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"Try reinstalling matplotlib?\n\nShyue Ping\n\nOn July 5, 2014 at 6:30:09 PM, Anubhav Jain (notifications@github.com) wrote:\n\nI am trying to plot band structures using the following code:\n\nfrom pymatgen import MPRester\nfrom pymatgen.electronic_structure.plotter import BSPlotter\n\nif **name** == \"**main**\":\... | 2014-07-06T01:30:07 | 2014-10-31T23:51:15 | 2014-07-07T04:47:13Z | MEMBER | {
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```
from pymatgen import MPRester
from pymatgen.electronic_structure.plotter import BSPlotter
if __name__ == "__main__":
MAPI_KEY = None # You must change this to your Materials API key! (or set MAPI_KEY env variable)
MP_ID = "mp-19017" # You mus... | {
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The following methods were added in Dos class:
\* get_element_spd_dos
\* get_site_spd_dos
Oszicar class was improved to suport non polarized calculations and MD calculations.
Volumetric Data output was not compatible with bader program from u-texas because of the header format of the CHGCAR files.
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"Can you try installing with pip? Do easy_install pip first.\n\nThe sandbox violation may also be due to dependency installations. The pymatgen,org install instructions also recommends that you install numpy and PyCifRW first manually before installing pymatgen.\n\nShyue Ping\n\nOn July 14, 2014 at 9:18:08 AM, jast... | 2014-07-14T16:18:07 | 2014-07-14T23:38:59 | 2014-07-14T23:38:59Z | NONE | {
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error: Setup script exited with error: SandboxViolation: os.open('/tmp/tmpqlHrBT/hZfPbu', 131266, 384) {}
The package setup script has attempted to modify files on your system
that are not within the EasyInstall build area, and has been aborted.
This package cannot... | {
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Useful when using the class for defect transformations.
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The function can be used to compute the defect concentrations for intermetals, and oxides
based on the raw defect energies or flip energies, and the input temperature
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the defect concentration plot or defect formation energies only.
In addition unit tests are added for dilute_solution_model
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I am troubled by XYZ reader now. For the attached XYZ text, if I use smartio.read_mol to read it. All the exponents in the last column will be removed, which leads to very strange structures.
20
6_methyl_12cyano
C 2.39132145462 -0.700993488928 -7.22293142224e-06
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"This is an optional dependency. That's why it is not in the official dependency. We generally try to keep core dependencies low.\n"
] | 2014-08-12T00:34:14 | 2014-08-12T04:04:41 | 2014-08-12T04:04:41Z | MEMBER | {
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} | possibly missing dependency PyDispatcher (not PyDispatch, btw!) fails [abinitio/workflows.py](https://github.com/materialsproject/pymatgen/blob/e47f1c3b32ec367df7a701976898d157718f0d7f/pymatgen/io/abinitio/workflows.py#L14) nosetest.
Add to requirements in installation section of docs?
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2) Added solute site preference finder in dilute_solution_model.py
3) Eliminated unused unittest
4) Updated docstrings
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"I think this is a known issue. The Voronoi coordination does not work for all structures. @hautierg can confirm since he wrote this.\n",
"If it is a known and unfixable issue, perhaps a better error message would\nhelp?\n\nOn Mon, Sep 8, 2014 at 4:05 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> I thi... | 2014-09-08T18:55:03 | 2014-09-09T22:03:48 | 2014-09-09T22:02:56Z | CONTRIBUTOR | {
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For mpid mp-559848, I am getting the following error when trying to calculate the coordination number for the sites in the structure.
## Code:
import MPRester
from pymatgen.analysis.defects.point_defects import ValenceIonicRadiusEvaluator
mpid = "mp-559848"
struct = MPRester().get_structure_by_material_id(mp... | {
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"you can use six.u\n\nOn Fri, Sep 12, 2014 at 2:14 PM, gmatteo notifications@github.com wrote:\n\n> unicode literals (i.e. u\"foo\") have been reintegrated in python3.3 (See\n> http://legacy.python.org/dev/peps/pep-0414/) but python3.2 does not\n> support them and the interpreter raises a SyntaxError exception.\n> ... | 2014-09-12T18:14:51 | 2014-09-12T19:13:48 | 2014-09-12T19:13:48Z | CONTRIBUTOR | {
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There are two tests that are failing in my branch due to unicode literals (see https://travis-ci.org/materialsproj... | {
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I have 3 unit tests failing in my branch in test_dilute_solution_model.
All of them use simpy so I guess it's due to a portability problem in sympy.
I'm using Python 2.7.3, sympy 0.7.5 and numpy 1.8..1
#
## ERROR: test_plot_data_with_chem_pot (pymatgen.analysis.defects.tests.test_dilute_solution_model.DiluteS... | {
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"Thanks for the changes. They are extremely useful.\n"
] | 2014-09-19T08:22:22 | 2014-09-19T15:25:32 | 2014-09-19T13:17:30Z | NONE | {
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I'm Nicolas Dardenne, Phd student at the UCL NAPS working with Geffroy Hautier as mentionned in a mail yesterday.
At the request of Matteo Giantomassi, I submit modifications of gaussianio directly to you. The changes were made in order to use gaussianio with fireworks for HTP and some minors changes to add some... | {
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https://computing.llnl.gov/tutorials/moab
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"Thanks for reporting this. It has been fixed and I have added a new unittest.\n"
] | 2014-10-07T19:09:30 | 2014-10-07T19:34:26 | 2014-10-07T19:33:33Z | NONE | {
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"Looks like expected behavior. s2 is just out of tolerance so no primitive cell is found. If you want to match s2 to s1, you can take the primitive cells and use attempt_supercell=True\n"
] | 2014-10-24T20:09:50 | 2014-12-09T17:11:59 | 2014-12-09T17:11:59Z | MEMBER | {
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} | Here's an example - note that git won't let me upload the JSON files, so you can obtain those here:
https://groups.google.com/forum/#!topic/pymatgen/HvqV79HQPHE
```
from pymatgen import Structure
from pymatgen.analysis.structure_matcher import StructureMatcher
s1 = Structure.from_file("s1.json")
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Added all option to interstitials.
high accuracy interstitial doesn't return face centers and edge centers.
Update to Zeo++ required.
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"This is a P1 structure. I am not sure why that would happen, given that it is practically a pass-through for P1 for get_primitive_standard. This should be debugged by @hautierg who implemented that method.\n",
"@hautierg Can you give an update on this? This bug is outstanding and severely affects the MP workflow... | 2014-11-07T03:45:14 | 2015-08-19T14:38:29 | 2015-08-19T14:38:29Z | CONTRIBUTOR | {
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} | We recently found some static runs give very different energy_per_atom results from the original relaxation results. It seems the get_primitive_standard_structure used for the static runs gives a different structure from the input structure.
Here's one example:
mpr=MPRester()
struct=mpr.get_structure_by_material_id(... | {
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} | In MIT and MP correction schemes, the F2 compound energy is supposed to be set by the correction scheme to get the gas phase energy correct. Currently, this correction isn't applied because F2 isn't in Composition.special_formulas. Either adding F2 to the special formulas, or setting the compound energy of F instead of... | {
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"Before I merge this, can you provide unittests for the new functionality pls? Thanks.\n",
"Ok, I will provide those and will re-submit. Thank you.\n"
] | 2014-11-18T01:17:28 | 2014-11-18T06:31:48 | 2014-11-18T06:31:48Z | CONTRIBUTOR | {
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} | Fixed the following in class Outcar in pymatgen/io/vaspio/vasp_output.py:
1 - Added parsing of ionic part of lepsilon in Outcar.
2 - Changed parsing of piezoelectric tensor units from e.Angstrom to C/m^2.
3 - Fixed results' data structure from numpy array to list.
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1 - Added parsing of ionic part of lepsilon in Outcar.
2 - Changed parsing of piezoelectric tensor units from e.Angstrom to C/m^2.
3 - Fixed results' data structure from numpy array to list.
Added tests in Class OutcarTest in pymatgen/io/vaspi... | {
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vasp_output.py in pymategen/io/vaspio/
test_vasp_output.py in pymategen/io/vaspio/tests
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"Not sure what the use case is. Ordering doesn't really make sense in this\ncase since they all have the same electrostatic energy -- might as well\njust do an enumeration.\nI agree that its a weird error though - I'll take a look\n\nOn Tue, Dec 9, 2014 at 12:14 PM, Shyue Ping Ong notifications@github.com\nwrote:\n... | 2014-12-09T17:14:09 | 2018-05-28T15:38:48 | 2018-05-28T15:38:48Z | MEMBER | {
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``` python
from pymatgen import Structure, Lattice
from pymatgen.transformations.standard_transformations import OrderDisorderedStructureTransformation
specie = {"Cu0+": 0.5, "Au0+": 0.5}
cuau = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.677), [specie], [... | {
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"Thanks for reporting this. We have actually fixed this issue in the bleeding edge repo code.\n\nWe will release a new version shortly.\n",
"Hey, thanks for your quick reply and fix.\n\nHowever, I can only confirm that 'pmg view JST.cif' looks good.\n\n'pmg view ABW.cif' looks like having oblique angles but it is... | 2014-12-12T11:14:30 | 2014-12-15T10:26:36 | 2014-12-12T13:39:44Z | NONE | {
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} | Consider following example cif files:
http://izasc.ethz.ch/fmi/xsl/IZA-SC/cif/ABW.cif
http://izasc.ethz.ch/fmi/xsl/IZA-SC/cif/ACO.cif
http://izasc.ethz.ch/fmi/xsl/IZA-SC/cif/JST.cif
Using 'pmg convert ABW.cif ABW-<version>.cssr' with pymatgen version = 2.10.6, 3.0.6 and 3.0.8:
2.10.6 & 3.0.6 certainly broken (wrong u... | {
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In _parse_kpoints, in io/vaspio/vasp_output, the execution of the following line
k.style = e.attrib["param"] if "params" in e.attrib else "Reciprocal"
always return "Reciprocal" as the style beacuse "params" is not in e.attrib.
Changing "params" to "param" will fix the issue.
regards
Kiran Mathew
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Also lot of bug fixes w.r.t. the dE and omega definitions and output generation.
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"As far as I can tell, this works perfectly fine. Can you give an example of where it fails?\n",
"when 'sym_potcar_map' is provided, the method 'set_symbols' of class Potcar appends potcar singles objects with its data variable set to 'sym_potcar_map[el]'.\nWhen 'sym_potcar_map' is not given, it actually goes to... | 2015-01-05T20:45:05 | 2015-01-05T22:52:47 | 2015-01-05T21:42:29Z | CONTRIBUTOR | {
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Solved it with np.round(a, decimals=10).
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"This is not a bug I think. Based on your output in line 39, I think you manually created the \"other_site\"? That site is As, not As3-. Pymatgen distinguishes between As3- and As as different species. That will make it such that the last site with As3- is a neighbor within a radius of 2.5 from the site you entered... | 2015-02-17T05:53:16 | 2015-02-17T17:59:47 | 2015-02-17T17:59:47Z | NONE | {
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} | Hello this is a rather small bug and it hasnt been problematic to deal with, but I figured it should be known for future releases. In structure.get_neighbors( site, rmax, index), when a site is passed in which does not belong to the unit cell and is an image, it will return the neighbors as well as the site itself.
F... | {
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"The jimage is not returned in get_neighbors. The index returned just simply tells you that the first NN site is O with a distance of 2.098 and corresponds to site # 8 in the structure. The distance already accounts for PBC, so you don't need to take that into account anymore.\n\nIf you really want to know what ima... | 2015-02-17T17:35:49 | 2015-02-18T12:54:18 | 2015-02-17T17:42:07Z | CONTRIBUTOR | {
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I would like to understand the image index which is returned by get_neighbors methods doing
```
s.get_neighbors(site, 3., include_index=True)
```
For example, I got
```
[(PeriodicSite: O (-3.0702, 1.4045, 3.7466) [0.3650, 0.1350, 0.7720],
2.0976135752472325,
8),
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"Can you pls supply the actual if file so that we can better advise on what might be the problem? \n\nShyue Ping\n\nOn March 5, 2015 at 01:03:01, wangnumber14 (notifications@github.com) wrote:\n\nI parse some cif files use the method \"CifParser\",\nwhile all the spacegroup names started with \"I\" are all parsed i... | 2015-03-05T09:02:54 | 2015-03-23T00:53:26 | 2015-03-20T13:53:32Z | NONE | {
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} | I parse some cif files use the method "CifParser",
while all the spacegroup names started with "I" are all parsed into "P", why?
for example, the icsd_044367.cif Li has the spacegroup_name "Im-3m", I use
SpacegroupAnalyzer(IStructure.from_file(icsd_044367.cif).get_spacegroup_symbol()
I get the result: Pm-3m
How ca... | {
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} | This pull request adds the convenience function `get_materials_id_references(<mp-id>)` and the according test in MPRester to make use of the new MP REST API [endpoint](https://github.com/materialsproject/materials_django/compare/89710d0bf172319455baa47419d7658010523465~1...master) `materials/mp-123/refs`. For the purpo... | {
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} | This pull request adds the convenience function `find_structure()` and according unit test to MPRester making use of the respective MP REST API [endpoint](https://github.com/materialsproject/materials_django/compare/materialsproject:00ec866...materialsproject:c368a32) ([Usage](https://gist.github.com/tschaume/fa8d0fc7e... | {
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} | This pull request extends the valid paths in `apps.borg.hive` to also accept directories without a `vasprun.xml`. VASP output in directories with either a POSCAR or a POSCAR and an OSZICAR is now assimilated by the `VaspToComputedEntryDrone`, too. The update in the valid paths requires more extensive checks regarding t... | {
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} | Hello Shyue,
I fixed the python 3 version bug in dilute solution model. In addition, I added a new command to compute defect concentrations. Since there are many steps in the computation, I created the command "pydii".
Thanks,
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