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https://api.github.com/repos/materialsproject/pymatgen/issues/501 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/501/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/501/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/501/events | https://github.com/materialsproject/pymatgen/pull/501 | 182,961,429 | MDExOlB1bGxSZXF1ZXN0ODkzMjMyMzM= | 501 | updates | {
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} | - feff: the absorbing atom can be specified by either its symbol or the site index. added test
- Bandstructure serialization fix: make the vbm and cbm projections consistent with the latest refactoring. The stray old style serialization in the Bandstructure class causes trouble if the projections are read in and the li... | {
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} | ## Summary
1 Ability to read CONTCAR files with more than 20 groups of atoms (in which case, the atoms and number of atoms are spread over more than just one line each)
2 Added test for the previous case.
3 Small fix in MultiStructureVis
4 Small fix in io.abinit.qadapters
## TODO (if any)
- Feature 1 is not compatible... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/503 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/503/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/503/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/503/events | https://github.com/materialsproject/pymatgen/issues/503 | 184,691,208 | MDU6SXNzdWUxODQ2OTEyMDg= | 503 | A question about the symmetry operations | {
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"spglib's symmetry operations are those that apply to that specific crystal. For example, if you have a supercell or a different setting, the actual symmetry operations are different from those in a standard conventional setting.\n\nThe pymatgen.symmetry.groups operations are those that apply the standard conventio... | 2016-10-23T13:46:41 | 2016-10-23T20:56:02 | 2016-10-23T20:56:02Z | CONTRIBUTOR | {
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} | <When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
- Pymatgen version: <Write "branch_name" if it is development version.>
- Python version: <Only 2.7.* and 3.* supported.>
- OS version: <If you are writing Windows he... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/504 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/504/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/504/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/504/events | https://github.com/materialsproject/pymatgen/issues/504 | 185,241,669 | MDU6SXNzdWUxODUyNDE2Njk= | 504 | Help retrieving names of all elements | {
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"Element is now an enum. If you want all the elements with Z 1-50, you simply do\n\n``` python\nfrom pymatgen import Element\nsymbols = [Element.from_Z(z).symbol for z in range(1, 51)]\n```\n\nI should point out that the code is from citrine's website. Pls contact them if you have problem with their code.\n",
"@s... | 2016-10-25T21:41:27 | 2016-10-27T00:25:11 | 2016-10-25T22:32:15Z | NONE | {
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} | Hi,
I am a new user of pymatgen and I am using version 4.4.9. I need some help.
1. I would like to create a list of all elements. I found some example code that does the job using this:
``` python
from pymatgen import MPRester, periodic_table
import itertools
allBinaries = itertools.combinations(periodic_table.all_... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/505 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/505/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/505/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/505/events | https://github.com/materialsproject/pymatgen/issues/505 | 185,976,068 | MDU6SXNzdWUxODU5NzYwNjg= | 505 | Some input sets override user_incar_settings | {
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} | ## System
- Pymatgen version: 4.3
- Python version: 2.7
## Summary
- The MVLSlabSet overrides user_incar_settings. Upon inspection, it seems as if MVLSlabSet.incar sets several of the parameters specific to that set after calling super, which is where the user_incar_settings are added. My quick fix added `incar.updat... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/506 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/506/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/506/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/506/events | https://github.com/materialsproject/pymatgen/issues/506 | 186,877,665 | MDU6SXNzdWUxODY4Nzc2NjU= | 506 | importing pymatgen takes a long time | {
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"I sped up the import a bit by disabling the spglib loading. But ultimately, the profiling tells me that the major factor is the creation of the Element enum type. That is however required for proper functioning. There is a way to speed up by ~50% if I disable unit checking, but that may break stuff. I will need to... | 2016-11-02T18:06:11 | 2016-11-03T15:57:39 | 2016-11-02T21:30:55Z | MEMBER | {
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} | ## System
* Pymatgen version: master
* Python version: 2.7.x
* OS version: Mac / Linux
## Summary
* Importing pymatgen objects takes a long time
* e.g., "from pymatgen import Composition" takes about 3 seconds on my machine; on NERSC it is like 10 seconds. These times vary depending on whether you run the t... | {
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"This approach is far too complicated. You just need to do:\n\n``` python\nfrom pymatgen import MPRester\nm = MPRester()\nfor s in m.get_structures(\"LiBeH3\"):\n print(s.lattice.abc)\n print(s.lattice.angles)\n```\n\nFor future reference, pls submit questions to the google groups. Github Issues are meant for... | 2016-11-07T19:19:17 | 2016-11-07T19:39:27 | 2016-11-07T19:33:34Z | NONE | {
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} | Hi,
I am using pymatgen (v4.5.0) to retrieve material data from materials project and extract the lattice parameters. When a material data is retrieved from Materials Project, it seems the lattice parameter data is buried into the cif data. It seems there are several options to write cif data, but not so much to retri... | {
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"All this sounds good. I await your pull request!\n",
"Just to update on this, I've got a `MagCifWriter` and `MagCifParser` in testing, and also a `MagSymmOp` and I'm working on a magnetic version of `SpaceGroup` too (have constructed a JSON file from a magnetic space groups data file which we have permission to ... | 2016-11-07T22:30:38 | 2017-05-24T13:36:23 | 2017-05-24T13:36:23Z | MEMBER | {
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magCIF is a relatively new standard (2014) for storing structures of magnetic materials. Adding magCIF functionality to pymatgen would be useful to (a) be able to incorporate existing magCIF structures into a Materials Project workflow and (b) to allow easier visualisation of magnetically ordered structur... | {
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} | * remove kwargs in inputsets: keep it simple
* fix parsing of the absorbing atom from the reciprocal space calculation outputs | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/510 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/510/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/510/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/510/events | https://github.com/materialsproject/pymatgen/issues/510 | 188,713,540 | MDU6SXNzdWUxODg3MTM1NDA= | 510 | Failed to read cifs files download from ICSD-Desktop | {
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"I fixed for all the ICSD files. I cannot fix the abinit version because the abinit version has serious problems. First, the symmetry positions is not properly preceded with a _. Second, the atomic positions reported are already replicated for symmetrically equivalent sites but the symm ops is not P1. This results ... | 2016-11-11T08:58:03 | 2017-02-01T02:43:57 | 2016-11-11T16:37:36Z | CONTRIBUTOR | {
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} | ## System
* Pymatgen version: 4.5.0
* Python version: 3.5.2
* OS version: macOS Sierra
## Summary
* Sometimes, Pymatgen failed to read cif files directly downloaded from ICSD-Desktop. The format of these cif files is slightly different from the standard one.
* Pymatgen also failed to deal with cif files ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/511 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/511/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/511/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/511/events | https://github.com/materialsproject/pymatgen/pull/511 | 189,048,077 | MDExOlB1bGxSZXF1ZXN0OTM1MjEwNjI= | 511 | improve readability of get_elt_projected_plots with colors. | {
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} | ## Summary
Adding colors to get_elt_projected_plots to make these plots more readable specially in compounds with more than 3 elements where other colored plots are not available.
## TODO
Coming up with better color combination later. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/512 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/512/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/512/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/512/events | https://github.com/materialsproject/pymatgen/issues/512 | 189,097,896 | MDU6SXNzdWUxODkwOTc4OTY= | 512 | Bandstructure class can't get bands properly after encoding with MontyEncoder | {
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} | ## System
* Pymatgen version: <4.5.0 pip>
* Python version: <2.7.12>
* OS version: <OSX 10.11.6>
## Summary
* Bandstructure.bands should be numpy.array consisting of float lists.
* but after `json.dumps(bs.as_dict(), cls=MontyEncoder)`, Bandstructure.bands turn to array consisting of dicts, and it's not ab... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/513 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/513/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/513/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/513/events | https://github.com/materialsproject/pymatgen/pull/513 | 189,456,442 | MDExOlB1bGxSZXF1ZXN0OTM4MTE4ODI= | 513 | fix from_dict() after bs dict() with MontyEncoder | {
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fix #512
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https://api.github.com/repos/materialsproject/pymatgen/issues/514 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/514/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/514/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/514/events | https://github.com/materialsproject/pymatgen/issues/514 | 189,535,030 | MDU6SXNzdWUxODk1MzUwMzA= | 514 | git push error on LFP_CHGCAR.gz | {
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"You just reforked? If not, pls delete your fork (making sure you still have your own local copy). Then refork, reclone, add whatever changes you need and push.\n\nI had to rebase the git branches because the total repo size is close to the Github limit. Unfortunately, that means the git history is no longer consis... | 2016-11-15T23:14:51 | 2016-11-15T23:44:47 | 2016-11-15T23:44:47Z | CONTRIBUTOR | {
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I download and update a fresh version of pymatgen (last commit 15 november). I just forked the repository. But if I tried to push commits on my own repository I got the following error :
```
open /Users/gvallver/git/pymatgen/test_files/path_finder/LFP_CHGCAR: no such file or directory
error: failed to pus... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/515 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/515/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/515/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/515/events | https://github.com/materialsproject/pymatgen/pull/515 | 190,281,556 | MDExOlB1bGxSZXF1ZXN0OTQzMzQzNjY= | 515 | Frequency and hessian matrix from gaussian output files | {
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} | ## Summary
* read in hessian matrix : need #P in route line
* read IR intensity, force constant and reduce mass
* compatibility break on frequency attributes of GaussianOutput object. Frequency is still a list for each frequency calculations and for each mode. But for each mode it contains a dictionary such as :
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/516 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/516/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/516/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/516/events | https://github.com/materialsproject/pymatgen/pull/516 | 191,035,145 | MDExOlB1bGxSZXF1ZXN0OTQ4MzM5NDE= | 516 | Optionnal possibility to specify that the saddle_point in the NEB sho… | {
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"I will merge but I will make some edits.",
"I pushed my changes. Can I request that we avoid introducing too much cruft and code that duplicates. When you have the exact same call to CubicSpline, that is a problem.\r\n\r\nAlso, when can we remove the old scipy spline? Pymatgen already pins the latest scipy as a ... | 2016-11-22T15:18:23 | 2016-11-22T19:31:54 | 2016-11-22T18:35:06Z | CONTRIBUTOR | {
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* Possibility to setup the spline in the NEB analysis so that the slope is zero for the saddle point (works only for new versions of scipy). | {
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} | ## Summary
* Added setup_spline method to NEBAnalysis.
* Added test for zero_slope at the saddle point option for splines in NEBAnalysis | {
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"Yes, you need to supply a symprec. If you want to try to get a standard setting, you can try using SpacegroupAnalyzer's get_conventional_standard_cell to get a conventional structure before writing it out with CifWriter. That still does not guarantee that a standard setting is always written though, but it should ... | 2016-11-23T21:24:46 | 2016-11-23T22:02:02 | 2016-11-23T22:02:02Z | CONTRIBUTOR | {
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} | ## System
* Pymatgen version: 4.5.2
* Python version: 2.7.12
* OS version: RHEL 6.8
## Summary
I want to use pymatgen to read in a POSCAR and output a cif with the symmetry information included a la FINDSYM.
However, when I write the cif file using the CifWriter, the spacegroup is still P1 and the symmet... | {
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"This is deliberate. Pybtex is only used in one place. There is no need to add it as a required dependency. Also, it uses a primiive 2to3 method of maintaining Py27 and Py3k compatibility, which makes it difficult of pymatgen to create condo packages using it."
] | 2016-11-25T01:18:51 | 2016-11-25T02:41:49 | 2016-11-25T02:41:49Z | CONTRIBUTOR | {
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} | <When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: <pip>
* Python version: <2.7.12.2>
* OS version: <Linux.>
## Summary
should add pybtex to requirement | {
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"EwaldSummation requires oxidation state decorated structures. That means they have Specie, which has oxi_state."
] | 2016-11-28T06:45:45 | 2016-11-28T08:02:46 | 2016-11-28T08:02:46Z | CONTRIBUTOR | {
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} | ## System
* Pymatgen version: 4.5.2
* Python version: 2.7.11
## Summary
It seems there is a tiny problem in the **compute_average_oxidation_state** function in **ewald.py** file in the directory analysis/ewald.py for two reasons.
(1) There is no attribute **oxi_state** but **oxidation_states** in the Element... | {
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} | ## Summary
An alternative interstitial finder was add, which works on the basis of a systematic structure-motif search in the unit cell by spanning a grid and using local order parameters for motif recognition. The interstitial finder is used in the Python Charged Defect Toolkit (PyCDT).
## TODO (if any)
Addi... | {
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"This is not a bug. make_supercell actually modifies the structure in place. For the non-working codes, you are effectively iteratively building larger and larger supercells within the same structure. That is why it never completes. The last example you wrote actually recreates the structure before making a superce... | 2016-11-29T16:32:35 | 2016-11-30T17:55:18 | 2016-11-30T17:32:01Z | NONE | {
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} | ## System
* Pymatgen version: 4.5.2
* Python version: 3.5.2
* OS version: OS X 10.10.5
## Summary
* structure.make_supercell() seems to hang after a certain number of iterative updates
* copying a structure also runs into the same problem
## Example code
This will not complete:
```python
wurzite_str... | {
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"Can we have a unittest for the new functionality pls?",
"THanks"
] | 2016-12-06T23:45:57 | 2016-12-07T17:26:27 | 2016-12-07T17:26:21Z | CONTRIBUTOR | {
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} | ## Summary
a few things are added to BoltztrapAnalyzer:
intrans as an input: it is a dictionary of inputs with which the boltztrap had been run before; it can be obtained via parse_intrans method from boltztrap.intrans file if BoltztrapAnalyzer is called via "from_files" method.
Justification:
when I call Bol... | {
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"I pushed a fix. Honestly, pprint doesn't look good with a structure in a dataframe. ",
"Thanks! I'll usually have separate columns for composition and spacegroup\nthat are more helpful from a visual standpoint anyway. The main thing is\nthat at least I can throw a Structure into a DataFrame and not have it\nhija... | 2016-12-07T21:28:22 | 2016-12-07T23:38:05 | 2016-12-07T22:41:31Z | MEMBER | {
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* Pymatgen version: master
* Python version: 2.7
## Summary
* I want to put Structure objects in a pandas Dataframe
* This works so long as I don't try to print the Dataframe or call a method like df.head(). This chokes if you put a Structure object in the DataFrame
* The reason for this is comple... | {
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Minor fix/cleanup to elastic tensor fitting. | {
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} | ## System
* Pymatgen version: 4.5.3
* Python version: 2.7
* OS version: Mac OS 10.11.4
## Summary
get_elt_projected_plots_color() assumes that a material has both CBm and VBM, and crashes if it doesn't.
## Example code
```python
vasprun = Vasprun('vasprun.xml', parse_projected_eigen=True)
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} | ## Summary
In the previous implementation only high-symmetry points are included in the KPOINTS file which result in a wrong band structure (I tested this on ZnS). So now, the from_prev_calc method either only adds the VBM and CBM k-points (mode=="Uniform") or add the entire high-symmetry k-points (mode =="Line")
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sorry I didn't update the tests before. It was failing because now we are adding more k-points in the Line-mode | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/529 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/529/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/529/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/529/events | https://github.com/materialsproject/pymatgen/pull/529 | 195,001,626 | MDExOlB1bGxSZXF1ZXN0OTc1NzIzOTA= | 529 | read the resume block of gaussian output file | {
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Read all resumes blocks in a gaussian output file and return them as a list of strings.
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https://api.github.com/repos/materialsproject/pymatgen/issues/530 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/530/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/530/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/530/events | https://github.com/materialsproject/pymatgen/pull/530 | 195,150,421 | MDExOlB1bGxSZXF1ZXN0OTc2ODAyODc= | 530 | adding the option "gap" to mode in MPHSEBSSet.from_prev_calc | {
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adding the option "gap" to the argument mode in MPHSEBSSet to distinguish between "uniform" and "gap" modes when ran from previous calculations. Also a test was added for the "gap" mode. Sometimes we want just to run the uniform k-points and don't need the CBM and VBM but the previous implementation didn'... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/531 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/531/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/531/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/531/events | https://github.com/materialsproject/pymatgen/pull/531 | 195,594,799 | MDExOlB1bGxSZXF1ZXN0OTc5OTg1NDk= | 531 | Bug fixes for Interstitial creation with no valence dictionary | {
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} | ## Summary
<When interstitial is created with no valences dictionary, ignore charge assignment>
* When interstitial is created with no valences dictionary, ignore charge assignment
## Additional dependencies introduced (if any)
## TODO (if any)
<Merge the Zeo++ python 3 changes and debug spglib errors>
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"I changed the fontsizes slightly and made them tunable, now it (by default) looks like this:\r\n\r\n\r\n",
"@computron, requests:\r\n\r\n1. as a user I'd prefer to set emin and emax directly ra... | 2016-12-14T19:13:29 | 2016-12-15T00:56:06 | 2016-12-15T00:55:20Z | MEMBER | {
"total": 0,
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A new band structure plotter that puts band structure and DOS on the same plot, aligned.
* Band structures include spin polarization
* Element projections on band structures supported
* Element and orbital projections on DOS supported
* Code is relatively straightforward to use, understand and modif... | {
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"Yes. For MP, the charges are analyzed to get an estimate of the oxidation state.",
"@albalu were you saying that these files are no longer needed for Bader charge analysis in the newest VASP / bader code? Please explain further...",
"@computron, I read the website more carefully again and it turns out it's sti... | 2016-12-15T00:59:57 | 2016-12-15T17:08:53 | 2016-12-15T01:03:11Z | CONTRIBUTOR | {
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} | I was wondering why LAECHG is set to True in MPStaticSet ? Is the only goal to generate AECCAR0-2 files for bader charge analysis? If yes, keeping it as False makes a big difference as these files (AECCAR0-2) are relatively large and shouldn't be printed by default if they are not generally needed. | {
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} | ## Summary
I've added the opt section to the qchem input file, which allows for constraining bond lengths, torsion angles, etc.
* Opt CONSTRAINT section added to qchem input files
* Opt section parser added
* unittest added
* unittest switch from unittest2 to unittest
## TODO (if any)
* only CONSTRAINT... | {
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} | Energy density conversion factor was off by a decimal place
Fixed the conversion factor to be easier to read
Updated the test and double checked it with another calculation
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} | ## Summary
For some reason, I could not get the projections to work for band structures stored in the old format. i.e., BandStructureSymmLine.from_old_dict() worked but did not do the projections correctly (calling get_projection_on_elements() resulted in failure).
This fixes that.
* BandStructureSymmLine.from... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/537 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/537/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/537/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/537/events | https://github.com/materialsproject/pymatgen/pull/537 | 197,274,679 | MDExOlB1bGxSZXF1ZXN0OTkxNzU4ODk= | 537 | bug fix in point_defects: incorrect usage of get attribute | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/538 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/538/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/538/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/538/events | https://github.com/materialsproject/pymatgen/issues/538 | 197,745,785 | MDU6SXNzdWUxOTc3NDU3ODU= | 538 | pathlib.Path.expanduser is available only for python3.5 | {
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} | * used in pymatgen.__init__.py for loading pmgrc
* it doesnt work for the other versons of python3(like 3.4 on tscc) | {
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"Pls fix the failing tests first. Thanks."
] | 2016-12-28T11:11:57 | 2016-12-28T15:49:34 | 2016-12-28T15:49:34Z | CONTRIBUTOR | {
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} | ## Summary
Improvements in chemenv : neighbors sets, tests, plotting.
* Image cell for neighbors in LightStructureEnvironments as an array of three integers (i.e. the neighbor is then the site with the index given translated by this array in fractional coordinates).
* Updated test structure_environments files.
... | {
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"Our approach for high symmetry k-point follows what is proposed by Setyawan et al.: Setyawan, W.; Curtarolo, S. Comput. Mater. Sci. 2010, 49 (2), 299–312. There the face centered A and B representations are not considered. This is only a representation and those are not recommended by the crystallographic communit... | 2017-01-04T07:02:00 | 2017-06-03T14:13:08 | 2017-06-03T14:13:08Z | NONE | {
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} | <When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: <4.5.7.>
* Python version: <Only 2.7.* and 3.* supported.>
## Summary
* In the source code, pymatgen.symmetry.bandstructure.py, it... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/541 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/541/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/541/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/541/events | https://github.com/materialsproject/pymatgen/pull/541 | 199,211,165 | MDExOlB1bGxSZXF1ZXN0MTAwNDY5NDk4 | 541 | small update of boltztrap.py | {
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"Thanks. Can you implement a few unittests to make sure it all works as expected? ",
"Thanks\r\n"
] | 2017-01-06T14:50:30 | 2017-01-06T16:40:50 | 2017-01-06T16:40:46Z | CONTRIBUTOR | {
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} | ## Summary
- bands check works for metals
- update the write_proj function to use properly the Orbital enum and new projections format
- added the k_el option to the get_thermal_conductivity function
(k_el = True is the default output k_0 -PF*T, as before. If False k_0 is returned)
- fixed a bug in the FERMI mod... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/542 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/542/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/542/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/542/events | https://github.com/materialsproject/pymatgen/pull/542 | 199,655,621 | MDExOlB1bGxSZXF1ZXN0MTAwNzU2MTg0 | 542 | Speed up Ewald summation | {
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Speeds up Ewald summation by doing more in-place math | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/543 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/543/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/543/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/543/events | https://github.com/materialsproject/pymatgen/issues/543 | 200,329,553 | MDU6SXNzdWUyMDAzMjk1NTM= | 543 | get_reconstructed_band_structure method outdated | {
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"@shyuep Unfortunately, this fix doesn't work as `BandStructure.bands` are `numpy` arrays.\r\n\r\nAs such, the line `eigenvals[Spin.up][i].append(e)` errors with:\r\n`AttributeError: 'numpy.ndarray' object has no attribute 'append'`\r\n\r\nThis is also the case I think for `BandStructure.projections`.\r\n\r\nI'm no... | 2017-01-12T10:24:49 | 2018-01-15T13:42:22 | 2018-01-15T13:42:22Z | MEMBER | {
"total": 0,
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} | ## System
* Pymatgen version: master/stable
* Python version: 2.7
## Summary
* The get `get_reconstructed_band_structure` method in `pymatgen/electronic_structure/bandstructure.py` contains references to `bs._bands` and `bs._kpoints`. These are obselete as the `BandStructure` class now uses the `bs.bands` and... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/544 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/544/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/544/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/544/events | https://github.com/materialsproject/pymatgen/issues/544 | 200,474,496 | MDU6SXNzdWUyMDA0NzQ0OTY= | 544 | Pymatgen won't work if installed with intel compilers | {
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"Can you provide an actual env that this occurs? What is the compilation method?",
"Also, where does it happen? \r\n\r\n1) in the compilation of pymatgen C source code (e.g. coords_utils_cython.c), in this case, it can be solved by configuring the compiler option; \r\n\r\n2) in the installation of dependent packa... | 2017-01-12T20:43:53 | 2018-06-07T15:40:08 | 2017-01-19T16:10:59Z | NONE | {
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} | I'm not sure how this should be fixed but it's kind of a recurring problem that can be easily forgotten.
Currently, pymatgen will throw "undefined symbol: _intel_fast_memcpy" errors when trying to use it if compiled using intel compilers. This seems like a silly problem that should be fixed either by throwing an err... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/545 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/545/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/545/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/545/events | https://github.com/materialsproject/pymatgen/pull/545 | 200,851,351 | MDExOlB1bGxSZXF1ZXN0MTAxNTg2MzUw | 545 | fix user_incar_settings bug in MPNonSCFSet and MPSOCSet | {
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"fix it."
] | 2017-01-15T06:11:16 | 2017-01-15T14:47:27 | 2017-01-15T14:47:27Z | CONTRIBUTOR | {
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* Fix user_incar_settings update issue in MPNonSCFSet and MPSOCSet and add corresponding unittest | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/546 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/546/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/546/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/546/events | https://github.com/materialsproject/pymatgen/issues/546 | 201,185,646 | MDU6SXNzdWUyMDExODU2NDY= | 546 | CIF test failing with Python 3.6 | {
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"Thanks. I implemented the fix as suggested."
] | 2017-01-17T06:19:57 | 2017-01-19T06:41:24 | 2017-01-19T06:41:13Z | MEMBER | {
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} | ## System
* Pymatgen version: 4.5.7
* Python version: 3.6.0
* OS version: macOS 10.12.2
## Summary
* `test_specie_cifwriter` fails in `test_cif.py`
* output of CifWriter() is basically correct, but ordering of species has changed, and thus atom labels change too
Output is:
```
_atom_site_occupancy... | {
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"Tests are failing. Pls fix."
] | 2017-01-18T20:17:23 | 2017-01-18T20:31:48 | 2017-01-18T20:19:56Z | CONTRIBUTOR | {
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} | ## Changes to elasticity module
Minor reorganization and bug fixes.
* elasticity classes/functions can now be imported from the top-level module, i. e. `from pymatgen.analysis.elasticity import ElasticTensor`.
* Minor bug fix concerning improper rotations with the option to exclude for TensorBase
* Added a tes... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/548 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/548/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/548/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/548/events | https://github.com/materialsproject/pymatgen/pull/548 | 201,696,307 | MDExOlB1bGxSZXF1ZXN0MTAyMTUyNDM4 | 548 | minor fix related to rounding errors in eigenvalue rotation | {
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Fixes failing test for deformation gradient generation in substrate analyzer. | {
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"Tests are failing because of use of pyhull. Pls try to use scipy.spatial where possible."
] | 2017-01-21T00:08:55 | 2017-01-23T18:01:41 | 2017-01-23T18:01:41Z | CONTRIBUTOR | {
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} | ## Summary
This PR introduces an adsorption site finder analysis tool in analysis/adsorption.py. Using it, one can enumerate symmetrically distinct adsorption sites on a slab and generate structures with molecular adsorbates at those sites.
* AdsorptionSiteFinder class, which has an find_adsorption_sites method ... | {
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"Pls add a unittest. and resubmit"
] | 2017-01-24T01:02:53 | 2017-01-24T01:33:37 | 2017-01-24T01:32:48Z | CONTRIBUTOR | {
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} | previously, if the conduction band minimum is equal to Fermi level, the code excludes it and return a neighbor data point.
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"Pls add a unit test before I merge."
] | 2017-01-24T01:33:02 | 2018-03-25T13:28:33 | 2017-01-24T01:33:29Z | MEMBER | {
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"@aykol is there any way to convert `Structure` to a pdb file (or string)?\r\n\r\nWe ([nglview](https://github.com/arose/nglview)) would like to support it too? cheers.\r\n\r\n(or even better, PR to `nglview` is welcome: https://github.com/arose/nglview/blob/master/nglview/adaptor.py)",
"@hainm thank you, it will... | 2017-01-24T19:57:27 | 2017-04-03T22:03:27 | 2017-01-24T19:58:51Z | CONTRIBUTOR | {
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} | ## Summary
* A handy function for quick visualization of pymatgen structures in jupyter notebook.
## Additional dependencies introduced (if any)
Optional dependency on an external package called chemview (https://github.com/gabrielelanaro/chemview). Will raise a proper import error upon use if chemview is no... | {
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modified BSE ouptut from the Fiesta code so modified reg pattern for BSEoutput
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"Thanks."
] | 2017-01-25T23:39:00 | 2017-01-26T00:18:09 | 2017-01-26T00:18:00Z | CONTRIBUTOR | {
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This PR introduces phonon related objects for archiving and plotting. The objects have been modeled on those contained in the electronic_structure module. No common class hierarchy has been introduced since the attributes of the electronic objects heavily rely on dictionaries containing Spin and Orbitals,... | {
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"This can be ignored for now.",
"I have this pre-link issue with mpi4py. Then, the program I ran shows... ImportError: Please install mpi4py. I use Anaconda, and \"conda list\" shows that mpi4py is already installed. Do you know how to fix this?"
] | 2017-02-01T17:41:08 | 2017-10-31T21:08:42 | 2017-02-01T23:24:00Z | NONE | {
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* Pymatgen version: 4.6.0
* Python version: 2.7.13 (Anaconda Distribution)
* OS version: Linux
## Summary
* Conda advises on installation that matsci dependencies are using dangerous pre-link scripts.
* Package matsci::palettable-2.1.1-py_0 uses a pre-link script
* Package matsci::pydispatcher-2.... | {
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} | Replace SpacegroupAnalyzer initialization argument keyword "tol" with "symprec" to match usage in SpacegroupAnalyzer class.
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"Go ahead and replace.",
"This was fixed in #558 and can be closed"
] | 2017-02-06T16:21:48 | 2017-03-31T22:35:30 | 2017-03-31T22:35:30Z | CONTRIBUTOR | {
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} | ## Order parameters were added that specifically recognize simple linear and bent coordination as well as coordination with a square and regular triangle (to form a pyramid with the central atom) and a square pyramidal OP (central atoms sits in basal plane).
To do:
- more unit tests (so far, only square pyramidal t... | {
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"@mbkumar, can you have a look at this issue?",
"This escaped my attention. I will check this at the earliest.\n\nOn Sep 11, 2017 3:34 PM, \"Nils Zimmermann\" <notifications@github.com> wrote:\n\n> @mbkumar <https://github.com/mbkumar>, can you have a look at this issue?\n>\n> —\n> You are receiving this because ... | 2017-02-08T00:26:04 | 2023-08-08T21:17:56 | 2023-08-08T21:17:55Z | NONE | {
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} | <When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: 4.6.1
* Python version: 2.7.13
## Summary
* when I use interstitial module, and set
interstitial=Interstitial(structure,valences... | {
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"@91bsjun Thanks for reporting. For later reference, here's before (top) and after (bottom) adding the suggested snippet:\r\n\r\n\r\n"
] | 2017-02-10T09:47:50 | 2023-05-29T16:03:50 | 2023-05-29T16:03:50Z | NONE | {
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} | `get_elt_projected_plots_color` is missing
```py
x_max = data['distances'][-1][-1]
plt.xlim(0, x_max)
```
Causes odd margins on the left and right side of the figure. | {
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"If you want to make a private repo of pymatgen, you need to clone the current version. Then create the private repo on github and clone that. Move the files from the clone to the private repo, and push it. The error you are seeing is probably due to the rebasing of pymatgen done a few months back. I suggest you cl... | 2017-02-10T18:44:03 | 2017-02-10T18:55:02 | 2017-02-10T18:55:02Z | MEMBER | {
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`[531e5b64ee126c2e0fba128fd0317662f36cbf02f651610ba085ba4354b96c6f] Object does not exist on the server: [404] Object does not exist on the server`
I think it's rel... | {
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} | * added class Paths: takes in a list of site indices that describes scattering path legs and generate corresponding custom scattering paths input file for feff.
* add unittests
* fall back to the deafult exhcnage setting for exafs
* some minor cleanups
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https://api.github.com/repos/materialsproject/pymatgen/issues/566 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/566/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/566/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/566/events | https://github.com/materialsproject/pymatgen/issues/566 | 207,676,881 | MDU6SXNzdWUyMDc2NzY4ODE= | 566 | Feature request for atom projected band structure | {
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"@hautierg Can you assign someone to implement this pls? I think this is indeed a useful feature to have.",
"Seems like this issue has been defunct for 6 years. Closing...."
] | 2017-02-15T00:30:10 | 2023-08-08T21:18:19 | 2023-08-08T21:18:18Z | NONE | {
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} | <When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
Python version 2.7 tested
## Summary
The documentation for BSPlotterProjected states "Class to plot or get data to facilitate the plot of band structure ... | {
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"You need to provide unittests that test the NpT functionality. The current pull request does not have that, only the old tests which only tests the NvT ensemble.\r\n\r\nPls run an NpT simulation with a simple small cell like Li2O or something and add the output file for NpT analysis.",
"Okay.",
"NpT output fil... | 2017-02-16T00:26:20 | 2017-02-16T20:52:55 | 2017-02-16T20:52:55Z | CONTRIBUTOR | {
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} | ## Summary
Make DiffusionAnalyzer class compatible with NPT-AIMD diffusion analysis.
* Added a new attribute *lattices*. For NVT simulation, the attribute is a one-item list; for NPT simulation, the attribute includes all lattice matrix, which is used in *get_drift_corrected_structures()*.
* Use fractional coord... | {
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"The tests are failing. Pls look at the Travis log. You used itertools.izip, which I htink in Python 3 is no longer available. Just use zip. Also, pls upgade to Py3 soon. Py27 support is now on its way out."
] | 2017-02-16T14:15:33 | 2017-02-16T14:54:41 | 2017-02-16T14:54:41Z | MEMBER | {
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} | ## Summary
Added a new function to the `Outcar` class to load in the average core potentials of each atom at all ionic steps. A test for this method was also added and is passing.
Some blank spaces at the end of lines were removed by vim python-mode- apologies for cluttering the pull request. | {
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"This is a unittest2 issue. Python 3.5 was still in beta when unittest2 was last released and it seems abandoned. Do you have a reason to use unittest2?\r\n\r\nEdit: I see now that it is in the source. This should probably be changed.",
"unittest2 is used in the pymatgen code. So the solution is to use a python v... | 2017-02-16T15:04:53 | 2017-02-16T21:20:23 | 2017-02-16T21:20:23Z | CONTRIBUTOR | {
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I am trying to run unittest of the master branch, but unittest2 seems incompatible with python 3.5.2
## System
pymatgen version: master branch
python version: python 3.5.2
conda version: 4.2.12
OS version: linux-64
## Summary
Running any test file returns:
```bash
ImportError: No module named 'unittest2'
... | {
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"There are failing tests. Pls check the travis log and fix pls. Thanks.",
"Thank you."
] | 2017-02-16T18:14:47 | 2017-02-17T14:30:36 | 2017-02-17T14:30:27Z | CONTRIBUTOR | {
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} | - get_average_eff_mass upgrade: now it returns values for all the energies,
using doping_level=False like other functions
- small patch for DOS run_type
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"Try to use the from_old_dict rather than from_dict method to deserialize the old format.",
"Did you actually try this?\r\n\r\n1. There is no from_old_dict() in the BandStructure class (only available for symm line band structures) and the first failure I get is for regular BandStructure\r\n2. Anyway, I had modif... | 2017-02-16T19:46:55 | 2017-02-18T00:45:15 | 2017-02-18T00:32:38Z | MEMBER | {
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## System
* Pymatgen version: master
* Python version: 2.7
* OS version: Mac
## Summary
* I am trying to back-convert old BandStructure and BandStructureSymmLine objects into the new format, and subsequently re-insert them into the database.
* I am successfully... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/572 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/572/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/572/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/572/events | https://github.com/materialsproject/pymatgen/pull/572 | 208,323,552 | MDExOlB1bGxSZXF1ZXN0MTA2NjYxNzU0 | 572 | PDAnalyzer.get_critical_compositions() | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/573 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/573/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/573/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/573/events | https://github.com/materialsproject/pymatgen/pull/573 | 208,391,987 | MDExOlB1bGxSZXF1ZXN0MTA2NzAxMDk0 | 573 | Class for I/O of exciting input | {
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"Thanks. However, can you make the following changes:\r\ni. This pull request is huge and affects a lot of files. A lot of the changes seem to be changing the permissions of the files. Pls keep your changes to only the specific files taht are modified.\r\nii. The class names should be CamelCase. So it should be Exc... | 2017-02-17T10:00:24 | 2017-02-20T14:38:17 | 2017-02-20T14:38:17Z | CONTRIBUTOR | {
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} | ## Summary
New class for the input of structure objects from the exciting input*.xml files, and the output of structures and bandstructure paths to exciting files.
## New Features
* `Structure.from_file` includes exciting files
* separate `excitingInput` object with `write_string` and `write_file` routines
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https://api.github.com/repos/materialsproject/pymatgen/issues/574 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/574/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/574/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/574/events | https://github.com/materialsproject/pymatgen/pull/574 | 208,504,135 | MDExOlB1bGxSZXF1ZXN0MTA2Nzc1NTE1 | 574 | New function to plot fermi surfaces using Mayavi tool | {
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"Great. Many thanks."
] | 2017-02-17T17:19:39 | 2017-02-17T17:21:08 | 2017-02-17T17:21:08Z | CONTRIBUTOR | {
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} | The function plot_fermi_surface of plotter module has been rewritten.
It now uses Mayavi package (mandatory) to calculate and potting the surface.
The dependency from ASE for reading CUBE files has been replaced with a new internal function.
It allows to plot fermi surfaces from cube file produces by both boltztrap ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/575 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/575/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/575/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/575/events | https://github.com/materialsproject/pymatgen/pull/575 | 208,565,730 | MDExOlB1bGxSZXF1ZXN0MTA2ODE4MDQ1 | 575 | Add rgb_legend style to BSDOSPlotter | {
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"note - element labels are now all black b/c the green \"K\" label in the ternary example is way too low-contrast to read"
] | 2017-02-17T21:44:46 | 2017-02-17T22:46:21 | 2017-02-17T22:46:20Z | MEMBER | {
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} | ## Summary
This PR adds a new style of legend to the BSDOSPlotter, the rgb_legend, which is by default False. If enabled, it can add a colored RGB triangle (ternaries) or RB bar (binaries) to show how the various colors on projected plots map to element ratios.
Note that the alternate (default) style is a more co... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/576 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/576/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/576/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/576/events | https://github.com/materialsproject/pymatgen/pull/576 | 208,594,539 | MDExOlB1bGxSZXF1ZXN0MTA2ODM4NjI5 | 576 | Pass the user defined symprec to spglib.get_ir_reciprocal_mesh | {
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## Summary
In SpacegroupAnalyzer the defined value of symprec is not propagated to spglib when calling the get_ir_reciprocal_mesh function, that instead uses a default of 1e-5. This may lead to unexpected behaviours and inconsistencies between the obtained space group and the list of irreducible kpoints. This pull... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/577 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/577/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/577/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/577/events | https://github.com/materialsproject/pymatgen/pull/577 | 208,620,217 | MDExOlB1bGxSZXF1ZXN0MTA2ODUxNTU0 | 577 | Third-order elastic constants fitting procedure | {
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} | ## Summary
This PR adds a fitting procedure that fits third-order elastic constants based on a central-difference scheme for finding first and second derivatives of the stress-strain relation.
* toec_fit function in elastic.py with unittest
* fixes a minor issue in generating eigenspace rotations related to defo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/578 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/578/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/578/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/578/events | https://github.com/materialsproject/pymatgen/pull/578 | 208,622,990 | MDExOlB1bGxSZXF1ZXN0MTA2ODUzMDg5 | 578 | BSDOS color interpolation update | {
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} | ## Summary
This is just a subtle change to the BSDOS coloring (both in the plot as well as in the legend). RGB values are interpolated based on square values. The reasoning is explained in this video:
https://youtu.be/LKnqECcg6Gw
Thanks to Matt Horton for pointing this out.
The squared values indeed lead t... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/579 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/579/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/579/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/579/events | https://github.com/materialsproject/pymatgen/pull/579 | 208,659,875 | MDExOlB1bGxSZXF1ZXN0MTA2ODcxNTc1 | 579 | Symprec variable fixed | {
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} | Symprec variable has been fixed:
- the default value now is 1e-3 consistent with other method in pymatgen
- it is also possible to pass a different symprec to BoltztrapRunner when
the list of kpoints has been generated with a different symprec.
This can be useful to cure the "factorization error" of BoltzTraP calcu... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/580 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/580/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/580/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/580/events | https://github.com/materialsproject/pymatgen/pull/580 | 208,742,306 | MDExOlB1bGxSZXF1ZXN0MTA2OTE0Mjcz | 580 | Simplex speedups | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/581 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/581/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/581/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/581/events | https://github.com/materialsproject/pymatgen/issues/581 | 208,757,936 | MDU6SXNzdWUyMDg3NTc5MzY= | 581 | Defining the correct usage of HighSymmKpath | {
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"I have no objection to issuing a warning or even raise an error if the structure does not correspond to primitive standard. Can you implement pls? Thanks."
] | 2017-02-19T23:59:22 | 2017-02-21T14:08:47 | 2017-02-21T14:08:47Z | CONTRIBUTOR | {
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} | ## Summary
I would like to signal a common misunderstanding that I have seen happen to many different people with the HighSymmKpath object.
HighSymmKpath is basically a hardcoded list of kpoints based on Setyawan-Curtarolo's paper, that uses the input structure just to get its spacegroup. On the other hand, at the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/582 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/582/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/582/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/582/events | https://github.com/materialsproject/pymatgen/issues/582 | 208,870,553 | MDU6SXNzdWUyMDg4NzA1NTM= | 582 | plotting fermi surface from vasp calculation | {
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"Hi,\r\nyou can run BoltztrapRunner using FERMI mode and selecting the index of the band you want to study.\r\nThen, you can import the output with BoltztrapAnalyzer and plot it with the function plot_fermi_surface.\r\nhere a general example:\r\n\r\nvrun = Vasprun('vasprun.xml.gz')\r\nbs = vrun.get_band_structure()... | 2017-02-20T12:48:38 | 2020-06-24T16:43:51 | 2017-02-20T14:37:22Z | NONE | {
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} | Hi,
I would like to ask about whether we could obtain Fermi surface and plot it via pymatgen (or other programs) from VASP calculations? I see the class BoltztrapRunner but not sure if it could achieve this task. Thank you very much. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/583 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/583/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/583/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/583/events | https://github.com/materialsproject/pymatgen/pull/583 | 208,976,927 | MDExOlB1bGxSZXF1ZXN0MTA3MDcyODg1 | 583 | Improvements to BSDOSPlotter legend | {
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} | ## Summary
Various improvements to fancy BSDOSPlotter legend
* Uses a separate inset axis to plot legend
* This ensures the aspect ratio of legend stays consistent for different band structures
* It also visually separates the legend from the background better
* Now rgb_legend style is by default True
The p... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/584 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/584/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/584/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/584/events | https://github.com/materialsproject/pymatgen/issues/584 | 209,006,276 | MDU6SXNzdWUyMDkwMDYyNzY= | 584 | error in plotting fermi surface | {
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"I have attached a small vasprun.xml (30 MB) that reproduces the error in the dropbox.\r\n\r\nhttps://www.dropbox.com/s/itz8etvh4424nwa/vasprun.xml?dl=0\r\n\r\nWould you like to take a look and see what might go wrong? Thank you very much.",
"If you run VASP using an automatic mesh, this is a typical error due to... | 2017-02-20T23:42:51 | 2017-03-09T23:22:19 | 2017-02-21T14:09:04Z | NONE | {
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} | After performing Spin Orbit Coupling calculation on VASP. I tried to use pymatgen to plot the fermi surface as followed:
```
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter, DosPlotter, BSDOSPlotter, BoltztrapPlotter
from pymatgen.electronic_structure.core... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/585 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/585/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/585/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/585/events | https://github.com/materialsproject/pymatgen/pull/585 | 209,155,067 | MDExOlB1bGxSZXF1ZXN0MTA3MTk0ODE5 | 585 | Warning for non standard structures in HighSymmKpath | {
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"Thanks.",
"My understanding is that if the lattice/structure doesn't match the primitive, then the output of HighSymmKPath will be incorrect.\r\n\r\nIf that's the case I would prefer an error, i.e., bad input should result in an error, not a warning. Under no circumstances should a code knowingly return bad outp... | 2017-02-21T14:06:18 | 2017-02-21T19:22:58 | 2017-02-21T14:08:30Z | CONTRIBUTOR | {
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} | ## Summary
This PR addresses the problem highlighted in issue #581 adding a warning if the lattice of structure does not match the one of the primitive standard. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/586 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/586/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/586/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/586/events | https://github.com/materialsproject/pymatgen/issues/586 | 209,221,416 | MDU6SXNzdWUyMDkyMjE0MTY= | 586 | generate explicit k-points generation for VASP | {
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"This is what the method MPNonSCF does:\r\n\r\n kpoints = Kpoints.automatic_density_by_vol(self.structure,\r\n self.reciprocal_density)\r\n mesh = kpoints.kpts[0]\r\n ir_kpts = SpacegroupAnalyzer(\r\n self.structur... | 2017-02-21T17:46:57 | 2017-02-24T18:20:30 | 2017-02-24T18:20:30Z | NONE | {
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} | I need to generate explicit k-points (considered symmetry of structure) for the vasp calculations (I also need it for correct Bootstrap fermi-surface calculation). I know that I could generate k-points among high symmetry lines in this way. However, I would need explicit k-points mesh for self consistent calculation (n... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/587 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/587/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/587/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/587/events | https://github.com/materialsproject/pymatgen/pull/587 | 209,465,693 | MDExOlB1bGxSZXF1ZXN0MTA3NDE1NDE5 | 587 | Correct error in factorization and update url of bolztrap | {
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* the url of boltztrap needs update
* the output should be "error in factorization" not "STOP error in factorization" at least in the version 1.2.5 | {
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} | ## Updates to adsorption module
A few updates to the adsorption module based on issues I've encountered and updates suggested by @richardtran415.
* AdsorbateSiteFinder.find_adsorption_sites can now take "subsurface" in its list of positions arguments. If specified, it will find adsorption sites based on subsur... | {
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} | ## Summary
Long pending modifications with respect to Zeo++ implemented.
* python3 compatibility for Zeo++ python bindings
* SpagegroupAnalyzer.get_symmetrized_structure fails for dense voronoi points. Voronoi points are pruned if close before passing to SpgA
* Zeo++ installation instructions added
## Add... | {
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} | * add 'numerical eos': the equation of state employed in the quasiharmonic Debye model described in Cormac's paper: 10.1103/PhysRevB.90.174107.
* refactor and cleanup eos.py module | {
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* file argument to saving dos plot is fixed.
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} | Dear master,
I wrote a new method named "get_projected_plots_dots_patom_pmorb" in plotter.py file. This is an extension of the old method "get_projected_plots_dots" and still in the class "BSPlotterProjected". Here are some features of this method:
- Get projections on specific atoms (e.g. Cu1, O3, Zn4) or on a g... | {
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* more object oriented implementation: makes it easier for adding more eoses
* added more unittests
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https://api.github.com/repos/materialsproject/pymatgen/issues/596 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/596/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/596/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/596/events | https://github.com/materialsproject/pymatgen/pull/596 | 210,165,629 | MDExOlB1bGxSZXF1ZXN0MTA3OTE0MDg3 | 596 | fixes to generate_adsorption_structures and tests | {
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Small update to adsorption module, fixes to structure generation for adsorbate structures
* AdsorbateSiteFinder can generate adsorption structures and pass arguments into the site finding function
* Relevant unittests added | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/598 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/598/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/598/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/598/events | https://github.com/materialsproject/pymatgen/pull/598 | 210,550,876 | MDExOlB1bGxSZXF1ZXN0MTA4MTYxOTAy | 598 | Reaction Balancing | {
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Cleaned up the reaction balancing.
Changed string formatting of reactions to avoid superfluous zeros and decimals. Also made the reaction strings consistent with each other (the formatting of different methods was slightly different).
Redefined and documented how Reactions are balanced by default. T... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/600 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/600/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/600/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/600/events | https://github.com/materialsproject/pymatgen/pull/600 | 210,971,646 | MDExOlB1bGxSZXF1ZXN0MTA4NDYyMDU3 | 600 | Refactoring of PDAnalyzer.get_element_profile | {
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} | ## Summary
* Refactor PDAnalyzer.get_element_profile to use get_critical_compositions instead of generating new PDs
* More helpful error message in Reaction for underdetermined reactants. I don't think there's a useful result to return in these cases.
* Better unittests for get_element_profile | {
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