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https://api.github.com/repos/materialsproject/pymatgen/issues/202 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/202/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/202/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/202/events | https://github.com/materialsproject/pymatgen/pull/202 | 65,327,439 | MDExOlB1bGxSZXF1ZXN0MzIyNzgwMDE= | 202 | Bug fix in solute defect parsing | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/203 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/203/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/203/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/203/events | https://github.com/materialsproject/pymatgen/issues/203 | 65,954,626 | MDU6SXNzdWU2NTk1NDYyNg== | 203 | Lattice parameters are not extracted from NWChem output | {
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"Thanks. That would be much appreciated.\nWe have not implement lattice parameters as we primarily use NWChem for molecular calculations at the moment. But I am sure this feature would be useful for many other users.\n",
"Very well then, I will open my fork of the code and start implementing the lattice parameter... | 2015-04-02T15:43:22 | 2015-04-07T16:58:11 | 2015-04-07T16:58:11Z | CONTRIBUTOR | {
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} | It seems that the lattice parameters are not extracted from the output of NWChem, a feature that would be nice to have. I wonder whether the developers feel positive about this development. I could implement it and present in a form of pull request if there is any possibility of such an improvement to get into the pack... | {
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} | This pull request implements parsing the lattice parameters from NWChem's output, if present. If lattice parameters are found in the output, an instance of `Structure` is created instead of `Molecule` and pushed in a separate list.
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"As far as I know, this is not an issue yet. Not sure about future. \n"
] | 2015-04-08T21:12:42 | 2015-04-14T00:36:16 | 2015-04-14T00:36:16Z | MEMBER | {
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```
from pymatgen import MPRester
from os import environ
mpr = MPRester(environ['MAPI_KEY'])
my_bs = mpr.get_bandstructure_by_material_id('mp-754937')
```
Output:
/Users/dwinston/.virtualenvs/mp/lib/python2.7/site-packages/requests/packages/urllib3/util/ssl_.py:79:... | {
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"Thanks for letting me know. I have just pushed a fix for potcar_setup. Is that the only one? I know that pmg works in Py3.\n\nShyue Ping\n\nOn April 12, 2015 at 2:21:35 PM, Michael Lamparski (notifications@github.com) wrote:\n\nVarious scripts in the scripts directory (such as potcar_setup) do not support Python 3... | 2015-04-12T21:21:34 | 2015-04-14T00:36:04 | 2015-04-14T00:36:04Z | CONTRIBUTOR | {
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```
python3 setup.py install
```
Then the scripts installed to `/usr/local/bin` will begin with `#!/path/to/python3`, causing them... | {
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"Thanks.\n"
] | 2015-04-13T14:42:08 | 2015-04-13T15:05:17 | 2015-04-13T14:51:26Z | CONTRIBUTOR | {
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Also, none of the tests called this method, so I added one.
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https://api.github.com/repos/materialsproject/pymatgen/issues/209 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/209/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/209/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/209/events | https://github.com/materialsproject/pymatgen/issues/209 | 68,223,180 | MDU6SXNzdWU2ODIyMzE4MA== | 209 | Bug in the updated dos code | {
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I am noticing this error when running the updated code on the same xml file:
Traceback (most recent call last):
File "./my_dos_plotter.py", line 53, in <module>
dp.add_dos_dict(cdos.get_site_spd_dos(cdos.structure.sites[0]))
File "/home/mbkumar/venv1/pymatgen/pymatgen/electronic_structure/dos.py",... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/210 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/210/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/210/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/210/events | https://github.com/materialsproject/pymatgen/issues/210 | 74,407,337 | MDU6SXNzdWU3NDQwNzMzNw== | 210 | electronic_structure.plotter.DosPlotter raises ValueError for some MP materials | {
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"This is really a data problem. I am not sure what is happening. But the energies has 581 elements and the densities has 601 elements. That cannot be the case.\n\nAlso, this seems to be non-spin-polarized, which is strange since we always do spin-polarized calculations. I suspect that the vasp run resulted in a bad... | 2015-05-08T15:48:31 | 2015-07-30T21:55:07 | 2015-07-30T21:55:07Z | MEMBER | {
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} | I'm getting a ValueError pertaining to numpy array shapes when trying to get the DOS plots for a couple of materials. Out of 500 sample materials, I found only two that fail to plot, so the problem may be upstream, e.g. the db data is misformatted. However, `MPRester.get_dos_by_material_id` succeeds in instantiating a ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/211 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/211/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/211/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/211/events | https://github.com/materialsproject/pymatgen/pull/211 | 76,729,551 | MDExOlB1bGxSZXF1ZXN0MzU1MTM3MDg= | 211 | Additional zeo++ functionality upon user request | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/212 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/212/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/212/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/212/events | https://github.com/materialsproject/pymatgen/pull/212 | 79,203,765 | MDExOlB1bGxSZXF1ZXN0MzU5ODgzMzc= | 212 | Cleaned up ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/213 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/213/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/213/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/213/events | https://github.com/materialsproject/pymatgen/issues/213 | 92,758,761 | MDU6SXNzdWU5Mjc1ODc2MQ== | 213 | semvar? | {
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"Generally, pymatgen follows pretty closely to semvar, though backwards incompatible changes do occur at what is so-called the minor version.\n\nThe evolution of pymatgen is too rapid to use standard semvar. Many “patches” in fact are new functionality development. The time between minor versions tend to be fairly ... | 2015-07-02T23:40:29 | 2015-07-03T00:31:54 | 2015-07-03T00:31:54Z | MEMBER | {
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} | What is this project's policy for version tagging? May I suggest using that of http://semver.org/?
There were some [deprecations](https://github.com/materialsproject/pymatgen/blob/master/CHANGES.rst#v305) introduced in v3.0.5 that are now incompatible changes as of v3.1. For example, the MP web code has a line
```
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"Below the affected code. It seems that `alpha` needs to be set to 90.\n\n```\n if new_matrix is None:\n #this if is to treat the case\n #where alpha==90 (but we still have a monoclinic sg\n new_matrix = [[a, 0, 0],\n [0, b,... | 2015-07-15T22:56:16 | 2015-07-30T21:48:02 | 2015-07-30T21:48:02Z | MEMBER | {
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} | In pymatgen 3.0.14, the `get_conventional_standard_structure` function crashes in line 618 with the error message: `local variable 'alpha' referenced before assignment`. For the special case with a monoclinic lattice type, a space group starting with 'C', and angle `landang[1][0] = 90`, the variable `alpha` is never ca... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/215 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/215/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/215/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/215/events | https://github.com/materialsproject/pymatgen/issues/215 | 97,518,983 | MDU6SXNzdWU5NzUxODk4Mw== | 215 | parsing of LORBIT and NELM by io.vaspio.Vasprun | {
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"I just pushed a fix to the NELM issue. But I cannot do anything about LORBIT. If the vasprun.xml does not report the right value, I can only leave it be. \n"
] | 2015-07-27T17:57:46 | 2015-07-28T04:18:26 | 2015-07-27T20:41:56Z | NONE | {
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} | vasprun.xml does not seem to read a numeric LORBIT correctly. When it is set in INCAR as an integer, it will be seen as a boolean tag and assigned False. The same could happen to other tags. Instead, OUTCAR has the right value, straight from INCAR.
NELM appears once in OUTCAR, but twice in vasprun.xml, one in 'electro... | {
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"My preference is if the anonymous formula is not built off the \"pretty formula\" but rather the reduced formula. ie. I would want Li2O2 to have anonymous formula for AB.\n",
"I am fine with this. Can someone fix this?\n"
] | 2015-07-30T17:54:15 | 2015-07-31T15:00:10 | 2015-07-31T15:00:10Z | CONTRIBUTOR | {
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} | The anonymous formula currently uses the list of special formulas to determine the reduced formula. For example, Li2O2 has anonymous formula A2B2 instead of AB. Is this desired functionality (and does anyone depend on it)?
As it is now, chemical substitutions applied to a structure can (sometimes) change its anonymous... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/217 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/217/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/217/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/217/events | https://github.com/materialsproject/pymatgen/pull/217 | 98,342,615 | MDExOlB1bGxSZXF1ZXN0NDEzMTgwMjU= | 217 | Allowing CIF data_* header to be prefixed with spaces and tabulations. | {
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"Thanks for the contribution. I will merge it.\n"
] | 2015-07-31T08:34:05 | 2015-07-31T14:00:28 | 2015-07-31T14:00:28Z | CONTRIBUTOR | {
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} | Current parser for CIF format files forbids CIF data_\* header to be prefixed with space, what is completely normal, according to IUCr's CIF syntax specification (http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax).
MWE (test.cif):
```
data_test_1
data_test_2
```
MWE (python script):
``` python
fro... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/218 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/218/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/218/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/218/events | https://github.com/materialsproject/pymatgen/issues/218 | 98,623,472 | MDU6SXNzdWU5ODYyMzQ3Mg== | 218 | pymatgen.io.vaspio.Incar() object copy method returns plain dict, rather than another object | {
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"You don't actually need to do .copy(). Just Incar(incar_old) will do.\n\nIn general, I don't want to override copy(). Incar inherits dict, which is why it returns a dict. For most purposes, an Incar is like a dict.\n"
] | 2015-08-02T17:23:05 | 2015-08-02T20:09:05 | 2015-08-02T20:09:05Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/219 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/219/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/219/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/219/events | https://github.com/materialsproject/pymatgen/issues/219 | 98,662,781 | MDU6SXNzdWU5ODY2Mjc4MQ== | 219 | Read WAVEDER(F) from Vasp LOPTICS runs? | {
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"Dear Miguel,\n\nI think this would be a nice addition. I have no idea how to read the WAVEDER without delving deep into the VASP source code to find out how it is generated (something I avoid). I think providing the facility to read the WAVEDERF is fine, as long as you document in the code that this is only useful... | 2015-08-03T03:11:45 | 2020-06-05T07:52:15 | 2015-08-04T00:59:07Z | CONTRIBUTOR | {
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} | Hello all,
we've recently been uncommenting a line (CALL WRT_CDER_BETWEEN_STATES_FORMATTED..) in vasp linear_optics.F which writes WAVEDERF, a formatted version of WAVEDER, to get the optical transition matrix elements, and we were thinking this could be a nice addition to vasp_output.py, since coupled with other band... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/220 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/220/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/220/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/220/events | https://github.com/materialsproject/pymatgen/pull/220 | 98,865,666 | MDExOlB1bGxSZXF1ZXN0NDE1MjUxMTc= | 220 | Add class for parsing WAVEDERF file | {
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"Thanks!\n"
] | 2015-08-04T00:53:20 | 2015-08-04T01:45:51 | 2015-08-04T00:58:48Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/221 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/221/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/221/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/221/events | https://github.com/materialsproject/pymatgen/pull/221 | 99,130,526 | MDExOlB1bGxSZXF1ZXN0NDE2NDU2MTc= | 221 | Multiple dielectricfunction elements in vasprun.xml | {
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"Thanks for the contribution. I made a minor modification to maintain Py3k compatibility.\n"
] | 2015-08-05T05:57:57 | 2015-08-05T15:11:19 | 2015-08-05T13:33:03Z | CONTRIBUTOR | {
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} | When [using the GW routines for the determination of frequency dependent dielectric matrix](http://cms.mpi.univie.ac.at/vasp/vasp/Using_GW_routines_determination_frequency_dependent_dielectric_matrix.html), there are multiple dielectricfuction elements in vasprun.xml, distinguished by element comments, and the Vasprun ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/222 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/222/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/222/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/222/events | https://github.com/materialsproject/pymatgen/issues/222 | 99,295,381 | MDU6SXNzdWU5OTI5NTM4MQ== | 222 | pymatgen.Structure.from_str() does not really implement arg "primitive", except for cif | {
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} | And it makes the primitive cell claim in the docstring of `pymatgen.Structure.from_file()` unexpected.
`pymatgen.Structure.from_str` looks like this:
``` python
@classmethod
def from_str(cls, input_string, fmt, primitive=False, sort=False):
...
if fmt == "cif":
parser = CifParser.from_string(input_string)
s =... | {
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"I am not sure how there can be a name conflict. The ase package is properly namespaced in pymatgen. You just do \n\n```\nfrom pymatgen.io.ase import AseAtomsAdaptor\n```\n\nThis works perfectly fine to me.\n",
"Hi shyuep,\nYes, that works fine, but when i do the following(structure is a Structure object):\n\n> >... | 2015-08-05T22:11:15 | 2015-08-06T01:57:45 | 2015-08-05T22:45:09Z | CONTRIBUTOR | {
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I just installed pymatgen version 3.1.5 and i was trying to use the aseadaptor from io/ase.py module. It seems like the module name clashes with the ase package and the statement 'from ase import Atoms' doesnt run evenafter installing ase. I was using version 3.1.0 before and didnt have any trouble using the adapto... | {
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"Thanks. I have fixed it the explicit kpoint parsing.\nThe get_kpoints doesn't really matter since numpy arrays are effectively lists for the most part. Is there a specific use case you find a problem with the numpy arrays?\n",
"No, not at all. It (kpoints.kpts) just didn't print out uniformly if there are lists ... | 2015-08-07T03:59:06 | 2016-04-20T04:55:04 | 2015-08-11T17:19:54Z | NONE | {
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``` python
#Assume explicit KPOINTS if all else fails.
style = Kpoints.supported_modes.Cartesian if style == "ck" \
else Kpoints.supported_modes.Reciprocal
kpts = []
kpts_weights = []
labels = []
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Initial code commits include place holder for Freysoldt correction, defect analyzer.
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Could change the original Locpot unit test so that it runs the... | {
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} | abinitio needs to be refactored to simply abinit to be consistent with the rest of the IO modules.
@gmatteo can you take care of this? I don't want to break anything in abipy because of what I do. But let me know if you prefer me to do it? For me, it's just a quick rename in an IDE.
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"You have an old spglib? Try doing python setup.py develop again first. \n\nShyue Ping\n\nOn August 13, 2015 at 12:25:59, Bharat Medasani (notifications@github.com) wrote:\n\nHello Shyue,\n\nI am getting the following error when trying to use SpacegroupAnalyzer.\n\nTraceback (most recent call last):\nFile \"BaBrF_v... | 2015-08-13T19:25:59 | 2015-08-13T19:42:13 | 2015-08-13T19:42:13Z | CONTRIBUTOR | {
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I am getting the following error when trying to use SpacegroupAnalyzer.
Traceback (most recent call last):
File "BaBrF_vacancy_scaling.py", line 9, in <module>
vac = Vacancy(uc, {}, {})
File "/Users/mbkumar/Research/Defects/pymatgen/pymatgen/analysis/defects/point_defects.py", line 284, in **init*... | {
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"Yeah, this is desired. If you want to to map a non-centrosymmetric\nstructure to its mirror image, you need the rotoinversions. Unless I'm\nmissing something....\n\nOn Wed, Aug 19, 2015 at 12:25 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> The Lattice.find_all_mappings can return aligned lattices that ... | 2015-08-19T16:25:11 | 2015-09-02T16:52:41 | 2015-09-02T16:52:41Z | MEMBER | {
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[[ 4.71115317 -0.32497418 -2.99516511]
[ -3.51444478 5.01683676 -0.34400454]
[ 0.1531054 -0.85080479 18.69400637]]
mapping with itself.
Is this really the desired behavior?
@wmdrichar... | {
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"Hi Comac,\n\nCan you pls move agl_thermal to under analysis. And have a more informative name than \"agl_\" (I have no idea what agl stands for). You also should not be commiting the distribute packages. \n"
] | 2015-08-22T01:29:04 | 2016-09-25T20:09:53 | 2016-09-25T20:09:53Z | NONE | {
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"Hello Nils,\n\nThanks for the code additions. IMO the VaspSet code needs slight changes to conform with the existing code. Please take a look at MITNEBVaspInputSet implementation for reference. Basically we are subclassing from MPVaspInputSet, all the settings and modifying them slightly. So the **init** function ... | 2015-08-25T01:47:48 | 2016-09-25T20:09:43 | 2016-09-25T20:09:43Z | CONTRIBUTOR | {
"total": 0,
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"Thanks for reporting this. I just pushed out a version taht fixes this.\n"
] | 2015-08-27T13:03:00 | 2015-08-27T15:32:38 | 2015-08-27T15:13:26Z | NONE | {
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} | I install pymatgen through pip on Ubuntu 14.04. When I run `pmg`, the following error info is outputed:
```
from: can't read /var/mail/__future__
/usr/local/bin/pmg: line 10: $'\nA master convenience script with many tools for vasp and structure analysis.\n': command not found
/usr/local/bin/pmg: line 12: __author__: ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/237 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/237/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/237/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/237/events | https://github.com/materialsproject/pymatgen/issues/237 | 103,895,917 | MDU6SXNzdWUxMDM4OTU5MTc= | 237 | Overlapping of labels when generating XRD pattern | {
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"Thanks for reporting this. But this is merely a problem that it is difficult to programmatically determine the optimal positions to place the labels. If you wish, you can turn off labels in the XRD plot, and then do the labels manually. I am also open to suggestions about how to allocate label positions.\n",
"I ... | 2015-08-30T02:45:05 | 2015-09-02T16:52:03 | 2015-09-02T16:52:03Z | NONE | {
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I'm trying to use `pymatgen`'s `XRDCalculator` to calculate XRD pattern,
``` python
from pymatgen.io.vaspio import Poscar
p=Poscar.from_file('POSCAR')
from pymatgen import Lattice, Structure
from pymatgen.analysis.diffraction.xrd import XRDCalculator
from IPython.display import Image, display
c = XRDCa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/238 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/238/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/238/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/238/events | https://github.com/materialsproject/pymatgen/issues/238 | 103,983,274 | MDU6SXNzdWUxMDM5ODMyNzQ= | 238 | pmg.analysis.structure_matcher.StructureMatcher() primitive_cell setting uses pmg.Structure.find_primitive_structure() without specifying tolerance. | {
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"@wmdrichards or @sdacek , can you please look into this? Thanks.\n",
"Do you have a specific case where this is an issue? Choosing default tolerances is kind of tricky, and this tolerance works as desired in almost all instances that I am aware of. You can always avoid calling Structure.find_primitive_structure(... | 2015-08-31T04:39:51 | 2015-09-18T22:47:18 | 2015-09-18T22:47:18Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/239 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/239/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/239/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/239/events | https://github.com/materialsproject/pymatgen/issues/239 | 104,189,739 | MDU6SXNzdWUxMDQxODk3Mzk= | 239 | In some cases pmg.symmetry.analyzer.SpacegroupAnalyzer.get_conventional_standard_structure() returns structure not matching the spacegroup it detects. | {
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"The `get_*_standard_structure` method first uses `spglib` to get a refined structure. That modifies the atoms such that they are in the expected symmetry positions. \r\n\r\nBut that really should only preserve or increase symmetry. It is odd that it actually decreases symmetry.\r\n\r\n@hautierg Can you investigate... | 2015-09-01T05:26:43 | 2022-10-22T20:20:58 | 2022-10-22T20:20:58Z | NONE | {
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st = m.get_structure_by_material_id('mp-542189')
spga = mg.symmetry.analyzer.SpacegroupAnalyzer(st, 0.1)
print(spga.get_spacegroup()) # C2/c
st1 = spga.get_conventional_standard_structure()
spga1 = mg.symmetry.analyzer.SpacegroupAnalyzer(st1, 0.1) # this symprec doesn't help
print(spga1.get_spacegroup()) #... | {
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"If we look at the VASP example, the selective dynamics are indicated as T/F, not 1 or 0. The unittests for the T/F case show that it works perfectly fine. \n\nTo do 1/0 is easy, but is this really needed?\n",
"not really, i used numpy arrays to automatically set the flags for slab relaxations as it would give me... | 2015-09-02T00:29:23 | 2015-09-03T14:15:57 | 2015-09-03T14:10:50Z | CONTRIBUTOR | {
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example serialized selective dynamics:
"selective_dynamics": [
{
"dtype": "float64",
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"Note quite sure what is happening, but I suspect the problem is that the original structure from MP is a primitive structure.\n"
] | 2015-09-03T16:42:53 | 2015-10-02T19:39:35 | 2015-10-02T19:39:35Z | NONE | {
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try:
``` python
st = m.get_structure_by_material_id('mp-542189')
mg.io.cif.CifWriter(st, 0.01).write_file('Cc.cif')
mg.io.cif.CifWriter(st, 0.... | {
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"Hello Alex,\n\nDanny forwarded your email. Thank you for adding your modifications and you are always welcome to contribute code and bug fixes.\n\nBlind removal of 6th line in LOCPOT file within pymatgen is a bad idea. The LOCPOT object created by pymatgen ignores the 6th line. If we are using those LOCPOTs (writt... | 2015-09-09T13:30:07 | 2016-09-25T20:09:44 | 2016-09-25T20:09:44Z | NONE | {
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"This is normal. But I added functionality to allow you to get specific data. Pull the latest changes and you should be ale to do what you want.\n"
] | 2015-09-15T21:16:14 | 2015-09-17T16:52:02 | 2015-09-17T16:51:31Z | CONTRIBUTOR | {
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entry = mpr.get_entries("mp-10",inc_structure="final")[0]
print entry.data
Output gives me an empty data dictionary. Is it normal?
MPRester.get_data work for me though.
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} | Minimal working example (syntactically valid CIF):
```
data_mwe
loop_
_tag
;
;
```
Error & trace:
``` python
In [6]: CifFile.from_file("mwe.cif")
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-6-14... | {
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"THanks for the nice contribution!\n"
] | 2015-09-21T05:44:04 | 2015-09-21T05:49:36 | 2015-09-21T05:49:27Z | CONTRIBUTOR | {
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} | - Support parsing hessian & projected hessian matrices from nwchem outputs.
- Support parsing raw frequencies.
- Unit tests are added and tested.
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"Sorry, I have just found constants in the core. Can I add several constants (h and c) ?\nGermain\n",
"Sure go ahead. Using scipy is fine too since we already incldue scipy as a dependency,\n"
] | 2015-09-22T18:59:22 | 2015-09-22T19:55:09 | 2015-09-22T19:55:09Z | CONTRIBUTOR | {
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Is it possible to use `scipy.constants` module in the implementation of methods or new dependencies are not recommended ?
Are standard physical constants accessible somewhere in pymatgen ?
Thanks
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"Thanks for the contributions!\n"
] | 2015-09-22T20:25:07 | 2015-09-22T20:27:41 | 2015-09-22T20:27:33Z | CONTRIBUTOR | {
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} | - fix compatibility issues between gaussian03/gaussian09
- new methods to read potential energy surface computed with gaussian
- new methods to read electronic transitions computed with TD-DFT
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"I'm not entirely sure what get_all_distance_and_image is supposed to return -- as far as I can tell, its a method that you created from part of the code from get_distance_and_image. I don't think it should be its own function because the sites that it returns are entirely dependent on the lattice representation, a... | 2015-10-02T18:35:33 | 2020-07-11T02:47:54 | 2020-07-11T02:47:54Z | MEMBER | {
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Try the following code::
```
from pymatgen.util.testing import PymatgenTest
cscl = PymatgenTest.get_structure("CsCl")
gen = SlabGenerator(cscl, (1, 1, 1), 10, 10)
o = gen.o... | {
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"Hi\nI got the same issues with large numbers of Kpoints or huge vasprun.xml files (several hundred of Mo). I guess there are too many xml tags/attribute in the file. In that cases I used Poscar class instead. I am working on it because, for the moment, that class does not return an electronic_strucure.Band object.... | 2015-10-08T01:58:36 | 2015-10-30T22:43:36 | 2015-10-30T22:43:36Z | NONE | {
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run = Vasprun(pwd+"/Band-DOS/vasprun.xml",parse_projected_eigen = True)
bands = run.get_band_structure(pwd+"/Band-DOS/KPOINTS",efermi = dosrun.efermi,line_mode = True)
plotter = BSPlotterProjected(bands)
graph = plotter.get_elt_projected_plots_color()
--- CODE end ---
when I use small vasprun.xml (500KB~1... | {
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"Thanks!\n"
] | 2015-10-09T09:50:32 | 2015-10-09T13:27:55 | 2015-10-09T13:27:48Z | CONTRIBUTOR | {
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Please check whether the method names comply with the pymatgen's style.
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- Unittests are added and tested.
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"thanks\n"
] | 2015-10-16T01:16:15 | 2015-10-16T01:41:36 | 2015-10-16T01:41:30Z | CONTRIBUTOR | {
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} | I've extended the constructor of Xdatcar to enable successful treatment of multiple consecutive preambles in XDATCAR. That case seems rare, but I've just encountered it.
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"Thanks for reporting this.\n"
] | 2015-10-20T17:03:24 | 2015-10-20T18:45:17 | 2015-10-20T18:45:00Z | NONE | {
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} | In line 704 and 705 of pymatgen/electronic_structure/bandstructure.py, the lines:
704 "name": (self._kpoints[b[0]].label + "-" +
705 self._kpoints[b[-1]].label)})
throw a variable compatibility error:
TypeError: unsupported operand type(s) for... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/259 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/259/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/259/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/259/events | https://github.com/materialsproject/pymatgen/pull/259 | 114,251,377 | MDExOlB1bGxSZXF1ZXN0NDkyNTc4NTc= | 259 | Enhance: GaussianOutput | {
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"I will fix my codes and then give a new pull request.\n"
] | 2015-10-30T11:23:29 | 2015-10-30T11:52:19 | 2015-10-30T11:52:19Z | CONTRIBUTOR | {
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} | The class `GaussianOutput` now supports parsing:
- Cartesian forces
- Frequencies
- Normal modes
Also add some unit tests.
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https://api.github.com/repos/materialsproject/pymatgen/issues/260 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/260/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/260/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/260/events | https://github.com/materialsproject/pymatgen/pull/260 | 114,258,244 | MDExOlB1bGxSZXF1ZXN0NDkyNjIwNTY= | 260 | Enhance: GaussianOutput | {
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"thanks!\n",
"I have added you to the list of authors for the gaussian module in recognition for your efforts.\n"
] | 2015-10-30T12:12:36 | 2015-10-30T22:45:41 | 2015-10-30T13:38:38Z | CONTRIBUTOR | {
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} | The class `GaussianOutput` now supports parsing:
- Frequencies
- Normal modes
- Cartesian forces
Python 3 compatible.
Unit tests are added.
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https://api.github.com/repos/materialsproject/pymatgen/issues/261 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/261/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/261/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/261/events | https://github.com/materialsproject/pymatgen/issues/261 | 114,371,239 | MDU6SXNzdWUxMTQzNzEyMzk= | 261 | Lattice.find_all_mappings test fails with latest numpy. | {
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"The new numpy version has a very bad bug with non contiguous data in np.inner calls:\nhttps://github.com/numpy/numpy/issues/6532\n",
"@shyuep Could you try with the 1.10.2rc1 release?\n",
"numpy 1.10.2rc1 seems to have fixed it\n",
"Yes, I confirm that too. Thanks !\n"
] | 2015-10-30T23:13:12 | 2015-11-14T15:31:33 | 2015-11-14T15:31:33Z | MEMBER | {
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} | Pls investigate. Error message below:
AssertionError:
Arrays are not almost equal to 5 decimals
(mismatch 100.0%)
x: array([[ 0.54756, -0.03654, -0.14159],
[ 0.06854, -0.38895, -0.89413],
[-1.78544, -0.24974, -0.0563 ]])
y: array([[ 0.2, -0.4, -1.4],
[ 0. , -0.4, -1. ],
[-0.6, -0.9, -0.... | {
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- Tests are added.
- Python3 compatible.
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https://api.github.com/repos/materialsproject/pymatgen/issues/264 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/264/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/264/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/264/events | https://github.com/materialsproject/pymatgen/pull/264 | 115,606,587 | MDExOlB1bGxSZXF1ZXN0NTAwMTQ2NTU= | 264 | Deformed structure set | {
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"Thanks. This looks great in terms of coding, but can you move the entire elasticity branch under the analysis package. The pymagen.X level if reserved for high-level abstraction. Specific property analyses are parked under pymatgen.analysis.\n",
"BTW, you do not need to withdraw the pull request. You simplt need... | 2015-11-06T22:50:32 | 2015-11-07T03:26:37 | 2015-11-07T03:26:37Z | CONTRIBUTOR | {
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} | Added the `elasticity` package, which includes modules
- tensors.py - `SQTensor` base class for 2-D tensors and relevant matrix operations
- stress.py - `Stress` class for various operations related to stress
- strain.py - `Deformation`, `Strain`, and `DeformedStructureSet` classes for operations related to structural... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/265 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/265/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/265/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/265/events | https://github.com/materialsproject/pymatgen/issues/265 | 115,769,340 | MDU6SXNzdWUxMTU3NjkzNDA= | 265 | Cannot understand Vasprun parser error in reading a vasprun.xml file - please advise | {
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"We use the python ElementTree XML parser for vasprun. While I think there is a way to change the error handling, it is generally not a good idea to ignore errors in XML. There is no way to ensure that the parsing gives reasonable results. \n\nI would say that if you know that there is a misprint, you can preproces... | 2015-11-08T23:28:31 | 2015-11-09T00:35:37 | 2015-11-09T00:35:37Z | NONE | {
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} | I get the error:
ParseError: mismatched tag: line 773, column 4
when using the Vasprun parser in pymatgen.io.vasp.outputs on a perfectly written out and converged vasprun.xml .. Any reason for this ?
The OUTCAR file yields a perfectly converged energy.
The line flagged in the vasprun.xml is one of the closing li... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/266 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/266/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/266/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/266/events | https://github.com/materialsproject/pymatgen/issues/266 | 116,118,986 | MDU6SXNzdWUxMTYxMTg5ODY= | 266 | A question about BSplotter() | {
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"Hi,\n\nGithub issues is for reporting bugs and feature requests. For such questions, please keep it in the pymatgen Google groups.\n",
"It is a common convention/practice in insulators and semiconductors to set the zero of energy at the VBM.\n\nGeoffroy\n\n> On 10 Nov 2015, at 15:37, 91bsjun notifications@github... | 2015-11-10T14:37:18 | 2015-11-10T14:52:16 | 2015-11-10T14:48:25Z | NONE | {
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} | Hi, I have a new question.
I want to know one of the operation in the bs_plot_data()
(In the class of BSplotter() )
why do this operation when non metalic band structure ?
> > > zero_energy = self._bs.get_vbm()['energy']
--- script ---
```
if self._bs.is_metal():
zero_energy = self._bs.efermi
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https://api.github.com/repos/materialsproject/pymatgen/issues/267 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/267/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/267/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/267/events | https://github.com/materialsproject/pymatgen/issues/267 | 116,468,243 | MDU6SXNzdWUxMTY0NjgyNDM= | 267 | use SlabGenerator.get_slab to generate a surface has a bug for ZnO(010) | {
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"Although I use get_sorted_structure() and get the right POSCAR format, I still want to know the reason. \n",
"Hi,\n\nPls post your technical questions to the pymatgen Google groups. Github issues are for reporting bugs and problems.\n\nAs for your specific problem, the structures returned by get_slab() is not s... | 2015-11-12T02:45:31 | 2015-11-12T06:52:36 | 2015-11-12T03:26:25Z | NONE | {
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My code is following:
ZnO=Structure.from_file("ZnO.cif",primitive=False)
Al55=SlabGenerator(ZnO,[0,1,0],5.3,5.0,lll_reduce=False,center_slab=False).get_slab()
IStructure.to(Al55,"poscar",filename="PO... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/268 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/268/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/268/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/268/events | https://github.com/materialsproject/pymatgen/pull/268 | 116,883,630 | MDExOlB1bGxSZXF1ZXN0NTA3MTEwMDY= | 268 | added explicit polar decomposition method to allow for more flexible … | {
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"Hmm... not quite sure why we need to implement an explicity polar decompositno method?\n",
"We were having an issue with the scipy dependency, since the polar method was implemented in sciyp/0.14.0 and some folks seem to be using older versions. Since it was the only scipy dependency in analysis.elasticity, I m... | 2015-11-14T01:03:46 | 2015-11-14T05:48:29 | 2015-11-14T05:48:29Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/269 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/269/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/269/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/269/events | https://github.com/materialsproject/pymatgen/issues/269 | 116,922,781 | MDU6SXNzdWUxMTY5MjI3ODE= | 269 | SlabGenerator.get_slab can not make sure the specific atom on the surface? | {
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"You can create the Slab first and then replace one of the surface atoms. The surface atoms is always the lowest or higher c fractional coordinate.\n",
"Thanks for your advice, I want to dope first and then create the slab, Pymatgen now can not satify this? \nThanks for your reply.\n",
"Not quite sure what you ... | 2015-11-14T12:40:46 | 2015-11-17T00:48:16 | 2015-11-14T15:51:40Z | NONE | {
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} | I want to use slabgenerator.get_slab to get (111)Fe.cif (2x2x2supercell) with one Cu dopant, and make sure that the Cu atom lies on the surface, or the atom sites the mesh origin(i.e., (0,0,0) site), how should I do? Whether Pymatgen.surface module supply this function?
I try use shift to adjust the surface, but the r... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/270 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/270/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/270/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/270/events | https://github.com/materialsproject/pymatgen/pull/270 | 117,575,307 | MDExOlB1bGxSZXF1ZXN0NTEwNzc0OTM= | 270 | Fiesta io | {
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} | - add io for Fiesta code (http://perso.neel.cnrs.fr/xavier.blase/fiesta/index.html): GW and BSE calculations with gaussian basis set.
- add time to io.nwchem.NwOutput
Nicolas Dardenne
UCL Belgium
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Mod to nwchem
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https://api.github.com/repos/materialsproject/pymatgen/issues/272 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/272/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/272/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/272/events | https://github.com/materialsproject/pymatgen/issues/272 | 117,867,602 | MDU6SXNzdWUxMTc4Njc2MDI= | 272 | pymatgen.core.periodic_table: block property | {
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"Your change appears to assign Lu and Lr to the \"f\"-block (rather than \nthe \"d\"-block). But perhaps that was intentional?\n- Randy\n\nOn 11/19/2015 10:33 AM, Shyue Ping Ong wrote:\n\n> Closed #272 https://github.com/materialsproject/pymatgen/issues/272 \n> via 91acf19 \n> https://github.com/materialsproject/p... | 2015-11-19T17:44:39 | 2015-11-19T19:54:59 | 2015-11-19T18:33:30Z | NONE | {
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} | Not being a materials scientist, perhaps I am simply naive, but I find some of the current block assignments to be surprising. The relevant code is:
> ```
> @property
> def block(self):
> """
> Return the block character "s,p,d,f"
> """
> block = ""
> if self.group in [1, 2]:
> block = "s"... | {
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} | Looking at the first few lines of the get_voronoi_polyhedra code:
> def get_voronoi_polyhedra(self, n):
> ...
> localtarget = self._target
> center = self._structure[n]
> neighbors = self._structure.get_sites_in_sphere(
> center.coords, VoronoiCoordFinder.default_cutoff)
Unless you... | {
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"Tess, I just pushed a quick fix that uses data obtained form the bilbao crystallographic server. Pls test it and see if it works. I haven't tried to really implement a true super-sub group matching. I merely saved the tree of relationships and used that for the super and sub group test.\n",
"Hi Shyue Ping, Thank... | 2015-11-20T01:10:19 | 2015-11-20T18:35:36 | 2015-11-20T15:33:07Z | CONTRIBUTOR | {
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"AbstractVaspINputSet is an abstract base class. You need to use one of the concrete implementations. E.g., MPVaspInputSet().get_all_vasp_input(s1).\n\nThis is not a bug.\n"
] | 2015-11-20T10:13:27 | 2015-11-20T13:55:00 | 2015-11-20T13:55:00Z | NONE | {
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} | from pymatgen.core import *
from pymatgen.io.vasp.sets import *
s1 = IStructure.from_file("tst.cif")
AbstractVaspInputSet.get_all_vasp_input(s1)
Here is the error.
File "<stdin>", line 1, in <module>
TypeError: unbound method get_all_vasp_input() must be called with AbstractVaspInputSet instance as first argument (g... | {
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} | - io.fiesta for code Fiesta (GW and BSE with gaussian basis set)
- modified nwchem with basis set option and time info
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"What command did you use to upgrade? \n",
"I used: \n\npip install pymatgen --upgrade --no-deps\n\nI also tried uninstalling, upgrading pyspglib, and the reinstalling with pip.\n\nSince I posted I have installed 3.2.7 successfully on other systems, but I am still encountering the same issue on the original compu... | 2015-11-25T16:37:25 | 2016-04-07T22:49:46 | 2015-11-25T20:18:31Z | NONE | {
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} | I upgraded to 3.2.7 and can no longer import pymatgen, and have the following error:
File "<stdin>", line 1, in <module>
File ".../lib/python2.7/site-packages/pymatgen/**init**.py", line 17, in <module>
from .io.smart import read_structure, write_structure, read_mol, write_mol
File "...0/lib/python2.7/site-pac... | {
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"This is not the correct implementation. You are changing anything that has a S. That is not correct. What happens with sulfates?\n\nThe correct way of dealing with sulfide is not mdify the sulfide itself, but to add it to the compound energies. That way, anything that has reduced_formula = \"S\" will be modified t... | 2015-12-02T23:39:03 | 2015-12-03T03:14:47 | 2015-12-03T03:14:47Z | CONTRIBUTOR | {
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"Thanks!\n"
] | 2015-12-03T10:10:59 | 2015-12-03T14:44:35 | 2015-12-03T14:19:40Z | CONTRIBUTOR | {
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- Basic support for parsing ADF output files.
- Python 2/3 compatible.
- Unit tests are added.
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"Try modifying the symprec. The default is pretty high. \n\nShyue Ping\n\nOn Thu, Dec 3, 2015 at 5:57 PM -0800, \"gcheon\" notifications@github.com wrote:\n\nHello,\n\nI'm trying to analyze a structure with no screw axes(I intentionally modified the structure to break that symmetry- the screw axis was the z axis, s... | 2015-12-04T01:57:42 | 2015-12-06T17:19:50 | 2015-12-06T17:19:49Z | CONTRIBUTOR | {
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I'm trying to analyze a structure with no screw axes(I intentionally modified the structure to break that symmetry- the screw axis was the z axis, so I copied the unit cell in a random position along the z axis. Structure on the bottom), but get_point_group() keeps saying that it has a screw axis(point group 32... | {
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"We cannot abandon pyhull completely for two undocumented reasons. Pymatgen is used in the Materials Project to generate phase diagrams. To make sure we can do it in a reasonably fast fashion, we use multiprocessing. The problem we had was that scipy's implementation of the convex hull does not work in multiprocess... | 2015-12-06T10:41:26 | 2015-12-06T17:19:16 | 2015-12-06T17:19:16Z | NONE | {
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the main problem I have with using pymatgen is that is uninstallable right now under a windows in 64 bit (32 bit seems to work though). The reason for this is the installation of pyhull. Is there any chance that pyhull could just be replaced by the scipy implementation?
As a side note, even the maintainer of ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/282 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/282/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/282/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/282/events | https://github.com/materialsproject/pymatgen/issues/282 | 120,646,413 | MDU6SXNzdWUxMjA2NDY0MTM= | 282 | Make electronic structure classes independent of Pyhull | {
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"Looks like this was fixed in [v2017.12.8](https://github.com/materialsproject/pymatgen/releases/tag/v2017.12.8)."
] | 2015-12-06T17:17:00 | 2023-05-29T18:24:20 | 2023-05-29T18:24:20Z | MEMBER | {
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} | Pyhull is still used in the BSPlotter. Can these be switched over to scipy's implementation? It does not seem too difficult for the electronic structure classes. The plan is to move to a Pyhull-free pymatgen for easier support on more platforms.
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} | Pyhull is still used in the Pourbaix. Can these be switched over to scipy's implementation? This seems a bit more work since the halfspace and other functions used by Pourbaix does not seem to have an equivalent in scipy.
The plan is to move to a Pyhull-free pymatgen for easier support on more platforms.
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"This is almost certainly a tolerance issue. You have one lattice vector that is 68A!\nTry playing around with the tolerances.\n\nShyue Ping\n\nOn December 8, 2015 at 10:03:28 PM, wangnumber14 (notifications@github.com) wrote:\n\nwhen I use\nsym=SpacegroupAnalyzer(IStructure.from_file(\"POSCAR\",False, False))\npri... | 2015-12-09T06:03:26 | 2015-12-15T03:15:22 | 2015-12-15T02:12:39Z | NONE | {
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sym=SpacegroupAnalyzer(IStructure.from_file("POSCAR",False, False))
prim = sym.get_primitive_standard_structure(international_monoclinic=False)
It has errors. It's the first time to see this error.
I got the messages in follows:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
prim = sym.get_primit... | {
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"I don't think this is actually doable. With *\\* 0.5, the behavior is specified by the **pow** magic function, which we can specify a behavior for the units. I have no idea what the math.sqrt function internally does to compute the sqrt. The same goes for math.pow and the functions.\n",
"If you read the official... | 2015-12-15T00:58:07 | 2015-12-15T03:21:34 | 2015-12-15T02:10:37Z | MEMBER | {
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} | I am playing with the pymatgen units class, which on the whole I find to be really nice.
I am having a problem with applying math.sqrt() on FloatWithUnit and am wondering why it is not supported.
i.e., this does not work:
```
from pymatgen.core.units import FloatWithUnit
import math
x = FloatWithUnit(9, "m^2 s^-2")
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"Note - there is a second commit that helps the unitized decorator function as expected when returning unit objects.\n"
] | 2015-12-15T01:32:52 | 2015-12-15T02:07:52 | 2015-12-15T02:07:52Z | MEMBER | {
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"Hi, unfortunately we cannot support all the different compilers. I have discussed with the spglib author and we think it's best if you use standard gcc to compile this.\n"
] | 2015-12-15T12:09:27 | 2016-01-18T19:17:41 | 2016-01-18T19:17:41Z | NONE | {
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Hi,
I had some issues building pymatgen-3.2.8.tar.gz on windows using Python 2.7.2 and MSVC 2008.
1. The spglib C files do not have topmost variable declarations. Trick used to was to rename all .c files to .cpp files:
find -nam... | {
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"Hello Kamal,\n\nThe svn access was modified slightly. Try the links to download Zeo++ and\nVoro++\n\nhttps://code.lbl.gov/scm/?group_id=97\n\nhttps://code.lbl.gov/scm/?group_id=108\n\nIn the Zeo++ trunk folder, cython folder is present.\\\nKeep in mind, there is a naming clash with zeo++ in pymatgen at present. I\... | 2015-12-22T16:21:00 | 2016-02-19T18:28:12 | 2016-02-19T18:28:12Z | NONE | {
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I would like to use interstitial package in pymatgen.
I installed cython, voro++ and zeo++ on a linux machine separately, but I don't see any cython_wrapper code as mentioned in the following link , and perhaps thats why I can't import zeo in python
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"Trying to cherrypick a particular commit, but not happening.\n"
] | 2015-12-25T18:40:03 | 2015-12-25T18:50:29 | 2015-12-25T18:50:19Z | CONTRIBUTOR | {
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"Fixed.\n"
] | 2016-01-02T04:00:06 | 2016-01-05T00:35:46 | 2016-01-05T00:35:46Z | MEMBER | {
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@hautierg Can you pls investigate since I don't know the BS code that well? Thanks.
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"For constructing supercells, it might be better to convert the Slab to a Structure first, e.g., Strcture.from_sites(slab)\n\nShyue Ping\n\nOn January 7, 2016 at 10:18:07 AM, rtrottie (notifications@github.com) wrote:\n\nCalling make_supercell (or using the pythonic \\* (#,#,#) ) on a slab produces the following er... | 2016-01-07T18:18:06 | 2016-01-08T16:08:54 | 2016-01-08T16:08:54Z | NONE | {
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File "/anaconda2/lib/python2.7/site-packages/pymatgen/core/structure.py", line 667, in **mul**
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"Thanks for the excellent contribution. However, I would like to suggest a few changes.\n\ni. the in_bound method seems to be more easily dealt with as max(lower, min(upper, value)). In fact, a variant is used in pymatgen.utils.num_utils.abs_cap.\n\nii. While the prototype structure is useful, the implementation is... | 2016-01-14T01:03:48 | 2016-02-05T15:56:44 | 2016-02-05T15:56:43Z | CONTRIBUTOR | {
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My thoughts were to put the entire class actually into the structure_analyzer.py, if this is wanted from other people, too.
prototype_structures.py is mainly a helper class to easily set up prototypic structures for the order parameter unit tests. But they could be generally also valuable ... | {
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Now it seems that I must create a new Poscar with the structure and include selective_dynamics at that point, rather than being able to set it after the fact.
Also, only a numpy array .tolist() seems to work, and not giving just an array.
[poscar_selective_dynamics... | {
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