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https://api.github.com/repos/materialsproject/pymatgen/issues/1901 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1901/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1901/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1901/events | https://github.com/materialsproject/pymatgen/pull/1901 | 654,364,094 | MDExOlB1bGxSZXF1ZXN0NDQ3MTA3MDM3 | 1,901 | ## fix openbabel 3.0 compatibility in lammps submodule | {
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"Thanks."
] | 2020-07-09T21:38:50 | 2020-07-09T22:14:43 | 2020-07-09T22:14:39Z | CONTRIBUTOR | {
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* Fix: small changes to important statements to align with openbabel 3.0 syntax
* Fix: removed casting to ASCII bytecode that was causing errors
* Feature: added as_dataframe method for XYZ and associated unit tests
## Additional dependencies introduced
* added imports for numpy and pandas to XY... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1902 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1902/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1902/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1902/events | https://github.com/materialsproject/pymatgen/pull/1902 | 654,835,748 | MDExOlB1bGxSZXF1ZXN0NDQ3NDgzODI5 | 1,902 | Update the download link and citations for enumlib | {
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"Thanks."
] | 2020-07-10T14:50:07 | 2020-07-10T15:08:30 | 2020-07-10T15:05:37Z | CONTRIBUTOR | {
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} | ## Summary
Enumlib has been migrated to github.
1. Update link of enumlib from Sourceforge to Github
2. Update the citations according to https://github.com/msg-byu/enumlib#brief-description | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1903 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1903/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1903/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1903/events | https://github.com/materialsproject/pymatgen/issues/1903 | 654,841,474 | MDU6SXNzdWU2NTQ4NDE0NzQ= | 1,903 | undefined symbol: _intel_fast_memcpy | {
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"This is a problem with the gcc mismatch on Linux. Do a `pip install --user --upgrade pymatgen` and it should disappear.",
"Since you're running conda, you can also try `conda install -c conda-forge pytmagen` too",
"Thanks, Matthew. \r\nconda install -c conda-forge pymatgen worked for me !!\r\nCentOS release 6.... | 2020-07-10T14:58:48 | 2020-07-11T17:08:13 | 2020-07-10T15:07:09Z | NONE | {
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I have tried loading Pymatgen both using intel and gcc at local cluster however the issue still persist.
Python 3.7.7 (default, May 7 2020, 21:25:33)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pymatgen
Traceback (most recent call ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1904 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1904/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1904/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1904/events | https://github.com/materialsproject/pymatgen/pull/1904 | 654,897,671 | MDExOlB1bGxSZXF1ZXN0NDQ3NTMzMzk2 | 1,904 | Fix serialisation of slabs with list scale_factor | {
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"Thanks @utf "
] | 2020-07-10T16:30:46 | 2020-07-10T16:32:33 | 2020-07-10T16:32:33Z | MEMBER | {
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} | ## Summary
A recent bug fix (1a3ce601c932ed80db14930da6e2c11a8a246771) introduced an incompatibility of the `Slab` class with the atomate `TransformerFW` and therefore broke surface workflows. Specifically, the `Slab` class now assumes the `scale_factor` input is a numpy array, whereas the `TransformerFW` supplies a... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1905 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1905/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1905/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1905/events | https://github.com/materialsproject/pymatgen/issues/1905 | 655,014,984 | MDU6SXNzdWU2NTUwMTQ5ODQ= | 1,905 | QChem Frequency Calculation Import Fails | {
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"Thanks @asmith97 for the report, would it be possible to share your output file to diagnose? @samblau could you assign someone to this, or know someone who could take a look?",
"I'm happy to take a look and diagnose. @asmith97, please provide your output, and I'll get right on it!",
"Thank you! I redid a frequ... | 2020-07-10T20:20:12 | 2020-07-14T02:17:33 | 2020-07-14T02:17:33Z | NONE | {
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} | I'm unable to use QCOutput to import data from a QChem frequency calculation. An error is thrown while loading the eigenvectors of the vibrational modes. I get an `IndexError: list index out of range` from `shape=(len(freqs), len(temp_freq_mode_vecs[0]), 3))` in line 558 of _read_frequency_data because temp_freq_mode_v... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1906 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1906/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1906/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1906/events | https://github.com/materialsproject/pymatgen/issues/1906 | 655,068,051 | MDU6SXNzdWU2NTUwNjgwNTE= | 1,906 | spglib bugs | {
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"I don't consider 1 as a bug. An atom existing at the same space is a bad structure.\r\n2 should be addressed and @mkhorton can deal with it.",
"For 1, we should at least make clear the None type is possible to be returned. Will address."
] | 2020-07-10T22:28:15 | 2023-08-13T16:33:43 | 2023-08-13T16:33:43Z | CONTRIBUTOR | {
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1. Duplicate atom in the structure
2. None magnetic moment assigned to sites in structure
[pymatgen_issue.zip](https://github.com/materialsproject/pymatgen/files/4905854/pymatgen_issue.zip)
<details><summary>Repro in zip archive</summary>
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"Please use conda install. The instructions are on pymatgen.org."
] | 2020-07-13T13:01:07 | 2020-07-13T15:06:12 | 2020-07-13T15:06:12Z | NONE | {
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```
Building wheels for collected packages: pymatgen, retrying
Building wheel for pymatgen (setup.py) ... error
ERROR: Complete output from command //anaconda3/bin/python -u -c 'import setuptools, tokenize;__file__='"... | {
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"Thanks."
] | 2020-07-14T01:37:07 | 2020-07-14T02:13:13 | 2020-07-14T02:13:07Z | CONTRIBUTOR | {
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* Fixes issue #1905
* All frequency information can now be correctly parsed even when Raman intensities are being calculated
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"Hi!\r\nThe label corresponds to the label from the ICOHPLIST. We could discuss alternatives but I preferred this as there can be multiple COHPs for a site combination.\r\n(Let me know if you have a better suggestion that is also comparably easy to use. I don't really want to think about which kind of image of the ... | 2020-07-14T21:25:05 | 2023-08-13T16:33:43 | 2023-08-13T16:33:43Z | CONTRIBUTOR | {
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} | Is there any reason for how an individual bond's COHP gets its label in the CompleteCOHP class (pymatgen.electronic_structure.cohp.py)? It seems to me that the labels are just distinct integers arbitrarily assigned to each bond. If that is the case, I suggest that we might switch to a labeling system where the label is... | {
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"Pls fix the pylint errors related to boltztrap2.py. The rest of the errors you can ignore for now.",
"Thanks.",
"@fraricci It seems that your changes caused the tests to fail. Can you fix the tests pls? Thanks.",
"it looks like it's not me:\r\n************* Module pymatgen/cli/feff_input_generation.py\r\npym... | 2020-07-15T17:07:43 | 2020-07-16T14:00:58 | 2020-07-15T20:02:10Z | CONTRIBUTOR | {
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"There are failing pylint tests. Pls fix before I merge."
] | 2020-07-17T23:14:28 | 2020-07-18T13:29:20 | 2020-07-18T13:29:20Z | CONTRIBUTOR | {
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} | ## Summary
* Add check for empty spectrum and negative intensities
* Fix the jump in intensities at the L2 and L3-edge junction by extrapolating L2-edge XANES
* Add tests
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"Thanks. \r\n\r\n1. Can you rename jarvisio to just Jarvis. The idea is that it is pymatgen.io.jarvis. For example, pymatgen.io.vasp, not pymatgen.io.vaspio (this was what we started with, but since IO is already in the earlier package, we don't need io again).\r\n2. Pls pin jarvis-tools to a specific version in re... | 2020-07-19T18:53:17 | 2020-07-19T22:00:58 | 2020-07-19T22:00:58Z | CONTRIBUTOR | {
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} | ## Summary
JARVIS-Tools module integration in Pymatgen.
* Creation of pymatgen.io.jarvis
* Fixed setup.cfg for jarvis modules
* Fixed requirements-optional.txt
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https://api.github.com/repos/materialsproject/pymatgen/issues/1913 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1913/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1913/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1913/events | https://github.com/materialsproject/pymatgen/issues/1913 | 661,081,298 | MDU6SXNzdWU2NjEwODEyOTg= | 1,913 | Running SpacegroupAnalyzer on enumerated structure returns wrong space group | {
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"The enumerated structure (ordered approximation) will necessarily be lower symmetry than the input disordered structure, so it's reasonable that it would no longer read as F-43m.",
"Ah, I see. So what about after relaxing the structure with DFT? Is there a function or way to \"rebuild\" the relaxed enumerated pr... | 2020-07-19T21:28:25 | 2020-07-21T16:55:32 | 2020-07-21T16:55:32Z | NONE | {
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Steps I took:
1. Input conventional cell (s.g. F-43m) and find the primitive cell using SpacegroupAnalyzer.find_primitive()
2. Enumerated using enumlib (i.e. EnumerateStructure... | {
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"Hi @haesunpark87, this code works for me, a core dump is likely some serious issue with your installation -- have you tried installing `pymatgen` using conda? Does `enumlib` work outside of pymatgen? (e.g. if you call `enum.x` directly?)",
"Dear Matthew, \n\nIt seems you are right. \nI ran the following code,\n\... | 2020-07-27T19:45:48 | 2020-07-29T18:11:04 | 2020-07-29T18:11:04Z | NONE | {
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} | **Describe the bug**
Error when modules from pymatgen.analysis.magnetism.analyzer are used.
**To Reproduce**
Steps to reproduce the behavior:
1. execute the following python script
!/usr/bin/env python3
-*- coding: utf-8 -*-
from pymatgen.core import Lattice, Structure
from pymatgen.analysis.magnetism.ana... | {
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"Hi @thienbinh92, this issues page is for reporting bugs, if you have a question could you ask it over at our user forum on https://matsci.org/pymatgen ? thanks!"
] | 2020-07-30T11:17:19 | 2020-07-30T16:47:28 | 2020-07-30T16:47:28Z | NONE | {
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} | Hello, I read this paper "Vacancy Ordering in O3-Type Layered Metal Oxide Sodium-Ion Battery Cathodes", Toumar described that pymatgen was used to generate potential structures and the formation energy vs Na concentration was plotted in figure 3. If I am right, the pymatgen's tutorial does not describe how to generate ... | {
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"Many thanks for addressing this @chc273.\r\n\r\nFor documentary purposes, I'm just noting we also noticed this issue on conda installs via Binder (which runs Ubuntu), and previously we also had some issues with Linux wheels via PyPI on #1868 that I think might be related.",
"> Many thanks for addressing this @ch... | 2020-07-30T18:04:59 | 2020-07-30T19:15:01 | 2020-07-30T19:15:01Z | CONTRIBUTOR | {
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} | ## Summary
Recently, we have seen some platform-dependent errors caused by this cython extension.
The known error is "illegal instructions (core dumped)" which cause crash of python. This error was found on conda installations. In particular, I have encountered issues on `ubuntu 18.04.4 LTS` (Matt raised this i... | {
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"Thanks @rkingsbury ",
"Tests pls ",
"@mkhorton Do you know where to find which pseudopotentials are currently recommended by VASP? There is [this](https://cms.mpi.univie.ac.at/vasp/vasp/Recommended_PAW_potentials_DFT_calculations_using_vasp_5_2.html) old page which is no longer maintained, but the current VASP... | 2020-07-31T18:38:39 | 2020-09-07T15:05:27 | 2020-08-13T20:18:40Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Revise `MPScanRelaxSet` per recent discussions
* LWAVE = False
* LREAL = Auto
* ENAUG = 2 * ENCUT
* remove ICHARG
* Add `MPScanStaticSet` in which we set LREAL=FALSE
## TODO
* Address question about MAGMOM in `MPStaticSet`
* Review POTCAR choices against VASP recommendations
* Update the ha... | {
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"Thank you. Can you pls add a unit test for the new functionality pls? Thanks.",
"hi @shyuep, there is no new functionality, just a small bug fix",
"The test would be to catch the bug you've encountered (e.g. with g.txt) so that future code modifications don't re-introduce the bug.",
"Yes, I understand that. ... | 2020-08-03T22:14:02 | 2020-08-10T08:51:29 | 2020-08-04T15:06:18Z | CONTRIBUTOR | {
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} | Hi pymatgen community!
In gaussian log, there are geometries outputted either in "standard" or "input" orientation or both together. The current implementation assumed that "input orientation" is always outputted but that is not the case (try e.g. [g.txt](https://github.com/materialsproject/pymatgen/files/5019019/g.... | {
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} | The new Compatibility interface (see #1826) provides a boolean `clean` argument to `process_entries` that determines whether or not previously-applied corrections are discarded when `process_entries` is called. We set this to `False` by default, but this has proven to be a bad choice. Myself, @shyamd and @awvio have al... | {
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"The actual change of this PR was changing a single value (0876de1) but to get linting to pass I had to make many changes in the local_env module.",
"Thanks for fixing everything."
] | 2020-08-07T02:43:55 | 2020-08-07T17:13:08 | 2020-08-07T17:12:59Z | MEMBER | {
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Changed the JMolNN tolerance parameter to match the that used by the JMol source code. | {
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"Thanks @mattmcdermott! Is there any reason this functionality couldn't just be added to the existing `ComputedStructureEntry` rather than made its own class? In general I feel we have too many `Entry` classes already. Interested to hear other's thoughts on this.\r\n\r\nSeparately, I'm working on creating an MPCon... | 2020-08-11T00:29:34 | 2020-08-13T17:23:22 | 2020-08-13T17:23:13Z | MEMBER | {
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} | ## Summary
- Added a new entry class called **GibbsComputedStructureEntry**. This is an extension to ComputedStructureEntry which
allows for the estimation of Gibbs free energy of formation, ΔGf(T), via a machine-learned model. This can be used to estimate temperature-dependent phase diagrams using MP data.
- Curr... | {
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"Actually closing for now, this looks to be something to do with the way an entry had been serialized in a database and then deserialized. I can't reproduce using more straightforward code. Although I would suggest that the code above is probably more robust than what's there as it works for the example below as we... | 2020-08-11T17:58:38 | 2020-08-11T21:01:09 | 2020-08-11T18:21:27Z | MEMBER | {
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} | **Describe the bug**
pymatgen.entries.compatibility.Compatibility.process_entries() is supposed to be clearing out the previous energy adjustments on an entry (the "clean" parameter is by default True). Doesn't look like it's doing it.
**To Reproduce**
Steps to reproduce the behavior:
- Load a ComputedEntry with... | {
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} | **Describe the bug**
The ``BabelMolAdaptor`` class fails when given ``IMolecule`` instead of ``Molecule`` objects.
**To Reproduce**
```python
from pymatgen import IMolecule
from pymatgen.io.babel import BabelMolAdaptor
m = IMolecule(["H","H"], [[1.,2.,3.],[4.,5.,6.]])
a = BabelMolAdaptor(m)
a.openbabel_mol
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1924 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1924/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1924/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1924/events | https://github.com/materialsproject/pymatgen/pull/1924 | 677,185,839 | MDExOlB1bGxSZXF1ZXN0NDY2MzQ2NDMw | 1,924 | Allow BabelMolAdaptor to convert IMolecules | {
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} | ## Summary
Instead of checking whether supplied objects are instances of ``Molecule``, ``BabelMolAdaptor`` now checks whether they are ``IMolecule``s instead (which is a superclass of ``Molecule`` so the old check still works). This fixes #1923.
## Checklist
Work-in-progress pull requests are encouraged, but p... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1925 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1925/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1925/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1925/events | https://github.com/materialsproject/pymatgen/pull/1925 | 677,202,883 | MDExOlB1bGxSZXF1ZXN0NDY2MzU5NjQw | 1,925 | simplify cleaning of EnergyAdjustment | {
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} | Replaces the code that removes previous `EnergyAdjustment` from `ComputedEntry` with a more robust alternative. See #1922 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1926 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1926/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1926/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1926/events | https://github.com/materialsproject/pymatgen/pull/1926 | 678,013,490 | MDExOlB1bGxSZXF1ZXN0NDY3MDM2ODQ5 | 1,926 | fix valence bug, add test | {
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"Many thanks @rkurchin !",
"On the test note, I agree this is unlikely to fail but I'll let the tests pass on CI first before merging. Your issue might be related to using `nose` which is now deprecated, `pytest` should be sufficient to run tests.\r\n\r\nWe're also asking new contributors to [fill out this form](... | 2020-08-12T22:20:01 | 2020-08-14T22:51:39 | 2020-08-12T23:56:36Z | CONTRIBUTOR | {
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} | Previously, asking for the valence property on an Element with full shells that wasn't noble (e.g. column 2 or 12) would cause an error. This resolves that.
## Summary
Include a summary of major changes in bullet points:
* Added a check for if the last orbital listed is fully-occupied and to choose that number... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1927 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1927/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1927/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1927/events | https://github.com/materialsproject/pymatgen/pull/1927 | 678,229,020 | MDExOlB1bGxSZXF1ZXN0NDY3MjExNTk4 | 1,927 | Updates to LobsterSet | {
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"I will close this one here and open up a new one. The automatic testing asks me to update the linting of a lot of code.... "
] | 2020-08-13T07:47:46 | 2020-08-13T08:31:42 | 2020-08-13T08:25:23Z | MEMBER | {
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} | ## Summary
I have just updated some values in the LobsterSet. Let me know if I should include more tests.
Best,
JG | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1928 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1928/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1928/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1928/events | https://github.com/materialsproject/pymatgen/pull/1928 | 678,257,246 | MDExOlB1bGxSZXF1ZXN0NDY3MjM0ODQ5 | 1,928 | Updates to LobsterSet | {
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"Sorry about that, adding an additional rule to ignore in the linter, and accidentally over-rode the default ignore list thereby triggering a lot of errors.\r\n\r\nIt should be fixed now if you merge in the latest master.",
"No worries - should have looked at the latest testss before starting with this pull reque... | 2020-08-13T08:33:24 | 2020-08-13T20:19:07 | 2020-08-13T20:19:03Z | MEMBER | {
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} | ## Summary
I have just updated some values in the LobsterSet. Let me know if I should include more tests.
There seem to be problems with the linting in the current main branch. I don't really want to fix all of them - there seem to be hundreds.
I will fix every failing test that seems to be related to my changes... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1929 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1929/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1929/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1929/events | https://github.com/materialsproject/pymatgen/issues/1929 | 679,126,086 | MDU6SXNzdWU2NzkxMjYwODY= | 1,929 | SpacegroupAnalyzer.get_conventional_standard_structure returns a wrong structure | {
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"Agreed this looks like a serious bug. I'm looking at these lines in particular:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/v2020.8.13/pymatgen/symmetry/analyzer.py#L547-L597\r\n\r\nI didn't write this code so it'll take me a while to understand what's meant to be happening here.",
"Interestingly, I... | 2020-08-14T12:31:49 | 2023-08-13T16:33:43 | 2023-08-13T16:33:43Z | CONTRIBUTOR | {
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} | **To Reproduce**
If I understand correctly, a structure and a symmetry-refined one have the same minimum distance between sites.
So, three structures `structure`, `conventional_refined`, and `spglib_refined` in the following script should have the same minimum distance.
```python
import numpy as np
from pymatgen... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1930 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1930/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1930/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1930/events | https://github.com/materialsproject/pymatgen/pull/1930 | 679,155,700 | MDExOlB1bGxSZXF1ZXN0NDY3OTgzMTg0 | 1,930 | Fix type of reciprocal lattice in KPathSeek | {
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"Thanks @Ian496!"
] | 2020-08-14T13:25:52 | 2020-08-14T18:19:01 | 2020-08-14T18:19:01Z | CONTRIBUTOR | {
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} | ## Summary
The abstract class of KPathSeek, KPathBase, expects a type of a reciprocal lattice as `pymatgen.core.lattice.Lattice`. This tiny PR fixes to cast a reciprocal lattice returned by `seekpath` into pymatgen's lattice class.
## Checklist
Before a pull request can be merged, the following items must be c... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1931 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1931/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1931/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1931/events | https://github.com/materialsproject/pymatgen/issues/1931 | 679,571,406 | MDU6SXNzdWU2Nzk1NzE0MDY= | 1,931 | Problems with Vasprun parsing dielectric vasprun.xml file | {
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} | I am trying to use pymatgen to read in the local field (RPA level) frequency dependent dielectric function.
I am using the input files from the SiC example on the vaspwiki page. The structure is SiC
```
<POSCAR>
system SiC
4.35
0.5 0.5 0.0
0.0 0.5 0.5
0.5 0.0 0.5
1 1
cart
0.00 0.00 0.00
0.25 0.25 0.25
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1932 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1932/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1932/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1932/events | https://github.com/materialsproject/pymatgen/pull/1932 | 680,523,799 | MDExOlB1bGxSZXF1ZXN0NDY5MDY2MDY5 | 1,932 | fix saving _acc_factor instead of _accf | {
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} | ## Summary
Fix `as_dict` in EwaldSummation to save `_acc_factor` and not `_accf`, to recreate the exact object as before. Previous tests did not catch this since the actual Ewald summation values remained within numerical tolerance (my bad for not catching this before).
## Checklist
Before a pull request can be ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1933 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1933/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1933/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1933/events | https://github.com/materialsproject/pymatgen/pull/1933 | 680,589,086 | MDExOlB1bGxSZXF1ZXN0NDY5MTIwODgw | 1,933 | MP2020 Compatibility refinements | {
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"FYI @awvio. When you are ready to update the .json.gz, the easiest way would be to open a pull request against [my branch](https://github.com/rkingsbury/pymatgen/tree/mp2020-refactor), which I can then merge so that it shows up here. Thanks!",
"@mkhorton @shyamd @shyuep I've reformatted the .yaml file to consoli... | 2020-08-17T23:42:20 | 2020-09-15T18:59:18 | 2020-09-15T18:36:40Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Refactor `MaterialsProject2020Compatibility` to utilize the new abstract compatibility interface (see #1826 ) instead of the legacy `CorrectionsList` class. Note that the `PotcarCorrection` class is still utilized, but not any other `Correction` cl... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1934 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1934/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1934/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1934/events | https://github.com/materialsproject/pymatgen/issues/1934 | 680,634,811 | MDU6SXNzdWU2ODA2MzQ4MTE= | 1,934 | Something wrong with the result of DosPlotter | {
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"I think the problem comes from stack=True. I had a similar result when trying to fill the a DOS plotted horizontally, while was ok if plotted vertically (as by BSDOSPlotter). Please, try with stack=False.\r\nI edited the code to solve the bug but I forgot to push it. I'll do it ASAP.",
"I have tried to solve thi... | 2020-08-18T02:11:47 | 2020-08-20T01:49:31 | 2020-08-20T01:45:16Z | NONE | {
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} | **Describe the bug**
when I use the BSDosPlotter model to draw BAND and DOS figure,I got a perfect result comparing to the one drawn by P4V and Origin.But,when I use the same data to draw single DOS picture with DosPlotter ,I got a very strange result .
**To Reproduce**
Follows are my script of DosPlotter:
im... | {
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"Not sure if @samblau or @espottesmith want to comment here? (or want to recommend someone who could)"
] | 2020-08-18T10:43:10 | 2023-08-13T16:33:44 | 2023-08-13T16:33:44Z | CONTRIBUTOR | {
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} | **Describe the bug**
The current version of MoleculeMatcher does not seem to be robust enough for practical applications.
**To Reproduce**
You can find a simplified code snippet below:
```python
import random
from pymatgen import Lattice, Structure, Molecule
from pymatgen.analysis.molecule_matcher import Mol... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1936 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1936/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1936/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1936/events | https://github.com/materialsproject/pymatgen/pull/1936 | 681,380,664 | MDExOlB1bGxSZXF1ZXN0NDY5Nzc4ODcz | 1,936 | Overhaul of PhaseDiagram plotting: adding Plotly backend | {
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"Looks fantastic, very exciting. Will need tests of course but otherwise will seems well structured.",
"Thanks @mattmcdermott ! This is going to be a really nice enhancement. This also includes the uncertainties support (for 2D plots at least), correct?",
"> Thanks @mattmcdermott ! This is going to be a really ... | 2020-08-18T22:30:23 | 2020-09-11T01:14:38 | 2020-09-11T01:13:46Z | MEMBER | {
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} | ## Summary
- Added `backend="plotly"` as a default argument to `PDPlotter`. Option `backend="matplotlib"` returns to existing plotting functionality.
- New features includes 2D scatter/line plot for binaries, and 3D scatter/mesh plots for ternaries and quaternaries. The latter include convex hull shading via Plotly... | {
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"Can you implement some tests to catch the bugs fixed pls? Thanks.",
"I implemented the tests. I also slightly changed the docstrings.",
"Thanks."
] | 2020-08-20T23:28:39 | 2020-08-21T15:10:12 | 2020-08-21T15:10:05Z | CONTRIBUTOR | {
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} | ## Summary
Two bug fixes:
* with the current implementation the Surface object can get weird results when instantiating with `reorient_lattice=True `and `coords_are_cartesian=True`. Fixed by switching to frac coords when needed.
* after dec6ecb6a9a80dbd4bfdfb924040cdfc7fe4ebb3 `Composition.to_reduced_dict` is no... | {
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"The results look perfect when I run the same test that was mentioned in issue #1935:\r\n```python\r\nN = 10\r\nmm = PermInvMatcher()\r\n\r\n# perturbing the atoms' position\r\nfor i in range(N):\r\n struct2 = struct.copy()\r\n struct_perturbed = struct.copy()\r\n struct_perturbed.perturb(0.3)\r\n _,_,_... | 2020-08-21T18:44:04 | 2020-10-05T12:28:39 | 2020-10-03T03:03:15Z | CONTRIBUTOR | {
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The main goal to implement a robust matching method between molecules. This implementation is based on [Kabsch algorithm]( https://en.m.wikipedia.org/wiki/Kabsch_algorithm) and on an excellent python package called [rmsd](https://github.com/charnley/rmsd). The code has been basically rewritten from scratc... | {
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"Hi @fekad, this looks useful but probably not something we'd want to merge into pymatgen. We're working on our own library for Jupyter visualization of crystal structur... | 2020-08-21T22:20:28 | 2020-08-25T01:24:15 | 2020-08-22T10:11:23Z | CONTRIBUTOR | {
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The tiny interface for visualising structures in jupyter notebook/lab using JSmol. The [`jupyter_jsmol`](https://github.com/fekad/jupyter-jsmol) package provides a widget (fully compatible with any other ipywidgets widgets) which is using the JSmol.
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"Thanks @rkingsbury "
] | 2020-08-22T00:53:08 | 2020-08-26T19:23:44 | 2020-08-26T19:22:32Z | CONTRIBUTOR | {
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- Remove ADDGRID
- Enforce `ISMEAR=-5` in all static calculations with `MPScanStaticSet`
Note:
We have learned that when `PREC=Accurate`, setting `ENAUG` has no effect. Although we considered removing ENAUG from the InputSet, ... | {
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"Hi @goodwilling, this is a Materials Project issue so would be better discussed at [matsci.org/materials-project](matsci.org/materials-project)\r\n\r\nIn brief, we're going through a series of large database updates, including this week expanding our band structures (from 54k -> 76k) and drastically improving the ... | 2020-08-26T11:47:39 | 2020-09-03T20:53:50 | 2020-09-03T20:53:50Z | NONE | {
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mpr.get_bandstructure_by_material_id("mp-867624")
or
https://www.materialsproject.org/rest/v2/materials/mp-867624/vasp/bandstructure?API_KEY=************
gives the error:
{
"valid_response": false,
"error": "too many indices for array: array is 0-dimensional, but... | {
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"Thanks @rwoodsrobinson !"
] | 2020-08-27T23:34:46 | 2020-08-29T02:00:51 | 2020-08-29T02:00:43Z | NONE | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Added spin parsing to SQSTransformation
* Added cluster parsing to SQSTransformation
* Added tests
* Fix .out file parsing bug
* Fix oxidation state and spin bug in periodic_table
## Checklist
Work-in-progress pull requests are encouraged... | {
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} | it was install，but it can only' import pymatgen'. if you 'import pymatgen.core' or 'import pymatgen.analysis' ,it would be that:
No module named 'pymatgen.analysis'; 'pymatgen' is not a package
on wind10 | {
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"I am confused. How do you know that the cart=False version is wrong? That is in the Zmatrix format. \r\n",
"> \r\n> \r\n> I am confused. How do you know that the cart=False version is wrong? That is in the Zmatrix format.\r\n\r\nI use Gaussview to visualize the two files and they are different.\r\n\r\ncart_outpu... | 2020-09-02T22:05:06 | 2023-08-13T16:33:45 | 2023-08-13T16:33:44Z | NONE | {
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} | **Describe the bug**
In some cases pymatgen.io.gaussian write_file() gives wrong output when cart_coords=False
**To Reproduce**
Here is the code to reproduce this issue.
```python
#!/usr/bin/env python
import pymatgen.io.xyz as xyzio
import pymatgen.io.gaussian as gaussianio
xyz_filename = "input.xyz"
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} | ## Summary
Merge pending changes to materialsproject.org and subsequent checking.
The intent of this PR is to better notify users of `MPRester` what the Materials Project database version is, and to notify the user if this version changes. | {
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"I don't think this functionality is implemented as a method anywhere, but I am unclear whether this requires its own method at all. Thinking about it in my head, this should not require more than 10 lines of code to do?",
"For this specific case, the `merge_sites` docstring claims `mode=='delete'` exists, does t... | 2020-09-04T04:49:07 | 2023-08-13T16:33:45 | 2023-08-13T16:33:45Z | CONTRIBUTOR | {
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} | I'd like to be able to embed one structure inside another. Roughly speaking, some of the sites should match exactly, while others may be quite different. The application that I have in mind is embedding a defect from a small supercell inside a larger supercell to cut down on the computational cost of the relaxation.
... | {
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* Use context managers for opening the input file and running the subprocess to ensure that both are properly closed
* Replace `ScratchDir` with `TemporaryDirectory` to eliminate non-obvious file deletion
Re: bullet point 2 - when the `S... | {
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"FYI @mattmcdermott @shyamd @awvio ",
"For certain, this requires new unittests.",
"> For certain, this requires new unittests.\r\n\r\nAbsolutely; tests added"
] | 2020-09-05T18:48:25 | 2021-07-15T14:31:38 | 2020-09-06T00:40:21Z | CONTRIBUTOR | {
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} | By analogy with `energy` and `energy_per_atom`, add `per_atom` attributes for other energies of a `ComputedEntry`:
* `correction_per_atom`
* `correction_uncertainty_per_atom`
* `uncorrected_energy_per_atom` | {
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TM = ['Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn',
'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd',
'La', 'Ce', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au']
I ... | {
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"Thanks. I have pushed the changes this time. For future reference, the instructions for how to contribute to pymatgen are at https://pymatgen.org/contributing . For a small change such as this, one way is to directly edit within Github itself, which will create a PR.",
"Thank you, I will do that next time.."
] | 2020-09-10T10:56:27 | 2020-09-10T23:48:17 | 2020-09-10T16:31:28Z | NONE | {
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} | Hello, I have been trying to use VornoiNN at large scale and noticed it does not scale well with large data set.
I noticed that trivial step in line 805 in pymatgen.analysis.local_env.VoronoiNN takes significant amount of time:
`sites = np.array(sites)[uniq_inds]`
The performance improves by about 10 fold over the ... | {
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"Thanks @rkingsbury. I noticed you commented out a test? Btw, NERSC is having load issues this morning so there are intermittent rester timeouts.",
"> Thanks @rkingsbury. I noticed you commented out a test? Btw, NERSC is having load issues this morning so there are intermittent rester timeouts.\r\n\r\nYes, that w... | 2020-09-10T18:33:19 | 2020-09-11T18:36:25 | 2020-09-11T18:34:35Z | CONTRIBUTOR | {
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} | The recent introduction of the `solid_compat` kwarg to `get_pourbaix_entries` began triggering a `DeprecationWarning` when the module was imported, because the kwarg defaulted to an instance of `MaterialsProjectCompatibility()`. This commit changes the interface slightly to avoid instantiating the class on import and t... | {
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"Thanks @rkingsbury !"
] | 2020-09-10T19:15:38 | 2020-09-20T19:14:27 | 2020-09-19T21:42:37Z | CONTRIBUTOR | {
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} | ## Summary
Migrate `MPScanRelaxSet` to the R2Scan metaGGA functional of Furness et al ([see paper](https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.0c02405)).
* use `R2SCAN` variant of SCAN
* Update test files and tests with R2Scan results
* Update docstrings with description and citation for R2Scan
Iterativ... | {
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"Many thanks @fraricci. For some context on the MPRester issue, some particularly large band structures fail due to a timeout on Cloudflare (which we cannot change). We use Cloudflare since it provides caching to reduce load on our servers and firewalls to prevent abuse. However, we're going to establish a second e... | 2020-09-15T11:19:33 | 2021-01-27T02:13:58 | 2020-10-10T01:17:02Z | CONTRIBUTOR | {
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} | This bug fix should solve the problem in issue #1941,
Example: mp-15077
Problem: for some reason some bandstructures on symmetry line in the MP
database contain the bands as dict(array). The BandStructureSymmLine.from_dict()
cannot handle this format. It creates the object but then the other methods
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"The DeprecationWarning message can have unexpected side effects.\r\n\r\non Windows 10, I encountered a case where thousands of DeprecationWarning come out if executing a python library on a terminal: \r\n\r\nDeprecationWarning: species_and_occu is deprecated\r\nUse site.species instead. This will be deprecated wit... | 2020-09-16T17:50:39 | 2020-10-12T17:23:36 | 2020-10-12T14:44:03Z | CONTRIBUTOR | {
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Various warnings emitted by pymatgen appear to be immune to filtering by the normal python approaches like `warnings.simplefilter("ignore")` or the `catch_warnings` context manager.
**To Reproduce**
For example, instantiating `MPRester()` raises a `DeprecationWarning` due to the upcoming cha... | {
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`TransformedStructure.append_transformation()` with `return_alternatives` breaks the structure one before the final.
**To Reproduce**
Here is an example code.
```
#!/usr/bin/env python
from pymatgen import Structure
from pymatgen.alchemy.materials import TransformedStructure
from pyma... | {
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`TransformedStructure.__str__()` removes `input_structure` from its history.
**To Reproduce**
Here is an example code.
```
#!/usr/bin/env python
from pymatgen import Structure
from pymatgen.alchemy.materials import TransformedStructure
from pymatgen.transformations.standard_transforma... | {
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"Thanks @cajfisher, this looks good but there are some linter errors (see failed tests):\r\n\r\n```\r\npymatgen/analysis/diffusion_analyzer.py:221:39: E261 at least two spaces before inline comment\r\npymatgen/analysis/diffusion_analyzer.py:222:18: E261 at least two spaces before inline comment\r\npymatgen/core/tra... | 2020-09-20T09:44:26 | 2022-01-09T14:51:25 | 2022-01-09T14:51:25Z | CONTRIBUTOR | {
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} | ## Summary
Fixes and changes to diffusion_analyzer.py:
* Now handles single-species systems correctly (specifically, when no framework atoms are present, calculation of framework drift is skipped)
* Various corrections to function descriptions (typo and grammar fixes, formatting and phrasing made consistent, et... | {
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"@tschaume , please take a look. the MPRester should now be able to get a url like this:\r\n\r\nhttps://nomad-lab.eu/prod/rae/api/repo/?file_pattern=vasprun*&external_id=mp-739635\r\n\r\n\r\nthe runner script is as follows:\r\n```\r\nimport os\r\nmaterial_ids = [\"mp-32800\"]\r\ntask_types = [TaskType.GGA_OPT, Task... | 2020-09-20T18:29:45 | 2021-09-23T18:12:13 | 2021-09-23T18:12:13Z | CONTRIBUTOR | {
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} | ## Summary
Update Nomad information
* Relink `get_download_info` in `ext/matproj.py` to the new URL: `https://nomad-lab.eu/prod/rae/api/repo/query?`
* Relink the `test_get_download_info` in the `ext/tests/matproj.py` to new URL
## TODO (if any)
This is a work in progress, I am still not able to run all the... | {
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"@mkhorton for the tests I just grabbed a bunch of random calculations and check that the grids matched.\r\nI actually check vs all 100K + calculations in my DB but only uploaded 300 to keep the file size small.",
"Thanks @jmmshn! Interesting you have to do a prime factorization with this too",
"This was amusin... | 2020-09-21T05:46:06 | 2020-09-25T16:32:37 | 2020-09-25T16:32:36Z | CONTRIBUTOR | {
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"Unless you want to communicate that people should be able to change `adj_per_atom` after instatiation, you probably want to set it with `self._adj_per_atom` (similar to eg `self._value` previously), likewise with `uncertainty`. Otherwise this looks good."
] | 2020-09-21T23:41:05 | 2020-09-29T17:49:45 | 2020-09-29T15:33:01Z | CONTRIBUTOR | {
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} | Populate the `cls` kwarg when creating `EnergyAdjustment` within `MaterialsProject2020Compatibility`. This information will be helpful in tracking the provenance of energy adjustments.
Now that the `cls` kwarg is populated as intended, executing `ComputedEntry.energy_adjustments` on an entry that has been processed... | {
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} | **Describe the bug**
MSD calculations fail when only one species is present in the system, as it is assumed all systems are ionic with framework atoms present in addition to the species of interest.
**To Reproduce**
Steps to reproduce the behavior:
1. Run DiffusionAnalzyer.from_structures using structures contain... | {
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"Hi @cajfisher, your comment is well-received but this is not likely to change at this point. The decision to use the term `Specie` is not made for grammatical reasons but for programmatical reasons: it is to unambiguously declare that this refers to a *single* species, vs., say, a list of multiple species. In term... | 2020-09-25T03:10:08 | 2020-09-30T03:52:48 | 2020-09-25T03:31:41Z | CONTRIBUTOR | {
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} | A number of functions and their descriptions (as well as the online manual) use the incorrect term "specie" to describe a single species. The singular and plural forms are both "species". ("Specie" refers to the physical form of money, usually coins.)
See, e.g., https://brians.wsu.edu/2016/05/31/specie/
https://thetr... | {
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"@mkhorton Pls review.",
"I'm fine merging this since the original `Specie` and `DummySpecie` are not deprecated but will remain as simple subclasses, so net disruption to the end user should be minimal.\r\n\r\nHowever, I'm mixed overall since it seems like the change doesn't produce net benefit, but will result ... | 2020-09-25T16:21:23 | 2020-09-29T15:32:17 | 2020-09-29T15:32:17Z | MEMBER | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Rename Specie and DummySpecie to Species and DummySpecies
* Specie and DummySpecie is allowed as a mapping for backwards compatibility.
* Corresponding changes to doc where possible.
* Pylint does not pass because of refactoring in chemenv and d... | {
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"Hi @hongyi-zhao, this is a dependency for the optional requirement `BoltzTrap2`, if you don't want to use BoltzTrap2 functionality you don't need to install this. To get it to work, you will want to install `cmake`, e.g. `snap install cmake` or `apt-get install cmake`",
"Thanks a lot. The following command solve... | 2020-09-27T05:41:24 | 2020-09-27T05:45:21 | 2020-09-27T05:45:21Z | CONTRIBUTOR | {
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The environment is Ubuntu 20.04, python 3.8.3 managed by pyenv, and latest git master version of pymatgen. See following for more info:
```
$ python --version
Python 3.8.3
$ pip install -r requirements-optional.txt
[...]
ERROR: Command errored out with exit status 1:
command: /home/werner/.pyenv... | {
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"Here, \"extra\" is a placeholder for the specific \"extra\" that you require.\r\n\r\nCurrently, you can choose from \"provenance\", \"ase\", \"vis\" or \"abinit\" (see [here](https://github.com/materialsproject/pymatgen/blob/4b406abb589b9df1b7fbc3ba52e375f6fd3ed37e/setup.py#L115)).\r\n\r\nAs with the BoltzTrap2 de... | 2020-09-27T05:54:40 | 2020-09-30T09:31:09 | 2020-09-30T03:51:21Z | CONTRIBUTOR | {
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The document told the following:
```
$ egrep -inR 'pymatgen\[extra\]' .
./docs_rst/introduction.rst:182: pip install pymatgen[extra]
```
But the output of the following installation command is not coherent with the above description:
```
$ pip install .[extra]
Looking in indexes: https://mirrors.aliyu... | {
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"@LuciusV My apologies for just seeing this now! Yes, the new PDPlotter (with Plotly backend) does not currently work with the `write_image()` function; that's my fault for missing that implementation when I wrote the code!\r\n\r\nUnfortunately, Plotly is quite difficult when it comes to saving high-quality figures... | 2020-09-28T13:24:26 | 2023-06-02T23:37:07 | 2020-10-30T19:55:25Z | NONE | {
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} | **Describe the bug**
If I try to .write_image() of ternary phase diagram with default backend, it fails.
**To Reproduce**
Steps to reproduce the behavior:
In jupyter notebook:
1. Make some 3-component PhaseDiagram
2. Make PDPlotter on this Phasediagram
3. Call write_image('something.svg'). PNG also fails.
4.... | {
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"Many thanks @nwinner, this is great! Thanks for breaking it off into a smaller PR too from the CP2k PR too, makes review easier.\r\n\r\nPlease make sure to include your details in [this form](https://forms.gle/JnisFb38QDR8QTFTA) so that you can be credited appropriately in the [pymatgen documentation](https://pyma... | 2020-09-29T06:04:53 | 2021-04-27T19:46:50 | 2020-10-03T03:14:37Z | CONTRIBUTOR | {
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} | ## Summary
Bader caller has been amended to allow for parsing VASP outputs (CHGCAR) as well as the Gaussian Cube format.
* Feature 1: pymatgen.io.cube module created for Cube object, which reads and stores volumetric data from cube file just as Chgcar does for CHGCAR files.
* Feature 2: BaderAnalysis now suppo... | {
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"Many thanks @fraricci ! This is a lot of very nice work.\r\n\r\nFor this point:\r\n\r\n> TODO: might by useful to implement a plotly version\r\n\r\nWe have plotly versions already (in another code, to be merged into pymatgen when they're fairly mature). We've been taking this strategy with the phase diagram plotti... | 2020-09-29T14:45:46 | 2020-10-10T01:18:16 | 2020-10-10T01:17:00Z | CONTRIBUTOR | {
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} | - BSPlotter now handle multiple bandstructures when they are on the same symmetry kpath.
- Usage: bsp = BSPlotter(sbs) or bsp = BSPlotter([sbs1,sbs2]); also bsp.add_bs(sbs2) or bsp.add_bs([sbs2,sbs3])
- Old plot_compare method still works but a warning will be raised.
- Differences in the distances scale are managed... | {
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> I'm not sure if related, but I had similar problem with MPSOCSet/MPStaticSet and MAGMOM. It might be worth having a look at this issue #1397. We solved it but we let it open for further checks.
_Originally posted by @fraricci in https://github.com/materialsproject/pymatgen/pull/1917#discussio... | {
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"@ucsdlxg Can you take a look?",
"Sure. I will take a look.\n\n> On Oct 10, 2020, at 9:45 PM, Shyue Ping Ong <notifications@github.com> wrote:\n> \n> \n> @ucsdlxg <https://github.com/ucsdlxg> Can you take a look?\n> \n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view ... | 2020-10-01T08:16:39 | 2023-08-13T16:33:47 | 2023-08-13T16:33:47Z | NONE | {
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} | **Describe the bug**
In the GB structure, some atoms are too close to each other (distance < rm_ratio*bond_length_in_bulk).
Similar results are also obtained for other bcc systems, with [100], [010], [001] as the rotation axis for the
twist GB and the primitive cell as the crystal bulk structure, together with ... | {
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"Thank you for reporting this @CompRhys ! Have you tested against the latest master branch? I believe what you are describing is the same bug that we caught and fixed in #1960 , which was just merged a few days ago. ",
"For me, using the your code snippet with the latest upstream pymatgen works properly, with the... | 2020-10-01T10:53:55 | 2020-10-01T17:14:36 | 2020-10-01T17:14:36Z | CONTRIBUTOR | {
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} | **Describe the bug**
`ComputedEntry.as_dict()` doesn't work with `energy_adjustments`
**To Reproduce**
```python
from pymatgen.entries.computed_entries import (
ComputedEntry,
ConstantEnergyAdjustment,
CompositionEnergyAdjustment,
TemperatureEnergyAdjustment,
ManualEnergyAdjustment,
)
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"Thanks @rkingsbury "
] | 2020-10-02T00:36:43 | 2020-10-02T03:10:37 | 2020-10-02T02:03:27Z | CONTRIBUTOR | {
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} | To facilitate testing in the absence of proprietary POTCAR files, `InputSet` have the option to write a `POTCAR.spec` file instead of an actual POTCAR. However, when a `POTCAR.spec` file is present, `Vasprun.get_potcars()` tries to read it, resulting in an error.
This PR causes Vasprun.get_potcars() to ignore POTCAR... | {
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"Thanks @mattmcdermott!"
] | 2020-10-03T00:49:16 | 2020-10-03T03:04:12 | 2020-10-03T03:04:12Z | MEMBER | {
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} | ## Summary
* Fix 1: phase labels now appear correctly for instances of CompoundPhaseDiagram and GrandPotentialPhaseDiagram
* Fix 2: shaded uncertainty window now appears correctly for terminal compounds in instances of CompoundPhaseDiagram and GrandPotentialPhaseDiagram
* Feature: uncertainty value appears in hove... | {
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"Nice -- very timely as I've actually been wanting to solve this issue as well! I frequently need to make phase diagrams of 10+ elements, which is essentially impossible (that's around when it starts taking hours). I came up with a \"phase diagram expansion\" solution (not actually in pymatgen). It's the `expand_pd... | 2020-10-03T17:43:17 | 2021-01-19T17:56:31 | 2021-01-19T17:56:31Z | CONTRIBUTOR | {
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} | ## Summary
Introduce a new `PhaseDiagram` based class to handle large disjoint data sets. Calculation of the convex hull of a data set scales with the dimensions and amount of data. Breaking up disjoint datasets into smaller patches reduces the complexity in both these regards and would allow for parallel computatio... | {
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"Many thanks for this @vorwerkc ! Since `paramdict` is freeform (for any settings not otherwise specified), perhaps it would be better to set this at the end as `**kwargs` instead? Otherwise this looks good to merge.",
"Hi @vorwerkc, I made a quick commit to illustrate what I meant by the \"kwargs\" comment, so n... | 2020-10-05T12:45:57 | 2020-12-02T21:02:27 | 2020-12-02T21:02:24Z | CONTRIBUTOR | {
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} | ## Summary
Small additional feature that allows the user to generate an exciting input file with additional parameters. The parameters are provided in the form of a nested dictionary, which allows to generate a full exciting input files with all elements and attributes.
* Additional arguments for io.exciting.Exci... | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed and justify why. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding one... | {
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"Can you upload a sample XSF file?",
"Sure thing, thanks a lot.\r\nSergiu\r\n\r\n[pymatgen_example.zip](https://github.com/materialsproject/pymatgen/files/5339451/pymatgen_example.zip)\r\n\r\n\r\n",
"Done. Now the default format uses atom symbols."
] | 2020-10-06T13:25:05 | 2020-10-11T02:44:29 | 2020-10-11T02:44:17Z | NONE | {
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**Describe the solution you'd like**
Please add the possibility to dump/read XSF files with atomic symbol (H,He,O) instea... | {
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"You can use the pymatgen.io.lammps to create LAMMPS format. Not all formats are given in fmt because LAMMPS require other parameters to be specified."
] | 2020-10-06T13:30:33 | 2020-10-11T02:37:03 | 2020-10-11T02:37:02Z | NONE | {
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**Describe the solution you'd like**
A simple format conversion described here: https://atomsk.univ-lille.fr/tutorial_lammps.php
Besr regards,
Sergiu | {
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"Thanks @utf!"
] | 2020-10-07T21:38:15 | 2020-10-08T06:03:43 | 2020-10-08T06:03:36Z | MEMBER | {
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} | A common pattern in many of the MP VASP input sets is to store the input kwargs in the constructor and then access them using `self.kwargs.get` in the `incar` and `kpoint` functions. Unfortunately, this can lead to discrepancies between the actual attributes of the input set and the data stored in the `kwargs` variable... | {
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"Thanks. I implemented the fix with a new test to ensure this does not recur.\r\n"
] | 2020-10-09T15:48:22 | 2020-10-11T02:36:07 | 2020-10-11T02:35:52Z | NONE | {
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} | **Describe the bug**
Neutron diffraction pattern can not be plot. A bug fix is suggested.
**To Reproduce**
Error always comes out if using the following script:
from pymatgen import Structure
from pymatgen.analysis.diffraction.neutron import NDCalculator
import sys
struc = Structure.from_file("Fe_mp-13_p... | {
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"Your statement is incorrect. C2/c and I2/b are both monoclinic. They even have the same space group (No. 15). It is just a different choice of axes. All this can be found in the International Tables for Space group No. 15."
] | 2020-10-11T01:54:32 | 2020-10-11T02:31:36 | 2020-10-11T02:31:36Z | CONTRIBUTOR | {
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Based on the descriptions in [this paper](https://pubs.acs.org/doi/pdf/10.1021/acs.chemmater.9b05047), see top left column on pp.3 for more info, I learned the following fact:
`
The (010) surface in C2/c is equivalent to the (001) surface in I2/b. And these two space groups are related through a change-of-b... | {
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"I just pin it to the without v for now."
] | 2020-10-12T15:17:22 | 2020-10-12T16:36:16 | 2020-10-12T16:36:15Z | NONE | {
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"This is related to the fact that numpy and cython does not exist in Python 3.9 yet. See https://github.com/pandas-dev/pandas/issues/32045 . Just keep pymatgen to python3.7 and 3.8 for now.",
"FYI for this, it looks like `tp_print` has been [removed in Python 3.9](https://docs.python.org/3.9/whatsnew/3.9.html#id3... | 2020-10-15T14:45:31 | 2020-10-16T23:17:24 | 2020-10-16T12:05:25Z | NONE | {
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} | **Describe the bug**
pymatgen fails to build with Python 3.9.0
```
pymatgen/util/coord_cython.c:22836:25: error: «PyTypeObject» {aka «struct _typeobject»} has no member named «tp_print»
22836 | __pyx_type___pyx_array.tp_print = 0;
```
**To Reproduce**
Steps to reproduce the behavior:
1. build with Python 3.... | {
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"+1 . I agree this would be very useful. ",
"I think it might be nicer to just change the `plt` argument to `ax` as I feel that is more natural to work with.\r\n\r\nThat said, to use the existing `plt` argument with subplots often the only thing you have to do is set the current axis to the axis you want to plot ... | 2020-10-17T15:17:38 | 2023-08-13T16:33:47 | 2023-08-13T16:33:47Z | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
It would be nice to be able to pass `matplotlib` axes objects to `PDPlotter` when using the `matplotlib` backend such that they can be easily incorporated into subplots.
**Describe the solution you'd like**
a `kwarg` called `axes` in PDPlotter that... | {
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"@shyamd feel free to add anything I missed\r\n",
"I think this might actually be a bug in `.normalize`. The unittest we have for `get_equilibrium_reaction_energy` passes, and it builds a `PhaseDiagram` from very simple `PDEntry` - they just have an energy and a composition. Using those entries,\r\n```\r\n[e.nor... | 2020-10-20T04:10:58 | 2021-01-27T15:26:18 | 2021-01-27T15:26:18Z | CONTRIBUTOR | {
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} | **Describe the bug**
`PhaseDiagram.get_equlibrium_reaction_energy()` fails when called on a stable entry from the phase diagram, and raises
```ValueError: None is unstable, the equilibrium reaction energy is available only for stable entries```
**To Reproduce**
```
with MPRester() as m:
entries = m.get_en... | {
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"Hi @jonathanjdenney, thanks for this.\r\n\r\nA few comments before merging, mostly just to follow Python conventions:\r\n\r\n* The file `pymatgen/analysis/Fstar/__pycache__/fstar.cpython-36.pyc` should be removed\r\n* The folder `pymatgen/analysis/Fstar/` should be renamed to `pymatgen/analysis/fstar/`\r\n* The fi... | 2020-10-20T17:51:34 | 2023-02-07T19:13:33 | 2023-02-07T19:13:32Z | CONTRIBUTOR | {
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} | ## Summary
Added f* diagram generator.
## Additional dependencies introduced (if any)
* List all new dependencies needed and justify why. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily impl... | {
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"I run that code on a vasprun that contains d orbilals projection without any error.\r\nCould you check that your vasprun has the needed data? In positive case,\r\nsend me that vasprun so that I can reproduce the error. @Yang-YM\r\n"
] | 2020-10-22T18:12:04 | 2023-08-13T16:33:48 | 2023-08-13T16:33:48Z | NONE | {
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} | When I want to plot the projected band structure using `BSPlotterProjected`, I find it not work if the `dictio` has d orbitals.
It gives the error :
```
C:\ProgramData\Anaconda3\lib\site-packages\pymatgen\electronic_structure\plotter.py:1058: MatplotlibDeprecationWarning: Adding an axes using the same arguments a... | {
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"In pymatgen's slab generator, the surface is in the x-y direction. The only question is whether the z direction is constrained to be orthogonal or not. By default the SlabGenerator makes non-orthgonal slabs that are the smallest possible for that surface. If you use Slab.get_orthogonal_c_slab, you then get the ort... | 2020-10-25T09:20:20 | 2020-10-25T15:04:33 | 2020-10-25T14:49:46Z | NONE | {
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} | Hi pymatgen developers,
I have lots of x-y axis orthorhombic slabs which is constructed by SlabGenerator. However, my problem is sensitive to the slab x-y angle (gamma) thus I would like to check if these slabs could be transformed into non-orthorhombic slabs.
The following picture (get from https://wiki.fysik.dt... | {
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"This should be ready to merge btw.",
"Thanks @utf"
] | 2020-10-27T01:12:14 | 2020-10-28T22:59:57 | 2020-10-28T22:27:04Z | MEMBER | {
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} | ## Summary
`Outcar.as_dict` method fails if the OUTCAR doesn't contain the average electrostatic potential at atomic cores. This can occur if `ICORELEVEL = 1` is set. I've fixed this behaviour and added a test.
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [... | {
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"This is too brief an error message for us to debug. I don't get this error."
] | 2020-10-30T19:48:10 | 2020-10-30T19:57:08 | 2020-10-30T19:57:08Z | NONE | {
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It says the module is not available, I have been using pymatgen for a year and have not came across anything like this before.
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"Thanks. Can you uncomment abinit in the setup.cfg and make sure the pydocstyle tests pass too? Thanks.",
"Hi, I've removed abinit from setup.cfg and fixed the doc strings as requested. All tests seem to be OK. ",
"Thanks."
] | 2020-11-05T16:14:30 | 2020-11-06T16:02:55 | 2020-11-06T16:02:55Z | CONTRIBUTOR | {
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* Use deterministic algorithm (not based on python set) to obtain list of elements before writing Abinit input file.
This is required to maintain compatibility with the original implementation of structure.types_of_specie and all the DFPT
results produced so far.
* Add refine_struct optional ar... | {
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"Thanks @gpetretto :-)"
] | 2020-11-06T15:35:43 | 2020-11-07T02:58:47 | 2020-11-07T02:58:45Z | CONTRIBUTOR | {
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Small bug fix in PhononBandStructureSymmLine. Added tests. | {
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"The phase used in the argument of Pourbaix.get_decomposition_energy must have a ratio of non-OH elements that matches the ratio corresponding to the pourbaix diagram in order to work. When you generate the pourbaix diagram, add a composition dictionary to match the entry whose stability you want to determine, e.g... | 2020-11-13T03:59:33 | 2023-09-20T02:07:38 | 2020-11-22T22:05:32Z | NONE | {
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I am new to pymatgen and am trying to use the Pourbaix diagram features to obtain a decomposition energy for a computed entry. However I keep encountering the ValueError associated with the get_decomposition_energy() method:
_ValueError: Composition of stability entry does not match Pourbaix Diagram_
... | {
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"I've also had this issue.",
"I just tried on my system and I cannot reproduce this. Can you try forcing a reinstall of ruamel?\r\n\r\n`pip install --force ruamel.yaml`",
"Forcing the reinstall gives me the following error messages:\r\n\r\nERROR: Cannot uninstall 'ruamel-yaml'. It is a distutils installed proje... | 2020-11-16T15:40:17 | 2021-01-16T00:50:07 | 2021-01-16T00:50:00Z | NONE | {
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} | **Describe the bug**
Error importing the pymatgen module.
```
>>> import pymatgen
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-2-a3a39e60e980> in <module>
----> 1 import pymatgen
~/an... | {
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"Can you provide your pymatgen version, VASP version, and a copy of the WAVECAR?",
"I have used pymatgen==2020.11.11 and vasp 5.4.4 version. I am unable to attach the WAVECAR file because the size of the file is very large (approx. 155 GB).",
"Do you have enough memory? The entire WAVECAR will be read in to mem... | 2020-11-16T20:46:46 | 2024-02-22T07:45:41 | 2023-06-23T02:49:22Z | NONE | {
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} | I trying to load the spin-orbit coupling WAVCAR but failed. I got the following error message:
```py
Traceback (most recent call last):
File "/lustre/project/k1388/shafiq/CSLD-AMSET/install4/bin/amset", line 33, in <module>
sys.exit(load_entry_point('amset', 'console_scripts', 'amset')())
File "/lustre/... | {
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"I think we can make it stricter. Explicitly set the type to \"unknown\" with a warning if it is not within the list of defined types. ",
"Might be more robust to set it to the METAGGA tag if that tag is specified, in terms of if additional meta GGAs are added in future.",
"Specifically this line:\r\n\r\n```\r\... | 2020-11-16T22:34:18 | 2021-07-15T14:31:39 | 2020-12-01T16:32:50Z | CONTRIBUTOR | {
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} | At present, `OUTCAR.run_type` incorrectly sets the `run_type` to 'GGA' when METAGGA is equal to `R2SCAN` or `RSCAN`. This commit adds support for these functionals in `run_type` and also adds a test for regular `SCAN` run_type, which was not previously covered by a test. | {
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"Thanks @jmmshn, going to merge this."
] | 2020-11-16T22:38:04 | 2020-12-01T16:31:55 | 2020-12-01T16:31:55Z | CONTRIBUTOR | {
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- Added ChargeInsertionAnalyzer class and tests
- Reformatted and ignoring .pre-commit-config.yaml | {
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"@haesunpark87 I recently noticed the same issue. The problem was due to the different pseudopotentials used for Li_sv. The PAW_PBE Li_sv in MP should be the `23Jan2001` version. Maybe the Li_sv you are using was `10Sep2004`. @mkhorton Is this something significant? I also have friends who had the same issues and s... | 2020-11-17T17:07:20 | 2021-03-09T02:23:49 | 2021-03-09T02:23:49Z | NONE | {
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} | I have calculated the energy of Li2O using the input setting made by **MPRelaxSet** module from pymatgen.
However, the calculated energy is way off from that in the MP data base(https://materialsproject.org/materials/mp-1960/#corrections-eqn).
The uncorrected energy differs by ~30meV/atom.
I used the POTCAR of Li_... | {
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"Thanks for the improvement @bayesfactor, apologies for letting such a brief PR sit for a while.",
"Since you are a first-time contributor, please do complete [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can credit you appropriately in the [documentation](https://pymatgen.org/team.html). We ask all cont... | 2020-11-18T19:39:29 | 2020-12-01T21:23:30 | 2020-12-01T16:41:59Z | CONTRIBUTOR | {
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} | 3D phase diagram plots have fonts that are so small they are nearly illegible. This PR has minor changes to aesthetics that take full use of the space in the plot and increase font size.
## Summary
Include a summary of major changes in bullet points:
* Larger fonts for component labels
* Changed 3D plot layou... | {
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"@utf @mkhorton see `smart_efermi` method based on Alex's code. Fermi level seems to be set in the `init` method of `Outcar`, `BSVasprun`, and `Wavecar`. It is also read from the DOS in `Vasprun`.\r\n\r\nWould it make sense to default to this method inside `Vasprun.get_band_structure()`? Where else in outputs.py w... | 2020-11-19T23:05:36 | 2021-07-15T14:31:41 | 2020-12-04T01:53:24Z | CONTRIBUTOR | {
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} | - Implement a `smart_efermi` property in `Vasprun` to detect cases in which the Fermi level reported by VASP crosses one of the bands, but the bands otherwise indicate insulating behavior. This issue sometimes causes `Vasprun` to report inaccurate bandgaps (for example, insulators may be reported to have zero bandgap)
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