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https://api.github.com/repos/materialsproject/pymatgen/issues/1101
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MDExOlB1bGxSZXF1ZXN0MTgwNjkxMjIz
| 1,101
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Mprest final struct
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[] | 2018-04-10T18:35:22
| 2019-04-04T02:45:03
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2018-04-10T19:47:00Z
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CONTRIBUTOR
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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 structure if `inc_structure=True` and only return the final structure if `inc_structure="Final"`. This seems counterintuitive to me, since the final structure is the one that actually corresponds to the calculated energy, and the rest of the MPRester uses the final structure by default, so this PR changes the default `inc_structure=True` behavior to include the final structure and allows for initial structures to be requested by `inc_structure="initial"`. Also added a test.
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MDExOlB1bGxSZXF1ZXN0MTgxMzI2MzI4
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|
Add cbm and vbm marker in BSPlotter when ylim is set
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[] | 2018-04-12T21:09:16
| 2018-04-12T22:41:32
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2018-04-12T22:41:32Z
|
MEMBER
|
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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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MDU6SXNzdWUzMTM5MDczNDk=
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_get_image() in pymatgen.analysis.local_env doesn't give correct image
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[] | null |
[
"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 most recent\nchange to get_image too. If you encounter further issues I’ll go back and\ntake another look.\n\nOn Thu, Apr 12, 2018 at 23:24, Anubhav Jain <notifications@github.com>\nwrote:\n\n> Closed #1103 <https://github.com/materialsproject/pymatgen/issues/1103>.\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1103#event-1572092081>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AC1rRAldoZQxeTR65cKOd8fmYh5qBRCAks5tn9QEgaJpZM4TSlF0>\n> .\n>\n",
"From what I can tell, the neighbors returned by VoronoiNN, MinimumDistanceNN, and perhaps all NN algorithms give back a Site objects that have the correct cartesian coordinates but the wrong image (e.g., fractional coordinates that don't correctly represent the image they are in). But, I don't have much time to debug. Just the code example above, here modified a bit to show the Cartesian distance at the end and how it is in agreement with a \"hacked\" image but not the reported image:\r\n\r\n```python\r\nfrom pymatgen import MPRester\r\nfrom pymatgen.analysis.local_env import MinimumDistanceNN\r\nimport numpy as np\r\n\r\nmpr = MPRester()\r\ns = mpr.get_structure_by_material_id(\"mp-685291\")\r\n\r\ncnn = MinimumDistanceNN(tol=0.5)\r\nnn = cnn.get_nn_info(s, 71)\r\nfor x in nn:\r\n if x[\"site\"].specie.symbol == \"Al\":\r\n print(x[\"site\"], s[71].distance(x[\"site\"], x[\"image\"])) # gives 15.85 - WRONG!\r\n print(x[\"site\"], s[71].distance(x[\"site\"], [0, 0, 0])) # gives 1.96 - RIGHT!\r\n print(x[\"site\"], np.linalg.norm(x[\"site\"].coords - s[71].coords)) # gives 1.96 - RIGHT!\r\n```\r\n\r\nAs far as I can tell the root of the image problem is the fractional coords of the site",
"Yeah, it’s definitely further down the callstack. I’ll track it down when\nI’m back in work next week — I think it’s either an issue with frac coords\non 0 or 1, or there’s a rounding of small numbers happening somewhere\nthat’s resulting in numbers being rounded the ‘wrong’ way. In any case,\nthere are alternative ways to get the image given that the Cartesian coords\nare correct, so hopefully should be an easy fix. Thanks for the detailed\nbug report.\n\nOn Fri, Apr 13, 2018 at 10:53, Anubhav Jain <notifications@github.com>\nwrote:\n\n> From what I can tell, the neighbors returned by VoronoiNN,\n> MinimumDistanceNN, and perhaps all NN algorithms give back a Site objects\n> that have the correct cartesian coordinates but the wrong image (e.g.,\n> fractional coordinates that don't correctly represent the image they are\n> in). But, I don't have much time to debug. Just the code example above,\n> here modified a bit to show the Cartesian distance at the end and how it is\n> in agreement with a \"hacked\" image but not the reported image:\n>\n> from pymatgen import MPResterfrom pymatgen.analysis.local_env import MinimumDistanceNNimport numpy as np\n>\n> mpr = MPRester()\n> s = mpr.get_structure_by_material_id(\"mp-685291\")\n>\n> cnn = MinimumDistanceNN(tol=0.5)\n> nn = cnn.get_nn_info(s, 71)\n>\n> for x in nn:\n> if x[\"site\"].specie.symbol == \"Al\"\n>\n> :\n> print(x[\"site\"], s[71].distance(x[\"site\"], x[\"image\"])) # gives 15.85 - WRONG!\n> print(x[\"site\"], s[71].distance(x[\"site\"], [0, 0, 0])) # gives 1.96 - RIGHT!\n> print(x[\"site\"], np.linalg.norm(x[\"site\"].coords - s[71].coords)) # gives 1.96 - RIGHT!\n>\n> As far as I can tell the root of the image problem is the fractional\n> coords of the site\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1103#issuecomment-381213753>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AC1rRGfJn3l2R-su4ObgR5fI8FwY-bVQks5toOYtgaJpZM4TSlF0>\n> .\n>\n",
"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 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_structure_by_material_id("mp-685291")
cnn = MinimumDistanceNN(tol=0.5)
nn = cnn.get_nn_info(s, 71)
for x in nn:
if x["site"].specie.symbol == "Al":
print(x["site"], s[71].distance(x["site"], x["image"])) # gives the WRONG distance for Al - way too far!!
print(x["site"], s[71].distance(x["site"], [0, 0, 0])) # gives the CORRECT distance for Al - this is the right image!
```
## Error message
none
## Suggested solution (if any)
haven't looked at the code
## Files (if any)
none
|
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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 a method of the object so that it can be explicitly tested (is there any particular reason to keep it as a nested function?)"
] | 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 label sometimes contains additional letters.
List of changes:
* parsing of element symbols in capital letters
* added an `errors` attribute to CifParser. It stores all the warnings and errors issued during the parsing.
* explicitly require pybtex for functions requiring it, instead of crashing (is an optional dependence)
* tests
While this increases the number of cif files parsed in the COD database, this can maybe introduce some regressions. Any comment about possible issues with the current modification?
|
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| 314,174,180
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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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| 314,261,132
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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 effectively appear as though it is the most electropositive.",
"I think NaN will just stay in the same place as it was initially in the list when sorted, so it wouldn't show up as either most or least electronegative unless it started in that list position\r\n\r\nSo elements with no electronegativity, when sorting, will just stay in the same place. But TBH I don't see that as a big issue. I'm more concerned with people designing mathematical functions that depend on electronegativity difference (or doing data mining with that) and the potential for infinity to be seen as a \"computable\" float.\r\n\r\nAs an example I am currently writing a NearNeighbor algorithm that might want to weight bonds with higher electronegativity difference more strongly - so something like a bond strength score that looks like (X1 - X2). However if I wasn't more careful in reading the docs or testing against ALL elements (like He, Ne, etc) then I could easily end up with pathological cases where the bond strength scores are infinity and I'm not sure why the NN algorithm is failing and perhaps just bonding everything to He / Ne / etc.",
"I can see the issue with the inf. But I also see the problem with using NaN. For example, there is now completely no predictability in sorting formulas. I can easily get LiHeN as well as HeLiN and LiNHe. Granted the ones with no electronegativities tend not to be compound formers, but it is an issue. For instance, HArF exist. There are a few He compounds at low temperatures. ",
"Ah now I understand why you want to be able to sort electronegativities and also why you chose +inf\r\n\r\nOk up to you. I think the two solutions are to just leave as-is, or if people want an explicit sort order to NaN (as in pretty formula) to have more complex code that gives a custom sort key, e.g.\r\n\r\n```\r\nsorted(my_list, key=lambda x: x if not math.isnan(x) else float(\"inf\"))\r\n```\r\n\r\nThis is admittedly ugly but explicit that you are intentionally putting undefined electronegativities at the end.\r\n\r\nFeel free to close ...",
"Ok, I have a solution that addresses both problems. We cab use Nan, but we modify the Element '__lt__' method to treat NaN as effectively infinity in the sort order. Will this address your needs? If so, pls implement with tests.",
"I implemented and fixed this. Just pull the latest changes.",
"Great, thanks!"
] | 2018-04-13T21:52:32
| 2018-04-14T16:42:41
|
2018-04-14T03:12:09Z
|
MEMBER
|
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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("No electronegativity for %s. Setting to infinity. "
"This has no physical meaning, and is mainly done to "
"avoid errors caused by the code expecting a float."
% self.symbol)
return float("inf")
```
* **I would suggest to return float("nan") instead**
* With float("inf") you can design functions and perform computations without knowing that you are doing anything wrong. e.g. a function like 1/electronegativity will return zero for unknown electronegativity, whereas it should really throw an error or return another invalid value like NaN. Otherwise, there is no way to really detect that 1/electronegativity did anything wrong - you get a perfectly ordinary float (zero) at the end.
* Note that my suggestion is in-line with what libraries like pandas does
|
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MDExOlB1bGxSZXF1ZXN0MTgxNzE4NzAw
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|
Ordered Dictionaries Removed
|
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[] | 2018-04-15T20:20:56
| 2018-04-15T21:12:17
|
2018-04-15T21:12:17Z
|
CONTRIBUTOR
|
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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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MDU6SXNzdWUzMTQ4NDI4OTI=
| 1,108
|
unnecessary line in all local_env classes
|
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[] | 2018-04-16T22:39:26
| 2018-04-16T23:49:08
|
2018-04-16T23:49:08Z
|
MEMBER
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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, never used!). The only reason for it seems to be a downstream code that @hillarypan is designing to benchmark the various CN algorithms where this variable is used as a container for the data stored in those benchmarks. This is crazy!
@hillarypan should explain whether this line of code is needed for the local_env methods to function apart from her own library (I think not). If not, then those lines should be removed from pymatgen where they do not belong and the benchmark code should handle the storage of coordination number data without contaminating the pymatgen code with extra lines.
## Suggested solution (if any)
* remove *all* ``self._cns = {}`` unless a good case can be made for their inclusion in **pymatgen**.
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| 314,847,290
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MDExOlB1bGxSZXF1ZXN0MTgyMDEwNTEx
| 1,109
|
AFLOW crystal prototype matcher + DisorderOrderedTransformation + pretty printing for disordered formulae
|
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[] | null |
[
"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 structure is a \"fluorite\" or a \"perovskite\" (especially if it's a less common crystal structure you may be previously unfamiliar with, but which has a common mineral name that can be easily googled).\r\n\r\nThe problem is that many structures don't StructureMatch against a prototype from the AFLOW library anyway -- either because there's been a partial species substitution, or there's too much local distortion even with loose structure matching tolerances, or maybe it's a layered structure and the interlayer spacing differs by too much, so it isn't perfect. But when it does work it can be useful."
] | 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 containing the prototype structures as SNLs.
* A `DisorderOrderedTransformation` to merge sites to create a disordered structure from an input ordered structure -- this is probably quite a niche transformation, but the intent here was to try and find a way to 'go back' to plausible disordered structures for the purposes of crystal prototype matching. This is useful if the disordered structure would structure match against a crystal prototype, while the ordered structure would not.
* A string util to create pretty formula like `Cu_{x}Au_{1-x} x=0.25` from a disordered Structure.
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* Better matching of ordered crystal structures derived to their original disordered prototype.
|
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MDExOlB1bGxSZXF1ZXN0MTgyMDEzODM2
| 1,110
|
taking out _cns
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[] | 2018-04-16T23:24:04
| 2018-04-16T23:30:33
|
2018-04-16T23:30:32Z
|
NONE
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Since I'm the only one using it (see issue #1108)
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| 315,193,254
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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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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.test_enumlib_caller.EnumlibAdaptorTest#test_timeout? Not sure why it's so low."
] | 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 preference for bonds with higher electronegativity difference.
Without any knowledge or "fitting", this method beat all other local_env methods currently in pymatgen on a benchmark test set of compounds including metals, minerals, and porous structures by a factor of two or more. The test set, which is still being expanded, is available here:
https://github.com/hillarypan/MaterialsCoord
## TODO
The method is complete and usable. However, it is possible we might fine tune the method later on if we see any issues that we didn't see in the current round of benchmarks. There are interested parties in this code that want to test this iteration of the NearNeighbor algo within pymatgen at the present time to help in the benchmarking process for diverse compound sets.
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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': 2.899999975486379,
'beta': 107.6337551894724,
'c': 2.899999975486379,
'gamma': 112.78479361412218,
'matrix': [[-1.703614, 1.712067, 1.605156],
[1.703614, -1.712067, 1.605156],
[1.703614, 1.712067, -1.605156]],
'volume': 18.727042432703485},
'sites': [{'abc': [0.0, 0.0, 0.0],
'label': 'Sn',
'species': [{'element': 'Sn', 'occu': 1}],
'xyz': [0.0, 0.0, 0.0]}]}
st = Structure.from_dict(s)
st.get_space_group_info()
```
The resulting error is:
```
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-11-fe0a28cf7159> in <module>()
1 from pymatgen import Structure
----> 2 Structure.from_dict(struc["input"]["structure"]).get_space_group_info()[0]
/Users/shyamd/codes/pymatgen/pymatgen/core/structure.py in get_space_group_info(self, symprec, angle_tolerance)
703 a = SpacegroupAnalyzer(self, symprec=symprec,
704 angle_tolerance=angle_tolerance)
--> 705 return a.get_space_group_symbol(), a.get_space_group_number()
706
707 def matches(self, other, **kwargs):
/Users/shyamd/codes/pymatgen/pymatgen/symmetry/analyzer.py in get_space_group_symbol(self)
136 (str): Spacegroup symbol for structure.
137 """
--> 138 return self._space_group_data["international"]
139
140 def get_space_group_number(self):
TypeError: 'NoneType' object is not subscriptable
```
The problem seems to be at:
```python
self._space_group_data = spglib.get_symmetry_dataset(
self._cell, symprec=self._symprec, angle_tolerance=angle_tolerance)
```
https://github.com/materialsproject/pymatgen/blob/master/pymatgen/symmetry/analyzer.py#L99-L100
I'm not even sure how to go about debugging spglib. Does anyone have an idea as to why its not giving back useful spacegroup info?
|
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MDExOlB1bGxSZXF1ZXN0MTgyNjE0OTYy
| 1,114
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Add uniform bandstructure fetching to MPRester
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[] | 2018-04-18T22:01:14
| 2018-04-18T23:18:03
|
2018-04-18T23:18:03Z
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MEMBER
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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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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 merged the two XRDPattern and NDPattern classes, moved the get_plot and other functions into a parent module. Right now, most of the differences are in the get_pattern method. There is still some duplication there, but it is something we can live with for now. Note that the names of some of the methods have been changed to make them more generic. Pls pull the latest changes and your NMR pattern should work. Thank you very much for the contribution.",
"@shyuep Thank you for your quick response. I pulled and checked the [latest code](https://github.com/materialsproject/pymatgen/commit/56d75aeecfd1ec7d078fe846baf16302fdb413c1). \r\nIt was nicely simplified, and the result looks good.\r\n\r\nWhen I come up with a solution of the issue of peak indexing, I will send pull-request. But now I don't need strict peak indexing in my research purpose; the fix might be procrastinated."
] | 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 unnecessary.
## TODO
### Fix peak indexing of forbidden reflection
The diffraction peak appearance is checked after group it by 2theta, in the present implementation of this code and XRDCalculator.
This means that a forbidden reflection seems to appear when the other reflection occurs at the same 2theta position. This behavior may confuse non-professional users.
### Make the plot function more generic
Now plot functions are implemented respectively in XRDCalculator and NDCalculator.
I think these should be integrated as a generic function because they are same except the name.
|
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|
Default QChem input sets, automatic input file checking, and PCM bug fixes
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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 qchem_io/inputs.py
* Updated tests and added an additional test to qchem_io/tests/test_inputs.py to work with the new dictionary standardization and to catch the reading errors that were present with the old regex patterns.
## TODO
Default input sets remain in a very basic, but functional, form and will be updated and expanded shortly.
|
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Update setup.py to use numpy>=1.14
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[] | 2018-04-19T23:29:40
| 2018-08-10T11:11:43
|
2018-04-19T23:42:53Z
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MEMBER
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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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| 316,085,875
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MDU6SXNzdWUzMTYwODU4NzU=
| 1,118
|
Alternate algo to reduce structure on the axb plane.
|
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[] | null |
[
"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_primitive_structure() works but because it iterates through a large number of possible reduced structures, it isn't fast enough. Since we only care about reducing the axb plane in our oriented unit cell, a simpler solution would be to just define the primitive basis vectors parallel to the hkl plane while maintaining the c vector and build a new oriented unit cell based on our new basis vectors.
Algo:
-Select a site as an origin.
-Find all equivalent sites to this site.
-Choose the two closest sites sitting on the same axb as our defined origin.
-The origin and the two sites define our a' and b' (making sure our a' and b' are not parallel of course).
-c'=c
-Build the new structure with the lattice defined by a', b', c' and the sites are inside a', b' and c'.
|
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MDExOlB1bGxSZXF1ZXN0MTgzMjA3MDU5
| 1,119
|
Fix a typo in Outcar.read_lepsilon()
|
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[] | 2018-04-21T05:28:06
| 2018-04-21T12:32:04
|
2018-04-21T12:32:03Z
|
CONTRIBUTOR
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`Outcar.read_lepsilon()` had a typo.
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MDExOlB1bGxSZXF1ZXN0MTgzMjU1MzQ2
| 1,120
|
Fix "TypeError" in case of input element is not in scattering length table
|
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[] | 2018-04-22T04:43:58
| 2018-04-22T05:41:15
|
2018-04-22T05:41:15Z
|
CONTRIBUTOR
|
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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 case, KeyError should occur here as expected.
I've entered the elements in the table and set the values as null.
But, this is the mistake.
I should have checked that carefully. Sorry😭😭
## Changes
* Drop the elements from neutron_scattering_length.json that the value of scattering length is unavailable
* Add assert of raised ValueError in that case
|
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| 1,121
|
Enable molecule-like rotations for structures.
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[] | 2018-04-23T15:40:37
| 2018-04-23T23:25:15
|
2018-04-23T23:25:15Z
|
CONTRIBUTOR
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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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| 317,002,662
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MDExOlB1bGxSZXF1ZXN0MTgzNTcyMjU1
| 1,122
|
fix to actually use search_cutoff
|
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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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A very minor fix - the parameter search_cutoff in the constructor of CrystalNN wasn't being used, this actually makes use of it.
|
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MDExOlB1bGxSZXF1ZXN0MTgzNTgxOTAx
| 1,123
|
Increased default cutoff in CrystalNN
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| 2018-04-23T23:15:41
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2018-04-23T23:15:41Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MTgzNjAxODY1
| 1,124
|
Add methods for getting phonon BS, DOS, and DDB output
|
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[] | 2018-04-24T02:01:02
| 2018-04-24T04:15:08
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2018-04-24T04:15:08Z
|
MEMBER
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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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MDExOlB1bGxSZXF1ZXN0MTgzOTI2NTA5
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|
Removed default dictionaries from sets
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[] | 2018-04-25T05:15:01
| 2018-04-25T13:05:45
|
2018-04-25T13:05:45Z
|
CONTRIBUTOR
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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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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 of the `CovalentBond` class and set it when initializing a `CovalentBond` object?
I can submit a pull request if the community think the feature is reasonable.
|
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Adaption to anticipated use of x_diff_weight
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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 ready. ",
"Sure. But \"Removed 2 bugs\" and the newer \"shortcomings\" are two separate things. Didn't anticipate more clean up, when I issued the first PR."
] | 2018-04-25T18:34:49
| 2018-04-25T22:54:01
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2018-04-25T22:49:44Z
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CONTRIBUTOR
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PCM functionality and testing for QChem inputs and sets
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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
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2018-05-02T21:25:18Z
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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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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 any performance problem. There are no loop more than 3 times.",
"Do not worry about the timeout. You just need to make sure that the tests for your new code passes. I usually take a look at the reasons for failure.",
"Great. That makes me feel a lot better."
] | 2018-04-26T05:11:04
| 2018-04-26T13:54:36
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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, the bond order can not be described by an int.
So what I finally do is to build another function `get_bond_order` which returns a float indicating the bond order. The bond order is calculated by the ideal bond lengths of different bond orders and the actual site distance. For example, if C-C bond is 1.54 A and C=C bond is 1.34 A and we have a distance of 1.4 A (benzene). Then the bond order is 2 - (1.4 - 1.34) / (1.54 - 1.34) = 1.7. I think this is enough to provide some qualitative information.
What I did is listed below in detail:
* Add a function `obtain_all_bond_lengths` as a wrapper of the bond length database.
* Add a function `get_bond_order` to calculate bond order
* Add a member method `get_bond_order` for class `CovalentBond` to indicate the bond order of the covalent bond.
* Refractor `get_bond_length` and `is_bonded` to make them more concise using new functions.
* Improve the behavior of `get_bond_length`. If data for the bond order requested is not available, a warning will be shown and the radius sum will be returned, instead of `None`, which is the same as the behavior when no bond order data is available for the species.
* Make bond lengths json file indented to provide convenience for inspection.
* Add tests for the bond order related functions.
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MDU6SXNzdWUzMTgwMTQ5NDM=
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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 have the option to check the value of symprec required to recognise the correct spacegroup for your structure and then to use this value as an argument for Interstitial."
] | 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 reduction function in Interstitial?
|
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Addressed some issues in CrystalNN and inserted a corresponding new unit test
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[] | 2018-04-26T18:27:26
| 2018-05-03T18:52:08
|
2018-05-03T18:52:08Z
|
CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MTg1MDQ2NzI1
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|
Update SNL remarks to 2017
|
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[] | 2018-04-30T19:47:27
| 2018-04-30T23:48:35
|
2018-04-30T20:05:12Z
|
NONE
|
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Update the remarks max to Twitter circa 2017 (280 character total)
|
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MDExOlB1bGxSZXF1ZXN0MTg1MDg0Njcw
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|
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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Reverts materialsproject/pymatgen#1132
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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 encapsulate the definition of a defect
- Defect generators are used to generate defects by automated algorithms
- DefectEntry encapsulates relevant data for defect thermodynamics including parameters from calculations
- Defect corrections apply corrections such as charge correction, band alignment, etc.
- DefectCompatability selects the corrections based on metadata from the corrections themselves
- DefectPhaseDiagram computes the defect phase diagram and relevant properties
Other Misc Features and Fixes:
- Travis Matplotlib settings were changed to default to Agg backend so that plottings tests would just work
- Added the ability to get all chempot facets in phase diagram ( necessary for defect phase diagram)
Regressions:
- Completely removed the old defects infrastructure including old transformations and CLI tool.
Future Work:
- Need to clean up and add Kumagai correction
- Need to build a good example notebook for this
|
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MDU6SXNzdWUzMTk1NDg5ODQ=
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Crash when using pymatgen.analysis.defects.point_defects.Interstitial
|
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[] | null |
[
"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 am encountering a crash when running the test script.
## Error message
```
<... snip ...>
Finding channels and pockets in Dijkstra network of 928 node(s). 928 are expected to compose pores.
Analyzed and assigned 928 nodes.
Identified 1 channels and 0 pockets.
928 nodes assigned to pores.
Traceback (most recent call last):
File "test_script.py", line 19, in <module>
interstitial = Interstitial(structure, radii=radii, valences=valences, oxi_state=True)
File "/Users/bcohen/anaconda3/envs/suzytest/lib/python3.6/site-packages/pymatgen/analysis/defects/point_defects.py", line 512, in __init__
coord_no, coord_sites, chrg = self._get_coord_no_sites_chrg(site)
File "/Users/bcohen/anaconda3/envs/suzytest/lib/python3.6/site-packages/pymatgen/analysis/defects/point_defects.py", line 547, in _get_coord_no_sites_chrg
if not site.specie.symbol == 'X':
AttributeError: 'int' object has no attribute 'specie'
```
## Suggested solution (if any)
Is it possible that the intention is for _get_coord_no_sites_chrg to call get_nn_info (which internally calls get_voronoi_polyhedra) rather than calling get_voronoi_polyhedra directly?
Making this modification causes code to run -- however not sure if capturing the correct physics ... I believe the polyhedra property used to calculate weight by default will be the polyhedral 'solid_angle' ... is that the correct 'weight' property for this purpose ... ?
```
def _get_coord_no_sites_chrg(self, site):
"""
Compute the coordination number and coordination charge
Args:
site:
pymatgen.core.sites.Site
"""
struct = self._structure.copy()
struct.append(site.specie.symbol, site.frac_coords)
vnn = VoronoiNN()
coord_no = vnn.get_cn(struct, -1, use_weights=True)
coord_sites = vnn.get_nn(struct, -1)
# In some cases coordination sites to interstitials include
# interstitials also. Filtering them.
def no_inter(site):
return not site.specie.symbol == 'X'
coord_sites = filter(no_inter, coord_sites)
coord_chrg = 0
if self._valence_dict:
for params in vnn.get_nn_info(struct, -1):
site = params['site']
weight = params['weight']
if not site.specie.symbol == 'X':
coord_chrg += weight * self._valence_dict[
site.species_string]
return coord_no, coord_sites, coord_chrg
```
## Files (if any)
The error reproduces for me with any POSCAR file tried -- but here is the one I'm interested in using ...
[POSCAR.txt](https://github.com/materialsproject/pymatgen/files/1967352/POSCAR.txt)
And for completeness -- minimal test script I use (same as linked from installation instructions)
```
import os
from pymatgen.analysis.defects.point_defects import Interstitial
from pymatgen.core.structure import Structure
structure = Structure.from_file(os.path.abspath('./POSCAR.txt'))
radii, valences = {}, {}
for element in structure.composition.elements:
radii[element.symbol] = element.atomic_radius
valence = element.group # Just a first guess..
if element.group > 12:
valence -= 10
valences[element.symbol] = valence
interstitial = Interstitial(structure, radii=radii, valences=valences, oxi_state=True)
interstitial._defect_sites
```
For some more context (if it helps) -- here is the actual computation wanting to run ...
```
from pymatgen.core.structure import Structure #For reading in structure files
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer #For checking tolerance to recognise correct spacegroup of supercell
from pymatgen.analysis.defects.point_defects import Interstitial, ValenceIonicRadiusEvaluator #For generating interstitials
# Load perfect supercell (in POSCAR format)
structure = Structure.from_file("./POSCAR.txt")
# Check pymatgen recognises the correct spacegroup for the input supercell at given tolerance
precision=0.01
spacegroup = SpacegroupAnalyzer(structure, symprec=precision, angle_tolerance=5)
print("")
print("The spacegroup of enargite should be 31")
print("What does pymatgen recognise the symmetry of the supercell as with a symmetry precision of "+str(precision)+"...?")
print(spacegroup.get_space_group_number())
print("")
print("May need to ensure interstitial finder uses the same tolerance..? (Default value is 1e-1?)")
print("")
### CHECK - need to make symprec equal to above???
# Use Voronoi analysis from pymatgen class 'Interstitial(Defect)' to identify all symmetrically distinct interstitial sites?
### Inputs for valences and radii redudnant when oxi_state=False, if allowing ValenceIonicRadiusEvaluator to analyse it
valences = {"As" : 5, "Cu" : 1, "S" : -2} #Set manually because evaluator gave Cu+ and Cu2+
#valences = {}
# Google search for ionic radii of above elements, taken from: http://abulafia.mt.ic.ac.uk/shannon/ptable.php
radii = {"As" : 0.335, "Cu" : 0.6, "S" : 1.84}
#radii = []
#evaluator = ValenceIonicRadiusEvaluator(structure)
find_interstitials = Interstitial(structure, radii=radii, valences=valences, site_type='voronoi_vertex', accuracy='Normal', symmetry_flag=True, oxi_state=True)
#find_interstitials = Interstitial(structure, radii=evaluator.radii, valences=evaluator.valences, site_type='voronoi_vertex', accuracy='Normal', symmetry_flag=True, oxi_state=False)
scaling_matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]] #Identity matrix, don't actually want to make supercell of my supercell
#print(find_interstitials.make_supercells_with_defects(scaling_matrix, "Cu"))
interstitial_supercells = find_interstitials.make_supercells_with_defects(scaling_matrix, "Cu")
print("Number of symmetrically unique interstitial sites is %s" %(len(interstitial_supercells)))
i = 0
for supercell in interstitial_supercells:
i = i + 1
filename = "supercell_POSCAR_"+str(i)+".vasp"
structure = supercell
structure.to(filename=filename)
```
@skw32
Many thanks! Let us know if we can provide more info to help track this down!
|
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MDExOlB1bGxSZXF1ZXN0MTg1NTg1NDkz
| 1,136
|
PCM Fixes and Outputs Update
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[] | 2018-05-02T23:20:11
| 2018-05-03T18:51:52
|
2018-05-03T18:51:52Z
|
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
* Substantial update of QChem output parsing (qchem_io/outputs.py) to be more streamlined and yield data in better formats to simplify the Atomate drone
* Output tests (qchem_io/tests/test_outputs.py) changed and supplemented to account for changes in output parsing
|
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MDU6SXNzdWUzMjAxMDU2MzQ=
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Random test errors in elasticity
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[] | 2018-05-03T22:48:31
| 2018-05-23T23:06:38
|
2018-05-23T23:06:38Z
|
MEMBER
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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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MDExOlB1bGxSZXF1ZXN0MTg1ODcwNjcw
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|
Elastic fix
|
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[] | null |
[
"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 unphysical. Wait for tests, but should be done. Also might be relevant to #743."
] | 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, but wanted to get some advice on what I might do, should I
(1) - issue a different warning that's more descriptive of the issue, but still return np.nan
(2) - raise an error
Let me know.
|
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MDExOlB1bGxSZXF1ZXN0MTg2MjMyNjU2
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|
Function for finding the dimensionality of connected subunits in a crystal structure.
|
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[] | null |
[] | 2018-05-06T23:38:41
| 2018-05-07T18:48:05
|
2018-05-07T18:48:05Z
|
CONTRIBUTOR
|
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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 wires.
See details at : Cheon, G.; Duerloo, K.-A. N.; Sendek, A. D.; Porter, C.; Chen, Y.; Reed, E. J. Data Mining for New Two- and One-Dimensional Weakly Bonded Solids and Lattice-Commensurate Heterostructures. Nano Lett. 2017. DOI: 10.1021/acs.nanolett.6b05229
|
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| 320,762,668
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MDExOlB1bGxSZXF1ZXN0MTg2MzIwMDIz
| 1,140
|
Small bug fix: Missing multiplication
|
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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_field_spin raises them if the element is not a metal or the oxidation state does not fit. I decided not to catch ValueErrors because they are raised if an invalid coordination or spin state are used. \r\nI hope this is sufficient.",
"Thanks!"
] | 2018-05-07T11:02:58
| 2018-05-08T13:55:13
|
2018-05-08T13:55:05Z
|
MEMBER
|
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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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MDU6SXNzdWUzMjE2NjI1NjY=
| 1,141
|
Clarify Symprec
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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 precision of measured atomic distances is within 0.01A."
] | 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 be switched around to be appropriate for loosely optimized structures and require the user to modify symprec for more 'precise' symmetry information.
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MDExOlB1bGxSZXF1ZXN0MTg3MDI1ODE0
| 1,142
|
extend the XYZ class
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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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MDExOlB1bGxSZXF1ZXN0MTg3MDY5OTk1
| 1,143
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Structure transform
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[] | 2018-05-09T23:59:48
| 2019-04-04T02:45:05
|
2018-05-10T02:34:58Z
|
CONTRIBUTOR
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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 generated for ieee standards, in cases the lattice vectors used to generate new bases are slightly non-orthogonal. This ensures, for example, that invariants won't change upon applying the tensor transformation.
* Tests for both methods
|
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MDU6SXNzdWUzMjIxNDU5MjY=
| 1,144
|
How to plot the bandstructure of the hybrid functional?
|
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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 want to plot the band-structure of the HSE06,and the output file was calculated by vasp.
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| 322,365,179
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MDExOlB1bGxSZXF1ZXN0MTg3NTE2NTY0
| 1,145
|
denser kpoints + more strict EDIFF independent of nsites
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[] | null |
[
"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/unconverged structure with the looser k-points (density=64) so I think it's better to change it in MPRelaxSet.\r\n\r\nAnother way of course would be to just change it in atomate. That's fine by me but I do think the k-point density is too low so better to just change it in MPRelaxSet.",
"I do not disagree, but this is not a decision that you can take. ",
"Of course; this is a suggestion. Please feel free to add other reviewers as well.",
"I'm confused about why you're getting different results, as far as I know, we've been using the same parameters the whole time (aside from the recent potcar issue and a minor change at some point in how k-point meshes were determined for very large unit cells). We should compare these results directly before making any changes.",
"A lot of this has been discussed before\r\n\r\nI think people should take a look at #665 \r\n\r\n",
"@montoyjh we definitely haven't been using the same k-point parameters the whole time\r\n\r\nThere were at least 3 and probably more phases of k-point settings:\r\n\r\n1. Initial settings by Michael Kocher, the very low mp ids would have this\r\n2. Post k-point mesh benchmarking by Geoffroy, in which the settings were modified from above but retained as a \"k-points per atom\" type scale\r\n3. Change to k-point density per reciprocal cell volume rather than per atom - with further changes to the way rounding k-points operates later on\r\n\r\nThere were probably even more steps in between. So I'm not surprised there are inconsistencies between historical and today's k-points.",
"Did you ever test just making EDIFF per atom more strict? Also your structure inconsistencies might have been potcar version dependent. We have 2001 potcars in MP. ",
"@shyamd , no I am just \"request\"ing to get rid of EDIFF_per_atom that likely would cause issues with large unitcells but my tests are limited to comparing these settings with some old runs (yes I checked with MP potcars). At this point, I am not sure what is a good test set. There should be a set of structures (5-10 maybe) that were run recently on MP so then I can compare the results of current defaults + some stricter settings. Based on my previous tests I say that the current defaults (atomate and MPRelaxSet) should change but change to what exactly I like to show it with a test set that everybody agrees on (i.e. everyone thinks the MP version of those structures is well converged).",
"Let us discuss this and settle this problem once and for all. Can one of you schedule a call with the key players? I will participate.",
"This could be done sometime in June 6-8 when we have our next coding session if you are available. I can also join and see if I can help. I have put together a document that compares some outputs from atomate defaults (w/ correct POTCARs) and MP data. They are generally consistent but with some clear outliers. The cases where they are not consistent (either structure or bandgap) requires a more careful investigation.\r\n\r\n[compare_with_MP.csv.zip](https://github.com/materialsproject/pymatgen/files/2018792/compare_with_MP.csv.zip)\r\n\r\nIn the meantime, please feel free to close this PR until I have a more solid test set and the reason for inconsistencies.",
"I think we should have a meeting before the coding session to discuss general strategy. The purpose of the coding session can be to implement that strategy"
] | 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 against things going wrong down the line.
Also related to atomate structure optimization discussion: https://github.com/hackingmaterials/atomate/issues/19
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MDExOlB1bGxSZXF1ZXN0MTg3NTYwOTc1
| 1,146
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v2 of CrystalNN
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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 relative
* change x_diff parameter behavior to activate more quickly
* support for zero-coordinated sites
* allow fingerprints to smoothly go to zero values
* minor code refactoring
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MDU6SXNzdWUzMjI2NDgxMDM=
| 1,147
|
Any plan for Dash/Zeal documentation?
|
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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 particular version of pymatgen\r\ngit checkout v2018.5.3\r\n# Use tasks.py in the pymatgen repo for a custom Sphinx-doc-building procedure.\r\ninvoke make-doc\r\n# \"-af\" adds the docset to your installed Dash and overwrites if already built\r\ndoc2dash docs -n \"pymatgen 2018.5.3\" -i docs/_images/pymatgen.png -u https://pymatgen.org/ -af\r\n```\r\nYou can grab my Dash docset for pymatgen 2018.5.3 [here](https://www.dropbox.com/s/2ll18eyelmq4922/pymatgen%202018.5.3.docset.tar.gz?dl=0) (need to `tar zxf` it).",
"I will add this to the invoke task and add a link to the docs for the always updated copy.",
"@dwinston Thanks! @shyuep I think it's better to push it to [Dash-User-Contributions](https://github.com/Kapeli/Dash-User-Contributions) as a native supported dash documentation at your convenience.",
"I have put the docs on pymatgen.org. See new section on offline docs.\r\n\r\nI am reluctant to do Dash-User-Contributions for now. The problem is that it is an extra step for me to submit there, and I do not really want to take the trouble to satisfy all the requirements, especially given that I do not know how many of pymatgen users actually use Dash instead of just going to pymatgen.org. (I use Dash and think it is great, but it is not something that everyone uses)",
" @shyuep thanks! This will also be great help. What's more I have 2 more suggestions.\r\n- the link of `.tar.gz` can't add as an feed of zeal, I'm wandering if changing to `.tar` will help.\r\n- the context column on left of page seems duplicate with the software, is there anyway, we can export the html without the context column?",
"Just to add that I have already added this to the User Contributed Docsets. You can now directly install it in Dash. The context column is also fixed. ",
"@shyuep Thanks in advance, I'm using it."
] | 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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MDU6SXNzdWUzMjI5NjQ3NDc=
| 1,148
|
add a "weight" attribute to the KPoint class
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[] | 2018-05-14T20:16:43
| 2023-08-08T21:25:30
|
2023-08-08T21:25:30Z
|
MEMBER
|
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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 better if the band structure had the kpoint weights embedded in it. This would be accomplished by:
- Adding a ``weight`` attribute to the ``KPoint`` class
- Parsing and including that weight when grabbing entries from Materials Project via MPRester
|
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| 323,004,738
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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 to fix.",
"Yes, it would be better to just move to python 3. In 2019, we are dropping Python 2 supprot for good in line with the other packages. An alternative is to roll back to earlier versions of pmg (v2017.*) that is compatible with Python 2."
] | 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/__init__.py:87: UserWarning:
Pymatgen will drop Py2k support from v2019.1.1. Pls consult the documentation
at https://www.pymatgen.org for more details.
at https://www.pymatgen.org for more details.""")
Traceback (most recent call last):
File "/Users/protik/pmg/bin/pmg", line 7, in <module>
from pymatgen.cli.pmg import main
File "/Users/protik/pmg/lib/python2.7/site-packages/pymatgen/cli/pmg.py", line 19, in <module>
from pymatgen.cli.pmg_plot import plot
File "/Users/protik/pmg/lib/python2.7/site-packages/pymatgen/cli/pmg_plot.py", line 13, in <module>
from pymatgen.analysis.diffraction.xrd import XRDCalculator
File "/Users/protik/pmg/lib/python2.7/site-packages/pymatgen/analysis/diffraction/xrd.py", line 15, in <module>
from .core import DiffractionPattern, DiffractionPatternCalculator, \
File "/Users/protik/pmg/lib/python2.7/site-packages/pymatgen/analysis/diffraction/core.py", line 50, in <module>
class DiffractionPatternCalculator(abc.ABC):
AttributeError: 'module' object has no attribute 'ABC'
```
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| 323,371,156
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MDExOlB1bGxSZXF1ZXN0MTg4MjQ2MTgw
| 1,150
|
NearNeighbors + StructureGraphs: some bug fixes, convenience methods + tests
|
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[] | null |
[
"(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 analysis.graphs to avoid a circular import.
Added two new NearNeighbor classes:
* Critic2NN -- this uses sum of atomic charge densities (to calculate bonds from Chgcars, you still need to use Critic2Caller directly)
* CutoffDictNN -- a very basic NN I've found useful for testing
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* None
|
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| 324,229,060
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MDExOlB1bGxSZXF1ZXN0MTg4ODkzMzM3
| 1,151
|
scrubbed units
|
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[] | 2018-05-18T00:20:01
| 2019-04-04T02:45:06
|
2018-05-18T01:15:41Z
|
CONTRIBUTOR
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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 have units until a more holistic approach can be implemented. This PR does that and adds a few tests to ensure no unitized floats are returned by the relevant methods.
|
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| 324,485,291
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MDU6SXNzdWUzMjQ0ODUyOTE=
| 1,152
|
Distance method of periodic site objects returns error
|
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[] | null |
[
"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)\r\ngoo.build_graph()\r\n```\r\n\r\nif you're looking to build a graph from a pymatgen struct, we have a `pymatgen.analysis.graphs` module, if you're interested in bonding specifically this is probably most easily accessible by picking a `NearNeighbor` class (e.g. CrystalNN) from `pymatgen.analysis.local_env`, and calling `CrystalNN().get_bonded_structure(struct)` -- you're welcome to drop me an email if this is at all relevant to you."
] | 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
```python
with open("./Ba3Nb5O15_exp.cif") as f:
lines = f.read()
struct = mg.Structure.from_str(lines, fmt='CIF')
foo = struct[0]
print(foo.distance(struct[1]))
```
## Error message
```
TypeError Traceback (most recent call last)
<ipython-input-26-7839243b4b78> in <module>()
4 struct = mg.Structure.from_str(lines, fmt='CIF')
5 foo = struct[0]
----> 6 print(foo.distance(struct[1]))
7 goo = Graph(struct)
8 goo.build_graph()
/home/nicholas/CODE/miniconda3/lib/python3.6/site-packages/pymatgen/core/sites.py in distance(self, other, jimage)
469 distance (float): Distance between the two sites
470 """
--> 471 return self.distance_and_image(other, jimage)[0]
472
473 def __repr__(self):
/home/nicholas/CODE/miniconda3/lib/python3.6/site-packages/pymatgen/core/sites.py in distance_and_image(self, other, jimage)
453 of the other site for which the distance applies.
454 """
--> 455 return self.distance_and_image_from_frac_coords(other._fcoords, jimage)
456
457 def distance(self, other, jimage=None):
/home/nicholas/CODE/miniconda3/lib/python3.6/site-packages/pymatgen/core/sites.py in distance_and_image_from_frac_coords(self, fcoords, jimage)
431 """
432 return self._lattice.get_distance_and_image(self._fcoords, fcoords,
--> 433 jimage=jimage)
434
435 def distance_and_image(self, other, jimage=None):
/home/nicholas/CODE/miniconda3/lib/python3.6/site-packages/pymatgen/core/lattice.py in get_distance_and_image(self, frac_coords1, frac_coords2, jimage)
1097 if jimage is None:
1098 v, d2 = pbc_shortest_vectors(self, frac_coords1, frac_coords2,
-> 1099 return_d2=True)
1100 fc = self.get_fractional_coords(v[0][0]) + frac_coords1 - \
1101 frac_coords2
/home/nicholas/CODE/miniconda3/lib/python3.6/site-packages/pymatgen/util/coord.py in pbc_shortest_vectors(lattice, fcoords1, fcoords2, mask, return_d2)
211 """
212 return cuc.pbc_shortest_vectors(lattice, fcoords1, fcoords2, mask,
--> 213 return_d2)
214
215
coord_cython.pyx in pymatgen.util.coord_cython.pbc_shortest_vectors()
/home/nicholas/CODE/miniconda3/lib/python3.6/site-packages/pymatgen/core/lattice.py in get_lll_frac_coords(self, frac_coords)
720 fractional coordinates in the lll basis.
721 """
--> 722 return np.dot(frac_coords, self.lll_inverse)
723
724 def get_frac_coords_from_lll(self, lll_frac_coords):
/home/nicholas/CODE/miniconda3/lib/python3.6/site-packages/pymatgen/core/lattice.py in lll_inverse(self)
461 return self._lll_inverse
462 else:
--> 463 self._lll_inverse = np.linalg.inv(self.lll_mapping)
464 return self._lll_inverse
465
/home/nicholas/CODE/miniconda3/lib/python3.6/site-packages/pymatgen/core/lattice.py in lll_mapping(self)
453 def lll_mapping(self):
454 if 0.75 not in self._lll_matrix_mappings:
--> 455 self._lll_matrix_mappings[0.75] = self._calculate_lll()
456 return self._lll_matrix_mappings[0.75][1]
457
/home/nicholas/CODE/miniconda3/lib/python3.6/site-packages/pymatgen/core/lattice.py in _calculate_lll(self, delta)
710 p = dot(a[:, k:3].T, b[:, (k - 2):k])
711 q = np.diag(m[(k - 2):k])
--> 712 result = np.linalg.lstsq(q.T, p.T, rcond=None)[0].T
713 u[k:3, (k - 2):k] = result
714
/home/nicholas/CODE/miniconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py in lstsq(a, b, rcond)
1959 work = zeros((lwork,), t)
1960 results = lapack_routine(m, n, n_rhs, a, m, bstar, ldb, s, rcond,
-> 1961 0, work, -1, iwork, 0)
1962 lwork = int(work[0])
1963 work = zeros((lwork,), t)
TypeError: must be real number, not NoneType
```
## Suggested solution (if any)
* This error only started happening after I upgraded from 2018.2.13 to 2018.5.14. Was something changed that broke distance calculation?
## Files (if any)
[CIF File](https://drive.google.com/open?id=1xjZcJMTRNXq_5yYZ5EqXlWNN7Hrr3tHu)
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| 324,652,714
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MDExOlB1bGxSZXF1ZXN0MTg5MjAyMjI0
| 1,153
|
Updates to LAMMPS modules
|
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[] | null |
[
"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.
* Simplified the parser for dump files. Instead of having an extra long list (Natoms * Ntimesteps) for atoms data, all data now is separated for each timestep.
* Fixed coordinate translation in `LammpsData` with non-orthogonal box using `LammpsBox`. The old constructor from a single structure is now `LammpsData.from_structure`. Since this is a high level constructor, this change is the only one that is backward compatible.
## Additional dependencies introduced (if any)
* None
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* The LAMMPS log parser seems buggy in my attempts using it. Should be easy to fix or even rewrite.
* Will look at other building blocks to see if any improvements needed.
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| 325,095,611
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MDU6SXNzdWUzMjUwOTU2MTE=
| 1,154
|
Missing file on pip install: hhi_data.csv
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[] | 2018-05-21T23:50:00
| 2018-05-21T23:55:49
|
2018-05-21T23:55:49Z
|
MEMBER
|
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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
```python
from pymatgen.analysis.hhi.hhi import HHIModel
h = HHIModel()
```
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MDExOlB1bGxSZXF1ZXN0MTg5NTE3NTkz
| 1,155
|
costdb_elements.csv also missing from setup.py
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[] | 2018-05-22T00:05:49
| 2018-05-22T00:06:13
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2018-05-22T00:06:13Z
|
MEMBER
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MDU6SXNzdWUzMjYzNzIwNzY=
| 1,156
|
some bugs found in electronic_structure.boltztrap
|
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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\nand it should be minus \r\nthanks a lot again!"
] | 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 the doping_levels in parse_outputtrans
2. electronic_structure.plotter.BoltztrapPlotter
all the np.sort must be change into sorted
3. electronic_structure.plotter.BoltztrapPlotter.plot_carriers
must be _carrier_conc rather than carrier_conc
## Suggested solution (if any)
1. i dont know how to solve it elegantly, the result from my outputtrans is like below
=================== INPUT VARIABLES ======================
4 Bandstyle: GENE
5 Set fermi: 0
6 Debug: 0
7 FermiE: 0.4639. step size: 0.0005 Ecut: 0.4000. # val. e: 96.000
8 Run type: CALC
9 Fourier expansion factor: 5
10 Calc type: BOLTZ
11 Fermi level range: (Ry) 0.1500
12 Max temperature: (K) 800.0 Temp step: (K) 50.0
13 Range around Ef where bands are given individual output (Ry) -1.0000
14 HISTO used for calculation of DOS
15 10 doping levels will be used
16 Doping levels to be output for, in carriers / cm^3:
17 0.100E+18 0.100E+19 0.100E+20 0.100E+21 0.100E+22-0.100E+18
18 -0.100E+19-0.100E+20-0.100E+21-0.100E+22
=========================================================
2. `2940 tlist = np.sort(cond['n'].keys())`
must to be changed into
`2940 tlist = sorted(cond['n'].keys())`
3. `3417 abs(self._bz.carrier_conc[temp] / (self._bz.vol * 1e-24)),`
must to be changed into
`3417 abs(self._bz._carrier_conc[temp] / (self._bz.vol * 1e-24)),`
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MDExOlB1bGxSZXF1ZXN0MTkwNjU2NzUy
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fix DeformStructureTransformation serialization
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[] | 2018-05-25T17:55:36
| 2018-05-25T18:35:32
|
2018-05-25T18:35:31Z
|
CONTRIBUTOR
|
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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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|
Move Critic2Caller import due to optional dependency / import error
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[] | 2018-05-29T17:36:37
| 2018-05-30T03:56:54
|
2018-05-30T03:56:54Z
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MEMBER
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## Summary
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 graphs of bonds in crystals)
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MDExOlB1bGxSZXF1ZXN0MTkyMjIwNTQ5
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|
removed old examples
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[] | 2018-06-02T22:22:55
| 2019-04-04T02:45:09
|
2018-06-02T23:35:11Z
|
CONTRIBUTOR
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Removes old examples from docs folder. Mainly to avoid confusion about some of the deprecated notebooks which were used to generate these, since they're still present in pymatgen.org/_static/ if someone has the old link.
|
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MDExOlB1bGxSZXF1ZXN0MTkyNTIyMTU0
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Using now copy's deepcopy in local_env instead of shallow copy
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[] | null |
[
"Can we have some tests pls?",
"Sure thing, Shyue Ping.\r\n(Kinda rhymes :-) )."
] | 2018-06-04T20:41:10
| 2018-06-06T14:00:58
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2018-06-06T14:00:58Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MTkyNTYyODg5
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|
Normalize reaction and reaction energy per reaction
|
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[] | 2018-06-05T00:39:16
| 2018-06-05T02:43:35
|
2018-06-05T02:43:35Z
|
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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MDExOlB1bGxSZXF1ZXN0MTkyODMxODc5
| 1,162
|
QChem updates for Atomate
|
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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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## Summary
Lots of polishing, formatting, and small to medium tweaks that were found to be necessary when building QChem functionality into Atomate and testing workflows.
* All parsed files are accessed with zopen to avoid issues with gzipped files. This precipitated compatibility issues with python 2.7 that were then resolved.
* Outputs parses walltime and cpu time and has an as_dict method.
* Inputs now makes sure all dictionary keys and values are lowercase and unique to avoid the same key being set to multiple different values due to differences in key capitalization.
* Small changes in default DFT parameters.
* Tests updated and improved throughout.
We would greatly appreciate if this could be merged as soon as possible and that a new version could be released immediately afterwards so that we can do a pull request for Atomate before Codebusters tomorrow. Thank you!
|
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MDExOlB1bGxSZXF1ZXN0MTkzMTAzOTc5
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Fix nelect implementation for disordered structures and fix a few basic bugs in vasp sets
|
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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, subclassing VaspInputSet is a better approach. In pycdt,\nDefectRelaxSet specifically addresses this situation.\n\n\n\nOn Thu, Jun 7, 2018 at 2:58 PM Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> *@shyuep* commented on this pull request.\n> ------------------------------\n>\n> In pymatgen/io/vasp/sets.py\n> <https://github.com/materialsproject/pymatgen/pull/1163#discussion_r193901345>\n> :\n>\n> > @@ -364,7 +364,7 @@ def incar(self):\n> incar['NUPDOWN'] = nupdown\n>\n> if self.structure._charge:\n>\n> I think we have to be careful about use cases here. Generally people\n> expect neutral vasp inputs - setting a charge is actually a very deliberate\n> thing that you want to do for special situations. That is why the\n> VaspInputSets ignore anything set in Structure - there is no guanrantee\n> someone will have an oxidation state decorated structure and in most\n> instances, I would assume people are supplying something they expect to be\n> neutral. Instead of trying to shoehorn this into the Structure object, I\n> think it is better to allow VaspInputSets to take in a net_structure_charge\n> which will be used to set nelect. Then remove the charge parameter for\n> structure.\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1163#discussion_r193901345>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AD2qkEi3ax7tPHddQyTUy8CJOQrDqxv1ks5t6aIGgaJpZM4UdKXH>\n> .\n>\n",
"All suggested changes have been made to the pull request and everything should be in order for merging. ",
"thanks\r\n"
] | 2018-06-06T18:39:55
| 2018-06-27T21:43:37
|
2018-06-27T21:43:35Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MTkzMTc0NzYx
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set nkpoints to the actual length of kpoint list
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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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## Summary
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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Improved StructureMotifInterstitial class
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[] | 2018-06-07T20:51:59
| 2018-06-07T21:50:45
|
2018-06-07T21:50:44Z
|
CONTRIBUTOR
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1) Runs faster (e.g., finds tetrahedral site in Si 4-5 times faster now than before).
2) More flexible (all motifs with specific order parameters can now be searched).
|
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| 330,713,565
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MDExOlB1bGxSZXF1ZXN0MTkzNjU2NDM0
| 1,166
|
Update MPRester tests in preparation of new MP DB release
|
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[] | 2018-06-08T15:55:15
| 2018-06-11T15:41:32
|
2018-06-11T15:41:32Z
|
MEMBER
|
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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 as a subset, as entry now matches more known ICSD IDs.
## TODO
It is expected that this PR will **not** test successfully until the new MP DB is released. I will update this PR when tests should re-run and this PR merged.
|
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MDU6SXNzdWUzMzA4MTk5NzY=
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|
support querying anonymous formula by string in addition to dict, e.g. "AB2C4"
|
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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 pymatgen import MPRester\r\n\r\nmpr = MPRester()\r\nmpr.query({\"formula_anonymous\": \"AB2C4\"}, [\"material_id\", \"pretty_formula\"])[:5]\r\n```\r\nOutput:\r\n> [{'material_id': 'mp-764906', 'pretty_formula': 'LiV2O4'},\r\n {'material_id': 'mp-675252', 'pretty_formula': 'Yb2MnS4'},\r\n {'material_id': 'mp-974038', 'pretty_formula': 'Ni2W4C'},\r\n {'material_id': 'mp-675143', 'pretty_formula': 'Eu(GdS2)2'},\r\n {'material_id': 'mp-7831', 'pretty_formula': 'MgIn2O4'}]\r\n"
] | 2018-06-08T22:24:49
| 2018-06-19T13:55:22
|
2018-06-19T13:55:22Z
|
NONE
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feature suggestion
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MDExOlB1bGxSZXF1ZXN0MTkzODAxNzMy
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|
Minor changes needed to support Abinit 8.8.2
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[] | 2018-06-10T00:02:04
| 2018-06-11T15:41:18
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2018-06-11T15:41:18Z
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CONTRIBUTOR
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MDU6SXNzdWUzMzA5NDExNjk=
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Extremely slow MinimumVIRENN analysis
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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 to ask @nisse3000 as I think it’s his algorithm",
"Hello @arosen93,\r\n\r\nI've had a look into the problem by using a pre-2018-04-20 version of pymatgen. What it made much faster was that the valences of all sites were predicted to be zero so that the ValenceIonicRadiusEvaluator didn't bother to use interpolated ionic radii based on the O'Keeffe data. It just set the radii to atomic radii to deal with this issue. The valences that I see now make mostly sense. Only, the one for H seems very weird to me.\r\nC 1\r\nC 2\r\nH -1\r\nMg 2\r\nO -2\r\n\r\nBut I guess the bottom line regarding the slow down is: the algorithm now does (much more) what you expect it to do. Maybe we should make it optional to use atomic radii instead of (interpolated) ionic radii to deal with zero valences in all sites. What's your take on this as a user?",
"Hi @nisse3000,\r\n\r\nOh, wow. Yes that change does make it do much more what I thought it did based on your order parameters paper. I didn't know it was pulling the atomic radii. And yes, those valences all seem appropriate except H like you said.\r\n\r\nAs a user, I think your suggestion is a good one. The current speed of the VIRENN algorithm makes it infeasible to use on a large database of materials (which, of course, is where automated approaches become essential). I think giving the user an option to use atomic radii, while not necessarily desirable compared to interpolated ionic radii, would be very helpful. Thanks for taking a look at this.",
"I would suggest to separate out the process of getting valences and getting radii\r\n\r\nThere are a few ways to get valence in pymatgen, including the quite fast \"get_oxi_state_by_guess\" method. In addition, sometimes a user might already know the valence from some other means (e.g., from ICSD valence assignments). Rather than re-determining the valences with BVAnalyzer, you should be able to just use those valences you already have from some other means in order to use it. It would only be a couple lines of code to either (i) only evaluate the valences if not already set by some other means (e.g, if the sites in the strucutre don't already have oxidation states) or (ii) simply require the user to put in a structure with valence states in there (e.g., by pre-processing with BVAnalyzer, get_oxi_state_by_guess, or some other means) in order to get the radii.\r\n\r\nIncidentally, we have been been doing a lot of tests of near neighbor algorithms and the new CrystalNN method we are developing seems to be doing considerably better than others, at least for typical metals / inorganic materials.",
"Also, I am looking at VIRENN code now and am surprised there is a 10 Angstrom search radius for looking for neighbors. I've found that such large search radii can take time to compute. \r\n\r\nIf I understand the algorithm correctly, you just care about neighbors within your atomic/ionic radius plus tolerance (usually will be on the order of 3-5 Angstroms). So you could just search for neighbors within that range instead of a 10 Angstrom radius which will speed things up a lot",
"Thanks @computron. I think as a user (and given the name of the VIRE algorithm) I just assumed that pymatgen was somehow estimating the oxidation states if not provided but see now that it defaults to atomic radii instead. At the least, I think it'd be helpful to make that clearer in whatever way is most appropriate. And I look forward to checking out CrystalNN! Looks very interesting.",
"Nevermind - the above about 10 Angstrom radius is not correct. But I do think you could start the algorithm which a much smaller radius (e.g. 7-8 Angstrom) and only increase it larger if necessary (automatically). For example, the code can increase the radius if no neighbors are found, or if the code (after finding the nearest neighbor) detects there is a chance for some ion to be greater than 7 Angstroms from the center and still fulfill the criteria of being a neighbor.",
"The main problem with VIRE right now is that BVAnalyzer is re-run for every site, which is very inefficient. This is a common problem with a lot of the NN classes. The [`_get_valences()`](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/local_env.py#L188) function is also not ideal because it has two nested try/excepts ... better would be to use AutoOxiStateTransformation (and making modifications to that if appropriate) than re-implementing this functionality in a private method in local_env\r\n * I agree with @computron that this behavior is ideally separated out (i.e. at the very least, if oxidation states are already present BVAnalyzer *should not* be run, and it would be good to be able to choose the oxidation-state decoration algorithm; again this could be added to AutoOxiStateTransformation)\r\n * I think `ValenceIonicRadiusEvaluator` should probably not be its own class anyway, and should be wrapped into the `MinimumVIRENN` class (it'll be a lot shorter/simpler if the transformation is used)\r\n\r\n@arosen93 \" I just assumed that pymatgen was somehow estimating the oxidation states if not provided but see now that it defaults to atomic radii instead. \" -- yes, pymatgen is actually estimating oxidation states and using ionic radii based on that. I do think it's doing something weird if it doesn't know the oxidation state however, incorporating co-ordination numbers from VoronoiNN. @nisse3000 can you comment on this? Was this in the VIRE paper?",
"Closing since this was partly addressed in https://github.com/materialsproject/pymatgen/pull/1630 (Oct 2019, thanks @utf), still slow, but not as slow! Happy to re-open if this continues to be a practical issue."
] | 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 caused it to be orders of magnitude slower and has not been fixed in the current 2018.5.22 release. Compared to `VoronoiNN`, the current implementation of `MinimumVIRENN` can be 100x slower or more.
## Example code
```python
from pymatgen.io.cif import CifParser
from pymatgen.analysis.local_env import MinimumVIRENN, VoronoiNN
import time
site_idx = 0
parser = CifParser('test.cif')
structure = parser.get_structures()[0]
t0 = time.time()
nn_object = MinimumVIRENN()
neighbors = nn_object.get_nn_info(structure,site_idx)
t1 = time.time()-t0
print('VIRE: '+str(t1))
t0 = time.time()
nn_object = VoronoiNN()
neighbors = nn_object.get_nn_info(structure,site_idx)
t2 = time.time()-t0
print('Voronoi: '+str(t2))
```
Results:
VIRE: 4.755153179168701
Voronoi: 0.028443098068237305
## Files (if any)
Please see attached for the `test.cif` file used in this example. Change the .txt extension to .cif before use.
[test.txt](https://github.com/materialsproject/pymatgen/files/2087561/test.txt)
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| 331,018,635
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MDU6SXNzdWUzMzEwMTg2MzU=
| 1,170
|
a typo in lattice.py: *a* lattice parameter.ATATClusterExpansion
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[] | 2018-06-11T01:07:37
| 2018-06-11T15:49:46
|
2018-06-11T15:49:46Z
|
NONE
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## System
* 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
```
@property
def a(self):
"""
*a* lattice parameter.ATATClusterExpansion
"""
return self._lengths[0]
@property
def b(self):
"""
*b* lattice parameter.
"""
return self._lengths[1]
```
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MDExOlB1bGxSZXF1ZXN0MTk0MTg5MzI5
| 1,171
|
Update plotter.py to remove matplotlib warning
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[] | 2018-06-12T07:30:28
| 2018-06-13T19:45:29
|
2018-06-13T19:45:29Z
|
CONTRIBUTOR
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remove warning "Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies the same functionality instead."
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MDU6SXNzdWUzMzE0NzQ1MTQ=
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GLIBC error when import pymatgen
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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), or [weaken the version dependencies](http://www.lightofdawn.org/wiki/wiki.cgi/NewAppsOnOldGlibc) so that pymatgen can work with the old libc-2.12.so. \r\n\r\nI hope this may help you.",
"Hi\r\nI am not the admin. We installed anaconda in our local cluster and I got that erreur after installing pymatgen.\r\nI tried to install pymatgen using pip but I got the same error with GLIBC.\r\nHow can I weaken the dependencies ?\r\nThanks",
"@gVallverdu \r\nHi again,\r\n\r\nJust a kind reminder: before executing pip install, did you use 'conda uninstall pymatgen‘? This is quite important. I found GLIBC error still exists if I don't use 'conda uninstall pymatgen'.\r\n\r\nAs for the method of 'weaken the version dependencies', actually I have provided the link in last reply, please see http://www.lightofdawn.org/wiki/wiki.cgi/NewAppsOnOldGlibc\r\n\r\nI know one of my friends used the workaround described in the abovewebpage to remove the GLIBC error. However, I didn't try it by myself, hence I cannot provide you more information here.\r\n\r\nBests\r\nFang",
"Hello\r\nYes, I did first remove pymatgen. But I wonder if the glibc error comes from pymatgen or its dependencies because pip installs only pymatgen (I guess the dependencies were installed with conda previously).\r\n\r\nI will follow the trick of your link. Thanks\r\n\r\n```\r\ngvallver@pyrene <~>\r\n--> conda uninstall pymatgen\r\nSolving environment: failed\r\n\r\nPackagesNotFoundError: The following packages are missing from the target environment:\r\n - pymatgen\r\n\r\n\r\n\r\ngvallver@pyrene <~>\r\n--> pip install pymatgen\r\nCollecting pymatgen\r\nRequirement already satisfied: numpy>=1.14.3 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pymatgen)\r\nRequirement already satisfied: tabulate in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/tabulate-0.8.2-py3.6.egg (from pymatgen)\r\nRequirement already satisfied: scipy>=1.0.1 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pymatgen)\r\nRequirement already satisfied: ruamel.yaml>=0.15.6 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pymatgen)\r\nRequirement already satisfied: palettable>=2.1.1 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/palettable-3.1.0-py3.6.egg (from pymatgen)\r\nRequirement already satisfied: pandas in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pymatgen)\r\nRequirement already satisfied: requests in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pymatgen)\r\nRequirement already satisfied: pydispatcher>=2.0.5 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/PyDispatcher-2.0.5-py3.6.egg (from pymatgen)\r\nRequirement already satisfied: sympy in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pymatgen)\r\nRequirement already satisfied: six in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pymatgen)\r\nRequirement already satisfied: matplotlib>=1.5 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pymatgen)\r\nRequirement already satisfied: spglib>=1.9.9.44 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pymatgen)\r\nRequirement already satisfied: monty>=0.9.6 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pymatgen)\r\nRequirement already satisfied: python-dateutil>=2 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pandas->pymatgen)\r\nRequirement already satisfied: pytz>=2011k in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from pandas->pymatgen)\r\nRequirement already satisfied: chardet<3.1.0,>=3.0.2 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from requests->pymatgen)\r\nRequirement already satisfied: idna<2.7,>=2.5 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from requests->pymatgen)\r\nRequirement already satisfied: urllib3<1.23,>=1.21.1 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from requests->pymatgen)\r\nRequirement already satisfied: certifi>=2017.4.17 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from requests->pymatgen)\r\nRequirement already satisfied: cycler>=0.10 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from matplotlib>=1.5->pymatgen)\r\nRequirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages (from matplotlib>=1.5->pymatgen)\r\nInstalling collected packages: pymatgen\r\nSuccessfully installed pymatgen-2018.6.27\r\nYou are using pip version 9.0.1, however version 10.0.1 is available.\r\nYou should consider upgrading via the 'pip install --upgrade pip' command.\r\n\r\ngvallver@pyrene <~>\r\n--> python\r\nPython 3.6.4 |Anaconda custom (64-bit)| (default, Jan 16 2018, 18:10:19) \r\n[GCC 7.2.0] on linux\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> import pymatgen\r\nTraceback (most recent call last):\r\n File \"<stdin>\", line 1, in <module>\r\n File \"/opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/pymatgen/__init__.py\", line 56, in <module>\r\n from .ext.matproj import MPRester\r\n File \"/opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/pymatgen/ext/matproj.py\", line 27, in <module>\r\n from pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\n File \"/opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/pymatgen/symmetry/analyzer.py\", line 19, in <module>\r\n import spglib\r\n File \"/opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/spglib/__init__.py\", line 35, in <module>\r\n from .spglib import (get_version,\r\n File \"/opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/spglib/spglib.py\", line 35, in <module>\r\n from . import _spglib as spg\r\nImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/spglib/_spglib.cpython-36m-x86_64-linux-gnu.so)\r\n>>> \r\n\r\n```",
"Hi, Germain, could you try '**pip install --user pymatgen**' as mentioned in my first response? Adding '--user' is used for installing pymatgen in the home directory without requiring any special privileges. \r\n\r\nIn addition, you can use this command to find the information of dependency:\r\n\r\n> readelf -s /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/spglib/_spglib.cpython-36m-x86_64-linux-gnu.so|grep GLIBC_2.14\r\n\r\nYou will find some information like this:\r\n\r\n88: 0000000000000000 0 FUNC GLOBAL DEFAULT UND memcpy@GLIBC_2.14 (4)\r\n801: 0000000000000000 0 FUNC GLOBAL DEFAULT UND memcpy@@GLIBC_2.14\r\n\r\nFurthermore, you can run the following command to print more information about the address of GLIBC_2.14:\r\n\r\n> readelf -V /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/spglib/_spglib.cpython-36m-x86_64-linux-gnu.so\r\n",
"Just compile glibc 2.14 yourself in your home directory and add the compiled lib to your LD_LIBRARY_PATH. See:\r\nhttps://stackoverflow.com/questions/35616650/how-to-upgrade-glibc-from-version-2-12-to-2-14-on-centos\r\n\r\nPymatgen will then work with Python 3.x. \r\n\r\nWarning: I found that Anaconda's conda executable crashes with Segmentation Fault error this way. To circumvent it, just reset your LD_LIBRARY_PATH to use the system default Glibc when you want to use conda (e.g., to update your package).",
"hey, I had this error on our cluster and solved it by installing an earlier version of `spglib`. The first way I found to fix it was to just use pip to install `pymatgen` then downgrade the version of `spglib`. Commands below:\r\n\r\n`pip install pymatgen; pip install spglib==1.9.8`",
"Closing this as outdated."
] | 2018-06-12T07:47:16
| 2023-06-18T17:50:31
|
2023-06-18T17:50:31Z
|
CONTRIBUTOR
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Hello
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 version: Scientific Linux release 6.9 (Carbon) x86_64
## Example code
```
Python 3.6.4 |Anaconda custom (64-bit)| (default, Jan 16 2018, 18:10:19)
[GCC 7.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pymatgen as mg
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/pymatgen/__init__.py", line 54, in <module>
from pymatgen.core import *
File "/opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/pymatgen/core/__init__.py", line 9, in <module>
from .structure import Structure, IStructure, Molecule, IMolecule
File "/opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/pymatgen/core/structure.py", line 30, in <module>
from pymatgen.core.lattice import Lattice
File "/opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/pymatgen/core/lattice.py", line 16, in <module>
from pymatgen.util.coord import pbc_shortest_vectors
File "/opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/pymatgen/util/coord.py", line 11, in <module>
from . import coord_cython as cuc
ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /opt/cluster/contrib/apps/anaconda/3/lib/python3.6/site-packages/pymatgen/util/coord_cython.cpython-36m-x86_64-linux-gnu.so)
>>>
```
Looking at `/lib64/libc.so.6` it is a sym link to `libc-2.12.so`. Thus I guess the lib version is too old ?
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MDExOlB1bGxSZXF1ZXN0MTk0MzkxMjUw
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Fixed issue in solid_angles function to deal with co-planar configurations (i.e., where denominator become zero).
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[] | 2018-06-12T20:00:26
| 2018-06-13T14:17:39
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2018-06-13T14:17:39Z
|
CONTRIBUTOR
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Also added a corresponding unit test and checked that it fails if I revert to previous version. @WardLT should double-check.
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Added MoleculeGraph class for representing bonds in molecules
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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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## Summary
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 manipulation, such as:
* Altering edges (bonds)
* Breaking edges (bonds)
* Detecting ring structures
* Splitting a molecule into components based on arbitrary alterations and deletions to the graph
* Auto-populating the graph after a substitution with a FunctionalGroup or Molecule
Anubhav Jain should review before this pull request is accepted.
## Additional dependencies introduced (if any)
* None
## TODO (if any)
More work could be done to effectively represent the MoleculeGraph (current drawing function is essentially copied from StructureGraph).
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Add in some additional Parsing logic for DFPT into Outcar
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[] | 2018-06-13T23:57:14
| 2018-06-28T15:53:32
|
2018-06-14T02:28:26Z
|
NONE
|
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## Summary
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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MDExOlB1bGxSZXF1ZXN0MTk0OTc4NDM2
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adding pymatgen to DoeCode
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[] | 2018-06-14T18:23:50
| 2018-08-10T11:11:58
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2018-06-14T18:30:33Z
|
MEMBER
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see FAQ's at https://www.osti.gov/doecode/faq
metadata can be updated as needed
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Interface
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[] | 2018-06-18T19:38:18
| 2018-06-23T01:44:38
|
2018-06-23T01:44:38Z
|
CONTRIBUTOR
|
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## Summary
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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MDExOlB1bGxSZXF1ZXN0MTk1OTkwOTI1
| 1,178
|
Fixed Charge/ Magnetization Parsing
|
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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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## Summary
* 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.
Example of this issue can be found by trying to create an Outcar object with the following file: [OUTCAR.gz](https://github.com/materialsproject/pymatgen/files/2117308/OUTCAR.gz)
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* None
|
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|
Pymatgen produces structure with duplicated atoms from CIF file
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[] | null |
[
"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+y, z'\r\n3 '-x, -y, z+1/2'\r\n4 '-x+y, -x, z+1/3'\r\n5 '-y, x-y, z+2/3'\r\n6 'x, y, z'\r\n```\r\n\r\nwhile I think it should read \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+5/6'\r\n2 'y, -x+y, z+1/6'\r\n3 '-x, -y, z+1/2'\r\n4 '-x+y, -x, z+1/3'\r\n5 '-y, x-y, z+2/3'\r\n6 'x, y, z'\r\n```\r\n\r\nIf you make this change, you no longer get duplicated atomic positions in the output.",
"Thank you Matthew,\r\n\r\nI will have a look at this. I did find it odd that there would be duplicate atoms if all I do is read the CIF file. However, if the CIF file incorrectly describes the symmetry equivalent positions then I suppose anything can happen.\r\n\r\nThank you very much,\r\n\r\n Huub\r\n\r\n-----------------------------------------------------------------------------------------------------\r\nHubertus van Dam, 631-344-6020, hvandam@bnl.gov\r\nBrookhaven National Laboratory\r\n\r\nFrom: Matthew Horton <notifications@github.com>\r\nReply-To: materialsproject/pymatgen <reply@reply.github.com>\r\nDate: Monday, June 25, 2018 at 10:56 PM\r\nTo: materialsproject/pymatgen <pymatgen@noreply.github.com>\r\nCc: \"Van Dam, Hubertus\" <hvandam@bnl.gov>, Author <author@noreply.github.com>\r\nSubject: Re: [materialsproject/pymatgen] Pymatgen produces structure with duplicated atoms from CIF file (#1179)\r\n\r\n\r\nI'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\nloop_\r\n\r\n_symmetry_equiv_pos_site_id\r\n\r\n_symmetry_equiv_pos_as_xyz\r\n\r\n1 'x-y, x, z'\r\n\r\n2 'y, -x+y, z'\r\n\r\n3 '-x, -y, z+1/2'\r\n\r\n4 '-x+y, -x, z+1/3'\r\n\r\n5 '-y, x-y, z+2/3'\r\n\r\n6 'x, y, z'\r\n\r\nwhile I think it should read\r\n\r\nloop_\r\n\r\n_symmetry_equiv_pos_site_id\r\n\r\n_symmetry_equiv_pos_as_xyz\r\n\r\n1 'x-y, x, z+5/6'\r\n\r\n2 'y, -x+y, z+1/6'\r\n\r\n3 '-x, -y, z+1/2'\r\n\r\n4 '-x+y, -x, z+1/3'\r\n\r\n5 '-y, x-y, z+2/3'\r\n\r\n6 'x, y, z'\r\n\r\nIf you make this change, you no longer get duplicated atomic positions in the output.\r\n\r\n—\r\nYou are receiving this because you authored the thread.\r\nReply to this email directly, view it on GitHub<https://github.com/materialsproject/pymatgen/issues/1179#issuecomment-400161602>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AEcvnpNpA93iluER8TsSSC6OMmfjZMSdks5uAaK1gaJpZM4Uvz37>.\r\n",
"Matthew,\r\n\r\nThank you for looking into this. I have reported your findings to ICSD and they have confirmed that there is an error in their CIF:\r\n\r\nYou are right. That is an mistake in ICSD. Somehow the translational part for two symmetries is missing. The suggestions of your colleague is correct. We will have to check, where the translational part got lost and correct this. For your case you can just add the two translational parts (+1/6 and +5/6 in the cif file and it will work correctly).\r\n\r\nI am sorry for the inconvenience.\r\n\r\nBest regards,\r\n\r\nStephan Rühl\r\n\r\nAnd as you can see they are looking to fix this problem (“your colleague” means you, as I did credit you by name for this discovery as I really didn’t do anything). I thought, you’d might like to know that your contribution is helping drive some changes.\r\n\r\nBest wishes,\r\n\r\n Huub\r\n\r\n-----------------------------------------------------------------------------------------------------\r\nHubertus van Dam, 631-344-6020, hvandam@bnl.gov\r\nBrookhaven National Laboratory\r\n\r\nFrom: Matthew Horton <notifications@github.com>\r\nReply-To: materialsproject/pymatgen <reply@reply.github.com>\r\nDate: Monday, June 25, 2018 at 10:56 PM\r\nTo: materialsproject/pymatgen <pymatgen@noreply.github.com>\r\nCc: \"Van Dam, Hubertus\" <hvandam@bnl.gov>, Author <author@noreply.github.com>\r\nSubject: Re: [materialsproject/pymatgen] Pymatgen produces structure with duplicated atoms from CIF file (#1179)\r\n\r\n\r\nI'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\nloop_\r\n\r\n_symmetry_equiv_pos_site_id\r\n\r\n_symmetry_equiv_pos_as_xyz\r\n\r\n1 'x-y, x, z'\r\n\r\n2 'y, -x+y, z'\r\n\r\n3 '-x, -y, z+1/2'\r\n\r\n4 '-x+y, -x, z+1/3'\r\n\r\n5 '-y, x-y, z+2/3'\r\n\r\n6 'x, y, z'\r\n\r\nwhile I think it should read\r\n\r\nloop_\r\n\r\n_symmetry_equiv_pos_site_id\r\n\r\n_symmetry_equiv_pos_as_xyz\r\n\r\n1 'x-y, x, z+5/6'\r\n\r\n2 'y, -x+y, z+1/6'\r\n\r\n3 '-x, -y, z+1/2'\r\n\r\n4 '-x+y, -x, z+1/3'\r\n\r\n5 '-y, x-y, z+2/3'\r\n\r\n6 'x, y, z'\r\n\r\nIf you make this change, you no longer get duplicated atomic positions in the output.\r\n\r\n—\r\nYou are receiving this because you authored the thread.\r\nReply to this email directly, view it on GitHub<https://github.com/materialsproject/pymatgen/issues/1179#issuecomment-400161602>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AEcvnpNpA93iluER8TsSSC6OMmfjZMSdks5uAaK1gaJpZM4Uvz37>.\r\n",
"Happy to hear this got resolved :)\n\nOn Wed, Jun 27, 2018 at 14:35, Hubertus van Dam <notifications@github.com>\nwrote:\n\n> Matthew,\n>\n> Thank you for looking into this. I have reported your findings to ICSD and\n> they have confirmed that there is an error in their CIF:\n>\n> You are right. That is an mistake in ICSD. Somehow the translational part\n> for two symmetries is missing. The suggestions of your colleague is\n> correct. We will have to check, where the translational part got lost and\n> correct this. For your case you can just add the two translational parts\n> (+1/6 and +5/6 in the cif file and it will work correctly).\n>\n> I am sorry for the inconvenience.\n>\n> Best regards,\n>\n> Stephan Rühl\n>\n> And as you can see they are looking to fix this problem (“your colleague”\n> means you, as I did credit you by name for this discovery as I really\n> didn’t do anything). I thought, you’d might like to know that your\n> contribution is helping drive some changes.\n>\n> Best wishes,\n>\n> Huub\n>\n> -----------------------------------------------------------------------------------------------------\n>\n> Hubertus van Dam, 631-344-6020, hvandam@bnl.gov\n> Brookhaven National Laboratory\n>\n> From: Matthew Horton <notifications@github.com>\n> Reply-To: materialsproject/pymatgen <reply@reply.github.com>\n> Date: Monday, June 25, 2018 at 10:56 PM\n> To: materialsproject/pymatgen <pymatgen@noreply.github.com>\n> Cc: \"Van Dam, Hubertus\" <hvandam@bnl.gov>, Author <\n> author@noreply.github.com>\n> Subject: Re: [materialsproject/pymatgen] Pymatgen produces structure with\n> duplicated atoms from CIF file (#1179)\n>\n>\n> I'm not sure if it's related to your problem, but the crystal doesn't look\n> quite right to me... the symmetry operations in the CIF file reads:\n>\n> loop_\n>\n> _symmetry_equiv_pos_site_id\n>\n> _symmetry_equiv_pos_as_xyz\n>\n> 1 'x-y, x, z'\n>\n> 2 'y, -x+y, z'\n>\n> 3 '-x, -y, z+1/2'\n>\n> 4 '-x+y, -x, z+1/3'\n>\n> 5 '-y, x-y, z+2/3'\n>\n> 6 'x, y, z'\n>\n> while I think it should read\n>\n> loop_\n>\n> _symmetry_equiv_pos_site_id\n>\n> _symmetry_equiv_pos_as_xyz\n>\n> 1 'x-y, x, z+5/6'\n>\n> 2 'y, -x+y, z+1/6'\n>\n> 3 '-x, -y, z+1/2'\n>\n> 4 '-x+y, -x, z+1/3'\n>\n> 5 '-y, x-y, z+2/3'\n>\n> 6 'x, y, z'\n>\n> If you make this change, you no longer get duplicated atomic positions in\n> the output.\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub<\n> https://github.com/materialsproject/pymatgen/issues/1179#issuecomment-400161602>,\n> or mute the thread<\n> https://github.com/notifications/unsubscribe-auth/AEcvnpNpA93iluER8TsSSC6OMmfjZMSdks5uAaK1gaJpZM4Uvz37>.\n>\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1179#issuecomment-400836761>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AC1rRI9aJ9FL8b80kU60N-JGwR0AgzLhks5uA_qkgaJpZM4Uvz37>\n> .\n>\n",
"A slightly different issue led me to this page. Sometimes, CIF files will have duplicate atoms especially if you open it in VESTA and convert it to .vasp file or POSCAR file. This is likely due to VESTA reading the file in P1 symmetry always. If you want to remove these duplicate/overlapping atoms from the structure, here's the code: \n`from pymatgen.core.structure import Structure`\n`structure = Structure.from_file(r'path/to/POSCAR')`\n`structure = structure.merge_sites(mode='delete')`\n`structure = structure.sort()`\n`structure.to(filename='your_file_name', fmt='cif')`\n\nNote, this is not the same as removing disorder. But it's a good place to start. "
] | 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 switching to Python 3.6.5 (with Python 2.7 I did not see this problem)
* The CIF-file, a small Python script demonstrating the problem, and the output I get are attached in
[pymatgen_in2se3_test.zip](https://github.com/materialsproject/pymatgen/files/2120649/pymatgen_in2se3_test.zip)
## Potential solution
I am perfectly happy if pymatgen detects and removes duplicated atoms before returning the structure to me.
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MDExOlB1bGxSZXF1ZXN0MTk2MzExNjMx
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Updated parameter that throws NoneType error when checking if structure is valid
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[] | 2018-06-21T01:12:36
| 2018-06-23T01:43:45
|
2018-06-23T01:43:45Z
|
CONTRIBUTOR
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## Summary
* 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)]
File "/home/sivonxay/.conda-envs/cms/code/pymatgen/pymatgen/core/structure.py", line 663, in distance_matrix
self.frac_coords)
File "/home/sivonxay/.conda-envs/cms/code/pymatgen/pymatgen/core/lattice.py", line 1057, in get_all_distances
v, d2 = pbc_shortest_vectors(self, fcoords1, fcoords2, return_d2=True)
File "/home/sivonxay/.conda-envs/cms/code/pymatgen/pymatgen/util/coord.py", line 213, in pbc_shortest_vectors
return_d2)
File "coord_cython.pyx", line 96, in pymatgen.util.coord_cython.pbc_shortest_vectors
File "/home/sivonxay/.conda-envs/cms/code/pymatgen/pymatgen/core/lattice.py", line 721, in get_lll_frac_coords
return np.dot(frac_coords, self.lll_inverse)
File "/home/sivonxay/.conda-envs/cms/code/pymatgen/pymatgen/core/lattice.py", line 462, in lll_inverse
self._lll_inverse = np.linalg.inv(self.lll_mapping)
File "/home/sivonxay/.conda-envs/cms/code/pymatgen/pymatgen/core/lattice.py", line 454, in lll_mapping
self._lll_matrix_mappings[0.75] = self._calculate_lll()
File "/home/sivonxay/.conda-envs/cms/code/pymatgen/pymatgen/core/lattice.py", line 711, in _calculate_lll
result = np.linalg.lstsq(q.T, p.T, rcond=None)[0].T
File "/home/sivonxay/.conda-envs/cms/lib/python3.6/site-packages/numpy/linalg/linalg.py", line 1953, in lstsq
0, work, -1, iwork, 0)
TypeError: must be real number, not NoneType
## Additional dependencies introduced (if any)
## TODO (if any)
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MDExOlB1bGxSZXF1ZXN0MTk2NDc4NDM4
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Faster Voronoi Tessellations
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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 realized that VoronoiNNFiltered is unnecessary as the functionality for filtering neighbors is already built into the base VoronoiNN class. \r\n\r\nI'm going to make a few changes to address that.",
"Ok, got that taken care of. If the test passes, I think this is ready for review.",
"Actually, I found another bug when running this on a larger dataset. Numerical issues with `_get_image`. Sorry, I should have run this on a large dataset first.",
"This PR is ready for review again, if the error in Travis is indeed unrelated. \r\n\r\nIn case it's relevant, the problem on the large dataset had to do with issues resolving the supercell image of atoms with fractional coordinates near 0 or 1. I avoided this problem by altering `Structure.get_all_neighbors` to return the supercell index used to generate each neighbor - bypassing the need to re-compute the supercell image. So, the issue listed in #1103 remains unfixed.\r\n\r\nAnother outstanding issue is that `get_all_neighbors` can return the supercell image, but `get_neighbors` cannot. Should I add a \"feature request\" Issue to make both operations have the same functionality?",
"I will merge. For get_neighbors, just implement it."
] | 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))` (`N` being the number of atoms), this method is faster for larger simulation cells.
The chart below shows the performance of this new code on a series of simple cubic supercells. The cross-over point in performance is at ~2 atoms/cell. So, my revised implementation of `get_all_nn_info` only uses the "compute all at once" method for cells with > 2 atom.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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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
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CONTRIBUTOR
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Pertains to Issue #1085.
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MDExOlB1bGxSZXF1ZXN0MTk2ODAwNTM5
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|
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 search
* make3d, add_hydrogen
* from_molecule_graph
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|
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.
## Additional dependencies introduced (if any)
None
## TODO (if any)
~~Need to add the image outputs to neighbor finding routines in Structure. I'll be working on those shortly, but wanted to open a PR to run unit tests because changing Lattice touches many parts of pymatgen.~~
|
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Add weaker equivalence test and node attributes to MoleculeGraph; add OpenBabel-based local environment strategy
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[] | 2018-06-26T16:33:58
| 2018-06-27T21:41:56
|
2018-06-27T21:41:56Z
|
CONTRIBUTOR
|
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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 through the molecule).
* Created class OpenBabelNN
* Added MoleculeGraph.equivalent_to
* Added MoleculeGraph.set_node_attributes, based on work done by Sam Blau and John Dagdelen.
## Additional dependencies introduced (if any)
None.
## TODO (if any)
Perform further testing on equivalent_to, and potentially expand support for dual weight/order storage in MoleculeGraph.
|
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add method get_critical_original_kink_ratio to interface_reactions module
|
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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 get_critical_original_kink_ratio to interface_reactions module, and the test of the function.
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| 337,117,255
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MDExOlB1bGxSZXF1ZXN0MTk4NDA4NzA0
| 1,187
|
Fractional NELECT
|
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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\nI can change the test so it uses a non-fractional pseudopotential but still runs the relevant code.\r\n"
] | 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_fractional_nelect', which defaults to False, to the DictSet class.
I added relevant code to MITMPRelaxSetTest.test_nelect for code coverage.
## Additional dependencies introduced (if any)
None.
## TODO (if any)
None.
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MDExOlB1bGxSZXF1ZXN0MTk4NTQ3MDg1
| 1,188
|
Allow fractional NELECT
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[] | 2018-07-01T22:49:52
| 2019-01-13T18:51:56
|
2018-07-02T16:35:16Z
|
CONTRIBUTOR
|
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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 dependencies introduced (if any)
None
## TODO (if any)
- Possibly add a flag to turn this on/off
- An alternative would be to add some code which checks if nelect is close to an integer value before rounding: `if abs(round(nelect) - nelect) < 0.001: nelect = int(round(nelect))`
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| 1,189
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Transformations module issue
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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 structures from experimental cif file as you mention in your paper.\r\n\r\nprim cell was built by \r\n<pre>\r\nstructure = Structure.from_file(\"LGPS.cif\")\r\nistructure = IStructure.from_file(\"LGPS.cif\")\r\n\r\n# add oxidation number\r\noxidation_state = {\"Li\":1, \"Ge\":4, \"S\": -2, \"P\":5, \"O\":-2, \"Mn\":2, \"Co\":2, \"Ni\":2}\r\nstructure.add_oxidation_state_by_element(oxidation_state)\r\n\r\n# adjust occupancy\r\n# 1. simplify Li occupancy to 0.625\r\n# 2. Ge/P sites fixed as Ge and P.\r\nfor i, site in enumerate(structure):\r\n if not site.is_ordered:\r\n if structure[i][\"Li+\"] == 0.466:\r\n structure[i] = {\"Li+\": 0.625}\r\n elif structure[i][\"Li+\"] == 0.74 or structure[i][\"Li+\"] == 0.81 or structure[i][\"Li+\"] == 0.86:\r\n structure[i] = {\"Li+\": 0.625}\r\n else:\r\n if round(site.coords[0], 6) == 4.3595:\r\n structure[i] = {\"Ge4+\": 1.0}\r\n elif round(site.coords[0], 6) == 0:\r\n structure[i] = {\"P5+\": 1.0}\r\n\r\n# make primitive cell\r\nanalyzer = SpacegroupAnalyzer(structure)\r\nprim_cell = analyzer.find_primitive()\r\nprint(prim_cell)\r\n\r\n---------------------------------------------\r\nFull Formula (Li20 Ge2 P4 S24)\r\nReduced Formula: Li10Ge(PS6)2\r\nabc : 8.719000 8.719000 12.639000\r\nangles: 90.000000 90.000000 90.000000\r\nSites (62)\r\n # SP a b c\r\n--- --------- ------- ------- -------\r\n 0 Li+:0.625 0.267 0.773 0.194\r\n 1 Li+:0.625 0.733 0.227 0.194\r\n 2 Li+:0.625 0.227 0.267 0.694\r\n 3 Li+:0.625 0.773 0.733 0.694\r\n 4 Li+:0.625 0.233 0.273 0.306\r\n 5 Li+:0.625 0.767 0.727 0.306\r\n 6 Li+:0.625 0.273 0.767 0.806\r\n 7 Li+:0.625 0.727 0.233 0.806\r\n 8 Li+:0.625 0.233 0.727 0.306\r\n 9 Li+:0.625 0.767 0.273 0.306\r\n 10 Li+:0.625 0.273 0.233 0.806\r\n 11 Li+:0.625 0.727 0.767 0.806\r\n 12 Li+:0.625 0.267 0.227 0.194\r\n 13 Li+:0.625 0.733 0.773 0.194\r\n 14 Li+:0.625 0.227 0.733 0.694\r\n 15 Li+:0.625 0.773 0.267 0.694\r\n 16 Li+:0.625 0.248 0.748 0\r\n 17 Li+:0.625 0.752 0.252 0\r\n 18 Li+:0.625 0.252 0.248 0.5\r\n 19 Li+:0.625 0.748 0.752 0.5\r\n 20 Li+:0.625 0.252 0.752 0.5\r\n 21 Li+:0.625 0.748 0.248 0.5\r\n 22 Li+:0.625 0.248 0.252 0\r\n 23 Li+:0.625 0.752 0.748 0\r\n 24 Li+:0.625 0 0.5 0.251\r\n 25 Li+:0.625 0.5 0 0.751\r\n 26 Li+:0.625 0.5 0 0.249\r\n 27 Li+:0.625 0 0.5 0.749\r\n 28 Li+:0.625 0 0 0.9454\r\n 29 Li+:0.625 0 0 0.4454\r\n 30 Li+:0.625 0.5 0.5 0.5546\r\n 31 Li+:0.625 0.5 0.5 0.0546\r\n 32 P5+ 0 0 0.69154\r\n 33 P5+ 0 0 0.19154\r\n 34 Ge4+ 0.5 0.5 0.80846\r\n 35 Ge4+ 0.5 0.5 0.30846\r\n 36 P5+ 0 0.5 0.5\r\n 37 P5+ 0.5 0 0\r\n 38 S2- 0 0.68857 0.40707\r\n 39 S2- 0 0.31143 0.40707\r\n 40 S2- 0.31143 0 0.90707\r\n 41 S2- 0.68857 0 0.90707\r\n 42 S2- 0.5 0.18857 0.09293\r\n 43 S2- 0.5 0.81143 0.09293\r\n 44 S2- 0.18857 0.5 0.59293\r\n 45 S2- 0.81143 0.5 0.59293\r\n 46 S2- 0 0.79557 0.09727\r\n 47 S2- 0 0.20443 0.09727\r\n 48 S2- 0.20443 0 0.59727\r\n 49 S2- 0.79557 0 0.59727\r\n 50 S2- 0.5 0.29557 0.40273\r\n 51 S2- 0.5 0.70443 0.40273\r\n 52 S2- 0.29557 0.5 0.90273\r\n 53 S2- 0.70443 0.5 0.90273\r\n 54 S2- 0 0.19901 0.79168\r\n 55 S2- 0 0.80099 0.79168\r\n 56 S2- 0.80099 0 0.29168\r\n 57 S2- 0.19901 0 0.29168\r\n 58 S2- 0.5 0.69901 0.70832\r\n 59 S2- 0.5 0.30099 0.70832\r\n 60 S2- 0.69901 0.5 0.20832\r\n 61 S2- 0.30099 0.5 0.20832\r\n</pre>\r\n\r\n\r\nIn here, Li is not ordered, so I choose 'OrderDisorderedStructureTransformation'\r\n<pre>\r\n>>> enum = OrderDisorderedStructureTransformation(symmetrized_structures=True)\r\n>>> enumerated = enum.apply_transformation(prim_cell, 100)\r\n\r\nTraceback (most recent call last):\r\n File \"enumerate_structure.py\", line 53, in <module>\r\n enumerated = enum.apply_transformation(prim_cell, 100)\r\n File \"/home/shared/anaconda3/envs/CCpy/lib/python3.6/site-packages/pymatgen/transformations/standard_transformations.py\", line 488, in apply_transformation\r\n sym_equiv = structure.find_equivalent_sites(ex)\r\nAttributeError: 'Structure' object has no attribute 'find_equivalent_sites'\r\n</pre>\r\n\r\nShould I use other transformation module?\r\n",
"This should be correct. But the input structure, prim_cell, should be a SymmetrizedStructure. You can get that from the spacegroup analyzer code. E.g.,\r\n\r\nanalyzer.get_symmetrized_structure()",
"Also, I should note that the OrderDisorder transformation by default already detects symmetry. The Symmetrized structure option should only be used if you already pre-determined the symmetry of the structure. In most instances, you should not use that."
] | 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 code
```
enum = OrderDisorderedStructureTransformation(symmetrized_structures=True)
enumerated = enum.apply_transformation(prim_cell, 100)
```
## Error message
```
Traceback (most recent call last):
File "enumerate_structure.py", line 53, in <module>
enumerated = enum.apply_transformation(prim_cell, 100)
File "/home/shared/anaconda3/envs/CCpy/lib/python3.6/site-packages/pymatgen/transformations/standard_transformations.py", line 488, in apply_transformation
sym_equiv = structure.find_equivalent_sites(ex)
AttributeError: 'Structure' object has no attribute 'find_equivalent_sites'
```
## Suggested solution (if any)
* The error may comes from wrong path after you upgrade Structure modules
## Files (if any)
* If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.
```
<contents of file 1>
```
|
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| 337,644,962
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MDExOlB1bGxSZXF1ZXN0MTk4Nzc1OTI3
| 1,190
|
Added a new order paramter (q_sq_face_cap_trig_pris) and unit test
|
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[] | null |
[
"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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MDU6SXNzdWUzMzc4NTY2MTI=
| 1,191
|
pymatgen does not support for python3.7
|
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[] | 2018-07-03T11:22:16
| 2018-07-06T06:37:24
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2018-07-06T06:37:24Z
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NONE
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MDExOlB1bGxSZXF1ZXN0MTk5MTE2NzQ5
| 1,192
|
Metallic radius
|
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[] | 2018-07-04T01:07:42
| 2018-07-07T14:27:23
|
2018-07-07T14:27:23Z
|
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
https://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page)
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MDExOlB1bGxSZXF1ZXN0MTk5NTI0NzAy
| 1,193
|
Update VoronoiNN cutoff dynamically
|
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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\nTraceback (most recent call last):\r\n File \"/home/travis/build/materialsproject/pymatgen/pymatgen/command_line/tests/test_enumlib_caller.py\", line 139, in test_timeout\r\n self.assertRaises(TimeoutError, adaptor._run_multienum)\r\nAssertionError: TimeoutError not raised by _run_multienum\r\n-------------------- >> begin captured logging << --------------------\r\npymatgen.command_line.enumlib_caller: DEBUG: Enumeration resulted in 0 structures\r\n--------------------- >> end captured logging << ---------------------\r\n```\r\n\r\nBut I just changed local_env.py, pretty sure that should be unrelated to enumlib?"
] | 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 find near neighbors)
- For some structures (e.g. mp-1096674), the cutoff is actually not enough and we hit the error.
This PR:
- sets a "maximum cutoff" equal to the length of the diagonal of the unit cell plus a small numerical tolerance
- if encountering a problem with the initial cutoff set by the user, it will double it until hitting the max cutoff
## Additional dependencies introduced (if any)
None
## TODO (if any)
* I didn't change the default cutoff of 10.0. I do think this could be scaled back to 8.0 or so and the algorithm would go much faster and not change any real results. The only issue is that it is *possible* that there is a structure where including all sites within 8 Angstroms and all sites within 10 Angstroms for consideration result in different answers, but both give valid Voronoi constructions. In these (probably extremely rare) cases, changing the default might change the answer. Someone could in principle test all MP structures and ensure that the results were the same with both cutoffs.
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Pymatgen does not support for Python3.7(PyYAML 3.13 has been installed)
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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.",
"I managed to build pymatgen from source with python3.7.\r\nI had to regenerate the C files with cython and install the dependencies with pip \r\ninstead of conda (at present there are few conda packages built for py3.7)",
"Noted.😇\r\nThank you for your kind reply.\r\n\r\nBest regards.\r\nWenT-Ethan\r\n\r\n\r\nOn Jul 7, 2018, at 08:16, gmatteo <notifications@github.com<mailto:notifications@github.com>> wrote:\r\n\r\n\r\nI managed to build pymatgen from source with python3.7.\r\nI had to regenerate the C files with cython and install the dependencies with pip\r\ninstead of conda (at present there are few conda packages built for py3.7)\r\n\r\n—\r\nYou are receiving this because you authored the thread.\r\nReply to this email directly, view it on GitHub<https://github.com/materialsproject/pymatgen/issues/1194#issuecomment-403168365>, or mute the thread<https://github.com/notifications/unsubscribe-auth/Am1t3ZOT53ECB4Ap0ZNB3lJtcUtr6dfxks5uD-_GgaJpZM4VE9Et>.\r\n\r\n",
"Many thanks. I merged the new Py37 compatibility code."
] | 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
* 1-2 short bullet points stating the problem.
## Example code
```python
# Example code generating error
```
## Error message
```
Collecting pymatgen
Downloading https://files.pythonhosted.org/packages/2c/f3/42a42cfe55dec0b7b8b5df383bc54baf36736ffcb3801c93cdbb7303ea83/pymatgen-2018.6.27.tar.gz (1.7MB)
100% |████████████████████████████████| 1.8MB 3.4MB/s
Requirement already satisfied: numpy>=1.14.3 in /usr/local/lib/python3.7/site-packages (from pymatgen) (1.14.5)
Requirement already satisfied: six in /usr/local/lib/python3.7/site-packages (from pymatgen) (1.11.0)
Requirement already satisfied: requests in /usr/local/lib/python3.7/site-packages (from pymatgen) (2.19.1)
Requirement already satisfied: ruamel.yaml>=0.15.6 in /usr/local/lib/python3.7/site-packages (from pymatgen) (0.15.42)
Requirement already satisfied: monty>=0.9.6 in /usr/local/lib/python3.7/site-packages (from pymatgen) (1.0.3)
Requirement already satisfied: scipy>=1.0.1 in /usr/local/lib/python3.7/site-packages (from pymatgen) (1.1.0)
Requirement already satisfied: pydispatcher>=2.0.5 in /usr/local/lib/python3.7/site-packages (from pymatgen) (2.0.5)
Requirement already satisfied: tabulate in /usr/local/lib/python3.7/site-packages (from pymatgen) (0.8.2)
Requirement already satisfied: spglib>=1.9.9.44 in /usr/local/lib/python3.7/site-packages (from pymatgen) (1.10.3.65)
Requirement already satisfied: matplotlib>=1.5 in /usr/local/lib/python3.7/site-packages (from pymatgen) (2.2.2)
Requirement already satisfied: palettable>=2.1.1 in /usr/local/lib/python3.7/site-packages (from pymatgen) (3.1.1)
Requirement already satisfied: sympy in /usr/local/lib/python3.7/site-packages (from pymatgen) (1.1.1)
Requirement already satisfied: pandas in /usr/local/lib/python3.7/site-packages (from pymatgen) (0.23.1)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /usr/local/lib/python3.7/site-packages (from requests->pymatgen) (3.0.4)
Requirement already satisfied: urllib3<1.24,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->pymatgen) (1.23)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages (from requests->pymatgen) (2018.4.16)
Requirement already satisfied: idna<2.8,>=2.5 in /usr/local/lib/python3.7/site-packages (from requests->pymatgen) (2.7)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib>=1.5->pymatgen) (1.0.1)
Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.7/site-packages (from matplotlib>=1.5->pymatgen) (2.7.3)
Requirement already satisfied: pytz in /usr/local/lib/python3.7/site-packages (from matplotlib>=1.5->pymatgen) (2018.5)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib>=1.5->pymatgen) (2.2.0)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib>=1.5->pymatgen) (0.10.0)
Requirement already satisfied: mpmath>=0.19 in /usr/local/lib/python3.7/site-packages (from sympy->pymatgen) (1.0.0)
Requirement already satisfied: setuptools in /usr/local/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib>=1.5->pymatgen) (39.2.0)
Building wheels for collected packages: pymatgen
Running setup.py bdist_wheel for pymatgen ... error
Complete output from command /usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/s_/58hrgzv50j108p9mnxm838bw0000gn/T/pip-install-126i33a8/pymatgen/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /private/var/folders/s_/58hrgzv50j108p9mnxm838bw0000gn/T/pip-wheel-h1tdlpza --python-tag cp37:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.13-x86_64-3.7
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen
copying pymatgen/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen
copying pymatgen/dao.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/compatibility.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/computed_entries.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/entry_tools.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/exp_entries.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/post_processors_abc.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/xcfunc.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/periodic_table.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/units.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/ion.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/libxcfunc.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/operations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/molecular_orbitals.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/spectrum.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/bonds.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/sites.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/lattice.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/structure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/composition.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/surface.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/defect_transformations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/standard_transformations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/transformation_abc.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/advanced_transformations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/site_transformations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/eos.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/energy_models.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/path_finder.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/reaction_calculator.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/find_dimension.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/diffusion_analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/surface_analysis.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/structure_matcher.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/pourbaix_diagram.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/wulff.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/local_env.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/phase_diagram.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/molecule_matcher.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/structure_analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/piezo.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/ewald.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/nmr.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/molecule_structure_comparator.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/thermochemistry.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/bond_valence.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/excitation.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/adsorption.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/graphs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/transition_state.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/quasiharmonic.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/substrate_analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/interface_reactions.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/convergence.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/num.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/plotting.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/coord.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/io_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/string.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/provenance.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/testing.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/serialization.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/optimization
copying pymatgen/optimization/linear_assignment_numpy.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/optimization
copying pymatgen/optimization/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/optimization
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/ext
copying pymatgen/ext/jhu.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/ext
copying pymatgen/ext/cod.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/ext
copying pymatgen/ext/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/ext
copying pymatgen/ext/matproj.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/ext
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/fiesta.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/ase.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/xyz.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/atat.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/aiida.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/nwchem.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/qchem.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/xr.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/lmto.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/zeopp.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/pwscf.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/babel.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/lobster.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/cssr.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/phonopy.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/cif.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/gaussian.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/xcrysden.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/adf.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/phonon
copying pymatgen/phonon/dos.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/phonon
copying pymatgen/phonon/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/phonon
copying pymatgen/phonon/plotter.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/phonon
copying pymatgen/phonon/bandstructure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/phonon
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pydii.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/feff_plot_dos.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_structure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_query.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_plot.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/feff_plot_cross_section.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_potcar.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_analyze.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_config.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/gaussian_analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/get_environment.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/feff_input_generation.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/groups.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/structure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/settings.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/maggroups.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/bandstructure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
copying pymatgen/vis/structure_vtk.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
copying pymatgen/vis/plotters.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
copying pymatgen/vis/structure_chemview.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
copying pymatgen/vis/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/cohp.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/dos.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/boltztrap.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/core.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/plotter.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/bandstructure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/bader_caller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/critic2_caller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/enumlib_caller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/aconvasp_caller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/gulp_caller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps
copying pymatgen/apps/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/alchemy
copying pymatgen/alchemy/materials.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/alchemy
copying pymatgen/alchemy/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/alchemy
copying pymatgen/alchemy/transmuters.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/alchemy
copying pymatgen/alchemy/filters.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/alchemy
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
copying pymatgen/analysis/elasticity/tensors.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
copying pymatgen/analysis/elasticity/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
copying pymatgen/analysis/elasticity/stress.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
copying pymatgen/analysis/elasticity/elastic.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
copying pymatgen/analysis/elasticity/strain.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
copying pymatgen/analysis/structure_prediction/volume_predictor.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
copying pymatgen/analysis/structure_prediction/substitution_probability.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
copying pymatgen/analysis/structure_prediction/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
copying pymatgen/analysis/structure_prediction/substitutor.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/cost
copying pymatgen/analysis/cost/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/cost
copying pymatgen/analysis/cost/cost.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/cost
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/xas
copying pymatgen/analysis/xas/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/xas
copying pymatgen/analysis/xas/spectrum.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/xas
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
copying pymatgen/analysis/defects/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
copying pymatgen/analysis/defects/dilute_solution_model.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
copying pymatgen/analysis/defects/point_defects.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
copying pymatgen/analysis/defects/surf_error.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv
copying pymatgen/analysis/chemenv/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/diffraction/neutron.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/diffraction/xrd.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/diffraction/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/diffraction/core.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/ferroelectricity
copying pymatgen/analysis/ferroelectricity/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/ferroelectricity
copying pymatgen/analysis/ferroelectricity/polarization.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/ferroelectricity
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/hhi
copying pymatgen/analysis/hhi/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/hhi
copying pymatgen/analysis/hhi/hhi.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/hhi
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/magnetism
copying pymatgen/analysis/magnetism/analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/magnetism
copying pymatgen/analysis/magnetism/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/magnetism
copying pymatgen/analysis/magnetism/jahnteller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/magnetism
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/structure_environments.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/voronoi.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/chemenv_config.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/func_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/math_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/defs_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/scripts_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/chemenv_errors.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/strategy_files
copying pymatgen/analysis/chemenv/coordination_environments/strategy_files/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/strategy_files
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/inputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/sets.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/outputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/db.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/abiobjects.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/qjobs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/tasks.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/abiinspect.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/events.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/abitimer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/works.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/scheduler_error_handlers.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/qadapters.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/calculations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/qutils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/netcdf.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/pseudos.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/wrappers.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/flows.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/launcher.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/nodes.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/scheduler_error_parsers.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/helpers.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/inputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/sets.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/outputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/exciting
copying pymatgen/io/exciting/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/exciting
copying pymatgen/io/exciting/inputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/exciting
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/input.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/sets.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/data.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/output.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
copying pymatgen/io/qchem_io/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
copying pymatgen/io/qchem_io/inputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
copying pymatgen/io/qchem_io/utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
copying pymatgen/io/qchem_io/sets.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
copying pymatgen/io/qchem_io/outputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/borg
copying pymatgen/apps/borg/queen.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/borg
copying pymatgen/apps/borg/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/borg
copying pymatgen/apps/borg/hive.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/borg
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/conversion_battery.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/insertion_battery.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/plotter.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/battery_abc.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/entries/MPCompatibility.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/MITCompatibility.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/core/reconstructions_archive.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/bond_lengths.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/func_groups.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/periodic_table.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/libxc_docs.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/analysis/icsd_bv.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/bonds_jmol_ob.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/bvparam_1991.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/op_params.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/cn_opt_params.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/ionic_radii.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Li2O.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/LiFePO4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Li10GeP2S12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/K2O2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Li3V2(PO4)3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Graphite.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/He_BCC.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/TiO2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/CsCl.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/BaNiO3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Li2O2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Si.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/NaFePO4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/VO2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Sn.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/SrTiO3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/symmetry/symm_data.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/symm_ops.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/symm_data.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/symm_ops.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/vis/ElementColorSchemes.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
copying pymatgen/command_line/OxideTersoffPotentials -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/analysis/structure_prediction/DLS_bond_params.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
copying pymatgen/analysis/cost/costdb_elements.csv -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/cost
copying pymatgen/analysis/defects/ionic_radii.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
copying pymatgen/analysis/diffraction/neutron_scattering_length.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/diffraction/atomic_scattering_params.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/hhi/hhi_data.csv -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/hhi
copying pymatgen/analysis/chemenv/coordination_environments/strategy_files/ImprovedConfidenceCutoffDefaultParameters.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/strategy_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/allcg.txt -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_2#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/H#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TY#3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PCPA#11.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/T#4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT_2#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TBT#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TI#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/T#5.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/AC#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SBSA#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SH#13.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HP#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/FO#7.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/H#11.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TBSA#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/L#2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DI#11.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TO_1#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DDPN#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TS#3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SMA#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PA#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TO_3#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PP#5.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#1.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SBT#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SC#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TC#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DD#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PBP#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/O#6.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SS#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT_3#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TL#3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PP#6.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/CO#11.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_3#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/ST#7.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/C#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HD#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BS_2#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PP#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SS#4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_1#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/C#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT_1#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/MI#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HB#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/ET#7.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/A#2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/O#6_explicit.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/T#6.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SA#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#5.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SY#4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HA#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PB#7.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SH#11.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TO_2#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BS_1#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/I#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DD#20.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/io/feff/MPEXAFSSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/MPELNESSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/MPXANESSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/MPEXELFSSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/vasp/MVLGWSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/MPHSERelaxSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/VASPIncarBase.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/MPRelaxSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/MITRelaxSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/vdW_parameters.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
running build_ext
building 'pymatgen.optimization.linear_assignment' extension
creating build/temp.macosx-10.13-x86_64-3.7
creating build/temp.macosx-10.13-x86_64-3.7/pymatgen
creating build/temp.macosx-10.13-x86_64-3.7/pymatgen/optimization
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c pymatgen/optimization/linear_assignment.c -o build/temp.macosx-10.13-x86_64-3.7/pymatgen/optimization/linear_assignment.o
In file included from pymatgen/optimization/linear_assignment.c:275:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
pymatgen/optimization/linear_assignment.c:21345:21: error: no member named 'exc_type' in 'struct _ts'
*type = tstate->exc_type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21346:22: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
*value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21347:19: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
*tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21354:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21355:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21356:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21357:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21358:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21359:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21414:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21415:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21416:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21417:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = local_type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21418:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21419:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21441:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21442:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21443:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21444:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = *type;
~~~~~~ ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
1 warning and 20 errors generated.
error: command 'clang' failed with exit status 1
----------------------------------------
Failed building wheel for pymatgen
Running setup.py clean for pymatgen
Failed to build pymatgen
Installing collected packages: pymatgen
Running setup.py install for pymatgen ... error
Complete output from command /usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/s_/58hrgzv50j108p9mnxm838bw0000gn/T/pip-install-126i33a8/pymatgen/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/s_/58hrgzv50j108p9mnxm838bw0000gn/T/pip-record-zlynknb9/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.macosx-10.13-x86_64-3.7
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen
copying pymatgen/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen
copying pymatgen/dao.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/compatibility.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/computed_entries.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/entry_tools.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/exp_entries.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/post_processors_abc.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/xcfunc.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/periodic_table.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/units.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/ion.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/libxcfunc.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/operations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/molecular_orbitals.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/spectrum.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/bonds.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/sites.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/lattice.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/structure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/composition.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/surface.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/defect_transformations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/standard_transformations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/transformation_abc.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/advanced_transformations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
copying pymatgen/transformations/site_transformations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/transformations
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/eos.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/energy_models.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/path_finder.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/reaction_calculator.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/find_dimension.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/diffusion_analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/surface_analysis.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/structure_matcher.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/pourbaix_diagram.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/wulff.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/local_env.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/phase_diagram.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/molecule_matcher.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/structure_analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/piezo.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/ewald.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/nmr.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/molecule_structure_comparator.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/thermochemistry.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/bond_valence.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/excitation.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/adsorption.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/graphs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/transition_state.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/quasiharmonic.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/substrate_analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/interface_reactions.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/convergence.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/num.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/plotting.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/coord.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/io_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/string.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/provenance.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/testing.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
copying pymatgen/util/serialization.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/optimization
copying pymatgen/optimization/linear_assignment_numpy.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/optimization
copying pymatgen/optimization/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/optimization
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/ext
copying pymatgen/ext/jhu.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/ext
copying pymatgen/ext/cod.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/ext
copying pymatgen/ext/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/ext
copying pymatgen/ext/matproj.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/ext
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/fiesta.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/ase.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/xyz.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/atat.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/aiida.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/nwchem.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/qchem.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/xr.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/lmto.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/zeopp.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/pwscf.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/babel.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/lobster.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/cssr.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/phonopy.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/cif.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/gaussian.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/xcrysden.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
copying pymatgen/io/adf.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/phonon
copying pymatgen/phonon/dos.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/phonon
copying pymatgen/phonon/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/phonon
copying pymatgen/phonon/plotter.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/phonon
copying pymatgen/phonon/bandstructure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/phonon
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pydii.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/feff_plot_dos.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_structure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_query.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_plot.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/feff_plot_cross_section.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_potcar.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_analyze.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg_config.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/gaussian_analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/get_environment.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/pmg.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
copying pymatgen/cli/feff_input_generation.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/cli
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/groups.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/structure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/settings.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/maggroups.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/bandstructure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
copying pymatgen/vis/structure_vtk.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
copying pymatgen/vis/plotters.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
copying pymatgen/vis/structure_chemview.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
copying pymatgen/vis/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/cohp.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/dos.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/boltztrap.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/core.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/plotter.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
copying pymatgen/electronic_structure/bandstructure.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/electronic_structure
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/bader_caller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/critic2_caller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/enumlib_caller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/aconvasp_caller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/command_line/gulp_caller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps
copying pymatgen/apps/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/alchemy
copying pymatgen/alchemy/materials.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/alchemy
copying pymatgen/alchemy/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/alchemy
copying pymatgen/alchemy/transmuters.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/alchemy
copying pymatgen/alchemy/filters.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/alchemy
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
copying pymatgen/analysis/elasticity/tensors.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
copying pymatgen/analysis/elasticity/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
copying pymatgen/analysis/elasticity/stress.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
copying pymatgen/analysis/elasticity/elastic.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
copying pymatgen/analysis/elasticity/strain.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/elasticity
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
copying pymatgen/analysis/structure_prediction/volume_predictor.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
copying pymatgen/analysis/structure_prediction/substitution_probability.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
copying pymatgen/analysis/structure_prediction/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
copying pymatgen/analysis/structure_prediction/substitutor.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/cost
copying pymatgen/analysis/cost/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/cost
copying pymatgen/analysis/cost/cost.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/cost
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/xas
copying pymatgen/analysis/xas/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/xas
copying pymatgen/analysis/xas/spectrum.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/xas
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
copying pymatgen/analysis/defects/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
copying pymatgen/analysis/defects/dilute_solution_model.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
copying pymatgen/analysis/defects/point_defects.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
copying pymatgen/analysis/defects/surf_error.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv
copying pymatgen/analysis/chemenv/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/diffraction/neutron.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/diffraction/xrd.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/diffraction/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/diffraction/core.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/ferroelectricity
copying pymatgen/analysis/ferroelectricity/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/ferroelectricity
copying pymatgen/analysis/ferroelectricity/polarization.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/ferroelectricity
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/hhi
copying pymatgen/analysis/hhi/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/hhi
copying pymatgen/analysis/hhi/hhi.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/hhi
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/magnetism
copying pymatgen/analysis/magnetism/analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/magnetism
copying pymatgen/analysis/magnetism/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/magnetism
copying pymatgen/analysis/magnetism/jahnteller.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/magnetism
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/structure_environments.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/voronoi.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
copying pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/chemenv_config.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/func_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/math_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/defs_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/scripts_utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
copying pymatgen/analysis/chemenv/utils/chemenv_errors.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/utils
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/strategy_files
copying pymatgen/analysis/chemenv/coordination_environments/strategy_files/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/strategy_files
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/inputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/sets.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/outputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/db.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/abiobjects.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/qjobs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/tasks.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/abiinspect.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/events.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/abitimer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/works.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/scheduler_error_handlers.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/qadapters.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/calculations.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/qutils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/netcdf.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/pseudos.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/wrappers.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/flows.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/launcher.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/nodes.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/scheduler_error_parsers.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
copying pymatgen/io/abinit/helpers.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/abinit
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/inputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/sets.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/outputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/exciting
copying pymatgen/io/exciting/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/exciting
copying pymatgen/io/exciting/inputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/exciting
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/input.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/sets.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/data.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
copying pymatgen/io/lammps/output.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/lammps
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
copying pymatgen/io/qchem_io/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
copying pymatgen/io/qchem_io/inputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
copying pymatgen/io/qchem_io/utils.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
copying pymatgen/io/qchem_io/sets.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
copying pymatgen/io/qchem_io/outputs.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/qchem_io
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/borg
copying pymatgen/apps/borg/queen.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/borg
copying pymatgen/apps/borg/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/borg
copying pymatgen/apps/borg/hive.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/borg
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/conversion_battery.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/analyzer.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/insertion_battery.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/plotter.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/apps/battery/battery_abc.py -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/apps/battery
copying pymatgen/entries/MPCompatibility.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/entries/MITCompatibility.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/entries
copying pymatgen/core/reconstructions_archive.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/bond_lengths.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/func_groups.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/periodic_table.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/core/libxc_docs.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/core
copying pymatgen/analysis/icsd_bv.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/bonds_jmol_ob.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/bvparam_1991.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/op_params.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/cn_opt_params.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
copying pymatgen/analysis/ionic_radii.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis
creating build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Li2O.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/LiFePO4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Li10GeP2S12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/K2O2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Li3V2(PO4)3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Graphite.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/He_BCC.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/TiO2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/CsCl.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/BaNiO3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Li2O2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Si.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/NaFePO4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/VO2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/Sn.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/util/structures/SrTiO3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/util/structures
copying pymatgen/symmetry/symm_data.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/symm_ops.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/symm_data.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/symmetry/symm_ops.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/symmetry
copying pymatgen/vis/ElementColorSchemes.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/vis
copying pymatgen/command_line/OxideTersoffPotentials -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/command_line
copying pymatgen/analysis/structure_prediction/DLS_bond_params.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/structure_prediction
copying pymatgen/analysis/cost/costdb_elements.csv -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/cost
copying pymatgen/analysis/defects/ionic_radii.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/defects
copying pymatgen/analysis/diffraction/neutron_scattering_length.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/diffraction/atomic_scattering_params.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/diffraction
copying pymatgen/analysis/hhi/hhi_data.csv -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/hhi
copying pymatgen/analysis/chemenv/coordination_environments/strategy_files/ImprovedConfidenceCutoffDefaultParameters.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/strategy_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/allcg.txt -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_2#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/H#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TY#3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PCPA#11.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/T#4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT_2#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TBT#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TI#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/T#5.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/AC#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SBSA#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SH#13.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HP#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/FO#7.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/H#11.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TBSA#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/L#2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DI#11.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TO_1#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DDPN#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TS#3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SMA#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PA#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TO_3#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PP#5.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#1.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SBT#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SC#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TC#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DD#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PBP#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/O#6.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SS#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT_3#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TL#3.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PP#6.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/CO#11.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_3#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/ST#7.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/C#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HD#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BS_2#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PP#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SS#4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_1#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/C#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT_1#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/MI#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HB#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/ET#7.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/A#2.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/O#6_explicit.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/T#6.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SA#8.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#5.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SY#4.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HA#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PB#7.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SH#11.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TO_2#9.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BS_1#10.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/I#12.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DD#20.json -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files
copying pymatgen/io/feff/MPEXAFSSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/MPELNESSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/MPXANESSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/feff/MPEXELFSSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/feff
copying pymatgen/io/vasp/MVLGWSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/MPHSERelaxSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/VASPIncarBase.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/MPRelaxSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/MITRelaxSet.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
copying pymatgen/io/vasp/vdW_parameters.yaml -> build/lib.macosx-10.13-x86_64-3.7/pymatgen/io/vasp
running build_ext
building 'pymatgen.optimization.linear_assignment' extension
creating build/temp.macosx-10.13-x86_64-3.7
creating build/temp.macosx-10.13-x86_64-3.7/pymatgen
creating build/temp.macosx-10.13-x86_64-3.7/pymatgen/optimization
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c pymatgen/optimization/linear_assignment.c -o build/temp.macosx-10.13-x86_64-3.7/pymatgen/optimization/linear_assignment.o
In file included from pymatgen/optimization/linear_assignment.c:275:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
pymatgen/optimization/linear_assignment.c:21345:21: error: no member named 'exc_type' in 'struct _ts'
*type = tstate->exc_type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21346:22: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
*value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21347:19: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
*tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21354:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21355:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21356:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21357:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21358:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21359:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21414:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21415:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21416:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21417:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = local_type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21418:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21419:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21441:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
pymatgen/optimization/linear_assignment.c:21442:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pymatgen/optimization/linear_assignment.c:21443:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pymatgen/optimization/linear_assignment.c:21444:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = *type;
~~~~~~ ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
1 warning and 20 errors generated.
error: command 'clang' failed with exit status 1
----------------------------------------
Command "/usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/s_/58hrgzv50j108p9mnxm838bw0000gn/T/pip-install-126i33a8/pymatgen/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/s_/58hrgzv50j108p9mnxm838bw0000gn/T/pip-record-zlynknb9/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/s_/58hrgzv50j108p9mnxm838bw0000gn/T/pip-install-126i33a8/pymatgen/
```
## Suggested solution (if any)
* If you have a suggestion on how to solve the issue, you may write it
here.
## Files (if any)
* If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.
```
<contents of file 1>
```
|
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https://github.com/materialsproject/pymatgen/pull/1195
| 339,082,935
|
MDExOlB1bGxSZXF1ZXN0MTk5ODU2MjI4
| 1,195
|
Add option to choose alternative settings for SpacegroupAnalyzer
|
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[] | null |
[] | 2018-07-06T22:00:39
| 2018-07-06T22:35:02
|
2018-07-06T22:35:02Z
|
MEMBER
|
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## Summary
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 then run SpacegroupAnalyzer again with one of those choices as appropriate.
This functionality is important if interested in e.g. Wyckoff co-ordinates in specific settings.
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* None
|
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| 339,093,875
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MDExOlB1bGxSZXF1ZXN0MTk5ODY0NjEy
| 1,196
|
Regenerate C files with cython 0.28.3 to support py3.7
|
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[] | 2018-07-06T23:09:51
| 2018-07-07T14:25:52
|
2018-07-07T14:25:51Z
|
CONTRIBUTOR
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Fix #1194
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MDExOlB1bGxSZXF1ZXN0MTk5ODY0NzU2
| 1,197
|
Fix py3.7 deprecation warnings
|
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[] | 2018-07-06T23:11:24
| 2018-07-07T14:26:19
|
2018-07-07T14:26:19Z
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CONTRIBUTOR
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MDU6SXNzdWUzMzk2NDMyODE=
| 1,198
|
CIF importing results in incorrect length assignment
|
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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[4]: 6.8179
In [5]: struct.lattice.b
Out[5]: 13.939
In [6]: struct.lattice.c
Out[6]: 16.143
```
CIF file:
```
_cell_length_a 6.8179
_cell_length_b 16.143
_cell_length_c 13.939
```
I must be missing something obvious here. What is it?
|
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MDU6SXNzdWUzNDAwMDM5NDM=
| 1,199
|
OUTCAR file fails to be loaded by the pymatgen.io.vasp.outputs.Outcar file due to electrostatic potential item in output
|
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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** two whitespaces in the regular expression parser. \r\n\r\nI'll work on this soon.",
"Update: can be fixed by changing the regular expression for table_pattern in the below snippet:\r\n\r\n```\r\n header_pattern = r\"\\(the norm of the test charge is\\s+[\\.\\-\\d]+\\)\"\r\n table_pattern = r\"((?:\\s+\\d+\\s?[\\.\\-\\d]+)+)\"\r\n footer_pattern = r\"\\s+E-fermi :\"\r\n\r\n pots = self.read_table_pattern(header_pattern, table_pattern, footer_pattern)\r\n\r\n```\r\nFrom\r\n```\r\n table_pattern = r\"((?:\\s+\\d+\\s?[\\.\\-\\d]+)+)\"\r\n```\r\nTo (adding a star to the middle whitespace \\s):\r\n```\r\n table_pattern = r\"((?:\\s+\\d+\\s*?[\\.\\-\\d]+)+)\"\r\n```\r\nI'll make a pull request for this later.\r\n\r\n\r\n",
"I just fixed it. ",
"See latest commit.",
"Thank you! "
] | 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 look like it)
* Python version: Python 3.6.5 |Anaconda, Inc.| (default, Apr 29 2018, 16:14:56)
* OS version: Linux (on NERSC)
## Summary
When I tried to parse an OUTCAR file, I got an error in parsing the electrostatic potential part of the output (which states the electrostatic potential at each ion in the system). The offending file is attached.
## Example code
```python
$python
>>>from pymatgen.io.vasp.outputs import Outcar
>>>a=Outcar("OUTCAR")
```
## Error message
```
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/global/homes/s/storrisi/.conda/envs/cms/lib/python3.6/site-packages/pymatgen/io/vasp/outputs.py", line 1622, in __init__
self.read_electrostatic_potential()
File "/global/homes/s/storrisi/.conda/envs/cms/lib/python3.6/site-packages/pymatgen/io/vasp/outputs.py", line 1749, in read_electrostatic_potential
pots = self.read_table_pattern(header_pattern, table_pattern, footer_pattern)
File "/global/homes/s/storrisi/.conda/envs/cms/lib/python3.6/site-packages/pymatgen/io/vasp/outputs.py", line 1726, in read_table_pattern
retained_data = tables[-1]
IndexError: list index out of range
```
## Suggested solution (if any)
My regular expression expertise is weak so it's unclear...
## Files (if any)
* If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.
[OUTCAR.txt](https://github.com/materialsproject/pymatgen/files/2182082/OUTCAR.txt)
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MDExOlB1bGxSZXF1ZXN0MjAwNTUwODQ2
| 1,200
|
Add grain boundary generator
|
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[] | null |
[
"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 on this pull request.\n> ------------------------------\n>\n> In pymatgen/core/grain_boundary_generator.py\n> <https://github.com/materialsproject/pymatgen/pull/1200#discussion_r201834982>\n> :\n>\n> > + normal_v_plane = np.cross(half_lattice.matrix[0], half_lattice.matrix[1])\n> + unit_normal_v = normal_v_plane / np.linalg.norm(normal_v_plane)\n> + translation_v = unit_normal_v * vacuum_thickness\n> +\n> + # construct the final lattice\n> + whole_matrix_no_vac = half_lattice.matrix\n> + whole_matrix_no_vac[2] = half_lattice.matrix[2] * 2\n> + whole_matrix_with_vac = whole_matrix_no_vac.copy()\n> + whole_matrix_with_vac[2] = whole_matrix_no_vac[2] + translation_v * 2\n> + whole_lat = Lattice(whole_matrix_with_vac)\n> +\n> + # construct the coords, move top grain with translation_v\n> + all_coords = []\n> + for site in bottom_grain:\n> + all_coords.append(site.coords)\n> + for site in top_grain:\n>\n> You mean one structure with twice top grain and twice bottom grain. e.g.\n> both top grain and bottom grain have N atoms. The grain boundary structure\n> has 2N atoms. The new structure has 4N atoms with some atoms overlapping\n> with each other. Is that correct?\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1200#discussion_r201834982>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AC1rRNbuhXnSVVb7HlGeY-q_xkWMEgukks5uFmWkgaJpZM4VKRZt>\n> .\n>\n",
"Now I've had some time to take a closer look at this, I had a few quick questions/comments:\r\n\r\n* Regarding \"# angle tolerance should be looser\" + `tol_angle = 100 * tol` -- why not just change the default kwarg here?\r\n* How does `lat_type` work? Why not just get the lattice type via spacegroup analyzer?\r\n* Will this work if you input the conventional unit cell and not the primitive? The `vol_ratio =` line seems to make certain assumptions about the input structure that I'm not sure I understand.\r\n\r\nThanks!",
"First, I just think the tolerance for angle should be smaller than that for distance when determining the lattice type, and do not want to use two tolerance parameters.\r\n\r\nSecond, when the function has 'lat_type' input parameter, then it has no concrete structure within it. If it has a structure, we will determine the lat_type from its structure properties (no lat_type input parameter needed). I just use the structure's lattice (a, b, c) and angle (alpha, beta, gamma) to determine the lat_type without using the spacegroup analyzer. I do not want the user to swap the a,b,c or angles. e.g. for hexagonal lattice, a=b!=c. gamma=120. Maybe spacegroup can do similar thing, I am not very familiar with it. Anyway, this part is quick.\r\n\r\nThird, you can use conventional cell to generate the GB. Only fcc and bcc can also use the primitive cell. But if you use conventional cell for bcc or fcc, the code cannot guarantee the smallest GB structure. \r\n\r\nDefinitely, the code may need to be optimized further. Open for any suggestions.\r\n\r\nThanks!",
"I suggest we do the following:\r\ni. The user supplies whatever cell he wants, and we define (100) etc. based on the supplied structure. If he chooses to use primitive, we assume (100) refers to the primitive a direction. We should not allow alternative structure input based on lat_type. That is a recipe for disaster as there will be multiple methods for generating structure.\r\nii. Angle tolerance should be a default parameter.\r\niii. Pls move the gb generator to pymatgen.analysis.gb for now and update all tests accordingly. We will decide whether it should be part of core in future.\r\n"
] | 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
GB plane, rotation axis, rotation angle. The second one is to generate GBs from given transformation matrices for each grain. It works for any general GB, including both twist, tilt GBs, etc.
It also contains functions that can generate all possible sigma values and from sigma value to generate rotation angles needed for the GB generator.
|
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