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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"This has been superseded by the new StructureMatcher.\n"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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} | I've modified the "substitute" function in /pymatgen/core/structure.py to add functional group from either user-defined molecule object, or from database functional_groups.json.
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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