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I_kwDOACgets4_Ivqb
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QCInput doesn't support multi-fragment molecule sections
|
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[] | 2021-11-21T00:13:39
| 2021-11-21T00:13:39
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NONE
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**Describe the bug**
Calculation inputs that represent any kind of fragment job (`fragmo` guess, BSSE, SCFMI/EDA, freezing string (FSM)) can't be read by the Q-Chem input parser. For this to work properly would probably require a fundamental rework of the parser and assumptions about what constitutes a molecule.
**To Reproduce**
An example freezing string input is:
```
$molecule
0 1
C 2.7338127436 -0.4160134456 0.0000555150
C 1.7178853475 0.7141682331 -0.0000169591
C 0.4025377415 0.6251382031 -0.0000634662
C -0.4023316027 -0.6250487458 -0.0000122605
C -1.7179140778 -0.7141571034 -0.0000591608
C -2.7339505731 0.4159341985 0.0000665089
H 3.3737854731 -0.3446793457 0.8772240969
H 3.3740118303 -0.3446632855 -0.8769523568
H 2.2651539065 -1.3927156272 0.0000061985
H 2.1625720004 1.7037046896 -0.0001543696
H -0.1622517588 1.5479329180 -0.0000165370
H 0.1625664852 -1.5477779268 -0.0000910372
H -2.1626281939 -1.7036793172 -0.0000730569
H -3.3741989948 0.3443338409 0.8770171024
H -3.3738611713 0.3447355997 -0.8771574867
H -2.2653870497 1.3926804143 0.0003763833
****
C -1.8991299412 -0.8590459370 0.2192241951
C -0.6641347605 -0.2013165452 -0.4233395587
C -0.5577337314 1.3223248314 -0.3463897004
C 0.5575523245 1.3223198718 0.3463956040
C 0.6640642376 -0.2013637083 0.4232178390
C 1.8992185075 -0.8589434214 -0.2192066620
H -1.7699867505 -1.9362978947 0.2767225427
H -2.7885620493 -0.6548659579 -0.3704992042
H -2.0612696879 -0.4792204329 1.2235249635
H -0.5195094384 -0.5990999255 -1.4288761716
H -1.2011460378 2.0979972505 -0.7394340887
H 1.2019536900 2.0968631625 0.7400557762
H 0.5193179975 -0.5992513516 1.4286977963
H 1.7701487194 -1.9361972610 -0.2768242764
H 2.7885499589 -0.6547638851 0.3706696282
H 2.0614837794 -0.4790142526 -1.2234472683
$end
$rem
method = hf
basis = sto-3g
jobtype = fsm
fsm_nnode = 10
fsm_ngrad = 3
fsm_mode = 2
fsm_opt_mode = 1
$end
```
(If you do decide to run this job, it should only take a minute tops.) To parse:
```python
from pymatgen.io.qchem.inputs import QCInput
qci = QCInput.from_file("fsm.in")
```
resulting in
```
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-4-b1d85d6646aa> in <module>
----> 1 qci = QCInput.from_file("fsm.in")
/dftman/home2/ericb/pyenv/versions/miniforge3-4.10.1-5/envs/atomate/lib/python3.9/site-packages/pymatgen/io/qchem/inputs.py in from_file(filename)
290 """
291 with zopen(filename, "rt") as f:
--> 292 return QCInput.from_string(f.read())
293
294 @classmethod
/dftman/home2/ericb/pyenv/versions/miniforge3-4.10.1-5/envs/atomate/lib/python3.9/site-packages/pymatgen/io/qchem/inputs.py in from_string(cls, string)
215 """
216 sections = cls.find_sections(string)
--> 217 molecule = cls.read_molecule(string)
218 rem = cls.read_rem(string)
219 # only molecule and rem are necessary everything else is checked
/dftman/home2/ericb/pyenv/versions/miniforge3-4.10.1-5/envs/atomate/lib/python3.9/site-packages/pymatgen/io/qchem/inputs.py in read_molecule(string)
576 footer = r"^\$end"
577 mol_table = read_table_pattern(string, header_pattern=header, row_pattern=row, footer_pattern=footer)
--> 578 species = [val[0] for val in mol_table[0]]
579 coords = [[float(val[1]), float(val[2]), float(val[3])] for val in mol_table[0]]
580 if charge is None:
IndexError: list index out of range
```
because `mol_table` is empty.
Note that the FSM block is a little different from the normal Q-Chem fragment input, which looks like
```
$molecule
0 1
---
0 1
C 2.7338127436 -0.4160134456 0.0000555150
C 1.7178853475 0.7141682331 -0.0000169591
C 0.4025377415 0.6251382031 -0.0000634662
C -0.4023316027 -0.6250487458 -0.0000122605
C -1.7179140778 -0.7141571034 -0.0000591608
C -2.7339505731 0.4159341985 0.0000665089
H 3.3737854731 -0.3446793457 0.8772240969
H 3.3740118303 -0.3446632855 -0.8769523568
H 2.2651539065 -1.3927156272 0.0000061985
H 2.1625720004 1.7037046896 -0.0001543696
H -0.1622517588 1.5479329180 -0.0000165370
H 0.1625664852 -1.5477779268 -0.0000910372
H -2.1626281939 -1.7036793172 -0.0000730569
H -3.3741989948 0.3443338409 0.8770171024
H -3.3738611713 0.3447355997 -0.8771574867
H -2.2653870497 1.3926804143 0.0003763833
---
0 1
C -1.8991299412 -0.8590459370 0.2192241951
C -0.6641347605 -0.2013165452 -0.4233395587
C -0.5577337314 1.3223248314 -0.3463897004
C 0.5575523245 1.3223198718 0.3463956040
C 0.6640642376 -0.2013637083 0.4232178390
C 1.8992185075 -0.8589434214 -0.2192066620
H -1.7699867505 -1.9362978947 0.2767225427
H -2.7885620493 -0.6548659579 -0.3704992042
H -2.0612696879 -0.4792204329 1.2235249635
H -0.5195094384 -0.5990999255 -1.4288761716
H -1.2011460378 2.0979972505 -0.7394340887
H 1.2019536900 2.0968631625 0.7400557762
H 0.5193179975 -0.5992513516 1.4286977963
H 1.7701487194 -1.9361972610 -0.2768242764
H 2.7885499589 -0.6547638851 0.3706696282
H 2.0614837794 -0.4790142526 -1.2234472683
$end
```
and though I haven't tested it, I'm assuming this will also fail.
I'm using version 2022.0.16 with Python 3.9.6 from conda-forge.
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| 1,060,468,105
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PR_kwDOACgets4u3jb4
| 2,303
|
More robust smart fermi method
|
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[] | null |
[
"Thanks @utf, this is very helpful. I followed up with the VASP folks on this, see [here](https://www.vasp.at/forum/viewtopic.php?p=20686). It sounds hopeful that this might be addressed in a future version."
] | 2021-11-22T18:26:43
| 2021-11-22T19:48:48
|
2021-11-22T19:48:48Z
|
MEMBER
|
{
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|
## Summary
VASP 6.1+ sometimes puts the Fermi level just inside a valence or conduction band. This is related to a change in VASP tetrahedron which is described here: https://www.vasp.at/forum/viewtopic.php?f=4&t=17981
There is already logic inside pymatgen to try and catch this bug, unfortunately it is not reliable and after some discussion with @mkhorton, we are not sure it can ever work.
I've made a new implementation that checks whether the Fermi level is just inside of band (controlled by a tolerance, by default set to 1 meV) and next to a band gap. If so, this is likely an error on VASPs part. In my testing I found this method much more reliable.
I'll note this is not enabled by default and is only included when calling `Vasprun.get_band_structure(efermi="smart")`.
@rkingsbury this may be relevant to you.
|
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PR_kwDOACgets4u4GuF
| 2,304
|
Fix to `get_continuous_path` method for line-mode band structures
|
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[] | null |
[
"\n[](https://coveralls.io/builds/47029579)\n\nCoverage decreased (-0.8%) to 83.372% when pulling **4b66ebc908cf8cb0322152d64f7491ccb2a84213 on munrojm:master** into **4b66ebc908cf8cb0322152d64f7491ccb2a84213 on materialsproject:master**.\n",
"Thanks for fixing @munrojm, I see the new test files to go with this fix but not the new test, happy to merge once that's been added."
] | 2021-11-22T22:08:30
| 2022-03-02T22:45:42
|
2022-03-02T22:22:58Z
|
MEMBER
|
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|
## Summary
This PR fixes a bug where band structure segments were missing in some cases due to an indexing issue with `0`.
## 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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| 1,061,186,071
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I_kwDOACgets4_QGoX
| 2,305
|
matplotlib 3.5 BSPlotterProjectedTest test error in electronic_structure test_plotter.py: ValueError: Number of rows must be a positive integer, not 5.5
|
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[
"Was fixed in a1e223a."
] | 2021-11-23T12:00:50
| 2021-12-14T09:44:49
|
CONTRIBUTOR
|
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**Describe the bug**
The BSPlotterProjectedTest test triggered by electronic_structure/tests/test_plotter.py has started failing with matplotlib 3.5. It was previously working with matplot 3.3 (I haven't tested matplotlib 3.4)
**To Reproduce**
Steps to reproduce the behavior:
1. Go to source dir
2. Run `PMG_TEST_FILES_DIR=./test_files/ python3 pymatgen/electronic_structure/tests/test_plotter.py`
3. See error
```
$ PMG_TEST_FILES_DIR=./test_files/ python3 pymatgen/electronic_structure/tests/test_plotter.py
.You do not want to sum projection over orbitals.
You do not want to sum projection over atoms.
Number of subfigures: 9
{'start_index': 0, 'end_index': 15, 'name': '\\Gamma-X'}
{'start_index': 16, 'end_index': 31, 'name': 'X-M'}
{'start_index': 32, 'end_index': 47, 'name': 'M-\\Gamma'}
{'start_index': 48, 'end_index': 63, 'name': '\\Gamma-R'}
{'start_index': 64, 'end_index': 79, 'name': 'R-X'}
{'start_index': 80, 'end_index': 95, 'name': 'M-R'}
dictio_d: {'Cu': ['dxy', 's', 'px'], 'O': ['px', 'py', 'pz']}
dictpa_d: {'Cu': ['3', '5'], 'O': ['1']}
E...The PostScript backend does not support transparency; partially transparent artists will be rendered opaque.
The PostScript backend does not support transparency; partially transparent artists will be rendered opaque.
....sssssssssssssssssss....The PostScript backend does not support transparency; partially transparent artists will be rendered opaque.
...The PostScript backend does not support transparency; partially transparent artists will be rendered opaque.
...
======================================================================
ERROR: test_methods (__main__.BSPlotterProjectedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/projects/build/pymatgen/pymatgen/electronic_structure/tests/test_plotter.py", line 220, in test_methods
self.plotter.get_projected_plots_dots_patom_pmorb(
File "/usr/lib/python3/dist-packages/pymatgen/electronic_structure/plotter.py", line 1651, in get_projected_plots_dots_patom_pmorb
plt.subplot(row + 1, 2, count)
File "/usr/lib/python3/dist-packages/matplotlib/pyplot.py", line 1268, in subplot
key = SubplotSpec._from_subplot_args(fig, args)
File "/usr/lib/python3/dist-packages/matplotlib/gridspec.py", line 595, in _from_subplot_args
gs = GridSpec._check_gridspec_exists(figure, rows, cols)
File "/usr/lib/python3/dist-packages/matplotlib/gridspec.py", line 223, in _check_gridspec_exists
return GridSpec(nrows, ncols, figure=figure)
File "/usr/lib/python3/dist-packages/matplotlib/gridspec.py", line 383, in __init__
super().__init__(nrows, ncols,
File "/usr/lib/python3/dist-packages/matplotlib/gridspec.py", line 47, in __init__
raise ValueError(
ValueError: Number of rows must be a positive integer, not 5.5
----------------------------------------------------------------------
Ran 38 tests in 43.123s
FAILED (errors=1, skipped=19)
```
**Desktop:**
- OS: Linux (Debian)
- Version 5.14.16
- Python 3.9.9
- matplotlib 3.5.0
- pymatgen 2022.0.16
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| 1,062,581,062
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I_kwDOACgets4_VbNG
| 2,306
|
Mistakes of argument type on the documentation
|
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[
"@mkhorton -- I think this can be closed.",
"Thanks for reporting @marinebox, this was fixed in https://github.com/materialsproject/pymatgen/commit/e1cbe781be6651fe9df08190e3620f97adadf22a",
"Also thanks @arosen93 for the reminder"
] | 2021-11-24T15:41:59
| 2022-03-29T20:55:59
|
2022-03-29T20:54:42Z
|
NONE
|
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The example of the argument of `gamma_automatic`([here](https://pymatgen.org/pymatgen.io.vasp.inputs.html#pymatgen.io.vasp.inputs.Kpoints.gamma_automatic)) is strange.
According to the source code, the type of `kpts` and `shift` should be tuple, but these are not tuple in the documentation.
In the other function([here](https://pymatgen.org/pymatgen.io.vasp.inputs.html#pymatgen.io.vasp.inputs.Kpoints)), Sphinx understands that the arguments are tuple. However, Sphinx does not understand the arguments of `gamma_automatic` are tuple.
From these points, it seems that Sphinx doesn't interpret the source code of gamma_automatic well.
I have no idea to fix this mistake, so I submit a new issue.
I found the same mistakes on `monkhorst_automatic`([here](https://pymatgen.org/pymatgen.io.vasp.inputs.html#pymatgen.io.vasp.inputs.Kpoints.monkhorst_automatic)) too.
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I_kwDOACgets4_Xxjm
| 2,307
|
VASP 6.2.1 OUTCAR not properly parsed for run stats
|
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[] | 2021-11-25T06:16:19
| 2021-12-17T19:03:48
|
2021-12-17T19:03:48Z
|
MEMBER
|
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**Describe the bug**
When parsing the attached OUTCAR (from VASP 6.2.1) with the current version of Pymatgen, the number of cores is not output correctly because instead of the OUTCAR reading `running on 64` it reads `running 64`. (The average memory used here is `N/A` by VASP, so `None` is appropriate.)
```
{'Average memory used (kb)': None,
'Maximum memory used (kb)': 212968.0,
'Elapsed time (sec)': 148.577,
'System time (sec)': 6.188,
'User time (sec)': 142.096,
'Total CPU time used (sec)': 148.284,
'cores': 'mpi-ranks,'}
```
**To Reproduce**
```python
from pymatgen.io.vasp import Outcar
out = Outcar('OUTCAR.txt')
print(out.run_stats)
```
[OUTCAR.txt](https://github.com/materialsproject/pymatgen/files/7600610/OUTCAR.txt)
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PR_kwDOACgets4vAFSM
| 2,308
|
Fix VASP 6.2.0+ # of cores in run_stats
|
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[
"\n[](https://coveralls.io/builds/44547772)\n\nCoverage decreased (-0.6%) to 83.121% when pulling **c5614ad9b04d0fbd090bb43ef36ce71a8c7e57c4 on arosen93:rosen-runstats** into **dd3737011e76520da1347d5db75db3a3f87e520f on materialsproject:master**.\n",
"@mkhorton, something appears to be up with the tests both here and in #2312. Here, for example, the tests passed successfully earlier. All I did was squash my commits, and now one of the tests simply stalls. Same thing but for a different test in #2312.",
"Thanks @arosen93 !"
] | 2021-11-25T06:49:34
| 2021-12-17T18:21:46
|
2021-12-16T23:32:31Z
|
MEMBER
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Addresses #2307 wherein the number of cores was not being parsed properly for a VASP 6.2.1 OUTCAR file. I have added a test for this new VASP file.
## Summary
- Correctly parses number of cores from VASP 6.2.0+ files
- Stores the number of cores as an `int` instead of `str`
|
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PR_kwDOACgets4vA9WR
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|
Removed double slashes for RST inline math
|
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[
"Many thanks @benedictsaunders ",
"HI @benedictsaunders, I saw you were a first-time contributor. So that we can acknowledge your contribution in [our documentation](https://pymatgen.org/team.html) please fill out [this form](https://forms.gle/JnisFb38QDR8QTFTA) if you have not already."
] | 2021-11-25T12:04:49
| 2022-01-06T22:49:20
|
2022-01-06T22:47:42Z
|
CONTRIBUTOR
|
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The double slashes were being misinterpreted in the current version of the documentation.
## Summary
* Replaced double backslases with ` \` as the `\\` was escaping and leading to no character bring printed in the rst math docstring.
## 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 e above checks. But it will be much moreyou 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_kwDOACgets4vBg7z
| 2,310
|
fix write Trajectory XDATACAR with variable lattice
|
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[
"\n[](https://coveralls.io/builds/44546398)\n\nCoverage decreased (-0.6%) to 83.124% when pulling **9b8995fdd168ea277308e6c0978b447beafdc951 on gpetretto:bugfix** into **dd3737011e76520da1347d5db75db3a3f87e520f on materialsproject:master**.\n",
"Many thanks @gpetretto "
] | 2021-11-25T15:05:02
| 2021-11-29T20:54:15
|
2021-11-29T20:54:11Z
|
CONTRIBUTOR
|
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## Summary
In the current implementation of the write_Xdatcar in Trajectory the lattice is either written only once if `constan_lattice==True` or never if `constan_lattice==False`. Fix to write it multiple times if the lattice is not constant.
Added a specific check in the tests.
|
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I_kwDOACgets4_eQQn
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Cannot import name 'SpeciesLike' from 'pymatgen.util.typing'
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[
"It is an issue with your install.",
"Hello @shyuep \r\nI tried to reinstall my pymatgen, but the above error message still appears, thank you for your time and help!"
] | 2021-11-27T03:53:15
| 2021-11-27T12:34:27
|
2021-11-27T03:58:53Z
|
CONTRIBUTOR
|
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When I use PyCharm to run lattice.py in core package, I got the following error message.
Is this because of a problem with my Installation process or I did not install other dependent libraries yet?
What should I do to solve my problem. thank!
~~~sh
raceback (most recent call last):
File "D:/Gitdownload/pymatgen/pymatgen/core/lattice.py", line 25, in <module>
from pymatgen.util.typing import ArrayLike
File "d:\gitdownload\pymatgen\pymatgen\util\typing.py", line 20, in <module>
from pymatgen.core.periodic_table import Element, Species, DummySpecies
File "d:\gitdownload\pymatgen\pymatgen\core\__init__.py", line 24, in <module>
from .sites import PeriodicSite, Site # noqa
File "d:\gitdownload\pymatgen\pymatgen\core\sites.py", line 21, in <module>
from pymatgen.util.typing import ArrayLike, SpeciesLike, CompositionLike
ImportError: cannot import name 'SpeciesLike' from 'pymatgen.util.typing' (d:\gitdownload\pymatgen\pymatgen\util\typing.py)
~~~
The `pymatgen.util.typing` code in pymatgen I cloned
~~~python
from pathlib import Path
from typing import Union, Sequence
import numpy as np
try:
from numpy.typing import ArrayLike
except ImportError:
ArrayLike = Union[Sequence[float], Sequence[Sequence[float]], Sequence[np.ndarray], np.ndarray] # type: ignore
from pymatgen.core.periodic_table import Element, Species, DummySpecies
from pymatgen.core.composition import Composition
VectorLike = Union[Sequence[float], np.ndarray]
MatrixLike = Union[Sequence[Sequence[float]], Sequence[np.ndarray], np.ndarray]
PathLike = Union[str, Path]
# Things that can be cast into a Species-like object using get_el_sp
SpeciesLike = Union[str, Element, Species, DummySpecies]
# Things that can be cast into a Composition
CompositionLike = Union[str, Element, Species, DummySpecies, dict, Composition]
~~~
My installation process
~~~sh
PS D:\StudyPymatgen\pymatgen> pip install -e .
Obtaining file:///D:/StudyPymatgen/pymatgen
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing wheel metadata ... done
Requirement already satisfied: numpy>=1.20.1 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (1.20.3)
Requirement already satisfied: spglib>=1.9.9.44 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (1.16.1)
Requirement already satisfied: matplotlib>=1.5 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (3.4.3)
Requirement already satisfied: palettable>=3.1.1 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (3.3.0)
Requirement already satisfied: pandas in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (1.3.2)
Requirement already satisfied: plotly>=4.5.0 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (5.3.1)
Requirement already satisfied: ruamel.yaml>=0.15.6 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (0.17.4)
Requirement already satisfied: sympy in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (1.8)
Requirement already satisfied: scipy>=1.5.0 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (1.7.1)
Requirement already satisfied: networkx>=2.2 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (2.5.1)
Requirement already satisfied: monty>=3.0.2 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (2021.8.17)
Requirement already satisfied: uncertainties>=3.1.4 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (3.1.5)
Requirement already satisfied: requests in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (2.26.0)
Requirement already satisfied: tabulate in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pymatgen==2022.0.16) (0.8.9)
Requirement already satisfied: pyparsing>=2.2.1 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from matplotlib>=1.5->pymatgen==2022.0.16) (3.0.6)
Requirement already satisfied: pillow>=6.2.0 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from matplotlib>=1.5->pymatgen==2022.0.16) (8.4.0)
Requirement already satisfied: kiwisolver>=1.0.1 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from matplotlib>=1.5->pymatgen==2022.0.16) (1.3.2)
Requirement already satisfied: cycler>=0.10 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from matplotlib>=1.5->pymatgen==2022.0.16) (0.11.0)
Requirement already satisfied: python-dateutil>=2.7 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from matplotlib>=1.5->pymatgen==2022.0.16) (2.8.2)
Requirement already satisfied: decorator<5,>=4.3 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from networkx>=2.2->pymatgen==2022.0.16) (4.4.2)
Requirement already satisfied: tenacity>=6.2.0 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from plotly>=4.5.0->pymatgen==2022.0.16) (8.0.1)
Requirement already satisfied: six in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from plotly>=4.5.0->pymatgen==2022.0.16) (1.16.0)
Requirement already satisfied: ruamel.yaml.clib>=0.1.2 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from ruamel.yaml>=0.15.6->pymatgen==2022.0.16) (0.2.6)
Requirement already satisfied: future in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from uncertainties>=3.1.4->pymatgen==2022.0.16) (0.18.2)
Requirement already satisfied: pytz>=2017.3 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from pandas->pymatgen==2022.0.16) (2021.3)
Requirement already satisfied: certifi>=2017.4.17 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from requests->pymatgen==2022.0.16) (2021.10.8)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from requests->pymatgen==2022.0.16) (1.26.7)
Requirement already satisfied: idna<4,>=2.5 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from requests->pymatgen==2022.0.16) (3.3)
Requirement already satisfied: charset-normalizer~=2.0.0 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from requests->pymatgen==2022.0.16) (2.0.8)
Requirement already satisfied: mpmath>=0.19 in d:\programdata\anaconda3\envs\studypymatgen\lib\site-packages (from sympy->pymatgen==2022.0.16) (1.2.1)
Installing collected packages: pymatgen
Running setup.py develop for pymatgen
Successfully installed pymatgen-2022.0.16
~~~
OS: windows 10
Pycahrm: 2021.2.1(Community Edition) 11.0.11 +9-b1504.16 amd64
python == 3.8
What I have done
> 1.Reinstallation follow the link `Setup for Developers (using GitHub)`: https://pymatgen.org/installation.html
Can't solve this problem so far!
|
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| 1,065,172,912
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PR_kwDOACgets4vFsY3
| 2,312
|
Clearer handling of magmom flag
|
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[
"\n[](https://coveralls.io/builds/44615262)\n\nCoverage decreased (-0.6%) to 83.13% when pulling **e6ba47bd4236e6cded188f1bc688e94ed55d03c1 on arosen93:rosen-clarifications** into **dd3737011e76520da1347d5db75db3a3f87e520f on materialsproject:master**.\n",
"This one is good to go. It's just that broken Mac Windows test holding it up.",
"Thanks @arosen93 !"
] | 2021-11-28T03:01:24
| 2021-12-20T19:57:56
|
2021-12-20T19:45:52Z
|
MEMBER
|
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## Summary
### Clearer Handling of Magnetic Moments
I have made a few additional clarifications to `pymatgen.io.vasp.sets`, primarily with regards to the handling of magnetic moments as a follow-up to #2301:
1. Clearer docstrings. This is rather self-explanatory.
2. Only print the warning about low magnetic moments on Co if the value is <= 1. If someone were to modify the default config to have high-spin Co, there is no longer a need for this warning. I had done this, and I found it somewhat bothersome.
3. If the user provides an integer for the magnetic moment, e.g. `site["magmom"] = 1`, then convert this to a float when `get_valid_magmom_struct()` is run. Previously, Pymatgen would crash when creating an `Incar()` object if the structure had an integer magnetic moment due to the lines below. https://github.com/materialsproject/pymatgen/blob/dd3737011e76520da1347d5db75db3a3f87e520f/pymatgen/io/vasp/sets.py#L3102-L3106
### Slight Adjustment to Handling of LASPH Warning
4. Extremely minor, but as a follow-up to #2297, I now check the `Incar()` object (rather than the `settings` variable) to see if `LASPH` is present. This is more robust.
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I_kwDOACgets4_hhBy
| 2,313
|
OPTIMADE Rester cannot find structures
|
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[
"I just tried the query you specified and for me it works.\r\nI ran it from the [binder page](https://mybinder.org/v2/gh/Materials-Consortia/optimade-tutorial-exercises/HEAD?filepath=notebooks%2Fdemonstration-pymatgen-for-optimade-queries.ipynb) of the Optimade tutorial. The pymatgen version I used is 2022.0.16\r\n\r\nPerhaps there was a problem with the internet connexion to the server, or there was another reason the server could not respond at the time.\r\nCould you retry the query to see if the issue is still there?\r\n\r\n ",
"The only way I made it work was to use string operations to build the url's instead of the join function.\r\n\r\n```\r\nurl = resource + f\"/v1/structures?filter={optimade_filter}&{fields}\"\r\n#url = join(resource, f\"v1/structures?filter={optimade_filter}&{fields}\")\r\n```\r\nAnd \r\n```\r\n#url = join(provider_url, \"v1/info\")\r\nurl = provider_url + \"/v1/info\"\r\n```\r\nThis builds strings like 'https://optimade.materialsproject.org/v1/info' instead of 'https://optimade.materialsproject.org\\v1/info'",
"Thanks for reporting this @oarcelus and following up @JPBergsma.\r\n\r\nI can't replicate the issue with the example on my local laptop (macOS), so I suspect it may be a platform-dependent issue related to the behaviour of `join`?",
"Perhaps `urljoin` is the better function to call.",
"Thanks for the inputs @mkhorton, indeed `urljoin` solves the problem in my case.\r\n\r\nFor the record, I am using Python 3.9 in Windows 10, and executing the string from PyCharm Community Edition 2021.2.2."
] | 2021-11-29T08:34:26
| 2021-11-30T08:22:54
|
NONE
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I am trying to use the OPTIMADE Rester. But when running the following lines
`from pymatgen.ext.optimade import OptimadeRester
opt = OptimadeRester('mp')
data = opt.get_structures(elements=['Li','Mn','O'], nelements=[1,3])`
I get the following error messages
> Failed to extract required information from https://optimade.materialsproject.org\v1/info: 'meta'
Could not retrieve required information from provider mp and url https://optimade.materialsproject.org\v1/structures?filter=(elements HAS ALL "Li", "Mn", "O") AND (nelements>=1 AND nelements<=3)&response_fields=lattice_vectors,cartesian_site_positions,species,species_at_sites: 'data'
{}
Process finished with exit code 0
Searching for this same URL's, both for the 'info' and 'structures' endpoints I get the expected responses, so I assume this is a bug of some kind. Is this the case?
|
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I_kwDOACgets4_i5Tj
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`OptimadeRester`: Add ability to request additional response fields
|
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[] | 2021-11-29T14:33:46
| 2021-11-29T21:04:20
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2021-11-29T20:07:13Z
|
CONTRIBUTOR
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We have just run into an issue (https://github.com/Materials-Consortia/optimade-tutorial-exercises/issues/8) where the pymatgen OPTIMADE tutorial fails to pull custom provider fields since #2244 was merged, as this PR (correctly) enforced the response fields required to create pymatgen structures from OPTIMADE responses, to the exclusion of all other fields.
As a quick fix, I suggest adding a `additional_response_fields` argument to the public methods of `OptimadeRester` that are used when constructing the query.
I am happy to knock up a PR if this is desired, but for now we will probably have to remove that section of the pymatgen tutorial.
(paging @mkhorton - the tutorials are now being used for a new workshop, hence the interest)
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PR_kwDOACgets4vIwXX
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Add ability to request additional OPTIMADE fields
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[
"\n[](https://coveralls.io/builds/44604585)\n\nCoverage decreased (-0.6%) to 83.127% when pulling **642431eba9b5d5ca99d2f757cf533036eb0798dc on ml-evs:ml-evs/optimade_response_fields** into **dd3737011e76520da1347d5db75db3a3f87e520f on materialsproject:master**.\n",
"Thanks @ml-evs, this is useful, I appreciate you have this working with the SNL objects too."
] | 2021-11-29T15:59:14
| 2021-11-29T20:07:14
|
2021-11-29T20:07:14Z
|
CONTRIBUTOR
|
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## Summary
Closes #2314 by adding the `additional_response_fields` argument when generating SNLs from OPTIMADE requests.
## 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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| 1,070,117,546
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PR_kwDOACgets4vVleW
| 2,316
|
Add missing elements to MPScanRelaxSet PBE .54 potentials
|
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[
"Since these are all additions not changes, they have my blessing!\r\n\r\nOpen to changes too but would be more discussion required.",
"As long as it doesn't change the workflow I have no objections either. Thanks for the docstring cleanup, too @arosen93 !",
"Great, thanks! I updated the hash accordingly, and it's now ready to be merged.",
"Thanks both!\r\n\r\nI see an unrelated test failure on this PR that will have to be addressed separately so will go ahead and merge."
] | 2021-12-03T01:03:23
| 2021-12-21T07:08:17
|
2021-12-03T17:10:00Z
|
MEMBER
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@rkingsbury and @mkhorton: Some elements that are currently in the VASP PAW .54 PBE library have defined pseudopotentials but aren't in the `MPScanRelaxSet.yaml` file because they never existed in the original PAW PBE set used in the GGA calculations on MP. This change won't influence anything in your R2SCAN workflow because: a) The jobs would have never run with these elements since no pseudopotentials were defined; b) none of these elements exist on MP right now because of the aforementioned statement.
Most of the elements I added have only one PAW PBE potential to use. In the case of multiple, I used the VASP-recommended set.
I know this breaks the hash for `MPScanRelaxSet.yaml`. It would need your blessing.
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I_kwDOACgets4_1Sxx
| 2,317
|
divide by zero encountered in true_divide error
|
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[
"Let me check this but I think it's just a warning that happens for some values of mu in the gap.\r\nDoes the final plot look reasonable?",
"You are right. It's just a warning and the plots are looking reasonable. Thanks :)"
] | 2021-12-03T20:17:46
| 2021-12-07T07:24:22
|
NONE
|
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I'm trying to use boltztrap2 module to plot conductivity, seeback etc but I get following error
```
---/lib/python3.6/site-packages/pymatgen/electronic_structure/boltztrap2.py:810: RuntimeWarning:
divide by zero encountered in true_divide
```
Could you help me to solve this issue?
script I use:
```
from pymatgen.electronic_structure.boltztrap2 import *
from monty.serialization import loadfn
from pymatgen.electronic_structure.plotter import BSPlotter
import matplotlib.pyplot as plt
vrun = Vasprun('vasprun.xml',parse_projected_eigen=True)
data = VasprunBSLoader(vrun)
bs = vrun.get_band_structure()
nele = vrun.parameters['NELECT']
st = vrun.final_structure
data = VasprunBSLoader(bs,structure=st,nelect=nele)
bztInterp = BztInterpolator(data,lpfac=10,energy_range=1.5,curvature=True,
save_bztInterp=True,fname='bztInterp.json.gz')
bztTransp = BztTransportProperties(bztInterp,temp_r = np.arange(300,1300,300), doping=10.**np.arange(16,23),
save_bztTranspProps=True,fname='bztTranspProps.json.gz')
bztPlotter = BztPlotter(bztTransp,bztInterp)
bztPlotter.plot_props('C','mu','temp',temps=[300,600,900], xlim=[-2, 7]).show()
```
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PR_kwDOACgets4vZNlJ
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|
Use f-string automatic string coercion: f"{str(x)}" -> f"{x}"
|
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[
"@shyuep The workflow \r\n\r\n```sh\r\npytest pymatgen/electronic_structure pymatgen/symmetry pymatgen/ext pymatgen/command_line\r\n```\r\n\r\ntimed out on Windows and macOS. There is no error, just that the operation was cancelled. Does this require fixing or is it a flaky test?",
"@shyuep Just resolved the merge conflicts here. Could you trigger a workflow run? Not sure why it didn't auto-trigger.",
"This caused test failures. I t hink it is not in line with the master branch. Pls resubmit after you have pull the latest from master.",
"Why merge and then revert? I did merge `master` just before I wrote that comment 3 days ago.",
"Because I merged and it caused all kinds of test failures. Pls merge master and resubmit a new PR.",
"Weird that it didn't trigger CI. But definitely should have checked its result before merging. Perhaps worth adding [`workflow_dispatch`](https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows#workflow_dispatch) to all CI tests to be able to trigger runs manually in cases where they fail to run automatically.\r\n\r\n"
] | 2021-12-04T17:45:18
| 2022-01-15T15:40:12
|
2022-01-12T19:20:28Z
|
MEMBER
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Related #2294.
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I_kwDOACgets4_9OsF
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Boltztrap2 module for 2D systems
|
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[
"I never used it for 2D systems. I think some changes are needed.\r\nPlease, have a look at BoltzTraP forum, this topic has been discussed multiple times in depth:\r\nhttps://groups.google.com/forum/#!forum/boltztrap"
] | 2021-12-07T07:34:14
| 2021-12-07T17:00:45
|
NONE
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Hi,
I'm using bolztrap2 module to compute thermoelectric coefficients of the 2D systems. Can I use straightforwardly this module for 2D systems if not what kind of changes do I need to make? For example, I generated the following plot for the WSe2 monolayer. Do I just need to change the unit (cm^-3 to cm^-2) here or is the plot is also wrong since my system is 2D?
A few more questions?
1. Is Hall carrier concentration implementation is reliable for 2D systems?
2. Is the unit of the conductivity that script generates same for 2D systems?
Thanks in advance
|
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Absorption
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[
"Thanks for opening this PR @yang-ruoxi!\r\n\r\nSince you're a new contributor, I have to manually approve the automatic tests. These should now be running.",
"Overall this looks good!\r\n\r\nThe main thing this is lacking right now is tests. You may be able to copy a test from the existing input sets (see `test_sets.py`) as a starting point. It would just need to test the main features of the input set, e.g. the `IPA` and `RPA` modes.\r\n\r\nThe other comment would be for `MPAbsorptionSet.yaml`, if it's only a few edits to the `MPRelaxSet.yaml` it would be better to make those changes inside `MPAbsorptionSet.__init__` so that you can inherit all the other settings from `MPRelaxSet.yaml`. The benefit of this approach is that if `MPRelaxSet.yaml` _does_ change in future, `MPAbsorptionSet` will automatically remain consistent.",
"* added AbsorptionSetTest and the corresponding test files ",
"\n[](https://coveralls.io/builds/50542160)\n\nCoverage decreased (-20.5%) to 63.581% when pulling **95cb764aa6f214c778f798250b7b1c96d9d11081 on yang-ruoxi:absorption** into **f61869ed20f942c00e7ba592d44ca5338ffbbb2f on materialsproject:master**.\n",
"Thanks @yang-ruoxi !"
] | 2021-12-08T04:42:11
| 2022-07-01T23:44:50
|
2022-07-01T23:44:40Z
|
MEMBER
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## Summary
* Added optical absorption input set for independent-particle approximation (IPA) and random-phase approximation (RPA), expected to be used with AbsorptionFW in atomate
* Added the AbsorptionSet.yaml for the default input set (IPA)
* Two modes are possible to choose from: IPA or RPA
* If IPA is chosen, it is assumed a previous 'ALGO = Normal' calculation needs to be done with the WAVECAR saved. This IPA calculation will use the previous WAVECAR, and set 'ALGO = Exact' and 'LOPTICS = TRUE' with a large number of NBANDS. One obtains the macroscopic frequency dependent dielectrics. Normally only `nbands_factor` is expected to be modified rather than directly modifying the `nbands`.
* If RPA is chosen, it is assumed an IPA calculation has to be done before hand with WAVECAR and WAVEDER saved.
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| 1,074,165,909
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I_kwDOACgets5ABniV
| 2,321
|
Pourbaix diagram is missing compounds
|
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[
"https://matsci.org/t/materials-project-database-release-log/1609/18\r\n\r\nUpgrading the pymatgen version from 2020.1.10 to 2022.0.16 worked.\r\n\r\n\r\n",
"Thanks for sharing your resolution @CFRP-07 !"
] | 2021-12-08T08:59:39
| 2021-12-08T19:28:25
|
2021-12-08T09:59:11Z
|
NONE
|
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Hello,
I am new to pymatgen and am trying to reproduce the Pourbaix diagram from the website in python. However, the plot seems to be missing some compounds and I can not figure out why.
Is it possible to resolve this?
Thanks!
My code:
`# Import necessary tools from pymatgen`
`from pymatgen import MPRester`
`from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, PourbaixPlotter`
`# Initialize the MP Rester`
`mpr = MPRester('MY-API-KEY')`
`# Get all pourbaix entries corresponding to the Fe-O-H chemical system.`
`entries = mpr.get_pourbaix_entries(["Fe", "Cu"])`
`# Construct the PourbaixDiagram object`
`pbx = PourbaixDiagram(entries, comp_dict={"Fe": 0.5, "Cu": 0.5},
conc_dict={"Fe": 1e-8, "Cu": 1e-8}, filter_solids=True)`
`# Construct the pourbaix analyzer`
`plotter = PourbaixPlotter(pbx)`
`plt = plotter.get_pourbaix_plot()`
`plt.show()`
Generated plot:
Plot from materials project website:
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| 1,074,997,696
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I_kwDOACgets5AEynA
| 2,322
|
Finish Wyckoff functionality in cif parsing/writing
|
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[] | null |
[
"You can use the SpaceGroupAnalyzer.get_symmetrized_structure to get the Wyckoff symbols.",
"I think this issue is more about propagating metadata already existing in the CIF, i.e. for Wyckoff symbols that have already been annotated, these could be parsed as site properties.",
"Yes, indeed the get_symmetrized structure works well if I want to find the Wyckoff symbols using spglib but as @mkhorton suggested, I desire to propagate existing metadata in CIFs produced by AFLOW's prototypying code.",
"As far as I know, that information is not parsed today. But if someone wants to take a crack at it, I am happy to include it.",
"Sounds good. I might try my hand in the coming months."
] | 2021-12-09T01:13:57
| 2022-01-12T22:32:37
|
CONTRIBUTOR
|
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**Is your feature request related to a problem? Please describe.**
I would like to use Pymatgen's wonderful structure manipulation functionality but cif parsing/manipulating/rewriting pipeline in Pymatgen doesn't preserve the wyckoff letters and multiplicities. I see in the code that it's planned for implementation in `site_properties`, that would be great.
**Describe the solution you'd like**
Parse wyckoff letters and multiplicities from cifs and write them to cifs.
|
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| 1,083,489,197
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PR_kwDOACgets4wA_cl
| 2,323
|
Add new automatic kpoint scheme that normalizes by lattice lengths
|
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[
"This one is good to go. It's just that broken Mac Windows test holding it up.",
"Many thanks for this @arosen93! Will be investigating failing tests shortly"
] | 2021-12-17T17:54:37
| 2022-01-07T00:58:16
|
2022-01-06T22:45:36Z
|
MEMBER
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## Summary
This PR creates a new automatic k-point generation scheme, `automatic_density_by_lengths`, which allows the user to specify a density of k-points in each dimension (rather than just for the entire volume). This is particularly important for slab calculations, because you almost always want 1 k-point in the vacuum dimension but don't want the vacuum space volume to influence your k-point generation otherwise.
For instance, doing `automatic_density_by_lengths(struct, [50, 50, 1])` would specify a k-point density of 50/a x 50/b x 1/c, with each rounded up to the next integer.
This is a more general implementation of the k-point scheme used in `MVLSlabSet` (reproduced below) and can be found in several papers from the Persson group, such as [this one](https://www.nature.com/articles/s41467-019-08356-1#Sec7).
https://github.com/materialsproject/pymatgen/blob/fcb84a1e129da3a3010b9f6b9cf18beddf39f245/pymatgen/io/vasp/sets.py#L2213-L2244
Tagging @oxana-a, @mhsiron in case they're curious.
|
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PR_kwDOACgets4wCdv0
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Pass magmoms and selective dynamics between ASE Atoms and Pymatgen Structure in ASEAtomsAdaptor
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[
"This one is good to go. It's just that broken Mac Windows test holding it up (although somehow one of the commits passed magically!).\r\n\r\nEdit: Made some improvements but still good to go now!",
"Thanks!"
] | 2021-12-18T22:40:52
| 2022-01-07T00:58:13
|
2022-01-06T22:47:07Z
|
MEMBER
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Currently, the `pymatgen.io.ase.ASEAtomsAdaptor` does not pass the magnetic moments or selective dynamics tags between the ASE `Atoms` and Pymatgen `Structure` objects (in either direction). As an example of where this came up for me recently, I was using the `mp_api` to fetch `Structure` objects from MP. When I convert them to ASE `Atoms` objects, they lose their magnetic moment site properties. It's not too hard to fix, so here it is.
This PR enables the passing back and forth of these site properties. Tests have been added. I also fixed the test `POSCAR` file, which had the wrong formula string at the top. This caused problems when comparing the ASE `Atoms` object and Pymatgen `Structure` object.
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I_kwDOACgets5Ar2Qv
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VASP Input Sets: Investigate LMAXTAU
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[
"Notifying @rkingsbury too as likely relevant for SCAN input sets.",
"Just to clarify for my own notes too: This is really only relevant if `LAPSH = True`.",
"Thanks @mkhorton ; if you change the SCAN sets just please make sure to check if any validation rules in the validation builder need to change (I don't think they do).",
"@munrojm, @janosh: We should probably consider updating this in the Atomate2 workflow......",
"The fix for this can ultimately be adapted from the relevant part in the Atomate2 PR: https://github.com/materialsproject/atomate2/pull/362",
"Apparently there is plenty of ambiguity about this... https://www.vasp.at/forum/viewtopic.php?p=23038. I would lean towards closing this issue as a result. If Kresse says it's fine, then I'm inclined to believe him.",
"We removed the the `_set_lmaxtau` helper entirely in https://github.com/materialsproject/atomate2/pull/362/commits/75c43baab2a3d3caa680da0892fcf7733b7c1bd9 in an attempt to fix this VASP error\r\n\r\n```txt\r\n -----------------------------------------------------------------------------\r\n| _ ____ _ _ _____ _ |\r\n| | | | _ \\ | | | | / ____| | | |\r\n| | | | |_) | | | | | | | __ | | |\r\n| |_| | _ < | | | | | | |_ | |_| |\r\n| _ | |_) | | |__| | | |__| | _ |\r\n| (_) |____/ \\____/ \\_____| (_) |\r\n| |\r\n| internal error in: asa.F at line: 479 |\r\n| |\r\n| internal error in YLM3LOOKUP: L or LP > LMAXCG |\r\n| L, LP, LMAXCG 7 1 6 |\r\n| |\r\n| If you are not a developer, you should not encounter this problem. |\r\n| Please submit a bug report. |\r\n| |\r\n -----------------------------------------------------------------------------\r\n```",
"@janosh: Let's close this as being not needed."
] | 2021-12-20T21:55:48
| 2023-09-03T19:42:38
|
2023-09-03T19:42:38Z
|
MEMBER
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Thanks @arosen93:
> If the PAW one-center expansion of the density has component up to L, then the one-center expansion of the kinetic energy density has components up to L+2. This means that as a rule of thumb, for s-elements: LMAXTAU=2, for p: LMAXTAU=4, and for d: LMAXTAU=6. If you are willing to live with the computational costs, the default for LMAXTAU ***should be safe in all cases, except those involving f-elements.*** [emphasis mine]
via https://www.vasp.at/wiki/index.php/LMAXTAU
Will likely add appropriate logic to appropriate VASP input sets.
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I_kwDOACgets5A5hxq
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get_conventional_standard_structure strips the structure of all site properties
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[
"Closing because of the discussion in #2330. "
] | 2021-12-26T18:28:14
| 2022-01-07T22:33:56
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2022-01-07T22:33:56Z
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MEMBER
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When using `pymatgen.symmetry.analyzer.SpacegroupAnalyzer`'s `get_conventional_standard_structure()`, all site properties in the pymatgen structure object (e.g. magnetic moments) are stripped.
Importantly, this also means that when using the MP API, doing `mpr.get_structure_by_material_id(mp_id, conventional_unit_cell=True)` does not return a structure with site properties.
Note: I think the issue is that when `get_refined_structure()` is called in `get_conventional_standard_structure()`, the site properties aren't re-introduced after the call to spglib [here](https://github.com/materialsproject/pymatgen/blob/2aeb9845102cae9bbc466a52d71f9df3ca28cad4/pymatgen/symmetry/analyzer.py#L305).
```python
from pymatgen.core import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
# Build structure
struct = Structure(
lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
species=["Mg", "O"],
coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
)
struct.add_site_property("magmom",[3.14]*len(struct))
# Test conventional cell transform
conventional_struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
print(conventional_struct.site_properties.get("magmom",None))
# ^ The above returns None
```
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I_kwDOACgets5A8jTw
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Group numbers for the lanthanides and actinides are strange
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[
"Thanks. Feel free to propose a conventional and implement a change. For me, group numbers don't really make any kind of sense of the TM and rare earth series. If you are planning to use it for ML purposes, I would say group number is probably one of the worst choices you can use. I for one don't believe the large body of work out there that utilizes this kind of features for ML.",
"tl;dr -- @shyuep: **Do you have a strong opinion on Option 1 vs. Option 2 below**?\r\n\r\nI definitely agree with you re: group number being used as a descriptor for ML. Besides, it's often highly correlated with many other properties anyway.\r\n\r\nMore simple than ML though, one might query a database of pymatgen structures for all entries containing halogens. If they did this query by looking for any structures with group 17 elements, Lu and Lr would unexpectedly come up too. \r\n\r\nTo back up what I'm going to suggest, here are a few points:\r\n- IUPAC understandably makes no explicit statement on the group number.\r\n- Currently, in pymatgen La and Ac are group 3 whereas Lu and Lr are group 17. However, Lu and Lr are more group-3-like than La and Ac, as argued [here](https://pubs.acs.org/doi/10.1021/ed059p634), so this is a point that should be resolved in a proposed change.\r\n- The lanthanoids and actinoids share common chemistry and should, in my view, not have different group numbers. \r\n\r\nWith the above points, the only solutions I can think of are:\r\n1. All lanthanoids and actinoids are in group 3.\r\n2. All lanthanoids and actinoids are in a ficticious group 19, which would be mentioned in the documentation.\r\n3. All lanthanoids and actinoids are not in group 3 but have `None` as the group number. This will likely pose a problem for down-stream ML tasks (even if it's not a preferred feature), and for this reason I do not advise it.\r\n4. Lu and Lr are in group 3, but the remaining lanthanoids and actinoids have `None` as the group number. Again, same problem as Option 3. For reference, this is what English language Wikipedia has decided upon.",
"I don't have a strong opinion, but I would note that the group is used to generate the periodic table layout. I don't mind them having an effective group number of 3. In any case, I wouldn't have used group 17 for halogens but rather specify the exact set of element (F, Cl, Br, I).",
"Closed in #2343."
] | 2021-12-28T05:06:01
| 2022-02-02T05:18:01
|
2022-02-02T05:18:00Z
|
MEMBER
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When accessing the `.group` property of a `specie` that is a lanthanide or actinide, the returned group number is quite unconventional. For instance, the group number for Yb is 16. For Lu it's 17. While there is certainly debate to be had around the group numbers for the lanthanides and actinides, I don't believe this choice would ever be considered one of the [conventional options](https://www.chemeurope.com/en/encyclopedia/Group_number_of_lanthanides_and_actinides.html).
```python
from pymatgen.core import Structure
struct = Structure(lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],species=["Yb", "O"],coords=[[0, 0, 0], [0.5, 0.5, 0.5]])
print(struct[0].specie.group)
# ^outputs 16
```
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Battery Analyzer for Anion Batteries
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[
"This sounds great."
] | 2021-12-29T22:48:11
| 2022-01-31T22:05:01
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2022-01-31T22:05:01Z
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CONTRIBUTOR
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Hello,
Currently, the pymatgen.apps.battery.analyzer module only can handle cation batteries, but there are several emerging battery chemistries with a negatively charged working ion, such as fluoride or chloride. I have some spare time in the next week, so I'll try to update the module to work for anion batteries in the same way as it currently does for cations. I think it will be pretty straight-forward, but please let me know if there are any special considerations to be aware of before I get the pull request ready.
Thanks
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Battery analysis for anion batteries [WIP]
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[
"@sthartman, I'm having the same issue with the test suite via GitHub Actions. I don't think it's due to any changes you introduced. (cc @mkhorton, this is a different one than before).",
"Hi @sthartman , I recently made sure all the tests are properly passing. Can you merge the latest master into your PR first? That should trigger a new test.",
"\n[](https://coveralls.io/builds/45605881)\n\nCoverage decreased (-0.6%) to 83.184% when pulling **2e0b63123c6ad6118fdf22a73dd9eaa658ea7c58 on sthartman:master** into **e115bda06170aa74d9f09a04fcd0867580505a71 on materialsproject:master**.\n",
"Thanks @shyuep, all the checks pass now. Let me know if the reduced coverage is an issue, I could make some more tests to get the other branches.",
"Great. Thanks. The slgihtly reduced coverage is not a big issue."
] | 2022-01-02T23:36:39
| 2022-01-13T16:56:18
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2022-01-13T16:56:18Z
|
CONTRIBUTOR
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## Summary
#2328
* Battery analysis now handles working ion with negative charge
* Added appropriate tests
## TODO (if any)
Pytest run from the command line finds no errors in the pymatgen/apps directory, where I made the changes, but I still need to figure out why the build as a whole is failing.
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Keep site properties after calling spglib in get_refined_structure() and find_primitive()
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[
"How does this work with magnetically ordered structures @arosen93? e.g. the primitive structure may not be large enough to retain the magnetic ordering from the input structure",
"@mkhorton:\r\n\r\nIn this PR, the site properties are carried over to any symmetrically equivalent site in the refined or primitive structure. However, the question you raised about longer range magnetic ordering is interesting to consider. I believe this is accounted for in `spglib`. \r\n\r\nAs you can see below, the `_cell` property is populated with the magnetic moment information:\r\nhttps://github.com/materialsproject/pymatgen/blob/4ae7d1b8013274b6848f09474839704890f4014a/pymatgen/symmetry/analyzer.py#L83\r\n\r\nWhen spglib is called, it should take into account the magnetic information when generating the primitive or refined unit cell: see [here](\r\nhttps://github.com/spglib/spglib/blob/0d2a1a50cdbd3413931b1376607b0fd1d83505ae/python/spglib/spglib.py#L93-L97).\r\n\r\nWhile worthwhile to consider, I don't think it matters all that much for this PR. The site properties are what they are -- not necessarily an expression of the ground truth. Sure, it's possible for new magnetic orderings to open up or be removed when the unit cell size is changed, but the site properties (e.g. as computed from VASP) are still valid.\r\n\r\n(The recent test issues are plaguing this PR as well, I should note)",
"@mkhorton, ah, do you mean the magnetic ordering site property specifically? I'm not too familiar with that one. Perhaps that shouldn't necessarily be carried over after the call to `spglib`. Instead of transferring all site properties, we could do just the `magmom` (and the `selective_dynamics`?) or we could just strip out any of the magnetic ordering site properties as a note of precaution. Do you have a preferred approach?",
"No, I do mean the `magmom` site property.\r\n\r\ne.g., consider a cell with two magnetic sites, one with a magmom +5, another with a magmom -5. Calling `get_primitive()` may return a cell with only a single magnetic site, but with what magmom value?",
"Thanks for the example. I see your point now.\r\n\r\nI was under the impression that `spglib` would not return a primitive cell in this case because of the provided magnetic character. This is perhaps worth a direct investigation to confirm. I'll put it on the to-do list.",
"My understanding is that spglib's treatment of magnetism is fairly basic. I believe there's some discussion on the spglib mailing list about this.\r\n\r\nFor our case, if we respect the magnetic moments (magmom) but pass them along as-is, but they're noisy (as they would be from VASP), then it would mean the returned primitive structure is likely incorrect. It's a tricky situation.",
"I see. Yes, that does add some complications to think about. \r\n\r\nIf we focus on `get_refined_structure()`, which itself is used in `get_conventional_standard_structure()`, does the same concern apply? For instance, if I have a one atom primitive cell with a magnetic moment of 5 and then make a conventional cell that has two atoms, they both would have magnetic moments of 5. Of course, in reality, the real magmoms might be [-5, 5], but that's a separate issue. I don't think there's any information loss this way, right? There's only information loss when making the primitive? If so, then maybe it makes sense to only pass properties for the `get_refined_structure()`.\r\n\r\n[Correct me if I'm wrong, of course. Trying to think about this visually].",
"Yes, it's not immediately obvious to me what the correct answer is here. For the refined structure, unfortunately the same logic applies I think (eg if getting the conventional crystallographic structure of a magnetically-ordered supercell, AFM NiO is the good test case here).",
"Ah, you're totally right. Good example. I don't think there is a satisfying solution in the end. Feel free to close this if you wish! I think it's somewhat of an ill-defined problem, unfortunately.",
"Ok, I'll close for now, but I am in favor of addressing this if we can find a good solution (and include appropriate tests for some of these tricky cases). I don't think you're the only person who's been tripped up by this.",
"Also my apologies for the work spent on this PR since we're not merging, but hopefully it can help someone pick up from here in the future.",
"Not at a problem at all! You brought up some important points, and it didn't take too long to do anyway.",
"@mkhorton: This has still been in the back of my mind, and I wanted to ask -- would a possible middle-ground solution be to provide an optional keyword argument that keeps the site magmoms where they are (just based on whatever spglib decides to do with the transformation)? You're right that there are edge-cases where we don't want to do this in general, but there are also a lot of systems where it would be perfectly fine.\r\n\r\nThe reason why I think something like this would be helpful is that if one is screening a large number of materials (e.g. from MP), a common approach is to take the converged magnetic moments and use those as the MAGMOM guess for downstream calculations. That's not possible if you need to convert the MP unit cell to a conventional cell in your workflow. The best option is to recalculate magnetic moments (naively with some trivial spin initialization or more exhaustively using the magnetic moment workflow), but this is time-consuming. A middle-ground solution, which is imperfect, is to just keep the magnetic moments on the atoms as they are from spglib. Sure, for antiferromagnetic NiO, it poses a problem. But for ferromagnetic bulk Fe, for example, it's perfectly fine.",
"Sure, I think that would be reasonable. Let's just make sure the docstring is explicit to warn users about caveats.",
"Sounds good! Thanks for the very helpful discussion. "
] | 2022-01-04T02:01:41
| 2022-01-14T21:56:16
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2022-01-07T18:24:35Z
|
MEMBER
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In `pymatgen.symmetry.analyzer.SpacegroupAnalyzer`, the `get_refined_structure()` and `find_primitive()` functions both strip Pymatgen structure objects of all their site properties, including magnetic moments. This PR carries over the site properties after calling `spglib`. Test have been added.
Addresses #2326.
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problem for "pymatgen.io.vasp.Poscar"
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[
"Pls provide the actual text POSCAR in the issue report. Giving an image is very difficult for me to try to reproduce the error.",
"> Pls provide the actual text POSCAR in the issue report. Giving an image is very difficult for me to try to reproduce the error.\r\n\r\nHere is my POSCAR file.\r\n\"\r\nCs1 Pb1 Br3\r\n1.0\r\n6.022257 -0.003742 -0.008211\r\n-0.024789 6.018620 0.014154\r\n0.008111 0.018091 6.002165\r\nCs Pb Br\r\n1 1 3\r\ndirect\r\n0.515001 0.498256 0.486467 Cs\r\n0.021258 -0.001505 -0.000947 Pb\r\n0.004667 0.002804 0.492459 Br\r\n-0.002320 0.516228 0.008898 Br\r\n0.497373 -0.006585 0.008383 Br\r\n\"\r\n\r\nHere is my code. As you can see, it is very simple code. but it doesn't work.\r\n\r\n``` python\r\n!pip install pymatgen==2020.11.11 # you need to install pymatgen in googlecolab using this command!\r\n \r\n# my code\r\nfrom pymatgen.io.vasp import Poscar\r\nposcar = Poscar.from_file('POSCAR') # in this part, the error occurs.\r\ncrystal = poscar.structure\r\ncrystal \r\n```",
"I can't reproduce this error. It actually works on my end. As for googlecolab, since I don't use that platform, I can't really test it out on there. As far as I can see, all the unittests indicate the code is functioning as it should and on my end, running your code works.",
"> I can't reproduce this error. It actually works on my end. As for googlecolab, since I don't use that platform, I can't really test it out on there. As far as I can see, all the unittests indicate the code is functioning as it should and on my end, running your code works.\r\n\r\nReally??. Oh. Thank you. maybe it is about the problem in googlecolab.\r\nI appreciate for your kind answer"
] | 2022-01-07T06:06:35
| 2022-01-09T11:25:09
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2022-01-08T16:32:37Z
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NONE
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Hi. I have found (probably) **Parsing Error** in the conversion process from "POSCAR" to "structure"
I wanted to convert my POSCAR file to structure object in pymatgen.
but there's something wrong in the library or my code.
Here is my situation
As you see, there is a vasp calculation directory containing **POSCAR** file which is standard format of the VASP.
and this code was available in january 5, 2020. in the **Googlecolab** environment.
But today, when I rerun the same code, the error that I did not see occurs.
I think there's something wrong in the **sre_parse.py** code.
I would really appreciate if you help me.
|
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I_kwDOACgets5BV8cd
| 2,332
|
Building will fail for Python 3.10
|
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[
"@chc273 Can you look into this?",
"@shyuep on it.",
"@shyuep This is mostly a Cython version issue. The older Cython generated the C code that does not work with python 3.10. It should have been fixed by your commits yesterday 40c1ff014908a08f11af05f58b252f8764df5bf7 \r\n\r\nI have tested on Ubuntu 20.04.3 LTS with a new python 3.10 conda env. I was able to build the cython code without problem. \r\n\r\n",
"Additionally, it seems that pip of python 3.10 does not find scipy 1.7.1 on my mac and ubuntu, changing https://github.com/materialsproject/pymatgen/blob/0ac6a086d248467a95f635d97ba6db377c9d0b7a/requirements.txt#L6 to 1.7.3 makes it work.",
"@sphuber I have confirmed that everything works fine but Boltztrap is still not compatible with 3.10. That's an optional dependency."
] | 2022-01-07T12:23:29
| 2022-01-08T22:53:47
|
2022-01-08T22:53:47Z
|
NONE
|
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**Describe the bug**
Building fails for Python 3.10 because the `pymatgen/optimization/neighbors.c` uses an undocumented struct member `use_tracing` that was removed. See this issue for reference: https://bugs.python.org/issue43760
I know that the package does not officially state support for Python 3.10, but wanted to give the heads-up.
**To Reproduce**
Try to build the package with Python 3.10 which should show the following stack trace (only last part pasted for clarity)
```
....
pymatgen/optimization/neighbors.c:25711:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘use_tracing’; did you mean ‘tracing’?
25711 | tstate->use_tracing = (tstate->c_profilefunc ||
| ^~~~~~~~~~~
| tracing
pymatgen/optimization/neighbors.c:25716:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘use_tracing’; did you mean ‘tracing’?
25716 | return tstate->use_tracing && retval;
| ^~~~~~~~~~~
| tracing
error: command '/usr/bin/gcc' failed with exit code 1
----------------------------------------
ERROR: Failed building wheel for pymatgen
```
**Desktop (please complete the following information):**
- Verified on Ubuntu 20.04
|
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I_kwDOACgets5BWGOh
| 2,333
|
Build broken on Python 3.8
|
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[] | null |
[
"Thanks. Indeed there are some really annoying crap happening with numpy binary compatibility between versions. For now, I have followed your recommendation to increment the numpy version.",
"Quick update that a new version of pymatgen was released which should fix these problems for now.",
"Thanks for the release and the update.",
"Thanks again for the quick action on this @shyuep but I am afraid this fix won't help. The real problem is when `pymatgen` is compiled with a more recent version of `numpy` and then is used with an older version. Since `pymatgen` doesn't specify an explicit version to build with in its `pyproject.toml`, it will automatically pick the latest. This is why things started failing when `numpy=1.22.0` was released on December 31. This now means that `pymatgen` builds can _only_ be run with `numpy==1.22.0` even though it is compatible with older versions as well.\r\n\r\nThis is a common problem and a common solution exists. One merely has to specify the minimum supported `numpy` version in the `[build]` section of the `pyproject.toml`. This works because `numpy` does guarantee forwards compatibility, so if you compile with an older version of `numpy` you _can_ run with a newer one, but not vice versa. The only problem of this approach that it puts a bit of a burden to keep these versions up to date in the `pyproject.toml`, however, there is a solution for this as well. Simply install the [`oldest-supported-numpy`](https://pypi.org/project/oldest-supported-numpy/) meta-package in the `pyproject.toml` and it will be done automatically.",
"But a minimum numpy version actually is specified in the pyproject.toml. It is not 1.22.0. ",
"Yes, but it shouldn't specify a _minimum_ version, but an _exact_ version, and ideally the lowest version that `pymatgen` supports. So if the current version of `pymatgen` is still compatible with `numpy==1.17.0` and up, you specify `numpy==1.17` in the build requirements.\r\n\r\nYou _can_ specify `numpy==1.21.4` for example, but than that would only ever be compatible with `numpy>=1.21.4` even though `pymatgen` could very well be compatible with older versions.\r\n\r\nSo to prevent all of these problems and be as loose as possible with restrictions, you should specify something like the following\r\n```toml\r\n[build-system]\r\nrequires = [\r\n \"wheel\",\r\n \"setuptools\",\r\n \"numpy==1.13.3; python_version=='3.5'\",\r\n \"numpy==1.13.3; python_version=='3.6'\",\r\n \"numpy==1.14.5; python_version=='3.7'\",\r\n # more numpy requirements...\r\n]\r\n```\r\nBut this can all be simplified by using the `oldest-compatible-numpy` meta-package to:\r\n```toml\r\n[build-system]\r\nrequires = [\"wheel\", \"setuptools\", \"oldest-supported-numpy\"]\r\n```"
] | 2022-01-07T13:20:22
| 2022-01-12T11:16:30
|
2022-01-07T17:34:44Z
|
NONE
|
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Building `pymatgen` on Python 3.8 currently seems broken, see for example [this recent action](https://github.com/materialsproject/pymatgen/runs/4733023541?check_suite_focus=true) on the `master` branch. The problem seems to be the well-known incompatibility of the `numpy` package used for building and the one used when running the tests, resulting in the exception:
```
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
```
I expect this has to do with the release of `numpy==1.22` about a week ago.
Recent comments [in this issue on `numpy`](https://github.com/numpy/numpy/issues/18709) suggest that the requirement of `numpy>=1.20.1` in `pymatgen`'s `pyproject.toml` have something to do with it and changing this to `numpy>=1.20.3` seems to alleviate the problem.
That being said, maybe using the [`oldest-supported-numpy`](https://pypi.org/project/oldest-supported-numpy/) meta-package in the `pyproject.toml` may be preferable and more robust a solution to prevent these problems from occurring in the future.
|
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| 1,096,719,827
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I_kwDOACgets5BXp3T
| 2,334
|
Invalid documentation in generate_all_slabs() for tol parameters
|
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[] | 2022-01-07T22:33:18
| 2022-01-15T06:57:01
|
2022-01-15T06:57:01Z
|
MEMBER
|
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**Describe the bug**
In the documentation below for `pymatgen.core.surface.generate_all_slabs()`, the description for the `tol` kwarg is incorrect. That description should be associated with the `ftol` kwarg. The `tol` kwarg is related to the symmetry (e.g. primitive cell search) tolerance. There is no docstring for the `ftol` kwarg.
https://github.com/materialsproject/pymatgen/blob/325269bf0db30aaea8caf7db6d98d161e7ec97a5/pymatgen/core/surface.py#L1771-L1773
I can open a PR when I get a spare moment.
|
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| 1,097,946,347
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PR_kwDOACgets4wvIL8
| 2,335
|
Corrected and Extended IO for Quantum Espresso Input Files
|
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[] | null |
[
"\n[](https://coveralls.io/builds/45494507)\n\nCoverage decreased (-0.6%) to 83.183% when pulling **2a0ec0e09641ac6c10bdc241f0279913cf1ab7ae on vorwerkc:qe-io** into **fb7706ce15913fd480daeb802b62ff73a408cefc on materialsproject:master**.\n",
"Great. Many thanks for the contribution!"
] | 2022-01-10T14:10:17
| 2022-01-10T15:10:57
|
2022-01-10T14:51:01Z
|
CONTRIBUTOR
|
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## Summary
This merge request fixes the parsing of QE input files. The previous code was based on an outdated QE code format, expecting curly brackets in the definition of CELL_PARAMETERS and ATOMIC_POSITIONS. The merge request adds a new test for the pymatgen.io.pwscf.PWInput.from_string function.
Additionally, the code now allows for to produce QE input files with various kpoints modes.
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PR_kwDOACgets4wwNn_
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Mixing Scheme
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[
"@mkhorton could you please re-trigger the tests? It appears the only failure is coming from XAS and if I understood you correctly, that should be fixed now?\r\n\r\n```\r\n___________________________ XASTest.test_stitch_l23 ____________________________\r\n\r\nself = <xas.tests.test_spectrum.XASTest testMethod=test_stitch_l23>\r\n\r\n def test_stitch_l23(self):\r\n self.l2_xanes.y[0] = 0.1\r\n with warnings.catch_warnings(record=True) as w:\r\n warnings.simplefilter(\"always\")\r\n XAS.stitch(self.l2_xanes, self.l3_xanes, 100, mode=\"L23\")\r\n> self.assertEqual(len(w), 6)\r\nE AssertionError: 5 != 6\r\n\r\npymatgen/analysis/xas/tests/test_spectrum.py:105: AssertionError\r\n```",
"I've re-triggered the tests, but may be worth merging from main branch again just in case. I see you did this yesterday.",
"Thanks! I did a git pull right before posting the comment today, but there\nappeared to be no changes.\n\nOn Tue, Jan 11, 2022 at 11:43 AM Matthew Horton ***@***.***>\nwrote:\n\n> I've re-triggered the tests, but may be worth merging from main branch\n> again just in case. I see you did this yesterday.\n>\n> —\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/2336#issuecomment-1010302351>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AAOR7VZ5K2NOARQJVGHY24DUVSB6DANCNFSM5LUOCTRQ>\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",
"I have not been able to reproduce this failing test, and other PRs are passing successfully. Can you try merging from the main branch again?",
"Done @mkhorton ; thanks for investigating. I can reproduce the failure locally; it only occurs on this branch and not on my local main branch. The question now is why? I can investigate but am not familiar with the XAS code. Do you have any thoughts on why/how `XAS.stitch` would be interacting with `ComputedEntry`?",
"> Done @mkhorton ; thanks for investigating. I can reproduce the failure locally; it only occurs on this branch and not on my local main branch. The question now is why? I can investigate but am not familiar with the XAS code. Do you have any thoughts on why/how `XAS.stitch` would be interacting with `ComputedEntry`?\r\n\r\nNevermind, found the problem; it was the changes in `StructureMatcher` (replacing np.bool and np.int with bool and int). Not sure why, but I reverted those and the test passes locally.",
"\n[](https://coveralls.io/builds/45637015)\n\nCoverage decreased (-0.5%) to 83.306% when pulling **89ebf076116a718a94c0be46671e5eae4be9cc9b on rkingsbury:scan-mixing-new** into **7672ea67b0434c2cb8422c3bb63ad6ae203c71bc on materialsproject:master**.\n",
"> Nevermind, found the problem; it was the changes in `StructureMatcher` (replacing np.bool and np.int with bool and int). Not sure why, but I reverted those and the test passes locally.\r\n\r\nThere are a bunch of numpy warnings about `np.bool` and `np.int` being deprecated throughout pymatgen that are pretty annoying for unit testing. I tried to change them all over in pymatgen the other day but gave up...",
"Yes--how a type hint change could cause a test failure in XAS I have no idea too. Anyway, separate issue to this PR which looks good, thank you!",
"CONGRATS, @rkingsbury!!!!!! ",
"> Yes--how a type hint change could cause a test failure in XAS I have no idea too. Anyway, separate issue to this PR which looks good, thank you!\r\n\r\nThanks @mkhorton ! To clarify, it wasn't the type hint but rather the change from `np.bool` and `np.int` to `bool` and `int`, respectively, in `StructureMatcher` that caused the XAS failure. Maybe a floating point precision issue or something? Not sure; I just know there are a ton of warnings about using the numpy types in pymatgen as @arosen93 said.",
"Thanks for the excellent test coverage for new features here too, definitely an example :)",
"Ahhh, nothing like merging a big PR on a Friday afternoon to close out the workweek 😄 ☺️ "
] | 2022-01-10T19:17:37
| 2022-01-14T22:48:05
|
2022-01-14T22:45:12Z
|
CONTRIBUTOR
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## Summary
Implementation of the SCAN / GGA(+U) mixing scheme. Mixing scheme code lives in the new file `mixing_scheme.py` and is implemented as a `Compatibility` class.
In addition to the core mixing scheme, this PR contains the following minor supporting changes:
* Changes to `MateraialsProjectAqueousCompatibility` that facilitate building Pourbaix diagrams with the mixing scheme. Previously, all H2 polymorphs were assigned the same energy by this class. Changes in this PR preserve energy differences among different polymorphs
* Additional kwargs to adjust the style of plots returned by `PourbaixPlotter`
* `EntrySet`: new methods `group_entries_by_composition`, `remove_non_ground_states`, and `is_ground_state`
* `MaterialsProjectCompatibility`: ensure that legacy corrections are only applied to GGA or GGA+U entries
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I_kwDOACgets5BeLnw
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Drift correction and framework ions in DiffusionAnalyzer
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[
"1. Yes unless you believe the framework is not moving much.\r\n2. Again, this really depends. If the ions are randomly moving and the average motion is close to 0, then it doesn't make a difference whether you include or not.\r\n3. I would definitely choose all ions other than the moving ions to be the famework. In this case, just Al. "
] | 2022-01-10T22:01:04
| 2022-01-13T15:00:56
|
2022-01-13T15:00:56Z
|
NONE
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The drift correction in `DiffusionAnalyzer` is automatically applied when calculating ionic diffusivity.
(1) Is it always required to include the drift correction for a trajectory?
(2) It makes sense to include it if all the ions moving in the same direction, but what if the ions are randomly moving around?
(3) If I want to calculate the diffusivities of different species in a same trajectory, should I use a same framework? For example, I have an AIMD calculated trajectory for LiAlO2. When using `DiffusionAnalyzer` to calculate Li diffusivity, Al+O will be the framework and the drift correction will be calculated based on Al+O displacements. Now, I also want to calculate the O diffusivity. Should I use the same framework (Al+O), or use Li+Al as the framework ions and recalculate the drift correction? Using the same framework makes more sense to me as the calculated Li and O diffusivities are based on the same framework.
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I_kwDOACgets5BfIe7
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ValueError: zero-size array to reduction operation maximum which has no identity
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[
"I think the reason is that you only have one species in your trajectory, therefore, your `framework_indices` is empty. A quick fix could be the following:\r\n```python:\r\nif len(framework_indices) == 0:\r\n dc = displacements\r\nelse:\r\n framework_disp = displacements[framework_indices]\r\n drift = np.average(framework_disp, axis=0)[None, :, :]\r\n dc = displacements - drift\r\n```\r\nIt looks like no one is maintaining the `DiffusionAnalyzer` module anymore. I asked a question about the drift and why it is required, but got no reply. If you know anything about it, I would like to hear your opinion. ",
"Dear Sir\r\n\r\nI am extremely sorry for being late. Sir, thank you very much for your kind reply. Sir, your suggestion solved the ValueError problem, however, now the following AttributeError is raised for the system of having a singly type species.\r\n\r\nAttributeError: 'DiffusionAnalyzer' object has no attribute 'dt'\r\n\r\nSir, can you please suggest how to solve this error. Thank you very much, Sir.\r\n\r\nAnd, Sir, regarding the drift, I am sorry that I have no idea about it."
] | 2022-01-11T05:50:56
| 2022-01-19T09:04:41
|
NONE
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Dear Sir
I am trying to calculate the diffusivity of Li ions on a Li metal surface from the VASP AIMD output files (XDATCAR, vasprun.xml) by using the pymatgen. I have used the following code:
--------------------------------------------------------------------------------------------------
%matplotlib inline
import numpy as np
import pickle
import matplotlib.pyplot as plt
import collections
import os
from pymatgen.core.trajectory import Trajectory
from pymatgen.core import Structure
from pymatgen.io.vasp.outputs import Xdatcar
from pymatgen.analysis.diffusion_analyzer import DiffusionAnalyzer, \
get_arrhenius_plot, get_extrapolated_conductivity
from pymatgen_diffusion.aimd.pathway import ProbabilityDensityAnalysis
#from pymatgen_diffusion.aimd.van_hove import VanHoveAnalysis
from pymatgen.io.vasp.outputs import Vasprun
traj = Trajectory.from_file("XDATCAR")
diff = DiffusionAnalyzer.from_structures(traj, 'Li', 298, 1, 1)
diff.plot_msd()
------------------------------------------------------------------------------------------------------
However, running the code in Jupyter notebook, I got the following error:
------------------------------------------------------------------------------------------
ValueError: zero-size array to reduction operation maximum which has no identity
------------------------------------------------------------------------------------------
I have checked the code for other system such as water. In that case the code works fine, however for a system of only one type of ions, the code gave me that error. Can you please suggest me the reason of this error and way to solve this issue. Thank you very much.
Best Regards
Arindam Sannyal
[VASP-Output.zip](https://github.com/materialsproject/pymatgen/files/7844016/VASP-Output.zip)
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I_kwDOACgets5BiQ8M
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Structure.get_sorted_structure does not preserve magmom site property
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[
"Hi @bocklund,\r\n\r\nI think this can be resolved by using the `Structure.add_site_property()` function, which is the preferred method of adding magnetic moments (and other site properties, like selective dynamics). I personally would recommend against trying to \"manually\" specify site properties, as they get stripped the moment you modify the structure.\r\n\r\nHere is your patched example:\r\n```python\r\nfrom pymatgen.core import Structure\r\nfrom pymatgen.io.vasp.sets import DictSet\r\nstruct = Structure.from_str(\"\"\"Cr2\r\n1.0\r\n2.849623 0.000000 0.000000\r\n0.000000 2.849623 0.000000\r\n0.000000 0.000000 2.849623\r\nCr\r\n2\r\ndirect\r\n0.000000 0.000000 0.000000 Cr\r\n0.500000 0.500000 0.500000 Cr\"\"\", fmt=\"POSCAR\")\r\n\r\n# See here!\r\nstruct.add_site_property(\"magmom\",[-5,5])\r\n\r\nassert all(hasattr(site, \"magmom\") for site in struct.sites) # passes\r\nassert all(hasattr(site, \"magmom\") for site in struct.get_sorted_structure().sites) # passes\r\n\r\nfrom pymatgen.io.vasp.sets import MPStaticSet\r\nassert all(hasattr(site, \"magmom\") for site in MPStaticSet(struct).structure.sites) # passes\r\nassert all(hasattr(site, \"magmom\") for site in MPStaticSet(struct, sort_structure=False).structure.sites) # passes\r\n```\r\n\r\nThis also confused me when I started out. I think that means we should make the documentation clearer.",
"Thank you @arosen93, understood. `add_site_property` seems to be the solution. Your PR in #2342 is definitely helpful, but I didn't know that the `add_site_property` method existed and so the improved docs/examples may not have helped me in this case.\r\n\r\nMy thought process was that the code around the exception that I got in `DictSet` accessed `magmom` as an attribute, so the principle of least surprise would suggest that I can interact with site properties as I would attributes. It seems like there's some asymmetry in that `Site.__getattr__` is overridden to access `Site.properties`, but there's not a symmetric `Site.__setattr__` method that sets `Site.properties`. ",
"I think this is a reasonable point. I would like to see the ability to do as you suggested because it is, arguably, the most intuitive route. I won't be able to make PR for this one, but perhaps you or someone else can improve upon that functionality.",
"@mkhorton -- I think this can be closed, but it's worth considering if a separate issue should be opened to address the pain point that @bocklund brought up.",
"Thanks for the reminder @arosen93, and thanks @bocklund for bringing this up -- it's true, I actually have not used the `.magmom` attribute myself and agree this looks confusing.\r\n\r\n>It seems like there's some asymmetry in that Site.__getattr__ is overridden to access Site.properties, but there's not a symmetric Site.__setattr__ method that sets Site.properties.\r\n\r\nThis seems like the fundamental cause. I would not close this issue until this has been addressed."
] | 2022-01-11T18:39:05
| 2022-03-29T20:58:39
|
CONTRIBUTOR
|
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**Describe the bug**
The `Structure.get_sorted_structure` method seems to clobber `magmom` attributes. As a consequence, all `DictSet` subclasses don't allow setting magnetic moments using site properties by default, since the default keyword argument `sort_structure=True` calls this method.
**To Reproduce**
```python
from pymatgen.core import Structure
from pymatgen.io.vasp.sets import DictSet
struct = Structure.from_str("""Cr2
1.0
2.849623 0.000000 0.000000
0.000000 2.849623 0.000000
0.000000 0.000000 2.849623
Cr
2
direct
0.000000 0.000000 0.000000 Cr
0.500000 0.500000 0.500000 Cr""", fmt="POSCAR")
struct.sites[0].magmom = -5
struct.sites[1].magmom = 5
assert all(hasattr(site, "magmom") for site in struct.sites) # passes
assert all(hasattr(site, "magmom") for site in struct.get_sorted_structure().sites) # fails
from pymatgen.io.vasp.sets import MPStaticSet
assert all(hasattr(site, "magmom") for site in MPStaticSet(struct).structure.sites) # fails
assert all(hasattr(site, "magmom") for site in MPStaticSet(struct, sort_structure=False).structure.sites) # passes
```
**Expected behavior**
These two lines should produce (effectively) the same INCAR with a correctly set MAGMOM tag:
```python
MPStaticSet(struct, user_incar_settings={"MAGMOM": False}, sort_structure=False).incar # Works
MPStaticSet(struct, user_incar_settings={"MAGMOM": False}, sort_structure=True).incar # Raises:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-21-d89e9d171cfc> in <module>
----> 1 MPStaticSet(struct, user_incar_settings={"MAGMOM": False}, sort_structure=True).incar
~/.envs/dft-env/lib/python3.9/site-packages/pymatgen/io/vasp/sets.py in incar(self)
1125 :return: Incar
1126 """
-> 1127 parent_incar = super().incar
1128 incar = Incar(self.prev_incar) if self.prev_incar is not None else Incar(parent_incar)
1129
~/.envs/dft-env/lib/python3.9/site-packages/pymatgen/io/vasp/sets.py in incar(self)
516 elif hasattr(site.specie, "spin"):
517 mag.append(site.specie.spin)
--> 518 elif str(site.specie) in v:
519 if site.specie.symbol == "Co" and v[str(site.specie)] <= 1.0:
520 warnings.warn(
TypeError: argument of type 'bool' is not iterable
```
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Pip cache not used in GitHub CI
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[
"Yes that would be helpful. I recently disabled the cache for debugging purposes. But I think we can re-enable them now."
] | 2022-01-11T21:17:46
| 2022-01-12T16:06:45
|
2022-01-12T16:06:45Z
|
MEMBER
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The GitHub test workflows for Linux, Mac and Windows all cache installed pip dependencies but then never check if there's a cache hit from previous runs. Would be great for saving time and energy to fix this soon.
https://github.com/materialsproject/pymatgen/blob/81e96a4a5739e383f921b7272db7ebf8b1710cb9/.github/workflows/test-linux.yml#L38-L44
Reusing cache requires setting an `id` on the cache step and then checking if there was a cache hit before rerunning the install:
```yml
- name: Cache pip
uses: actions/cache@v2
id: pip-cache
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Install dependencies
if: steps.pip-cache.outputs.cache-hit != 'true'
run: |
pip install -r requirements.txt
```
Also, in the Mac and Windows workflows, there's no need for `if: startsWith(runner.os, 'macOS')` etc.
https://github.com/materialsproject/pymatgen/blob/81e96a4a5739e383f921b7272db7ebf8b1710cb9/.github/workflows/test-mac.yml#L34-L47
Since v20.1, `pip` provides a platform agnostic way of getting the cache location: [`pip cache dir`](https://pip.pypa.io/en/stable/cli/pip_cache).
Happy to submit a PR for this.
|
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I_kwDOACgets5BivYQ
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|
Incorrect Oxidation States with add_charges_from_oxi_state_guesses Method
|
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[] | 2022-01-11T21:19:37
| 2022-01-11T21:19:37
|
NONE
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**Describe the bug**
I’ve noticed that the add_charges_from_oxi_state_guesses method in the pymatgen.core.composition module provides incorrect oxidation state numbers for materials which only contain one atom of an element in a material that can undergo charge disproportionation, such as BiO2.
**To Reproduce**
This function (using the add_charges_from_oxi_state_guesses method) shows the oxidation states results with and without doubling the formula unit.
```
from pymatgen import Composition
materialsToTest = ["LuNiO3", "BiO2", "Ag13(BiI4)14", "Li5Co5(SbO6)2", "LuFe2O4"]
def OxidationStateCalc(formula):
chemical = Composition(formula)
oxStates = list(chemical.add_charges_from_oxi_state_guesses())
oxStates = [str(element) for element in oxStates]
return oxStates
doubleUp = [f"({mat})2" for mat in materialsToTest]
for i in range(len(materialsToTest)):
print(f"{materialsToTest[i]}: {list(OxidationStateCalc(materialsToTest[i]))} {list(OxidationStateCalc(doubleUp[i]))}")
```
Output:
```
LuNiO3: ['Lu3+', 'Ni3+', 'O2-'] ['Lu3+', 'Ni2+', 'Ni4+', 'O2-']
BiO2: ['Bi0+', 'O0+'] ['Bi3+', 'Bi5+', 'O2-']
Ag13(BiI4)14: ['Ag+', 'Ag2+', 'Bi3+', 'I-'] ['Ag+', 'Bi3+', 'Bi5+', 'I-']
Li5Co5(SbO6)2: ['Li+', 'Co2+', 'Co3+', 'Sb3+', 'Sb5+', 'O2-'] ['Li+', 'Co2+', 'Sb3+', 'Sb5+', 'O2-']
LuFe2O4: ['Lu3+', 'Fe2+', 'Fe3+', 'O2-'] ['Lu3+', 'Fe2+', 'Fe3+', 'O2-']
```
**Expected behavior**
For BiO2, the expected oxidation states are ['Bi3+', 'Bi5+', 'O2-'], but instead the method returns ['Bi0+', 'O0+']. Another example is LuNiO3, where the expected oxidation states are ['Lu3+', 'Ni2+', 'Ni4+', 'O2-'], but the method returns ['Lu3+', 'Ni3+', 'O2-'].
**Desktop**
- OS: Windows
- Version 10.0.19043 Build 19043
**Additional context**
Based on my observations, it's only for materials which only have one 'charge disproportionation atom' where the function doesn't work correctly (for materials where there are two or more charge disproportionation atoms, it works as expected - see LuFe2O4).
As a workaround, I tried doubling the formula unit (f”({mat})2”), and that seems to give the correct oxidation states for such cases. However, this greatly increases computation time, and gives different results for some materials that don’t require cell doubling, e.g. Ag13(BiI4)14, which changes from ['Ag+', 'Ag2+', 'Bi3+', 'I-'] without cell doubling to ['Ag+', 'Bi3+', 'Bi5+', 'I-'] with cell doubling. Is there a better way to resolve this issue?
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PR_kwDOACgets4w1Yy2
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Clarify docstring for core.surface.generate_all_slabs() and structure.add_site_property()
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[
"\n[](https://coveralls.io/builds/45554453)\n\nCoverage decreased (-0.6%) to 83.184% when pulling **a71c84fbc9b9056f3e7cde13b0a34cbdad468f4b on arosen93:rosen-docs** into **81e96a4a5739e383f921b7272db7ebf8b1710cb9 on materialsproject:master**.\n",
"Thanks!"
] | 2022-01-12T04:34:02
| 2022-01-13T15:01:46
|
2022-01-13T15:01:42Z
|
MEMBER
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Addresses #2334 and #2339.
- The docstring for `generate_all_slabs()` was missing the description for the `ftol` kwarg and had the wrong description for the `tol` kwarg.
- I added examples on how to use `structure.add_site_property()` for adding magnetic moments and selective dynamics because, when I was a new user, I found this unclear and tried to do what was attempted in #2339.
|
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PR_kwDOACgets4w1ZIh
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Update row and group number for lanthanoids/actinoids
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[
"\n[](https://coveralls.io/builds/46097286)\n\nCoverage decreased (-0.4%) to 83.434% when pulling **433e7d8819cb9a40a98b18e81d434ef85fd4c5a9 on arosen93:rosen-group** into **81e96a4a5739e383f921b7272db7ebf8b1710cb9 on materialsproject:master**.\n",
"Before accepting this PR, I ask that you give it a look to see if there are any obvious spots where this could have unintended side-effects (like the periodic table plotting, which is specifically addressed).",
"@mkhorton, should be good now. Thanks for the review!",
"Thanks!"
] | 2022-01-12T04:37:32
| 2022-01-31T22:02:12
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2022-01-31T22:02:08Z
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## Purpose
This PR addresses #2327 wherein the group number for lanthanoids and actinoids was set to unconventional values of 3-17 depending on the element. The row was also set to the fictional values of 8 and 9, which is equally unconventional (although convenient for plotting).
## Changes
- The group number for all lanthanoids and actinoids are now 3 as a matter of convention. Usually, a value of 3 or none is accepted. I chose 3 primarily to avoid `None`.
- The row number for all lanthanoids and actinoids is now 6 and 7, respectively. This is generally accepted.
- The documentation for `pymatgen.core.periodic_table.ElementBase.from_row_and_group` has to be modified accordingly, as there is no longer a 1:1 map between row+group and element. Here, the old convention for row and group (i.e. row 8 and 9 for lanthanoids/actinoids and groups 3-17) should be used. This also means the function does not change in its inputs/outputs compared to before.
- I have added tests for row and group attributes as well as `from_row_and_group()`, none of which had tests to the best of my knowledge.
## Additional Checks
Since this change influences the way the periodic table is represented, I confirmed that the `print_periodic_table()` function still functions. Indeed, it does:
```python
from pymaten.core.periodic_tale import ElementBase
ElementBase.print_periodic_table()
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Rf Db Sg Bh Hs Mt Ds Rg Cn Nh Fl Mc Lv Ts Og
La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr
```
I also ran `from pymatgen.util.plotting.periodic_table_heatmap` on a dataset of my own and checked that it stayed the same before and after the proposed PR.
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PR_kwDOACgets4w2H-z
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Add caching to all GH workflows
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"\n[](https://coveralls.io/builds/45570143)\n\nCoverage decreased (-0.6%) to 83.183% when pulling **568ca1c08dec9dd4c5149a4ac49e54a53b0586dd on janosh:gh-ci-caching** into **81e96a4a5739e383f921b7272db7ebf8b1710cb9 on materialsproject:master**.\n",
"Thanks."
] | 2022-01-12T09:31:47
| 2022-01-12T16:08:02
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2022-01-12T16:06:46Z
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MEMBER
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Closes #2340.
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GH workflows check not on fork
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"I think it is useful to keep it for forks. The tests help inform the developer whether his code is working or not.",
"> The tests help inform the developer whether his code is working or not.\r\n\r\nThis is already taken care of by the emails everyone gets from the workflows running on this repo. The fork runs are just additional noise. Plus, they often fail even when the runs on this repo succeed (presumably because of missing `${{ secrets.PMG_MAPI_KEY }}`).",
"I see. Then go ahead and implement a PR then. Thanks.",
"This may need to be revisited, it's useful for people to run actions on their forks _before_ opening an PR to ensure tests are passing appropriately. I was just working with @arepstein to try to figure out why the tests and coverage reports were not running on his repo, for example.\r\n\r\nWith that said, I want to be responsive to concerns about noise, too many emails etc., so open to suggestions for changes. ",
"@mkhorton lint on local machine shouldn’t be onerous since all the packages are pure python and we have provided a precommit hook. For tests, we expect most people to be working on a fairly isolated part of the code and just testing one small file. The full test suite will run when a PR is submitted. The GitHub actions shouldn’t be taking the place of a local isolated test. It is very expensive to be running 20min tests for a change in one method in one module. ",
"I think it's a matter of preference for the individual developer, I think it's reasonable for a developer to want their fork to be running the same tests (guaranteed the same) as the main pymatgen repo.\r\n\r\nAlso, while straight forward to use the pre-commit hook for experienced developers, it is still an additional barrier to entry for first-time contributors.",
"I see both sides of this, but I would lead toward supporting the PR that has been merged (i.e. removing GH actions from forks). I have had several situations where the GH actions on my pymatgen fork somehow get out of sync with upstream, so I get the noisy emails about test failures _even when tests in my PR are passing_. This undermined my confidence that GH actions tests on forks are meaningful, so I often ignore them and rely on local tests instead.",
"I think it is a matter of being conscious. Each full test suite run is X SUs = Y joules = Z CO2 emitted. It is profligate use of resources, even if we are not actually charged money. Similarly, you wouldn't ask people to print out the entire Pymatgen if they need a paper copy of one method. ",
"As a more general comment, I feel it would really benefit our community of occasional contributors if we could stabilize our CI and testing standards. In the few years I've been contributing to pymatgen I feel there have been a large number of changes to the linters, CI infrastructure, etc. that have been rather disorienting to keep up with. I think we should try to more firmly establish what the standards and testing expectations are, document them clearly on our contributing page, and try not to change them. We can't expect occasional volunteer contributors to keep up with frequent changes.",
"Yes, fair enough, I'm sympathetic to concerns about energy usage too.\r\n\r\nI think the main problem with the current set up is that if someone _does_ want to enable actions on their fork, assuming we leave it disabled by default, they have to make a commit to change the actions .yml file, which then would also be included in their PR.\r\n\r\nMaybe we can leave this conversation open for a while for others to comment too. Thanks for adding your experiences too @rkingsbury -- it's important to hear.",
"@rkingsbury I think some context is necessary. The Python language evolves (e.g., f-strings, type annotations, etc). So I don't think it is reasonable to expect that linting requirements stay the same. That said, I think the linters have been reasonably stable for some time now. There was some initial iteration when we were figuring out what kind of linting was important, but by and large, we have not changed the linters for some time (other than internal changes to the linters themselves).\r\n\r\nPymatgen has always set itself out to promote best software practices. That means code style, documentation, and more recently, typing (gradually). In the past, enforcement was purely through the maintainers eyeballing the code and let's just say that due to bandwidth issues, a bad job was done (mostly on me). Some parts of the code simply was allowed to get away with no documentation, bad code style and we ended up with a technical debt that we are still dealing with today.\r\n\r\nThe linters help both the maintainers and the contributors. Take for example, black. Nowadays, instead of worrying about every single whitespace between every operator, I just focus on writing the logic and then letting black do its thing. The result is less load on me as a contributor as well. Pylint and pydocstyle impose requirements that are supposed to be imposed in the first place (e.g., asking for documentation on every.single.public.method). Mypy just checks types, where they exist. The linters set the expectations clear on what is required for a contribution to pymatgen.\r\n\r\nI would argue that if you compare pymatgen to other codes where the imposition of such linters is not as strict, you'd much rather read a pymatgen code and work on it than other codes. Most other codes that we have had in the Materials Project has not lasted beyond one or two years (including other codes that I started and allowed to degenerate due to lack of bandwidth).\r\n\r\n",
"One more addition: I see the linters as basically the \"Custodian\" for code. Those of us in this field spend our waking hours trying to automate calculations. Why should code management be any different? If one day there is an AI that can simply take the intent of a developer and translate it into beautiful code, I would happily adopt it. For now, I can only automate the feedback process to the contributor. It is my view that relaxing the linting requirements might gain us some contributors in the short run but would lead to such a degeneration that in the medium to long run, pymatgen would be unreadable and unmaintainable and no one would want to work on it anymore.",
"Yes @shyuep I 100% agree the linters, etc. are valuable, and unquestionably help keep our code quality high. The many layers of CI testing in pymatgen have made me a better coder for sure. I just think it's important that we communicate the standards to our developer community as clearly and frequently as we can, and keep the CI infrastructure as stable as we reasonably can (or at least try to change it in a predictable way or at predictable intervals). I don't know a great way to solve this and it's really a separate discussion; apologies for starting a tangent here.\r\n\r\nToday's example is what prompted my comment. Today @arepstein and I got confused about coveralls not working, which prompted him to reach out to @mkhorton , which caused them to spend time troubleshooting when in fact the root cause was a change in our CI system. In this case it's a change I'm in favor of; however in general I think changing the way the test infrastructure is set up carries risk of confusion and wasted time, as happened today. Similar things have happened to me a few times before. \r\n\r\nAs to the question on this PR, a compromise solution would be to keep the linting test active for all forks (which I think would be valuable, as sometimes local linting does not give the same results as the CI), but disable all the heavier tests.",
"Oh dear, didn't expect this change to trigger such a discussion. 😅 Lots of good points raised here! Don't want to drag this out so will keep my 2 cents as short as possible:\r\n\r\n> [from @mkhorton] ... it's useful for people to run actions on their forks before opening an PR to ensure tests are passing appropriately.\r\n\r\nI don't see all that much use in that. GH allows marking PR as drafts specifically so that people can submit unfinished work, announce their intent for a change and let others know they're working on it while actual upstream CI runs against it.\r\n\r\n> [from @shyuep] The full test suite will run when a PR is submitted. The GitHub actions shouldn’t be taking the place of a local isolated test.\r\n\r\nThat!\r\n\r\n> [from @mkhorton] I think it's reasonable for a developer to want their fork to be running the same tests (guaranteed the same) as the main pymatgen repo.\r\n\r\nI experienced many times the same thing @rkingsbury reported, i.e. that my fork's CI fails even when upstream CI is green. I'm curious, has anyone ever gotten CI to pass in a fork?\r\n\r\nThe GH actions running in a fork were never guaranteed the same as in this repo since all test workflows insert a secret:\r\n\r\n```yml\r\n env:\r\n PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}\r\n```\r\n\r\nOf course users could insert their own `PMG_MAPI_KEY` into repo secrets but then you're back to asking extra setup steps from potentially inexperienced devs.\r\n\r\n> [from @mkhorton] Also, while straight forward to use the pre-commit hook for experienced developers, it is still an additional barrier to entry for first-time contributors.\r\n\r\nI feel like this barrier was lowered dramatically by tools like [`pre-commit`](https://pre-commit.com). This is perhaps where @rkingsbury's point of communicating code quality standards more clearly applies the most. The steps needed to setup linting locally are just 2 lines of code\r\n\r\n```sh\r\npip install -U pre-commit # only needed once\r\npre-commit install\r\n```\r\n\r\nAfter that, all linters run before every commit so you get feedback before even pushing to your fork. It's super fast and only runs on changed files, i.e. very time+energy efficient. I found this very helpful as I no longer need to wait 5 mins for linting in CI to complain about some annoying whitespace issues, `black` auto-fixes at commit time, aborts commit, I do `git add .` to include fix, commit again, it passes, happy days. 😄\r\n\r\nSince `pymatgen` already has a `.pre-commit-config.yaml` file, there's very little work to communicate this workflow clearly to all contributors. Just add the 2 shell lines above to the GH PR template and to the contributing guide or readme.\r\n\r\nIn fact, as I discussed with @arosen93 on Sunday, you may want to adopt [pre-commit.ci](https://pre-commit.ci) on this repo as that does away with the need for inexperienced people to setup linters altogether. Once enabled, pre-commit.ci applies linter fixes to PRs automatically without the user having to do anything. It's free for open source repos and always will be. Here's an example of what it looks like in practice: https://github.com/janosh/ml-matrics/pull/3\r\n\r\n@shyuep I bet that would save you a bunch more time. 😄 ",
"Here are my thoughts, as briefly as possible:\n\n1) I like the lowered noise as a result of this PR. Similar to what @shyuep said, I tend to run only the one or two tests I need locally. And I have no qualms opening a WIP PR for further refinement. Never had a need for the CI test suite on forks. Not sure I ever got them to pass. Always ignored them. \n\n2) I agree that adding instructions for how to use the pre-commit hook would be wise. \n\n3) I like @janosh's suggestion of pre-commit CI. The fewer mundane things people need to think about, the better. ",
"One more point in support of pre-commit.ci so it's not just a random guy like me recommending it: many big orgs and repos have adopted it:\r\n\r\n- Python Software Foundation (PSF):\r\n - https://github.com/python/typeshed\r\n- Python Packaging Authority (PyPA):\r\n - https://github.com/pypa/virtualenv\r\n - https://github.com/pypa/wheel\r\n- Testing out of the box (TOX)\r\n - https://github.com/tox-dev/tox\r\n - https://github.com/tox-dev/tox-docker\r\n - https://github.com/tox-dev/tox-pipenv\r\n- Pytest\r\n - https://github.com/pytest-dev/pytest\r\n - https://github.com/pytest-dev/pytest-cov\r\n\r\nAnd prob others I'm not aware of.",
"@janosh Yes, you triggered a constitutional crisis. This is the pymatgen equivalent of the Jan 6 insurrection. :-)"
] | 2022-01-12T18:37:09
| 2022-02-22T11:43:17
|
2022-01-12T19:20:02Z
|
MEMBER
|
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Would be good to add a check to all GH workflows so that they don't run on forks.
```yaml
jobs:
test:
if: github.repository_owner == 'materialsproject'
# ...
```
Would save compute and it's annoying to keep getting emails about failed runs on my fork when submitting PRs:
<img width="866" alt="Screen Shot 2022-01-12 at 18 35 01" src="https://user-images.githubusercontent.com/30958850/149201290-17cd935b-6b8a-4f83-a2fe-5f9167bbee01.png">
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PR_kwDOACgets4w4HkJ
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Revert "Use f-string automatic string coercion: f"{str(x)}" -> f"{x}""
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[] | 2022-01-12T19:30:58
| 2022-01-21T20:16:21
|
2022-01-12T19:31:04Z
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Reverts materialsproject/pymatgen#2318
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PR_kwDOACgets4w4SP7
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Prevent GH actions from running on forks
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[] | null |
[
"\n[](https://coveralls.io/builds/45579054)\n\nCoverage decreased (-0.6%) to 83.183% when pulling **531561d8d1dd55b3104d923c585861340c2223f0 on janosh:no-ci-on-forks** into **e04bf536e0245805f0f42860ca81ed1582e62314 on materialsproject:master**.\n",
"Thanks."
] | 2022-01-12T20:36:11
| 2022-01-13T15:10:49
|
2022-01-13T15:01:17Z
|
MEMBER
|
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For #2345.
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I_kwDOACgets5Brm24
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|
Rename master to main
|
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[
"It has always been master. It is the other repos that rename themselves to main to serve some woke bullshit. I am not bowing to this kind of crap. You can ask the ones which are called main to go back to master. ",
"I agree that dropping the name `master` doesn't actually help with any entrenched societal problems (i.e. the reasoning behind this decision doesn't make much sense) but now it's there and it's even 2 letters shorter so why not use it. 😄 ",
"1. The change involves costs. It may be a net benefit to some developers (who work with pymatgen and fireworks etc.) but it is a net negative for me since all my repos are named master. Now I have to spend time renaming all of them. And all the downstream developers have to repull to main. \r\n2. Because we have to take a stand against this kind of hypersensitive BS that the intolerant left imposes on us. We can always come up with new BS. What if I say as an Asian, I take offense to the color yellow being used for any plots with negative connotations? Should we ban the use of the color or the word yellow then? There is no end to the funny crap we can come up with. \r\n\r\nIncidentally, the word \"master\" has many meanings. One of them is synonymous with \"main\". It also means someone with great proficiency or knowledge. The whole argument of master vs main is basically trying to dumb down the English language to the singular historical meaning. People should just move on and deal with problems with practical solutions rather than imposing this kind of nonsense on what I consider free speech.",
"Can't argue with any of your points except one: From my own experience, transitioning from `master` to `main` (on dozens of repos) wasn't much work.",
"One more note: I understand your point that the transition from `master` to `main` is a hassle with no benefits in and of itself. But at least GitHub makes it as smooth as possible by notifying every fork of upstream default branch changes including instructions what to do about it. This is what I recently got for my pandas fork after they renamed `master` to `main`:\r\n\r\n\r\n",
"Well, ease aside, I maintain that principles trump all these considerations. I simply refuse to allow the woke to tell me what to say or think. I am open to reason and logic, not bullshit. So nothing will be done about this. That is the end of this conversation.",
"I do apologize if I came across as being aggressive. I am aware I can be a bit too direct sometimes. It is just a reaction to a long list of this kind of thing I have to put up with in various fora. I recognize that it is not too difficult to do. But since pymatgen has always been using master, we have decided to keep it as is. Thanks for raising this anyway.",
"Thanks for asking about this @janosh, I can offer some perspective about the other codes you mentioned. We had an internal discussion on this issue and ultimately it was left as a decision with the individual package maintainers.\r\n\r\nMany of us decided to go ahead and rename to `main` for a few reasons: it was following the [lead of GitHub](https://github.blog/changelog/2020-10-01-the-default-branch-for-newly-created-repositories-is-now-main/) and [others](https://about.gitlab.com/blog/2021/03/10/new-git-default-branch-name/) in the community, the switch itself was painless for us, we wanted to respect [those who feel strongly about this issue](https://betterprogramming.pub/github-replacing-master-with-main-is-a-huge-win-for-inclusion-in-tech-bf517478275b), and there is also an argument that `main` is a better name regardless in the context of distributed version control.\r\n\r\nHowever, there are other factors too, especially for a long-running code where a branch rename might cause a lot of disruption for existing users and, of course, even when weighing all these factors we may reach different conclusions, as demonstrated here -- it's ok for us to disagree.\r\n\r\nUltimately, because it touches on social issues, questions like this are among the most difficult to tackle in open source and in a public forum where it can be difficult to have a nuanced conversation, so I'm grateful for polite discussion on these topics when they happen.",
"Thanks for the thoughtful responses. @shyuep No need to apologize. IMO you raised valid counter points. And like @mkhorton said, disagreements are part of the process.\r\n\r\nIt was a small concern anyway what the primary branch is called. I'm grateful you guys put so much thought and effort into the tools built around MP. Great thing for the materials community that they're free to use for everyone. 👍 "
] | 2022-01-13T15:39:01
| 2022-01-19T08:26:33
|
2022-01-13T15:43:56Z
|
MEMBER
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Bit annoying that the primary branch is inconsistently named across MP repos. Many still use `master` ([pymatgen](https://github.com/materialsproject/pymatgen), [custodian](https://github.com/materialsproject/custodian), [mapidoc](https://github.com/materialsproject/mapidoc), ...) while some have adopted GitHub's new default `main` ([fireworks](https://github.com/materialsproject/fireworks), [matbench](https://github.com/materialsproject/matbench), [maggma](https://github.com/materialsproject/maggma), ...). Has led me to merge/rebase the wrong branch on a few occasions. Any chance everything could move to `main`?
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PR_kwDOACgets4xEBsI
| 2,349
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Provide an option to keep site properties when calling spglib
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[
"\n[](https://coveralls.io/builds/45652538)\n\nCoverage decreased (-0.6%) to 83.315% when pulling **ab6cfd13de4371eaacbf543b924aaeff91525bd9 on arosen93:rosen-siteprops** into **ef6a4b09940531083bab1b587b3d80445163cfae on materialsproject:master**.\n",
"@mkhorton, hopefully this should be better.",
"Great. Thanks."
] | 2022-01-14T22:26:23
| 2022-01-18T03:12:22
|
2022-01-15T14:55:42Z
|
MEMBER
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As discussed in greater detail in #2330, this PR provides a new keyword option (`keep_site_properties`) in various `structure.symmetry.analyzer` functions to keep the site properties on the sites after a transformation. The docstring makes it clear that this may lead to undesirable side-effects as a result of the transformation, such as a loss of long-range magnetic ordering or antiferromagnetism.
|
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PR_kwDOACgets4xEQyZ
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Correction of small bugs in Lobster module
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"\n[](https://coveralls.io/builds/45649985)\n\nCoverage decreased (-0.6%) to 83.306% when pulling **adf3368150ae6bb49098c6bcbad26c4e155df18e on JaGeo:master** into **0604210825c8bb2e38d5e0e8cce32a5fc265c3e6 on materialsproject:master**.\n",
"All tests pass now. Let me know if I should do anything else. Thank you ",
"Thanks."
] | 2022-01-15T00:54:37
| 2022-01-15T14:55:08
|
2022-01-15T14:55:04Z
|
MEMBER
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## Summary
This is a pull request to correct small bugs in the Lobster module (set and environment classes). I have added tests to ensure they will not show up again.
Test files were zipped which led to more changes.
Let me know if there are suggestions.
|
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PR_kwDOACgets4xFY8n
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Fix CI status badge
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[
"Closed because, actually, I'm not 100% sure about this. Will just open an issue.",
"\n[](https://coveralls.io/builds/45687645)\n\nCoverage decreased (-0.6%) to 83.316% when pulling **8313f18c5cad747699bbb0f4dcc46cb1105e513e on arosen93:rosen-ci** into **ef6a4b09940531083bab1b587b3d80445163cfae on materialsproject:master**.\n",
"I think this can be reopened. You just need to update both [the image URL](https://github.com/materialsproject/pymatgen/pull/2351/files#diff-7b3ed02bc73dc06b7db906cf97aa91dec2b2eb21f2d92bc5caa761df5bbc168fR1) as well as the link it points to.\r\n\r\nBtw, you can test both URLs directly in comments. For instance, this renders as:\r\n\r\n```md\r\n[](https://github.com/materialsproject/pymatgen/actions/workflows/test-linux.yml)\r\n```\r\n\r\n[](https://github.com/materialsproject/pymatgen/actions/workflows/test-linux.yml)\r\n\r\nFor markdown readmes, you can also copy this snippet directly from the [action's page](https://github.com/materialsproject/pymatgen/actions/workflows/test-linux.yml):\r\n\r\n\r\n",
"Thanks for the help, @janosh! I was confused about if the badge would reflect actions from people submitting PRs or the main branch. I also wasn't sure how to test it out, so thank you for the tips!\r\n\r\n@shyuep, this one was merged a bit prematurely (no harm done). The image URL just [needs to be updated](https://github.com/arosen93/pymatgen/commit/21d60fd3c5ed5d0700d89cb6d5cfa599979c7c37), per @janosh's comment."
] | 2022-01-15T06:51:44
| 2022-01-17T22:36:56
|
2022-01-17T15:52:18Z
|
MEMBER
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The CI status badge isn't loading on the README because the test workflow got renamed. This should fix it.
|
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PR_kwDOACgets4xIkc5
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Format + typo fixes
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[
"\n[](https://coveralls.io/builds/45679059)\n\nCoverage decreased (-0.6%) to 83.317% when pulling **6517cef8726ab009c42626fadcc2455ac161c974 on janosh:fixes** into **8128f3062a334a2edd240e4062b5b9bdd1ae6f58 on materialsproject:master**.\n",
"@shyuep Ready for review. Would be great to get this in before any conflicts arise."
] | 2022-01-17T09:04:44
| 2022-01-31T21:06:41
|
2022-01-17T15:25:06Z
|
MEMBER
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3rd time's the charm (#2294, #2318).
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| 1,106,227,908
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PR_kwDOACgets4xKyLh
| 2,353
|
Improve passing of site properties between ASE Atoms object and Pymatgen Structure/Molecule objects (and vice versa)
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[
"\n[](https://coveralls.io/builds/45710406)\n\nCoverage decreased (-0.6%) to 83.323% when pulling **c38e7f33f3d290cf0d7da8a77468ab6f5685c808 on arosen93:rosen-ase** into **d72686269bd513c2edd8fb219de9011334fbdf7d on materialsproject:master**.\n",
"Thanks @arosen93 !"
] | 2022-01-17T20:16:38
| 2022-01-18T22:04:31
|
2022-01-18T21:31:22Z
|
MEMBER
|
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- When creating a Pymatgen `molecule` object from an ASE `Atoms` object using `pymatgen.io.ase.AseAtomsAdaptor.get_molecule()`, the `molecule.charge` and `molecule.spin_multiplicity` are now appropriately set. Before, they would always be set to their default values of 0 and 1, respectively.
- Now, _all_ Pymatgen site properties are passed to the ASE Atoms object (and vice versa).
|
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I_kwDOACgets5CAroh
| 2,354
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DataFrame returned from get_pattern() in TEMCalculator has NaN values
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[] | 2022-01-18T23:46:50
| 2022-01-18T23:46:50
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NONE
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**Describe the bug**
When I use the [get_pattern()](https://github.com/materialsproject/pymatgen/blob/905fa8592423f51784b9e83e02c53bb0c6ea0aa3/pymatgen/analysis/diffraction/tem.py#L278) method for [TEM diffraction](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/diffraction/tem.py) to create a DataFrame for future reference, the **Position**, **Intensity**, and **Film radius** columns all show `NaN`.
This is because in lines 298-304 of the [tem.py](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/diffraction/tem.py) file, the column names (`field_names`) are defined in such a way that those three columns are named differently than in the Dict object with the reference data (`dict1` in lines 307-313, stored inside `rows_list`).
Thus, when `df = pd.DataFrame(rows_list, columns=field_names)` is called, the [constructor's behavior](https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html) for `columns=` is to "If data contains column labels, will perform column selection instead."
Consequently, it tries to select the columns defined in `field_names` and it cannot find those three columns in `rows_list`.
**To Reproduce**
```
from pymatgen.core import Structure
from pymatgen.analysis.diffraction.tem import TEMCalculator
struct = Structure.from_file(filename) # any POSCAR will do, perhaps a simple one like Ni FCC.
tem = TEMCalculator()
dp = tem.get_pattern(struct)
dp.head()
```
**Expected behavior**
All data should be populated.
**Screenshots**
**Desktop (please complete the following information):**
- OS: Windows 11
**Additional context**
I think the fix is pretty simple, based on my own testing, change the names in `dict1`, at construction time ([lines 307-313](https://github.com/materialsproject/pymatgen/blob/905fa8592423f51784b9e83e02c53bb0c6ea0aa3/pymatgen/analysis/diffraction/tem.py#L307)), to be the same as those defined in `field_names` ([lines 298-304](https://github.com/materialsproject/pymatgen/blob/905fa8592423f51784b9e83e02c53bb0c6ea0aa3/pymatgen/analysis/diffraction/tem.py#L298)).
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| 1,107,888,918
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I_kwDOACgets5CCQsW
| 2,355
|
Broken Phase Diagram Energies
|
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[] | null |
[
"This was an issue with ComputedEntry entries having the same entry_id. Not sure where this id was generated."
] | 2022-01-19T09:58:55
| 2022-01-19T13:24:25
|
2022-01-19T13:23:30Z
|
NONE
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Between v2022.0.9 and v2022.0.10 calculating the phase diagram breaks. For a simple phase field (Mn, Fe, O) the energies above the hull are all 0 meV atom-1 in v2022.0.10 with entry in stable_entries and no entries in unstable_entries.
All entries should either be in stable_entries or unstable_entries
Working with python3.8 on ubuntu
|
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PR_kwDOACgets4xSE3Z
| 2,356
|
Minor cleanup of bader_caller.py + new get_partial_charge() convenience function
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[
"\n[](https://coveralls.io/builds/45782579)\n\nCoverage decreased (-0.6%) to 83.33% when pulling **671fd7f6a15261715c594694e4e3aad5e4b47d6f on arosen93:rosen-bader** into **fd553a8e80935d77df285fed1a14d7bf63669c14 on materialsproject:master**.\n",
"Thanks."
] | 2022-01-19T19:17:20
| 2022-01-25T18:25:49
|
2022-01-25T14:49:36Z
|
MEMBER
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I'll be adding a `chargemol_caller.py` soon, so this is a PR that does some minor cleanup of things I've found in `bader_caller.py` in the process.
- Add a new convenience function `get_partial_charge()`, which is just the negative of the `get_charge_transfer()`. This is to parallel the forthcoming `chargemol_caller.py`.
- Removes unused function kwarg. Adds missing docstrings for function args
- Adds code comments to describe the sign convention of "charge" and "charge transferred", which is a bit unclear on its own.
- Moved the `get_filepath()` function out of `bader_caller.py` (where it's not being used) to `critic2_caller.py` (where it is being used).
|
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Create a ChargemolAnalysis command line caller (for DDEC6, CM5 analysis)
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[
"\n[](https://coveralls.io/builds/45815529)\n\nCoverage decreased (-0.7%) to 83.306% when pulling **c6d38b11dadf4ed5ada3f98cb7bf58a34960eb62 on arosen93:rosen-ddec** into **6753761b1f332b70507b8e019114ac65c45b5c75 on materialsproject:master**.\n",
"@oxana-a, @mhsiron -- this is now completed. If you have any feature requests or changes you suggest, please let me know! Thanks to @mhsiron for kicking this one off.",
"Great thanks!"
] | 2022-01-19T19:26:21
| 2022-01-31T16:41:02
|
2022-01-31T16:39:31Z
|
MEMBER
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# Purpose
This PR introduces `pymatgen.command_line.chargemol_caller` with a `ChargemolAnalysis` class that functions in an analogous way as `BaderAnalysis` but for DDEC6/CM5 population analyses. It analyzes the output files from [Chargemol](https://sourceforge.net/projects/ddec/files/) and can also execute Chargemol on its own given a VASP directory of CHGCAR, AECCAR0, AECCAR2, and POTCAR files. Tests have been added for all user-facing functions with NaCl (spin-unpolarized) and O3 (spin-polarized) test systems. The only place a test wasn't added was for the execution of Chargemol, as it requires Pymatgen to have the same license if we were to integrate the binary into the Pymatgen repo.
Currently, the `ChargemolAnalysis` class can return: partial atomic charges (both DDEC and CM5), spin moments (if a spin-polarized calculation was run), dipoles, the sum of bond orders, a bond order mapping between every pair of atoms (including the spin-polarization of those bonds), and R^2/R^3/R^4 moments. Currently, the `ChargemolAnalysis` is written to be compatible with VASP, but it should only require minor updates if someone wanted to make it compatible with other codes (e.g. Gaussian, CP2K).
# Minimal Example
```python
from pymatgen.command_line.chargemol_caller import ChargemolAnalysis
path = "/path/to/my/vasp/run"
ca = ChargemolAnalysis(path)
print(ca.summary)
```
which would return
```python
{
"ddec": {
"partial_charges": List[float],
"spin_moments": List[float],
"dipoles": List[float],
"rsquared_moments": List[float],
"rcubed_moments": List[float],
"rfourth_moments": List[float],
"bond_order_sums": List[float],
"bond_order_dict": Dict
},
"cm5": {
"partial_charges": List[float],
}
}
```
-----
Note: This is built off of work originally by @mhsiron (with permission) -- see [here](https://github.com/mhsiron/pymatgen/blob/ads_wf/pymatgen/command_line/ddec6_caller.py) for the original. The PR here adds a number of features not available in the original version (e.g. CM5 charges), refactors the code a fair bit, and fixes several bugs (e.g. related to bond orders, data types).
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PR_kwDOACgets4xSJ6s
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Don't perform dict type-check on the MAGMOM flag in io.vasp.sets (fixes downstream Atomate issue)
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[
"\n[](https://coveralls.io/builds/45807775)\n\nCoverage decreased (-0.6%) to 83.328% when pulling **5792dcb1a66814c4390ad64b73dd2f899fa32cdd on arosen93:rosen-mags** into **d5370df167e92aa4293a1bd15cc49c327be46cbd on materialsproject:master**.\n",
"Thanks @arosen93. Noting that this reverts the warning recently introduced in pymatgen v2022.0.17 via #2301 "
] | 2022-01-19T19:46:06
| 2022-01-20T22:08:07
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2022-01-20T22:08:06Z
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- Addresses https://github.com/materialsproject/pymatgen/commit/9cfef441c16fd4c68290b80bb0383d52a0a8c0fe#r64164646 by reverting the type-check on the MAGMOM key-value pair.
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I_kwDOACgets5CEnc7
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Fix yaml.safe_load() deprecation warnings
|
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[
"Btw, `pyyaml` [also exports a `load()` function](https://pyyaml.org/wiki/PyYAMLDocumentation) so it wouldn't throw an error to use `pyyaml.load()` for people who don't have `ruamel.yaml` but it would no longer be \"safe\". Not sure if that's an issue? I guess we could monkey-patch it:\r\n\r\n```py\r\ntry:\r\n from ruamel.yaml import YAML\r\n\r\n yaml = YAML(typ=\"safe\", pure=True)\r\nexcept ImportError:\r\n try:\r\n import ruamel_yaml as yaml # type: ignore # noqa\r\n except ImportError:\r\n import yaml # type: ignore # noqa\r\n\r\n yaml.load = yaml.safe_load\r\n```",
"Closed in d7cfd8a."
] | 2022-01-19T20:05:24
| 2022-01-19T21:41:23
|
2022-01-19T21:41:23Z
|
MEMBER
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My `pytest` and `fireworks` logs are full of `yaml.safe_load()` deprecation warnings originating in `pymatgen` and `monty`.
```py
site-packages/monty/serialization.py:85: PendingDeprecationWarning:
load will be removed, use
yaml=YAML(typ='unsafe', pure=True)
yaml.load(...)
instead
return yaml.load(fp, *args, **kwargs)
site-packages/pymatgen/analysis/local_env.py:51: PendingDeprecationWarning:
safe_load will be removed, use
yaml=YAML(typ='safe', pure=True)
yaml.load(...)
instead
default_op_params = yaml.safe_load(f)
site-packages/pymatgen/analysis/local_env.py:54: PendingDeprecationWarning:
safe_load will be removed, use
yaml=YAML(typ='safe', pure=True)
yaml.load(...)
instead
cn_opt_params = yaml.safe_load(f)
```
Would be nice to fix those to have readable logs again. Should be doable by turning this
https://github.com/materialsproject/pymatgen/blob/905fa8592423f51784b9e83e02c53bb0c6ea0aa3/pymatgen/core/__init__.py#L11-L17
into this
```py
try:
from ruamel.yaml import YAML
yaml = YAML(typ="safe", pure=True)
except ImportError:
try:
import ruamel_yaml as yaml # type: ignore # noqa
except ImportError:
import yaml # type: ignore # noqa
```
and then replace all `yaml.safe_load()` with `yaml.load()`. What do you say?
|
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PR_kwDOACgets4xSPDc
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flake8 add per-file-ignores = __init__.py: F401
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[
"This has become quite the opinionated PR with more monkey patching than expected.\r\n\r\nSince the `safe_load` method will be removed soon, something like the mess I'm creating here will become necessary unless `pymatgen` decides to be more opinionated about the YAML parser it requires users to have. I.e. by saying everyone must install `ruamel.yaml` you'd have a more dependable interface.",
"Let me do this. ruamel is already a requirement in pymatgen anyway.",
"I just pushed a fix. This PR should not be necessary unless you see I missed something.",
"@shyuep Cool thanks! Fix looks good. I left the\r\n\r\n```\r\nper-file-ignores =\r\n # F401: imported but unused\r\n __init__.py: F401\r\n```\r\n\r\npart of this PR cause I think that's an improvement. What do you think?",
"Ok!"
] | 2022-01-19T20:16:10
| 2022-01-19T21:45:08
|
2022-01-19T21:44:05Z
|
MEMBER
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~Closes #2359.~ Closes nothing.
#2359 was closed in d7cfd8a4a6a00fce1860f1a4d2ed0a3830520dbc.
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I_kwDOACgets5CF-Wm
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Incorrect Gvec generation in Wavecar class of pymatgen.io.vasp.outputs module
|
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[
"@RyanNKHall: Just a head's up, the line you want is probably\r\n\r\n```python\r\nself.encut = np.fromfile(f, dtype=np.float64, count=1)[0]\r\n```\r\nWithout the `[0]` indexing, `self.encut` is returned as a length-one array instead of a float.",
"Thanks @arosen93. I actually spotted this the other day too. It doesn't seem to cause any issues without it because I think most functions that use encut would be able to unpack the value from a size 1 array but I guess it could cause issues and it's more correct to reference the value.\r\n\r\nI noticed there's a variable that's unpacked a few lines down that indexes the array in this way and it's obvious now that a numpy function would create an array by default.\r\n",
"This is now addressed via #2410. @RyanNKHall or @mkhorton, looks like you can close this one.",
"Addressed via #2410 \r\nThanks @arosen93 for completing the PR and @mkhorton for the support."
] | 2022-01-20T04:56:22
| 2022-03-07T08:20:42
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2022-03-07T08:19:27Z
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NONE
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**Describe the bug**
Within the `pymatgen.io.vasp.outputs` module's `Wavecar` class is a function called `_generate_G_points` (line 5012) that generates the G vectors for the plane wave expansion of the wavefunction using the cutoff energy from the Wavecar file and the kpoints. This function fails to generate the correct number of Gpoints when tested against a range of VASP version 5 Wavecar files. I found the issue arises due to the _encut attribute, which represents the cutoff energy for the plane wave expansion being cast to an integer type in the Wavecar class init function (line 4833). I was able to fix the bug by leaving encut as a float.
**To Reproduce**
Steps to reproduce the behavior:
1. Use the example WAVECAR file provided. It was generated for Silicon (mp149 in materials project) with hybrid functionals and a Monkhorst-pack grid of 9 x 9 x 9. The resultant Wavecar file contains 35 kpoints, 96 bands and has an encut of 245.345 when not cast to an integer -> this is cast to 245 in the original code
2. I have provided a test Python script called Wavefunction.py that creates an instance of the Wavecar class with the WAVECAR file to reproduce the error
3. A value error "Incorrect value of vasp_type given..." is produced on the third kpoint (ink = 2) (the casting/rounding does not affect the first two iterations likely because the kpoint magnitude is small)
4. Adding a print statement to outputs.py if statement that raises the value error provides some more verbose information on the issue. Specifically, adding: `print("\n# Gpoints:", len(self.Gpoints[ink]), "# plane waves:", nplane, "# extra Gpts:", len(extra_gpoints), "\n")` before the value error is raises will display to the terminal the number of Gpoints generated versus the required number nplane. In this example, 244 Gpoints are generated instead of the expected 253.
5. If you modify line 4833 of outputs.py from:
```
# extract kpoint, bands, energy, and lattice information
self.nk, self.nb, self.encut = np.fromfile(f, dtype=np.float64, count=3).astype(np.int_)
```
to:
```
self.nk, self.nb = np.fromfile(f, dtype=np.float64, count=2).astype(np.int_)
self.encut = np.fromfile(f, dtype=np.float64, count=1)
```
The error/issue is resolved. I have not tested this with earlier VASP WAVECAR outputs
Provide any example files that are needed to reproduce the error,
especially if the bug pertains to parsing of a file.
**Expected behavior**
The `_generate_G_points` should generate the correct number of Gpoints for the specified VASP WAVECAR type e.g. std, gam, or ncl
**Files required to reproduce error**
[bug_report.zip](https://github.com/materialsproject/pymatgen/files/7902425/bug_report.zip)
**Desktop (please complete the following information):**
- OS: Windows 11 education
**Additional context**
Feel free to contact me via email:
ryan.n.hall@unsw.edu.au
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PR_kwDOACgets4xUVjd
| 2,362
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Clean up conditional typing.Literal imports
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[
"@shyuep There's one error here that says to contact you about changes to an input set. In this case just a whitespace change.\r\n\r\n```py\r\n=================================== FAILURES ===================================\r\n_____________________ SetChangeCheckTest.test_sets_changed _____________________\r\n\r\nself = <vasp.tests.test_sets.SetChangeCheckTest testMethod=test_sets_changed>\r\n\r\n def test_sets_changed(self):\r\n # WARNING!\r\n # These tests will fail when you change an input set.\r\n # They are included as a sanity check: if you want to change\r\n # an input set, please make sure to notify the users for that set.\r\n # For sets starting with \"MVL\" this is @shyuep, for sets starting\r\n # with \"MP\" this is @shyuep and @mkhorton.\r\n os.chdir(MODULE_DIR / \"..\")\r\n input_sets = glob.glob(\"*.yaml\")\r\n hashes = {}\r\n for input_set in input_sets:\r\n with open(input_set) as f:\r\n hashes[input_set] = hashlib.sha1(f.read().encode(\"utf-8\")).hexdigest()\r\n known_hashes = {\r\n \"MVLGWSet.yaml\": \"f4df9516cf7dd923b37281172c662a70fa32bebc\",\r\n \"MVLRelax52Set.yaml\": \"eb538ffb45c0cd13f13df48afc1e71c44d2e34b2\",\r\n \"MPHSERelaxSet.yaml\": \"2bb969e64b57ff049077c8ec10e64f94c9c97f42\",\r\n \"VASPIncarBase.yaml\": \"19762515f8deefb970f2968fca48a0d67f7964d4\",\r\n \"MPSCANRelaxSet.yaml\": \"dfa9fee19178cb38c6a121ce6096db40693478e8\",\r\n \"MPRelaxSet.yaml\": \"4ea97d776fbdc7e168036f73e9176012a56c0a45\",\r\n \"MITRelaxSet.yaml\": \"1a0970f8cad9417ec810f7ab349dc854eaa67010\",\r\n \"vdW_parameters.yaml\": \"66541f58b221c8966109156f4f651b2ca8aa76da\",\r\n }\r\n \r\n> self.assertDictEqual(\r\n hashes,\r\n known_hashes,\r\n \"These tests will fail when you change an input set. \"\r\n \"They are included as a sanity check: if you want to \"\r\n \"change an input set, please make sure to notify the \"\r\n \"users for that set. \"\r\n 'For sets starting with \"MVL\" this is @shyuep, '\r\n 'for sets starting with \"MP\" this is @shyuep and @mkhorton.',\r\n )\r\nE AssertionError: {'MITRelaxSet.yaml': '1a0970f8cad9417ec810f7[471 chars]4d4'} != {'MVLGWSet.yaml': 'f4df9516cf7dd923b37281172[471 chars]6da'}\r\nE {'MITRelaxSet.yaml': '1a0970f8cad9417ec810f7ab349dc854eaa67010',\r\nE 'MPHSERelaxSet.yaml': '2bb969e64b57ff049077c8ec10e64f94c9c97f42',\r\nE 'MPRelaxSet.yaml': '4ea97d776fbdc7e168036f73e9176012a56c0a45',\r\nE 'MPSCANRelaxSet.yaml': 'dfa9fee19178cb38c6a121ce6096db40693478e8',\r\nE 'MVLGWSet.yaml': 'f4df9516cf7dd923b37281172c662a70fa32bebc',\r\nE 'MVLRelax52Set.yaml': 'eb538ffb45c0cd13f13df48afc1e71c44d2e34b2',\r\nE 'VASPIncarBase.yaml': '19762515f8deefb970f2968fca48a0d67f7964d4',\r\nE - 'vdW_parameters.yaml': '04bb09bb563d159565bcceac6a11e8bdf0152b79'}\r\nE + 'vdW_parameters.yaml': '66541f58b221c8966109156f4f651b2ca8aa76da'} : These tests will fail when you change an input set. They are included as a sanity check: if you want to change an input set, please make sure to notify the users for that set. For sets starting with \"MVL\" this is @shyuep, for sets starting with \"MP\" this is @shyuep and @mkhorton.\r\n\r\n/home/runner/work/pymatgen/pymatgen/pymatgen/io/vasp/tests/test_sets.py:84: AssertionError\r\n```",
"Thanks. Pls update the hashes so that the tests pass. @mkhorton Pls review.",
"\n[](https://coveralls.io/builds/45817925)\n\nCoverage decreased (-0.6%) to 83.34% when pulling **776dabac89585ad7b9a5274f53515aa09ecf39e3 on janosh:qa** into **6753761b1f332b70507b8e019114ac65c45b5c75 on materialsproject:master**.\n",
"Will probably break using most recent versions on Google colab which is stuck on 3.7.12 ",
"People using Google collab can use older versions. ",
"@CompRhys `pip`/`conda` won't even try to install the latest `pymatgen` on Colab since @shyuep bumped `python_requires` to 3.8 in https://github.com/materialsproject/pymatgen/commit/d00945491e9b53548ea8a6755a002c2066ad0ac9 2 weeks ago. Not until Google updates their runtime.",
"@janosh is right the most recent version already throws errors on google colab so my point doesn't really have bearing on this PR. I thought it would still work but I just hadn't merged recent changes onto my branch that I use with my colab workflow.",
"@shyuep What was the reason for dropping py37? I'd assumed it had something to do with `numpy` but that doesn't appear to be the case.",
"Numpy 1.22 dropped py37. ",
"Thanks."
] | 2022-01-20T11:08:20
| 2022-01-31T21:41:58
|
2022-01-25T14:47:47Z
|
MEMBER
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Since `pymatgen` is now py38+, can get rid of conditional `typing.Literal` imports.
Also, brings `.pre-commit-config.yaml` up to date and adds `pyupgrade` commit hook.
|
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I_kwDOACgets5CIN7c
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|
TypeError in _get_potcar_symbols()
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[
"Will have a look at it as soon as I am back from my vacation ... (On Monday)\r\n\r\nIt's just there to warn users if they use the POTCARs including these keywords. If you know how to fix it, please go ahead. Errors seem to be new, though...\r\n\r\nAnd, thanks for putting all the work into this. 🙂",
"I guess one way to fix it would be\r\n\r\n```diff\r\n- if \"SHA256\" in data or \"COPYR\" in data: \r\n+ if b\"SHA256\" in data or b\"COPYR\" in data: \r\n```\r\n\r\nbut I was a bit confused by this error as I didn't expect the result `f.read()` to be a `bytes` object in the first place. Since `data` is prob supposed to be `str`, turning \"SHA256\" into `bytes` string wouldn't be the right fix here.",
"Yeah, same. I hope it is not again some test data problem in atomate. 🙈",
"Don't think so. Since `zopen` is coming from `monty` maybe @shyuep can comment how to handle this.",
"At least in pymatgen, the tests seem to be working: \r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/fd553a8e80935d77df285fed1a14d7bf63669c14/pymatgen/io/lobster/tests/test_lobster.py#L2012",
"zopen does not do anything to the encoding. It merely passes through to io.open or gzip or bzip2 based on the file extension. So this is not related to zopen. In general, python has become more strict on binary vs text types. So you might have to properly handle the encoding conversions.",
"@JaGeo Thanks, yes I saw the tests pass here. The difference is prob that in `atomate` the POTCAR is gzipped so the returned IO stream comes from `gzip.open()` instead of python's `open()`.\r\n\r\n@shyuep You mean check the type and handle the comparison accordingly?\r\n\r\n```py\r\nif isinstance(data, bytes):\r\n if b\"SHA256\" in data or b\"COPYR\" in data:\r\n # ...\r\nelse:\r\n if \"SHA256\" in data or \"COPYR\" in data: \r\n\r\n",
"No, you should handle the encoding of \"data\" first. If it is supposed to be a string, it needs to be converted to unicode first. The comparison should be based on unicode, not bytes. Then everything that follows using data should treat it as a proper unicode."
] | 2022-01-20T15:34:00
| 2022-01-20T20:19:57
|
2022-01-20T20:19:57Z
|
MEMBER
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`class Lobsterin()._get_potcar_symbols()` causes [CI errors in `atomate`](https://github.com/hackingmaterials/atomate/runs/4871532128?check_suite_focus=true#step:8:115)
https://github.com/materialsproject/pymatgen/blob/fd553a8e80935d77df285fed1a14d7bf63669c14/pymatgen/io/lobster/inputs.py#L612-L633
```sh
with zopen(POTCAR_input, "r") as f:
data = f.read()
> if "SHA256" in data or "COPYR" in data:
E TypeError: a bytes-like object is required, not 'str'
```
Triggered by PR: https://github.com/hackingmaterials/atomate/pull/738
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I_kwDOACgets5CIpBl
| 2,364
|
Handling partial periodic boundary conditions
|
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[
"This is definitely desired. I would be happy to discuss.",
"Thanks for the interest. Here are some considerations that I hope will be useful as a starting point.\r\n\r\nThe distinction between the `Molecule` and `Structure` objects always worked well for me in general. Other codes (e.g. ASE, aiida) handle all cases of partial periodic boundary conditions (PPBC) in a single object, with the information about PPBC stored as a list of 3 booleans. Introducing such a classification in pymatgen when two objects already exist may lead to some confusion: is a Molecule an entity with 0 PBC? Is a Structure an entity with 3 PBC? \r\nAnother important point is how much breaking of backward compatibility would be allowed to implement such a feature. Objects that involve PBC (or the lack of it) include Structure/Molecule, Lattice, Site/PeriodicSite and their use is ubiquitous in pymatgen. Considering that the need for this feature apparently did not emerge for more than 10 years, it would seem unreasonable to cause a large disruption in the rest of the code just to introduce it. \r\nDepending on the solution implemented it can be that the same physical object could be represented with two different python objects. Would this be acceptable? \r\nMy impression is that, when considering its representation, a physical object with PPBC is \"closer\" to a `Structure` than to a `Molecule`. For example, a 1D object is still associated with the concept of a lattice (even though it is basically just one number), while an object with no PBC does not need it at all.\r\nIn principle defining the periodicity with the triplet of boolean is not strictly necessary. A 1D object could be defined by a \"lattice\" consisting of a single float and set of 2D cartesian coordinates plus 1D fractional coordinates. Without the need to specify its direction in a 3D cartesian space. However this, aside from being messy to handle, would be limiting in the definition of the system. There could be good reasons for defining the 1D system along the x-axis rather than the z-axis. It seems that the DFT codes that support this kind of input may have different conventions. For this reason in the following I focused on the idea of the PBC defined in a 3D cartesian space.\r\n\r\nThat said, and given that this would be a new feature in an already existing and widely used package, I don't think there are too many options to add the support for PPBC. I will list those that I can think of, in order of increasing impact for the rest of the existing code. I also tried to outline a (non exhaustive) list of pros and cons.\r\n\r\n* Create new subclass(es) of `SiteCollection` to handle the specific cases of PPBC. Two distinct possibilities are the introduction of two new classes (a 1DStructure plus a 2DStructure) or a single class for generic PPBC.\r\n * pros: \r\n * little impact on existing code. Support for these classes could be introduced at different times and only if needed.\r\n * should be relatively easy to implement. Some code duplication could be avoided with an additional abstraction layer (e.g. `PeriodicSiteCollection`) that handles common functionalities between the new PPBC object(s) and `Structure`\r\n * cons: \r\n * more objects to maintain separately\r\n * probably more new objects needed that play the role of Lattice and Site?\r\n * in the option with single new object, this may end up overlapping with Structure and Molecule if 3D or 0D PBC are allowed inside it.\r\n\r\n* Implement a new (non abstract) class from which `Structure` inherits. Such a new class can have a pbc=(bool, bool, bool) attribute and will be the reference for handling PPBC. `Structure` would subclass it and have pbc=(True, True, True) fixed. (False, False, False) is forbidden and remains a distinct object from `Molecule`.\r\n * pros: \r\n * not much disruption for the existing code\r\n * most of the code could probably be in the parent class\r\n * switching to accepting an instance of the base class (e.g. in the input generator of some code) should be relatively painless if only methods of the base class are used.\r\n * cons: \r\n * ambiguity when handling the case pbc=(True, True, True). Both the new object and `Structure` could be used.\r\n * potential issues in the inheritance tree due to the presence of `IStructure`. Should an immutable PPBC object exist as well? How would the final inheritance tree be?\r\n * a bit disappointing not accepting the pbc=(False, False, False) option, but adding the `Molecule` in the inheritance tree would introduce additional complications with little benefit.\r\n * new objects for Lattice and Site may be needed as well with associated coding and maintenance efforts required.\r\n\r\n* Add the pbc=(bool, bool, bool) directly in `Structure`. (False, False, False) is forbidden and remains a distinct object from `Molecule`:\r\n * pros: \r\n * no new objects. Might be easier for both users and developers to have a single entry point and a single object to maintain.\r\n * if everything is made consistently, Lattice and Site could be updated to handle pbc as well and remove the need for new specific objects.\r\n * cons: \r\n * likely disruptive for a large part of the existing code. When `Structure` is used it currently means a 3D PBC. Passing a Structure with PPBC will still respect the API but PPBC will not be really supported by most of the code. Checks should be added almost everywhere. Alternatively the user should be responsible for using a proper 3D periodic `Structure`, with the risk of failures or, worse, unexpected behavior.\r\n * still does not allow for pbc=(False, False, False)\r\n\r\n* Create a new object that handles all kind of PBC, from 0 to 3, replacing `Molecule` and `Structure` in the long run or coexisting with them. I honestly listed this just for completeness, because I believe that this would wreak havoc in all depending codes and drop the nice distinction between `Structure` and `Molecule` with very little to gain.\r\n\r\nThese were my personal thoughts about it. I would be glad to hear comments and if other options should be considered.\r\n\r\n",
"Thanks for the thoughtful suggestions. Oddly, my inclination is to do the last one - a new SiteCollection subclass for all kinds of PBC. The general idea is that this new class would mainly be used for 1D and 2D for now, and the design should be such that we can make Molecule and Structure to subclass it with little difficulty. There are some codes where we'd want to support any PBC, and there are some codes where only certain types of PBC are supported (molecules and 3D crystals). The analogy I would make is that you should write a Polygon class from which specific implementations like Square, Triangle, Hexagon, Pentagon can be derived. Maybe 90% of the time people only work with Squares and Triangles and so, we have special subclasses for them. But Hexagons, Pentagons or even Heptadecagons can be defined as just polygons in general.\r\n\r\nYour second suggestion is fine too, though preferably, I don't want to treat Molecules separate from other kinds of PBC.\r\n\r\n",
"@mkhorton You should weigh in since this is a major change.",
"I should add that you should not worry about IStructure for now. The intent is really to get rid of it soon. There is very little benefit to keeping IStructure and IMolecule.",
"Thanks @shyuep.\r\n\r\nFor the motivation of this feature, I agree and I also have been in touch with several people who would like PPBCs. They're useful for a number of reasons (2D materials, mixed basis set codes, classical modelling codes, etc.).\r\n\r\nFor the implementation, I think we should first acknowledge that to define PBCs, a `Lattice` should be required. E.g., the `Lattice` defines the periodicity. At present, all lattices in _pymatgen_ are 3D lattices. While defining a 2D lattice is technically possible, I think in practice it would see limited use -- even 2D materials are often more practically described with a 3D lattice, so that fractional co-ordinates can be used to describe atomic positions.\r\n\r\nSo one option to consider might be a property on `Lattice`. By default, `Lattice.periodic = (True, True, True)`. This can then optionally be changed as necessary, and `Structure` will continue to work as-is except for any features that need to take the Lattice periodicity into account.\r\n\r\nIn this way, the periodicity of a `SiteCollection` is defined by the `Lattice` associated with the sites within it, in much the same way as it currently works when the `PeriodicSite` contains lattice information.",
"Thanks for your comments. So let me try to summarize your main suggestions.\r\n\r\nOne option would be to have a single a tree like this:\r\n<img width=\"190\" alt=\"pbc1\" src=\"https://user-images.githubusercontent.com/8665734/151958250-45324fea-9a23-486f-ae05-5c893c8b40ba.png\">\r\n\r\nI think this is not so dissimilar from what I had in mind in my second option in the previous post:\r\n<img width=\"160\" alt=\"pbc2\" src=\"https://user-images.githubusercontent.com/8665734/151958353-5c6bd470-a497-401a-9289-211cdbbc9ba1.png\">\r\n\r\nThe first being @shyuep preferred option. \r\n\r\nThe suggestion from @mkhorton seems to go in the opposite direction. No new classes and instead add the `periodic` attribute to `Lattice`, so that `Structure` can handle PPBC. I have just one doubt: do I understand correctly that you would require that a reasonable 3D lattice should always be defined, so that the main reference will still be the fractional coordinates? My initial idea was to consider a `Lattice` with a 3x3 Matrix, but to basically ignore the axes of the directions with no periodicity. However the latter would indeed leave ambiguity in the definition of fractional coordinates for PPBC and how to store them in the serialized version (currently they are stored as fractional coordinates).\r\n\r\nDoes this summarizes correctly your positions?\r\n\r\nWhile we personally have a slight preference for the creation of a new class (let's call it `System` at this stage, just for reference. Suggestions on the name are welcome, if this would be the chosen option), I am still afraid that there will be some issues including Molecule as a subclass. Some examples are\r\n* as also pointed out by @mkhorton, the defining property of a system with PBC is the presence of a `Lattice`. So, while `System` needs to have a `lattice` attribute, this is basically meaningless for a Molecule. This might force to handle this special case of the lattice attribute in the base class.\r\n* `System` will still be a SiteCollection. While `Structure` is a collection of `PeriodicSite`s, Molecule is a collection of `Site`s. What should `System` contain? `PeriodicSite` seems the obvious choice, but `Molecule` will be a subclass of `System` while having `Site`s internally.\r\n\r\nHandling all the different cases in the base class can be more challenging to implement and maintain. If to avoid these kind of issues all the methods and properties of `System` need to be overridden in `Molecule`, what would be the benefit of having it as a subclass of `System`?\r\n\r\nIf you are interested, I would be available to try to work on this. In that case I can open a WIP PR to discuss other points in more details. However, since this is a major change, I think that a clear decision about which solution to implement should preferably come from your side.",
"Thanks. I have thought about it further. I think we can go with your original scheme (option B), i.e., keep Molecule and Structure as separate branches. We then adopt @mkhorton suggestion that we define PBC in terms of the lattice basis vectors. This will be integrated into PeriodicSites and Structure, which can be something with arbitrary PBC (with 3D being default). To be honest, I think it is difficult to do pure strategization without seeing a real concrete example of what it would look like. I think a WIP PR with a barebones implementation (maybe it does not need to be in Structure in the first instance if it makes it easier to write) would be useful to stimulate ideas and discussion."
] | 2022-01-20T17:13:54
| 2022-05-26T18:15:13
|
2022-05-26T18:15:13Z
|
CONTRIBUTOR
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**Is your feature request related to a problem? Please describe.**
We (I and @davidwaroquiers) were thinking about what would be the best option to handle objects with partial periodic boundary conditions.
In particular this would be helpful for defining the inputs of codes that support calculations with this option.
**Describe the solution you'd like**
A potential solution would be to extend the Structure object to support partial PBC or introduce a new object specific to these cases.
We mainly wanted to know if this was ever considered in pymatgen and, if not, start a discussion about whether this could be a desirable feature to implement.
**Describe alternatives you've considered**
A trivial solution is to use a Structure with some vacuum in the non-periodic directions. This, however, forces to keep somewhere else the information about which directions are periodic and all the operations on the Structure need to pass through a series of if statements.
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PR_kwDOACgets4xWACm
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Fix Lobsterin()._get_potcar_symbols()
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[
"\n[](https://coveralls.io/builds/45803835)\n\nCoverage decreased (-0.6%) to 83.33% when pulling **e181a7fb800d7dff1a1074bc0be25f10e8558034 on janosh:fix_get_potcar_symbols** into **fd553a8e80935d77df285fed1a14d7bf63669c14 on materialsproject:master**.\n",
"Can add a test for this if anyone wants one.",
"Thanks.",
"Thanks for merging. When's the next release due? This fix blocks https://github.com/hackingmaterials/atomate/pull/738 which makes `atomate` compatible with latest `pymatgen`.",
"Would like to point out this pull request related to atomate as well: https://github.com/materialsproject/pymatgen/pull/2358 . Would be happy if we could wait for this one as well before a new atomate version might be released. We ran into issues in the static workflow due to this.",
"@JaGeo Cool! I'd seen the CI error but not @arosen93's PR yet. Thought I'd have to dig into that one too. :)\r\n\r\nYes, we'll definitely have to wait for #2358 before releasing `atomate`.",
"@JaGeo, should be done shortly! A user reported an issue when using the `LobsterSet` with `StaticFw` due to a change I merged a little while back (https://github.com/materialsproject/pymatgen/commit/9cfef441c16fd4c68290b80bb0383d52a0a8c0fe#r64164646). I'll admit, I'm not exactly sure of the cause after digging into it, but I'm just reverting my change for now."
] | 2022-01-20T19:18:55
| 2022-01-20T20:40:02
|
2022-01-20T20:19:58Z
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Closes #2363.
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np.bool/np.int deprecation warnings
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"Great, thanks for taking care of this! "
] | 2022-01-22T21:04:20
| 2022-01-23T00:08:05
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2022-01-23T00:05:40Z
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MEMBER
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Currently, Pymatgen has several areas where there are `np.bool` and `np.int` deprecation warnings. Similar to #2359, it would be nice to address this in part so `pytest` (here and in other downstream projects) isn't cluttered.
> c:\users\asros\github\pymatgen\pymatgen\analysis\structure_matcher.py:556: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> mask = np.zeros((len(struct2), len(struct1), fu), dtype=np.bool)
> c:\users\asros\github\pymatgen\pymatgen\analysis\structure_matcher.py:757: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> if LinearAssignment(mask).min_cost > 0: # pylint: disable=E1101
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I_kwDOACgets5CQyKJ
| 2,367
|
Vasprun().final_energy does not report energy(sigma->0) for VASP 6 & Vasprun and Outcar final energies are inconsistent
|
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[] | null |
[
"I think the reason is mostly historical. And I am fine with changing everything to default to e_0_energy unless @mkhorton has any concerns.",
"Good to know. Based on the details below, I think it is actually **a VASP 6+ bug for `Vasprun`** but a historical decision for `Outcar`.\r\n\r\nI did some digging into this, and I now see what was trying to be done. For `Vasprun`, it appears this was a workaround to address a bug in VASP 5.x.x, which had the correct `e_0_energy` in the OUTCAR but _not_ in certain parts of the `vasprun.xml`. For full details, I direct you to the VASP forum post [here](https://www.vasp.at/forum/viewtopic.php?f=3&t=16942), which I've independently confirmed. It discusses the issue in full.\r\n\r\nIn short, `e_wo_entrp` was actually `e_0_energy` by mistake in the ionic steps section of the `vasprun.xml` file before VASP 6. As the user noted, \"I could currently use the `e_wo_entrp` from `calculation/energy` [for `e_0_energy`] since that contains the value that I want, however should this bug ever be fixed my code will start returning the wrong value.\" This is exactly what Pymatgen did, and indeed, in VASP 6+ when the bug was fixed, `Vasprun` now returns the wrong energy value.\r\n\r\nThe `Outcar` scenario seems to just be purely a historical decision. No bug -- just a design choice, albeit one that is perhaps not expected.\r\n\r\nI will propose a set of fixes shortly.",
"Thanks for the report -- I concur with using `e_0_energy`, I'll respond with any further queries in the PR thread #2369. Thanks for the comprehensive post-mortem on this @arosen93 ",
"Closed via #2369"
] | 2022-01-22T21:43:55
| 2022-01-25T02:32:46
|
2022-01-25T02:32:45Z
|
MEMBER
|
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@shyuep, @mkhorton: There is a bug with the `final_energy` property in `Vasprun` for VASP 6+, and the `final_energy` property in `Outcar` is somewhat unintuitive.
## Background
For the attached VASP 6 files below, there are the three types of energies in the output for the final step.
Vasprun.xml:
```
<i name="e_fr_energy"> -33.16377435 </i>
<i name="e_wo_entrp"> -33.15237262 </i>
<i name="e_0_energy"> -33.15807349 </i>
```
OUTCAR:
```
free energy TOTEN = -33.16377435 eV
energy without entropy= -33.15237262 energy(sigma->0) = -33.15807349
```
Here is a quote from the VASP manual in the [ISMEAR section](https://www.vasp.at/wiki/index.php/ISMEAR) to motivate what I'm going to discuss below, although getting the sigma->0 extrapolated energy is important regardless of ISMEAR.
> The Gaussian smearing method leads to very reasonable results in most cases. Within this method **it is necessary to extrapolate from finite SIGMA results to SIGMA=0 results**. You can find an extra line in the OUTCAR file: energy( SIGMA→0 ), giving the extrapolated results.
## Vasprun
For the attached files, the `Vasprun` prints out the `e_wo_entrp` as the `final_energy`. It's because of the codeblock below, where it detects that `e_wo_entrp` and `e_0_energy` are different and takes the former.
It's not particularly clear to me, however, why it's taking the former when you'd almost universally want the energy in the sigma --> 0 limit (there are no vdW corrections here despite the warning message). **NOTE**: Turns out the code is not what it looks like at first glance. It's to fix a confusing `vasprun.xml` bug in VASP 5 (see comment below), but it ends up breaking in VASP 6.
https://github.com/materialsproject/pymatgen/blob/ae3f1b77d75b397735ee7cf16fcd77d8f487d85e/pymatgen/io/vasp/outputs.py#L621-L629
## Outcar
To add to the confusion a bit, the `Outcar` prints out the `e_fr_energy` instead as the `final_energy`. Again, I would have naively assumed that it would output the `e_0_energy`. There are few situations where I'd actually want `e_fr_energy`. Either way, it is not great that it is a different `final_energy` than that generated with `Vasprun`.
This can be traced back to the following line, which looks for `TOTEN` and then uses that energy for `final_energy`.
https://github.com/materialsproject/pymatgen/blob/ae3f1b77d75b397735ee7cf16fcd77d8f487d85e/pymatgen/io/vasp/outputs.py#L1795
## Example
```python
from pymatgen.io.vasp import Vasprun,Outcar
vr = Vasprun('Vasprun.xml.gz')
print(vr.final_energy) # -33.15237262
out = Outcar('OUTCAR.gz')
print(out.final_energy) # -33.16377435
# Note: The energy(sigma->0) is -33.15807349.
```
[OUTCAR.gz](https://github.com/materialsproject/pymatgen/files/7919351/OUTCAR.gz)
[vasprun.xml.gz](https://github.com/materialsproject/pymatgen/files/7919352/vasprun.xml.gz)
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| 1,111,747,163
|
I_kwDOACgets5CQ-pb
| 2,368
|
Get the Seitz symbol of the space group symmetries for a specific crystal structure.
|
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[] | 2022-01-23T02:03:45
| 2022-01-23T03:45:29
|
CONTRIBUTOR
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For wurtzite MnO, the description given by ICSD is as follows:
```
$ cat ICSD_CollCode262928.cif
#(C) 2021 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure. All rights reserved.
data_262928-ICSD
_database_code_ICSD 262928
_audit_creation_date 2012-08-01
_chemical_name_common 'Manganese oxide (1/1)'
_chemical_formula_structural 'Mn O'
_chemical_formula_sum 'Mn1 O1'
_chemical_name_structure_type Wurtzite#ZnS(2H)
_exptl_crystal_density_diffrn 4.44
_citation_title
;
New crystal structure: synthesis and characterization of hexagonal wurtzite Mn
O
;
loop_
_citation_id
_citation_journal_full
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary 'Journal of the American Chemical Society' 2012 134 8392 8395 JACSAT
loop_
_citation_author_citation_id
_citation_author_name
primary 'Nam Ki Min'
primary 'Kim Yong-Il'
primary 'Jo Younghun'
primary 'Lee Seung Mi'
primary 'Kim Bog G.'
primary 'Choi Ran'
primary 'Choi Sang-Il'
primary 'Song Hyunjoon'
primary 'Park Joon T.'
_cell_length_a 3.3717
_cell_length_b 3.3717
_cell_length_c 5.3855(7)
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 120.
_cell_volume 53.02
_cell_formula_units_Z 2
_space_group_name_H-M_alt 'P 63 m c'
_space_group_IT_number 186
loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 '-x, -x+y, z+1/2'
2 'x-y, -y, z+1/2'
3 'y, x, z+1/2'
4 'x-y, x, z+1/2'
5 'y, -x+y, z+1/2'
6 '-x, -y, z+1/2'
7 'x, x-y, z'
8 '-x+y, y, z'
9 '-y, -x, z'
10 '-x+y, -x, z'
11 '-y, x-y, z'
12 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Mn2+ 2
O2- -2
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_occupancy
Mn1 Mn2+ 2 b 0.33333 0.66667 0.01096 0.04952 1.
O1 O2- 2 b 0.33333 0.66667 0.37547 0.03911 1.
```
I also read [the following description](https://doi.org/10.1016/j.physleta.2020.126494) of this material:
If I understand it correctly, it seems that the [`Seitz symbol of the space group`](https://www.cryst.ehu.es/html/cryst/help_pop-up/seitz_symbol.html) is used here.
In order to get the symmetric representations used in above paper, I tried the following steps using `pymatgen` on Ubuntu 20.04.3 LTS:
```
$ pyenv shell datasci
$ pip install -U pymatgen
$ pip list|grep pymatgen
pymatgen 2022.1.20
$ ipython
Python 3.9.1 (default, Feb 10 2021, 15:30:33)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.31.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
In [2]: from pymatgen.core import Lattice, Structure, Molecule, IStructure
In [3]: s=IStructure.from_file('ICSD_CollCode262928.cif')
/home/werner/.pyenv/versions/3.9.1/envs/datasci/lib/python3.9/site-packages/pymatgen/io/cif.py:1164: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
warnings.warn("Issues encountered while parsing CIF: %s" % "\n".join(self.warnings))
In [4]: a = SpacegroupAnalyzer(s, 0.1)
In [20]: a.get_symmetry_operations()
Out[20]:
[Rot:
[[1. 0. 0.]
[0. 1. 0.]
[0. 0. 1.]]
tau
[0. 0. 0.],
Rot:
[[ 1. -1. 0.]
[ 1. 0. 0.]
[ 0. 0. 1.]]
tau
[0. 0. 0.5],
Rot:
[[ 0. -1. 0.]
[ 1. -1. 0.]
[ 0. 0. 1.]]
tau
[0. 0. 0.],
Rot:
[[-1. 0. 0.]
[ 0. -1. 0.]
[ 0. 0. 1.]]
tau
[0. 0. 0.5],
Rot:
[[-1. 1. 0.]
[-1. 0. 0.]
[ 0. 0. 1.]]
tau
[0. 0. 0.],
Rot:
[[ 0. 1. 0.]
[-1. 1. 0.]
[ 0. 0. 1.]]
tau
[0. 0. 0.5],
Rot:
[[0. 1. 0.]
[1. 0. 0.]
[0. 0. 1.]]
tau
[0. 0. 0.5],
Rot:
[[ 1. 0. 0.]
[ 1. -1. 0.]
[ 0. 0. 1.]]
tau
[0. 0. 0.],
Rot:
[[ 1. -1. 0.]
[ 0. -1. 0.]
[ 0. 0. 1.]]
tau
[0. 0. 0.5],
Rot:
[[ 0. -1. 0.]
[-1. 0. 0.]
[ 0. 0. 1.]]
tau
[0. 0. 0.],
Rot:
[[-1. 0. 0.]
[-1. 1. 0.]
[ 0. 0. 1.]]
tau
[0. 0. 0.5],
Rot:
[[-1. 1. 0.]
[ 0. 1. 0.]
[ 0. 0. 1.]]
tau
[0. 0. 0.]]
```
But I still can't find the intuitive information from the `pymatgen`'s output which is corresponding to what is described in the aforementioned paper. Any hints for building the relationship between them will be highly appreciated. See [here](https://github.com/qzhu2017/PyXtal/issues/187) for relevant discussion.
Regards,
HZ
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| 1,111,749,464
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PR_kwDOACgets4xc44S
| 2,369
|
Return the correct Vasprun().final_energy for VASP 6+ and change the default Outcar().final_energy to be energy(sigma->0)
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[] | null |
[
"@mkhorton -- this is ready for your review at your next convenience.",
"\n[](https://coveralls.io/builds/45904732)\n\nCoverage decreased (-0.6%) to 83.338% when pulling **c5b8d495e400e49a66aad90ddbb2ca31c91ee8f9 on arosen93:rosen-energy** into **4813709cbccd35543e192cef6b7cf78153624cd6 on materialsproject:master**.\n",
"Hi @arosen93, this looks great. My only questions:\r\n\r\n1. Can you add some comments (or change file names) to make clear what version of VASP was used to generated e.g. `vasprun.xml.etest1.gz`\r\n2. The VASP forum post was perhaps a little vague on this, do you know if this behavior definitely changed with 6 (6.1.0?) vs 6.1.2, 6.2.1 etc?\r\n\r\nFor point 2., in particular I'm aware of a large quantity of calculations that were generated with a VASP 6 beta which may incorrectly report its version number. I assume there's no alternative we can take here, i.e. that we just have to trust the version number reported and use that for the `if` statement, rather than another method of being able to figure out if the bug is present?",
"@mkhorton:\r\n1. Certainly, I can make that clearer. \r\n2. I have checked and confirmed that VASP 6.1.0 (and the VASP 6 pre-release used by @rkingsbury) both have the `vasprun.xml` change.\r\n\r\nRe your point 2 follow-up: There is indeed a workaround. The workaround would be to just delete the `if` statement entirely. The codeblock below works for any version of VASP. It's just kind of messy and unnecessary for VASP 6.1.0+, but it will still work for VASP 6.1.0+. The only side-effect is there will be rounding in the 8th digit of the energy (negligible). We can just have this block regardless of version number if you'd prefer.\r\n\r\nhttps://github.com/materialsproject/pymatgen/pull/2369/files#diff-0d68150cedc59844e2cd1ea9f15543fe522b072531e5050fde8a4fe4bee3baf3R625-R628\r\n\r\nEdit: Actually, I could just check to see if both solutions yield the (essentially) the same answer. If they do, it's probably VASP 6+ so just use the normal `e_0_energy`. If they differ, it's probably a messed up `vasprun.xml` and take the latter.",
"I won't refer to the ASE code on this for licensing reasons (though I'm sure it's wonderful!)\r\n\r\n> Actually, I could just check to see if both solutions yield the (essentially) the same answer. If they do, it's probably VASP 6+ so just use the normal e_0_energy. If they differ, it's probably a messed up vasprun.xml and take the latter.\r\n\r\nThis sounds like a great solution.",
"I'm perhaps over-paranoid about edge cases (eg old results that are reporting an incorrect VASP version) but I know in a large enough database these edge cases always happen sooner or later.",
"Yes, good points all around. I will implement a check that is not dependent on the version number just in case. Will get back to you on this!",
"This should do the trick! I now compare the energy computed from two methods: 1) By taking the final `e_0_energy` from the last ionic step, and 2) from the \"bugfix\" approach discussed on the VASP forum. If Option 1 and Option 2 are the same, we'll just take Option 1 because that's what it should be if the `vasprun.xml` is correct (and should occur for VASP 6+). If they differ by 1e-7 or more, we'll take Option 2 because it's a sign that there's something wrong with the `vasprun.xml` (expected for VASP < 6).\r\n\r\nI also added comments to the tests to indicate the version numbers.",
"Perfect, thanks @arosen93 !"
] | 2022-01-23T02:17:49
| 2022-01-25T01:48:41
|
2022-01-25T01:28:34Z
|
MEMBER
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## The Problem
This is to address #2367. In short, there are two issues:
1. `Vasprun().final_energy` does not report `e_0_energy` (the desired energy quantity) for VASP 6+. In an attempt to address the VASP 5.x.x bug documented [here](https://www.vasp.at/forum/viewtopic.php?f=3&t=16942) where `e_wo_entrp` and `e_0_energy` were swapped, Pymatgen seems to have an unintended side-effect of returning energies that are not extrapolated to sigma-->0 for VASP 6+ when the bugfix is no longer needed.
2. `Outcar().final_energy` always reports `e_fr_energy`, which is rarely the desirable quantity. Fortunately, there is no bug with `e_0_energy` in the OUTCAR. This was just a design decision but one that is not intuitive and also inconsistent with the expected behavior of `Vasprun().final_energy`.
## Changes in this PR
1. Bugfix: `Vasprun().final_energy` now returns `e_0_energy` as expected. For VASP < 6, the energies should be the same as before to within 7 decimal places. For VASP 6+, the energies will differ by whatever the difference between `e_wo_entrp` and `e_0_energy` was, as the former was incorrectly returned before.
2. Improvement: `Outcar().final_energy` now prints out `e_0_energy` (also called "energy(sigma->0)" in the OUTCAR) rather than `energy_fr_energy` (also called "free energy TOTEN" in the OUTCAR). This is to be consistent with `Vasprun().final_energy` and because it is generally the desired quantity.
3. Feature addition: `Outcar()` now has two new attributes: `.final_energy_wo_entrp` and `final_fr_energy`, which correspond to `e_wo_entrp` and `e_fr_energy`, respectively. The user can fetch whichever one of the three they desire now, although `.final_energy` gives you the value you'd want in virtually all cases.
## Tests
It is crucial that we get this right, so I am including here some tests (attached) that use different versions of VASP (as well as different IVDW and different ISMEAR for good measure). Four of these are added to the test suite. The desired solution is the `energy(sigma->0)` column, which is taken from the last `energy(sigma->0)` line of the OUTCAR, which has no known issues.
### Tests with Main Branch Pymatgen
I draw your attention to Run 3 and Run 6. The `Vasprun` is not producing the correct energy for VASP 6+.
Also, Run 2 and Run 3 are the same material and settings. If you relied solely on the `Vasprun` final energy, you might incorrectly think that VASP 6.2.1 changed the energy by 0.05 eV when in reality it was a parsing error.
The differences in `Outcar` are just because it was outputting `e_fr_energy` (design decision).
```
Run, energy(sigma->0), Vasprun, Outcar, VASP version
1, -15.89355325, -15.89355325 eV, -15.92106087, 5.4.1
2, -11.18981538, -11.18981538 eV, -11.217323, 5.4.1
---> 3, -11.18986774, -11.1348525 eV, -11.21737536, 6.2.1 <---
4, -15.02557351, -15.02557351 eV, -15.05308113, 5.4.1
5, -15.92852842, -15.92852842 eV, -16.01840921, 5.4.1
---> 6, -33.15807349, -33.15237262 eV, -33.16377435, 6.2.1 <---
```
### Tests with this PR
Everything is as expected now, regardless of version number.
There is slight fluctuation in the eighth decimal place for the `Vasprun` final energy with VASP 5.x.x because I updated how the `vasprun.xml` bugfix is handled to be more robust, at the expense of a rounded 8th decimal place. See the [VASP forum post](https://www.vasp.at/forum/viewtopic.php?f=3&t=16942) for details.
```
Run, energy(sigma->0), Vasprun, Outcar, VASP version
1, -15.89355325, -15.89355324 eV, -15.89355325, 5.4.1
2, -11.18981538, -11.18981538 eV, -11.18981538, 5.4.1
3, -11.18986774, -11.18986774 eV, -11.18986774, 6.2.1
4, -15.02557351, -15.02557351 eV, -15.02557351, 5.4.1
5, -15.92852842, -15.92852843 eV, -15.92852842, 5.4.1
6, -33.15807349, -33.15807349 eV, -33.15807349, 6.2.1
```
[tests.zip](https://github.com/materialsproject/pymatgen/files/7919790/tests.zip)
|
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I_kwDOACgets5CREHZ
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[Not actually a problem] Ionic step energies in Vasprun() w/ vdW interactions are missing the vdW component
|
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[
"Closed because of a misunderstanding on my part. Apologies. I missed the first three keys of the `vasprun.ionic_steps[-1]` dict, which show the expected values. The values I reported above were in the `electronic_steps` part of the dict. It's been a long day of debugging..."
] | 2022-01-23T04:24:06
| 2022-01-23T05:19:53
|
2022-01-23T05:15:06Z
|
MEMBER
|
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In troubleshooting my PR for #2369, I stumbled upon a different but related error involving `Vasprun` and vdW calculations (not sure if this is VASP6-specific or not, but it probably is).
For the attached `vasprun.xml.gz` file, doing
```python
from pymatgen.io.vasp.outputs import Vasprun
Vasprun('vasprun.xml.gz').ionic_steps
```
yields the following energies for the final step:
```
'e_fr_energy': -15.03838978,
'e_wo_entrp': -14.95586691,
'e_0_energy': -15.01088215
```
However, none of these energies contain the vdW contribution. The data should actually be:
```
<i name="e_fr_energy"> -15.92115453 </i>
<i name="e_wo_entrp"> -15.83863167 </i>
<i name="e_0_energy"> -15.89364691 </i>
```
I assume that it was desired to have the vdW contributions as part of the ionic step entries, although perhaps I'm mistaken.
[OUTCAR.gz](https://github.com/materialsproject/pymatgen/files/7919769/OUTCAR.gz)
[vasprun.xml.gz](https://github.com/materialsproject/pymatgen/files/7919770/vasprun.xml.gz).
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PR_kwDOACgets4xeI2p
| 2,371
|
Pass oxidation states between Pymatgen structure/molecule and ASE Atoms
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[
"\n[](https://coveralls.io/builds/45866319)\n\nCoverage decreased (-0.6%) to 83.344% when pulling **31f9f33cd3ea19aec9196163b285f8fbe512aace on arosen93:rosen-ase-props** into **4813709cbccd35543e192cef6b7cf78153624cd6 on materialsproject:master**.\n",
"Thanks."
] | 2022-01-24T04:41:44
| 2022-01-25T18:06:15
|
2022-01-25T14:47:27Z
|
MEMBER
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This hopefully should be my last update in my quest to enhance the `AseAtomsAdaptor`.
In this PR:
1. Oxidation states are now passed from Pymatgen structure/molecule objects to ASE atoms objects. Since these aren't `site_properties`, they never got transferred. This is the main change.
2. Charges passed from Pymatgen to ASE now get assigned "intelligently" in the ASE Atoms object such that the ASE-recommended `atoms.get_charges()` function retrieves them.
3. Several new tests have been added to the test suite, most importantly a check that doing Atoms --> Structure --> Atoms as well as Structure --> Atoms --> Structure result in identical objects before/after the transformation cycle. This is an important check that was missing, as it's very easy for a property to be lost in the translation if not coded appropriately. This will also help future-proof the module if/when others make changes.
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PR_kwDOACgets4xf1IV
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Added file_path parameter to ComputedEntry and fixed entry_id in Vasprun.get_computed_entry
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[
"Sorry about the delay in reviewing this PR. However, I don't think file path is a key parameter that needs an attribute by itself. The entry object already has a \"data\" attribute that allows you to store variables in there. Can you rewrite this to just store the file path in the data attribute? Thanks.",
"@shyuep Thanks for taking the time to review this PR. I have now updated this as requested.",
"\n[](https://coveralls.io/builds/56023906)\n\nCoverage: 71.152% (-3.8%) from 74.981% when pulling **bf7b82933d78e708ae8f1024fda1445caf6d1381 on robertcdickson:master** into **21852078f6e365dc96c70384a28ea0096b5743d0 on materialsproject:master**.\n",
"Closing this for now since it's causing a [test failure](https://github.com/materialsproject/pymatgen/actions/runs/3940836292/jobs/6742446403). Feel free to re-open if not stale.\r\n\r\n```py\r\n try:\r\n vasprun = Vasprun(file_path)\r\n except Exception as ex:\r\n logger.debug(f\"error in {file_path}: {ex}\")\r\n return None\r\n \r\n> self._data[\"file_path\"] = file_path\r\nE TypeError: list indices must be integers or slices, not str\r\n\r\npymatgen/apps/borg/hive.py:142: TypeError\r\n```"
] | 2022-01-24T13:52:19
| 2023-01-17T16:03:10
|
2023-01-17T15:53:03Z
|
NONE
|
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## Summary
Include a summary of major changes in bullet points:
* file_path parameter added to ComputedEntry
* fixed problem with generating entry_id in get_computed_entry method of Vasprun
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* Nothing else needs done. [WIP] added as this is my first commit to project.
## 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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I_kwDOACgets5CUpCu
| 2,373
|
pmg config CLI fails
|
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[
"Thanks for reporting this. This is due to a recent change in the way yaml files are handled in ruamel.yaml. \r\nI just fixed it in the code."
] | 2022-01-24T14:16:49
| 2022-01-24T14:21:35
|
2022-01-24T14:20:58Z
|
NONE
|
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**Describe the bug**
Cannot configure POTCAR setup as "pmg config" fails to add keywords to .pmgrc.yaml
**To Reproduce**
Fresh install with conda:
$ conda create --name my_pmg python=3.8
$ conda activate my_pmg
$ conda install -c conda-forge pymatgen
run "pmg config --add", for example:
pmg config --add PMG_DEFAULT_FUNCTIONAL PBE_52
throws error:
(pmg2) s1351949@SCE-SOPA-00584:~/TEMP/VASP$ pmg config --add PMG_DEFAULT_FUNCTIONAL PBE_52
Traceback (most recent call last):
File "/home/s1351949/miniconda3/envs/pmg2/bin/pmg", line 11, in <module>
sys.exit(main())
File "/home/s1351949/miniconda3/envs/pmg2/lib/python3.8/site-packages/pymatgen/cli/pmg.py", line 297, in main
args.func(args)
File "/home/s1351949/miniconda3/envs/pmg2/lib/python3.8/site-packages/pymatgen/cli/pmg_config.py", line 217, in configure_pmg
add_config_var(args)
File "/home/s1351949/miniconda3/envs/pmg2/lib/python3.8/site-packages/pymatgen/cli/pmg_config.py", line 202, in add_config_var
dumpfn(d, SETTINGS_FILE, default_flow_style=False)
File "/home/s1351949/miniconda3/envs/pmg2/lib/python3.8/site-packages/monty/serialization.py", line 119, in dumpfn
yaml.dump(obj, fp, *args, **kwargs)
TypeError: dump() got an unexpected keyword argument 'default_flow_style'
**Expected behavior**
Add PMG_DEFAULT_FUNCTIONAL keyword to .pmgrc.yaml file
**Desktop (please complete the following information):**
- OS:Linux
- Python 3.8.12
- fresh conda environment for pmg
|
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https://github.com/materialsproject/pymatgen/pull/2374
| 1,112,921,211
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PR_kwDOACgets4xgotM
| 2,374
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Added property symbol_list to class SiteCollection.
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[
"Thanks for the suggested contribution. But since this is a method that is a one-liner and not that frequently used, I am not in favor of adding it to the already long list of Structure properties/methods.",
"Thanks for your comment @shyuep. I agree that there are already plenty of methods / properties in `Structure`. In this particular case though, I think it would be really nice to have a method / property that outputs a list of *strings* of atom identifiers (e.g. chemical symbols). The rationale is that, as many other postprocessing codes need this information as an input, the unique format of `species` in pymatgen makes it difficult to directly use `species` as input to other codes. I would imagine such routine to be rather common, as from my own experience, I have to write this one line of code many times. and would really appreciate if you could provide some comment / suggestion. Thanks again!"
] | 2022-01-24T17:12:45
| 2022-01-24T18:17:21
|
2022-01-24T17:18:32Z
|
CONTRIBUTOR
|
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## Summary
* Added a new property, symbol_list, within the class SiteCollection in core/structure.py. This property returns the list of chemical symbols of all atoms in the collection. This property may be useful for postprocessing purposes, as the "species" property does not return a list of strings.
## Additional dependencies introduced (if any)
No additional dependency is needed.
## TODO (if any)
N/A
## 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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| 1,112,983,963
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PR_kwDOACgets4xg10K
| 2,375
|
Extend get_symmetric_site to non laue slabs
|
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[
"Thanks. Can you add a unittest for the non-Laue part of the code pls? The tests should be in pymatgen/core/tests/test_surface.py",
"Hello, I modified the function test_get_symmetric_sites in pymatgen/core/tests/test_surface.py to test the new version of the get_symmetric_site function.\r\n\r\n> Thanks. Can you add a unittest for the non-Laue part of the code pls? The tests should be in pymatgen/core/tests/test_surface.py\r\n\r\n",
"\n[](https://coveralls.io/builds/46298151)\n\nCoverage decreased (-0.5%) to 83.451% when pulling **82309e9fa68008ed15e4fd68c3f0d3306981b0bb on bcamino:master** into **41e171b5aeae63bf73c130f7ef451fd77aa46e0f on materialsproject:master**.\n",
"Hi @shyuep, is there anything else I should do about this PR? Thanks for your help (first time submitting a PR here).\r\nCheers,\r\nBruno",
"I apologize for this, but there is a conflict due to some recent changes. Can you resolve the conflict? @CFritz145 Do you mind taking a look and see if there are any issues with this change to support non-laue slabs? Thanks.\r\n",
"Sure thing, I'll take a look at the PR later during the day. Thanks for letting me know",
"> I apologize for this, but there is a conflict due to some recent changes. Can you resolve the conflict? @CFritz145 Do you mind taking a look and see if there are any issues with this change to support non-laue slabs? Thanks.\r\n\r\nHello, the only conflict I am seeing is the piece of code I replaced in get_symmetric_site. Is there more to that? Cheers, Bruno",
"I seen no issue with compatibility, however I thinks there's a simpler solution to all of this. \r\n\r\nThe point of this PR is to identify symmetric surface sites by generalizing what we consider a \"symmetric slab\". A slab doesn't need Laue symmetry (centrosyymetric) to be symmetric as implied by the PR, e.g. a mirror plane perpendicular to the c-axis of the slab or a screw axis along c would make it possible to symmetric sites between two surfaces. The get_symmetric_site() method of the Slab class is a bit outdated and uses the get_laue() class to determine slab symmetry, so yes that needs to be changed. However the operation you proposed to identify slab symmetry is believe is already taken care of by the .is_symmetric() function which **previously operated under the assumption that a slab is symmetric IFF it has Laue symmetry**. This was modified a few months ago to now take into account any symmop along the c-axis that gets you the same sites on both sides of the slab (essentially treating symmetry the slab like its 2D symmetry as you proposed). @bcamino correct me if I'm wrong but would replacing the operations proposed in the PR with the .is_symmetric() function accomplish the same thing?",
"Hi @CFritz145, thank you for your response. The goal of this PR is twofold:\r\n\r\nthe first, as you identified, is to use is_symmetric() rather than is_laue in defining the symmetry of a slab. \r\n\r\nthe second is being able to get the symmetric site that sits on the other side of the same slab. In the current version of get)symmetric_site(), there are instances in which the point found by this function is symmetric indeed, but in the neighbouring cell. If you want to replicate this behaviour you can use:\r\n\r\nbulk = Structure.from_spacegroup(\"Fm-3m\", Lattice.cubic(6.63), [\"Cu\"], [[0, 0, 0]])\r\nadsorbate = Molecule('O',[[0.0, 0.0, 0.0]])\r\nsubstrate = SlabGenerator(initial_structure=bulk,miller_index=[1,0,0],min_slab_size=15.,min_vacuum_size=10.,center_slab=True).get_slab()\r\nads_sites = AdsorbateSiteFinder(substrate)\r\nsub_ads = ads_sites.adsorb_both_surfaces(adsorbate,repeat=[1,1,1])[0] \r\n\r\nIn the first adsorption structure, the first oxygen is placed at [0.5000, 0.5000, -0.8103] and duplicated at [0.0000, -0.0000, 0.8103] (all fractional coordinates). This latter point was obtained by applying the \r\nRot:\r\n[[ 1. 0. 0.]\r\n [ 0. -1. 0.]\r\n [ 0. 0. -1.]]\r\ntau\r\n[0.5 0.5 0. ]\r\nsymmetry operator. This duplicated oxygen atom is equivalent to the first one, but it is in the cell (0,0,-1). This doesn’t cause problems in a plane wave code where slabs are simulated as 3D structures with a vacuum region between slabs. However, I’m interested in generating structure with pymatgen for the CRYSTAL code. CRYSTAL uses localised atomic orbital generated Bloch functions as basis set and treats the slabs as 2D systems. Therefore, I do need to have the symmetric adsorbate on the side of the same slab. In addition, having both adsorbates on the same slab makes it easier to visualise the structures. \r\n\r\nThe proposed methodology (centering the slab at z=0 and getting the symmetry operators) ensures this is true.\r\n\r\nPlease let me know if you require any more information about this PR.\r\n\r\nCheers,\r\n\r\nBruno",
"Hi @bcamino \r\n\r\nThank you for the explanation. \r\n\r\nSo the heart of the issue here seems to be that the symmetry operators return a fractional coordinate outside the periodic boundary condition. In the block of code you sent, for example, the return slab had an O atom appended to a position at c < 0 which poses problems in CRYSTAL. This PR solves this issue by ensuring the fractional coordinates remain inside the PBC ie between 0 and 1. Let me know if this may work as an alternative:\r\n\r\nAfter identifying a symmetric surface frac_coord using .get_symmetric_site(), the function will create a PeriodicSite with the dummy site. This is just a crystal site with the lattice information in it so that it can determine the frac_coords. With our dummy PeriodicSites, we can use the class method .to_unit_cell() which ensures the site will remain inside the bounds of the lattice. Then we return the frac_coord or cartesian_coord. This will avoid any symmetric positions being added outside the PBC. \r\n\r\nJust trying to seeing if there might be a more parsimonious solution, but if there's an underlying issue that .to_unit_cell() can't solve here, I see no issue in the PR from my side.",
"Hi @CFritz145,\r\n\r\nthank you! That does sound like a better plan. I’m going to modify this PR to use this approach. \r\n\r\nOne more thing: in the current implementation, if no slab satisfied the is_laue() condition, the site2 that was generated by the last symmop is returned. However, this would be a non symmetrical slab. What do you think about adding a check at the beginning of get_symmetric_site that checks if the initial slab is symmetric? I believe having an initial symmetric slab is a condition to obtain a symmetric one with adsorbates on both surfaces (please correct me if I’m wrong). \r\n\r\nIf you think this is a good idea, in case of an initial non symmetric slab, should the function raise a warning message and return None?\r\n\r\nThank you so much for your help.\r\n\r\nCheers,\r\n\r\nBruno",
"Hi @bcamino \r\n\r\nGlad I could help. \r\n\r\nIn regards to returning an assymetric site, you are right, it will return something regardless of whether or not it found a symmetric site. I originally planned submit a PR on this but lost track of it somewhere down the line. \r\n\r\nIf you want, you can copy this block of code i modified along time ago into the PR, it should be able to address everything talked about here. The idea is to return a Nonetype instead of an actual coordinate if no symmetric site was found. Feel free to modify as you see fit.\r\n\r\n` def get_symmetric_sites(self, points, cartesian=False):\r\n \"\"\"\r\n This method uses symmetry operations to find equivalent sites on\r\n both sides of the slab. Works mainly for slabs with Laue\r\n symmetry. This is useful for retaining the non-polar and\r\n symmetric properties of a slab when creating adsorbed\r\n structures or symmetric reconstructions.\r\n\r\n Arg:\r\n point: Fractional coordinate.\r\n\r\n Returns:\r\n point: Fractional coordinate. A point equivalent to the\r\n parameter point, but on the other side of the slab\r\n \"\"\"\r\n\r\n ops = SpacegroupAnalyzer(self).get_symmetry_operations(cartesian=cartesian)\r\n\r\n # Each operation on a point will return an equivalent point.\r\n # We want to find the point on the other side of the slab.\r\n found_site = False\r\n for op in ops:\r\n # skip any symmops that don't bring the site to the other side of the slab \r\n if all((op.rotation_matrix[2] == [0, 0, 1])):\r\n continue\r\n\r\n slab = self.copy()\r\n sites2 = op.operate_multi(points)\r\n\r\n # Add dummy site to check the overall structure is symmetric\r\n for site2 in sites2:\r\n slab.append(\"O\", site2, coords_are_cartesian=cartesian)\r\n for point in points:\r\n slab.append(\"O\", point, coords_are_cartesian=cartesian)\r\n\r\n try:\r\n if slab.is_symmetric():\r\n found_site = True\r\n break\r\n except TypeError:\r\n # error related to spacegroup analysis\r\n pass\r\n \r\n if found_site:\r\n psite = PeriodicSite('O', site2, slab.lattice, to_unit_cell=True,\r\n coords_are_cartesian=cartesian)\r\n site2 = psite.coords if cartesian else psite.frac_coords\r\n return sites2\r\n else:\r\n warnings.warn('Cannot add symmetric site!')\r\n return None\r\n`",
"Please let me know once this PR is ready. Thanks",
"Hello @shyuep , after some more tests I don't think this PR will be necessary, so I will close it now. Thank you, Bruno"
] | 2022-01-24T18:15:44
| 2022-05-31T16:36:46
|
2022-05-31T16:36:46Z
|
NONE
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## Summary
* The current version of get_symmetric_site relies on slabs to have Laue symmetry. Treating a slab as a 3D object introduces symmetry operators that duplicate a site to a neighbouring cell in the z direction. This introduces two possible issues:
* some of the operators will duplicate the point to be on the same side of the slab in a neighbouring cell rather than on the other side;
* if the slab is to be used in a code such as CRYSTAL17 that treats slabs as objects with 2D symmetry, all the atoms need to be in the same unit cell (at least along the z direction)
* To solve the issue, I propose this approach:
* center the slab and the point at z=0
* get the symmetry operators to this structure
* apply the symmops to the point coordinates. If the resulting point is at -z coordinate (where z was the coordinate of the original point), check the slab is symmetric (rather than laue)
* if the slab is symmetric return the coordinates of the point
## Additional dependencies introduced (if any)
* No additional dependencies were added
## TODO (if any)
* None for this functionality
## 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.
[New_get_symmetric_site.ipynb.zip]
Jupyter Notebook showing the tests I performed for the new functionality.
(https://github.com/materialsproject/pymatgen/files/7935219/New_get_symmetric_site.ipynb.zip)
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I_kwDOACgets5CXGO8
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import problem cannot import name 'Structure' from 'pymatgen' (unknown location)
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[
"You should open an issue with pycdt. As noted [here](https://pymatgen.org/#major-announcement-v2022-0), `from pymatgen import Structure, Element` should now be `from pymatgen.core import Structure, Element`. You can refer to the aforementioned page for additional details.\r\n\r\npycdt will either need to update their import statements (recommended) or rely on a version of pymatgen before v2022.",
"It looks like someone has already opened a pull request for this here: https://github.com/mbkumar/pycdt/pull/10/files",
"> You should open an issue with pycdt. As noted [here](https://pymatgen.org/#major-announcement-v2022-0), `from pymatgen import Structure, Element` should now be `from pymatgen.core import Structure, Element`. You can refer to the aforementioned page for additional details.\r\n> \r\n> pycdt will either need to update their import statements (recommended) or rely on a version of pymatgen before v2022.\r\n\r\nThanks for your answer above\r\nMay I know how could I install an old version of pymatgen ? ",
"Sure, you can see the list of Pymatgen versions [here](https://pypi.org/project/pymatgen/#history). You could, for instance, install version 2021.3.9 via `pip install pymatgen==2021.3.9`.",
"@FrankSays pycdt accepted the PR, so hopefully updating to the latest PyCDT will fix this problem.",
"@mkhorton, looks like you can close this one."
] | 2022-01-25T02:28:01
| 2022-03-07T19:10:58
|
2022-03-07T19:10:58Z
|
NONE
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When I used pycdt, it give error as:
it did not happen in old version.
File "/public1/home/sch1893/apps/miniconda3/envs/pycdt/bin/pycdt", line 4, in <module>
__import__('pkg_resources').run_script('pycdt==2.0.5', 'pycdt')
File "/public1/home/sch1893/apps/miniconda3/envs/pycdt/lib/python3.9/site-packages/pkg_resources/__init__.py", line 651, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/public1/home/sch1893/apps/miniconda3/envs/pycdt/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1448, in run_script
exec(code, namespace, namespace)
File "/public1/home/sch1893/apps/miniconda3/envs/pycdt/lib/python3.9/site-packages/pycdt-2.0.5-py3.9.egg/EGG-INFO/scripts/pycdt", line 40, in <module>
from pycdt.core.defects_analyzer import ComputedDefect
File "/public1/home/sch1893/apps/miniconda3/envs/pycdt/lib/python3.9/site-packages/pycdt-2.0.5-py3.9.egg/pycdt/core/defects_analyzer.py", line 24, in <module>
from pycdt.utils.parse_calculations import SingleDefectParser
File "/public1/home/sch1893/apps/miniconda3/envs/pycdt/lib/python3.9/site-packages/pycdt-2.0.5-py3.9.egg/pycdt/utils/parse_calculations.py", line 32, in <module>
from pycdt.core.chemical_potentials import MPChemPotAnalyzer
File "/public1/home/sch1893/apps/miniconda3/envs/pycdt/lib/python3.9/site-packages/pycdt-2.0.5-py3.9.egg/pycdt/core/chemical_potentials.py", line 18, in <module>
from pymatgen import Structure, Element
ImportError: cannot import name 'Structure' from 'pymatgen' (unknown location)
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I_kwDOACgets5CXaRZ
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Empty `.pmgrc.yaml` file produces error with `yaml.safe_load` (or `yaml.load`) and `update`
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[
"I already fixed it in the latest release. BUt if your pymatgen is 2022.0.17, that is the old version.",
"Hi,\r\nI have a similar problem:\r\nwhen enter: pmg config --add PMG_VASP_PSP_DIR /home/myname/PYMATGEN_POTCAR/POT_GGA_PAW_PBE/\r\nerror:\r\n**Existing /home/myname/.pmgrc.yaml backed up to /home/linwen/.pmgrc.yaml.bak\r\nTraceback (most recent call last):\r\n File \"/home/myname/anaconda3/envs/vasp_highThroughComputer/bin/pmg\", line 11, in <module>\r\n sys.exit(main())\r\n File \"/home/myname/anaconda3/envs/vasp_highThroughComputer/lib/python3.7/site-packages/pymatgen/cli/pmg.py\", line 440, in main\r\n return args.func(args)\r\n File \"/home/myname/anaconda3/envs/vasp_highThroughComputer/lib/python3.7/site-packages/pymatgen/cli/pmg_config.py\", line 218, in configure_pmg\r\n add_config_var(args)\r\n File \"/home/myname/anaconda3/envs/vasp_highThroughComputer/lib/python3.7/site-packages/pymatgen/cli/pmg_config.py\", line 203, in add_config_var\r\n dumpfn(d, SETTINGS_FILE, default_flow_style=False)\r\n File \"/home/myname/anaconda3/envs/vasp_highThroughComputer/lib/python3.7/site-packages/monty/serialization.py\", line 119, in dumpfn\r\n yaml.dump(obj, fp, *args, **kwargs)\r\nTypeError: dump() got an unexpected keyword argument 'default_flow_style'**\r\n",
"As noted above, please upgrade your pymatgen to the latest version. ",
"I have installed pymatgen with \"conda install pymatgen\"\r\nThen, conda update pymatgen\r\nBut, conda list\r\nMy postman's version is pymatgen-2022.0.17\r\nHow to update pymatgen to the latest version?",
"You are on py37. That the latest version for that python version. I suggest you go to py38 or 39. Py37 is very old. ",
"> You are on py37. That the latest version for that python version. I suggest you go to py38 or 39. Py37 is very old.\r\n\r\nThank you for your reply.\r\nIt works."
] | 2022-01-25T05:09:52
| 2022-03-27T07:53:59
|
2022-01-25T15:54:36Z
|
NONE
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The bug in https://github.com/materialsproject/pymatgen/issues/2373 seems to produce an empty `.pmgrc.yaml` configuration file for me
```python
Traceback (most recent call last):
File "/usr/local/bin/pmg", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.7/dist-packages/pymatgen/cli/pmg.py", line 440, in main
return args.func(args)
File "/usr/local/lib/python3.7/dist-packages/pymatgen/cli/pmg_config.py", line 218, in configure_pmg
add_config_var(args)
File "/usr/local/lib/python3.7/dist-packages/pymatgen/cli/pmg_config.py", line 203, in add_config_var
dumpfn(d, SETTINGS_FILE, default_flow_style=False)
File "/usr/local/lib/python3.7/dist-packages/monty/serialization.py", line 119, in dumpfn
yaml.dump(obj, fp, *args, **kwargs)
TypeError: dump() got an unexpected keyword argument 'default_flow_style'
```
After using the fallback of `export PMG_MAPI_KEY={MP_API_KEY}`, an error is later produced when trying to load the empty config file:
```python
from pymatgen.core import Composition
```
```python
/usr/local/lib/python3.7/dist-packages/pymatgen/core/__init__.py in <module>()
59
60
---> 61 SETTINGS = _load_pmg_settings()
62 locals().update(SETTINGS)
/usr/local/lib/python3.7/dist-packages/pymatgen/core/__init__.py in _load_pmg_settings()
49 with open(SETTINGS_FILE) as f:
50 d_yml = yaml.safe_load(f)
---> 51 d.update(d_yml)
52 except OSError:
53 # If there are any errors, default to using environment variables
TypeError: 'NoneType' object is not iterable
```
The workaround is to delete the empty file, and only use the `export` command above or use the [latest changes](https://github.com/materialsproject/pymatgen/issues/2373#issuecomment-1020151373) (which I'm sure will go into a new release soon), or to make the empty file read:
```yaml
PMG_MAPI_KEY: <my-api-key>
```
[](https://colab.research.google.com/github/sparks-baird/piro/blob/main/piro/notebooks/BaTiO3-Example-Colab.ipynb)
`pymatgen` version is `2022.0.17`.
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| 1,113,528,470
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I_kwDOACgets5CXxiW
| 2,378
|
pmg command becomes not to work
|
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[
"You need to replace the `<MY_PSP>`, etc. with the actual variables relevant for your system. ",
"Dear shyuep, \r\n\r\nThank you for your comment.\r\nI reset the locations of potcar files like\r\n`pmg config -p ~/POT_GGA_PAW_PBE_52 ~/vasp_potentials`\r\n`pmg config --add PMG_VASP_PSP_DIR ~/vasp_potentials`\r\n\r\nMy settings and pmg command works after that.\r\nIn my case, empty .pmgrc.yaml was created and it caused my trouble. I found that a similar situation was already reported in #2377. My pmg command recovered after deleting the .pmgrc.yaml file.\r\n\r\nThank you again for your help.\r\n "
] | 2022-01-25T07:35:10
| 2022-01-26T02:30:48
|
2022-01-25T14:54:25Z
|
NONE
|
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|
Dear all,
I installed pymatgen through conda. Installation of pymatgen was OK.
However, after setting up the location of POTCAR files according to the instruction in the official web page, pmg command become not t work anymore. In the the setting up of the POTCAR files, I run these command.
> pmg config -p <EXTRACTED_VASP_POTCAR> <MY_PSP>
> pmg config --add PMG_VASP_PSP_DIR <MY_PSP>
> pmg config --add PMG_DEFAULT_FUNCTIONAL PBE_52
The following error messages appear when pmg command with any option is run.
###############################
Traceback (most recent call last):
File "/home/kuwabara/anaconda3/envs/pymatgen/bin/pmg", line 7, in <module>
from pymatgen.cli.pmg import main
File "/home/kuwabara/anaconda3/envs/pymatgen/lib/python3.10/site-packages/pymatgen/cli/pmg.py", line 15, in <module>
from pymatgen.core import SETTINGS
File "/home/kuwabara/anaconda3/envs/pymatgen/lib/python3.10/site-packages/pymatgen/core/__init__.py", line 54, in <module>
SETTINGS = _load_pmg_settings()
File "/home/kuwabara/anaconda3/envs/pymatgen/lib/python3.10/site-packages/pymatgen/core/__init__.py", line 44, in _load_pmg_settings
d.update(d_yml)
TypeError: 'NoneType' object is not iterable
###############################
I uninstalled pymatgen and reinstall. The problem is not resolved.
- OS: Ubuntu 20.04.3 LTS (on WSL2, Windows10)
- pymatgen 2022.1.24
- python 3.10.2
|
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| 1,114,009,850
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PR_kwDOACgets4xkKXz
| 2,379
|
Flynt
|
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[] | null |
[
"\n[](https://coveralls.io/builds/45936403)\n\nCoverage decreased (-0.6%) to 83.373% when pulling **8b697ed4fa702bb2b7ddefb4d9fb9a60fa6a3657 on janosh:flynt** into **5a05f662d35ab3c0d93f252f1c73e813e87c75f6 on materialsproject:master**.\n"
] | 2022-01-25T15:11:19
| 2022-01-25T19:29:19
|
2022-01-25T19:01:30Z
|
MEMBER
|
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|
[`flynt`](https://github.com/ikamensh/flynt) auto-converts old string literal formatting to [faster](https://realpython.com/python-f-strings/#speed) and more concise f-strings.
|
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| 1,114,285,248
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PR_kwDOACgets4xlEiQ
| 2,380
|
flynt --aggressive
|
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[
"\n[](https://coveralls.io/builds/45955901)\n\nCoverage decreased (-0.6%) to 83.372% when pulling **04d7a99182cfea007e048b1e5700208bb4e721c3 on janosh:flynt-aggressive** into **6c31f7e38268986bd23110c2fbd4f14a09042a2a on materialsproject:master**.\n"
] | 2022-01-25T19:35:03
| 2022-01-26T19:04:01
|
2022-01-26T18:28:34Z
|
MEMBER
|
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Same as #2379 but using `flynt`'s `--aggressive` flag and more careful checking of changes.
|
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| 1,114,509,441
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PR_kwDOACgets4xlzWv
| 2,381
|
Weighted average position with PBC
|
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[
"\n[](https://coveralls.io/builds/46011293)\n\nCoverage decreased (-0.6%) to 83.39% when pulling **0d26db1b7167db6efa81b3192317609efa221bee on jmmshn:defect_finder** into **72849371a03ffda519e1f590776001b9076c9cd8 on materialsproject:master**.\n",
"Thanks. But I am not sure this shuld be in Lattice. I am not even sure how the weighted average is defined - fractional or cartesian coords? If this method is mainly for defect finding, it can be implemented in the defects package.",
"So this is coded for `frac_coords` but I think that since the transformation is linear the weighted average position can just be transformed with `get_cartesean_coord`.\r\n\r\nI need this for some defect code development but I imagine that people might have a need to average some scalar property on a few sites and get an effective coarse-grained value.\r\nThe situation above seems pretty general and this function will allow us to easily do that.\r\n ",
"Well, the main purpose of such a function that I can think of is to do something like calculating moment of inertias (atomic mass weighted position). In any case, I don't think it should be done in Lattice. It is at best a SiteCollection method. And everything should be done with cartesian coords (fractional coord averaging doesn't make much sense since the PBC can cause the correct fractional coordinates for neighbors to be quite different).",
"> It is at best a SiteCollection method\r\n\r\nI'll look at this.\r\n\r\n> fractional coord averaging doesn't make much sense since the PBC can cause the correct fractional coordinates for neighbors to be quite different\r\n\r\nThe code in this PR specifically deals with PBC so that even if the provided positions in the list \"wraps\" the average point does not. \r\nAn example will be averaging the following points.\r\n```\r\n [0.6, 0.7, 0.5],\r\n [0.9, 0.8, 0.5],\r\n [0.1, 0.2, 0.5],\r\n [0.1, 0.95, 0.5],\r\n```\r\nGives the same result as averaging:\r\n```\r\n[[0.6, 0.7, 0.5],\r\n [0.9, 0.8, 0.5], \r\n[1.1, 1.2, 0.5], \r\n[1.1, 0.95, 0.5]]\r\n```\r\nBecause the code understands that the last 2 points should be wrapped. This allows users to not be super worried about providing the exactly correct period image index.\r\n",
"What is the practical usage for allowing for weighted positions? To calculate centre of mass?",
"The origin of this was that I needed to take the weighted average of a scalar disturbance field on a bunch of atoms.\r\nThen I realized that crossing the boundary condition what going to be a problem so this function is just the math of how to deal with average positions across PCB.",
"Although I do acknowledge that if people use a set of points that are spread across the entire unit cell, the answer of where the COM is non-unique. It's only unique if the points are close together to begin with.",
"Will include this code with the defect position finder "
] | 2022-01-26T00:52:06
| 2022-02-21T03:16:06
|
2022-02-21T03:16:06Z
|
CONTRIBUTOR
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## Summary
* Added function to find the weighted average of positions in a periodic lattice
* Added test
This is in preparation for a provenance agnostic defect position identification
|
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I_kwDOACgets5CcalE
| 2,384
|
structure.as_dict()["charge"] is None even though structure.charge == 0
|
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[
"I agree. As for why it is self._charge, I think that stores the input charge given by the user. But in other cases, the charge of the structure is given by the sum of the oxidation states of the species where available. In general, charge on a structure is pretty arbitrarily defined. "
] | 2022-01-26T08:20:19
| 2022-01-26T18:36:32
|
2022-01-26T18:36:32Z
|
MEMBER
|
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```python
from pymatgen.core import Structure
structure = Structure(
lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
species=["Mg", "O"],
coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
)
print(structure.charge) # prints 0
print(structure.as_dict()["charge"]) # prints None
assert structure.charge == structure.as_dict()["charge"]
```
As demonstrated in the above example, when `structure.charge` is left at the default value of 0, the `.as_dict()["charge"]` is returned as `None`. It would be ideal if these were consistent (i.e. the latter should be 0, in my opinion).
Is there a specific reason why `self._charge` is used below instead of `self.charge`?
https://github.com/materialsproject/pymatgen/blob/6c31f7e38268986bd23110c2fbd4f14a09042a2a/pymatgen/core/structure.py#L2205-L2211
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PR_kwDOACgets4xmkHR
| 2,385
|
Autoflake
|
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[
"\n[](https://coveralls.io/builds/45961062)\n\nCoverage decreased (-0.6%) to 83.371% when pulling **c3592de6d003fd0439af90d3ddf19bd5c0b81b4c on janosh:autoflake** into **6c31f7e38268986bd23110c2fbd4f14a09042a2a on materialsproject:master**.\n"
] | 2022-01-26T08:26:47
| 2022-01-26T19:04:00
|
2022-01-26T18:28:13Z
|
MEMBER
|
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Add `--ignore-init-module-imports` to `autoflake` hook in `.pre-commit-config.yaml`. Applies all the other rules across the code base.
|
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| 1,115,046,053
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I_kwDOACgets5CdkCl
| 2,386
|
crystal orientation of slab in all directions
|
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[
"Not quite sure what you mean. If you are referring to the lattice directions, that can be obtained from the Slab.lattice object.",
"Ok, maybe my question was not clear.\r\nSuppose that I created a slab that has the crystal direction say [1-100] (for HCP family as an example) of the slab surface. Now, I want to know the two crystallographic directions that are orthogonal to one another and also to [1-100] direction. ",
"The c lattice vector is always the normal to the plane for Slab objects. The plane itself is defined by vectors a and b. Those are not always perpendicular to c. There is no reason why they must be. If you want them to be perpendicular, you can use the get_orthgonal_c_slab method. \r\n\r\nAs an aside, these questions should be posed on the matsci.org forum since they are not \"issues\" with pymatgen per se. ",
"As I understood, slab.miller_index provides the crystallographic direction along the c vector. \r\nYes, a and b do not have to be orthogonal to create a slab and just need to be normal to c vector. However, c vector does not necessarily always represent the crystallographic direction of the surface. A crystallographic orientation of a slab surface, say (1-10), can be along the c vector that is [0 0 c_z]. I wonder if it is possible to find (by pymatgen) the crystallographic direction along a and b vectors even if they are not orthogonal. \r\n\r\nIn other words, as I can find miller index of the slab surface, can I also find similar along a and b vectors?\r\n\r\nThanks for the link. "
] | 2022-01-26T13:55:47
| 2022-01-27T04:30:42
|
2022-01-26T14:36:24Z
|
NONE
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I created a slab by SlabGenerator of pymatgen.core.surface. I see the miller_index of the slab surface. However, I also want to know the crystal orientation of other two orthogonal directions. How is it possible by pymatgen?
|
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PR_kwDOACgets4xnvV7
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|
Fix readme badges
|
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[
"While we're at it, what do you think of converting the readme to Markdown? RST is a pain to write.",
"\n[](https://coveralls.io/builds/45969046)\n\nCoverage decreased (-0.6%) to 83.373% when pulling **dfd56f6706c44ef35716280786fe796b6fcbd025 on janosh:readme-badges** into **6c31f7e38268986bd23110c2fbd4f14a09042a2a on materialsproject:master**.\n",
"Sphinx uses RST. I would prefer not to have to handle two different documentation formats. The README is basically a cut and paste of the introduction RST. "
] | 2022-01-26T14:51:41
| 2022-01-27T08:10:07
|
2022-01-26T18:26:48Z
|
MEMBER
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Follow-up to #2351.
- uniform shield.io readme badges
- brought onto 1 line
- fix GH CI badge
- add PyPI download badge
## Before
## After
|
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| 1,115,229,169
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PR_kwDOACgets4xoIgb
| 2,388
|
Store the actual charge and spin_mult in structure.as_dict()
|
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[
"Pls add a test to make sure the new behavior is correct. Thanks.",
"\n[](https://coveralls.io/builds/45976139)\n\nCoverage decreased (-0.6%) to 83.375% when pulling **b706b6560ea94f1444bb48d0cdb960b255ec850d on arosen93:rosen-charge** into **6c31f7e38268986bd23110c2fbd4f14a09042a2a on materialsproject:master**.\n",
"Thanks."
] | 2022-01-26T16:39:16
| 2022-01-26T18:36:43
|
2022-01-26T18:27:50Z
|
MEMBER
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Addresses #2384.
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| 1,115,343,191
|
PR_kwDOACgets4xodGj
| 2,389
|
PDEntry.__repr__ include name attr if not fallback value
|
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[
"Thanks. I don't have a problem with this. The repr is purely for end user readability."
] | 2022-01-26T18:19:23
| 2022-01-26T19:03:11
|
2022-01-26T18:26:11Z
|
MEMBER
|
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Override `Entry.__repr__` in `PDEntry` to include the `name` if its not the fallback value of reduced composition.
**Before**
```py
PDEntry("LiFeO2", 53, name="mp-757614")
>>> PDEntry : Li1 Fe1 O2 with energy = 53.0000
```
**After**
```py
PDEntry("LiFeO2", 53, name="mp-757614")
>>> PDEntry : Li1 Fe1 O2 (mp-757614) with energy = 53.0000
PDEntry("LiFeO2", 53)
>>> PDEntry : Li1 Fe1 O2 with energy = 53.0000
```
Added a test for both cases.
We could also do
```py
PDEntry mp-757614 : Li1 Fe1 O2 with energy = 53.0000
```
if preferred.
|
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| 1,115,365,672
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PR_kwDOACgets4xohzh
| 2,390
|
Fix PDEntryTest.test_get_name() CI error
|
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[
"I already fixed it."
] | 2022-01-26T18:46:46
| 2022-01-26T20:09:17
|
2022-01-26T20:09:16Z
|
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CI didn't finish on #2389 before merge but threw an error. I hope this fixes it.
|
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PR_kwDOACgets4xo1uJ
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|
Compat.process_entry
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[
"\n[](https://coveralls.io/builds/45980918)\n\nCoverage decreased (-0.6%) to 83.375% when pulling **4f87d606bc831e3294ffa2fd0c0c0a93f80e3d35 on janosh:compat.process_entry** into **a13843919e6fe57fad7e1056b2af260462bb76cb on materialsproject:master**.\n"
] | 2022-01-26T20:33:32
| 2022-01-27T16:05:58
|
2022-01-27T16:05:58Z
|
MEMBER
|
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`Compatibility.process_entry()` needlessly does its work twice to check if it got a result. More EAFP to use `try/except`.
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| 1,116,094,824
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PR_kwDOACgets4xq2vn
| 2,392
|
Drop OrderedDict
|
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[
"@shyuep There are some YAML related `mypy` errors. Not sure if that's related to the recent YAML changes:\r\n\r\n```\r\nmypy pymatgen/entries/correction_calculator.py\r\n\r\npymatgen/entries/correction_calculator.py:480: error: \"YAML\" has no attribute \"YAML\"\r\npymatgen/entries/correction_calculator.py:488: error: \"YAML\" has no attribute \"comments\"\r\npymatgen/entries/correction_calculator.py:489: error: \"YAML\" has no attribute \"comments\"\r\npymatgen/entries/correction_calculator.py:490: error: \"YAML\" has no attribute \"comments\"\r\npymatgen/entries/correction_calculator.py:491: error: \"YAML\" has no attribute \"comments\"\r\npymatgen/entries/correction_calculator.py:492: error: \"YAML\" has no attribute \"comments\"\r\npymatgen/entries/correction_calculator.py:493: error: \"YAML\" has no attribute \"comments\"\r\nFound 7 errors in 1 file (checked 1 source file)\r\n```\r\n\r\n```py\r\n yml = yaml.YAML()\r\n yml.default_flow_style = False\r\n contents = yml.load(outline)\r\n\r\n contents[\"Name\"] = name\r\n\r\n # make CommentedMap so comments can be added\r\n contents[\"Corrections\"][\"GGAUMixingCorrections\"][\"O\"] = yaml.comments.CommentedMap(o)\r\n contents[\"Corrections\"][\"GGAUMixingCorrections\"][\"F\"] = yaml.comments.CommentedMap(f)\r\n contents[\"Corrections\"][\"CompositionCorrections\"] = yaml.comments.CommentedMap(comp_corr)\r\n contents[\"Uncertainties\"][\"GGAUMixingCorrections\"][\"O\"] = yaml.comments.CommentedMap(o_error)\r\n contents[\"Uncertainties\"][\"GGAUMixingCorrections\"][\"F\"] = yaml.comments.CommentedMap(f_error)\r\n contents[\"Uncertainties\"][\"CompositionCorrections\"] = yaml.comments.CommentedMap(comp_corr_error)\r\n```",
"\n[](https://coveralls.io/builds/46003559)\n\nCoverage decreased (-0.6%) to 83.38% when pulling **0498587d46934de9d6ff20e99da624e5d9e82e57 on janosh:drop-ordered-dict** into **a13843919e6fe57fad7e1056b2af260462bb76cb on materialsproject:master**.\n",
"Thanks.",
"Just to avoid potential confusion, CPython dicts were insertion ordered even in 3.6. It was just considered an implementation detail and not guaranteed across other Python implementations."
] | 2022-01-27T11:26:33
| 2022-01-28T06:43:57
|
2022-01-27T16:05:21Z
|
MEMBER
|
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Python 3.6 is [EOL since 23 Dec 2021](https://endoflife.date/python) and regular `dict`s are insertion-ordered since Python 3.7 so safe to replace `OrderedDict`.
|
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| 1,116,327,115
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PR_kwDOACgets4xroUd
| 2,393
|
Write k-point grids to QE input file
|
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[
"\n[](https://coveralls.io/builds/46004527)\n\nCoverage decreased (-0.6%) to 83.38% when pulling **7fd109a7143350b5dba492dfb4aa755b5a602d8a on vorwerkc:qe_kpoints_output** into **a13843919e6fe57fad7e1056b2af260462bb76cb on materialsproject:master**.\n",
"Thanks."
] | 2022-01-27T14:57:47
| 2022-01-27T16:04:49
|
2022-01-27T16:04:49Z
|
CONTRIBUTOR
|
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Fixes a formatting bug in the output of k-grids in Quantum Espresso input files.
Additionally, the pull request adds a news test for the output of k-grids in Quantum Espresso input files.
|
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PR_kwDOACgets4xsiJ2
| 2,394
|
Fix issue with gzipped DOSCAR files in Lobster module
|
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[
"\n[](https://coveralls.io/builds/46012333)\n\nCoverage decreased (-0.6%) to 83.385% when pulling **08ff11c436018a2ffd8c8a81fdfd5d0865d83edc on JaGeo:master** into **72849371a03ffda519e1f590776001b9076c9cd8 on materialsproject:master**.\n",
"Thanks."
] | 2022-01-27T18:13:22
| 2022-01-27T20:17:34
|
2022-01-27T20:17:27Z
|
MEMBER
|
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## Summary
This pull request fixes an issue with gzipped DOSCAR files in the Lobster module.
I also included a test.
|
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PR_kwDOACgets4xsv-P
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Q-Chem Updates
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"\n[](https://coveralls.io/builds/46014173)\n\nCoverage decreased (-0.6%) to 83.39% when pulling **9c3b416d6dd77b94189a8cb4e3a3510375877a34 on samblau:qchem** into **72849371a03ffda519e1f590776001b9076c9cd8 on materialsproject:master**.\n",
"Thanks."
] | 2022-01-27T19:31:20
| 2022-01-27T20:17:11
|
2022-01-27T20:17:06Z
|
CONTRIBUTOR
|
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## Summary
All minor points, though important:
* Fixed SCF parsing in the presence of a specific warning
* Parsing new errors associated with failing CPSCF in analytic frequencies to enable Custodian handling
* Multiple NBO7 parsing fixes + new tests
|
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PR_kwDOACgets4xwAOz
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[WIP] Fixed the mask_sphere function in cube.py
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[
"\n[](https://coveralls.io/builds/46044516)\n\nCoverage decreased (-0.6%) to 83.392% when pulling **b83b8031d324e387c02c6deb1b2f9deebf8cb9ac on adam-kerrigan:masked_sphere_correction** into **07794afb624f7613b3dbcebdf0034cab4c9ee7ea on materialsproject:master**.\n",
"Thanks @adam-kerrigan!\r\n\r\n@jmmshn, do you have any thoughts on this? I remember you having issues with masking in `VolumetricData`/`Chgcar`.",
"https://github.com/materialsproject/pymatgen/blob/fedfdd0a69b75d9d7890942954a4ffa3604ac4ba/pymatgen/analysis/defects/utils.py#L1272\r\nI think these are indeed the same. I think the right thing to do is to refactor the distance mask code into Volumetric data, since my old code used a \"private\" function for that part it should be minimally invasive.\r\n",
"I think using the sphere function of the lattice instead of distances would still be better though as you aren't spawning massive grids for what is often only a couple of hundred points around a site. This is why I thought just returning the indices for the mask might be ideal also, so you could store several sites and not have to use them one at a time for fear of OOMing but I don't think that is what people would expect returned from a mask function. \r\n\r\nI think personally, in my unqualified-to-address-the-scale-of-the-task opinion, I would also prefer it was refactored into VolumetricData (with that being moved into core, with a sub-class for charge densities and another for local potentials etc?) and used as a parent for cubes as well as chgcars etc but I don't know how many other classes are using specifically the Chgcar class or this Cube one that would then need to be made more general.\r\n\r\nOn the code you linked @jmmshn I can see it is called in the function above. Here you define sites whereby the charge density is a minimum and integrate around it. I was wondering if you could tell me what you were using this for? I've just started looking at critical points and haven't seen many uses for cage points and am interested to learn more.",
"> On the code you linked @jmmshn I can see it is called in the function above. Here you define sites whereby the charge density is a minimum and integrate around it. I was wondering if you could tell me what you were using this for? I've just started looking at critical points and haven't seen many uses for cage points and am interested to learn more.\r\n\r\nThe code in there was used in this paper to identify candidate cation insertion sites with low steric interactions.\r\n\r\nhttps://www.nature.com/articles/s41524-020-00422-3",
"> I think using the sphere function of the lattice instead of distances would still be better though as you aren't spawning massive grids for what is often only a couple of hundred points around a site. This is why I thought just returning the indices for the mask might be ideal also, so you could store several sites and not have to use them one at a time for fear of OOMing but I don't think that is what people would expect returned from a mask function.\r\n\r\nI can see pros and cons here but I think we should always err on the side of more explicitly and less efficient unless an efficiency bottleneck is actually encountered. Also returning the indices of the mask still might not allow for fast access even if the data is much smaller. My general impression is that the masking operation in NumPy is pretty fast and looping over indices is pretty slow.",
"I agree completely that being more explicit over being more efficient is the right way to go, however this function returns a spherical mask by calling get_points_in_sphere(), over creating a distance matrix for the entire array and then using that to create another array based on a conditional. I think arguments can be made both ways for explicitness. \r\n\r\nFor an idea of comparison between the two I ran them both using a reasonably small sized grid (140x112x378) and obviously the _dist_mat function is invariant to radius (0.98 seconds per site) where as there was a greater than 300 times speed up for radii of 1.6 and under (0.0028 seconds per site) and 50 times speed up for radii of 3.2 and under (0.019 seconds per site). This meant I could look at every site in the file (912) in under 3 seconds for a typical ionic radius length, in under 20 seconds for 3.2 Ang which is massive and this all compared to 15 minutes using the _dist_mat method.\r\n\r\nRegarding your thoughts on the indices vs masking I don't think the function you linked uses any masking. From what I can see it just does multiplication between two arrays of one of density one of bools. Again I ran a quick test and for a 1.6 Ang radius masking this way takes 0.01 seconds to create the new array, indexing takes 0.00006. But I think what is important about this note is the memory efficiency. When working with voxel data I think considerations around memory are important, as the data itself can be huge. Storing the whole array in several places (3 times as the output of a meshgrid, another 3 times as a vstack) feels excessive when there is a way to do it without copying the array once.\r\n\r\nI have attached the tests I did incase you want to have a play around.\r\n[test.zip](https://github.com/materialsproject/pymatgen/files/7978916/test.zip)\r\n\r\n",
"Sorry, I had a brain fart there. I forgot that the mask needs to be generated for each origin.\r\nSo this all makes sense to me now.\r\n\r\n> I think personally, in my unqualified-to-address-the-scale-of-the-task opinion, I would also prefer it was refactored into VolumetricData (with that being moved into core, with a sub-class for charge densities and another for local potentials etc?)\r\n\r\nI also agree with this, but this has to be done without too much disruption to the codebase so we might not be able to change what we used defined in `VolumetricData` and where it is defined.\r\nMaybe we can add a `PeriodicField` class somewhere (either in `pymatgen.io` or `pymatgen.core`) that contains some common stuff between the VASP and CUBE codes.\r\nSince these voxel data is usually used in post-processing I lean towards creating a file or even an `io/common` directory to hold similar codes.\r\n@mkhorton Thoughts? \r\n"
] | 2022-01-28T17:30:03
| 2024-08-03T19:01:57
|
CONTRIBUTOR
|
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## Summary
Include a summary of major changes in bullet points:
* The mask_sphere function returned a mask of distance values that doesn't vary with site
* Changed this use the get_points_in_sphere from Lattice
## TODO (if any)
* A discussion about what this returns:
* I think just returning the indices rather than a full array would be better.
* Was it intentional to multiply by distance or is how I have set it up now (just 1 or 0)
* Should I type hint the functions?
## 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.
- [ ] 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.
|
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PR_kwDOACgets4xx994
| 2,397
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Delete overdue deprecations
|
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[
"\n[](https://coveralls.io/builds/46060118)\n\nCoverage decreased (-0.6%) to 83.451% when pulling **ce3615803666b28726e56f1a1fd11c3676b06c60 on janosh:drop-deprecated** into **07794afb624f7613b3dbcebdf0034cab4c9ee7ea on materialsproject:master**.\n",
"Beat me to it. I was just about to point out the AiiDA deprecation.",
"There were some more things where I couldn't easily figure out from `git blame` when it was last changed and if it might be time to get rid of that as well. Maybe @shyuep can comment on those:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/07794afb624f7613b3dbcebdf0034cab4c9ee7ea/pymatgen/analysis/interface_reactions.py#L629-L634\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/ce3615803666b28726e56f1a1fd11c3676b06c60/pymatgen/analysis/defects/dilute_solution_model.py#L42-L56\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/0af8a0c66bd54a3dc83a3f33792d48ca0bf22632/pymatgen/analysis/elasticity/elastic.py#L408-L414",
"The first one at least seems like a very recent module from @mattmcdermott.\n\nEdit: Apologies. The specific line highlight didn't render from my phone. ",
"Thanks.",
"It doesn't matter. If it has been indicated as depreacted, we can remove it now. If someone complains, we then add it back as necessary. Most of these are very old indeed."
] | 2022-01-29T18:07:58
| 2022-01-31T16:39:10
|
2022-01-31T16:37:44Z
|
MEMBER
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Noticed that a bunch of stuff has deprecation messages saying it would be removed in pmg `2020.*`. This PR removes those functions and methods since we're already at v2022.1.24.
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I_kwDOACgets5Cp-GF
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Is MaterialsProjectCompatibility deprecated?
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[] | 2022-01-29T18:52:15
| 2023-05-26T23:04:26
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2023-05-26T23:04:26Z
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MEMBER
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MaterialsProjectCompatibility does not issue a deprecation warning. @rkingsbury said it used to. Was this removed intentionally? Should it be reinstated?
```py
from pymatgen.entries.compatibility import MaterialsProjectCompatibility
mpc = MaterialsProjectCompatibility()
processed_entries = mpc.process_entries(unprocessed_entries, verbose=True)
>>> 5034it [00:00, 24523.19it/s]
0%| | 0/5034 [00:00<?, ?it/s]
pymatgen/entries/compatibility.py:287: UserWarning: No structure or oxide_type
parameter present. Note that peroxide/superoxide corrections are not as reliable
and relies only on detection of specialformulas, e.g., Li2O2.
warnings.warn(
100%|██████████| 5034/5034 [00:00<00:00, 9655.80it/s]
```
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PR_kwDOACgets4xyePf
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ASEAtomsAdaptor: magmom/charge site properties in Structure/Molecule become initial (rather than final) magmoms/charges in Atoms object
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[
"\n[](https://coveralls.io/builds/46075357)\n\nCoverage decreased (-0.6%) to 83.391% when pulling **e578fca0d451231cf18cf92c9a17e0353b8b18ce on arosen93:rosen-asemags** into **07794afb624f7613b3dbcebdf0034cab4c9ee7ea on materialsproject:master**.\n"
] | 2022-01-30T08:49:20
| 2022-01-31T16:38:43
|
2022-01-31T16:38:43Z
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MEMBER
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**Summary**:
In this PR, the naming convention for the magnetic moments (and charges) are modified such that "magmom" in the pymatgen `Structure`/`Molecule` object is set as the _initial_ magnetic moment in ASE rather than the _final_ when using the `ASEAtomsAdaptor`. Looks like I still had a bit of refinement left to do here.
**Motivation**:
- In ASE, the `.magmom` attribute for an atom returns the initial magnetic moment, not the final magnetic moment. For consistency, the same convention should be used for the "magmom" site property in `Structure`/`Molecule`.
- In ASE, the final magnetic moments are only ever added after a calculation has completed, so in most practical use-cases of the `ASEAtomsAdaptor`, only the initial magnetic moments would be present. In this case, one would likely anticipate the input (i.e. initial) magnetic moments set in the `Atoms` object to be the magmom values used when constructing an INCAR in pymatgen from the `Structure`. For this to happen, the "magmom" site property must be mapped to ASE's initial magnetic moment.
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Update zeo++ installation steps
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[
"\n[](https://coveralls.io/builds/46095020)\n\nCoverage decreased (-0.6%) to 83.425% when pulling **d60d53273b721b5d09580552c78bcbae293755be on arosen93:rosen-zeo** into **07794afb624f7613b3dbcebdf0034cab4c9ee7ea on materialsproject:master**.\n",
"Can you put these in the docs_rst instructions too? A lot of people just search on pymatgen.org/installation for these instructions.",
"Good idea! Should be done now.",
"Thanks @arosen93 !"
] | 2022-01-30T08:59:52
| 2023-06-03T02:25:23
|
2022-01-31T20:45:24Z
|
MEMBER
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Closes #2255.
The Zeo++ installation steps in `pymatgen.io.zeopp` are extremely out of date. I've modernized them and added the reference that should be cited when using Zeo++.
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PR_kwDOACgets4xyhFE
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Use setup-python automatic pip caching in CI
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"\n[](https://coveralls.io/builds/46064662)\n\nCoverage decreased (-0.6%) to 83.394% when pulling **76088c3f1e8512f50f792b753a0ed65c237ac625 on janosh:gha-auto-pip-cache** into **07794afb624f7613b3dbcebdf0034cab4c9ee7ea on materialsproject:master**.\n",
"Note by default this caching mechanism uses the combined hash of all files matching `**/requirements.txt` as the restore key. In case of the `linting` workflow for example, we actually want this to be `requirements-dev.txt`:\r\n\r\n```yml\r\n- uses: actions/setup-python@v2\r\n with:\r\n cache: pip\r\n cache-dependency-path: requirements-dev.txt\r\n```\r\n\r\nhttps://github.com/actions/setup-python#caching-packages-dependencies"
] | 2022-01-30T10:10:21
| 2022-01-31T16:37:13
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2022-01-31T16:36:11Z
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MEMBER
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Since Nov 2021, `setup-python` GitHub action supports automatic `pip` dependency caching:
https://github.blog/changelog/2021-11-23-github-actions-setup-python-now-supports-dependency-caching
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I_kwDOACgets5CraO-
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Highlight selected points in plotly PDPlotter
|
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[
"Would also be nice to be able to pass in additional information for the hover labels i.e. a DOI for the entry etc ",
"Additionally if using `PDEntry` `entry_id = getattr(entry, \"entry_id\", \"no ID\")` doesn't grab the name as `PDEntry` calls the identifier `name`",
"> Sometimes I want to plot a phase diagram and highlight points that are not on the convex hull. It would be nice to be able to give a list of entry names that would then be highlighted in a separate list to \"stable\" and \"above hull\".\r\n\r\nThis should be doable, but I don't yet know a clean way to do it in Plotly. The most straightforward approach would be to define a new trace that would correspond to \"Highlighted\" points, but because the stable and unstable entries are already split into two traces, you would need to create four separate traces now: 1) Highlighted - Stable, 2) Highlighted - Unstable, 3) Unhighlighted - Stable, 4) Unhighlighted - Unstable. Since this is kind of gross I'd rather not do it that way. However, if you think this would be okay (or even preferred?) let me know.\r\n\r\nI think the better way is probably to add a `Button` in plotly, so that you can restyle the phase diagram. The issue with that is there doesn't seem to be way to hide specific points without leaving some weird stuff behind. I tried setting their opacity to zero, but it leaves behind some artifacts that look kind of gross. (See picture where I try to hide all but one stable point and one unstable point). For the stable points, it seems to leave behind gray lines that I can't get rid of, and the legend labels also get messed up.\r\n\r\n> Would also be nice to be able to pass in additional information for the hover labels i.e. a DOI for the entry etc\r\n\r\n> Additionally if using PDEntry entry_id = getattr(entry, \"entry_id\", \"no ID\") doesn't grab the name as PDEntry calls the identifier name\r\n\r\n^ I should be able to address these!\r\n\r\n\r\n",
"@janosh does the stuff you were doing with groups for the frontier plot offer any nice solutions for highlighting here?",
"@CompRhys I don't see how without changes to `PDPlotter` which might turn into a mess.\r\n\r\nBut since `PDPlotter` returns a Plotly figure object, you can just apply changes to any of its traces as you see fit:\r\n\r\n\r\n\r\n```py\r\nfrom pymatgen.analysis.phase_diagram import PDPlotter, PhaseDiagram\r\nfrom pymatgen.ext.matproj import MPRester\r\n\r\nentries = MPRester().get_entries(\"Fe-O\")\r\nentries += MPRester().get_entries(\"Fe\")\r\nentries += MPRester().get_entries(\"O\")\r\n\r\npd = PhaseDiagram(entries)\r\n\r\nfig = PDPlotter(pd).get_plot()\r\n\r\nunstable = [trace for trace in fig.data if trace.name == \"Above Hull\"][0]\r\n\r\nunstable[\"marker\"][\"size\"] = [10] * (len(unstable[\"x\"]) - 1) + [40]\r\n```\r\n",
"> The issue with that is there doesn't seem to be way to hide specific points without leaving some weird stuff behind.\r\n\r\n@mattmcdermott I assume you could `zip` over the `x`, `y` and `hovertext` attributes of a trace and populate new lists with the existing points based on conditions, then overwrite the existing attributes with the new lists. Something like:\r\n\r\n```py\r\ntrace = [trace for trace in fig.data if trace.name == \"Above Hull\"][0]\r\n\r\nnew_x, new_y, new_hover = [], [], []\r\nfor x, y, h in zip(trace.x, trace.y, trace.hovertext):\r\n if (x < 0.5) and (y > 1):\r\n new_x.append(x)\r\n new_y.append(y)\r\n new_hover.append(h)\r\n\r\ntrace.x = new_x\r\ntrace.y = new_y\r\ntrace.hovertext = new_hover\r\n```\r\n\r\nHaven't tried it though. And it's a lot of work too.",
"@CompRhys FYI, I finally added this feature in https://github.com/materialsproject/pymatgen/pull/3032.\r\n\r\n"
] | 2022-01-30T19:04:52
| 2023-06-03T00:55:13
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2023-06-03T00:55:13Z
|
CONTRIBUTOR
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Sometimes I want to plot a phase diagram and highlight points that are not on the convex hull. It would be nice to be able to give a list of entry names that would then be highlighted in a separate list to "stable" and "above hull".
@mattmcdermott Is this something that seems reasonable to be able to add?
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The Vasprun parser does not store site_properties in the ionic_steps structure objects
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"organizations_url": "https://api.github.com/users/Andrew-S-Rosen/orgs",
"repos_url": "https://api.github.com/users/Andrew-S-Rosen/repos",
"events_url": "https://api.github.com/users/Andrew-S-Rosen/events{/privacy}",
"received_events_url": "https://api.github.com/users/Andrew-S-Rosen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Closed because, to my surprise, the total magnetization doesn't appear to be in the `vasprun.xml` file. I guess that can only be parsed from OUTCAR."
] | 2022-01-30T21:04:05
| 2022-01-30T23:07:16
|
2022-01-30T23:07:15Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Example:
```python
from pymatgen.io.vasp.outputs import Vasprun
v = Vasprun('vasprun.xml.gz')
v.ionic_steps[-1]["structure"].site_properties
```
The above example does not return "magmom" site properties in the returned structure object.
[vasprun.xml.gz](https://github.com/materialsproject/pymatgen/files/7966917/vasprun.xml.gz)
|
{
"login": "Andrew-S-Rosen",
"id": 8674072,
"node_id": "MDQ6VXNlcjg2NzQwNzI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8674072?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Andrew-S-Rosen",
"html_url": "https://github.com/Andrew-S-Rosen",
"followers_url": "https://api.github.com/users/Andrew-S-Rosen/followers",
"following_url": "https://api.github.com/users/Andrew-S-Rosen/following{/other_user}",
"gists_url": "https://api.github.com/users/Andrew-S-Rosen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Andrew-S-Rosen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Andrew-S-Rosen/subscriptions",
"organizations_url": "https://api.github.com/users/Andrew-S-Rosen/orgs",
"repos_url": "https://api.github.com/users/Andrew-S-Rosen/repos",
"events_url": "https://api.github.com/users/Andrew-S-Rosen/events{/privacy}",
"received_events_url": "https://api.github.com/users/Andrew-S-Rosen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2403/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
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"heart": 0,
"rocket": 0,
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|
https://api.github.com/repos/materialsproject/pymatgen/issues/2403/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
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