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https://api.github.com/repos/materialsproject/pymatgen/issues/801 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/801/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/801/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/801/events | https://github.com/materialsproject/pymatgen/issues/801 | 252,371,190 | MDU6SXNzdWUyNTIzNzExOTA= | 801 | Pathological error in VoronoiCoordFinder for slabs | {
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"How to use the `allow_pathological`?",
"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 2017-08-23T18:16:09 | 2023-08-08T21:20:31 | 2023-08-08T21:20:30Z | CONTRIBUTOR | {
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} | There is an issue for some slab structures where a `RunTimeError` occurs stating the structure is pathological. I think this may be due to the code being unable to properly create a convex hull for surface sites where there are neighboring atoms in the vacuum. There is a tag called `allow_pathological` that bypasses th... | {
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} | Suggest just calling it write_file to be consistent with other io.
Not sure if backwards compatibility needs to be maintained since I have no idea where this object is used in MP.
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"I already fixed this last time. But tests are still failing on Py27. ",
"@shyuep Could you accept my pull request and check it again. Actually, I did a simple fix and it works for both python 2.x and python 3.x (I checked).",
"I already fixed the map problem. Your pull req has merge conflicts with the main pym... | 2017-08-24T14:43:45 | 2017-08-24T15:03:40 | 2017-08-24T14:46:16Z | CONTRIBUTOR | {
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} | … in plotter.py file.
These changes make the usage of "map" function suitable with both python 2.x and python 3.x
## Summary
Short few sentences, and summary of the major changes in bullet
points
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new... | {
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"Thanks!"
] | 2017-08-24T18:22:01 | 2017-12-14T04:17:39 | 2017-08-24T18:49:25Z | NONE | {
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} | ## Summary
The method min_freq in the PhononBandStructure object returns the wrong q-point. In its current form, the method would return the q-point with the index of the band that contains the minimum instead of using the index of the minimum frequency.
Fix: Change self.qpoints[i[0]] in line 106 to self.qpoints[... | {
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} | ## Summary
The AdsorbateSiteFinder class now has a new parameter "top_surface=True" which will adsorb molecules on the top surface if True and bottom surface if False. This is useful for studying the adsorption of nonsymmetric surfaces. A new function that utilizes this is adsorb_both_surfaces. A new parameter calle... | {
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"There is a test error. You need to check your tests and fix.",
"I am not sure how to deal with this situation in a pythonic way. The fix I wrote looks not professional. You may improve it. Thanks."
] | 2017-08-24T22:44:03 | 2017-08-25T00:14:50 | 2017-08-25T00:13:30Z | CONTRIBUTOR | {
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When Vasprun() parses vasprun.xml , it generally first checks the convergence status (electronic and ionic). However, there is no electronic or ionic step in BSE calc. This fix is to ignore the convergence checking of BSE vasprun.xml. | {
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"The code should not convert LAMMPS to POSCAR. It should just allow a person to get a structure.",
"There is never a reason to write code to convert one file format to another. If you are able to get a structure from LAMMPSDAta, you can already pass the structure to the Poscar class to get the Poscar object. The ... | 2017-08-24T23:33:33 | 2017-08-25T15:33:59 | 2017-08-25T13:54:15Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Add the code to transform from the format of the lammps Data to vasp POSCAR.
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, ad... | {
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fix parsing BSE vasprun error | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/811 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/811/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/811/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/811/events | https://github.com/materialsproject/pymatgen/pull/811 | 253,017,511 | MDExOlB1bGxSZXF1ZXN0MTM3NzU2ODQ3 | 811 | Bug fix for LMPDATA to Structure object | {
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"Pls run Pycharm -> Reformat code first. Your code does not conform to Python PEP8."
] | 2017-08-25T21:04:16 | 2017-08-25T22:43:35 | 2017-08-25T22:43:35Z | CONTRIBUTOR | {
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} | ## Summary
I add a variable "atom_style" to tell the LammpsData format.
The difference of atomic mass for some elements is small, e.g. Pt, Ce. Now set the criteria to 0.05.
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed. While a... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/812 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/812/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/812/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/812/events | https://github.com/materialsproject/pymatgen/pull/812 | 253,096,129 | MDExOlB1bGxSZXF1ZXN0MTM3Nzk5NDI0 | 812 | surface_analysis.py ver1 | {
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} | ## Summary
surface_analysis.py and its corresponding test file test_surface_analysis.py has been added. This is to partially address Issue #767 . The current version contains a class called SurfaceEnergyAnalyzer, which takes in a dictionary of a list of Vasprun objects for a set of slab calculations. The key is the ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/813 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/813/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/813/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/813/events | https://github.com/materialsproject/pymatgen/pull/813 | 253,122,561 | MDExOlB1bGxSZXF1ZXN0MTM3ODExODg0 | 813 | Documentation of spectrum module | {
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} | ## Summary
Add document to functions in core/spectrum module
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https://api.github.com/repos/materialsproject/pymatgen/issues/814 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/814/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/814/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/814/events | https://github.com/materialsproject/pymatgen/issues/814 | 253,482,233 | MDU6SXNzdWUyNTM0ODIyMzM= | 814 | enumlib_caller: makestr.x deprecated | {
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"Ok. If you can fix these, it would be great. In general, I use only latest enumlib since that has significant speed advantages with the latest symmetry handling.",
"Hello,\r\n\r\nThe supporting files provided indeed work, thank you.\r\nHowever, please update the error message in pymatgen that is misleading.\r\n\... | 2017-08-28T23:09:48 | 2019-07-08T13:29:02 | 2017-10-13T22:23:25Z | MEMBER | {
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} | An FYI: I noticed that makestr.x has been deprecated in enumlib, replaced by [makeStr.py](https://github.com/msg-byu/enumlib/tree/master/aux_src). I don't know if these are interchangeable, but we should probably update `enumlib_caller` at some point in case the code diverges more in future. (Also, I think [this test](... | {
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"I don't see a unit test."
] | 2017-08-28T23:38:01 | 2017-08-30T00:08:19 | 2017-08-30T00:08:19Z | NONE | {
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} | ## Summary
oxi_state_guesses could take a long time for Compositions with large numbers of sites and many degrees of freedom (oxidation states) per site. If enabled, this feature allows one to try to limit the number of sites used by reducing the formula to at most max_sites before the analysis.
Notes:
* althoug... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/817 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/817/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/817/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/817/events | https://github.com/materialsproject/pymatgen/pull/817 | 253,576,187 | MDExOlB1bGxSZXF1ZXN0MTM4MTIzMjIx | 817 | MAINT: Numerical stability for symmetrise + finer control over tolerance | {
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"Thanks. However, there seems to be a test error? You can click on the travis-ci above to see the error.",
"Thanks as well for accepting ;)"
] | 2017-08-29T08:55:39 | 2017-08-29T16:43:34 | 2017-08-29T15:23:54Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Followup to #760
* Improved numerical stability in the symmetrise code. Previously if *O(i, j)* denotes the the symmetry operation to map atom *i* unto *j* it could end up with a chain of *O(3, 4) O(2, 3) O(1, 2)* even if *O(1, 4)* was already available. Mathematically this does not matter, but in l... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/818 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/818/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/818/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/818/events | https://github.com/materialsproject/pymatgen/pull/818 | 254,193,014 | MDExOlB1bGxSZXF1ZXN0MTM4NTY4OTU1 | 818 | Parsing energies from gen_scfman module in Qchem 5 | {
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"Thanks!"
] | 2017-08-31T02:38:26 | 2017-08-31T03:51:57 | 2017-08-31T03:51:57Z | CONTRIBUTOR | {
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} | ## Summary
In Qchem 5 there is new scf module called gen_scfman, unfortunately the scf output is slightly different from the default module. Also, I added .eggs/ to the git ignore file. I saw a few egg related ignore so hopefully that is alright.
* parse energies from gen_scfman output
*unittest added
## TODO... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/819 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/819/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/819/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/819/events | https://github.com/materialsproject/pymatgen/pull/819 | 254,745,076 | MDExOlB1bGxSZXF1ZXN0MTM4OTY4ODA1 | 819 | Bug fix for Hubbard-U in Vasprun, and added basic vdW support | {
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"Thanks! However, I don't think the use_vdw and del_vdw should eb within the Incar object. In general, the Incar etc. input files are generically defined to support any functional or calculation type. For actual settings, these should be implemented in the vasp input sets (in pymatgen.io.vasp.sets.py). Can you impl... | 2017-09-01T20:34:01 | 2017-09-01T23:40:50 | 2017-09-01T23:40:50Z | NONE | {
"total": 0,
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} | ## Summary
Fixed a bug for Hubbard calculations in Vasprun, and added basic van-der-Waals support.
* Hubbard: If LDAUJ is not specified in INCAR, Vasprun.as_dict() will raise a VaspParserError because the lengths of the LDAUU and LDAUJ lists are different. This problem has already been resolved in Vasprun.hubbard... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/820 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/820/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/820/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/820/events | https://github.com/materialsproject/pymatgen/pull/820 | 254,774,057 | MDExOlB1bGxSZXF1ZXN0MTM4OTkwMjUy | 820 | fix slab set as_dict issue and add unittest | {
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"total": 0,
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} | ## Summary
MVLSlabSet.as_dict was failing due to a change in __init__ argument name without the corresponding assignment of attribute. I'm not sure this is the best way to do it, but this seems to fix the issue. Might want to check, @richardtran415. Also added a unittest. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/821 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/821/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/821/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/821/events | https://github.com/materialsproject/pymatgen/pull/821 | 254,776,380 | MDExOlB1bGxSZXF1ZXN0MTM4OTkxOTQ5 | 821 | Add critic2 command line caller for topological analysis, includes new graph class | {
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"I've updated `StructureGraph` this morning to remove some of the rough edges. I'm a lot happier with it now.\r\n\r\nEven though it's quite minimal, I've submitted this PR to (a) solicit feedback and make it easier for people to test and (b) signal my intent to work on this, so that if anyone intends to work on so... | 2017-09-02T00:17:31 | 2017-09-07T05:25:16 | 2017-09-06T22:47:13Z | MEMBER | {
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} | # Add critic2 command line caller
Critic2 provides a more advanced Bader analysis, giving information on critical points present in the charge density and connections between these critical points. This allows us to obtain bonding information directly from the charge density, but also provides a whole range of addit... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/822 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/822/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/822/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/822/events | https://github.com/materialsproject/pymatgen/pull/822 | 254,900,791 | MDExOlB1bGxSZXF1ZXN0MTM5MDYxODY3 | 822 | Kpath fix | {
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"Pls fix the failing tests.",
"Sorry, I have found a few problems in this PR.\r\n\r\n- Simply adding the test for the presence of \"A\" in the spg symbol does not guarantee to give a proper standard primitive cell for the face centered orthorhombic spacegroups:\r\n```\r\nfrom pymatgen import MPRester\r\nfrom pyma... | 2017-09-03T21:09:11 | 2017-09-04T16:49:43 | 2017-09-04T16:06:35Z | CONTRIBUTOR | {
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} | ## Summary
Modifications to account for space group naming conventions changes in spglib
* Fix in pymatgen.symmetry.bandstructure.HighSymmKpath class
* Fix in pymatgen.symmetry.analyzer.SpacegroupAnalyzer class
* Tests for both modifications | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/823 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/823/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/823/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/823/events | https://github.com/materialsproject/pymatgen/pull/823 | 255,096,122 | MDExOlB1bGxSZXF1ZXN0MTM5MTk2NjEx | 823 | Kpath fix: rebased to pymatgen master and centering issue fixed | {
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"Thanks. But while I appreciate the extremely comprehensive tests, this is adding 230 files (one for each structure), and each file is not exactly small. Any chance the structures can be generated usinng code on the fly? It should be a simple matter to pass a crystal lattice and use Structure.from_spacegroup to gen... | 2017-09-04T17:53:25 | 2017-09-16T03:39:45 | 2017-09-16T03:39:45Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Modifications to account for space group naming conventions changes in spglib.
* Fix in pymatgen.symmetry.bandstructure.HighSymmKpath class
* Fix in pymatgen.symmetry.analyzer.SpacegroupAnalyzer class
* Tests for both modifications
## Centering convention fix
```
from pymatgen import MPRester
f... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/824 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/824/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/824/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/824/events | https://github.com/materialsproject/pymatgen/issues/824 | 255,147,488 | MDU6SXNzdWUyNTUxNDc0ODg= | 824 | Is get_primitive_structure has bug? | {
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"get primitive just returns a primitive cell, typically the niggli or LLL reduced version. This is not always the same as the rhom version. They are nevertheless the same structure.",
"@shyuep OK, I understand. Thank you for explanation"
] | 2017-09-05T03:00:20 | 2017-09-05T11:23:57 | 2017-09-05T11:20:34Z | NONE | {
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} | I am just pip installed the latest pymatgen, the python version is 2.7
I want to do primitive cell conversion on Bi2Se3 structure. The cif file is space group 166 in hexagonal mode, while the primitive cell should be rhombohedral. So I do the following
```
import pymatgen as mp
structure = mg.Structure.from_f... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/825 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/825/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/825/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/825/events | https://github.com/materialsproject/pymatgen/issues/825 | 255,369,293 | MDU6SXNzdWUyNTUzNjkyOTM= | 825 | FloatWithUnit does not play nicely with numpy arrays | {
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"Use arraywithunit\n\nOn Wed, Sep 6, 2017, 00:06 Brandon Bocklund <notifications@github.com>\nwrote:\n\n> from pymatgen.core.units import FloatWithUnitimport numpy as np\n>\n> scaling_array = np.array([0.5, 1, 2, 4])\n> one_ev = FloatWithUnit(1, 'eV')\n> # does not raise, drops unit (should be eV)# see the first\n>... | 2017-09-05T18:36:14 | 2023-08-08T21:20:46 | 2023-08-08T21:20:46Z | CONTRIBUTOR | {
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} | ``` python
from pymatgen.core.units import FloatWithUnit
import numpy as np
scaling_array = np.array([0.5, 1, 2, 4])
one_ev = FloatWithUnit(1, 'eV')
# does not raise, drops unit (should be eV)
# see the first
scaling_array*one_ev
# raises
one_ev*scaling_array
from pymatgen.core.units import Array... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/826 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/826/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/826/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/826/events | https://github.com/materialsproject/pymatgen/pull/826 | 255,412,266 | MDExOlB1bGxSZXF1ZXN0MTM5NDIzNzIy | 826 | resolving two small issues with periodic table data | {
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"Pls fix the values not in the json, but rather the yaml version in pymatgen/dev. That is supposed to be \"base data\" that we edit on. We then convert that yaml to json using the scipt in pymatgen/dev.",
"ok I just changed this value inside pymatgen/dev_scripts/periodic_table.yaml",
"@shyuep The script does no... | 2017-09-05T21:19:21 | 2017-11-01T13:52:50 | 2017-09-06T01:04:06Z | CONTRIBUTOR | {
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} | ## Summary
both changes are very small:
* Electrical resistivity for Te is 1000010<sup>-8</sup> in periodic_table.json but it should be 10000 10<sup>-8</sup> equal to 1e-4 ohm.m consistent with here ( http://periodictable.com/Elements/052/data.html ) for example
* to have every Element property as float, I set... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/827 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/827/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/827/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/827/events | https://github.com/materialsproject/pymatgen/issues/827 | 255,414,570 | MDU6SXNzdWUyNTU0MTQ1NzA= | 827 | Possible bug in local_env.py or PeriodicSite/Lattice, incorrect jimage? | {
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"It's a numerical issue because the third cell angle is 120 degrees. Does that make sense?\r\n\r\n\r\n",
"Hi Nils -- from your attached image, the neighbor from 1 (0,0) to 2' (0,1) makes sen... | 2017-09-05T21:28:46 | 2017-09-12T22:07:34 | 2017-09-12T22:07:34Z | MEMBER | {
"total": 0,
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} | ## System
* Pymatgen version: 2017.9.1 (development)
* Python version: 3.6.0
* OS version: macOS 10.12.6
## Summary
Would appreciate a sanity check here. I'm looking at a single layer of MoS2 from a .cif file ([attached](https://raw.githubusercontent.com/mkhorton/pymatgen/e807247f43153a71b6f3389120c623c3d7e1... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/828 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/828/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/828/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/828/events | https://github.com/materialsproject/pymatgen/pull/828 | 255,475,537 | MDExOlB1bGxSZXF1ZXN0MTM5NDY4ODg2 | 828 | Code style fix | {
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"Thanks!"
] | 2017-09-06T04:16:02 | 2017-09-11T05:06:58 | 2017-09-11T05:06:54Z | CONTRIBUTOR | {
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} | ## Summary
Fixed code style in interface_reaction module.
* Modified docstring to conform to pymatgen standard.
* Modified code style to conform to PEP 8 requirements. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/829 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/829/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/829/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/829/events | https://github.com/materialsproject/pymatgen/pull/829 | 255,835,829 | MDExOlB1bGxSZXF1ZXN0MTM5NzMwNjE2 | 829 | Fix the bug for str conversion with tilted box | {
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} | ## Summary
For lammpsData,
1), The lattice vector a should be along x direction.
2), The plane formed by lattice vectors a, b should be perpendicular with z direction.
Thus we need to rotate input structure's lattice so that it conforms to the above requirements, from which we can get the new lattice. The atomic... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/830 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/830/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/830/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/830/events | https://github.com/materialsproject/pymatgen/pull/830 | 255,841,007 | MDExOlB1bGxSZXF1ZXN0MTM5NzM0MjUy | 830 | Adding two volume predicting schemes | {
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} | ## Summary
* Reference lattice scaling scheme (RLS) improved on top of ConditionalVolumePredictor in MatMiner.
* Data-mined lattice scaling scheme (DLS) improved on top of VolumePredictor in MatMiner (Sayan Roychowdhury and Anubhav Jain).
* Unittests are also provided. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/831 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/831/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/831/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/831/events | https://github.com/materialsproject/pymatgen/pull/831 | 256,084,875 | MDExOlB1bGxSZXF1ZXN0MTM5OTE1ODU2 | 831 | Add critic2 command line caller for topological analysis | {
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"09/12: Updated to account for changes due to #827, added method to extract molecules from periodic crystals for #833",
"can you fix the merge conflicts? I will then merge the pull req.",
"Great, thanks. The graph library this uses (networkx) just had a big 2.0 release, so I'm going to update to that/run some t... | 2017-09-07T22:07:39 | 2017-09-29T17:21:17 | 2017-09-29T17:21:17Z | MEMBER | {
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} | This is an update of a [previous pull request](https://github.com/materialsproject/pymatgen/pull/821), fixing a few bugs and adding some new features (e.g. `StructureGraph.diff()` to, for example, easily compare two different neighbor-detection strategies).
From a technical point of view it's ready to merge, unless ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/832 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/832/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/832/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/832/events | https://github.com/materialsproject/pymatgen/issues/832 | 256,160,640 | MDU6SXNzdWUyNTYxNjA2NDA= | 832 | How to vary slab thickness when creating slab? | {
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"Hi, everyone. no one help?",
"The min_slab_thickness and min_vacuum_thickness arguments to the SlabGenerator?\r\n\r\nBTW, for questions on usage, please us the Google groups. Github issues is meant for reporting bugs and feature requests."
] | 2017-09-08T07:08:37 | 2017-09-11T05:03:36 | 2017-09-11T05:03:36Z | NONE | {
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I am trying to use pymatgen to create slab structure. I want to create a single and a double quintuple layer of Bi2Se3.
Bi2Se3 has spacegroup 166, and the conventional cell of hexagonal setting has 15 atom layers along c axis which is 3 quintuple layer (as show in [this picture](https://www.resea... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/833 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/833/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/833/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/833/events | https://github.com/materialsproject/pymatgen/issues/833 | 256,223,127 | MDU6SXNzdWUyNTYyMjMxMjc= | 833 | extract molecules from organic crystal | {
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"I don't believe this is currently implemented (perhaps others can correct me) -- but I may be able to help implement something that does this. I think you're right that the closest we currently have is a nearest neighbour algorithm.\r\n\r\nDo you have any constraints on your inputs? Do they just contain molecules,... | 2017-09-08T11:20:55 | 2023-01-24T16:00:59 | 2018-09-07T18:42:55Z | CONTRIBUTOR | {
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} | If I've got a cif file for a small organic molecule crystal, how could I convert it to a Molecule object?
I've looked through the document but my closest match is some nearest neighbor algorithm... Maybe I've missed something?
If the feature is not yet implemented, I hope I can be of help. I plan to:
1. build a ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/834 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/834/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/834/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/834/events | https://github.com/materialsproject/pymatgen/pull/834 | 256,383,175 | MDExOlB1bGxSZXF1ZXN0MTQwMTM0NDIx | 834 | fixed spacing for Electrical resistivity of Si and Ge (very small change) | {
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} | ## Summary
fixed spacing for Electrical resistivity of Si and Ge. For example in Ge the resistivity was 5000010... rather than 50000 10... and that would prevent correct parsing. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/835 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/835/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/835/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/835/events | https://github.com/materialsproject/pymatgen/pull/835 | 256,860,712 | MDExOlB1bGxSZXF1ZXN0MTQwNDQ5MzI5 | 835 | Corrected image location computation in local_env.py | {
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"Can we have a few unittests confirming the new definition pls? @mkhorton example of MoSi2 would be a good one."
] | 2017-09-11T22:26:12 | 2017-09-11T23:29:31 | 2017-09-11T23:29:31Z | CONTRIBUTOR | {
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} | I've changed the way the images locations are computed in local_env.py according to @mkhorton and @shyuep's comments in issue #827
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https://api.github.com/repos/materialsproject/pymatgen/issues/836 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/836/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/836/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/836/events | https://github.com/materialsproject/pymatgen/issues/836 | 257,374,177 | MDU6SXNzdWUyNTczNzQxNzc= | 836 | Bug in io.gaussian.GaussianOutput | {
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} | Hi, all! I belive I've found a bug in io.gaussian module at line 1301. Luckily I think it's easy to fix.
```
if not charge:
charge = self.charge
```
When a user tries to set the charge of the generated input file to 0, i.e., the parameter `charge = 0`, the statement `not charge` will be considered as ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/837 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/837/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/837/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/837/events | https://github.com/materialsproject/pymatgen/pull/837 | 257,560,721 | MDExOlB1bGxSZXF1ZXN0MTQwOTU5NDM0 | 837 | New argument max_row in periodic heating map | {
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} | ## Summary
- Add argument "max_row" in period table heat map. That way one can control the number of rows shown in the heat map.
- Add unittests | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/838 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/838/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/838/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/838/events | https://github.com/materialsproject/pymatgen/pull/838 | 258,205,269 | MDExOlB1bGxSZXF1ZXN0MTQxNDMxMTE3 | 838 | Kpath fix with on-the-fly structures for tests and some comments | {
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"There are two test errors (see travis). The errors are:\r\n\r\n```\r\n======================================================================\r\nERROR: test_kpath_acentered (pymatgen.symmetry.tests.test_kpaths.HighSymmKpathTest)\r\n----------------------------------------------------------------------\r\nTraceback ... | 2017-09-16T03:41:54 | 2017-09-16T22:38:35 | 2017-09-16T22:38:35Z | CONTRIBUTOR | {
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} | ## Summary
Modifications to account for space group naming conventions changes in spglib.
* Fix in pymatgen.symmetry.bandstructure.HighSymmKpath class
* Fix in pymatgen.symmetry.analyzer.SpacegroupAnalyzer class
* Tests for both modifications, this time generating structures within tests
* A few comments to ex... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/839 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/839/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/839/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/839/events | https://github.com/materialsproject/pymatgen/pull/839 | 258,559,172 | MDExOlB1bGxSZXF1ZXN0MTQxNjU5OTYw | 839 | Gibbs free energy of a material with respect to Pourbaix stable domains | {
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"I am not sure the __eq__ test for phase diagrams is a good idea. In fact, I am not even sure tehre should be an __eq__ implementation for a PD. When would such a function be used?",
"It's not for the pd itself, it's just for a single PDEntry. We use it primarily to test if a list of entries contains a specific ... | 2017-09-18T17:29:18 | 2017-09-19T02:26:43 | 2017-09-19T02:26:43Z | MEMBER | {
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Some revisions and simplification to existing routines.
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https://api.github.com/repos/materialsproject/pymatgen/issues/840 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/840/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/840/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/840/events | https://github.com/materialsproject/pymatgen/pull/840 | 258,577,813 | MDExOlB1bGxSZXF1ZXN0MTQxNjcyNzQy | 840 | avoid importing palettable | {
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Fixes a performance regression that has caused the time taken by `import pymatgen` to rise by about 50%.
In short, palettable imports matplotlib, undoing all of pymatgen's hard work to avoid exactly that.
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"Thanks."
] | 2017-09-18T20:03:31 | 2017-09-18T20:25:32 | 2017-09-18T20:25:27Z | CONTRIBUTOR | {
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* Fix formatting of lattice in `Poscar.get_string` to respect the `significant_digits` argument | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/842 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/842/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/842/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/842/events | https://github.com/materialsproject/pymatgen/issues/842 | 259,131,223 | MDU6SXNzdWUyNTkxMzEyMjM= | 842 | BoltztrapRunner discards bands with no warning | {
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"I agree, and I would say a parameter should be set to allow people to choose to discard a certain % or none at all. I will leave @hautierg and @computron to comment and implement.",
"I think the relevant person here is @fraricci to implement and @hautierg to comment on the procedure (as per the explicit comment ... | 2017-09-20T11:32:53 | 2017-09-29T13:14:49 | 2017-09-29T13:14:49Z | MEMBER | {
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} | The `BoltztrapRunner` class discards the top 10% of bands when writing the eigenvalues to the input files needed by BoltzTraP. In some cases this can cause the valence band maximum and conduction band minimum to be discarded, leading to BoltzTraP errors. I understand the rationale for discarding these bands (i.e. that ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/843 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/843/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/843/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/843/events | https://github.com/materialsproject/pymatgen/pull/843 | 259,155,172 | MDExOlB1bGxSZXF1ZXN0MTQyMDkzNjE3 | 843 | Import pymatgen.util.serialization | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/844 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/844/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/844/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/844/events | https://github.com/materialsproject/pymatgen/issues/844 | 259,338,477 | MDU6SXNzdWUyNTkzMzg0Nzc= | 844 | More general algo to avoid breaking of specific bonds for SlabGenerator | {
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} | The get_slabs() method of the SlabGenerator class has a parameter called bonds that allow the users to specify which terminations to avoid based on whether this specific bond is broken (e.g. PO4 or PS4 bonds). However, this leads to many missing possible terminations in more complicated structures such as LiFePO4. A mo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/845 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/845/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/845/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/845/events | https://github.com/materialsproject/pymatgen/pull/845 | 259,593,578 | MDExOlB1bGxSZXF1ZXN0MTQyNDE2NTYy | 845 | Add MVLNPTMDSet with unittest | {
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} | ## Summary
Add `MVLNPTMDSet` class
* Add MVLNPTMDSet for AIMD input set in NpT ensemble
* Add unittest
* Minor docstring change | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/846 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/846/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/846/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/846/events | https://github.com/materialsproject/pymatgen/issues/846 | 259,626,574 | MDU6SXNzdWUyNTk2MjY1NzQ= | 846 | Not all relevant species in a facet are reported by Pourbaix Plotter | {
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"@kristinpersson Maybe get one of your folks working on the Pourbaix stuff to look into this?",
"@ashtonmv Hey Michael, using the pymatgen.analysis.pourbaix.plotter functions you can enable the labeling of all the entries in a Pourbaix domain. I think the problem in this specific case is due to the way the Pourb... | 2017-09-21T20:44:29 | 2023-05-29T15:46:38 | 2023-05-29T15:46:38Z | NONE | {
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} | ## Summary
* This is a feature request. I would like to be able to report *all* stable species in each facet of a Pourbaix diagram, much like what happens on the MaterialsProject website Pourbaix app. Instead, what currently shows up is a single species.
## Example code
```python
from pymatgen.analysis.pourba... | {
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} | This pull request will address issue #844
This method of generating slabs will repair slabs with more broken bonds than the allotted max_broken_bonds parameter instead of omitting them. Because this can lead to a large number of possible terminations, for now, I’ve made the repair of broken bonds optional. Default ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/848 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/848/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/848/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/848/events | https://github.com/materialsproject/pymatgen/pull/848 | 259,701,660 | MDExOlB1bGxSZXF1ZXN0MTQyNDk2MTQw | 848 | add combine_neb_plots method | {
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"When is this going to be done?",
"This might be merged. The error of ModuleNotFoundError: No module named 'pip._vendor.requests.adapters' seems not related to this code."
] | 2017-09-22T04:45:21 | 2017-10-10T20:52:40 | 2017-10-10T20:52:40Z | NONE | {
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} | add combine_neb_plots method.
Due to this method:
move test_files/neb_analysis/neb1/start/OUTCAR to test_files/neb_analysis/neb1/neb/00/
move test_files/neb_analysis/neb1/end/OUTCAR to test_files/neb_analysis/neb1/neb/04/
Finally, remove test_files/neb_analysis/neb1/start and test_files/neb_analysis/neb1/end | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/849 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/849/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/849/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/849/events | https://github.com/materialsproject/pymatgen/pull/849 | 259,709,670 | MDExOlB1bGxSZXF1ZXN0MTQyNTAxNDEz | 849 | Adding phonopy-related functions | {
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} | ## Summary
- Basic functions that convert structure objects between pymatgen and phonopy.
- Function that generates a list of atomic displaced pmg structures (for phonon calculations).
## Additional dependencies introduced (if any)
* phonopy
## TODO (if any)
Implement functions that extract modulated pmg st... | {
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to remove in the calculation of transport properties | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/851 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/851/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/851/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/851/events | https://github.com/materialsproject/pymatgen/pull/851 | 260,790,530 | MDExOlB1bGxSZXF1ZXN0MTQzMjU4Nzcz | 851 | Added many more OPs and made normalization procedure more robust | {
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"At this juncture, I think you need to rethink your approach. Basically, there is far too many permutations of order parameters to just hard code them into if statements. I suggest storing the parameters in some sensible json/yaml file, and the *short* code then uses the data from the file without the many if state... | 2017-09-26T22:32:21 | 2017-10-16T20:38:52 | 2017-10-16T20:38:49Z | CONTRIBUTOR | {
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} | Added order parameters for:
- single-bond case
- trigonal planar
- square planar
- pentagonal planar
- square pyramid (previous one (sq_pyr_legacy) recognizes any pyramidal motif with neighbors on the basal plane being on a circle)
- trigonal pyramid
- pentagonal pyramid
- hexagonal pyramid
-... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/852 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/852/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/852/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/852/events | https://github.com/materialsproject/pymatgen/pull/852 | 261,507,107 | MDExOlB1bGxSZXF1ZXN0MTQzNzkwMzA3 | 852 | Reverted slab argument to structure in MVLSlabSet | {
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"This is fine with me."
] | 2017-09-29T01:31:22 | 2017-09-29T02:11:11 | 2017-09-29T02:11:03Z | CONTRIBUTOR | {
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} | Can we revert the constructor syntax of MVLSlabSet such that it takes a "structure" kwarg instead of a "slab"? My reasoning for this is twofold:
* Input structures to MVLSlabSet aren't always slabs, e.g. when doing reference bulk calculations, but they are always structures
* Having "slab" as the input argument na... | {
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} | from a VASP POSCAR
The docs previously had this example for generating a
Structure object from a VASP POSCAR file:
```python
from pymatgen.io.vasp import Poscar
poscar = Poscar.from_file("POSCAR")
struct = poscar.struct
```
The correct attribute is `poscar.structure`.
This pull request updates the `usa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/855 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/855/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/855/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/855/events | https://github.com/materialsproject/pymatgen/issues/855 | 262,271,143 | MDU6SXNzdWUyNjIyNzExNDM= | 855 | Adsorption finder: AttributeError: 'Structure' object has no attribute 'center_of_mass' | {
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"Right, the center_of_mass is a property that was added to the slab object\nrecently as a property. I added it to the adsorption code so that it would\nbe able to adsorb one surface or the other or both. Changing the structure\nto a slab object should work, but @montoyjh@lbl.gov do you think I should\njust change i... | 2017-10-03T00:39:52 | 2017-10-03T23:20:46 | 2017-10-03T23:20:46Z | MEMBER | {
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* Pymatgen version: 2017.9.23
* Python version: 3.6.2
* OS version: Windows 10 (not an OS issue)
## Summary
When using the `AdsorptionSiteFinder`, I get a `center_of_mass` issue when reading a structure from a `CONTCAR` or other VASP file.
## Example code
```python
from pymatgen import Structu... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/856 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/856/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/856/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/856/events | https://github.com/materialsproject/pymatgen/pull/856 | 262,561,333 | MDExOlB1bGxSZXF1ZXN0MTQ0NTExMTkx | 856 | Asf fix | {
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"\n[](https://coveralls.io/builds/28491945)\n\nCoverage decreased (-38.6%) to 38.141% when pulling **e6694758020c46e2cfc8db9ccc47ff4a28679bc7 on montoyjh:asf_fix** into **482ee1dea30aa940da8c736b1f146efdedb507ff on materialsproject:master**.\n"
] | 2017-10-03T19:45:42 | 2020-02-03T09:25:26 | 2017-10-03T20:36:37Z | CONTRIBUTOR | {
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Fix for issue #855 and a few things cleaning up cartesian conversion to fractional coords and vice versa. | {
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} | ## Summary
Couldn't find this in pymatgen already. Patch to add a comparator which matches occupancies in StructureMatcher. Used for SQS generation, to match a disordered pymatgen Structure to its appropriate SQS template file.
(Also included another commit to delete a stray print statement in my previous PR...)
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/858 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/858/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/858/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/858/events | https://github.com/materialsproject/pymatgen/pull/858 | 262,945,040 | MDExOlB1bGxSZXF1ZXN0MTQ0Nzg2NzY1 | 858 | Drift in Outcar | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/859 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/859/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/859/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/859/events | https://github.com/materialsproject/pymatgen/pull/859 | 263,272,330 | MDExOlB1bGxSZXF1ZXN0MTQ1MDI1NzY2 | 859 | Add I/O for ATAT’s mcsqs lattice format | {
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} | ## Summary
Input/output for [ATAT](https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/), for use with the mcsqs tool.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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"Pls do not keep adding to the same pull request. merge the current origin to your fork properly and submit NEW pull requests in future."
] | 2017-10-05T22:49:31 | 2017-10-08T00:02:21 | 2017-10-07T23:17:05Z | CONTRIBUTOR | {
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} | ## Summary
This pull request removes the need for differentiating two surfaces when building an adsorbed slab with adsorbates on both sides. Therefore the use of COM in the AdsorbateSiteFinder() class as well as the option to adsorb at the bottom or top is also remove. The algorithm will rollback to Joseph Montoya's... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/861 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/861/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/861/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/861/events | https://github.com/materialsproject/pymatgen/issues/861 | 263,681,582 | MDU6SXNzdWUyNjM2ODE1ODI= | 861 | Error: Connection must be made over secure https. | {
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"Materials project is down right now because of maintenance. This is not an\nerror in the code.\n\nOn Sat, Oct 7, 2017, 5:09 PM Bruno Abreu Calfa <notifications@github.com>\nwrote:\n\n> System\n>\n> - Pymatgen version: pymatgen==2017.9.23\n> - Python version: 3.6.3\n> - OS version: Mac OS X 10.12.6\n>\n> S... | 2017-10-08T00:09:37 | 2023-05-29T15:44:22 | 2023-05-29T15:44:22Z | NONE | {
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} | ## System
* Pymatgen version: `pymatgen==2017.9.23`
* Python version: 3.6.3
* OS version: Mac OS X 10.12.6
## Summary
Something wrong (apparently related to secure https) is happening in the call to `requests.post`. The same script I'm running used to work a while ago.
## Example code
You may consider ... | {
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"Sorry, but I have to insist on more comprehensive unittests of the functionality before I merge. If you look at https://coveralls.io/github/materialsproject/pymatgen, a lot of modules in the chemenv package have some of the lowest coverages. You just need to sort by the \"Missed\" category.\r\n\r\nPls add proper u... | 2017-10-10T08:30:01 | 2017-10-13T22:22:57 | 2017-10-13T22:22:48Z | CONTRIBUTOR | {
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} | ## Summary
* Radial distribution and angular distribution figures in chemenv
* Clear environments
* Added citation for chemenv
* Minor addition in memory policy in io.abinit.qadapters | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/863 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/863/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/863/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/863/events | https://github.com/materialsproject/pymatgen/pull/863 | 264,677,448 | MDExOlB1bGxSZXF1ZXN0MTQ2MDE3OTI3 | 863 | Molecular Orbitals Functionality | {
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"Pls fix failing tests.",
"Fixed failed composition test"
] | 2017-10-11T17:49:53 | 2017-10-16T20:36:57 | 2017-10-16T20:36:57Z | CONTRIBUTOR | {
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} | ## Summary
* Feature 1: added atomic orbital energies to periodic table data
* Feature 2: collect atomic orbitals for all elements in a composition to predict band character with MolecularOrbitals class
## TODO (if any)
* Feature 2 has no concept of covalent bonding or the orbital energies of ions | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/864 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/864/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/864/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/864/events | https://github.com/materialsproject/pymatgen/pull/864 | 264,720,331 | MDExOlB1bGxSZXF1ZXN0MTQ2MDUwMDQy | 864 | ATAT ordering fix | {
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} | Hopefully this should fix it. I wrote a bad test though really, because it was failing even with a correct output... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/865 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/865/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/865/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/865/events | https://github.com/materialsproject/pymatgen/issues/865 | 265,211,211 | MDU6SXNzdWUyNjUyMTEyMTE= | 865 | Improvements needed for io.lammps.data | {
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"Go ahead and make the changes.",
"After struggling for weeks, here I will list a few upcoming major changes to the entire `io.lammps` package. Yes it will certainly break some code, but I don't see many API usage depending on methods or attributes of `LammpsData` or `LammpsForceFieldData`. \r\n\r\n1. `LammpsData... | 2017-10-13T08:39:08 | 2017-11-08T04:46:03 | 2017-11-08T04:46:03Z | CONTRIBUTOR | {
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} | A few issues with the current implementation I would like to discuss with whoever involved in this module.
* A list of lists of floats is now used as the data structure for each long section like "atoms", "bonds", etc. Since each column has its specific meaning, can we store the data using a list of dicts instead? T... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/866 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/866/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/866/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/866/events | https://github.com/materialsproject/pymatgen/pull/866 | 265,416,540 | MDExOlB1bGxSZXF1ZXN0MTQ2NTUyNzA2 | 866 | Request for enumlib tester (PR is to add makeStr.py support) | {
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} | ## Summary
Tests for enumlib have been incorrectly skipped for a while if `enum.x` was present (they only ran if `multienum.x` was present, which is an old version).
When running these tests myself on current pymatgen, I get test failures -- `self.assertEqual(len(structures), 10)` will fail with `len(structures)=... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/867 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/867/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/867/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/867/events | https://github.com/materialsproject/pymatgen/pull/867 | 265,683,807 | MDExOlB1bGxSZXF1ZXN0MTQ2NzIyNDU2 | 867 | Correction in io/abinit/qadapters | {
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} | ## Summary
Correction of io/abinit/qadapters (mem is now the default behavior) | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/868 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/868/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/868/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/868/events | https://github.com/materialsproject/pymatgen/issues/868 | 266,356,280 | MDU6SXNzdWUyNjYzNTYyODA= | 868 | CIF reading error | {
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"This CIF file is bad. atom_site_label is defined twice. Just change the last atom_site_label to something like atom_site_lbl and pymatgen parses it correctly."
] | 2017-10-18T04:24:39 | 2017-10-18T04:30:10 | 2017-10-18T04:30:10Z | MEMBER | {
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} | ## System
* Pymatgen version: 2017.10.16
* Python version: 3.x
## Summary
Reading certain CIF files leads to error even though it can be read in VESTA, ChemCraft, or other visualizers.
## Example code
```python
import pymatgen as pm
mof = pm.Structure.from_file('mof.cif')
```
## Error message
`... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/869 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/869/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/869/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/869/events | https://github.com/materialsproject/pymatgen/pull/869 | 267,772,841 | MDExOlB1bGxSZXF1ZXN0MTQ4MjA3Nzg1 | 869 | Fix bug in POSCAR parsing | {
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"This fix seems to be causing a lot of existing tests to fail? https://travis-ci.org/materialsproject/pymatgen/builds/291690908\r\n\r\nThe test file [here](https://github.com/materialsproject/pymatgen/blob/master/test_files/POSCAR) claims it's LiFePO4 but it's actually Fe4P4O16, I'm not sure if that's intentional o... | 2017-10-23T18:36:56 | 2017-10-24T15:27:09 | 2017-10-23T18:42:15Z | NONE | {
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} | Bug in POSCAR parsing from file looking for POTCAR by name only
Misses extensions such as .gz .orig, .relax1.gz , etc.
Fixed by looking for POTCAR in filename | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/870 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/870/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/870/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/870/events | https://github.com/materialsproject/pymatgen/pull/870 | 268,071,380 | MDExOlB1bGxSZXF1ZXN0MTQ4NDI2ODU5 | 870 | Magnetic analysis module + improvements to MagOrderingTransformation | {
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"Thanks!"
] | 2017-10-24T15:11:39 | 2017-10-27T23:45:24 | 2017-10-27T23:45:01Z | MEMBER | {
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} | ## Summary
A magnetic analysis module with some helpful methods + backwards-compatible improvements to MagOrderingTransformation to handle more complex cases + tests for same. Also a few general bugfixes.
More features will be added to the module in future, but it'd be useful to merge this now.
## Additional d... | {
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Add some additional filename wildcards for mcsqs input
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
* Feature 1 supports a, but not b. | {
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"Thanks\r\n"
] | 2017-10-24T21:49:25 | 2017-10-24T21:50:27 | 2017-10-24T21:50:21Z | CONTRIBUTOR | {
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} | Should fix JHU servlet issue. Was using a static INCAR from the test files, rather than generating it on the fly, and JHU updated their system to parse magmoms for symmetry. | {
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} | ## Summary
Add more filename wildcards for mcsqs input
## Additional dependencies introduced (if any)
## TODO (if any) | {
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"This is not a good name. SEe how VaspInput is defined.",
"I renamed the class name to PostFEFFSet to make the name more specific about the class' function, similar to the class names defined in the VaspInput. "
] | 2017-10-27T19:53:40 | 2017-10-30T21:05:39 | 2017-10-30T21:05:39Z | CONTRIBUTOR | {
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} | ## Summary
Add PostFEFFSet class to pymatgen.io.feff that allows post-processing of FEFF input files from an existing FEFF input files directory. Unittest files have been added accordingly | {
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} | @rwoodsrobinson noticed that bandstructures for a number of materials were returning negative values from `Bandstructure.get_direct_band_gap()`, which was because the sampling over the bands didn't consistently account for the spin down bands when determining the valence band maxima.
This PR should fix that, and add... | {
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"I said this before - merge the origin with your fork and submit a new pull request. This pull request contains all the code from previous pull requests.",
"Will do, sorry about that"
] | 2017-10-27T23:07:49 | 2017-10-28T05:02:02 | 2017-10-28T05:02:02Z | CONTRIBUTOR | {
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} | ## Summary
Removed import of MPRester to calculate chemical potential range. Temporarily set chemical potential range for a nonstoichiometric slab as an optional parameter. A future release will handle the calculation of the chemical potential range automatically. Added class method to plot binding energy vs clean s... | {
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} | - Fixed the POTCAR parsing bug in POSCAR again
- Updated the tests so they are appropriate conditioned for a test folder with multiple POSCARs and POTCARs
- Added in electrostatic potential parsing at each atom in OUTCAR
- Moved drift to an Outcar attribute
- Used a more sensible regex for parsing the drift | {
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} | ## Summary
Add PostFEFFSet class to pymatgen FEFF io used for post-processing of FEFF input files, with modified FEFF set test files. | {
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"Should wait for tests ... for some reason py2 tests were failing when I created the branch - even before I made any changes. Could not figure out the reason for this."
] | 2017-11-01T00:00:11 | 2018-04-04T19:40:23 | 2017-11-01T13:49:18Z | MEMBER | {
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} | ## Summary
Adds some new features for order-disorder transformation
* A new DiscretizeOccupanciesTransformation that will discretize the site occupancies in a structure, e.g., 0.62, 0.19, 0.19 to 0.6, 0.2, 0.2 - according to tunable tolerances.
* Test for above
* A new option for EnumerateStructureTransformatio... | {
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} | ## Summary
added a function to get symmetrically equivalent k-points to a given k-point to then be used to obtain band degeneracies via get_kpoint_degeneracy. I did not define degeneracy as default properties of cbm and vbm since they will be None most of the time as usually bs.structure is None. Also, I did not def... | {
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"Can you also add a test to ensure this doesn't happen again."
] | 2017-11-02T15:32:44 | 2017-11-02T16:29:28 | 2017-11-02T15:36:36Z | NONE | {
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Fixed by switching to the logic used in PDEntry. | {
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* Added a test for is_element in computed entry | {
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} | The APIs for dealing with symmetry operations from `SpacegroupAnalyzer` and `PointGroupAnalyzer` objects have a lot of differences. This pull request adds a `PointGroupAnalyzer.get_symmetry_operations()` method, that mirrors the `SpacegroupAnalyzer.get_symmetry_operatsion()` method. | {
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} | I am trying to run the EnumlibAdapter code, but wrap that code with a monty timeout
e.g.,
```
with timeout(4):
try:
# run EnumlibAdapter
except TimeoutError:
# handle timeout
```
But this doesn't work because EnumlibAdapter catches all exceptions that might occur inside of it in two pla... | {
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"@mkhorton Pls handle this. Thanks.",
"Will do, thanks for the report.\r\n\r\n@cyz11 do you have a test file to share please?",
"Regarding the first issue, it should work regardless of if an underscore or period is used as the delimiter -- this was because the magCIF standard changed during development, but the... | 2017-11-05T05:16:57 | 2017-11-06T21:58:21 | 2017-11-06T21:58:21Z | NONE | {
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} | I had problems when reading a magnetic cif file generated by ISOCIF.
It seems the 'parse_magmoms' method in cif.py have some problems.
First, the keys in data
'_atom_site_moment_crystalaxis_x'
'_atom_site_moment_crystalaxis_y'
'_atom_site_moment_crystalaxis_z'
'_atom_site_moment_label'
should be changed into
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"Pls add tests for the new fixes.",
"Will add the test file from @cyz11",
"Both issues should be fixed now, tests added."
] | 2017-11-06T18:26:28 | 2017-11-06T21:46:43 | 2017-11-06T21:46:43Z | MEMBER | {
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} | See http://comcifs.github.io/magCIF.dic.html for more information
Fixes issue 1 of 2 in #886 | {
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"If this is merged, could you please release a new version of pymatgen so that I can use this updated feature in matminer?"
] | 2017-11-07T18:39:03 | 2017-11-09T04:14:38 | 2017-11-09T04:14:38Z | CONTRIBUTOR | {
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} | Commit 42df22fe0d2488c539914f58ed90961411eaec46 added a `get_symmetry_operations` method to the `PointGroupAnalyzer` class.
It also introduced a bug, where the symmetry operations returned only included those found from the initial analysis of a molecule, instead of the complete set of symmetry operations for the c... | {
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"I will merge now. BUut go ahead and introduce pandas as a dependency. I foresee we will be doing so soon enough given that there are clear advantages to using pandas for many types of analysis."
] | 2017-11-08T04:36:06 | 2017-11-08T04:46:03 | 2017-11-08T04:46:03Z | CONTRIBUTOR | {
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} | ## Summary
`io.lammps.data` has been completely rewritten to fix the formatting issue. Closes #865
* `LammpsForceFieldData` has been merged into `LammpsData`, with `force_field` and `topology` as optional args.
* Data in each line is now stored in a dict rather than a plain list in order to distinguish floats f... | {
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} | Was previously just returning the string instead of writing to file. Thanks @josuav1 for the report. | {
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"This is truly a nonsensical class name and approach. It even violates what an \"InputSet\" as defined by pymatgen is. An InputSet is not a collection of input; it is a collection of RULES that create input. \r\n\r\nDo you see the equivalent class in pymatgen.io.vasp.sets? Of course not. If you just want to collect... | 2017-11-08T21:17:20 | 2017-11-09T01:04:31 | 2017-11-09T01:04:31Z | CONTRIBUTOR | {
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Add PostFEFFSet used for post-processing of FEFF input from a directory contains FEFF input files. Useful when existing FEFF input needs some adjustment. | {
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"Thanks for the fixes.",
"There are failed tests on Py2 or 3. Pls fix.\r\n\r\nhttps://circleci.com/gh/materialsproject/pymatgen/7263?utm_campaign=build-failed&utm_medium=email&utm_source=notification"
] | 2017-11-10T00:49:20 | 2017-11-12T22:55:13 | 2017-11-12T22:02:35Z | CONTRIBUTOR | {
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} | added fix_denominator (bool) to DiscretizeOccupanciesTransformation:
if True, will enforce a common denominator for all species. This prevents a mix of denominators (for example, 1/3, 1/4) that might require large cell sizes to perform an enumeration.
added Test; successful
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https://api.github.com/repos/materialsproject/pymatgen/issues/895 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/895/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/895/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/895/events | https://github.com/materialsproject/pymatgen/issues/895 | 273,114,230 | MDU6SXNzdWUyNzMxMTQyMzA= | 895 | Is it possible to convert symmetrized cif file to discard symmetry cif file while retaining the original inequivalent labels? | {
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"You can write a script to do it.",
"Also the `SpacegroupAnalyzer.get_symmetrized_structure()` method can help with this by grouping equivalent sites, but there's no guarantee it'll get the same grouping as the original CIF (this depends on what tolerances you use for the symmetry analysis)."
] | 2017-11-11T03:20:30 | 2017-11-11T16:23:35 | 2017-11-11T15:09:06Z | NONE | {
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} | Dear developers,
For example, I have a symmetrized cif file called "sym.cif" with spacegroup 31 and atom info like below
Te Te1 2 0.0000000000000 0.2072200000000 0.6463300000000 1
Te Te2 2 0.0000000000000 0.2984500000000 0.1022900000000 1
Te Te3 2 0.0000000000000 0.6463100000000 0.3535... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/896 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/896/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/896/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/896/events | https://github.com/materialsproject/pymatgen/pull/896 | 273,128,231 | MDExOlB1bGxSZXF1ZXN0MTUyMDQ3NDA1 | 896 | handle NoneType entries | {
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} | ## Summary
Mute MPRestError if the given criteria have no corresponding entries.
* `rester.get_entries_in_chemsys` throws MPRestError if no entry matches the given criteria. For example, a query in chemical system C-O-N:
```python
from pymatgen.ext.matproj import MPRester
rester = MPRester()
mp_entries =... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/897 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/897/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/897/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/897/events | https://github.com/materialsproject/pymatgen/pull/897 | 273,531,051 | MDExOlB1bGxSZXF1ZXN0MTUyMzEyNjY4 | 897 | Fix rounding errors in py2 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/898 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/898/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/898/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/898/events | https://github.com/materialsproject/pymatgen/pull/898 | 273,559,429 | MDExOlB1bGxSZXF1ZXN0MTUyMzMzNzM3 | 898 | Make the conversion battery module useful for multivalent cations | {
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"Pls add a test first. I do not merge things without tests.",
"I will close this pull request and send off a new pull request with unittest."
] | 2017-11-13T20:03:23 | 2018-01-06T08:25:40 | 2018-01-06T08:25:40Z | CONTRIBUTOR | {
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} | Applied the same treatment as we did for insertion electrodes. When the ion oxidation state is 2+, the voltage reduced to half, and the capacity multiplied by 2.
## Summary
* Previously, the code works for LIB. However, it ignores the valence state of multivalent cations such as Mg and Ca, and treat it like Li. ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/899 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/899/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/899/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/899/events | https://github.com/materialsproject/pymatgen/pull/899 | 273,765,923 | MDExOlB1bGxSZXF1ZXN0MTUyNDg0OTYx | 899 | fix pmg plot --xrd | {
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} | ## Summary
fix `pmg plot --xrd POSCAR`
error message:
```plain
AttributeError: 'Namespace' object has no attribute 'xrd'
``` | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/900 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/900/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/900/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/900/events | https://github.com/materialsproject/pymatgen/issues/900 | 274,027,637 | MDU6SXNzdWUyNzQwMjc2Mzc= | 900 | what happened to LammpsData.from_structure classmethod? | {
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"Sorry it was removed in the recent PR because\r\n\r\n1. A LAMMPS data file usually contains more information than a structure does. \r\n2. There is no reason to place the molecule in the center of the simulation box, or alter the simulation box size simply based the size of input molecule. \r\n\r\nTo work with pmg... | 2017-11-15T04:01:17 | 2017-11-15T19:56:38 | 2017-11-15T19:56:38Z | CONTRIBUTOR | {
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} | it used to be there until the recent PR. @adengz why did you remove it? it is very useful to have it in there for generating data files for general structure objects. | {
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