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"Thanks for letting us know. I have fixed the issue and pushed out the latest release (1.2.4) which should not have this problem, and with some new bug fixes.\n"
] | 2012-02-26T12:10:46 | 2012-02-26T14:52:41 | 2012-02-26T14:52:41Z | NONE | {
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Therefore the _load__pt_data function fails with a "IOError: [Errno 2] No such file or directory:"
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"Error fixed. Occupancy fractions that result in ambiguous numbers to remove (>.1 from an integer) now raise an error\n"
] | 2012-04-20T14:57:49 | 2012-04-20T18:36:36 | 2012-04-20T18:36:36Z | MEMBER | {
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} | The OrderDisorderTransformation fails with an non-intuitive error when the actual cell is too small to perform ordering. E.g., if you use a primitive cell of a NMC material, the cell only contains one atom with a 0.33 Ni, 0.33 Co, 0.33 Mn occu. This has not enough atoms to perform ordering.
The transformation should ... | {
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"ODST now supports BEST_FIRST algo. Working on a better one\n"
] | 2012-04-20T15:00:52 | 2019-08-26T21:38:29 | 2019-08-26T21:38:29Z | MEMBER | {
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"There's a num_structures argument that used to be in **init** I've moved it to apply_transformation. As a default it is set to one and so only one structure is calculated. If you want more structures you need to increase that number\n",
"Ok.\n"
] | 2012-04-20T15:25:17 | 2014-06-23T17:11:42 | 2012-04-20T17:27:22Z | MEMBER | {
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"Geoffroy, any update on this? \n"
] | 2012-11-17T16:56:37 | 2014-09-18T13:43:51 | 2014-09-18T13:43:51Z | MEMBER | {
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} | It appears that get_most_compact_basis has a anychange local variable that is effectively unused. Right before the final part of the "while" loop, it sets anychange=True followed by if anychange: break.
Also, unittests are needed to know what is the expected output of this method.
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On systems without a functional scipy.spatial.Delaunay this will always fail.
Maybe use_external_qhull cou... | {
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"This has been superseded by the new StructureMatcher.\n"
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} | I am not sure whether to classify this as a bug. But it is a very odd thing.
Try the following code
logging.basicConfig(level=logging.DEBUG)
# Use the POSCAR.LiFePO4 from the test_files.
p = Poscar.from_file("test_files/POSCAR.LiFePO4", check_for_POTCAR=False)
s = p.structure
from pymatgen.analysis.structure_fitter ... | {
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} | Line 191 of pymatgen/electronic_structure/bandstructure.py in installation tree has a conditional line
```
if len(projections) != 0 and self._structure is None:
```
that will fail (crash) when projections is NoneType. This line is preceded by the line 187
```
self._projections = projections if projections e... | {
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This assumption is not valid. Esp when releasing packages, the tests directories are all excluded from the final package. The code base should stand on its own without the tests directory... | {
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} | Go to "test_files" and do
../scripts/matgenie.py compare Li2O.cif POSCAR.Li2O
Both are Li2O. Second one is a big-ish supercell. The code fails with a TypeError after a while, given below:
Traceback (most recent call last):
File "../scripts/matgenie.py", line 423, in <module>
args.func(args)
File "../scripts... | {
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> > > import pymatgen
> > > myprocar=pymatgen.io.vaspio.vasp_output.Procar('PROCAR')
> > > Traceback (most recent call last):
> > > File "<stdin>", line 1, in <module>
> > > File "/share/apps/virtualenv/mastenv/lib/python2.7/site-packa... | {
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"I'm not sure why the indentations didn't display properly above...please let me know if there are problems...\n",
"The reason why this problem occured is because a numpy array was supplied as a selective dynamics when it is expecting a list. I have changed the code to support both. Thanks for reporting this.\n"
... | 2013-04-02T22:41:43 | 2013-04-02T23:05:12 | 2013-04-02T22:58:05Z | CONTRIBUTOR | {
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Traceback (most recent call last):
File "test_selectivedynamics.py", line 9, in <module>
mypos.selective_dynamics=mysd
File "/share/apps/virtualenv/mastenv/lib/python2.7/site-packages/pymatgen/io/vaspio/vasp_input.py", line 141, in **setattr**
if value:
ValueError... | {
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"It is a conscious design decision to not treat an Element and a Specie with zero oxidation state the same. A zero oxidation state means that someone has consciously assigned a oxidation state, which then allows the computation of things like Ewald summations. An Element means that no one has specified an oxidation... | 2013-04-18T21:36:18 | 2013-04-19T18:18:24 | 2013-04-19T18:18:24Z | CONTRIBUTOR | {
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} | It seems these two methods don't do the same thing:
(rs1 is a StructureEditor)
rs1.remove_species([Element('Li')])
rs1.remove_species([Specie('Li', 0)])
Why is this the case? It makes it difficult to use remove_species()
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"Btw, for battery purposes I can get around this by using:\n\nmin(e for e in el.oxidation_states if e>1)\n\nwhere el is an Element. But maybe V should be changed anyway?\n",
"I am not sure how to solve this problem very robustly. Different people have different definitions of what constitute a \"common\" oxidatio... | 2013-04-19T23:00:15 | 2013-04-19T23:08:29 | 2013-04-19T23:08:29Z | MEMBER | {
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} | It looks like only +5 is listed as a common oxidation state of Vanadium:
el = Element('V')
print el.common_oxidation_states
> > (5,)
Should +2, +3, and +4 also be on the list?
Note that some of the BatteryAnalyzer code in a different Materials Project repo needs to know how far you can reduce a metal. Currently it w... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/18 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/18/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/18/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/18/events | https://github.com/materialsproject/pymatgen/pull/18 | 13,762,372 | MDExOlB1bGxSZXF1ZXN0NTQyNTI0MA== | 18 | Pull request for abinitio | {
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"Thanks Matteo. I just merged the pull request. There is one minor failure in my unittests though. This was the error:\n\n# \n\n## ERROR: test_read_Si2 (pymatgen.io.abinitio.tests.test_netcdf.GSR_Reader_TestCase)\n\nTraceback (most recent call last):\n File \"/Users/shyuepingong/Documents/Aptana Studio 3 Workspace... | 2013-04-29T14:25:27 | 2014-07-04T02:48:18 | 2013-04-29T16:48:15Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/19 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/19/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/19/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/19/events | https://github.com/materialsproject/pymatgen/pull/19 | 13,771,047 | MDExOlB1bGxSZXF1ZXN0NTQyOTY3NQ== | 19 | solved problem with test_netcdf | {
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"Thanks Matteo. I have made a minor mod. I think the skip test should be NC_VERSION != 4.\nYou can now merge the master branch of the main branch to your fork to keep it up to date.\n\nThanks for the great work on the abinit support!\n",
"Right, I made a mistake!\nThank you.\n\nOn Mon, Apr 29, 2013 at 7:30 PM, Sh... | 2013-04-29T17:22:31 | 2014-07-04T02:48:17 | 2013-04-29T17:28:27Z | CONTRIBUTOR | {
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} | Hi Shyue,
the problem with the netcdf test is hopefully solved in this revision. I was trying to support both scipy.io.netcdf as well as netcdf4 although the two APIs are not 100% compatible. netcdf4 is more flexible that the interface provided by scipy that only supports netcdf3. Now the test is skipped if netcdf4 i... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/20 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/20/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/20/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/20/events | https://github.com/materialsproject/pymatgen/pull/20 | 13,849,174 | MDExOlB1bGxSZXF1ZXN0NTQ3MDcwNA== | 20 | fix conflict with ape.py (removed in my branch) | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/21 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/21/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/21/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/21/events | https://github.com/materialsproject/pymatgen/issues/21 | 13,854,867 | MDU6SXNzdWUxMzg1NDg2Nw== | 21 | having trouble generating POTCAR with sym_potcar_map set | {
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"The sym_potcar_map is meant to be used with a raw potcar string. It is not a mapping of symbol to symbol. \n\nRegards,\nShyue Ping\n\nOn Wednesday, May 1, 2013 at 12:29 PM, cmgtam wrote:\n\n> Code version is apparently 2.7.0b, pulled today at 11:17.\n> Below I have compared sym_potcar_map=None with sym_potcar_map... | 2013-05-01T16:29:20 | 2013-05-01T17:13:38 | 2013-05-01T17:13:38Z | CONTRIBUTOR | {
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Below I have compared sym_potcar_map=None with sym_potcar_map set.
> > > mypotcar = pymatgen.io.vaspio.Potcar(symbols=['Si','C','O'], functional="PBE", sym_potcar_map=None)
> > > mypotcar[0].enmax
> > > 245.345
> > > mypotcar = pymatgen.io.vaspio.Potcar(symbol... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/22 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/22/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/22/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/22/events | https://github.com/materialsproject/pymatgen/pull/22 | 13,964,095 | MDExOlB1bGxSZXF1ZXN0NTUzMTE5Mw== | 22 | minor change in smart_element_or_specie | {
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"Hi there,\n\nI can't reproduce the error. You cannot just specify voronoi_data as site properties because there are only some properties allowed. But otherwise, I can't reproduce the error. Can you give me the exact forms of the variables voronoi_lattice, s and c? For example, the following works just fine:\n\nSt... | 2013-05-16T21:22:40 | 2013-05-17T19:59:43 | 2013-05-17T19:59:43Z | CONTRIBUTOR | {
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} | When trying to initialize Structure in core/structure.py, I am getting an error message.
Input to initializer:
1) lattice of type "pymatgen.core.lattice.Lattice"
2) species of type "List of strings"
3) coords of type "List of numpy arrays of size 3"
4) coords_are_cartesian=True
5) site_properties=dict{"property_nam... | {
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"Hi Matteo, \n\nThis is a known issue. Can you install pyhull using \"pip install pyhull --upgrade\"? Thanks. \n\nShyue Ping\n\nOn Tuesday, May 21, 2013 at 11:49 AM, gmatteo wrote:\n\n> Hi,\n> I've just merged mpmaster in my private branch. I ran the unit tests \n> and many tests were failing in phasediagram due... | 2013-05-21T15:49:27 | 2014-01-15T18:09:10 | 2014-01-15T18:09:10Z | CONTRIBUTOR | {
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I've just merged mpmaster in my private branch. I ran the unit tests
and many tests were failing in phasediagram due to the fact that now we
require pyhull >=1.3.8.
I tried to install the new version of pyhull via setup.py but the installation fails
with the following error
sudo python setup.py install
...
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equal by RMSD
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} | The index error for methane is fixed.
MoleculeMatcher is fine for complex molecule, I will add these molecules to the unittest.
Meanwhile, I am thinking a better solution for simple molecules.
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} | 1) Add a new IsomorphismMolAtomMapper that calculates the RMSD of all the possible graph isomorphsim mapping and match the atoms using the one with smallest RMSD. The isomorphisms is enumerated by OpenBabel library.
2) Add 21 molecule for unittest
3) Add unit test for the group_molecules(), to_dict() and from_dict() ... | {
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Additional files functional_groups.py and functional_groups.json were also added under /pymatgen/core directory.
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The is raised because the function is supposed to be a helper function, however it is also called directly by the unittest class. Just renamed the function to a name not starting with "test", the direct calling form unittest is avoi... | {
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"Hello Shyue, \n\nI updated the tests and fixed the issues related to testing. Can you please check it again.\n\nThanks,\nBharat\n",
"Hi Bharat, you need to issue a new pull request. \n\nRegards,\nShyue Ping\n\nOn Tuesday, August 6, 2013 at 4:12 PM, Bharat Medasani wrote:\n\n> Hello Shyue, \n> I updated the tes... | 2013-08-02T17:36:53 | 2014-07-04T02:47:50 | 2013-08-07T19:53:35Z | CONTRIBUTOR | {
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} | zeoio module adds classes and functions for interface with Zeo++ cython wrapper.
It has dependency on Zeo++.
Zeo++ code can be obtained using "svn checkout https://codeforge.lbl.gov/anonscm/zeo"
The cython wrapper is in trunk/cython_wrapper.
Thanks,
Bharat
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I addressed the issues related to previous pull request.
a) The tests are working.
b) Defects package is moved inside analysis.
I updated comments and tests for io.zeoio, command_line.gulp_caller and analysis.defects.point_defects
modules. defects.point_defects is still a work in progress. Some duplicate funct... | {
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} | See the comments in units.py for a discussion about the main differences between the protocol implemented in Unit and ArrayWithUnit.
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"Thanks for letting us know. We will fix the error message. But yes, this means the DOS is not available for that ID/. \n\nRegards,\nShyue Ping\n\nOn Friday, September 6, 2013 at 7:47 AM, cmgtam wrote:\n\n> Okay:\n> \n> > > > a.get_dos_by_material_id(\"mp-24972\")\n> \n> Strange error - does this mean there is no ... | 2013-09-06T14:47:54 | 2013-09-06T17:08:37 | 2013-09-06T17:08:37Z | CONTRIBUTOR | {
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> > > a.get_dos_by_material_id("mp-24972")
> > > <pymatgen.electronic_structure.dos.CompleteDos object at 0x15b74710>
Strange error - does this mean there is no dos for that material ID?:
> > > a.get_dos_by_material_id("mp-510408")
> > > Traceback (most recent call last):
> > > File "<stdin>", line 1, in <mo... | {
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} | myval
pymatgen.analysis.defects.point_defects.ValenceIonicRadiusEvaluator instance at 0x7841560
myval.radii
{'Mn': 0.785 pm, 'O': 1.26 pm, 'La': 1.172 pm}
I like working with Angstroms better anyway, but it was a little confusing.
VERSION
2.8.0
DATE
Sep 6 2013
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"Thanks David, for the changes. However, this is an issue with some of the changes to the PD Plotter. The current PDPlotter supports 2, 3, and 4 component PDs. Does the ordering parameter work for all three types?\n"
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"Pls send a nwchem input file that is supposed to be parsed properly. Nidhi, I am assigning this issue to you together with the parsing of COSMO files. Pls fix it and report back.\n"
] | 2013-09-21T00:33:39 | 2015-12-06T17:26:36 | 2015-12-06T17:26:36Z | CONTRIBUTOR | {
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Currently, space is not allowed in the value of theory_directives. Because, NwInput use "theory_directives[theory][toks[0]] = toks[-1]" to parse the theory_directives in the NwInput.from_string().
For example, Lei uses "vectors input atomic". After NwInput.from_string() it will become "vectors atomic".
Luc... | {
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I've been refactoring a lot of code in abinitio and I've added new features. Sorry for pushing such a big patch.
In the forthcoming pull requests, I will try to commit localized changes in order to facilitate the work of the project leader. Note that now abinitio requires two external packages: pyYAML and ... | {
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I'm gradually moving to pymatgen the new workflows for Phonon calculations with Abinit.
Many of these new features will require Abinit 7.6 that is presently under development.
Note that now abinitio uses the configuration directory $HOME/.abinit/abipy to store important
configuration parameters. The unit tes... | {
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"Hi Matteo, \n\nMay I know how is the behavior of iround different from the behavior of python’s round? I think python’s round already gives the behavior you want. \n\nShyue Ping\n\nOn Monday, October 28, 2013 at 0:31, gmatteo wrote:\n\n> You can merge this Pull Request by running\n> git pull https://github.com/g... | 2013-10-27T16:31:51 | 2014-07-04T02:47:23 | 2013-10-27T16:38:07Z | CONTRIBUTOR | {
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I am including the fix for failing test #3.
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Camel case for Tersoff_pot class.
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} | When trying to get the unit cell from symmetry.finder.SymmetryFinder for the structure with mpid "mp-25145", I am getting error.
Code:
struct = mp.get_structure_by_material_id("mp-25145")
uc = SymmetryFinder(struct).get_conventional_standard_structure()
## Error:
ValueError Traceback (... | {
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} | When generating the voronoi nodes, a single ionic radii was used for each species in the structure.
Now, when multiple oxidation states of a single species are present in the structure, different ionic radii for different oxidation states are used.
Also, coordination number is used as input to compute the ionic rad... | {
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Missing ionic radii for lanthanides and actinides and other elements added.
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in determining the ionic radii.
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"Hi there,\n\nI apologize but there was a small bug in the previous release which broke the tasks API. We have just fixed it and released a bug fix. It should work now. \n\nIn any case, if your goal is only to get the relaxed geometry, you just need to query for the structure of a material, which by default is the ... | 2014-02-16T19:28:45 | 2014-03-12T22:47:44 | 2014-03-12T22:47:44Z | CONTRIBUTOR | {
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I'm trying to get `tasks` JSON reply.
First I go to https://www.materialsproject.org/rest/v1/materials/Fe2O3/vasp?API_KEY=MYAPIKEY
There I get (added newlines for clarity)
``` json
{"created_at": "2014-02-16T09:34:09.995518", "valid_response": true, "version": {"pymatgen": "2.9.1", "db": "2014.02.13", "rest": "... | {
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"David,\n\nI merged most of these changes. But I think add_oxidation state by site fraction needs to be fixed. The oxidation states seem to be assigned in order of the Composition dict. But the dict has no pre-defined order. That can lead to extremely unpredictablee behavior. For example, you may specify [2, 3] for... | 2014-02-19T13:01:50 | 2014-06-27T11:40:14 | 2014-02-20T16:42:57Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/75 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/75/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/75/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/75/events | https://github.com/materialsproject/pymatgen/pull/75 | 28,108,969 | MDExOlB1bGxSZXF1ZXN0MTI4Mjc5OTQ= | 75 | Voronoi face centers are also included in the interstitial sites | {
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Latest Zeo++ required.
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The route finally taken was to add a method to Composition (not change Composition) that returns an ordered list of tuples (element/species, occupation). The ele... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/77 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/77/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/77/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/77/events | https://github.com/materialsproject/pymatgen/pull/77 | 29,397,115 | MDExOlB1bGxSZXF1ZXN0MTM1NDk5NDg= | 77 | Zeo++ high accuracy option enabled | {
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"Hi Bharat,\n\nThanks for the additions. Can you modify your code to use monty.tempfile.ScratchDir for the portions that uses temp dirs and files. That is a much cleaner way of doing this. The usage is simply:\n\n``` python\nwith ScratchDir(...):\n do something\n```\n",
"Sure.\n\nOn Thu, Mar 13, 2014 at 4:02 P... | 2014-03-13T22:56:08 | 2014-07-02T02:21:06 | 2014-03-14T00:31:27Z | CONTRIBUTOR | {
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by using an additional keyword accuracy="High" when initializing.
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} | When lattice periodicity of ordered sites doesn't match the periodicity of disordered sites (but when they have the same spacegroup), the wrong periodicity is used by spglib, missing some valid enumerations.
Example structure that should have 2 distinct orderings:
```
#\#CIF1.1
######################################... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/79 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/79/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/79/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/79/events | https://github.com/materialsproject/pymatgen/issues/79 | 30,707,705 | MDU6SXNzdWUzMDcwNzcwNQ== | 79 | VASP KPOINTS file with Line_mode | {
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"Hi Germain,\n\nThanks for reporting the issue. I have applied your fix and contributions.\n\nAs for the line-mode, I know that VASP uses Line-mode. But because of the way the Enum design pattern works, I can't use \"-\" in the class. In any case, VASP does not actually look for \"Line-mode\". They only look at the... | 2014-04-02T17:24:55 | 2018-01-11T14:43:54 | 2014-04-30T17:45:34Z | CONTRIBUTOR | {
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} | Hi !
I am new in pymatgen and I try to use it to produce KPOINTS file for band structure calculations with VASP. I use HighSymmKpath and Kpoints classes to produces the kpoints file.
Here is the source code
``` python
import pymatgen as mg
from pymatgen.symmetry.bandstructure import HighSymmKpath
from pymatgen.io.vas... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/80 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/80/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/80/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/80/events | https://github.com/materialsproject/pymatgen/pull/80 | 31,122,616 | MDExOlB1bGxSZXF1ZXN0MTQ1MzE0MjI= | 80 | Warn the user if CifParser raises KeyError | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/81 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/81/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/81/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/81/events | https://github.com/materialsproject/pymatgen/issues/81 | 31,532,972 | MDU6SXNzdWUzMTUzMjk3Mg== | 81 | test suite has 3 failures | {
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"Thanks for reporting this. There is a bug in the ewald module that we are trying to fix now. The tests in the current updated branch should pass for now.\n"
] | 2014-04-15T07:58:53 | 2014-09-18T13:40:20 | 2014-09-18T13:40:20Z | CONTRIBUTOR | {
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======================================================== FAILURES =========================================================
_______________________________________ EwaldElectrostaticModelTest.test_get_energy _______________________________________
self = <pym... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/82 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/82/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/82/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/82/events | https://github.com/materialsproject/pymatgen/issues/82 | 31,551,781 | MDU6SXNzdWUzMTU1MTc4MQ== | 82 | get_conventional_standard in pymatgen.symmetry.finder.SymmetryFinder changes symmetry | {
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"@hautierg Can you fix this soon pls? This is really a major issue. There is no guarantee that the band structures are right if the symmetry is not preserved.\n",
"I assume the method is now pymatgen.symmetry.analyzer.SpacegroupAnalyzer? I can't reproduce this. symprec is set to 0.1, and SpacegroupAnalyzer correc... | 2014-04-15T13:14:34 | 2015-08-19T08:13:24 | 2015-08-19T08:13:24Z | MEMBER | {
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} | Using https://www.materialsproject.org/materials/mp–715572/, when converting the primitive cell to conventional standard, the space group changes from C2 to P1. Given that this is just a basis transformation, this really should be the case.
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"Fixed.\n"
] | 2014-04-30T14:13:04 | 2014-04-30T17:30:26 | 2014-04-30T17:30:26Z | CONTRIBUTOR | {
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} | As it stands, only .cif files have the primitive cell taken after structure import. It appears as though they also have their sites sorted. To achieve consistency across structure file types, I suggest we add primitive_cell and sort_structure tags to the read_structure method. The CifParser may also need this flag adde... | {
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"I didn't get any warning running this.\n\nOn Wed, Apr 30, 2014 at 4:08 PM, Anubhav Jain notifications@github.comwrote:\n\n> try the following, you'll get many DeprecationWarnings\n> \n> from sklearn import linear_model\n> from pymatgen import Composition\n> \n> clf = linear_model.LinearRegression()\n> \n> print Co... | 2014-04-30T23:08:50 | 2014-04-30T23:38:00 | 2014-04-30T23:38:00Z | MEMBER | {
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from sklearn import linear_model
from pymatgen import Composition
clf = linear_model.LinearRegression()
print Composition("LiFePO4")
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"Thanks for reporting the issue. Do you have a proposed solution? How about instead of a strict cutoff like 1e-8, we look at the delta in occupation between bands?\n",
"I would try to get rid of the partial occupations. rerun wiht tetrahedra ?\n\n ----- Original Message ----- \n From: Shyue Ping Ong \n To: mat... | 2014-05-05T15:46:16 | 2015-12-06T17:26:12 | 2015-12-06T17:26:12Z | NONE | {
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This may be related to the definition of valence band maximum and conduction band minimum with occupation of "occu > 1e-8" in vasp_output.py
For example. In a static run. band gap occurs between band 96 and 97 for one calculation.
The occupation and energy ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/88 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/88/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/88/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/88/events | https://github.com/materialsproject/pymatgen/pull/88 | 34,967,771 | MDExOlB1bGxSZXF1ZXN0MTY3MTM4NDk= | 88 | Add functionality in Procar class | {
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} | Add convenient properties and method to the Procar class in order to get the number of k-points, the number of bands and to get the projection of bands on elements.
The method `get_projection_on_elements(s)` was written from the same method in the BandStructure class.
The PROCAR file is parsed faster than the vasprun.x... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/89 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/89/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/89/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/89/events | https://github.com/materialsproject/pymatgen/issues/89 | 34,985,355 | MDU6SXNzdWUzNDk4NTM1NQ== | 89 | LDA Potcar.from_file() doesn't work on some LDA potcars | {
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"If I understand correctly, this is an issue with VASP POTCARs. Is there another way to auto-detect which POTCAR it is other than the main line? e.g. by the parameters of La vs La_s? That might be a more robust fix so that pymatgen works across all VASP users, rather than just the ones that have updated their POTCA... | 2014-06-04T17:56:41 | 2014-06-06T15:29:28 | 2014-06-06T15:29:28Z | CONTRIBUTOR | {
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} | The first line of LDA POTCARs are inconsistent. E.g. for POTCAR.La_s, the line is
La: PAW 5s5p 6s5d4f valence
There is actually no occurance of La_s in the file, making it impossible to retrieve the Potcar.symbol from a generated POTCAR file. The only solution is to manually change the POTCAR files in the VASP_PSP dir... | {
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} | struct=mpr.get_structure_by_material_id("mp-8654")
print XRDCalculator(symprec=0.1).get_xrd_data(struct)
The error message is:
line 235, in get_xrd_data
coeffs[:, :, 0] \* np.exp(-coeffs[:, :, 1] \* s2), axis=1)
IndexError: too many indices
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https://api.github.com/repos/materialsproject/pymatgen/issues/91 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/91/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/91/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/91/events | https://github.com/materialsproject/pymatgen/issues/91 | 35,120,602 | MDU6SXNzdWUzNTEyMDYwMg== | 91 | Options to specify data range in get_xrd_data | {
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} | XRD calculator takes very long time to generate patterns for targets with short wavelength. Adding limits of calculation range will accelerate data production, such as 2-theta range or highest index.
struct=mpr.get_structure_by_material_id("mp-19017")
for target in ["Fe", "Cu", "Cr", "Co", "Mo", "Ag"]:
t=datetime.... | {
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File "/usr/local/lib/python2.7/dist-packages/pymatgen/analysis/diffraction/xrd.py", line 298, in get_xrd_plot
for two_theta, i, hkls in self.get_xrd_data(structure):
ValueError: too many values to unpack
Correction :
for two_theta, i, hkls, d in self.get_xrd_data(structure):
get_xrd_data retur... | {
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} | In pymatgen/dependencies/spglib-1.6.0/_spglib.c, the line 191:
sprintf(symbol, "%s (%d)", symbol, num_spg);
this function call will have undefined behavior because the source buff and target buff have an overlap.
That will lead to the wrong results when calling get_spacegroup_symbol() in some systems. For... | {
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} | Add method `read_core_state_eigen()` to class `Outcar` in module `vasp_output.py` in order to read core state eigenenergies which are not available in vasprun.xml (see VASP keywords CL*).
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"Update - I think I left out a few steps in the diagram above. It looks like the code is skipping the \"three-phase\" regions like 4 & 5. Rather is doing 1->2->3->6->8 in the updated diagram below\n\n",
"The pr... | 2014-06-23T17:11:42 | 2014-06-23T18:02:46 | 2014-06-23T18:01:03Z | MEMBER | {
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The problem is that when I run the co... | {
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"Actually, this is not an issue with spglib. It is not really an issue at all. What happened is that pairs of coordinates are being negated. E.g., you have 0.750000 0.810832 0.020666 -> 0.750000 -0.810832 -0.020666 -> 0.750000 0.189168 0.979334 (to unit cell). This is because the get_primitive_standard_structure s... | 2014-06-24T19:03:15 | 2014-06-25T01:37:39 | 2014-06-25T00:33:38Z | CONTRIBUTOR | {
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from pymatgen.matproj.rest import MPRester
from pymatgen.symmetry.finder import SymmetryFinder
fro... | {
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"Hello Prateek,\n\nThanks for reporting it.\nIn the ValenceIonicRadiusEvaluator, its a compromise between not having any value and assigning the radius of the nearest oxidation state. This worked reasonably well for P4+, but is failing for S- in identifying the closest oxidation state. Could you please post the mpi... | 2014-07-02T00:21:59 | 2014-09-18T13:39:47 | 2014-09-18T13:39:47Z | NONE | {
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I have been trying to use pymatgen to automatically charge decorate structures, so that I can evaluate their ionic radius. I have considered two ways.
1. Using AutoOxiStateDecorationTransformation to first charge decorate a structure and then use specie.ionic_radius to evaluate the ionic radius for each unique spe... | {
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In addition the Interstitial class in analysis/defects/point_defects.py is updated for more usage scenarios.
Update to Zeo++ code is required.
Bug fix in ValenceIonicRadiusEvaluator class
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Nose got confused due to the presence of "_test" in function name. Removed "_test" to prevent the confusion.
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