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https://api.github.com/repos/materialsproject/pymatgen/issues/1101 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1101/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1101/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1101/events | https://github.com/materialsproject/pymatgen/pull/1101 | 313,041,493 | MDExOlB1bGxSZXF1ZXN0MTgwNjkxMjIz | 1,101 | Mprest final struct | {
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} | ## Change default behavior of MPRester.get_entries with inc_structure
Someone pointed out on the forum that the rester was returning different structures with `MPRester.get_entry_by_material_id` and `MPRester.get_structure_by_material_id`. This is because `get_entry_by_material_id` will include the initial structur... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1102 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1102/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1102/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1102/events | https://github.com/materialsproject/pymatgen/pull/1102 | 313,888,350 | MDExOlB1bGxSZXF1ZXN0MTgxMzI2MzI4 | 1,102 | Add cbm and vbm marker in BSPlotter when ylim is set | {
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} | Now, one can set ylim and get cbm and vbm markers at the same time with the BSPlotter. If I should do anything else, just let me know.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1103 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1103/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1103/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1103/events | https://github.com/materialsproject/pymatgen/issues/1103 | 313,907,349 | MDU6SXNzdWUzMTM5MDczNDk= | 1,103 | _get_image() in pymatgen.analysis.local_env doesn't give correct image | {
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"Actually based on the fractional coordinates of the near neighbor Al site, the get_image seems to be OK. So the problem might lie upstream of the get_image method",
"I am closing this for now, need to make sure I am using distance correctly ...",
"There was some discussion on this on the PR Nils made for the m... | 2018-04-12T22:20:05 | 2023-08-08T21:23:02 | 2023-08-08T21:22:59Z | MEMBER | {
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} | ## System
* Pymatgen version: master
## Summary
* pymatgen.analysis.local_env.NearNeighbors#_get_image doesn't give the correct image
* Looks like @mkhorton did an initial implementation and @nisse3000 made the most recent changes to it
## Example code
```python
mpr = MPRester()
s = mpr.get_s... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1104 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1104/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1104/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1104/events | https://github.com/materialsproject/pymatgen/pull/1104 | 313,910,514 | MDExOlB1bGxSZXF1ZXN0MTgxMzQzMjMw | 1,104 | CifParser updates | {
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"I refactored the parse_symbol function to handle the symbols in capital letters and removed the explicit usage of a list of elements. I modified the list of special cases to handle the possible problematic symbols I have encountered so far. This should comply with the requests.\r\n\r\nI also moved the function as ... | 2018-04-12T22:34:01 | 2019-02-16T01:11:10 | 2018-04-16T16:33:03Z | CONTRIBUTOR | {
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} | ## Summary
This PR mainly addresses the problem of having element symbols in capital letters, as in several cif files present in the COD database. This happens both in the _atom_site_type_symbol and in the _atom_site_label keys. Notice that in the latter case a simple str.title() does not solve the problem as the la... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1105 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1105/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1105/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1105/events | https://github.com/materialsproject/pymatgen/pull/1105 | 314,174,180 | MDExOlB1bGxSZXF1ZXN0MTgxNTM4MzUz | 1,105 | split Brunner algos into three classes | {
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"I need tests for all of them.",
"Note that there are some conflicts. You need to do a merge and fix them first."
] | 2018-04-13T16:34:20 | 2018-04-14T20:22:17 | 2018-04-14T20:22:17Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1106 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1106/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1106/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1106/events | https://github.com/materialsproject/pymatgen/issues/1106 | 314,261,132 | MDU6SXNzdWUzMTQyNjExMzI= | 1,106 | return values for undefined numbers | {
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"While I in principle do not have objections to this, NaN has other problems. For example, float(\"NaN\") > 0 and float(\"NaN\") < 0 both return False. If you do `sorted([float(\"NaN\"), 0, 1, -1, 2])`, that effectively returns `[nan, -1, 0, 1, 2]`. That means that all elements with no electronegativity will effect... | 2018-04-13T21:52:32 | 2018-04-14T16:42:41 | 2018-04-14T03:12:09Z | MEMBER | {
"total": 0,
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} | ## Summary
* pymatgen sometimes returns float("inf") if a value is not found - just search for float("inf") or look specifically at the code for electronegativity below
```
@property
def X(self):
if "X" in self._data:
return self._data["X"]
else:
warnings.warn... | {
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} | ## Summary
Unnecessary ordered dictionaries were removed. This should fix testing issues
Short few sentences, and summary of the major changes in bullet
points
* OrderedDict removed from input.py
* OrderedDict removed from test_input.py | {
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} | @hillarypan this pertains directly to your commits!
## System
* Pymatgen version: master
## Summary
A recent commit adds the following line to all local env classes:
```
self._cns = {}
```
This line looks to be pointless. The ``_cns`` variable is not referenced anywhere in pymatgen (only defined, ne... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1109 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1109/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1109/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1109/events | https://github.com/materialsproject/pymatgen/pull/1109 | 314,847,290 | MDExOlB1bGxSZXF1ZXN0MTgyMDEwNTEx | 1,109 | AFLOW crystal prototype matcher + DisorderOrderedTransformation + pretty printing for disordered formulae | {
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"I am not sure why we would want to bother. We already have our own prototypes and matchers. Is the AFLOW any better?",
"Up to you. I found it useful for Strukturbericht symbols mostly.",
"I think the advantage of a formal prototype library like this is mostly pedagogical, e.g. it's useful to know if a structur... | 2018-04-16T23:00:17 | 2018-09-24T17:40:37 | 2018-09-24T17:40:37Z | MEMBER | {
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} | ## Summary
* A class to match Structures against crystal prototypes from the 'AFLOW Library of Crystal Prototypes', http://aflowlib.org/CrystalDatabase/ -- the terms of use on their website is to cite them if using their encyclopedia so I've made sure to include citations in the docstrings, and also in the JSON file... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1110 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1110/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1110/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1110/events | https://github.com/materialsproject/pymatgen/pull/1110 | 314,851,619 | MDExOlB1bGxSZXF1ZXN0MTgyMDEzODM2 | 1,110 | taking out _cns | {
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} | Since I'm the only one using it (see issue #1108) | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1111 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1111/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1111/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1111/events | https://github.com/materialsproject/pymatgen/pull/1111 | 315,193,254 | MDExOlB1bGxSZXF1ZXN0MTgyMjY2MDU4 | 1,111 | Added PCM and Solvent sections to QChem input and tests | {
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"Pls sort out the codacy reviews.",
"I believe that Julian has resolved the initial issues here. Could this please be merged in? Thanks!"
] | 2018-04-17T19:11:26 | 2018-04-18T19:31:55 | 2018-04-18T19:31:55Z | NONE | {
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} | ## Summary
Added PCM (polarizable continuum model) and solvent sections in QChem input and in corresponding unit tests
* PCM section now included in input
* Solvent section also included in input
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https://api.github.com/repos/materialsproject/pymatgen/issues/1112 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1112/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1112/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1112/events | https://github.com/materialsproject/pymatgen/pull/1112 | 315,194,293 | MDExOlB1bGxSZXF1ZXN0MTgyMjY2ODMy | 1,112 | Implementation of a new NN method | {
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"FYI there are failing tests but pretty sure they have nothing to do with this PR",
"the problem was the EnumlibTest timing out (unrelated to this PR)\r\n\r\nRestarting the CircleCI test fixed it. Going to try rebuilding Travis as well.\r\n\r\nMaybe you want to bump up the timeout in pymatgen.command_line.tests.t... | 2018-04-17T19:14:46 | 2018-04-17T21:55:18 | 2018-04-17T21:55:18Z | MEMBER | {
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} | ## Summary
This PR implements a new NearNeighbor method to the list already available in local_env.py
The method is my own custom algorithm for determining near neighbor. Briefly, it is based on post-processing Voronoi solid angle weights with additional considerations for site distance as well as optional prefer... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1113 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1113/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1113/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1113/events | https://github.com/materialsproject/pymatgen/issues/1113 | 315,613,879 | MDU6SXNzdWUzMTU2MTM4Nzk= | 1,113 | Problem with SPG lib getting spacegroup info | {
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"Can you post this on the spglib Github issues page?",
"Good point. I should have gone there in the first place. ",
"This was fixed in spglib"
] | 2018-04-18T19:35:22 | 2018-07-11T20:46:05 | 2018-07-11T20:46:05Z | NONE | {
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} | For some reason spglib is returning None for this structure. I figured it should at worst return P1 spacegroup info.
```python
from pymatgen import Structure
s = {'@class': 'Structure',
'@module': 'pymatgen.core.structure',
'lattice': {'a': 2.899999975486379,
'alpha': 108.04703882787179,
'b': 2.8999999... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1114 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1114/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1114/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1114/events | https://github.com/materialsproject/pymatgen/pull/1114 | 315,657,649 | MDExOlB1bGxSZXF1ZXN0MTgyNjE0OTYy | 1,114 | Add uniform bandstructure fetching to MPRester | {
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} | ## Summary
Adds `line_mode=True` kwarg to `MPRester.get_bandstructure_by_material_id`. If false, returns uniform bandstructure if available. Adds test. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1115 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1115/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1115/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1115/events | https://github.com/materialsproject/pymatgen/pull/1115 | 315,720,765 | MDExOlB1bGxSZXF1ZXN0MTgyNjYwOTc5 | 1,115 | Add new class for calculate neutron diffraction pattern | {
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"Many thanks Yuta. I will merge this now, but I will be making some changes. The XRD and NMR code shares a lot of common pieces. So I think it would make sure to have a parent class and have XRD, NMR etc. inherit from that. I will implement this shortly.",
"@resnant I have just pushed my changes. Basically, I mer... | 2018-04-19T04:06:24 | 2018-04-19T15:17:35 | 2018-04-19T04:29:50Z | CONTRIBUTOR | {
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} | ## Summary
Closes #1070
Add powder neutron diffraction (ND) calculator based on analysis.diffraction.xrd.XRDCalculator.
The change of code is slight.
Main changes by using neutron instead of X-ray are as follows:
1. Atomic scattering length is a constant.
2. Polarization correction term of Lorentz factor is ... | {
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"I believe that all issues have been resolved. Could this please be merged in? Thank you!"
] | 2018-04-19T20:13:52 | 2018-04-20T16:49:43 | 2018-04-20T16:49:43Z | CONTRIBUTOR | {
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} | ## Summary
* Added default QChem input sets (qchem_io/sets.py)
* Added automatic input file checking at the top of qchem_io/inputs.py. Also added the function lower_and_check_unique to qchem_io/utils.py that standardizes a dictionary to help with the checking.
* Fixed problems with some of the regex patterns in q... | {
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} | ## Summary
`numpy.linalg.lstsq` raises a `TypeError: must be real number, not NoneType` if user has numpy<1.14 installed because the default value of `rcond` changed from -1 to None. Ensures user has a compatible numpy install (already set in requirements.txt). | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1118 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1118/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1118/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1118/events | https://github.com/materialsproject/pymatgen/issues/1118 | 316,085,875 | MDU6SXNzdWUzMTYwODU4NzU= | 1,118 | Alternate algo to reduce structure on the axb plane. | {
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"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid and someone wants to take it on."
] | 2018-04-20T00:33:36 | 2023-08-08T21:23:42 | 2023-08-08T21:23:42Z | CONTRIBUTOR | {
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} | Part of the SlabGenerator class. We want to build a slab from the most reduced oriented unit cell as possible in order to reduce computational cost and maintain kpoint density of the ouc and slab. The current method of doing this (sift through all possible structures with the c direction constrained) using get_primitiv... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1119 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1119/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1119/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1119/events | https://github.com/materialsproject/pymatgen/pull/1119 | 316,463,718 | MDExOlB1bGxSZXF1ZXN0MTgzMjA3MDU5 | 1,119 | Fix a typo in Outcar.read_lepsilon() | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1120 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1120/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1120/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1120/events | https://github.com/materialsproject/pymatgen/pull/1120 | 316,548,698 | MDExOlB1bGxSZXF1ZXN0MTgzMjU1MzQ2 | 1,120 | Fix "TypeError" in case of input element is not in scattering length table | {
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} | ## Summary
Remove the elements from neutron_scattering_length.json
that the value of scattering length is unavailable.
This change fixes the following error in case of the input element is not the table.
in neutron.py, line 162:
`TypeError:` unsupported operand type(s) for *: 'NoneType' and `'float'`
In this... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1121 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1121/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1121/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1121/events | https://github.com/materialsproject/pymatgen/pull/1121 | 316,869,072 | MDExOlB1bGxSZXF1ZXN0MTgzNDc2Mzcz | 1,121 | Enable molecule-like rotations for structures. | {
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} | ## Summary
* enable molecule-like rotations of arbitrary sites by some angle around some axis at some anchor for pymatgen.core.Structure.
## Additional dependencies introduced
None
## TODO
Nothing | {
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"also the default radius for finding NN was changed to 7.0, found through Nils that 6.0 is too small for certain materials (e.g., Tl site of mp-861993)"
] | 2018-04-23T22:15:26 | 2018-04-23T23:25:00 | 2018-04-23T23:25:00Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1123 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1123/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1123/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1123/events | https://github.com/materialsproject/pymatgen/pull/1123 | 317,015,302 | MDExOlB1bGxSZXF1ZXN0MTgzNTgxOTAx | 1,123 | Increased default cutoff in CrystalNN | {
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} | ## Summary
Add `MPRester` methods to get phonon dispersion, density of states, and ABINIT Derivative Data Base (DDB) output. Add unit test.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1125 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1125/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1125/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1125/events | https://github.com/materialsproject/pymatgen/pull/1125 | 317,481,116 | MDExOlB1bGxSZXF1ZXN0MTgzOTI2NTA5 | 1,125 | Removed default dictionaries from sets | {
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} | ## Summary
default dictionaries weren't referenced properly, and I think it makes sense to put all the defaults in the __init__
* Fix 1 defaults dictionaries
* Fix 2 pep8 line length
## TODO (if any)
Unittests need to added @samblau | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1126 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1126/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1126/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1126/events | https://github.com/materialsproject/pymatgen/issues/1126 | 317,513,158 | MDU6SXNzdWUzMTc1MTMxNTg= | 1,126 | Feature request: bond order of covalent bonds | {
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"Yes, this feature would be great. Thank you in advance and please submit a pull request (with unittests) when you are ready. ",
"Note that you can now also get bond orders from `pymatgen.analysis.local_env.OpenBabelNN` also where bond orders are returned as neighbor weights."
] | 2018-04-25T07:41:36 | 2018-09-12T20:10:42 | 2018-09-12T20:10:42Z | CONTRIBUTOR | {
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} | Function `is_bonded` in `bonds.py` is able to find if 2 sites are bonded according to bond length data stored. It's great. I think it's natural to automatically judge the bond order between the 2 sites, and `is_bonded` can return an int bond order instead of a bool. Further, why not make `bond_order` a member variable ... | {
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"If you removed bugs, that means that these bugs were not tested originally. Pls include tests to show that the bugs are removed.",
"@shyuep, the class is from @computron. I'm currently testing in-depth and finding these bugs. Will be added to unit tests.",
"Ok. But pls submit PR only when you are more or less ... | 2018-04-25T18:34:49 | 2018-04-25T22:54:01 | 2018-04-25T22:49:44Z | CONTRIBUTOR | {
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"Not sure why the AppVeyor build was canceled, but I believe this is ready to be merged in. Thanks!",
"I'm about to push a bunch of additional stuff to my repos. I'll do a new pull request soon that includes everything from this one as well as more"
] | 2018-04-25T20:45:34 | 2018-05-02T21:25:57 | 2018-05-02T21:25:18Z | CONTRIBUTOR | {
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} | ## Summary
* PCM bug fixes for QChem inputs (qchem_io/inputs.py) and accompanying tests (qchem_io/tests/test_inputs.py)
* PCM functionality included in QChem default input sets (qchem_io/sets.py)
* Added tests for QChem default input sets (qchem_io/tests/test_sets.py
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https://api.github.com/repos/materialsproject/pymatgen/issues/1129 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1129/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1129/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1129/events | https://github.com/materialsproject/pymatgen/pull/1129 | 317,879,849 | MDExOlB1bGxSZXF1ZXN0MTg0MjI3ODky | 1,129 | Add bond order property of a CovalentBond | {
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"I found there are so many tests that with some bad luck travis-ci will time out. Is it possible for new PRs to test only codes that are modified? In ideal condition maybe we should test over the whole project, but currently we are so close to the time limit of travis-ci. Any ideas?\r\nIMHO my code does not induce ... | 2018-04-26T05:11:04 | 2018-04-26T13:54:36 | 2018-04-26T13:54:36Z | CONTRIBUTOR | {
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} | ## Summary
Add bond order property of a CovalentBond (Issue #1126) . Initially I plan to change `is_bonded` to return an int indicating bond order. After some reflection I think this is a bad idea:
* According to the semantics, `is_bonded` should return a Boolean instead of an int.
* In some cases, like in benzene... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1130 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1130/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1130/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1130/events | https://github.com/materialsproject/pymatgen/issues/1130 | 318,014,943 | MDU6SXNzdWUzMTgwMTQ5NDM= | 1,130 | Feature request: Symmetry tolerance for Interstitial? | {
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"Apologies, from looking into the source code for the 'symmetry_reduced_voronoi_nodes' function that is used in Interstitial it looks like by default the high_accuracy flag is not set and then by default symprec=1e-1 for the symmetry finder.\r\n\r\nSo I updated the issue to a feature request since it may be nice to... | 2018-04-26T12:49:25 | 2023-08-08T21:25:02 | 2023-08-08T21:25:02Z | NONE | {
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} | I'm currently trying to use Interstitial to generate symmetrically distinct defects but I've been unable to find out what default tolerance is used for recognising the symmetry of the structure.
Is there a way to relate to the numerical values used in the symprec argument for the SpacegroupAnalyzer for the symmetry... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1133 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1133/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1133/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1133/events | https://github.com/materialsproject/pymatgen/pull/1133 | 319,062,305 | MDExOlB1bGxSZXF1ZXN0MTg1MDg0Njcw | 1,133 | Revert "Update SNL remarks to 2017" | {
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"@shyamd Your code failed the tests. Pls resubmit a revised PR."
] | 2018-04-30T22:51:19 | 2018-08-10T11:11:26 | 2018-04-30T22:51:28Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1134 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1134/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1134/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1134/events | https://github.com/materialsproject/pymatgen/pull/1134 | 319,414,704 | MDExOlB1bGxSZXF1ZXN0MTg1MzM5MDg4 | 1,134 | Major refactor of defects module | {
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"@shyuep This is ready to merge. "
] | 2018-05-02T05:31:26 | 2020-05-12T15:47:25 | 2018-07-14T14:21:58Z | NONE | {
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} | ## Summary
The old defects module was basically unparseable. This is complete refactor to be more DB/pythonic and provide objects for defects, defect entries, corrections, defect phase diagrams and a compatibility layer to autodetect how to apply corrections.
Major New Features:
- Basic defect objects encapsula... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1135 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1135/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1135/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1135/events | https://github.com/materialsproject/pymatgen/issues/1135 | 319,548,984 | MDU6SXNzdWUzMTk1NDg5ODQ= | 1,135 | Crash when using pymatgen.analysis.defects.point_defects.Interstitial | {
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"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 2018-05-02T13:18:59 | 2023-08-08T21:25:17 | 2023-08-08T21:25:17Z | NONE | {
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} | ## System
* Pymatgen version:
2018.4.20
* Python version:
Python 3.6.5 :: Anaconda, Inc.
* OS version:
macOS 10.12.6
## Summary
Attempting to use pymatgen to find Interstitials via Zeo++ Voronoi analysis. I followed installation/setup directions from here http://pymatgen.org/installation.html#zeo -- and ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1136 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1136/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1136/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1136/events | https://github.com/materialsproject/pymatgen/pull/1136 | 319,743,914 | MDExOlB1bGxSZXF1ZXN0MTg1NTg1NDkz | 1,136 | PCM Fixes and Outputs Update | {
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} | ## Summary
* PCM bug fixes for QChem inputs (qchem_io/inputs.py) and accompanying tests (qchem_io/tests/test_inputs.py)
* PCM functionality included in QChem default input sets (qchem_io/sets.py)
* Added tests for QChem default input sets (qchem_io/tests/test_sets.py
* Substantial update of QChem output parsing (... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1137 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1137/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1137/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1137/events | https://github.com/materialsproject/pymatgen/issues/1137 | 320,105,634 | MDU6SXNzdWUzMjAxMDU2MzQ= | 1,137 | Random test errors in elasticity | {
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} | The elasticity test have errors due to some numpy issue. There are also a number of invalid values in numpy.
See https://circleci.com/gh/materialsproject/pymatgen/7783
Pls fix. @montoyjh | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1138 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1138/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1138/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1138/events | https://github.com/materialsproject/pymatgen/pull/1138 | 320,122,940 | MDExOlB1bGxSZXF1ZXN0MTg1ODcwNjcw | 1,138 | Elastic fix | {
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"I would suggest raising an error as the safest route. Then end users are forced to explicitly handle these errors. Such errors can cause significant problems in analysis.",
"Thanks for the feedback. I've implemented as suggested with a wrapper for the relevant functions that will throw an error if the tensor is... | 2018-05-04T00:30:05 | 2018-05-04T13:22:52 | 2018-05-04T13:22:52Z | CONTRIBUTOR | {
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} | This addresses the primary issue in #1137.
The invalid value issues are related to negative arguments of a square root function in sound velocity and thermal conductivity models. Currently these functions return np.nan if, say, G_VRH is negative because of bad input data and issue the warning. I can change this, b... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1139 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1139/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1139/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1139/events | https://github.com/materialsproject/pymatgen/pull/1139 | 320,639,300 | MDExOlB1bGxSZXF1ZXN0MTg2MjMyNjU2 | 1,139 | Function for finding the dimensionality of connected subunits in a crystal structure. | {
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} | Functions for finding the dimensionality of connected subunits in a crystal structure. This method differs from get_dimensionality() function in structure_analyzer in that it finds the dimensionality of the material even when the material is not layered along low-index planes, or does not have flat layers/molecular wir... | {
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"Fix the exception being caught to a less extensive one. And if you fix this bug, pls include a unittest to ensure it does not happen again.",
"I will work on it. It might take some time.",
"I included a test for the static method mu_so. Moreover, only AttributeErrors are caught in the mu_so method. get_crystal... | 2018-05-07T11:02:58 | 2018-05-08T13:55:13 | 2018-05-08T13:55:05Z | MEMBER | {
"total": 0,
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} | ## Summary
Fixes a broken multiplication. Without it, mu_so does not work correctly and always returns "None".
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"This has been discussed before. The default should be strict. In most instances, you want to err on the side of treating structures as different rather than treating them the same. Pymatgen is not meant to be a code for computational materials scientists. When people discuss symmetry of crystal structures, the pre... | 2018-05-09T17:41:46 | 2018-05-09T23:58:46 | 2018-05-09T23:57:06Z | NONE | {
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} | The comments in SpacegroupAnalyzer state that the default symprec is 1E-3, when it is really 1E-2 right now. It also suggests that loosely optimized structures should use a symprec of 1E-1, and this is the default in MP.
Can we get some clarity on what the intended default **should** be? Also, should the defaults b... | {
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"Can you implement a few simple tests pls? Thanks.",
"I did it and push a new commit. It seems it appears already here.",
"Thanks."
] | 2018-05-09T20:05:52 | 2018-05-11T15:18:29 | 2018-05-11T15:18:22Z | CONTRIBUTOR | {
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} | ## Summary
some float formats were not recognized when reading an xyz file. Only this one was read: 0.500e-09 and 0.7766e3. That floats were not recognized by the regex and are now read correctly:
* 0.100E+01
* 0.100D+02
* 0.100d+2
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https://api.github.com/repos/materialsproject/pymatgen/issues/1143 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1143/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1143/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1143/events | https://github.com/materialsproject/pymatgen/pull/1143 | 321,765,213 | MDExOlB1bGxSZXF1ZXN0MTg3MDY5OTk1 | 1,143 | Structure transform | {
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} | ## Summary
Additional functionality to Tensor class to allow for transformations corresponding to changes in structure basis.
* adds a method to the Tensor class that allows one to transform from the implicit basis of one structure to that of a second structure.
* added a method to refine rotation matrices generat... | {
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"Pls see http://matgenb.materialsvirtuallab.org for examples. Plotting hybrid and non-hybrid bandstructures is no different. Also, pls use the Google groups for questions. The Github Issues is meant for reporting bugs and feature requests. Thanks."
] | 2018-05-11T02:24:21 | 2018-05-11T02:28:54 | 2018-05-11T02:28:43Z | NONE | {
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"I forgot to change the kpoints density: not ready to merge yet.",
"You really shouldn't be modifying MPRelaxSet unless you have the consensus of the whole MP team. @computron @montoyjh Is this something that was discussed?",
"We haven't really discussed this. This is one solution. I do get inconsistent/unconve... | 2018-05-11T16:52:42 | 2018-06-06T16:33:52 | 2018-06-06T16:33:52Z | CONTRIBUTOR | {
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} | ## Summary
Making EDIFF independent of number of atoms is mainly to avoid errors in large unit cells. I tested the EDIFF=1e-5 with 120 ABC structures and had structures more consistent with the Materials Project both in terms of lattice constants and energy. Even if it is a slight overkill, I think it's good insurance... | {
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"noticed an issue, closing this PR until fixed.",
"Ok I think this is ready now - note that travis tests appear to be flaky, not sure why those are failing (CircleCI is fine)"
] | 2018-05-11T20:22:24 | 2018-05-12T00:12:56 | 2018-05-12T00:12:56Z | MEMBER | {
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} | ## Summary
This PR improves the accuracy of CrystalNN, particularly for layered systems.
* Intelligent search cutoff (prevent Voronoi errors for large layer distances)
* Redo weighting scheme to penalize large solid angles resulting from open structures
* change distance cutoffs to be absolute rather than relat... | {
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"The following worked for me:\r\n```\r\nconda create -n doc2dash_pmg python=3.6\r\nconda activate doc2dash_pmg\r\n# include optional dependencies to make those docs too\r\npip install \"pymatgen[provenance]\"\r\npip install doc2dash\r\npip install invoke\r\ncd <local_git_checkout_of_pymatgen>\r\n# make docs for a p... | 2018-05-14T01:44:25 | 2018-05-25T03:02:25 | 2018-05-14T06:07:26Z | CONTRIBUTOR | {
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} | I think pymatgen is big enough to have a documentation for [Dash](https://kapeli.com/dash)/[Zeal](https://zealdocs.org/). I tried [doc2dash](https://github.com/hynek/doc2dash) on pymatgen but it didn't work. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1148 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1148/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1148/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1148/events | https://github.com/materialsproject/pymatgen/issues/1148 | 322,964,747 | MDU6SXNzdWUzMjI5NjQ3NDc= | 1,148 | add a "weight" attribute to the KPoint class | {
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} | When accessing the kpoints of a calculation, it's sometimes helpful to know the weights of each k-point. For example, we currently want the k-point weights in order to compute branch point energies.
Right now, we pull the band structure and regenerate the weights again using SpacegroupAnalyzer. But it would be bette... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1149 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1149/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1149/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1149/events | https://github.com/materialsproject/pymatgen/issues/1149 | 323,004,738 | MDU6SXNzdWUzMjMwMDQ3Mzg= | 1,149 | Cannot use pmg command in macOS | {
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"The \"quick fix\" for you here is to use Python 3. This error was not caught earlier because tests are no longer being run for pymatgen using Python 2. @shyuep I'm not sure what is your preferred way to patch this for py2 compatibility in the meantime, so I'm just leaving this comment rather than submitting a PR t... | 2018-05-14T22:32:02 | 2018-05-15T00:44:59 | 2018-05-15T00:44:59Z | NONE | {
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## System
* Pymatgen version: 2018.5.3
* Python version: 2.7.10
* OS version: macOS 10.13.4 (17E202)
## Summary
Trying to setup POTCARs using `pmg`. The `pmg` command fails in general.
## Example code
```python
➜ pmg
/Users/protik/pmg/lib/python2.7/site-packages/pymatgen... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1150 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1150/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1150/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1150/events | https://github.com/materialsproject/pymatgen/pull/1150 | 323,371,156 | MDExOlB1bGxSZXF1ZXN0MTg4MjQ2MTgw | 1,150 | NearNeighbors + StructureGraphs: some bug fixes, convenience methods + tests | {
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"(CI errors are unrelated to this PR)"
] | 2018-05-15T20:29:06 | 2018-05-16T08:10:37 | 2018-05-16T08:10:37Z | MEMBER | {
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} | ## Summary
Fixed a few minor bugs in pymatgen.analysis.graphs, now supports molecules too (including via NearNeighbor class; will box them first).
Added `get_local_order_parameters` and `get_bonded_structure` convenience methods to NearNeighbor base class. The former is adapted from Nils' code, moved here from an... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1151 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1151/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1151/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1151/events | https://github.com/materialsproject/pymatgen/pull/1151 | 324,229,060 | MDExOlB1bGxSZXF1ZXN0MTg4ODkzMzM3 | 1,151 | scrubbed units | {
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} | ## Summary
Some of the methods in the elastic tensor classes get (incorrectly) unitized, which can lead to problems in postprocessing. In the long term, I think the elastic tensor classes should be refactored to better support units, but in the short term I think it's probably best to scrub the quantities which hav... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1152 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1152/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1152/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1152/events | https://github.com/materialsproject/pymatgen/issues/1152 | 324,485,291 | MDU6SXNzdWUzMjQ0ODUyOTE= | 1,152 | Distance method of periodic site objects returns error | {
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"Looks like your 2018.5.14 upgrade didn't upgrade numpy properly. `pip install \"numpy>=1.14\"` and you should be fine.",
"But setup.py in 2018.5.14 already stipulate setup_requires numpy>=1.14",
"@mtdg-wagner btw, I don't know what your specific application is, but I noticed:\r\n\r\n```\r\ngoo = Graph(struct)\... | 2018-05-18T17:02:52 | 2018-05-18T18:06:05 | 2018-05-18T17:18:38Z | CONTRIBUTOR | {
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} | When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
* Pymatgen version: 2018.5.14
* Python version: 3.6.5
* OS version: Ubuntu 16.04 LTS
## Summary
* Site distance method returns error
## Example code
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1153 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1153/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1153/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1153/events | https://github.com/materialsproject/pymatgen/pull/1153 | 324,652,714 | MDExOlB1bGxSZXF1ZXN0MTg5MjAyMjI0 | 1,153 | Updates to LAMMPS modules | {
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"The failing test on Appveyor is due to your lammps changes. Pls fix.",
"Test fixed on AppVeyor. The failed test on Travis is not relevant to this PR. "
] | 2018-05-19T19:06:41 | 2018-05-22T18:28:23 | 2018-05-22T18:28:23Z | CONTRIBUTOR | {
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} | ## Summary
For historical reasons, non-orthogonal simulation box was not properly treated in the original LAMMPS interface. This PR addresses all the issues left with those less used boxes.
* Added a `LammpsBox` class, useful for building the data input file and parsing simulation box info in dump files.
* Sim... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1154 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1154/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1154/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1154/events | https://github.com/materialsproject/pymatgen/issues/1154 | 325,095,611 | MDU6SXNzdWUzMjUwOTU2MTE= | 1,154 | Missing file on pip install: hhi_data.csv | {
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} | ## System
* Pymatgen version: 2018.2.13
* Python version: 3.6
* OS version: mac OS 10.13.4
## Summary
* When trying to instantiate `HHIModel()` via a pip installed pymatgen, a FileNotFoundError is raised for hhi_data.csv
* This file is located in the correct folder in the repo
## Example code
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"Thanks for reporting it, I will take care of that as soon as possible.\r\n",
"thanks a lot!\r\nand there is still one thing to fix\r\nwhile using the electronic_structure.plotter.BoltztrapPlotter module\r\nif anything about mu, like plot_seebeck_mu, plot_conductivity_mu\r\nthe mu_steps didnt minus the e-fermi\r\... | 2018-05-25T03:53:23 | 2023-05-29T18:46:55 | 2023-05-29T18:46:55Z | NONE | {
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} | When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
* Pymatgen version: <2018.4.20>
* Python version: <3.5>
* OS version: <linux-x86_64>
* Boltztrap version:<1.2.5>
## Summary
1. cannot correctly read th... | {
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} | ## Summary
Fixed serialization issue as `Deformation` is not `MSONable`, with a proper test.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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Fixes an issue where `MaterialsProjectCompatibility` raises an import error if optional dependency `networkx` not installed, due to use of analysis.local_env classes.
(we could also just make networkx a core dependency, it's quite light and pure Python; it's currently used for creating and analyzing gr... | {
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"Can we have some tests pls?",
"Sure thing, Shyue Ping.\r\n(Kinda rhymes :-) )."
] | 2018-06-04T20:41:10 | 2018-06-06T14:00:58 | 2018-06-06T14:00:58Z | CONTRIBUTOR | {
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} | ## Summary
Normalize reaction formula. Also provide reaction energy per reaction formula in kJ/mol.
* Reaction formula is normalized by the second reactant.
* Reaction energy in kJ/mol for per mol of normalized reaction is calculated in get_kinks method.
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"All checks have passed. I believe this is ready to be merged in. We would greatly appreciate if it could be merged and a new version could be released this evening so that we're ready to go for Codebusters tomorrow morning. Thanks! "
] | 2018-06-05T20:48:44 | 2018-06-06T12:15:03 | 2018-06-06T12:15:03Z | CONTRIBUTOR | {
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Lots of polishing, formatting, and small to medium tweaks that were found to be necessary when building QChem functionality into Atomate and testing workflows.
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"I concur with Shyue on this. Using an extrinsic property stored in\nStructure to influence the behavior of VaspInputSets is not a good idea.\nYou are adding a specific use case and pushing it on unsuspecting\nusers/developers. These use cases are hard to identify later on and\nunderstand in general.\n\nIMO, subcla... | 2018-06-06T18:39:55 | 2018-06-27T21:43:37 | 2018-06-27T21:43:35Z | CONTRIBUTOR | {
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"Pls implement tests."
] | 2018-06-07T00:25:36 | 2018-06-07T13:58:04 | 2018-06-07T13:58:04Z | CONTRIBUTOR | {
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previous implementation would return 0 if kpoints is auto-generated and 1 otherwise both of which are not the expected behavior.
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2) More flexible (all motifs with specific order parameters can now be searched). | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1166 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1166/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1166/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1166/events | https://github.com/materialsproject/pymatgen/pull/1166 | 330,713,565 | MDExOlB1bGxSZXF1ZXN0MTkzNjU2NDM0 | 1,166 | Update MPRester tests in preparation of new MP DB release | {
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} | **do not merge** (see `TODO` below)
## Summary
Tested values are changed in the new MP DB due to additional compounds
* Update non-existent compound for interface reactions test, as MnO3 exists in new MP db
* Update tested db entry values. Relax places=7 constraint on assertion.
* Test for expected icsd ids ... | {
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"If you are referring to a Materials Project database field accessible via e.g. `MPRester.query`, this is available as [`formula_anonymous`](https://github.com/materialsproject/mapidoc/blob/3bea594cdfd0e8186cc535414fd1cbe13a86e4b3/materials/formula_anonymous/README.md). For example:\r\n\r\n```python\r\nfrom pymatge... | 2018-06-08T22:24:49 | 2018-06-19T13:55:22 | 2018-06-19T13:55:22Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1168 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1168/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1168/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1168/events | https://github.com/materialsproject/pymatgen/pull/1168 | 330,928,079 | MDExOlB1bGxSZXF1ZXN0MTkzODAxNzMy | 1,168 | Minor changes needed to support Abinit 8.8.2 | {
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"Any ideas @computron? I noticed you have added a lot of nice changes to the `local_env` class lately. The [4.6.2018 version](https://pypi.org/project/pymatgen/2018.4.6/) is the last one that still works reasonably efficiently with the `MinimumVIRENN` algorithm.",
"I haven’t touched MininumVIRENN, you might want ... | 2018-06-10T05:11:55 | 2020-07-11T02:43:18 | 2020-07-11T02:42:48Z | MEMBER | {
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} | ## System
* Pymatgen version: 2018.4.20 -- 2018.5.22 (present)
* Python version: 3.6.5
* OS version: Issue occurs on Windows and Linux
## Summary
The `MinimumVIRENN` algorithm in `pymatgen.analysis.local_env` used to be quite fast, but a change was introduced in the 2018.4.20 release of Pymatgen that has cau... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1170 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1170/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1170/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1170/events | https://github.com/materialsproject/pymatgen/issues/1170 | 331,018,635 | MDU6SXNzdWUzMzEwMTg2MzU= | 1,170 | a typo in lattice.py: *a* lattice parameter.ATATClusterExpansion | {
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* Pymatgen version: master branch (Latest commit 03bb94e)
* Python version: any
* OS version: any
## Summary
* there is typo in lattice.py, line 361
## Suggested solution (if any)
* remove "ATATClusterExpansion"
## Files (if any)
* pymatgen/pymatgen/core/lattice.py
```
@prope... | {
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"Hi, Germain, I also encountered this import error of pymatgen-2018.6.27 that was installed by anaconda with python3 (same error with python2).\r\nI solved this problem by using\r\n\r\n> pip install --user pymatgen\r\n\r\nIf you still have the problem, you may consider to update your GLIBC (if you are the admin), o... | 2018-06-12T07:47:16 | 2023-06-18T17:50:31 | 2023-06-18T17:50:31Z | CONTRIBUTOR | {
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I have recently installed anaconda and pymatgen in our lab server and I got an error about GLIBC when I try to import pymatgen. It seems there is something wrong with gcc and cython. Do you know how can I fix this ?
## System
* Python version: Python 3.6.4 Anaconda
* Pymatgen version: 2018.6.11
* OS ve... | {
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"Pls fix failing tests. Thanks.\r\n",
"Should be good now. Sorry about that; put my test files in the wrong directory."
] | 2018-06-13T21:19:44 | 2018-06-14T18:38:56 | 2018-06-14T18:38:56Z | CONTRIBUTOR | {
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Previously, pymatgen.analysis.graphs.StructureGraph represented both Structures and Molecules. However, functionality for Molecules was limited. This splits StructureGraph into two classes: StructureGraph and MoleculeGraph, and adds a series of features to the MoleculeGraph that are useful for molecular m... | {
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Modifying OUTCAR's parsing logic. The big change is the addition of parsing of internal strain tensors from DFPT calcs. There is some additional logic for parsing the ionic portion of the dielectric and piezoelectric tensor if DFPT is on. | {
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metadata can be updated as needed | {
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Fix bug when two reactants are the same composition.
* Fix get_kinks method and _get_reaction method to handle the case when two reactants have the same reduced composition. | {
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"can you put in a unit test pls?",
"@sivonxay in this PR, you're then skipping parsing electrostatic potential completely ? Would it be possible to fix parsing instead? (e.g. I think if every `-` sign in that block was replaced with a leading space ` -` this would fix it?)",
"Thanks @sivonxay !"
] | 2018-06-20T00:12:40 | 2018-09-24T22:52:57 | 2018-09-24T22:52:57Z | CONTRIBUTOR | {
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* Fix 1 - Outcar parsing error : "ValueError: could not convert string to float: "
Occasionally, reading the outcar results in an error when the "average electrostatic potential at core" contains values <-100. This is caused by the charge parsing incorrectly finding the electrostatic potential at core.
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"there is a method to remove duplicate atoms in Structure.",
"I'm not sure if it's related to your problem, but the crystal doesn't look quite right to me... the symmetry operations in the CIF file reads:\r\n\r\n```\r\nloop_\r\n_symmetry_equiv_pos_site_id\r\n_symmetry_equiv_pos_as_xyz\r\n1 'x-y, x, z'\r\n2 'y, -x... | 2018-06-20T18:58:39 | 2025-02-28T22:04:49 | 2018-06-25T15:54:03Z | NONE | {
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} | ## System
* Pymatgen version: 2018.6.11
* Python version: 3.6.5 |Anaconda, Inc.| (default, Apr 29 2018, 16:14:56)
* OS version: Red Hat Linux 2.6.32-220.el6.x86_64
## Summary
* Reading a CIF file for In2Se3 from the ICSD produces a structure with 2 atoms in the same position.
* This problem arose after swi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1180 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1180/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1180/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1180/events | https://github.com/materialsproject/pymatgen/pull/1180 | 334,301,801 | MDExOlB1bGxSZXF1ZXN0MTk2MzExNjMx | 1,180 | Updated parameter that throws NoneType error when checking if structure is valid | {
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* Updated parameter that throws NoneType error when checking if structure is valid
Fixes the following error:
File "/home/sivonxay/.conda-envs/cms/code/pymatgen/pymatgen/core/structure.py", line 299, in is_valid
all_dists = self.distance_matrix[np.triu_indices(len(self), 1)]
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"Pls fix the conflicts first. Also, if the limit is just 2 atom/cell, I wouldn't bother with making a conditional thing just for it. It introduces code complexity for a very minor case. People who are just doing one atom/cell can just wait a bit more. ",
"Not yet ready to merge. While making the merges, I realize... | 2018-06-21T14:48:25 | 2018-06-25T15:30:36 | 2018-06-25T15:30:36Z | CONTRIBUTOR | {
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} | ## Summary
Added methods to accelerate the computation of Voronoi tessellations for an entire simulation cell. Our current implementation computes the tessellation for each atom, this new implementation computes it once for the entire cell. As the time to compute the Voronoi tessellation scales with `O(N log(N))` (`... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1182 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1182/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1182/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1182/events | https://github.com/materialsproject/pymatgen/pull/1182 | 334,625,140 | MDExOlB1bGxSZXF1ZXN0MTk2NTUxNzY5 | 1,182 | Fixed issue with partial occupancies in VoronoiNN and added corresponding new unit test. | {
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"@shyuep, the Travis build failed, but the reason is not the local_env module. Merge?"
] | 2018-06-21T19:24:41 | 2018-06-23T01:38:23 | 2018-06-23T01:38:23Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1183 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1183/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1183/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1183/events | https://github.com/materialsproject/pymatgen/pull/1183 | 334,961,412 | MDExOlB1bGxSZXF1ZXN0MTk2ODAwNTM5 | 1,183 | Add several functions to BabelMolAdaptor | {
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"Thanks!"
] | 2018-06-22T17:36:06 | 2018-06-23T01:37:33 | 2018-06-23T01:37:32Z | CONTRIBUTOR | {
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} | ## Summary
Add several functions to BabelMolAdaptor, including rotor conformer search, confab conformer search and make3d, add_hydrogen etc. Also add support for reading a molecule from a MoleculeGraph object.
* systematic/random/weighted rotor conformer search
* confab conformer search
* gen3d conformer searc... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1184 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1184/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1184/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1184/events | https://github.com/materialsproject/pymatgen/pull/1184 | 335,855,914 | MDExOlB1bGxSZXF1ZXN0MTk3NDQ5MzAy | 1,184 | Add Supercell Image to Neighbor-Finding Routines | {
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"Note, this may provide a route to fix #1103",
"I've added \"return supercell\" to all of neighbor-finding routines I could find. This PR is ready for review."
] | 2018-06-26T14:46:29 | 2018-06-26T16:45:46 | 2018-06-26T16:45:46Z | CONTRIBUTOR | {
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} | ## Summary
Adding the ability to output to all routines that determine nearest neighbors. Detecting which image a neighbor comes from given its coordinates (Cartesian or fraction) can be complicated for neighbors near the edges of cells, and this change allows algorithms to avoid needing to perform such operations.
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1185 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1185/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1185/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1185/events | https://github.com/materialsproject/pymatgen/pull/1185 | 335,902,213 | MDExOlB1bGxSZXF1ZXN0MTk3NDgzNDMy | 1,185 | Add weaker equivalence test and node attributes to MoleculeGraph; add OpenBabel-based local environment strategy | {
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} | ## Summary
Added a new class to pymatgen/analysis/local_env.py which wraps OpenBabel bond-detecting functionality for Molecules; also added to MoleculeGraph, including an isomorphism-based equivalence test and a way to keep track of the species and coordinates of each node in the graph (rather than having to track t... | {
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"@shyuep Hi Prof. Ong, it seems that the checks are all completed but the status is still pending. May I know what I could do to get this pull request merged? Thanks!"
] | 2018-06-29T06:19:38 | 2018-07-18T22:01:36 | 2018-07-18T22:01:36Z | CONTRIBUTOR | {
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} | ## Summary
Added method get_critical_original_kink_ratio to interface_reactions module. The point is to provide users with the critical mixing ratios between ORIGINAL reactant compositions, not normalized ones. These original mixing ratio would more useful and straightforward for experimentalists.
* Added method ... | {
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"I see that the tests failed with 'OSError: You do not have the right POTCAR with functional PBE and label H1.25 in your VASP_PSP_DIR'. I was under the impression that these fractional hydrogen pseudopotentials were included with VASP as they were included in mine, and the test completed fine on my computer.\r\n\r\... | 2018-06-29T19:49:26 | 2018-07-01T22:07:10 | 2018-06-30T03:54:44Z | CONTRIBUTOR | {
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} | ## Summary
In the DictSet provided in pymatgen.io.vasp.sets, fractional NELECT values are not allowed. For almost all purposes, this is not a problem. However, I am using the DictSet to prepare calculations that use the fractional hydrogen pseudopotentials, giving an incorrect NELECT value. I added a flag 'allow_fra... | {
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} | ## Summary
Removed unnecessary int(round(...)) from two locations when computing the NELECT value. While for most cases this should be an integer, there are some cases where a fractional value is expected; one use case is pseudo-hydrogen, which has a fractional charge for passivating bonds.
## Additional dependen... | {
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"I am not sure what you are supplying as prim cell. Please provide a more detailed example code. Basically I cannot reproduce the error, and there is an actual unittest which passes on that particular method. ",
"Actually, I'm trying to follow your publication about LMPX. I'd like to generate enumerated structure... | 2018-07-02T08:01:27 | 2018-07-02T16:19:42 | 2018-07-02T16:13:43Z | NONE | {
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} | When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
* Pymatgen version: latest version
* Python version: 3.6
* OS version: CentOS
## Summary
* Attribute error in strandard_transformations
## Example cod... | {
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"Provide a description so that I know what this PR is about?",
"The new order parameter recognizes square-face capped trigonal prismatic coordination environments (IUPAC symbol: TPRS-7; CN = 7)."
] | 2018-07-02T20:03:09 | 2018-07-07T14:27:38 | 2018-07-07T14:27:38Z | CONTRIBUTOR | {
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} | ## Summary
Fixed some bugs in surface_analysis.py. Added metallic radius to periodic_table.py .
Credits:
Zachariasen, W. H. (1973). Metallic radii and electron configurations of the 5f-6d metals. Journal of Inorganic and Nuclear Chemistry, 35(10), 3487–3497. https://doi.org/10.1016/0022-1902(73)80357-4
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"@shyuep I am not sure why the test is failing. The error says:\r\n\r\n```\r\n======================================================================\r\nFAIL: test_timeout (pymatgen.command_line.tests.test_enumlib_caller.EnumlibAdaptorTest)\r\n----------------------------------------------------------------------\r\... | 2018-07-05T16:28:25 | 2018-08-10T11:12:11 | 2018-07-07T14:27:09Z | MEMBER | {
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} | ## Summary
Currently, VoronoiNN takes in a static cutoff, and if neighbors are not found within that cutoff, it gives an error and quits.
Two problems:
- the default cutoff is very high to avoid such problems, making the default unnecessarily slow for most structures (which do not need a 10 Angstrom cutoff to fi... | {
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"Right now, many things do nto specifically support Python 3.7 yet. I don't think there is a specific code issue with pymatgen - more likely it just requires a regeneration of the c extension code from cython. Give us a few weeks for the rest of the scientific dependencies to catch up before we update pymatgen.",
... | 2018-07-06T06:35:24 | 2018-07-07T14:26:54 | 2018-07-07T14:25:51Z | NONE | {
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} | When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
* Pymatgen version: <Write "branch_name" if it is development version.>
* Python version: <Python3.7>
* OS version: <MacOS High Sierra 10.13.5>
## Summary
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Adds a `choice` kwarg to select alternative origin, axes settings.
Due to how spglib's python interface works, the easiest way to use this functionality is to use SpacegroupAnalyzer to do an initial analysis, use `.get_available_choices()` to list out other choices that are supported by spglib, and the... | {
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"The default behavior is to reduce the cell to a primitive cell, which can result in swapping of crystal axes. To turn off this behavior, pls use `Structure.from_file(\"MIL-47.cif\")` or set `primitive=False` in the `get_structures` method."
] | 2018-07-09T23:36:52 | 2018-07-10T14:06:17 | 2018-07-10T14:06:17Z | CONTRIBUTOR | {
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} | https://github.com/numat/RASPA2/blob/master/structures/mofs/cif/MIL-47.cif
Importing the above MIL-47.cif results in lattice lengths different from what is listed in the cif file. Why is this?
```
In [2]: mof = CifParser("MIL-47.cif")
In [3]: struct = mof.get_structures()[0]
In [4]: struct.lattice.a
Out[... | {
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"I think I figured out the bug; if the electrostatic potential at an ion is only of order 1 (e.g. -5 instead of -50) then there are going to be two spaces between the ion index and the value, i.e.\"1 -5\" versus \"1 -5\". (It works fine if there are 0 spaces, too). Hence, there needs to be provision for one **or**... | 2018-07-10T20:56:36 | 2018-07-13T17:13:09 | 2018-07-13T15:44:05Z | CONTRIBUTOR | {
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} | This is my first time submitting an issue so I hope that what I've written below is the appropriate level of detail. Thanks for everything you guys do!
## System
* Pymatgen version: "2018.5.14" (Slightly older version, but I checked the history of the file in question to see if this had been fixed and it didn't ... | {
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"Yep, that’s correct. And then we find which sites overlap in the 4N\nstructure within a given threshold (eg using scipy’s kdTree), and then use\nthat to flag which sites are co-incident in the 2N structure.\n\nOn Wed, Jul 11, 2018 at 13:52, Xiang-Guo Li <notifications@github.com>\nwrote:\n\n> *@ucsdlxg* commented ... | 2018-07-10T23:33:25 | 2018-07-13T15:11:43 | 2018-07-12T15:57:05Z | CONTRIBUTOR | {
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} | ## Summary
This generator provides two methods to generate grain boundaries (GBs) from bulk conventional cell (fcc, bcc can from the primitive cell), and works for Cubic, Tetragonal, Orthorhombic, Rhombohedral, and Hexagonal systems. The first one is to generate GBs from given parameters, which includes
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