1.21.5/lib/python3.9/site-packages/numpy/core/include -I/nix/store/afi0ysqw20yiiw2gr2d28dx40bc4ddf8-python3-3.9.10/include/python3.9 -c pymatgen/optimization/linear_assignment.c -o build/temp.linux-x86_64-3.9/pymatgen/optimization/linear_assignment.o
> gcc: error: pymatgen/optimization/linear_assignment.c: No such file or directory
> gcc: fatal error: no input files
> compilation terminated.
> error: command '/nix/store/pja9g36cy32z3d51942jqk91a6l2d5nv-gcc-wrapper-10.3.0/bin/gcc' failed with exit code 1
For full logs, run 'nix log /nix/store/5d5alw8d51lpaacpnmhkzaby4l4dsjhc-python3.9-pymatgen-2022.2.7.drv'.
```
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PR_kwDOACgets4yWiVh
| 2,427
|
Move cython to setup_requires
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[
"Thanks.",
"\n[](https://coveralls.io/builds/46419483)\n\nCoverage decreased (-0.6%) to 83.449% when pulling **542067ecbd0a5a61416d9942d173da77fd980af5 on jonringer:patch-1** into **a160fca5669e95ddb700b1fef0323b58b96532ce on materialsproject:master**.\n"
] | 2022-02-10T06:30:18
| 2022-02-10T17:09:01
|
2022-02-10T15:06:11Z
|
CONTRIBUTOR
|
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## Summary
Move cython to `setup_requires`. Allows for availability to be checked before attempting to build native extensions. Avoiding #2426
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [ ] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
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| 1,130,484,448
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I_kwDOACgets5DYdLg
| 2,428
|
Ih point group symmetry operations
|
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[] | null |
[
"The list of point group symmetry operations in pymatgen are mainly dealing with the crystallographic point groups (Ih is not crystallographic since it has 5-fold rotations). So you will need to look for them in texts. That said, it is relatively easy to generate the whole list if you define the main 5-fold, 3-fold and 2-fold axes using the Operations class and generate the whole list."
] | 2022-02-10T17:08:05
| 2022-02-10T17:14:04
|
2022-02-10T17:14:04Z
|
NONE
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I was trying to find out the symmetry operations of the point of Ih. But I did not find a symbol corresponding to it to generate a PointGroup object.
I would really appreciate the symbol to generate the symmetry operations of Ih point group.
|
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PR_kwDOACgets4yh2x_
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|
Partial periodic boundary conditions
|
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[
"\n[](https://coveralls.io/builds/49489353)\n\nCoverage decreased (-0.7%) to 83.291% when pulling **9dfe1665eef558d5b8511c1055a682ebdc5b1e99 on gpetretto:ppbc** into **6bbe18e33348ba0175c423ac8f9533d02b7fbc75 on materialsproject:master**.\n",
"Thanks for this PR @gpetretto! I appreciate the write-up and detailed thoughts, I'll take some time to read it over and think about the concerns raised.",
"Hi @mkhorton, sorry for the bothering, but do you have any update on this?",
"Thanks for your patience @gpetretto and thank you for the reminder (it was necessary! apologies, been busy recently).\r\n\r\nI've had a look over the PR now and it looks good to me. I like this approach overall. I'm not familiar enough to guarantee the Cython code is correct so I will trust you and the tests on this.\r\n\r\nDo you have any remaining concerns?",
"Thanks for the reply @mkhorton. Just to be sure, do you mean that the comments in the opening post do not need further discussion and things can stay roughly as they are in the current PR? \r\nIf that is the case, should I just add the tests and finalize the PR?",
"Yes, I would agree with finalizing the PR and using this approach. If anyone disagrees however or has further input, now is the time to comment!",
"I fixed a few points and added tests. If there are no other comments this sohuld be ready for a review and merge.",
"Thanks"
] | 2022-02-11T14:56:56
| 2022-05-26T18:06:21
|
2022-05-26T18:06:14Z
|
CONTRIBUTOR
|
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### Summary
As a follow up to #2364 I am opening this PR to discuss about the introduction of partial periodic boundary conditions (PPBC).
### Details
This first draft is based on these main points:
* PPBC are introduced at the level of `Lattice` with a tuple of three bool in the `pbc` attribute, defining the periodic boundary conditions along the three edges of the lattice.
* Objects having a `Lattice` get their periodic boundary conditions from it. This avoids inconsistencies among different objects. i.e. `PeriodicSite` and `Structure` have the same reference to define the PBC.
* `Molecule` and `Structure` stay on two different branches of the inheritance tree starting from `SiteCollection`, even though `Molecule` could be thought of a subset of the case where `pbc=(False, False, False)`.
* fractional coordinates remain the main reference for `PeriodicSite`. This ensures the backward compatibility with the serialised data and avoids the ambiguity of what `frac_coords` would mean in PPBC. This implies that a somewhat meaningful 3D Lattice should be defined even with PPBC.
Based on these, the changes required to the code are relative small and seems that backward compatibility could be easily preserved (at least, all the tests pass).
In practice, the main changes are the addition of the `pbc` attribute and the updates to take it into account in functions related to distances and where `to_unit_cell` is True. Since distances are calculated in a few key functions, the changes should propagate to all functions that rely on these.
Being a first draft I did not add any test and changed the docstrings in just a few places. I also did not run the checks for the coding style.
I am not used to write cython code, so some additions in coord_cython.pyx could probably be optimised. Also, the standard implementation of `pbc_shortest_vectors` relies on the LLL reduced lattice and makes it incompatible with the `pbc`. Is there a specific reason for that, aside from the use of the `lll_frac_tol` argument? I switched to the standard lattice if the crystal is not 3D periodic.
### Example
```python
coords = [[0,0,0],
[0.9, 0.9, 0.9]]
l = Lattice(np.eye(3) * [1,2,3], pbc=(True, False, True))
s = Structure(lattice=l, coords=coords, species=["Si"]*len(coords))
print(s.distance_matrix[0, 1])
```
gives 1.82756669, instead of 0.37416574 with `pbc=(True, True, True)`.
### Comments
Assuming that the main points listed above are fine, here are some more considerations.
It would be relevant to to decide if this new feature should stay directly in `Structure` (as implemented here) or a new intermediate class should be introduced between `SiteCollection` and `Structure`, with `Structure` having `pbc=(True, True, True)` fixed.
If the PPBC stay in `Structure`, how to handle its subclasses (e.g. `Slab`, `Interface`, `SymmetrizedStructure`)? I suppose that for most of them PPBC would not make sense.
How should all the objects that accept a `Structure` behave? For example running the `SpacegroupAnalyzer` should not be meaningful for PPBC. Should these make checks on `pbc` and raise?
Could objects like the `StructureMatcher` be adapted to work with PPBC?
Concering `Lattice`:
* should the `pbc` attribute be immutable?
* should `pbc=(False, False, False)` be allowed?
* some methods may be considered ambiguous. Methods like `get_niggli_reduced_lattice`, `get_wigner_seitz_cell` will keep working while ignoring `pbc`, but are likely to return inconsistent results for PPBC. Should they raise an error? Methods like `scale` should still act on the whole lattice, or modify only the periodic directions?
Concerning `Structure`:
* some methods like `get_primitive_structure`, `get_orderings` could probably be adapted to work with PPBC, but I suppose it will not be straightforward. Should this be done?
* Should the writing to a file be allowed in PPBC as if it was a normal `Structure`? Are there file formats that support PPBC?
* how should a Structure with PPBC be scaled? (e.g. `__mul__`)
While it would not necessarily be the best option, I would say that allowing PPBC only in a new class, parent of `Structure`, should avoid easily all the problems related to checks in cases where a fully periodic `Structure` is expected.
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PR_kwDOACgets4ynFBh
| 2,430
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Remove deprecated structure_2_lmpdata()
|
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[
"\n[](https://coveralls.io/builds/46570777)\n\nCoverage remained the same at 83.481% when pulling **14df0164b47f30a047cd362febc18abb01f0277f on janosh:unpin-dev-reqs** into **6ec393bdfa5bdbc3548bc47b89b9c9fb159793b5 on materialsproject:master**.\n"
] | 2022-02-12T15:27:14
| 2022-02-15T17:40:48
|
2022-02-15T17:18:17Z
|
MEMBER
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Also unpins dev requirements. I noticed they are kept very close to the latest versions anyway which `pip` auto-installs by default so this simply removes the need to update the version numbers manually.
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I_kwDOACgets5DyZDV
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AttributeError when using .atomic_numbers on a disordered structure
|
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[] | 2022-02-14T13:11:26
| 2022-02-14T16:49:41
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2022-02-14T16:49:41Z
|
MEMBER
|
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**Describe the bug**
Accessing `atomic_numbers` on a disordered structure throws `AttributeError: specie`.
<details>
<summary>full error trace</summary>
```py
AttributeError Traceback (most recent call last)
~/.venv/py310/lib/python3.10/site-packages/pymatgen/core/structure.py in atomic_numbers(self)
270 def atomic_numbers(self) -> Tuple[int]:
271 """List of atomic numbers."""
--> 272 return tuple(site.specie.Z for site in self) # type: ignore
273
274 @property
~/.venv/py310/lib/python3.10/site-packages/pymatgen/core/structure.py in <genexpr>(.0)
270 def atomic_numbers(self) -> Tuple[int]:
271 """List of atomic numbers."""
--> 272 return tuple(site.specie.Z for site in self) # type: ignore
273
274 @property
~/.venv/py310/lib/python3.10/site-packages/pymatgen/core/sites.py in __getattr__(self, a)
77 if a in p:
78 return p[a]
---> 79 raise AttributeError(a)
80
81 @property
AttributeError: specie
```
</details>
**To Reproduce**
```py
from pymatgen.transformations.standard_transformations import SubstitutionTransformation
from pymatgen.ext.matproj import MPRester
struct = MPRester().get_structure_by_material_id("mp-19017")
disord_struct = SubstitutionTransformation(
{"Fe": {"Fe": 0.75, "C": 0.25}}
).apply_transformation(struct)
disord_struct.atomic_numbers
```
**Expected behavior**
Either a tuple of dicts (for the disordered sites) or a more helpful error message saying this is not supported.
|
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| 1,137,820,572
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PR_kwDOACgets4y0Cpa
| 2,432
|
Fix and add some type annotations
|
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[] | null |
[
"\n[](https://coveralls.io/builds/46555065)\n\nCoverage decreased (-0.6%) to 83.443% when pulling **7a53d56ccbd6086050b7e6f421ae0bbceebfd9d6 on janosh:fix-type-annos** into **555a788348d5aa8e1d5fdfa20cffa859ec1e475e on materialsproject:master**.\n"
] | 2022-02-14T20:43:07
| 2022-02-15T17:26:57
|
2022-02-15T17:17:31Z
|
MEMBER
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[Docs](https://docs.python.org/3/library/typing.html#typing.Tuple):
> To specify a variable-length tuple of homogeneous type, use literal ellipsis, e.g. [Tuple](https://docs.python.org/3/library/typing.html#typing.Tuple)[int, ...]. A plain Tuple is equivalent to Tuple[Any, ...], and in turn to [tuple](https://docs.python.org/3/library/stdtypes.html#tuple).
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PR_kwDOACgets4y2XhV
| 2,433
|
Fix Structure.apply_operation() return val
|
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"\n[](https://coveralls.io/builds/46555597)\n\nCoverage decreased (-0.6%) to 83.439% when pulling **c44f0d5c547817103fda935e9e400bce285a0f75 on janosh:fix-struct-apply_operation** into **555a788348d5aa8e1d5fdfa20cffa859ec1e475e on materialsproject:master**.\n"
] | 2022-02-15T10:52:58
| 2022-02-15T17:25:36
|
2022-02-15T17:17:09Z
|
MEMBER
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`Structure.apply_operation()` says it returns modified structure but didn't.
|
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PR_kwDOACgets4y3xkm
| 2,434
|
Small changes to Lobster classes
|
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[] | null |
[
"\n[](https://coveralls.io/builds/46582749)\n\nCoverage decreased (-0.6%) to 83.482% when pulling **f2caba9f57f9a4c17c7379aefacfb792dcb1a2a8 on JaGeo:master** into **df44a54129f468e2a506cb3ed674a75b70d344b3 on materialsproject:master**.\n"
] | 2022-02-15T16:47:11
| 2022-02-16T00:14:20
|
2022-02-15T23:43:17Z
|
MEMBER
|
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## Summary
I have changed the energy range for the standard Lobster computation. This is partially related to a VASP 6.0 problem with Fermi levels at the bottom of the band gap.
Furthermore, I have enabled the use of Loewdin charges to determine cation and anions and respective coordination environments based on the assessment of cation and anion bonds.
I have also included and/or adapted the tests.
|
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PR_kwDOACgets4y6u8_
| 2,435
|
Remove unused mypy ignores
|
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[
"\n[](https://coveralls.io/builds/48165920)\n\nCoverage decreased (-0.7%) to 83.272% when pulling **db6268f413cffca8cf79ec1f159afb4c9253efbe on janosh:no-unused-mypy-ignore** into **1a2bf238bf87123b09ab8a207f50a9f4eeb13d68 on materialsproject:master**.\n",
"@shyuep Given how slow `mypy` is, is there a good reason for deleting the cache on every run?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/9bdf9fb8eebf4bef66f8a3541cfd27ba8ee1bccf/.github/workflows/lint.yml#L28-L32",
"When it is cached, the results may be inaccurate. In any case, the speed is not a big limiting factor for CI.",
"@shyuep Just fixed the merge conflicts and remaining `mypy` errors.",
"CI error seems unrelated?\r\n\r\n```py\r\ndef predict_mp(self, model_name, mp_id):\r\n \"\"\"\r\n Predict using the http://megnet.crystals.ai/ API.\r\n \"\"\"\r\n response = None\r\n url = self.url + f\"/predict_mp/{model_name}/{mp_id}\"\r\n try:\r\n response = self.session.get(url)\r\n if response.status_code in [200, 400]:\r\n return response.json()\r\n raise ValueError(f\"REST query returned with error status code {response.status_code}\")\r\n except Exception as ex:\r\n msg = f\"{ex}. Content: {response.content}\" if hasattr(response, \"content\") else str(ex)\r\n> raise ValueError(msg)\r\nE ValueError: REST query returned with error status code 503. Content: ...\r\n```",
"The CI errors are related to the MP website being down."
] | 2022-02-16T10:54:48
| 2022-04-11T20:58:18
|
2022-04-11T20:58:06Z
|
MEMBER
|
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Might want to add
```cfg
[mypy]
warn_redundant_casts = true
warn_unused_ignores = true
check_untyped_defs = true
```
to `setup.cfg` in future though currently emits too many type errors to deal with.
|
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PR_kwDOACgets4y-DR_
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|
[WIP] Add comments and type hints
|
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[
"\n[](https://coveralls.io/builds/46629515)\n\nCoverage decreased (-0.6%) to 83.481% when pulling **39f203529819f151827c9c147c331af9a5cd7209 on penicillin0:add-type-vasp-input** into **394e0d71bf1d1025fcf75498cbb16aa3f41ce78c on materialsproject:master**.\n"
] | 2022-02-17T06:38:41
| 2022-06-14T00:07:38
|
2022-06-14T00:07:38Z
|
CONTRIBUTOR
|
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## Summary
The function for vasp's io is used often, so I made the type more explicit.
This is also for the safety and uniformity of the types.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [ ] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [ ] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [ ] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
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I_kwDOACgets5ELU1B
| 2,437
|
Structure doesn't recognize Yaml files it writes
|
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[] | 2022-02-18T21:50:45
| 2022-02-24T14:47:49
|
2022-02-24T14:47:49Z
|
MEMBER
|
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```py
from pymatgen.core import Structure
from pymatgen.ext.matproj import MPRester
mp_id = "mp-2201"
struct = MPRester().get_structure_by_material_id(mp_id)
struct.to(filename=f"{mp_id}.yml")
Structure.from_file(filename=f"{mp_id}.yml")
>>> ValueError: Unrecognized file extension!
```
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PR_kwDOACgets4zIBDu
| 2,438
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Fix `Structure.from_file()` for `.yml` extension
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"\n[](https://coveralls.io/builds/46704312)\n\nCoverage decreased (-0.6%) to 83.483% when pulling **8427738c341d2230647c83e7b3924920f1a1faeb on janosh:fix-structure-from-yml** into **394e0d71bf1d1025fcf75498cbb16aa3f41ce78c on materialsproject:master**.\n",
"Thanks."
] | 2022-02-18T21:54:44
| 2022-02-24T14:49:01
|
2022-02-24T14:47:49Z
|
MEMBER
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Also adds a test for this.
Closes #2437.
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PR_kwDOACgets4zM4qb
| 2,439
|
added wswq parser
|
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[
"\n[](https://coveralls.io/builds/46720329)\n\nCoverage decreased (-0.6%) to 83.486% when pulling **a3f8f941ab48daaee588de4929573da75ca4c9ce on jmmshn:parse_WSWQ** into **394e0d71bf1d1025fcf75498cbb16aa3f41ce78c on materialsproject:master**.\n",
"Thanks @jmmshn :)"
] | 2022-02-21T03:15:21
| 2022-02-23T16:16:27
|
2022-02-22T23:31:42Z
|
CONTRIBUTOR
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# WSWQ Parsing
VASP has a "secret" file WSWQ representing the matrix elements of <W | S | W(Q)>
Where W is the plane-wave wavefunction of the present calculation and W(Q) is the wavefunction of some perturbed calculation.
These matrix elements can be used to calculate the finite-difference of the wavefunction overlaps as you distort as structure.
This has applications for evaluating the electron-phonon interactions as we have done in the NONRAD code:
https://github.com/mturiansky/nonrad
Having this parser here I think makes a bit more sense especially if someone wants to make a workflow involving this stuff.
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PR_kwDOACgets4zPwES
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|
Add pydocstyle pre-commit hook
|
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"\n[](https://coveralls.io/builds/46744919)\n\nCoverage decreased (-0.6%) to 83.48% when pulling **326af0eb1a1926a398a1f7379c535ce301fa5099 on janosh:pydocstyle** into **394e0d71bf1d1025fcf75498cbb16aa3f41ce78c on materialsproject:master**.\n",
"Thanks."
] | 2022-02-21T19:04:39
| 2022-02-24T18:20:10
|
2022-02-24T17:05:03Z
|
MEMBER
|
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Brings pre-commit.ci more in line with GHA `lint.yml` so people can be more confident CI won't complain once checks pass locally.
Adds a few type hints along the way.
|
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PR_kwDOACgets4zP2X6
| 2,441
|
Add CITATION.cff
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[
"\n[](https://coveralls.io/builds/46746727)\n\nCoverage decreased (-0.6%) to 83.482% when pulling **a78eb0ce018fd5a10c7bbac7c050c8361e551f41 on janosh:citation** into **394e0d71bf1d1025fcf75498cbb16aa3f41ce78c on materialsproject:master**.\n",
"Thanks. But let's still keep the readme citation as well since some people may not be aware of the CFF file. ",
"> Thanks. But let's still keep the readme citation as well since some people may not be aware of the CFF file.\r\n\r\nSure thing. Though its not just the file, it's also prominently displayed on the repo's landing page side bar."
] | 2022-02-21T19:42:40
| 2022-02-22T11:06:51
|
2022-02-22T00:18:18Z
|
MEMBER
|
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GitHub supports adding citation metadata to repos. This PR moves instructions on how to cite `pymatgen` from readme into the `CITATION.cff` file which GH uses to then display citations in BibTeX and APA formats in the side bar. See [docs for details](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files).
Looks like this:
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I_kwDOACgets5EUT4f
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Missing ``kpath`` property in ``HighSymmKPath`` breaks VASP Kpoints
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[] | 2022-02-21T19:53:13
| 2022-02-21T20:40:05
|
2022-02-21T20:40:05Z
|
NONE
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**Describe the bug**
The ``kpath`` property was removed from the ``pymatgen.symmetry.bandstructure.HighSymmKPath``. This now breaks the VASP Kpoints object ``pymatgen.io.vasp.inputs.Kpoints`` if one tries to instantiate a Kpoints instance using the ``automatic_linemode()`` method as it makes use of the ``kpath`` property
**To Reproduce**
Steps to reproduce the behavior:
Setup any arbitrary structure and a ``HighSymmKpath`` instance and try to initialize a Kpoints object using the ``pymatgen.io.vasp.inputs.Kpoints.automatic_linemode()`` method
**Expected behavior**
Well, it should not crash.
**Desktop (please complete the following information):**
- OS: Linux
- Version 2022.0.17
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| 1,148,441,020
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I_kwDOACgets5Ec9G8
| 2,444
|
pmgrc.yaml not created when installing pymatgen (Python 3.8, pymatgen 2022.2.10)
|
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[
"This is a warning, not an error. The pmgrc file stores certain settings that is needed if you are generating VASP input files, using the materials project, etc. This warning can be ignored if you are not planning on using those.",
"This warning was also updated in https://github.com/materialsproject/pymatgen/commit/cc9dabf49f553fff2700aa514f31a3d17f99b18c, and will be slightly different in the next version: if the `.pmgrc.yaml` is not present at all, the warning will not be generated.\r\n\r\nThis change was the result of a change in behavior in YAML parsers resulting in corruption of this file for some users.",
"Thank you for the swift and informative replies!"
] | 2022-02-23T18:31:13
| 2022-02-23T22:20:25
|
2022-02-23T18:50:23Z
|
NONE
|
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Hello,
After installing pymatgen using 'pip pre-commit pymatgen' from my environment in bash and trying to import a function (OCPCalculator from the ocp module) I receive the following message from the terminal.
**warnings.warn(f"Error loading .pmgrc.yaml: {ex}. You may need to reconfigure your yaml file.")**
I checked in my home directory and found that no yaml file had been created anywhere that I could see. I am running from the Compute Canada Niagara cluster. Can you please tell me the likely cause of the problem and/or possible solutions?
**Expected behavior**
I would expect the module to import without this error.
**Desktop (please complete the following information):**
- OS: [Linux CentOS 7]
Best wishes
|
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I_kwDOACgets5EeDL1
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`ChemicalPotentialDiagram` fails on interior point selection for some systems
|
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[
"Just for posterity, here is a copy of the kind of error that is produced in Qhull when selecting an incorrect interior point (Zr-O-N system as before, with `default_min_limit=-20`)\r\n\r\n```\r\nscipy.spatial._qhull.QhullError: QH6023 qhull input error: feasible point is not clearly inside halfspace\r\nfeasible point: -10 -10 \r\n halfspace: 0.5 0.5 \r\n at offset: 10.012997585 and distance: 0.01299758500000081 \r\nThe halfspace was at index 0\r\n\r\nWhile executing: | qhull H \r\nOptions selected for Qhull 2019.1.r 2019/06/21:\r\n run-id 961326389 Halfspace _maxoutside 0\r\n\r\nTraceback (most recent call last):\r\n File \"/root/.local/lib/python3.9/site-packages/ddtrace/contrib/flask/helpers.py\", line 36, in wrapper\r\n return wrapped(*args, **kwargs)\r\n File \"/root/.local/lib/python3.9/site-packages/flask/app.py\", line 1516, in full_dispatch_request\r\n rv = self.dispatch_request()\r\n File \"/root/.local/lib/python3.9/site-packages/ddtrace/contrib/flask/helpers.py\", line 25, in wrapper\r\n return func(pin, wrapped, instance, args, kwargs)\r\n File \"/root/.local/lib/python3.9/site-packages/ddtrace/contrib/flask/patch.py\", line 494, in _traced_request\r\n return wrapped(*args, **kwargs)\r\n File \"/root/.local/lib/python3.9/site-packages/flask/app.py\", line 1502, in dispatch_request\r\n return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)\r\n File \"/root/.local/lib/python3.9/site-packages/ddtrace/contrib/flask/wrappers.py\", line 25, in trace_func\r\n return wrapped(*args, **kwargs)\r\n File \"/root/.local/lib/python3.9/site-packages/dash/dash.py\", line 1344, in dispatch\r\n response.set_data(func(*args, outputs_list=outputs_list))\r\n File \"/root/.local/lib/python3.9/site-packages/dash/_callback.py\", line 151, in add_context\r\n output_value = func(*func_args, **func_kwargs) # %% callback invoked %%\r\n File \"/app/mp_web/apps/phasediagram/phasediagram.py\", line 353, in update_table\r\n chempot_fig = chempot_diagram.get_plot()\r\n File \"/root/.local/lib/python3.9/site-packages/pymatgen/analysis/chempot_diagram.py\", line 150, in get_plot\r\n fig = self._get_2d_plot(elements=elems, label_stable=label_stable)\r\n File \"/root/.local/lib/python3.9/site-packages/pymatgen/analysis/chempot_diagram.py\", line 228, in _get_2d_plot\r\n domains = self.domains.copy()\r\n File \"/root/.local/lib/python3.9/site-packages/pymatgen/analysis/chempot_diagram.py\", line 509, in domains\r\n return self._get_domains()\r\n File \"/root/.local/lib/python3.9/site-packages/pymatgen/analysis/chempot_diagram.py\", line 179, in _get_domains\r\n hs_int = HalfspaceIntersection(hs_hyperplanes, np.array(interior_point))\r\n File \"_qhull.pyx\", line 2813, in scipy.spatial._qhull.HalfspaceIntersection.__init__\r\n File \"_qhull.pyx\", line 357, in scipy.spatial._qhull._Qhull.__init__\r\nscipy.spatial._qhull.QhullError: QH6023 qhull input error: feasible point is not clearly inside halfspace\r\nfeasible point: -10 -10 \r\n halfspace: 0.5 0.5 \r\n at offset: 10.012997585 and distance: 0.01299758500000081 \r\nThe halfspace was at index 0\r\n\r\nWhile executing: | qhull H \r\nOptions selected for Qhull 2019.1.r 2019/06/21:\r\n run-id 961326389 Halfspace _maxoutside 0\r\n```",
"Closing with c70ca529586d848134c2e0e4d9362a0e37d1fdde"
] | 2022-02-24T00:38:54
| 2022-02-25T18:58:45
|
2022-02-25T18:58:45Z
|
MEMBER
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**Describe the bug**
The `ChemicalPotentialDiagram` class currently fails upon initialization for some systems using MP data (e.g., Zr-O-N) due to improper selection of an interior point to be passed to Qhull.
The current logic implemented in pymatgen is to use the mean of the elemental limits/bounds as the interior point, however, it would be just as easy to use the minimum (or some offset from the minimum).
**To Reproduce**
```python
with MPRester() as mpr:
entries = mpr.get_entries_in_chemsys("Zr-O-N")
cpd = ChemicalPotentialDiagram(entries)
```
**Expected behavior**
The interior point is always selected logically, such that it never leads to a Qhull error.
**Desktop (please complete the following information):**
- OS: Mac
- Version 2022.2.10
**Additional context**
I have implemented a fix and will address soon!
|
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I_kwDOACgets5EeKjM
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|
`ChemicalPotentialDiagram.get_plot()` needs better default limits for cleaner plotting
|
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[
"Thanks for taking care of this @mattmcdermott, it was actually an issue in our website issue tracker :)\r\n\r\nPart of the issue also seems to be font size related too, I wonder if we can pull the axes labels further from the plot so they don't overlap.",
"@mkhorton For sure, gonna try to address that as well in #2447. Will try to have it done by tomorrow.",
"I was not able to figure out how to add space between the axis label and the axis; as far as I can tell, this is not a Plotly feature. (I also couldn't make a hack with HTML breaks to do it either). However, I have changed the size of the ticks and tick labels to help with the visual clarity in #2447 -- I think it looks much better now! ",
"Closing with c70ca529586d848134c2e0e4d9362a0e37d1fdde"
] | 2022-02-24T01:28:11
| 2022-02-25T18:58:21
|
2022-02-25T18:58:20Z
|
MEMBER
|
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**Is your feature request related to a problem? Please describe.**
Chemical potential diagrams tend to look pretty gross with the current defaults, especially for MP data. See screenshot from the new MP website below:
**Describe the solution you'd like**
What is needed is some logic for automatically "deleting" extra whitespace for elemental domains. See new screenshot below:
**Describe alternatives you've considered**
The only alternative is the manual setting of limits, which is tedious and not possible for the MP website.
**Working solution**
I have a working solution for this and will address in an upcoming PR.
|
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PR_kwDOACgets4zYOi5
| 2,447
|
Fix bug in `ChemicalPotentialDiagram` initialization (interior point), improve default plots
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[
"\n[](https://coveralls.io/builds/46873292)\n\nCoverage decreased (-0.7%) to 83.374% when pulling **961f2cd298e3b3575d7998f794ca6c72515e1b7e on mattmcdermott:cpd_fix** into **03e8b9981535acace1fc84406c8c027626ebbad4 on materialsproject:master**.\n",
"@mkhorton I think this is good to go",
"Thanks @mattmcdermott ! This is super helpful :)"
] | 2022-02-24T01:40:52
| 2022-02-25T18:56:41
|
2022-02-25T18:56:11Z
|
MEMBER
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## Summary
Include a summary of major changes in bullet points:
* Bug fix: changed method of determining interior point for Qhull algorithm to improve stability (see Issue #2445)
* Bug fix: better default plotting by re-assignment of minimum limit when `get_plot()` is called (see Issue #2446)
## Additional dependencies introduced (if any)
None
## TODO (if any)
* Linting, some docstring fixes
* Further testing on my end to make sure this actually works in most cases
## Checklist
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
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PR_kwDOACgets4zapgH
| 2,448
|
Allow to switch off print of ChemEnv citation
|
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[
"I would say - why print citations at all? I don't think any other part of the code prints citations. E.g., pymatgen doesn't print a citation everytime something is done. I would suggest turning it off by default. I think the citation is prominently displayed in all the documentation.",
"I would be fine with this. I can remove it and add the reference for the technical paper in the documentation."
] | 2022-02-24T16:33:20
| 2022-02-24T17:04:44
|
2022-02-24T17:04:44Z
|
MEMBER
|
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## Summary
I am adding a small parameter to switch off the ChemEnv citation print. This will make it easier to use ChemEnv in other program packages. I am also updating the citation of ChemEnv.
I am tagging @davidwaroquiers here, so that he knows.
Let me know if I should do anything additionally.
|
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PR_kwDOACgets4z0g1k
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Bump `actions/checkout` in GitHub CI to v3
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"\n[](https://coveralls.io/builds/47007120)\n\nCoverage decreased (-0.8%) to 83.369% when pulling **b7542b69cef567c539e1742d3ad44eea958b2bf5 on janosh:actions-checkout-v3** into **3d40b31b076aa10d49dbba59a712348c40ee98d3 on materialsproject:master**.\n"
] | 2022-03-02T11:03:03
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2022-03-02T14:43:00Z
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MEMBER
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Only change appears to be that [runtime was updated from node v14 to v16](https://github.com/actions/checkout/releases/tag/v3.0.0).
|
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PR_kwDOACgets4z3KqF
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|
Add monty `cached_class` to other compatibility schemes
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[
"Thanks @munrojm!\r\n\r\nFor the record, in private communication @munrojm noted that the decoding changes from ~7s to ~0.3s in our benchmark case of a set of entries in the `Fe-O` system, so a huge improvement.",
"\n[](https://coveralls.io/builds/47032454)\n\nCoverage decreased (-0.8%) to 83.37% when pulling **7b27d26b9f8de818b9b0306c80a55bc346d90c1c on munrojm:master** into **4b66ebc908cf8cb0322152d64f7491ccb2a84213 on materialsproject:master**.\n",
"@mkhorton @munrojm fwiw, we just did performance testing using the new `cached_class` proposed in https://github.com/materialsvirtuallab/monty/pull/691 comparing to the old or no `cached_class` and the performance stays basically unchanged in all 3 cases.\r\n\r\n\r\n```py\r\nfrom mp_api.client import MPRester\r\n\r\n%%timeit\r\nMPRester().get_entries(\"Fe-O\")\r\n>>> 1.17 s ± 181 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\r\n```\r\n\r\n@mkhorton do you remember what kind of testing you did? perhaps changes in the `mp_api` mean the `cached_class` no longer offers any speed benefits? in which case removing it altogether from `MaterialsProject2020Compatibility` would also solve @CompRhys's pickling issue reported in https://github.com/materialsproject/pymatgen/issues/3898"
] | 2022-03-03T00:28:45
| 2024-07-01T12:53:36
|
2022-03-03T00:41:24Z
|
MEMBER
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## Summary
This PR adds the `@cached_class` decorator from monty to the `MaterialsProject2020Compatibility` and `MaterialsProjectAqueousCompatibility` classes. This fixes slow decoding of large lists of entry object which greatly impacts the new `MPRester` client.
## Additional dependencies introduced (if any)
None
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
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PR_kwDOACgets4z_QGq
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Type hints
|
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[
"\n[](https://coveralls.io/builds/47100065)\n\nCoverage decreased (-0.8%) to 83.37% when pulling **7dcb5287dc50a75a7792d8c197159912b1233209 on janosh:type-hints** into **3376f27a9c5a4cac1590169f2212361ab6c94388 on materialsproject:master**.\n",
"@janosh -- nice update to the typehints. I have a general question based on this. For something like `kwarg = None`, which is better programming practice: `kwarg: int = None` or `kwarg: int | None = None`? ",
"@arosen93 Thanks! `kwarg: int | None = None` is strictly speaking more correct but unless you set `mypy`'s [`--no-implicit-optional`](https://mypy.readthedocs.io/en/stable/command_line.html#cmdoption-mypy-no-implicit-optional) flag (which I usually don't) then the two are equivalent.",
"Good to know, thanks! :)",
"Thanks!"
] | 2022-03-05T09:25:23
| 2022-03-10T00:00:34
|
2022-03-10T00:00:31Z
|
MEMBER
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Add some more type hints in `electronic_structure/plotter.py`, `bandstructure.py`, `io/vasp/outputs.py`.
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PR_kwDOACgets4z_VxQ
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Future annotations
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[
"\n[](https://coveralls.io/builds/47217777)\n\nCoverage decreased (-0.9%) to 83.24% when pulling **4d44b489c98a3c5ff36c4b73a987c217bf907c36 on janosh:future-annotations** into **eaa2b6287520f6e59730d9a0697e2d8f841f8bfb on materialsproject:master**.\n",
"Note to future `pymatgen` maintainers: `pymatgen` makes heavy use of variadic args (`**kwargs` in particular, 438 hits occurrences across the code base, and another 57 `*args`) which unfortunately can't yet be annotated. There's a `mypy` issue https://github.com/python/mypy/issues/4441 from 2018 about this limitation still unclosed. Though it looks like the recently accepted PEP 646 slated for py3.11 with its `Unpack` type might make it easier to allow using `TypedDict`s to annotate `**kwargs` (at least `pyright` seems keen to try it: https://github.com/microsoft/pyright/issues/3002). IMO definitely sth to explore once that becomes possible.",
"Hi @janosh, thanks for the PR -- can you point me to where in the PEP the `x | None` syntax is preferred over `Optional[None]`?\r\n\r\nI was reading elsewhere that the new preferred option for kwargs may be to omit the `Optional` entirely, e.g. just `your_kwarg: x = None`, and that `mypy` will respect this.",
"> I was reading elsewhere that the new preferred option for kwargs may be to omit the `Optional` entirely, e.g. just `your_kwarg: x = None`, and that `mypy` will respect this.\r\n\r\n@mkhorton That's right! As I was discussing with @arosen93 over in https://github.com/materialsproject/pymatgen/pull/2451#issuecomment-1060296902, `kwarg: int | None = None` and `kwarg: int = None` are equivalent unless you set `mypy`'s [`--no-implicit-optional`](https://mypy.readthedocs.io/en/stable/command_line.html#cmdoption-mypy-no-implicit-optional) flag.\r\n\r\n\r\n",
"@mkhorton Regarding your 1st question, I believe [604 is the PEP](https://peps.python.org/pep-0604/#proposal) you're looking for.\r\n\r\n> We will also be able to write `t | None` or `None | t` instead of `Optional[t]`:\r\n> \r\n> ```py\r\n> isinstance(None, int | None)\r\n> isinstance(42, None | int)\r\n> ```",
"Thanks, so just to summarize:\r\n\r\n* `Optional[x]` and `x | None` are equally accepted, with neither specifically preferred (presumably the latter is easier since it skips the import)\r\n* The implicit optionals, though accepted by `mypy` by default, are not currently \"officially\" preferred (i.e., no guidance from Python/PEPs on this)\r\n\r\nHappy to merge this regardless since it looks cleaner, I just want to make sure we have guidelines for future PRs.",
"Yes, whether you allow implicit optionals is up to personal preference afaik. Seems more pythonic to me so I would leave it enabled.\r\n\r\n> I just want to make sure we have guidelines for future PRs.\r\n\r\nWe already do actually. This will all be handled automatically by pre-commit.ci in the future since we're using the [`pyupgrade`](https://github.com/asottile/pyupgrade) hook. It will [auto rewrite all type hints](https://github.com/asottile/pyupgrade#pep-585-typing-rewrites) to use the [new leaner](https://github.com/asottile/pyupgrade#pep-604-typing-rewrites) [syntax](https://github.com/asottile/pyupgrade#remove-quoted-annotations) in files that have the `__future__`'s import.\r\n\r\nThe only thing left to decide really is whether that `from __future__ import annotations` should be added to all files automatically."
] | 2022-03-05T11:53:26
| 2022-03-11T06:42:32
|
2022-03-11T03:00:02Z
|
MEMBER
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Convert annotations to future syntax available through import in Python 3.7 upwards. [See PEP 563](https://www.python.org/dev/peps/pep-0563/#id6).
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I_kwDOACgets5FLGC2
| 2,453
|
Feature Suggestion: DOS-related descriptors (e.g. d-band center, upper d-band edge)
|
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[] | 2022-03-06T07:03:13
| 2022-03-09T20:00:58
|
2022-03-09T20:00:58Z
|
MEMBER
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Given that we already have tools to parse DOS data in Pymatgen, it would be great to add some DOS-related descriptors. Some ideas include:
- d-band center
- Plotting the Hilbert transform of the local, projected DOS
- Upper d-band edge (i.e. highest peak position of the Hilbert transform of the projected DOS)
Other suggestions are welcome. I plan to implement these.
|
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| 1,160,717,725
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I_kwDOACgets5FLyWd
| 2,454
|
Slab generator cuts strong bonds
|
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[
"Hi @cedenoruel, I have not had chance to investigate this yet, but is it the case that this still happens even if you do not add oxidation states and skip that `add_oxidation_state_by_element` line? I'm wondering if the bond logic is oxidation-state dependent or not. e.g. is `(\"P\", \"O\"): 3` different to `(\"P5+\", \"O2-\": 3)`?",
"Hi @mkhorton , you are right, the bond logic is indeed oxidation-state dependent. \r\n`` bonds={(\"P5+\", \"O2-\": 3)}`` solves the issue. Thank you very much."
] | 2022-03-06T21:15:48
| 2022-03-08T12:57:16
|
2022-03-08T12:57:16Z
|
NONE
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Hi pymatgen developers.
I am generating slab structures for an inorganic crystal containing a phosphate ion (KH2PO4).
I would like to have no broken P--O bonds so I used the `bonds={("P", "O"): 3}`
```
from pymatgen.core.structure import Structure
KDP = Structure.from_file("input.cif")
KDP.add_oxidation_state_by_element({"K": 1, "H": 1, "P": 5, "O": -2})
all_slabs = generate_all_slabs(KDP, 1, min_slab_size=10, min_vacuum_size=10, bonds={("P", "O"): 3},
center_slab=False,symmetrize=False, lll_reduce=False,ftol=0.00001,tol=0.00001,repair=True)
```
However, when I inspect the symmetric **slab(001)**, **phosphate bond is broken.**
I attached here my input CIF file.
[KDP_Nelmes_295K.zip](https://github.com/materialsproject/pymatgen/files/8193491/KDP_Nelmes_295K.zip)
Any comments would be highly appreciated. Thank you very much for this very useful tool.
|
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| 1,160,784,241
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PR_kwDOACgets40ArtG
| 2,455
|
s-, p-, d-band properties: band filling, band center, band width, skewness, kurtosis, upper band edge
|
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[
"\n[](https://coveralls.io/builds/47217139)\n\nCoverage decreased (-0.7%) to 83.376% when pulling **b227fef96d359f4ffe5d2f2b5043703ed1125d19 on arosen93:rosen-dband** into **adafd2207e6c111560e3a98fc1353aa049c88076 on materialsproject:master**.\n",
"@montoyjh I imagine you're not doing much catalysis anymore these days, but if you have any requests along these lines, please let me know!",
"@mkhorton, ~when you get a moment, could you help out with this? Locally, my tests pass, but I'm having trouble resolving them here.~\r\n\r\nNever mind. Got it!",
"Okay, this is ready for your review :)",
"Thanks @arosen93, this looks great! Will merge shortly. I take it on faith that the values presented in the unit tests are reasonable.\r\n\r\nOne (excessively nit-picking) question, why `get_band_width` in the method name, but `bandwidth` (no space) in the docstring?",
"@mkhorton: Thanks!\r\n\r\nRe: unit tests, yup they're as reasonable as I can possibly assure. A few papers had codes to calculate these parameters in the SI, and I benchmarked my implementation against theirs.\r\n\r\nRe: naming, oops yeah that's because in the literature they often called it \"bandwidth\", but that would make it incompatible with `get_band_center`, `get_band_kurtosis`, etc.. I'll change the docstring right now."
] | 2022-03-07T01:14:26
| 2022-03-10T10:01:31
|
2022-03-09T20:00:58Z
|
MEMBER
|
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## Summary
This PR seeks to add additional features to `pymatgen.electronic_structure.dos` for various orbital-projected DOS properties used in catalysis, including:
- The orbital-projected band center, as defined by [Hammer and Norskov, _Surf. Sci._, 1995](https://www.sciencedirect.com/science/article/pii/0039602896800070)
- The band filling, band width, skewness, and kurtosis of the orbital-projected DOS, as defined by [Xin et al., _PRB_, 2014](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.89.115114)
- The Hilbert transformation of the orbital-projected DOS, which is relevant for the Newns-Anderson model of adsorption
- The Hilbert transform-based upper band edge, as defined by [Xin et al., _PRB_, 2014](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.89.115114)
To benchmark my implementation, I have reproduced the d-band center and upper d-band edge for an example material reported in [Xin et al.](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.89.115114) (included in the test suite). I have also reproduced the band filling, band width, skewness, and kurtosis from [Li et al.](https://pubs.acs.org/doi/abs/10.1021/acscatal.9b05248) (also in the test suite).
Additional changes:
- Fixed several typehint issues with `Orbital` vs. `OrbitalType` in the `CompleteDos` class
Closes #2453.
|
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| 1,162,515,877
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I_kwDOACgets5FSpWl
| 2,456
|
Building model of adding an oxygen atom
|
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[] | null |
[
"Please visit matsci.org for questions of usage. Github Issues should be used for reporting Issues and Bugs only."
] | 2022-03-08T11:01:07
| 2022-03-08T12:57:05
|
2022-03-08T12:57:04Z
|
NONE
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Hi pymatgen developers:
I want to add H atoms to the systems randomly, and maintain the distance between H and O , the steps are shown in the figure,
and which function can help me to realize this process?
Any comments would be highly appreciated. Thank you very much.
|
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I_kwDOACgets5FYddY
| 2,457
|
Missing matches from ZSLGenerator
|
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[] | 2022-03-09T14:51:30
| 2023-07-03T15:18:34
|
2023-07-03T15:18:34Z
|
CONTRIBUTOR
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**Describe the bug**
I noticed that some of the lattice matches I was getting with MPInterfaces' matching algorithm were missing in pymatgen's implementation with the same matching parameters. After a closer look, I narrowed the issue down to the transformation indices generated in `ZSLGenerator.generate_sl_transformation_sets()`. This happens when `int(self.max_area / film_area)` (or `substrate_area`, same issue) rounds down. Since this value is used as the second argument in the `range()` function, the list comprehension only iterates up to `int(self.max_area / film_area) - 1`, and as a result, we miss some indices at the upper limit.
In the specific example I was working on (script below), the matched area is just below my `max_area`, and this missing index results in no matches. This issue occurs only when `value % 1 < 0.5`, and a simple `np.ceil()` would solve it. Here's a small script to reproduce this:
**To Reproduce**
Simply run this script, and currently, it will not return any matches. By converting the `int()` to `np.ceil()`, we get 4 matches below the `max_area` of 100 A^2.
```python
import numpy as np
from pymatgen.analysis.interfaces import ZSLGenerator
from pymatgen.core.surface import SlabGenerator
from pymatgen.ext.matproj import MPRester
m = MPRester()
match_params = {
'max_area': 100,
'max_angle_tol': 0.02,
'max_length_tol': 0.05,
'max_area_ratio_tol': 0.1,
'bidirectional': False
}
film_bulk = m.get_structure_by_material_id('mp-13', conventional_unit_cell=True)
substrate_bulk = m.get_structure_by_material_id('mp-134', conventional_unit_cell=True)
miller_index = (1, 1, 1)
film_slab = SlabGenerator(film_bulk, miller_index, 10, 10).get_slabs()[0]
substrate_slab = SlabGenerator(substrate_bulk, miller_index, 10, 10).get_slabs()[0]
zsl_gen = ZSLGenerator(**match_params)
matches = list(zsl_gen(film_vectors=film_slab.lattice.matrix[:2],
substrate_vectors=substrate_slab.lattice.matrix[:2]))
def get_area(vec1, vec2):
vec3 = np.cross(vec1, vec2)
return np.sqrt(np.dot(vec3, vec3))
if matches:
for i, match in enumerate(matches):
subs_sl_vecs = match.substrate_sl_vectors
film_sl_vecs = match.film_sl_vectors
print(f'For match {i}, substrate SC has area {get_area(subs_sl_vecs[0], subs_sl_vecs[1])} '
f'and film SC has area {get_area(film_sl_vecs[0], film_sl_vecs[1])}')
```
**Expected behavior**
There should be a match with roughly 94 A^2 average supercell area with the given `match_params`.
I can fix this and write some unit tests and do a PR if needed.
|
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Alchemy type hints
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"`actions/checkout@v3` (now with default `fetch-depth: 1`) run time went from 38s to 21s.",
"\n[](https://coveralls.io/builds/47249066)\n\nCoverage decreased (-0.8%) to 83.38% when pulling **696ecd20d24cf4753f747fcf624be5a1914cee69 on janosh:alchemy-types** into **ddba2ea6c030cdcc8ccc7d08f6ee099e0ea15888 on materialsproject:master**.\n",
"Thanks as always @janosh ! :) "
] | 2022-03-10T16:39:53
| 2022-03-11T06:36:13
|
2022-03-11T03:00:31Z
|
MEMBER
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945d8daabe type annotations for pymatgen/alchemy/materials.py
3c3e9417fb type annotations for pymatgen/transformations/transformation_abc.py
696ecd20d2 remove `fetch-depth: 0` from lint actions/checkout
|
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I_kwDOACgets5FfQLB
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bug report on macOS with python3.7
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[
"Pls delete your .pmgrc file and try again.",
"it works like a charm. Thanks. Dr. Ong. \r\nIt bothered me for 2 weeks..."
] | 2022-03-10T23:10:21
| 2022-03-11T00:02:53
|
2022-03-10T23:11:21Z
|
NONE
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**Describe the bug**
I have an issue to. import the Composition module when installing latest pymatgen on a macOS using conda with python3.7
it takes long time to import and finally failed and get this error :
Successfully installed future-0.18.2 plotly-5.6.0 pymatgen-2022.0.17 ruamel.yaml-0.17.21 tenacity-8.0.1 uncertainties-3.1.6
(mat) jason$ python convert2formula.py --input oqmd_com_ckpt4049.txt
Traceback (most recent call last):
File "convert2formula.py", line 8, in <module>
from pymatgen.core.composition import Composition
File "/Users/jason/opt/anaconda3/envs/mat/lib/python3.7/site-packages/pymatgen/core/__init__.py", line 61, in <module>
SETTINGS = _load_pmg_settings()
File "/Users/jason/opt/anaconda3/envs/mat/lib/python3.7/site-packages/pymatgen/core/__init__.py", line 50, in _load_pmg_settings
d_yml = yaml.safe_load(f)
File "/Users/jason/opt/anaconda3/envs/mat/lib/python3.7/site-packages/ruamel/yaml/main.py", line 1118, in safe_load
return load(stream, SafeLoader, version)
File "/Users/jason/opt/anaconda3/envs/mat/lib/python3.7/site-packages/ruamel/yaml/main.py", line 1071, in load
return loader._constructor.get_single_data()
File "/Users/jason/opt/anaconda3/envs/mat/lib/python3.7/site-packages/ruamel/yaml/constructor.py", line 121, in get_single_data
return self.construct_document(node)
File "/Users/jason/opt/anaconda3/envs/mat/lib/python3.7/site-packages/ruamel/yaml/constructor.py", line 126, in construct_document
data = self.construct_object(node)
File "/Users/jason/opt/anaconda3/envs/mat/lib/python3.7/site-packages/ruamel/yaml/constructor.py", line 154, in construct_object
data = self.construct_non_recursive_object(node)
File "/Users/jason/opt/anaconda3/envs/mat/lib/python3.7/site-packages/ruamel/yaml/constructor.py", line 189, in construct_non_recursive_object
data = constructor(self, node)
File "/Users/jason/opt/anaconda3/envs/mat/lib/python3.7/site-packages/ruamel/yaml/constructor.py", line 696, in construct_undefined
node.start_mark,
ruamel.yaml.constructor.ConstructorError: could not determine a constructor for the tag 'tag:yaml.org,2002:python/object/apply:ruamel.yaml.comments.CommentedMap'
in "/Users/jason/.pmgrc.yaml", line 1, column 1
**To Reproduce**
Steps to reproduce the behavior:
Provide any example files that are needed to reproduce the error,
especially if the bug pertains to parsing of a file.
**Expected behavior**
A clear and concise description of what you expected to happen.
**Screenshots**
If applicable, add screenshots to help explain your problem.
**Desktop (please complete the following information):**
- OS: Mac latest version
- Version Montery M1 Max
**Additional context**
Add any other context about the problem here.
|
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I_kwDOACgets5Fu1zB
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Add option to disable the progress bar for MPRester query
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[
"I just pushed an option called `show_progress_bar` to allow you to disable it.",
"@shyuep: excellent, thank you. Btw, there's an even easier way to do it: I think you can just change `tqdm(...)` to `tqdm(..., disable=not show_progress_bar)`. Up to you, what you've done should fix the issue.",
"Hmmm thanks. I will leave it. I don't even understand why we need to initialize tqdm if we are not bothering with the progress bar.",
"Presumably because most users will want the progress bar, I'd think. Then it's just less lines of code (no `if` statements), but as I said it's really neither here nor there. Thanks for the quick fix. Will this be released in the next minor version?",
"It will be released in the next version.",
"@munrojm, is there a way to do this in the new `mp_api`? I was just wondering this the other day.",
"> @munrojm, is there a way to do this in the new `mp_api`? I was just wondering this the other day.\r\n\r\nYes, currently there is an environment variable you can set to mute all progress bars. My plan is to also implement it as a input to the generic search methods. "
] | 2022-03-15T16:28:06
| 2022-03-19T00:32:56
|
2022-03-15T16:56:29Z
|
CONTRIBUTOR
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https://github.com/materialsproject/pymatgen/blob/c37ba66cce99e93557b5e44d697059e2c93c0869/pymatgen/ext/matproj.py#L923-L1044
There seems to be no way to disable the progress bar for these queries. This breaks the progress bar/output stream depending on Jupyter and other things. It's a simple improvement and should be added. For example, a simple `verbose` default in the `MPRester.query` method should suffice.
I'm happy to fix and open a PR.
|
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| 1,170,313,234
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I_kwDOACgets5FwZAS
| 2,461
|
Broken `MagneticSpaceGroupTest.test_symmetry_ops()`?
|
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[
"Hi @janosh, I wrote that test, not intentional, I imagine it was an omission. Thanks for flagging it."
] | 2022-03-15T22:07:04
| 2022-03-22T17:11:03
|
2022-03-22T17:11:03Z
|
MEMBER
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`msg_1` isn't being tested unlike `msg_(2|3|4)`. Is this intentional?
https://github.com/materialsproject/pymatgen/blob/a740053063c8d0864f23d697a45bcafef3aaadf4/pymatgen/symmetry/tests/test_maggroups.py#L78-L85
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PR_kwDOACgets40oInA
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Allow for passing of Structure/Molecule kwargs in ASEAtomsAdaptor and add new charge_spin_check kwarg to Molecule/IMolecule
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"\n[](https://coveralls.io/builds/47479449)\n\nCoverage decreased (-0.7%) to 83.387% when pulling **285c41b582fb63c60af80153f2762d21b553a85f on arosen93:rosen-aseio** into **a740053063c8d0864f23d697a45bcafef3aaadf4 on materialsproject:master**.\n"
] | 2022-03-17T22:16:39
| 2022-03-24T23:00:52
|
2022-03-22T18:43:51Z
|
MEMBER
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## Summary
This PR serves three purposes:
1. When using the `ASEAtomsAdaptor.get_structure()` or `.get_molecule()` commands, optional kwargs to the `Structure()` and `Molecule()` classes can now be passed, such as the `validate_proximity` kwarg.
3. When instantiating a `Molecule()` or `IMolecule()` object, a new optional kwarg `charge_spin_check` can be passed. By default, the value is `True` and does not change the behavior of the existing `Molecule()`/`IMolecule()` classes. If `charge_spin_check=False`, then a `ValueError` will not be raised if the charge and spin multiplicity are incompatible.
3. The type-hint for the `spin_multiplicity` of a `Molecule` is now `int` instead of `float` to be consistent with the documentation and physical reality.
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| 1,174,101,471
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PR_kwDOACgets40rob2
| 2,463
|
Fix ValueError when cations, anions are not detected (LobsterEnv)
|
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"\n[](https://coveralls.io/builds/47509279)\n\nCoverage decreased (-0.7%) to 83.387% when pulling **806629043b85562b592b4a9e3ea5f7abceae8431 on JaGeo:master** into **a740053063c8d0864f23d697a45bcafef3aaadf4 on materialsproject:master**.\n",
"Thanks.",
"Thank you!"
] | 2022-03-18T23:14:04
| 2022-03-22T15:44:33
|
2022-03-22T15:42:40Z
|
MEMBER
|
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## Summary
This fixes a problem in the tool to determine coordination environments based on a Lobster analysis. In case, there are no cations, anions in the compound, a more useful error message is raised. In such a case, cation-anion bonds cannot be used to determine coordination environments. I have also added tests for this case.
|
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I_kwDOACgets5F-5hz
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[Not an issue actually] Counterintuitive behavior with assign_site_properties in AdsorbateSiteFinder
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[] | 2022-03-19T00:00:09
| 2022-03-19T03:14:54
|
2022-03-19T00:18:05Z
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MEMBER
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Edited: What I originally had was invalid and should be ignored.
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I_kwDOACgets5F_QV3
| 2,465
|
PDplotter plotly backend ternary diagram default colors are terrible
|
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[
"Hi @Youjin1985, please try the matplotlib backend. The 3D ternary plot is intended primarily for _interactive_ use, where the plot can be rotated to allow it to be read more easily, rather than for publication figures.\r\n\r\nI am working personally on a 2D version of this plot with the plotly backend, but not sure when I'll finish this. PRs also welcome."
] | 2022-03-19T08:29:52
| 2023-06-03T00:55:14
|
2023-06-03T00:55:14Z
|
NONE
|
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Hi,
Black font on black markers, completely invisible!
It's nowhere near publication quality plot, please change default look or allow customisation by arguments of PDPlotter.
|
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PR_kwDOACgets40swk3
| 2,466
|
Types for `pymatgen/symmetry/groups.py`
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[
"Just for the record, seems a bit odd that `class SymmetryGroup` implements `__getitem__`. `__iter__` to loop through all sym-ops would make more sense to me but that's absent. What's the meaning of an index into a group of symmetry operations that are implemented as a `set()`, i.e. have no inherent order anyway?",
"\n[](https://coveralls.io/builds/47586389)\n\nCoverage decreased (-0.7%) to 83.379% when pulling **2ae5cfdcce92b6c670afa9784cfabfc39b3f84b7 on janosh:types-symmetry-group** into **a740053063c8d0864f23d697a45bcafef3aaadf4 on materialsproject:master**.\n",
"Thanks for adding the test case!"
] | 2022-03-20T11:05:23
| 2022-03-22T17:56:50
|
2022-03-22T17:11:03Z
|
MEMBER
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2a0ed0e2df add type hints to `pymatgen/symmetry/groups.py`
3b7b6ab3ae `yesqa **/*.py`
e876dc99b9 fix `MagneticSpaceGroupTest.test_symmetry_ops()` unused 1st test case (closes #2461)
91f7942549 improve doc strings for `fractional_composition` + `reduced_composition`
21d5183b57 delete dead code
872da47137 fix typo
|
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PR_kwDOACgets40yBEb
| 2,467
|
Allow for nearest neighbor algorithms other than VoronoiNN in get_surface_sites
|
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[
"Ah, I see this is using the weight VN polyhedra. This is a bit too much work for me to want to mess around with it. Abandoning for now."
] | 2022-03-22T02:22:20
| 2022-03-22T02:41:04
|
2022-03-22T02:41:04Z
|
MEMBER
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The `get_surface_sites()` function when dealing with surfaces is hard-coded to use `VoronoiNN`. However, this is no particular reason to do so, and in fact it would be nice to let the user choose their own preferred method (e.g. `CrystalNN`). This PR gives the user that option with a new kwarg called `local_env`.
|
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PR_kwDOACgets40zjZ7
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Import ABC from collections.abc for Python 3.10 compatibility
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[
"\n[](https://coveralls.io/builds/47575501)\n\nCoverage decreased (-0.7%) to 83.381% when pulling **46d1ee36c7237c25ee5bb757420366e342e3bf26 on tirkarthi:fix-collections** into **a740053063c8d0864f23d697a45bcafef3aaadf4 on materialsproject:master**.\n"
] | 2022-03-22T11:28:08
| 2022-03-22T11:57:32
|
2022-03-22T11:41:39Z
|
CONTRIBUTOR
|
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## Summary
Import ABC from `collections` was deprecated and removed in Python 3.10. Use `collections.abc` .
## Additional dependencies introduced (if any)
* List all new dependencies needed and justify why. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. Provide a justification why that dependency is needed.
Especially frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* Feature 1 supports A, but not B.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [ ] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [ ] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [ ] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
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PR_kwDOACgets401RKh
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Fix bad `ValueError` message in `SimpleVaspToComputedEntryDrone.assimilate()`
|
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[
"@shyuep Wait, I need to appease the linter first. 😆 ",
"Also, I'm always wary when changing strings f-strings about potential errors. So tests passing is important here.",
"I will fix it. Don't worry. I will issue a new release shortly."
] | 2022-03-22T18:37:52
| 2022-03-22T19:35:18
|
2022-03-22T18:42:49Z
|
MEMBER
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Plus a few type hints and f-strings.
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I_kwDOACgets5GOLY3
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|
Circular import when importing SpaceGroup
|
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[
"Glad to learn about `typing.TYPE_CHECKING` though, that was new to me! Seems useful",
"Damn it, that fix over in #2471 is not going well. 😄 \r\nI should prob stop doing other stuff and focus on it. And run tests locally instead of waiting for CI emails to come back."
] | 2022-03-23T13:25:55
| 2022-03-25T02:15:10
|
2022-03-25T02:15:10Z
|
CONTRIBUTOR
|
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**Describe the bug**
The most recent release (2022.3.22) introduced a circular import error the SpaceGroup class
**To Reproduce**
Running the line...
``` python
from pymatgen.symmetry.groups import SpaceGroup
```
...produces the following error...
``` python
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\jacks\anaconda3\envs\pmg_env\lib\site-packages\pymatgen\symmetry\groups.py", line 25, in <module>
from pymatgen.core.lattice import Lattice
File "C:\Users\jacks\anaconda3\envs\pmg_env\lib\site-packages\pymatgen\core\__init__.py", line 19, in <module>
from .structure import IMolecule, IStructure, Molecule, Structure
File "C:\Users\jacks\anaconda3\envs\pmg_env\lib\site-packages\pymatgen\core\structure.py", line 51, in <module>
from pymatgen.symmetry.maggroups import MagneticSpaceGroup
File "C:\Users\jacks\anaconda3\envs\pmg_env\lib\site-packages\pymatgen\symmetry\maggroups.py", line 19, in <module>
from pymatgen.symmetry.groups import SymmetryGroup, in_array_list
ImportError: cannot import name 'SymmetryGroup' from partially initialized module 'pymatgen.symmetry.groups' (most likely due to a circular import) (C:\Users\jacks\anaconda3\envs\pmg_env\lib\site-packages\pymatgen\symmetry\groups.py)
```
**Additional context**
The bug was accidentally introduced by @janosh in this commit: https://github.com/materialsproject/pymatgen/commit/2a0ed0e2df6d6e151e54695997071bef0a43d66f
Looks like the issue is with line 25 (`from pymatgen.core.lattice import Lattice`) which produces the circular import.
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PR_kwDOACgets404gIT
| 2,471
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Fix circular import in `pymatgen.symmetry.groups`
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[
"No worries! Thanks for the quick response and fix. 😄 ",
"It is odd that this was not caught in any of the tests earlier? All the tests passed.",
"@shyuep Yes, I'm trying to figure out why not.",
"@shyuep I had the same thought... but I'm able to successfully reproduce this error in a clean conda env using the single import line. It is also triggering an error in [my own tests](https://github.com/jacksund/simmate/runs/5655518452?check_suite_focus=true). No idea why though is not showing up in pymatgen's tests",
"Yeah. I have also noticed that the CI full test suite is sometimes selective about what tests they run or which ones fail..... This occurred with the old nose and now with pytest as well. It is very strange.",
"\n[](https://coveralls.io/builds/47628463)\n\nCoverage decreased (-0.7%) to 83.385% when pulling **d24702ee19486948e4c388843b93db8005f6f013 on janosh:fix-circular-import** into **ff4d66cc237734a7abec8cb8e14e8901626b36c2 on materialsproject:master**.\n"
] | 2022-03-23T13:36:40
| 2022-03-25T02:15:10
|
2022-03-25T02:15:10Z
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MEMBER
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Closes #2470.
@jacksund Sorry about that. But thanks for the detailed error report!
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I_kwDOACgets5GSBtm
| 2,472
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Question about Ewald minimizer
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[] | 2022-03-24T07:44:20
| 2022-03-24T07:44:20
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NONE
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I have a POSCAR file of Na3Zr2Si2PO12 (mp-532695).
I'd like to substitute Zr2 -> HfZr at POSCAR file and get a minimum Ewald sum structure by using pymatgen.
So I tried to use Ewald minimizer, but I can't understand about the parameter of Ewald minimizer especially m_list.
Can I get a example of Ewald minimizer module? or more explain about the m_list at Ewald minimizer.
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PR_kwDOACgets408i3L
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Dead code
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"\n[](https://coveralls.io/builds/47655395)\n\nCoverage decreased (-0.7%) to 83.389% when pulling **bb7b4c165f17f2b485e29e18c6220cb9350e77f8 on janosh:dead-code** into **ff4d66cc237734a7abec8cb8e14e8901626b36c2 on materialsproject:master**.\n"
] | 2022-03-24T11:57:06
| 2022-03-25T07:59:26
|
2022-03-25T02:14:57Z
|
MEMBER
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Restoring/deleting some dead code.
Test cases that pass were restored. Code that seemed outdated was deleted.
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I_kwDOACgets5GfMSg
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(Un?)popular opinion: pymatgen is too OOP
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[
"While I agree some stateless stuff can be non-objects (e.g., pymatgen.util are mostly methods based), I should outline the basic principles. OOP can be used as either a state tool or an organizational tool. MPRester actually does have states - the session, API key and the url. Similarly, SpacegroupAnalyzer wraps around spglib to get the spacegroup data only once. Can we rewrite such that they are all method-based? Sure. That would require every single method to replicate the API key, the url and multiple calls to spglib to get back the same info for processing, even if you are doing a single structure. \r\n\r\nEven for the plotters, many have rather sophisticated analyses bundled into the plotting that are valuable in and of itself. There can be multiple ways of plotting the same information (e.g., PDPlotter.get_element_profile). It also enables options like plotting figures on top of each other in certain ways (e.g., DOSPlotter). Again, you can always argue we can write a plot_X method to just plot a figure in one way and add arguments or alternative methods to get a different plot. But my view is that it is more messy than the current approach.\r\n\r\nI am open to hearing other opinions from others and where we can streamline things.",
"@shyuep Thanks for taking the time to reply! Good points!\r\n\r\nTo clarify what I'm suggesting: For `SpacegroupAnalyzer`, I was thinking of a function like\r\n\r\n```py\r\nanalyze_spg(\r\n struct: Structure,\r\n sym_data: list[str] = None\r\n)\r\n```\r\n\r\nwhich by default returns the full dict received from `spglib.get_symmetry_dataset(struct, symprec)` (plus potential further analysis results from pmg itself if they're cheap and often used) to avoid the need for repeated `spglib` calls. If user knows they only want a subset of keys, they pass `sym_data = ['international', 'number', 'crystal_sys', ...]`. Similar to the 2nd arg of `MPRester.query()` where you pick all the stuff you need.\r\n\r\n> That would require every single method to replicate the API key, the url and multiple calls to spglib to get back the same info for processing, even if you are doing a single structure.\r\n\r\nTrue, splitting `MPRester` into separate functions requires each function to accept an API key. Though internally, that could be handled by a decorator so you only need to implement it once (some people object to decorators changing function signature. I'm not saying this approach is without downsides). On the user-side this problem is already solved. The API key is read from `.pmgrc.yaml` if not passed explicitly, so you wouldn't have to pass it to every function.\r\n\r\nRegarding the plots I have to admit I haven't used them to the point where I've tried to combine them or looked at any intermediate data analysis they do. So I'm talking at a very high level here. But if plotting classes can/are also used for data analysis, that sounds like insufficient separation of concerns. For the most part, I think plotting code should solely be responsible for visualizing data. Analyzing or bringing that data into the right shape should be handled by other functions, which like you said can be useful on their own.\r\n\r\nLet me repeat, this issue is not super actionable and I was never expecting any immediate changes from it. Just wanted to voice this opinion so that perhaps it gets taken into consideration in future development.",
"I personally think having decorators change function signatures is a very bad practice. Most people have a hard time knowing how to call something. If they have to hunt down the decorator implementation to figure it out, it is much worse. ",
"> I am open to hearing other opinions from others and where we can streamline things.\r\n\r\nDrive-by comment. For generative modeling I'll probably be running tens of thousands of structures (if not many more) through `SpaceGroupAnalyzer(pmg_struct).get_refined_structure()` or similar. Not sure if the overhead of class instantiation for each structure vs. a function as mentioned by @janosh is enough overhead to be noticeable, especially compared to the cost of sampling structures from a pretrained generative model (can vary by orders of magnitude depending on the choice of model). I'd guess it's probably not so bad in that context.\r\n\r\nAside: really enjoying using pymatgen as a toolkit to help with generating modeling pre- and post-processing in [xtal2png](https://github.com/sparks-baird/xtal2png)😄\r\n\r\nRelated discussion: https://github.com/sparks-baird/auto-paper/discussions/3",
"@janosh I will close this as it is not an \"Issue\" per se. Feel free to post a similar thing in Github Discussion. I will outline my general philosophy:\r\n1. Stateless, unique functionality - methods\r\n2. Things which look like objects (e.g., Structure) - OOP\r\n3. Things which have state - OOP preferred.\r\n\r\nAs a compromise, I think we can make some of the more commonly used stuff into methods within the common objects. For example, Structure.get_space_group_info() or the Structure.to(...). We can easily add a Structure.refine(). The bigger question is how many times do people really use the method and whether it is worth adding it to a long list of Structure.X methods. For things like Structure.to, I think it is quite clear there is major usage and value. This obviates the need to call specific IO packages. But this is not always the case.",
"Of course, closing is fine. I agree with your general philosophy. I probably wouldn't like `pymatgen` otherwise. Just to be clear though, I wasn't advocating for more methods (by which I mean functions callable on a class instance). I think less methods and more standalone and/or pure functions could make `pymatgen` even easier to use in some of [the above cases](https://github.com/materialsproject/pymatgen/issues/2474#issue-1182581920)."
] | 2022-03-27T16:15:57
| 2022-06-22T16:04:00
|
2022-06-22T15:43:25Z
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MEMBER
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Let me preface by saying I understand `pymatgen` is a mature code base with a large user base (for a research code), hence any breaking changes to the interface will be a slow and painful process. So feel free to close this issue if it's an unwelcome discussion.
---
The point I would like to raise is that many parts of `pymatgen` are packaged into classes even though it's stateless functionality that should really be procedural. On average classes tend to be more verbose with larger surface area for bugs. It can also be harder to reason about than the equivalent procedural code, especially if the code is stateless and could be a pure function instead.
Examples that stand out include:
- [`MPRester`](https://pymatgen.org/pymatgen.ext.matproj.html#pymatgen.ext.matproj.MPRestError): could be a function that always closes the session before returning. Leaving a session open for repeated API calls should require an explicit context manager IMO rather than sth that works both ways, but where only one way of using is recommended.
- [`SpacegroupAnalyzer`](https://pymatgen.org/pymatgen.symmetry.analyzer.html?highlight=spacegroup#pymatgen.symmetry.analyzer.SpacegroupAnalyzer): There's no need to bind space group analysis to a structure. Adds overhead invoking lots of classes if you want to analyze lots of structures. If it's about binding together related functionality, that's what modules are for. No need to wrap it in another layer (i.e. a class inside a module).
```py
# current
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
SpacegroupAnalyzer(structure).get_crystal_system()
# simpler
import pymatgen.symmetry.analyzer as psa
psa.get_crystal_system(structure)
```
- `SpectrumPlotter` | `VoltageProfilePlotter` | `PhononDosPlotter` | `PDPlotter` | ... : All the `XyzPlotter` classes are perhaps the most clear-cut case. Does plotting ever require persistent state? If there's no need for state, why use classes, a tool built for binding functionality to state? For stuff like `Compositions` and `Structures`, this makes perfect sense. It allows implementing comparison operators (`if struct1 == struct2`) and methods for neatly manipulating the internal state without having to pass it around. I see the appeal of classes there. But with plots, you have some finished state and now you want to see it. There's no use case for checking that 2 `PDPlotter` instances will give the same plot. Instead using classes here results in the IMO slightly awkward `get_plot()` API:
```py
from pymatgen.analysis.phase_diagram import PhaseDiagram, PDPlotter
pd = PhaseDiagram(processed_entries)
plotter = PDPlotter(pd)
fig = plotter.get_plot()
```
Wanting the plot is a given, no? A function that returns the plot always without having to ask for it would make more sense:
```py
from pymatgen.analysis.phase_diagram import PhaseDiagram, plot_pd
pd = PhaseDiagram(processed_entries)
fig = plot_pd(pd)
```
I was going to give more examples but realize now this is turning into an essay. So I'll stop here.
Happy to discuss more in comments if any changes in this direction aren't out of the question.
|
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PR_kwDOACgets41Lgi1
| 2,475
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Cp2k 1.0
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[
"Linting says that X | Y syntax requires python 3.10. This syntax was added in by Shyue, so I think that it should be alright. Please let me know if I should revert.",
"I think this problem can be solved by using `from __future__ import annotations`?",
"Oh you're right I didn't realize I'd removed that. Added it back in and also replaced ruamel with the newer import.",
"\n[](https://coveralls.io/builds/47763876)\n\nCoverage decreased (-0.9%) to 83.261% when pulling **ff66690bde430e2f5dcbfa0c0b9df92cd28f5887 on nwinner:cp2k-1.0** into **2e91dbb4948261002d28802c1e06492364b3cc31 on materialsproject:master**.\n"
] | 2022-03-28T19:37:13
| 2022-09-29T20:26:04
|
2022-03-28T22:44:44Z
|
CONTRIBUTOR
|
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## Summary
First major update to the CP2K IO module. Unless some changes are desired by devs. I think I'll title this v1.0 for the module.
inputs.py:
* Feature 1: New SectionList allows for repeated section names. Analogous to KeywordList
* Feature 2: New strict set action for less error prone custodian modifications.
* Feature3: Kpoints can know be generated automatically using SpacegroupAnalyzer. While CP2K generally doesn't use kpoints, this is convenient for the few times where you do.
* Fix 1: Resolved input file parsing issues for list of sections and for potential info in restart files
sets.py
* Feature 1: Updated defaults to align with expected usage of CP2K better.
outputs.py:
* Features 1: Parse calculation type
* Fix 1: Resolved errors with stress and ionic step parsing
* Fix 2: Fixed issues in DOS parsing.
* Fix 3: Previously would fail for metallic systems, since they are not that common in cp2k calculations
utils.py:
* Feature 1: Updated to align with new set.
* Feature 2: new truncation radius function to correct for user error in setting radius for hybrid functionals.
## Additional dependencies introduced (if any)
* No new dependencies, but this version changes several defaults as compared to CP2K internal defaults. This version assumes a modern version of CP2K is being used, and so better flags can be set than the legacy defaults.
Before a pull request can be merged, the following items must be checked:
- [ x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [ x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [ x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [ x] Tests have been added for any new functionality or bug fixes.
- [ x] All linting and tests pass.
|
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PR_kwDOACgets41Of6C
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Make `Composition` and `ChemicalPotential` special binary methods return `NotImplemented`
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[
"This PR is getting larger than expected.\r\n\r\nAnyway, for potential reviewers: the only interesting changes are in \r\n\r\n- abdafc7\r\n- 82b225b\r\n- 8e4a7eb\r\n- 7579245",
"[1 failing test left](https://github.com/materialsproject/pymatgen/runs/5740699569?check_suite_focus=true#step:6:52).\r\n\r\nJust had a look. It's because `this_sites` and `other_sites` here are no longer the same:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/8650675d098997edbdca5e2839f1a78c5fe2987f/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py#L2074-L2075\r\n\r\nNot sure how I broke this. Will investigate later.",
"\n[](https://coveralls.io/builds/47878971)\n\nCoverage decreased (-0.7%) to 83.262% when pulling **44387d289fafe6250f456cc2b234015a8932a5e2 on janosh:comp-comparison-return-notimplemented** into **8650675d098997edbdca5e2839f1a78c5fe2987f on materialsproject:master**.\n"
] | 2022-03-29T12:33:06
| 2022-04-04T19:18:51
|
2022-04-04T19:15:32Z
|
MEMBER
|
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Follow up to https://github.com/materialsproject/pymatgen/pull/2291#discussion_r746839280.
Quoting the docs:
> [NotImplemented](https://docs.python.org/3.6/library/constants.html#NotImplemented) should be returned by the binary special methods (e.g. __eq__(), __lt__(), __add__(), __rsub__(), etc.) to indicate that the operation is not implemented with respect to the other type
I also added tests for this.
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PR_kwDOACgets41P-30
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Remove `from __future__ import annotations` in electrode base class due to bug
|
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[
"\n[](https://coveralls.io/builds/47797396)\n\nCoverage decreased (-0.0002%) to 84.008% when pulling **38be5b65af40b76a85fe2dbdea7843265960da78 on mkhorton-patch-1** into **8650675d098997edbdca5e2839f1a78c5fe2987f on master**.\n",
"Without knowing exactly what bug we're talking about, an issue between dataclasses and future annotations _was_ reported and fixed in Cpython.\r\n\r\nhttps://github.com/python/cpython/pull/9518\r\n\r\nThe fix was backported all the way to 3.7 though. So which exact python version are we talking about? Early 3.7?",
"We're talking about Python 3.9",
"Thanks for linking the issue btw, I was looking around the Python bug tracker too, to find candidates for the cause, but it's still unclear at this point.",
"Here is the full traceback for future reference:\r\n\r\n```Traceback (most recent call last):\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/uvicorn/protocols/http/h11_impl.py\", line 375, in run_asgi\r\n result = await app(self.scope, self.receive, self.send)\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/uvicorn/middleware/proxy_headers.py\", line 75, in __call__\r\n return await self.app(scope, receive, send)\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/fastapi/applications.py\", line 211, in __call__\r\n await super().__call__(scope, receive, send)\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/starlette/applications.py\", line 112, in __call__\r\n await self.middleware_stack(scope, receive, send)\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/starlette/middleware/errors.py\", line 181, in __call__\r\n raise exc\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/starlette/middleware/errors.py\", line 159, in __call__\r\n await self.app(scope, receive, _send)\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/starlette/exceptions.py\", line 82, in __call__\r\n raise exc\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/starlette/exceptions.py\", line 71, in __call__\r\n await self.app(scope, receive, sender)\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/starlette/routing.py\", line 656, in __call__\r\n await route.handle(scope, receive, send)\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/starlette/routing.py\", line 259, in handle\r\n await self.app(scope, receive, send)\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/starlette/routing.py\", line 61, in app\r\n response = await func(request)\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/fastapi/applications.py\", line 163, in openapi\r\n return JSONResponse(self.openapi())\r\n File \"/Users/jasonmunro/Documents/DEVELOP/emmet/emmet-api/./emmet/api/core/api.py\", line 47, in custom_openapi\r\n openapi_schema = get_openapi(\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/fastapi/openapi/utils.py\", line 387, in get_openapi\r\n definitions = get_model_definitions(\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/site-packages/fastapi/utils.py\", line 24, in get_model_definitions\r\n m_schema, m_definitions, m_nested_models = model_process_schema(\r\n File \"pydantic/schema.py\", line 548, in pydantic.schema.model_process_schema\r\n File \"pydantic/schema.py\", line 589, in pydantic.schema.model_type_schema\r\n File \"pydantic/schema.py\", line 241, in pydantic.schema.field_schema\r\n File \"pydantic/schema.py\", line 495, in pydantic.schema.field_type_schema\r\n File \"pydantic/schema.py\", line 839, in pydantic.schema.field_singleton_schema\r\n File \"/Users/jasonmunro/anaconda3/envs/pymatgen_develop/lib/python3.8/abc.py\", line 102, in __subclasscheck__\r\n return _abc_subclasscheck(cls, subclass)\r\nTypeError: issubclass() arg 1 must be a class\r\n```",
"Looks like it's an issue with `pydantic`. There's an open PR since Jan 17 yet to be merged. Maybe we all upvote to give it some prio.\r\n\r\nhttps://github.com/samuelcolvin/pydantic/pull/3681",
"Ok, even though this is not \"our\" bug, since it is causing problems elsewhere and it's only a type hint change, I've gone ahead and reverted it in this one file for now. We can re-instate it later when the pydantic bug is fixed."
] | 2022-03-29T18:18:07
| 2022-10-10T17:53:53
|
2022-03-29T20:09:10Z
|
MEMBER
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Suspect some interaction with `dataclasses` and `pydantic` but root cause of bug is still unclear.
Notifying @munrojm (can you add some context to this PR in case it helps others?) and also notifying @janosh since it relates to whether we should have these imports everywhere by default or not.
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PR_kwDOACgets41SJ6b
| 2,478
|
[WIP] Relaxation Transformation
|
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[
"\n[](https://coveralls.io/builds/47815160)\n\nCoverage decreased (-0.8%) to 83.258% when pulling **acadab7ebd9bd82a8fe701291d5f18bb8f696a1d on nwinner:patch-2** into **02ac6df9b8f70d13ccd23040818afb86d8b17f36 on materialsproject:master**.\n",
"Hmmm... this is an odd transformation since it does not have any rules associated with it. All it does is to log that you have performed a process and this is the final structure. While conceptually I see the reason for it, I definitely wouldn't call it RelaxationTransformation and I would definitely suggest including metadata related to the transformation - at minimum, a name plus a dict of metadata. Maybe ExternalTransformation or MetaTransformation? The name can be something like \"VaspRelaxation\", and the dict can be the parameters. I can definitely see other use cases like \"ExtSlabGenerator\" or \"MDJiggle\", etc. I guess this is the mother of transformations that does some arbitrary thing to the structure that is not easily encoded in a series of Python steps.",
"Closing this as outdated. @nwinner Feel free to ping for reopen if you want to pick this up again."
] | 2022-03-30T05:04:38
| 2023-05-08T19:56:59
|
2023-05-08T19:56:59Z
|
CONTRIBUTOR
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Sometimes, we have calculations with continue from a previous calculation. For example, you run a coarse relaxation followed by a fine relaxation in separate fireworks. In that case, it would be convenient to have a Transformation which represents that relaxation that can be part of the second calculation's transformation history, rather than starting from the coarse-relaxed structure.
Perhaps this should be named something else, though? Relaxation is probably the most common potential use case, but it could be more general perhaps. Open to suggestions.
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I_kwDOACgets5GryEv
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pymatgen version: 2022.3.24 -- TransformedStructure.structures didn't work!!!
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[
"Pls provide an actual series of code that I can use to reproduce the error.",
"**To Reproduce**\r\nfrom pymatgen.alchemy.transmuters import CifTransmuter\r\nfrom pymatgen.transformations.standard_transformations import SubstitutionTransformation, RemoveSpeciesTransformation\r\ntrans = []\r\ntrans.append(SubstitutionTransformation({\"Fe\":\"Mn\"}))\r\ntrans.append(RemoveSpeciesTransformation([\"Li\"]))\r\ntransmuter = CifTransmuter.from_filenames([\"test_files/LiFePO4.cif\"], trans)\r\nstructures = transmuter.transformed_structures",
"Have you solve this problem?",
"The history of structures is in the history attribute. After your last line, add print(structures[0].history) and you will see both structures. Or if you pprint.pprint(structures[0].structures), that has the entire list of structures too. \r\n\r\n"
] | 2022-03-30T05:07:52
| 2022-04-06T14:18:48
|
2022-04-06T14:17:28Z
|
NONE
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**Describe the bug**
I made some transformations on a structure, output **final_structure** and **structures**. But I found these two properties are the same. It means **structures** property didn't work. And I view its source code. I found it's due to the **input_structure** key within **hdict** is removed by no reason.
**Show the phenomenon**
When you debug and stop on the 155th line, you can see the **hdict**, and the **input_structure** still exists.
However, when you stop on the 156th line, the **input_structure** is gone. I don't know why.
**To Reproduce**
you can try my example code, and pymatgen version is 2022.3.24 on Ubuntu.
`
from pymatgen.alchemy.transmuters import CifTransmuter
from pymatgen.transformations.standard_transformations import SubstitutionTransformation, RemoveSpeciesTransformation
trans = []
trans.append(SubstitutionTransformation({"Fe":"Mn"}))
trans.append(RemoveSpeciesTransformation(["Li"]))
transmuter = CifTransmuter.from_filenames(["test_files/LiFePO4.cif"], trans)
structures = transmuter.transformed_structures
`
**Expected behavior**
In my example, I want my **structures[0].structures** contains each structures in history, not only the last transformed structure.
|
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I_kwDOACgets5Gt2Tr
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Vasprun fails to read in ML-based MD results
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[
"Thanks for raising this issue @pjf295 and for sharing an example `vasprun.xml`. I have not had chance to try this functionality myself yet but agree the MLFF output should also be available. It seems reasonable a user may want to access the MLFF steps separately from the AIMD steps? If both were available via a combined output, do you have any thoughts about how to indicate which method was used for a given ionic step to the user?",
"Dear Matthew,\n\n It is nice to hear from you. I have often read your comments on the discourse pymatgen server. The machine-learned force field functionality in Vasp offers a significant (tens of times) speed up for MD calculations. While I have not verified it at this point, it would also appear that the scaling with system size is very favorable as well (for purely machine learned systems). As you may know, the typical option for the ML FF is to run in ML_ISTART = 1 mode. In this scenario, a machine learning potential is used, but based upon a Bayesian approach for monitoring systematic error, the system performs occasional ab-initio calculations and update its ML FF. This means that such simulations have intermixed ab-initio and ML FF MD data. For many use cases, it is useful to carry out autocorrelation-based Green-Kubo analysis of steady state trends for tasks such as doing diffusion analysis or as I am have been exploring recently predicting friction values (by monitoring of the force data using Green-Kubo formalism). The only realistic way to handle this is to have the data as one integral object. This would also be the case for example of large systems that are undergoing crystallization. To this end, I would suggest the addition of new Boolean dictionary elements for the ionic_steps object such as is_abinitio and is_MLFF. This way one could distinguish if necessary between the two, but existing classes (such as DiffusionAnalyzer) would not experience indigestion or have to be rewritten to handle the new information. Note that some of the energy terms will be missing in a ML FF approach (an unfortunate side effect of ML). On the other hand, the scaling improvements will hopefully allow the study of nucleation and crystallization behavior which often require long simulation times and/or large system sizes.\n\n I am very much an amateur at Python, but I have enjoyed a large improvement in productivity in using Pymatgen and am very grateful for your (and other team member) efforts in improving Pymatgen and its associated tools. I worked for over 25 years as a senior research at a large national laboratory (AIST) in Japan and recently moved to university (Keio). I have found that the use of pymatgen and associated tools such as matminer is an expedient approach to introducing students into world of simulations. Keep up the good work. I would be happy to comment more on the ML topic, but I suspect that you are more proficient at Python and I am looking at the situation from the viewpoint of workflows.\n\nBest wishes,\n Paul Fons\n\n\n\nPaul Fons\n***@***.***\n\nProfessor\nKeio University, Faculty of Science and Technology, Department of Electronics and Electrical Engineering\n\n〒223-8522 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan\nKeio University Faculty of Science and Technology Yagami Campus.\n\n〒223-8522 横浜市港北区日吉3-14-1 慶應義塾大学理工学部電気情報工学科 23-315 \n\n\n\n> On Apr 1, 2022, at 4:02, Matthew Horton ***@***.***> wrote:\n> \n> \n> Thanks for raising this issue @pjf295 and for sharing an example vasprun.xml. I have not had chance to try this functionality myself yet but agree the MLFF output should also be available. It seems reasonable a user may want to access the MLFF steps separately from the AIMD steps? If both were available via a combined output, do you have any thoughts about how to indicate which method was used for a given ionic step to the user?\n> \n> —\n> Reply to this email directly, view it on GitHub, or unsubscribe.\n> You are receiving this because you were mentioned.\n> \n\n",
"XDATCAR format does not change for vasp5.4 and vasp6.3. Can pymatgen analyze MD results from XDATCAR? ",
"While it is true that the XDATCAR format is unchanged, there is much more information in the vasprun file including velocities and forces. I would like to use the force information in particular.",
"I realize that this change is probably not a high priority item, but I was curious if there was a rough timeline of when support for the new machine learning tags will be added.",
"It would be helpful if someone outlined the new format of the vasprun.xml file for me. The implementation is actually easy once the format is known.\r\n",
"I have finished implementing an initial version of Vasprun parsing of ML-MD runs. It is now in master.",
"How do you pass md_data into DiffusionAnalyzer.from_files\r\ne.g.\r\nanalyzer = DiffusionAnalyzer.from_files([\"vasprun.xml\"], specie=\"Li\", smoothed=False)",
"There is a DiffusionAnalyzer.from_structures. The md_data key contains all the structures. I have no idea what the timestep of the calculations are since I don't use this feature of VASP at all.",
"Ok thanks. So from_structures is updated but not from_ files. The time step is no different than a typical vasp md calculation (still based on POTIM); however, one might use NBLOCK to reduce output but this is not a new feature.\n\nSent from my iPhone\n\n> On May 19, 2022, at 4:58 PM, Shyue Ping Ong ***@***.***> wrote:\n> \n> \n> There is a DiffusionAnalyzer.from_structures. The md_data key contains all the structures. I have no idea what the timestep of the calculations are since I don't use this feature of VASP at all.\n> \n> —\n> Reply to this email directly, view it on GitHub, or unsubscribe.\n> You are receiving this because you commented.\n",
"I'm still having trouble getting this to work.\r\n\r\nThis reads vasprun.xml but I can't seem to excess the md_data:\r\nanalyzer = DiffusionAnalyzer.from_files([\"vasprun.xml\"], specie=\"Li\", smoothed=False)\r\n\r\nIf I do the following:\r\nanalyzer = DiffusionAnalyzer.from_structures([\"vasprun.xml\"], specie=\"Li\", temperature=700.0, time_step=1, step_skip=1, smoothed=False)\r\n\r\nI get \r\n```\r\n 590 if i == 0:\r\n 591 structure = s\r\n--> 592 p.append(np.array(s.frac_coords)[:, None])\r\n 593 l.append(s.lattice.matrix)\r\n 594 if initial_structure is not None:\r\n\r\nAttributeError: 'str' object has no attribute 'frac_coords'\r\n```",
"Sorry, but you need to read the method signatures and documentation carefully. AS the method name implies, DiffusionAnalyzer.from_structures takes in a list of structures, not a list of vasprun.xml files. I will provide a basic example here but ultimately, you have to be the one reading the documentation and figuring this out.\r\n\r\n```python\r\nv = Vasprun(\"vasprun.xml\")\r\nstructures = [d[\"structure\"] for d in v.md_data]\r\nanalyzer = DiffusionAnalyzer.from_structures(structures, ....)\r\n```",
"Dear Prof. @shyuep , I ran with `ML_ISTART = 2`, no calculation was exported, but the predicted structures and velocities in the vasprun.xml file. The following error appears for my case:\r\n```\r\n---------------------------------------------------------------------------\r\nIndexError Traceback (most recent call last)\r\n/var/folders/13/76vrjtyn2kgckfh7v76ndv900000gn/T/ipykernel_6381/266408610.py in <module>\r\n 2 # \"tem-800/out_vasprun.xml_3\", \"tem-800/out_vasprun.xml_4\",\r\n 3 file800 = [\"tem-800/out_vasprun.xml_5\"]\r\n----> 4 analyzer800 = DiffusionAnalyzer.from_files(file800, specie=\"Li\", smoothed=False)\r\n 5 #analyzer3 = DiffusionAnalyzer.from_files(file3, specie=\"Li\", smoothed=\"max\")\r\n 6 plt800 = analyzer800.get_msd_plot()\r\n\r\n~/miniconda3/lib/python3.8/site-packages/pymatgen/analysis/diffusion_analyzer.py in from_files(cls, filepaths, specie, step_skip, ncores, initial_disp, initial_structure, **kwargs)\r\n 742 offset = (-(v.nionic_steps - offset)) % step_skip\r\n 743 \r\n--> 744 return cls.from_vaspruns(\r\n 745 vr(filepaths), specie=specie, initial_disp=initial_disp, initial_structure=initial_structure, **kwargs\r\n 746 )\r\n\r\n~/miniconda3/lib/python3.8/site-packages/pymatgen/analysis/diffusion_analyzer.py in from_vaspruns(cls, vaspruns, specie, initial_disp, initial_structure, **kwargs)\r\n 672 \r\n 673 s = get_structures(vaspruns)\r\n--> 674 step_skip, temperature, time_step = next(s)\r\n 675 \r\n 676 return cls.from_structures(\r\n\r\n~/miniconda3/lib/python3.8/site-packages/pymatgen/analysis/diffusion_analyzer.py in get_structures(vaspruns)\r\n 654 \r\n 655 def get_structures(vaspruns):\r\n--> 656 for i, vr in enumerate(vaspruns):\r\n 657 if i == 0:\r\n 658 step_skip = vr.ionic_step_skip or 1\r\n\r\n~/miniconda3/lib/python3.8/site-packages/pymatgen/analysis/diffusion_analyzer.py in vr(filepaths)\r\n 737 offset = 0\r\n 738 for p in filepaths:\r\n--> 739 v = Vasprun(p, ionic_step_offset=offset, ionic_step_skip=step_skip)\r\n 740 yield v\r\n 741 # Recompute offset.\r\n\r\n~/miniconda3/lib/python3.8/site-packages/pymatgen/io/vasp/outputs.py in __init__(self, filename, ionic_step_skip, ionic_step_offset, parse_dos, parse_eigen, parse_projected_eigen, parse_potcar_file, occu_tol, separate_spins, exception_on_bad_xml)\r\n 357 # add the tailing information in the last step from the run\r\n 358 to_parse = \"<calculation>\".join(new_steps)\r\n--> 359 if steps[-1] != new_steps[-1]:\r\n 360 to_parse = f\"{preamble}<calculation>{to_parse}{steps[-1].split('</calculation>')[-1]}\"\r\n 361 else:\r\n\r\nIndexError: list index out of range\r\n```",
"Thank you for your note. I probably didn’t explain myself well. I realize that the XDATCAR file is available, however, I need force data which is in the vasprun.xml file. Unfortunately, the Vasprun class does not read molecular dynamics data generated using machine learning at all. For example, a 40,000 step MD simulation generated using ML, none of the ML force-field data is read in. I have parsed the velocity and force data directly from the Vasprun file using awk and related tools, but it is in the interests of the pymatgen project to be able to read in such data directly. The speed-ups associated with ML are very large and will enable carrying out simulations for much longer times and potentially larger system sizes so it is important to support such features.\n\n\nPaul Fons\n***@***.***\n\n\n\n> On Apr 7, 2022, at 11:31, thienbinh92 ***@***.***> wrote:\n> \n> \n> XDATCAR format does not change for vasp5.4 and vasp6.3. Can pymatgen analyze MD results from XDATCAR?\n> \n> —\n> Reply to this email directly, view it on GitHub <https://github.com/materialsproject/pymatgen/issues/2480#issuecomment-1091015108>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQT5S3CPBGKYCB67UE3HYC3VDZCHDANCNFSM5SB3FHSA>.\n> You are receiving this because you were mentioned.\n> \n\n",
"@pjf295 I understand this is a new feature of VASP and there are some pymatgen users who might need it. But you must understand that pymatgen is an open source project contributed by volunteers, not a commercial software with paid software engineers. The way new features happen is if a volunteer happens to need a new function and they add support for that feature and submit a PR. Neither myself nor any other user has stepped up to rigorously implement MLFF support because none of us actually need it at the moment.\r\n\r\nIf you want to implement it properly and submit a PR, we will be happy to review it."
] | 2022-03-30T12:58:56
| 2022-10-11T10:42:55
|
2022-05-18T19:28:17Z
|
NONE
|
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**Describe the bug**
Vasp 6.3.0 includes the ability to use machine learning (ML) to generate force fields (FF) based upon ab-initio results. Ths results is a large speed up in calculation speeds. The ML process mixes both ab-initio MD with ML FF results based upon a Bayesian approach. This results in the vasprun.xml file containing both ab-initio results and ML based results. The ML based XML results include positions, forces, and velocities, but ab-initio energies. The Vasprun class init reads in a vasprun.xml file generated with ML FF without error, but it ignores all of the ML results and only includes the (typically widely temporally spaced) ab-initio results.
[vasprun.xml.gz](https://github.com/materialsproject/pymatgen/files/8380576/vasprun.xml.gz)
[XDATCAR.gz](https://github.com/materialsproject/pymatgen/files/8380577/XDATCAR.gz)
**To Reproduce**
Steps to reproduce the behavior:
See the attached INCAR.txt file for the relevant input cards. Machine learning must be turned on to reproduce the results
Provide any example files that are needed to reproduce the error,
especially if the bug pertains to parsing of a file.
I have also attached gzipp'd versions of XDATCAR and vasprun.xml for a demonstration run with 100 integration steps. The XDATCAR contains 100 different structures for each of the MD steps. The vasprun.xml file also contains all 100 steps, but reading in the vasprun.xml file using the Vasprun init (run = Vasprun('vasprun.xml') leads to a vasprun object only containing a small fraction of the ionic steps in the MD simulation (e.g. only those in which ab-initio steps were performed) leaving out all of the FF results.
**Expected behavior**
The vasprun object should contain the ionic steps for all MD steps. Perhaps another flag should be set to indicate that the results were generated using ab-initio or ML FF processes.
**Desktop (please complete the following information):**
Pymatgen version 2022.3.7
Behavior host independent (Mac and Linux have the same symptoms)
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https://github.com/materialsproject/pymatgen/pull/2481
| 1,186,808,401
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PR_kwDOACgets41VL_5
| 2,481
|
bug fix for bsplotter and bztInterpolator
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[
"\n[](https://coveralls.io/builds/47842442)\n\nCoverage decreased (-0.7%) to 83.264% when pulling **fe6db1cd1574c5c1890fab78a00eaf0bb9b4df58 on fraricci:bugfix_bsplotter_bztinterp** into **02ac6df9b8f70d13ccd23040818afb86d8b17f36 on materialsproject:master**.\n"
] | 2022-03-30T18:06:09
| 2022-04-04T19:14:55
|
2022-04-04T19:14:55Z
|
CONTRIBUTOR
|
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I fix two bugs:
- the units of vbm and cbm in the BztInterpolator were wrong and leading to a wrong energy range.
- BSPlotter in case of metallic bands and zero_to_efermi=False was broken.
|
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PR_kwDOACgets41aXny
| 2,482
|
Fix `{StructureGraph,MoleculeGraph}.sort()`
|
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[
"\n[](https://coveralls.io/builds/47886499)\n\nCoverage decreased (-0.7%) to 83.272% when pulling **497f0e5054e7db4d2520a4d14fd636ad8fe49bc3 on janosh:fix-sort-struct-graph** into **02ac6df9b8f70d13ccd23040818afb86d8b17f36 on materialsproject:master**.\n",
"Thanks @janosh !"
] | 2022-03-31T16:25:14
| 2022-03-31T18:42:50
|
2022-03-31T18:40:13Z
|
MEMBER
|
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Plus add tests for `{StructureGraph,MoleculeGraph}.sort()`.
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PR_kwDOACgets41hmIX
| 2,483
|
Fix errors on entries_charge/entries_discharge attributes
|
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[
"\n[](https://coveralls.io/builds/48335796)\n\nCoverage decreased (-0.7%) to 83.277% when pulling **6b068a4d149395ad07e1d4e032de9ae265a549cb on peikai:master** into **827ad4ee1e85bd723e0d29ef9ce8f708c44a1e61 on materialsproject:master**.\n",
"Pls add a test to check for this bug.",
"> Pls add a test to check for this bug.\r\n\r\nWe can test discharge profiles of the entry mp-246 (TiF3) with these codes:\r\n\r\n```python\r\ncomposite_A_list = [entry.composition.reduced_formula for entry in voltage_pair.entries_discharge]\r\ncomposite_B_list = [entry.composition.reduced_formula for entry in voltage_pair.entries_charge]\r\n```\r\nwhich are only two steps discharge based on MP Database V2021.05.13,\r\n\r\n| reaction | composite_A | composite_B |\r\n|----------------------------------------|----------------|----------------|\r\n| 1.5 Li + TiF3 -> 0.5 Li3TiF6 + 0.5 Ti | ['TiF3'] | ['Li3TiF6', 'Ti'] |\r\n| 1.5 Li + 0.5 Li3TiF6 -> 3 LiF + 0.5 Ti | ['Li3TiF6', 'Ti'] | ['Ti', 'LiF'] |\r\n\r\nObviously, the composite_A should be the composite in charged state, and composite_B is the composite in discharged state. However, the bug is that the composite_A actually comes from voltage_pair.entries_discharge in the codes above. \r\n\r\nHence, I found the aforementioned bug and fixed it in this PR.\r\n",
"Thanks. What I meant is that since you detected this bug, a unittest should be added to the test_conversion_battery.py to check that this fix is done properly. It also ensures that future people will not make changes that result in this bug again. Thanks.",
"I have found out the meaningfulness of a unittest. Now, a test function has been added to check phase components at each discharge step. This unittest will be able to notice the above bug. Thanks!",
"Thanks."
] | 2022-04-02T08:18:36
| 2022-04-18T01:23:15
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2022-04-18T01:23:10Z
|
CONTRIBUTOR
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The results that entries_discharge and entries_discharge attributes returned in _pymatgen/apps/battery/conversion_battery.py_ were confused. I fixed this problem that entries in charge/discharged state should be the entries from step1/step2, respectively.
We can find evidence in similar attribute, vol_discharge, that properties in discharge states should be retrieved from the step2.
```python
vol_discharge = sum(
abs(curr_rxn.get_coeff(e.composition)) * e.structure.volume
for e in step2["entries"]
if e.composition.reduced_formula != working_ion
)
```
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[pre-commit.ci] pre-commit autoupdate
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[] | 2022-04-04T19:00:56
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2022-04-04T19:14:35Z
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CONTRIBUTOR
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<!--pre-commit.ci start-->
updates:
- [github.com/asottile/pyupgrade: v2.31.0 → v2.31.1](https://github.com/asottile/pyupgrade/compare/v2.31.0...v2.31.1)
- [github.com/psf/black: 22.1.0 → 22.3.0](https://github.com/psf/black/compare/22.1.0...22.3.0)
- [github.com/pre-commit/mirrors-mypy: v0.930 → v0.942](https://github.com/pre-commit/mirrors-mypy/compare/v0.930...v0.942)
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I_kwDOACgets5HIqnA
| 2,485
|
Vasp 6.3 and new units for dipole moments
|
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[] | null |
[
"Thanks for catching this! Concerning to have such a big change that wasn't in the release notes / change log."
] | 2022-04-05T16:45:44
| 2022-04-26T21:51:49
|
2022-04-26T21:51:49Z
|
CONTRIBUTOR
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I noticed that (at least) version 6.3 of VASP has changed the units for the dipole (LCALC=True) from, i.e.:
Ionic dipole moment: p[ion]=( 0.00000 0.00000 19.70306 ) **electrons** Angst
to
Ionic dipole moment: p[ion]=( 0.00000 0.00000 -19.70306 ) **|e|** Angst
This means that these vectors needs to be multiplied by -1 to recover previous values.
In particular, to get the correct value of the polarization (as computed in the analysis.ferroelectricity.polarization),
the electronic dipole need to be multiplied by -1, since the ionic part is computed separately (p_ion is not from outcar).
I propose a fix in this pull request #2486
But, any comments and suggestion are welcome.
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PR_kwDOACgets41rGfw
| 2,486
|
fix dipole moments units
|
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[
"Could you add a quick test to this @fraricci? Then will merge ASAP",
"Thanks @fraricci! Looks like test failures are unrelated (CrystalAIResterTest.test_query) so will go ahead and merge"
] | 2022-04-05T16:50:37
| 2022-04-20T18:16:14
|
2022-04-20T18:16:14Z
|
CONTRIBUTOR
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Fix for the new units in recent vasp versions (at least 6.3, maybe even before).
Discussed in #2485
|
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I_kwDOACgets5HKIa-
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Bader analysis via Pymatgen is extremely slow
|
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[
"If we believe bader doesn't modify anything, we can do the analysis without copying to scratch. Feel free to make the modifications to pymatgen and submit a PR.",
"I'm also fine with these changes, but interested:\r\n\r\n> Use chgsum.pl AECCAR0 AECCAR2.pl directly. Don't read in the AECCARs via Pymatgen. This would require chgsum.pl to be in the PATH in addition to just the bader executable.\r\n\r\nIs this substantially faster? If so, why is pymatgen's parsing so slow, comparatively?\r\n\r\n> Repeat this step but yield the spin densities if the calculation is spin-polarized.\r\n\r\nCan `bader` handle the spin densities automatically, or does it require writing out a new CHGCAR with just the spin channel included (i.e., requiring the extra I/O step)?",
"I have to do some benchmarking on the individual steps. If the AECCAR summing ends up being comparable, then it's easier to just leave that step in Pymatgen. Right now, the CHGCAR file is also parsed in that step, so we will want to avoid that at the least.\r\n\r\nRegarding spin densities, a new CHGCAR file will need to be written, which is usually done via `chgsplit.pl CHGCAR` if using the VTST scripts.\r\n\r\nI'll do some digging into this because there's definitely something _substantially_ increasing the overall runtime. I'll report back.",
"@arosen93 I just want to clarify that in pymatgen, the default is to go through the Python objects because we never know where the CHGCAR can come from. For example, we can conceivably download a CHGCAR from MP and do a Bader analysis, which would require writing it out. However, the IO is extremely slow (we are parsing hundreds of MB or Gb and then writing them out). I think a good compromise would be simply to have a wrapper that deals with simple Bader analysis on existing files without IO for the majority of cases where we are doing analysis on local files.",
"@shyuep -- Thanks. I agree with everything you said. I still need to do some benchmarking to confirm the rate-limiting step is what I think it is, but I'm a bit over-subscribed at the moment. I will come back to this and my other opened issues... in time."
] | 2022-04-05T23:31:14
| 2023-08-08T19:14:54
|
2023-08-08T19:14:54Z
|
MEMBER
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**Describe the bug**
When using the `bader_caller` in Pymatgen (specifically `bader_analysis_from_path`), it can take many times longer to run a Bader analysis than just using the standalone scripts provided by the Henkelman group. I suspect this is related to excessive file I/O related to reading in the CHGCAR, AECCAR0, and AECCAR2 every time and also writing out the CHGCAR again every time (in addition to the summed AECCARs, but that is necessary). I've run Bader analyses on systems with hundreds of atoms, and it never takes more than a minute or so, but with Pymatgen the same analysis can take tens of minutes in comparison.
We should track down the bottleneck here and then figure out how to fix this. I think having an option to do the following would be ideal:
- Copy the AECCAR0, AECCAR2, CHGCAR, and POTCAR files to scratch (is this even necessary? I don't think `bader` will overwrite anything).
- Use `chgsum.pl AECCAR0 AECCAR2.pl` directly. Don't read in the AECCARs via Pymatgen. This would require `chgsum.pl` to be in the PATH in addition to just the `bader` executable.
- Run `bader CHGCAR -ref CHGCAR_sum`. Repeat this step but yield the spin densities if the calculation is spin-polarized.
At no point in the above should the CHGCAR be read or written, in contrast with the current approach.
Tagging @mkhorton since we briefly discussed this earlier today.
|
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| 1,195,366,763
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PR_kwDOACgets41xhnC
| 2,488
|
Fix DOS docstring
|
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[] | 2022-04-07T01:27:52
| 2022-04-07T01:29:18
|
2022-04-07T01:29:17Z
|
MEMBER
|
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Fixes a typo in the docstrings for the new `CompleteDos` properties I introduced in #2455.
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PR_kwDOACgets41x1gO
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Remove redundant operation
|
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[
"\n[](https://coveralls.io/builds/48070886)\n\nCoverage decreased (-0.7%) to 83.275% when pulling **6349dfac44a058e1954613090d19e14ad53dc3f3 on arosen93:rosen-band** into **040c45a68f7c787e062078aca28c3532c7c817e9 on materialsproject:master**.\n"
] | 2022-04-07T03:43:00
| 2022-04-07T11:34:27
|
2022-04-07T11:34:26Z
|
MEMBER
|
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Removed a redundant mathematical operation in the `CompleteDos` properties. The line `energies = dos.energies - dos.efermi` was included in two places. I deleted the second instance.
https://github.com/materialsproject/pymatgen/blob/040c45a68f7c787e062078aca28c3532c7c817e9/pymatgen/electronic_structure/dos.py#L860-L864
Apologies for not catching this during the previous docstring cleanup.
|
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PR_kwDOACgets42GlLx
| 2,490
|
Speed up to group structures by equivalence
|
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[
"\n[](https://coveralls.io/builds/48213263)\n\nCoverage decreased (-0.7%) to 83.276% when pulling **e65f680502b70dfd7117222cc0dae730592c4036 on lan496:speedup-group-structures** into **a82f60db3e4af40e2f21ed2cb968ffc398cf3a75 on materialsproject:master**.\n",
"Thanks."
] | 2022-04-12T13:34:12
| 2022-04-12T23:32:19
|
2022-04-12T16:16:57Z
|
CONTRIBUTOR
|
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## Summary
- Speed up `StructureMatcher.group_structures` by skipping redundant transformations on given structures.
`group_structures` calls `fit` or `fit_anonymous` to compare two structures in a given list. Every time `fit` or `fit_anonymous` are called, the structures are reduced by searching their primitive cell and performing Niggli reduction (if specified). However, these reductions can be skipped because we can perform the reductions on given structures at once. This PR introduces `skip_structure_reduction` flag to remove the duplicated reductions in `group_structures`.
## Benchmark
I have confirmed the following test case with 16 structures is about 4x faster than before (0.2039 s -> 0.0593 s).
```python
import os
import json
from time import time
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.util.testing import PymatgenTest
from monty.json import MontyDecoder
if __name__ == '__main__':
with open(os.path.join(PymatgenTest.TEST_FILES_DIR, "TiO2_entries.json")) as fp:
entries = json.load(fp, cls=MontyDecoder)
s_list = [e.structure for e in entries]
print(f"{len(s_list)} structures")
sm = StructureMatcher()
start = time()
out = sm.group_structures(s_list)
elapsed = time() - start
print(f"{elapsed:.4f} s")
assert list(map(len, out)) == [4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1]
```
## Checklist
Before a pull request can be merged, the following items must be checked:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
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PR_kwDOACgets42IEiy
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|
Update corrections.py
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[] | null |
[
"\n[](https://coveralls.io/builds/48225994)\n\nCoverage decreased (-0.7%) to 83.277% when pulling **f3c8c2c53cbcdf348c6b2c3531235ae3bf3a0e22 on kavanase:master** into **834dc9c507f0ceb735887be2db358be37c52a4d7 on materialsproject:master**.\n"
] | 2022-04-12T19:38:21
| 2022-04-19T14:35:02
|
2022-04-19T14:35:02Z
|
CONTRIBUTOR
|
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Specify `dtype` in numpy array generation
## Summary
Due to the new `VisibleDeprecationWarning` in `numpy` for creating arrays from ragged nested sequences, the `dtype` must be specified when generating the arrays, otherwise the following three warnings are printed for each defect correction calculated:
```
/home/dngsykes/miniconda3/envs/toolbox/lib/python3.8/site-packages/pymatgen/analysis/defects/corrections.py:102: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
list_axis_grid = np.array(entry.parameters["axis_grid"])
/home/dngsykes/miniconda3/envs/toolbox/lib/python3.8/site-packages/pymatgen/analysis/defects/corrections.py:103: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
list_bulk_plnr_avg_esp = np.array(entry.parameters["bulk_planar_averages"])
/home/dngsykes/miniconda3/envs/toolbox/lib/python3.8/site-packages/pymatgen/analysis/defects/corrections.py:104: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
list_defect_plnr_avg_esp = np.array(entry.parameters["defect_planar_averages"])
```
This has been fixed in the PR code
|
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| 1,202,641,339
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PR_kwDOACgets42JOGh
| 2,492
|
Add pylint pre-commit hook
|
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[
"\n[](https://coveralls.io/builds/48233648)\n\nCoverage decreased (-0.7%) to 83.276% when pulling **cc0a69945317307853844d153a0cc180ca72f330 on lan496:pylint-hook** into **834dc9c507f0ceb735887be2db358be37c52a4d7 on materialsproject:master**.\n",
"Thanks.",
"`pylint` doesn't play nicely with `pre-commit` for the reasons discussed in https://github.com/PyCQA/pylint/issues/5293. I don't think adding it to the `.pre-commit-config.yaml` is a good idea as it means everyone who has installed or will install commit hooks on the pymatgen repo will now encounter this error when trying to commit:\r\n\r\n```\r\npylint...................................................................Failed\r\n- hook id: pylint\r\n- exit code: 1\r\n\r\nExecutable `pylint` not found\r\n```\r\n\r\nThe situation before was that people would only get an error in CI if the code they added offended `pylint`.",
"@janosh Hi. Thanks for pointing out the discussion on `pylint`.\r\nI understand your concern is the situation that people who are unaware or forget `pip install -r requirements-dev.txt` encounter the error when trying to commit. I agree that this PR additionally requires people to install `requirements-dev.txt`, but I think it is a good thing to prepare linters in their local. So, I prefer adding instructions in [Coding Guidelines](https://pymatgen.org/contributing.html) or introducing extra dependencies (like `pip install -e \".[dev]\"`) to removing `pylint` from `.pre-commit-config.yaml`.",
"@lan496 Adding setup instructions for contributors is definitely an improvement. But in practice those are often not consulted and even if, they would still increase the burden on contributors. Given how many community contributions `pymatgen` receives, I think it's very valuable to keep the barrier to entry as low as possible.\r\n\r\nI'm not a `pylint` user myself so don't know if there are any downsides to this approach, but I think it should work to just change these two lines:\r\n\r\n```diff\r\n - repo: local\r\n hooks:\r\n - id: pylint\r\n name: pylint\r\n entry: pylint\r\n- language: system\r\n+ language: python\r\n types: [python]\r\n args: [-sn, --rcfile=pylintrc]\r\n+ additional_dependencies: [pylint]\r\n```\r\n\r\nThat will make pre-commit install `pylint` automatically.\r\n\r\nAlso, since `pylint` has been running on this project continuously, there are no legacy violations. So with this change, I think there wouldn't be a need to skip the `pylint` hook in pre-commit.ci."
] | 2022-04-13T01:33:08
| 2022-04-16T14:20:19
|
2022-04-13T17:04:54Z
|
CONTRIBUTOR
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## Summary
[The linter workflow](https://github.com/materialsproject/pymatgen/blob/master/.github/workflows/lint.yml) in GitHub actions uses `pylint`, but `.pre-commit-config.yaml` did not call it. This PR adds `pylint` in `.pre-commit-config.yaml`.
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I_kwDOACgets5HrxqP
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analysis/adsorption.py add_adsorbate is not working
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[
"Hi @zuhalcakir not sure if this is still an issue (the original issue seems more like a bug from the ASE side).\r\n\r\n```\r\nase==3.23.0\r\nnumpy==2.1.3\r\npymatgen==2024.10.29\r\n```\r\n\r\nWith the following code snippet I seem to get the correct structure ([POSCAR_with_ads](https://github.com/user-attachments/files/17686248/POSCAR_with_ads.txt)):\r\n```python\r\n\r\n\r\nfrom pymatgen.analysis.adsorption import AdsorbateSiteFinder\r\nfrom pymatgen.core import Molecule\r\nfrom pymatgen.io.ase import AseAtomsAdaptor\r\nfrom pymatgen.io.vasp import Poscar\r\n\r\n\r\nposcar = Poscar.from_file(\"POSCAR\")\r\natoms = AseAtomsAdaptor.get_atoms(poscar.structure)\r\nslab = AseAtomsAdaptor.get_structure(atoms)\r\n\r\nmol = Molecule(\r\n species=[\"N\", \"N\"],\r\n coords=[[0, 0, 0], [0, 0, 1.1]]\r\n)\r\n\r\nads_site_finder = AdsorbateSiteFinder(slab)\r\npmg_ads_struct = ads_site_finder.add_adsorbate(\r\n mol,\r\n [5.3, 3.0, 28], # above #33 nitrogen\r\n translate=True,\r\n reorient=False,\r\n )\r\n# ase_struct = AseAtomsAdaptor.get_atoms(pmg_ads_struct)\r\n\r\nfinal_poscar = Poscar(pmg_ads_struct)\r\nfinal_poscar.write_file(\"POSCAR_with_ads\")\r\n\r\n```\r\n\r\nMeanwhile, it would be really helpful if you could provide a self-contained and **complete** code snippet when reporting any further issues in the future. This will make it easier for us to recreate that issue. Thanks in advance!\r\n\r\n"
] | 2022-04-13T02:05:54
| 2024-11-09T06:31:23
|
NONE
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**Describe the bug**
add_adsorbate function is not working properly.
**To Reproduce**
Steps to reproduce the behavior:
atoms = read(contcar)
pym_slab = pym_ase.get_structure(atoms)
mol = molecule('N2')
pym_mol = Molecule(species=[atom.symbol for atom in mol], coords=[atom.position for atom in mol])
asf = AdsorbateSiteFinder(pym_slab)
pym_ads_struct = asf.add_adsorbate(pym_mol, atom_pos, translate=True, reorient=False)
ase_struct = pym_ase.get_atoms(pym_ads_struct)
**Provide any example files that are needed to reproduce the error,**
especially if the bug pertains to parsing of a file.
Co Mo
1.00000000000000
5.3315851301465687 0.0000000000000000 0.0000000000000000
2.6657925650732843 4.6172881651462907 0.0000000000000000
0.0000000000000000 0.0000000000000000 35.2362736039142277
Co Mo N
16 16 2
Selective dynamics
Direct
0.8333333333333357 0.3333333333333357 0.2837984547517323 F F F
0.3333333333333357 0.8333333333333357 0.2837984547517323 F F F
0.0000000000000000 0.0000000000000000 0.3455703248226669 F F F
0.5000000000000000 0.0000000000000000 0.3455703248226669 F F F
0.1666666666666643 0.1666666666666643 0.4073421948936016 F F F
0.6666666666666643 0.6666666666666643 0.4073421948936016 F F F
0.8333333333333357 0.8333333333333357 0.4691140649645362 F F F
0.3333333333333357 0.8333333333333357 0.4691140649645362 F F F
0.5044306276791102 0.0001186248577321 0.5272432715239195 T T T
0.0092446198272882 0.5070564411120697 0.5292001621916322 T T T
0.1444638655056341 0.1807118082041121 0.5872388278721111 T T T
0.1566301557079408 0.6580435955302947 0.5904734080209274 T T T
0.6772674607093401 0.6575287989674415 0.5874959318275438 T T T
0.3143157855111828 0.3418129800672944 0.6502164922642319 T T T
0.0129632841176543 -0.0375154377356958 0.7078850390182233 T T T
0.5414389580794525 -0.0453114478106517 0.7131104262811178 T T T
0.3333333333333357 0.3333333333333357 0.2837984547517323 F F F
0.8333333333333357 0.8333333333333357 0.2837984547517323 F F F
0.0000000000000000 0.5000000000000000 0.3455703248226669 F F F
0.5000000000000000 0.5000000000000000 0.3455703248226669 F F F
0.6666666666666643 0.1666666666666643 0.4073421948936016 F F F
0.1666666666666643 0.6666666666666643 0.4073421948936016 F F F
0.8333333333333357 0.3333333333333357 0.4691140649645362 F F F
0.3333333333333357 0.3333333333333357 0.4691140649645362 F F F
0.0052486070172410 -0.0112179742650929 0.5288025104996794 T T T
0.5066254008294978 0.5137602311377656 0.5330124549416291 T T T
0.6311291354527444 0.1542261721847707 0.5922300970749093 T T T
0.8142536428867365 0.3437874211517009 0.6496358026207728 T T T
0.8351093464793909 0.8331609981746062 0.6531777338056198 T T T
0.3237339769862948 0.8575962783790190 0.6461829842804433 T T T
0.0114431532232512 0.4088432135581262 0.7178108625756642 T T T
0.4539508169619021 0.5154486384014929 0.7153779500404396 T T T
0.6672293050703286 0.6492728128413993 0.7460181013054595 T T T
0.3701582110482037 0.2669813289058624 0.7454620336850959 T T T
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
**Expected behavior**
A clear and concise description of what you expected to happen.
ase_struct = pym_ase.get_atoms(pym_ads_struct)
File "/depot/jgreeley/apps/envs/pymatgen_ase_bell_brown/lib/python3.8/site-packages/pymatgen/io/ase.py", line 56, in get_atoms
return Atoms(symbols=symbols, positions=positions, pbc=pbc, cell=cell,
File "/depot/jgreeley/apps/envs/pymatgen_ase_bell_brown/lib/python3.8/site-packages/ase/atoms.py", line 233, in __init__
self.new_array('positions', positions, float, (3,))
File "/depot/jgreeley/apps/envs/pymatgen_ase_bell_brown/lib/python3.8/site-packages/ase/atoms.py", line 458, in new_array
a = np.array(a, dtype, order='C')
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (34,) + inhomogeneous part.
**Screenshots**
If applicable, add screenshots to help explain your problem.
**Desktop (please complete the following information):**
- OS: CentOS 7
- Version
**Additional context**
Add any other context about the problem here.
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PR_kwDOACgets42T35s
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|
Fix scipy deprecation warnings
|
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"\n[](https://coveralls.io/builds/48326618)\n\nCoverage decreased (-0.7%) to 83.272% when pulling **3aa44fe7d9720f496a5a1c1ccd95088b7e8c1690 on arosen93:rosen-dep** into **827ad4ee1e85bd723e0d29ef9ce8f708c44a1e61 on materialsproject:master**.\n"
] | 2022-04-16T02:04:23
| 2022-04-20T03:33:11
|
2022-04-19T14:34:47Z
|
MEMBER
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Fixes a few depractation warnings.
|
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PR_kwDOACgets42UGol
| 2,495
|
Clean up tests
|
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[
"Hey, just say your comment for the lobster tests. I think I forgot to include one assertion... \r\n\r\nCould you add \"self.assertEqual(icooplist_bise, self.icoop_bise.icohplist)\" to line 621 of test_lobster.py? I think this should work. Otherwise, I will put this on my ToDo.\r\n",
"\n[](https://coveralls.io/builds/48328119)\n\nCoverage decreased (-0.8%) to 83.267% when pulling **576ea8841cae664805162db41673eaec28f700f8 on janosh:fix-flake8** into **827ad4ee1e85bd723e0d29ef9ce8f708c44a1e61 on materialsproject:master**.\n",
"@JaGeo Wow, you spotted that TODO quickly! 😄 \r\n\r\nThanks, I added your code snippet.",
"Thanks 🙂. "
] | 2022-04-16T09:53:40
| 2022-04-19T14:35:33
|
2022-04-19T14:35:32Z
|
MEMBER
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Boring part of this PR: Fix some flake8 violations.
Worth reviewing are changes to
- `PathFinderTest.test_image_num()`
- dulong-petit test case in `ElasticTensorExpansionTest.test_thermal_expansion_coeff()`
|
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PR_kwDOACgets42US_Y
| 2,496
|
Improvement of pre-commit hook settings for `pylint`
|
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[
"\n[](https://coveralls.io/builds/48331133)\n\nCoverage decreased (-0.7%) to 83.272% when pulling **0aacddddb8e47b282ba151e5e4043bc97175f71d on lan496:pylint-hook** into **827ad4ee1e85bd723e0d29ef9ce8f708c44a1e61 on materialsproject:master**.\n",
"Oops, looks like `pylint` is too slow for pre-commit.ci (timeout after 180 seconds). I guess it needs to be skipped after all.",
"I have restored to skip `pylint` in pre-commit.ci due to the timeout limitation.\r\nI believe it is ready to be merged after all other tests are passed!"
] | 2022-04-16T15:26:03
| 2022-04-20T00:38:13
|
2022-04-19T14:34:36Z
|
CONTRIBUTOR
|
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Improvement of settings for `pylint` in `.pre-commit-config.yaml`, continuation of https://github.com/materialsproject/pymatgen/pull/2492 (@janosh, thank you for telling me the snippet!)
- I have confirmed `pylint` is now automatically installed when pre-commit hooks are called.
- Adding instructions to set up optional dependencies in docs.
|
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PR_kwDOACgets42dl2Z
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|
Fix link to Bader code in docstring
|
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[] | null |
[
"Might make sense to run a link checker on the docs to catch broken links automatically. Looks like there are some that cover all pymatgen-relevant markup languages, i.e. HTML, MD and rST: https://github.com/lycheeverse/lychee (can be run [as an action](https://github.com/lycheeverse/lychee-action))."
] | 2022-04-20T02:51:37
| 2022-04-20T19:53:39
|
2022-04-20T03:25:26Z
|
MEMBER
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Closes #1874. Fixes a broken URL in the docstring.
|
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I_kwDOACgets5IFkL2
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|
Add a kwarg to avoid POTCAR checking in correction scheme
|
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[
"Closed in fad0576eb85af458cdc18daf4df9e861c75971ed"
] | 2022-04-20T09:26:30
| 2023-07-11T05:30:03
|
2023-07-11T05:30:02Z
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MEMBER
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This mainly concerns the `MaterialsProject2020Compatibility` scheme, so I'm CC'ing @rkingsbury here.
https://github.com/materialsproject/pymatgen/blob/dcc4576fb8fb89b7adc2f31158654392348e6498/pymatgen/entries/compatibility.py#L941-L944
The above codeblock checks the POTCAR symbols when getting a correction. While this is a very useful tool, I don't know that it should be _required_ to obtain a correction. For instance, my entry objects don't have any data about POTCARs in them, but I can't get the corrections without commenting out this codeblock.
@rkingsbury: Are you opposed to me adding a kwarg `check_potcar` to `get_adjustments()` or to `__init__` to optionally bypass this check? I feel like the difference between this and `check_potcar_hash=False` is potentially confusing though. In the case of `check_potcar_hash`, the POTCARs are still check but just their symbols and not the hash itself. Any suggestions?
For additional context, see #3142.
|
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I_kwDOACgets5IFmQo
| 2,500
|
Improve useability of the `MaterialsProject2020Compatibility` Scheme
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[] | 2022-04-20T09:33:31
| 2022-04-20T20:23:25
|
MEMBER
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Another one for @rkingsbury regarding `MaterialsProject2020Compatibility`.
# Issue 1: Oxide Type
If the `.data` field is empty in a `ComputedEntry`, the compatibility scheme fails because of the bottom line. We should copy the section from the sulfide correction and call `oxide_type()` if a `structure` object is attached and switch the line below to `.data.get("oxide_type")` so it doesn't crash if empty.
https://github.com/materialsproject/pymatgen/blob/bb259c6bf3faabc3ab9fbd011b660a35cad469a8/pymatgen/entries/correction_calculator.py#L237-L241
# Issue 2: Clarification on run_type
We should provide some documentation about the `.parameters["run_type"]` check, as the user may not know in advance that they need to specify "GGA" or "GGA+U" for this. Additionally, if it's not set at all, you get a `CompatibilityError`, which wasn't clear to me originally.
https://github.com/materialsproject/pymatgen/blob/bb259c6bf3faabc3ab9fbd011b660a35cad469a8/pymatgen/entries/compatibility.py#L474-L482
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PR_kwDOACgets42gLBb
| 2,501
|
No complex
|
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[
"Thanks @jmmshn! More descriptive PR titles would be appreciated though :) \r\n\r\nWas this because of issues with serialization when leaving them as complex?",
"> Was this because of issues with serialization when leaving them as complex?\r\n\r\nSorry for the short title. Yes, I'm trying to make this more JSON friendly."
] | 2022-04-20T16:08:39
| 2022-04-20T18:16:11
|
2022-04-20T18:14:12Z
|
CONTRIBUTOR
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# Removed complex numbers from the definition of WSWQ
- split the complex numbers into a real and imaginary parts
- added test for proper orthonormality of WSWQ
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Can't import pymatgen.core "No module named 'pymatgen.core'"
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[
"I have no idea what pymatgen.py is. I suspect it is because you named your script pymatgen and by default, python uses the package in the current directory. Rename the code to some other name.",
"of course! thanks."
] | 2022-04-20T23:48:31
| 2022-04-21T23:51:26
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2022-04-21T02:05:00Z
|
NONE
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I've used pip install pymatgen with Python 3.9.1 on Windows 10 to install pymatgen, but I'm getting the following error:
Traceback (most recent call last):
File "D:\code\pymatgen\pymatgen.py", line 1, in <module>
import pymatgen.core as mg
File "D:\code\pymatgen\pymatgen.py", line 1, in <module>
import pymatgen.core as mg
ModuleNotFoundError: No module named 'pymatgen.core'; 'pymatgen' is not a package
I have also tried to install the previous 2 versions but still getting the same error though I can already see it in the pip list
pymatgen 2022.3.22
i am not using a virtual environment and i dont want to install conda its too big
What am I missing?
|
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|
FEFF: support Molecule as input
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[
"This is ready for review. Note that there is one non-deterministic test failure that sometimes occurs and sometimes passes:\r\n\r\n```\r\nE AssertionError: 'PATH[72 chars]6884 1 Fe\\n-5.133990 -0.916498 -5.379918 1 Fe\\[188 chars]0 Fe' != 'PATH[72 chars]6884 2 Fe\\n-5.133990 -0.916498 -5.379918 2 Fe\\[188 chars]0 Fe'\r\nE Diff is 831 characters long. Set self.maxDiff to None to see it.\r\n\r\npymatgen/io/feff/tests/test_inputs.py:411: AssertionError\r\n```\r\n\r\nThis is because the potential indices of Fe and O sometimes get reversed (where Fe is 2 and O is 1), but sometimes they don't. It's not completely clear to me whether the changes in this PR have triggered the non-determinism (I don't think so), but perhaps we can restructure the test to make it more robust? I'm open to suggestions there.",
"This failure also appears to be non-deterministic, and could occur for the same reason (element names and numbers getting mixed up)\r\n\r\n```\r\n______________________ FeffInputSetTest.test_get_feffPot _______________________\r\n\r\nself = <feff.tests.test_sets.FeffInputSetTest testMethod=test_get_feffPot>\r\n\r\n def test_get_feffPot(self):\r\n POT = str(self.mp_xanes.potential)\r\n d, dr = Potential.pot_dict_from_string(POT)\r\n> self.assertEqual(d[\"Co\"], 1, \"Wrong symbols read in for Potential\")\r\nE AssertionError: 2 != 1 : Wrong symbols read in for Potential\r\n\r\npymatgen/io/feff/tests/test_sets.py:61: AssertionError\r\n\r\n```",
"I think I've found a fix for the non-deterministic test failures. Please hold off on merging though, as I want to also double check handling of charged clusters (and whether the `ION` card should be set when there is a charge). I have an email in to one of the devs about this and will follow up soon.",
"\n[](https://coveralls.io/builds/52561510)\n\nCoverage increased (+0.1%) to 63.368% when pulling **e4b7299ccd3bce812f0b55b10fbea9a2d1370bd6 on rkingsbury:feff** into **beac8d5361d8f5332c7335be3ce31b41cb131e31 on materialsproject:master**.\n",
"OK, ready for review! I have gotten clarification about how calculations involving charged structures should be set up. Full support for that may be a bit involved, so in this PR I have opted to 1) detect when charged structures are used to instantiate an InputSet and 2) raise an exception or a warning as appropriate to alert the user that some manual editing is needed in that case. I've also added in the code comments what is supposed to be done.\r\n\r\nI will experiment with adding support for automatic `ION` tags but I think that's best for a separate PR.",
"Friendly reminder about this PR, which is ready for review. If any changes are needed, I'd like to do them soon b/c I have shifted to other kinds of calculations and my memory about the details of FEFF IO will become fuzzy soon :)\r\n\r\nRegarding support for charged `Molecule`:\r\n\r\n> I will experiment with adding support for automatic `ION` tags but I think that's best for a separate PR.\r\n\r\nInstead of waiting for a separate PR, I have added here minimal support for ION tags via `user_tag_settings`, with an associated warning message that is triggered if 1) the input `Molecule` has a net charge and 2) `the user has not supplied the IONS key in `user_tag_settings`. The changes correctly produce multiple `ION` tags in the output file when `IONS` is included in the `user_tag_settings`.",
"Thanks @rkingsbury, apologies for the delay with review -- features are very welcome."
] | 2022-04-25T21:58:31
| 2022-09-29T18:04:18
|
2022-09-28T17:32:15Z
|
CONTRIBUTOR
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## Summary
This PR includes minimal changes to FEFF I/O to support the use of non-periodic input structures (e.g., `Molecule` rather than `Structure` objects). Tested with `MPXANESSet`. This also includes a fix for an edge case in which there is only a single absorbing atom present. When that occurs, some changes were necessary to ensure that the single absorbing atom does not get listed twice in the POTENTIALS section of the input file.
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Corruption of `.pmgrc.yaml` still happening
|
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[
"No idea. I don't even know why MPRester needs to write to the pmgrc file. @mkhorton should look into this and make sure it is proper json and/or put it in another file. rc files are for configuration variables. The current ones that I see are not.",
"Maybe it's not `MPRester()` after all. At least I couldn't reproduce the corruption intentionally by running this code in a loop 100 times.\r\n\r\n```py\r\nimport os\r\nfrom ruamel.yaml import YAML\r\n\r\nSETTINGS_FILE = os.path.join(os.path.expanduser(\"~\"), \".pmgrc.yaml\")\r\nyaml = YAML()\r\n\r\ntry:\r\n with open(SETTINGS_FILE) as f:\r\n d = dict(yaml.load(f))\r\nexcept OSError:\r\n d = {}\r\n\r\nd = d or {}\r\n\r\nif \"MAPI_DB_VERSION\" not in d:\r\n d[\"MAPI_DB_VERSION\"] = {\"LOG\": {}, \"LAST_ACCESSED\": None}\r\nelse:\r\n # ensure data is parsed as dict, rather than ordered dict,\r\n # due to change in YAML parsing behavior\r\n d[\"MAPI_DB_VERSION\"] = dict(d[\"MAPI_DB_VERSION\"])\r\n\r\nif \"LOG\" in d[\"MAPI_DB_VERSION\"]:\r\n d[\"MAPI_DB_VERSION\"][\"LOG\"] = dict(d[\"MAPI_DB_VERSION\"][\"LOG\"])\r\n\r\ndb_version = \"2020_09_08\"\r\n\r\n# store a log of what database versions are being connected to\r\nif db_version not in d[\"MAPI_DB_VERSION\"][\"LOG\"]:\r\n d[\"MAPI_DB_VERSION\"][\"LOG\"][db_version] = 1\r\nelse:\r\n d[\"MAPI_DB_VERSION\"][\"LOG\"][db_version] += 1\r\n\r\n# alert user if db version changed\r\nlast_accessed = d[\"MAPI_DB_VERSION\"][\"LAST_ACCESSED\"]\r\nif last_accessed and last_accessed != db_version:\r\n print(\r\n f\"This database version has changed from the database last accessed ({last_accessed}).\\n\"\r\n f\"Please see release notes on materialsproject.org for information about what has changed.\"\r\n )\r\nd[\"MAPI_DB_VERSION\"][\"LAST_ACCESSED\"] = db_version\r\n\r\n# write out new database log if possible\r\n# bare except is not ideal (perhaps a PermissionError, etc.) but this is not critical\r\n# and should be allowed to fail regardless of reason\r\ntry:\r\n with open(SETTINGS_FILE, \"w\") as f:\r\n yaml.dump(d, f)\r\nexcept Exception as exc:\r\n print(exc)\r\n```",
"Well, I searched the entire code for any dump commands using Pycharm. The only dump commands operating on the pmgrc are in pmg_config and MPRester. These are the only places where corruption can occur. ",
"This is/was definitely due to a change in behavior in `ruamel.yaml`.\r\n\r\nSpecifically, data from .pmgrc.yaml was now being loaded as non-native Python data types, and then when written back out, was written out with a lot of extra metadata to preserve these non-native data types. In my view this is a bug, because the .pmgrc.yaml should have been loaded as a `dict` and this was the original behavior.\r\n\r\nThe reason the write occurs in `MPRester` is to keep a local log of database version accessed: a common point of confusion for MPRester users, based on support questions, is when and why retrieved data can change. By storing a local log of database version accessed, we can warn when database version changes. It's obviously important for anyone doing science with this data (+ wanting their science to be reproducible) that they're mindful of the database version.\r\n\r\nI've lost (some) confidence in `ruamel.yaml` as a result of this, because this will not be an issue that only affects .pmgrc.yaml, but could affect any of our yaml parsing.",
"@mkhorton I get that you want to keep a log, but I think that can be done using a separate file? pmgrc should really be about config variables and edits to it should be minimal. You can always store a `.mprester_log.yaml` or something.",
"Sure, we can keep it separately, but it doesn't change the fundamental issue that `ruamel.yaml` (for some versions) cannot do a round-trip read/write anymore.",
"Seems like it's not that much to ask to be able to write to a yaml file. But if a file `.mprester_log.yaml` is really added, could it be inside `site_packages` so as not to proliferate $HOME dir files?\r\n\r\n> Specifically, data from .pmgrc.yaml was now being loaded as non-native Python data types, and then when written back out, was written out with a lot of extra metadata to preserve these non-native data types.\r\n\r\nI noticed that too and assumed this was the cause of the problem.\r\n\r\nPerhaps the simplest \"hot fix\" for now would be to make this change:\r\n\r\n```py\r\ntry:\r\n with open(SETTINGS_FILE) as f:\r\n- d = dict(yaml.load(f))\r\n+ d = json.loads(json.dumps(yaml.load(f)) # will recursively convert ruamel.yaml subclass of OrderedDict to dict\r\nexcept (OSError, TypeError):\r\n # TypeError: 'NoneType' object is not iterable occurs if SETTINGS_FILE exists but is empty\r\n d = {}\r\n```\r\n\r\nCan add it to #2507 if you approve.",
"> fundamental issue that `ruamel.yaml` (for some versions) cannot do a round-trip read/write anymore.\r\n\r\nAre the affected `ruamel.yaml` version ranges known? Then we could only allow newer versions in `setup.py`.",
"@mkhorton I get that. I think the main issue is the definition of primitives supported in python. In any case, a log file is a minor thing and we can even just rely on a text dump for that.\r\n\r\n@janosh Let's not hotfix anything. The bottom line is that config files is not the same as log files. Log files are meant to be write often, and read rarely. Config files are the exact opposite. And no, you should not dump files into site_packages. $HOME is about the cleanest place to put it. Just make sure it is a hidden file (starting with a \".\"). Fixing the ruamel version should be done, but let's fix this whole thing properly independent of the ruamel issue.",
"Not sure writing to `.pmgrc.yaml` really needs fixing. One reason why config files are usually in formats like yaml, json, toml, cfg, etc. and not in whatever language you're coding in is because config files with their highly restricted syntax are much easier to parse and auto-update, i.e. write to. From what I understand, that's even the _main_ reason why some projects have transitioned their packaging from `setup.py` to `setup.cfg`.",
"@janosh I understand that. But what MPRester is writing is *not* a config. It is basically a *log*. ",
"Ok, I think we're decided about the MPRester log -- let's move it to a separate file. I'm ok with this in `site_packages` if this would be robust against version updates.\r\n\r\n@janosh, what was your specific suggestion for `.pmgrc.yaml`, assuming this log is no longer present?\r\n\r\nFor configuration in other projects, we've started using [`pydantic Settings`](https://pydantic-docs.helpmanual.io/usage/settings/) which is very elegant.",
"@mkhorton Pls do not use site_packages. I think it is bad form. Site packages is meant for package data. Just put it in the same $HOME directory as the pmgrc but as a different file name. ",
"> @janosh, what was your specific suggestion for `.pmgrc.yaml`, assuming this log is no longer present?\r\n\r\n@mkhorton Not sure what you mean? This?\r\n\r\n```py\r\nd = json.loads(json.dumps(yaml.load(f)) # will recursively convert ruamel.yaml subclass of OrderedDict to dict\r\n```\r\n\r\nBut as @shyuep said, the better solution would be to pin to unaffected `ruamel.yaml` version ranges."
] | 2022-04-26T10:33:41
| 2022-04-26T21:36:22
|
2022-04-26T21:36:22Z
|
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Pinging @shyuep as I think this was supposed to be fixed in https://github.com/materialsproject/pymatgen/issues/2421.
Using `MPRester` still corrupts `.pmgrc.yaml`:
```yaml
dictitems:
MAPI_DB_VERSION:
LAST_ACCESSED: '2020_09_08'
LOG: {'2020_09_08': 1}
PMG_DEFAULT_FUNCTIONAL: PBE_54
PMG_MAPI_KEY: **********************
PMG_VASP_PSP_DIR: /Users/janosh/dev/vasp/pseudo-potentials
state:
_yaml_format: !!python/object/new:ruamel.yaml.comments.Format
state: !!python/tuple
-
- {_flow_style: false}
_yaml_line_col: !!python/object:ruamel.yaml.comments.LineCol
col: 0
data:
PMG_DEFAULT_FUNCTIONAL: [0, 0, 0, 24]
PMG_MAPI_KEY: [1, 0, 1, 14]
PMG_VASP_PSP_DIR: [2, 0, 2, 18]
line: 0
MAPI_DB_VERSION:
LOG:
'2020_09_08': 2
LAST_ACCESSED: '2020_09_08'
```
leading on subsequent `MPREster` calls to
```py
pymatgen.ext.matproj.MPRestError: REST query returned with error status code 403
```
Is this due to an outdated `ruamel.yaml` on my machine?
```
pip list | grep ruamel
ruamel.yaml 0.17.20
ruamel.yaml.clib 0.2.6
```
If so, should update the min version in `setup.py`:
```py
"ruamel.yaml>=0.15.6"
```
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PR_kwDOACgets42z5uk
| 2,507
|
Report exceptions in `MPRester.__init__()` when trying to read/write `SETTINGS_FILE`
|
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[
"\n[](https://coveralls.io/builds/48585235)\n\nCoverage decreased (-0.7%) to 83.278% when pulling **74ee108dd1d7db531bbf4be575814eca8ad7b535 on janosh:mprester-init-exception-handling** into **da8d0a996584b716e2f9a6f2e3fdf9a94d80454a on materialsproject:master**.\n",
"This has been superseded by recent changes.",
"@shyuep The changes were largely orthogonal. You don't think it would be a good idea to catch `TypeError` correctly when trying to read an empty `MP_LOG_FILE` (formerly `SETTINGS_FILE`)?",
"I would rather not catch the error and just let it fail. Then people will fix the code to make it robust again this kind of errors.\r\n\r\nCatching errors should be for errors we expect. E.g., if a file is potentially unavailable or unwritable. If errors are a result of bad code or assumptions, those should not be caught but rather fixed.",
"That was my motivation as well except I thought it'd be more likely to get fixed properly when there's a warning than when it fails silently."
] | 2022-04-26T15:29:59
| 2022-04-28T20:59:56
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2022-04-26T21:45:08Z
|
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Relates to #2506.
Changes `MPRester.__init__()` to print exceptions when trying to read/write `SETTINGS_FILE` instead of swallowing them silently. This might help identify the underlying issue leading to `.pmgrc.yaml` corruption.
|
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