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https://api.github.com/repos/materialsproject/pymatgen/issues/601 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/601/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/601/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/601/events | https://github.com/materialsproject/pymatgen/pull/601 | 211,497,411 | MDExOlB1bGxSZXF1ZXN0MTA4ODM2NDI2 | 601 | BSDOSPlotter figure size option | {
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} | ## Summary
Sometimes long kpaths result in figures where kpoint labels overlap each other. Allowing user to change figure size can stretch the figure out so this does not occur. Defaults to previous default size dimensions (11, 8.5) if user does not specify.
## Additional dependencies introduced (if any)
N/A
... | {
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"@hautierg Can you comment?",
"The fix seems pretty straightforward, I'm quite happy to implement as long as this is definitely a bug and I'm not missing something.",
"Thanks. Yes, if you can fix it, it would be great.",
"Sounds good to me. Thanks!\n> On 03 Mar 2017, at 21:23, Shyue Ping Ong <notifications@gi... | 2017-03-03T16:54:10 | 2017-03-07T14:21:59 | 2017-03-07T14:21:59Z | MEMBER | {
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} | When parsing a hybrid band structure using the `Vasprun.get_band_structure()` method with `linemode=True`, the band energies for any k-points that are not zero weighted are ignored.
If the `Vasprun` object is initialised with `parse_projected_eigen=True` the projections for each band are also read from the vasp outp... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/603 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/603/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/603/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/603/events | https://github.com/materialsproject/pymatgen/pull/603 | 211,753,436 | MDExOlB1bGxSZXF1ZXN0MTA5MDE5ODA3 | 603 | add list_keys to Incar | {
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"Pls add unittest.",
"Unittest for new list_keys LANGEVIN_GAMMA has been added."
] | 2017-03-03T17:35:01 | 2017-03-04T00:33:32 | 2017-03-04T00:33:32Z | CONTRIBUTOR | {
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} | ## Summary
Add "LANGEVIN_GAMMA" to list_keys in class Incar.
## Additional dependencies introduced (if any)
NA
## TODO (if any)
NA | {
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"Many thanks. Sorry for the lateness in merging. I was thinking if there are better ways to structure the class. For now, this looks great!",
"No problem at all, I'm not convinced this is the best way of doing it either, but I think it works for now. Thanks for merging!",
"I have just pushed a bunch of changes ... | 2017-03-04T01:07:13 | 2017-04-13T00:46:33 | 2017-04-11T00:07:13Z | MEMBER | {
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} | ## Summary
New proposal for `electronic_structure.core.Magmom` class to simplify working between scalar and vector-type magnetic moments for collinear and non-collinear electronic structure calculations.
Internally implements a spin quantization axis, following exactly the specification of `SAXIS` tag in VASP doc... | {
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} | Hybrid band structures created with `linemode=True` now discard any projections for weighted k-points.
Fixes #602 | {
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} | ## System
* Pymatgen version: master
* Python version: 2.7
* OS version: MacOS
## Summary
It seems there is a bug in core/surface.py#L584:
Line in question is:
```uvw, cosine, l = max(candidates, key=lambda x: (x[1], -l))```
It seems it should be:
```uvw, cosine, l = max(candidates, key=lambda x: (x[... | {
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"Hi,\r\nI want to point out that this is related to the issue #374. The problem originates from the fact that spglib at some point started to use and return the symbol of the a-centered structure for some of the base-centered orthorhombic lattices (spacegroups 38 to 41. Notice that mp-773965 has spacegroup 40). See... | 2017-03-07T18:58:50 | 2023-08-08T21:18:43 | 2023-08-08T21:18:43Z | CONTRIBUTOR | {
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* Pymatgen version: 4.6.2
* Python version: 2.7
* OS version: Mac
## Summary
* seems like HighSymmKpath have a problem with symmetries with spage group number 40 (see the example below also tried mp-12364 returned None)
## Example code
```python
from pymatgen import MPRester
from pymatgen.s... | {
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"Thanks. Pls implement the change and submit a PR."
] | 2017-03-08T16:59:18 | 2017-03-31T22:35:53 | 2017-03-31T22:35:53Z | 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: appears to be present in 4.7.0
* Python version: 2.7.x
* OS version: CentOS 5
## Summary
* During a testing discussion, Daniil real... | {
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See issue #610
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} | When fixing #602 I didn't check that the band structure had projections before discarding those corresponding to weighted k-points. As such trying to run `vr.get_band_structure()` when projections are not loaded results in an error.
This pull request fixes that bug.
However, this and #543 highlight the need for p... | {
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} | Something has been broken in the plotter module, in the last version 4.7.0
I got huge fonts and lines plotting DOS and Phase Diagrams.
Probably the same happens for other kind of plots. | {
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"I fixed it for flask-paginate. Can you check if there are problems for others?",
"@shyuep Thanks, it also happenes on `smoqe` and `tabulate` when installing in python3.6.\r\nBesides, does `palettable` on the matsci channel need an update?",
"I just fixed all of them. I can update palettable.",
"@shyuep Thank... | 2017-03-10T02:41:59 | 2017-03-11T02:22:19 | 2017-03-10T15:04:25Z | 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(conda)
* Python version: 2.7 and 3.6
* OS version: linux
## Summary
In the matsci channel, some dependency have name with `py_0... | {
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} | ## Refactor elasticity symmetry reduction of tensors
Abstracts the symmetry reduction algorithm, implements a unit-test, and cleans up a few unused imports.
* pymatgen.analysis.elasticity.tensors.symmetry_reduce takes a list of tensors and reduces it to a set of symmetrically equivalent tensors. The function ret... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/617 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/617/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/617/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/617/events | https://github.com/materialsproject/pymatgen/pull/617 | 213,585,160 | MDExOlB1bGxSZXF1ZXN0MTEwMjg3ODk5 | 617 | minor bug fix | {
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} | ## Summary
* Minor bug fix for fraction coordinates and Cartesian coordinates conversion. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/618 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/618/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/618/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/618/events | https://github.com/materialsproject/pymatgen/pull/618 | 213,646,482 | MDExOlB1bGxSZXF1ZXN0MTEwMzIxODk5 | 618 | Minor bug fix on TOEC fitting | {
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} | * Fixes bug in which equilibrium stress wasn't being substituted properly into stencil for third-order elastic constant fitting with stencil resolutions other than 7
* Adds unit test to check TOEC fitting with stencil resolutions other than 7
* Uses scipy's central_diff_weights in TOEC function and deletes pymatgen f... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/619 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/619/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/619/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/619/events | https://github.com/materialsproject/pymatgen/pull/619 | 214,089,100 | MDExOlB1bGxSZXF1ZXN0MTEwNjMyODY2 | 619 | remain site_properties if exist when replace Element | {
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"This does not make sense. If you replace an element, the likelihood is that the site properties will change.",
"Also, the tests failed.",
"Yes, I see it, sorry.\n\n2017年3月15日 00:11，\"Shyue Ping Ong\" <notifications@github.com>写道：\n\nThis does not make sense. If you replace an element, the likelihood is that\nt... | 2017-03-14T14:26:26 | 2017-03-15T13:28:29 | 2017-03-15T13:28:29Z | CONTRIBUTOR | {
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remain site_properties if exist when replace Element | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/620 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/620/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/620/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/620/events | https://github.com/materialsproject/pymatgen/pull/620 | 214,549,348 | MDExOlB1bGxSZXF1ZXN0MTEwOTU5MDg2 | 620 | Toec new | {
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"I'm going to close this for now, want to do a bit more refactoring of the Strain functionality."
] | 2017-03-15T22:48:37 | 2017-03-16T17:03:10 | 2017-03-16T17:03:10Z | CONTRIBUTOR | {
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} | ## Minor edits to elastic tensor
Fixes a few issues in elasticity related to using a tolerance for independent deformation finding and summary output for derived properties.
* Elastic tensors can return a dictionary of derived properties and structure-derived properties
* Independent strain-deformation finding u... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/621 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/621/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/621/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/621/events | https://github.com/materialsproject/pymatgen/issues/621 | 214,640,290 | MDU6SXNzdWUyMTQ2NDAyOTA= | 621 | Set attribute to the Site object. | {
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"Note that sites are supposed to be immutable. So you cannot set any properties at all. The coords are internally represented by an private array. So what [4] does is that you get a copy of the array, and then you are modifying that copy. I don't think there is an easy way to change the code such that [4] raises an... | 2017-03-16T09:17:48 | 2017-03-16T13:05:13 | 2017-03-16T13:05:13Z | CONTRIBUTOR | {
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If you are using a Site object, as attributes are almost all properties you cannot directly set it.
```
In [1]: site = mg.Site(3, [0, 0, 0])
In [2]: site
Out[52]: Site: Li (0.0000, 0.0000, 0.0000)
In [3]: site.x = 2
---------------------------------------------------------------------------
AttributeE... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/622 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/622/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/622/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/622/events | https://github.com/materialsproject/pymatgen/pull/622 | 215,191,383 | MDExOlB1bGxSZXF1ZXN0MTExNDA4ODcy | 622 | quasi-harmonic debye approximation | {
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* added tests | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/623 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/623/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/623/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/623/events | https://github.com/materialsproject/pymatgen/pull/623 | 215,542,772 | MDExOlB1bGxSZXF1ZXN0MTExNjQxNDkz | 623 | Removed mutable default parameters. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/624 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/624/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/624/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/624/events | https://github.com/materialsproject/pymatgen/pull/624 | 216,480,345 | MDExOlB1bGxSZXF1ZXN0MTEyMjczOTg0 | 624 | add logging to boltztrap | {
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} | ## Summary
Current boltztrap run with the output only in console, there is few log for us to know what pymatgen have down.
So I add logging to run method and BoltztrapError class, i have test a little, and hope everything will work. | {
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} | ## Summary
If the conduction band minimum (cbm) is the same or slightly smaller than the Fermi level, the code cannot find the cbm. Instead, the code returns the second smallest number and, in turn, gets the wrong band gap.
* Changes a '>' to a '>='
* Adds a unit test for InN (mp-22205) to guard against regress... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/626 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/626/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/626/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/626/events | https://github.com/materialsproject/pymatgen/pull/626 | 216,825,265 | MDExOlB1bGxSZXF1ZXN0MTEyNDg0Nzkz | 626 | Contributions from UCLouvain group | {
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"Many thanks."
] | 2017-03-24T15:43:44 | 2017-03-24T18:37:42 | 2017-03-24T16:17:32Z | CONTRIBUTOR | {
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} | ## Summary
Contributions from UCLouvain group.
* Add support for Abinit 8.2.2
* Improved support for DFPT calculations
* Add support for `angdeg` in Structure.from_dict
* Fix minor py3k portability issues | {
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} | ## Summary
<Short few sentences, and summary of the major changes in bullet
points>
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
<List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, addin... | {
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* Fix typo
* Add unit test | {
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} | ## Refactor Elasticity
This PR features a refactoring of the classes in analysis.elasticity to allow for more efficient higher order elastic tensors.
* Renames TensorBase to Tensor
* Introduces NthOrderElasticTensor and ElasticTensorExpansion, which inherit attributes of Tensor and can be used to calculate stres... | {
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} | ## Adds unit tests and a miscellaneous fixes to higher order elastic tensors
* Fixes an issue with subclass structure in new elastic tensors
* Renames central_diff_fit to diff_fit, since central difference stencils are no longer required
* Adds unit tests for elastic tensor expansion and subclasses | {
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"(note - if you don't like the ``import *``, just do ``from pymatgen.analysis.elasticity.elastic import ElasticTensor`` and you get the same error)",
"Ah, I failed to protect a sympy-dependent section of the new code with the\nconditional. I'll fix shortly.\n\nOn Fri, Mar 31, 2017 at 11:36 AM, Anubhav Jain <noti... | 2017-03-31T18:36:11 | 2017-03-31T20:03:05 | 2017-03-31T19:12:29Z | MEMBER | {
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## System
* Pymatgen version: master
* Python version: 2.7
* OS version: mac
## Summary
* See example code
## Example code
```python
from pymatgen.analysis.elasticity.elastic import *
```
## Error message
```
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "... | {
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} | ## Summary
In the case of Pourbaix diagrams for 3 or more elements, weights of multi-entries were incorrectly computed. Weights were fixed by using an algorithm based on the Rouche-Capelli Theorem.
## Additional dependencies introduced (if any)
No additional dependencies were introduced.
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"Note: the downstream consequence of this is that all MP structures for gas phase compositions (e.g., H2, F2, N2, etc) have e_above_hull = 0. This means that even if you have some really bad H2 structure that is nothing like the real solid and doesn't contain any bonds, it will still show e_above_hull = 0. It makes... | 2017-04-04T18:59:32 | 2017-04-06T02:58:31 | 2017-04-06T02:58:31Z | 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: 4.6.0+
* Python version: 2.7
* OS version: linux (nersc mendel)
## Summary
* Gascorrection collapses the energy_per_atom and E^hull... | {
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"I have just pushed a fix. Thanks for reporting this."
] | 2017-04-06T01:30:07 | 2017-04-06T02:44:21 | 2017-04-06T02:44:04Z | NONE | {
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this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: 4.3.16-py27_0
* Python version: Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15)
IPython 5.1.0
* OS versio... | {
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"Try BSDOSPlotter, that's the one I wrote and IMO much prettier than BSPlotter",
"Erm, that does not solve the SymmLine vs non-SymmLine issue? ",
"It only solves the issue of needing to play around with a lot of parameters to get the plotting to work. You should just be able to feed in a DOS and BSSymmLine obje... | 2017-04-07T14:11:49 | 2023-08-08T21:19:30 | 2023-08-08T21:19:30Z | MEMBER | {
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} | I am thinking that the Bandstructure capabilities need a bit of an overhaul. Recently, I have tried to plot a few bandstructures from a few vasp runs (not from MP), but found that I had to play around with several parameters until I finally got it to work. For example,
1. Vasprun.get_band_structure returns two types... | {
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} | Modified Outcar __init__ method:
* Check for ISPIN = 2 and if so set self.spin = True
* Check for LNONCOLLINEAR = T and if so set self.noncollinear = True
* Check for LCALCPOL = T and if so run read_lcalcpol
Modified Outcar read_lcalcpol method:
* If self.spin = True, read spin polarized dipole moment to propert... | {
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} | 1) Support for fixed atoms for constrained geometry optimizations.
2) Support for method keyword. Add it to constructor parameter and omit old exchange keyword in case that it is already coverred by method.
3) Refractor "$opt" section data structure. | {
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"Thanks. Yes, there was a change in the internal representation of the projected BS for efficiency. Your suggested change should fix it. I just pushed the change."
] | 2017-04-12T06:20:54 | 2017-04-12T14:38:52 | 2017-04-12T14:38:03Z | CONTRIBUTOR | {
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} | ## System
* Pymatgen version: 4.7.3
* Python version: 2.7.10
* OS version: Ubuntu 15.10
## Summary
* BSPlotterProjected.get_projected_plots_dots_patom_pmorb fails, complaining about an IndexError
* This appears to be because BSPlotterProjected is expecting the underlying BandStructureSymmLine.projections[S... | {
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## Summary
Proposal for a simple `MagSymmOp` class. This subclasses `SymmOp`, adding a time reversal operator. It also includes an `operate_magmom()` method which acts to transform the magnetic moment on an atom when a magnetic symmetry operation is performed.
This is used for #508 and also in a new `MagneticSp... | {
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<Short few sentences, and summary of the major changes in bullet
points>
*Na-H bond length from CCCBDB added to bond_lengths.json
*Bond length is 1.887Å
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} | ## Summary
Currently, it's non-obvious how a user would add a custom `LDAUU` value to their `user_incar_settings` that would be used in the general case (regardless of what anions are in the input structure).
From my reading of `sets.py` it seems like if a user wants to set (e.g.) a custom `LDAUU` value for Fe, t... | {
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"We should not be changing the precision of the data. What we should do is to edit the is_metal method to account for floating point numerical accuracy and allow for up to a 4th decimal place difference."
] | 2017-04-19T15:58:50 | 2017-04-25T23:17:43 | 2017-04-25T23:17:43Z | CONTRIBUTOR | {
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Excerpt from vasprun.xml:
```
...
<i name="efermi"> 2.71196589 </i>
<total>
<array>
<dimension dim="1">gridpoints</dimension... | {
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"Shuldn't the second threshold be -1e-4, rather than 1e-4?",
"No, the example in #648 would still be categorized as metallic in that case. ",
"Let's think about the intent of that method. Basically, the code is asking if there are eigenvalues that are both above and below the efermi level in a band. If there is... | 2017-04-19T16:17:15 | 2017-04-19T18:09:55 | 2017-04-19T18:09:55Z | CONTRIBUTOR | {
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} | See [https://github.com/materialsproject/pymatgen/issues/648#issuecomment-295325994](https://github.com/materialsproject/pymatgen/issues/648#issuecomment-295325994). | {
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the default type of p.communicate() is bytes in python3, the log info will not display as we wish. | {
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} | ## Summary
`Outcar.read_freq_dielectric()` had a typo when assigning the dielectic tensor components to full tensors, making the data stored in `self.dielectric_tensor_function` have asymmetric off-diagonal elements. This update fixes this.
* `read_freq_dielectric()` now generates symmetric dielectric tensors. | {
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"@dwinston I currently see this warning when I use python 3.6, but I think `pytex` is dependency only for python 2.x."
] | 2017-04-24T23:31:13 | 2017-05-11T11:06:02 | 2017-04-24T23:32:06Z | MEMBER | {
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} | MPRester users are having issues decoding SNL objects due to `pybtex` no longer being installed by default by pymatgen. This issue was raised before as #519. I would love to have `pybtex` required, but as an alternative, this PR adds a user warning to install extras.
* Emits `UserWarning` if cannot import `pybtex`
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"Hey @blondegeek,\r\nI can give it a shot next week and see if I can construct something quickly. Will let you know ASAP.",
"@nisse3000 Thanks very much! Please let me know if there's any way I can be helpful.",
"@shyuep, I think that this issue can be closed because the trigonal bipyramidal order parameter wa... | 2017-04-25T23:24:05 | 2017-09-11T22:45:53 | 2017-09-11T22:45:53Z | CONTRIBUTOR | {
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} | @nisse3000 How difficult would it be to add the order parameter for trigonal bipyramidal coordination to OrderParameters in pymatgen.analysis.structure_analyzer?
Example of structure with trigonal bipyramid coordination:
Hexagonal manganate YMnO3
[https://materialsproject.org/materials/mp-19385/](https://material... | {
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"I think MXYZ and XYZ classes should be merged.",
"I was thinking about it. But, are you sure? It will change the API. e.g. molecules (list) vs molecule. Of course, we can do ad-hoc stuff to make it file dependent, then we will force the user to test the type of molecule.",
"I mean the molecule property can be ... | 2017-04-26T22:26:49 | 2017-04-28T00:17:35 | 2017-04-28T00:17:35Z | CONTRIBUTOR | {
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* Add support for "velocity" section to QChem module to AIMD setup.
* Add class QcNucVeloc to parse QChem AIMD velocity output. | {
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} | ## Summary
Minor fixes and edits to pymatgen elasticity module
* Updated DeformedStructureSet symmetry functionality, now works as intended, added unittest
* PEP8 cosmetic adjustments to newer code
## TODO (if any)
Larger refactor of stress-strain functionality, fitting, and some extended properties from t... | {
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} | ## Summary
2 new structure analysis features
* A JMolCoordFinder that automatically determines coordination number based on an emulation of the JMol autoBond algorithm
* A get_dimensionality() function that returns whether a structure is formed of 1D chains/molecules, 2D layers, or is 3D interconnected
+ test... | {
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"Pymatgen is at version 4.7.4. There is no version 5.0 at the moment. \r\n\r\nI need the example file to know the problem. The likelihood is that there is an illegal character in the file which causes the unicode decoding (which is expected for a POTCAR file) to not work. \r\n\r\nAlso, can you elaborate on the \"ha... | 2017-05-08T03:24:53 | 2017-05-14T17:04:21 | 2017-05-14T17:04:21Z | NONE | {
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} | ## System
* Pymatgen version: 5.0
* Python version: 2.7 as primary, though 3 installed
* OS version: Fedora 25
## Summary
Running a code to get density of states (that runs fine in Debian Jessie) returns the following error in Fedora 25.
` UnicodeDecodeError: 'utf8' codec can't decode byte 0xb0`
Pymat... | {
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"Let's do the first. Thanks for finding the cause.\r\n\r\nAs an aside, I wrote DeformedStructureSet mostly to preserve some legacy functionality of an older codebase that I inherited, but I've never used it for anything practical (I mostly use atomate/MPWorks for managing calculations of ECs). If there's any addi... | 2017-05-09T22:21:51 | 2017-05-09T23:12:42 | 2017-05-09T23:12:42Z | NONE | {
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} | ## System
* Pymatgen version: **master 4.7.5**
* Python version: **3.6.1**
* OS version: **Fedora 25**
## Summary
* analysis/elasticity/strain.py: DeformedStructureSet() returns a [dict_keys](https://docs.python.org/3/library/stdtypes.html#dictionary-view-objects) object in python 3 (rather than a list in py... | {
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* Ensures deformations attribute of deformed structure set is a list | {
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"Can you provide an example code?",
"[point_group_example.txt](https://github.com/materialsproject/pymatgen/files/992427/point_group_example.txt)\r\n\r\nSorry forgot to upload",
"Thanks for the report. I have fixed the bug (it is actually not due to bad detection of rotation axes, but rather wrong classificatio... | 2017-05-10T15:47:34 | 2017-05-14T16:41:42 | 2017-05-14T16:31:22Z | NONE | {
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this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: <4.7.2>
* Python version: <3.6.1>
* OS version: <OpenSUSE 13.1>
## Summary
* <If you pass 8 carbon atoms at the corners of a cube ... | {
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"Hi Shyue\r\n\r\nFor the most part I am OK with the change. \r\n\r\nThe part I would hedge a bit on is the enforcement of even/odd mesh as per VASP documentation. This is unrelated to your change since it was there before, but I just would take the opportunity to revisit it.\r\n\r\nPretend there are two materials w... | 2017-05-10T19:42:36 | 2017-05-17T04:06:08 | 2017-05-15T23:39:38Z | MEMBER | {
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} | ## People who definitely need to look at this code and comment
* @computron @kristinpersson @hautierg @zbwang @johnson1228 @montoyjh @wmdrichards
I will leave this in the branch for three days. After that, I will merge if there are no comments.
## Summary
* Today's kpoint generation scheme is highly ineffici... | {
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} | Now if compute_forces is set to False, will allow __str__ method to print without error from trying to calculate self.forces.
## Summary
- Bug fix with printing the EwaldSummation object with default value of compute_force
## Additional dependencies introduced (if any)
N/A
## TODO (if any)
N/A | {
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"When you entered the issue, the template specifically asks for several pieces of information with regards to the type of OS and system. Pls indicate all that information. The single error message that you gave above is not enough for us to go on.\r\n\r\nAlso, the pymatgen installation instructions specifically rec... | 2017-05-15T09:21:50 | 2017-05-15T13:00:38 | 2017-05-15T13:00:38Z | NONE | {
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} | I am learning how to use pymatgen . But I have a problem on installing pymatgen, the method I use is 'python setup.py install'. When I install pymatgen, it has a error . The error is 'error LNK2019: unresolved external symbol _round referenced in function
___pyx_pf_8pymatgen_4util_18coord_utils_cython_pbc_shortest_v... | {
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"(just look at the diff)"
] | 2017-05-15T19:59:19 | 2017-05-15T20:21:38 | 2017-05-15T20:21:38Z | MEMBER | {
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"(Looks like CI failures are a result of https://github.com/materialsproject/pymatgen/commit/66a78e5d00a394d7c2a9b1365c533d4176b0e27c, since CI doesn't have a MAPI key defined? All tests in this PR should pass okay otherwise.)",
"Many thanks. I will merge for now. I am not sure why JSON would be slower than sqlit... | 2017-05-17T04:09:07 | 2017-05-17T18:38:19 | 2017-05-17T05:02:46Z | MEMBER | {
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} | ## Summary
* A magnetic version of `SpaceGroup`, with information on all 1651 magnetic space groups. Magnetic space groups are commonly supplied in one of two settings ('BNS' and 'OG'); this class uses BNS as the canonical setting but can also be initialized with the OG label/number. More information on this can be ... | {
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} | Class retrieves a binary blob from the sqlite database and converts it to a byte `array`. At some point, the `array` constructors changed from accepting a string to accepting a buffer.
At present, I can't find a constructor that works in both Python 2.7 and Python 3.6, so have wrapped it in a try/except.
Apologie... | {
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caught by `if isinstance(…, str)` statement leading to no SQL query
being generated. | {
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} | ## Summary
Added color differentiation between plot_1 and plot_2 in plot_compare, an option to print a legend, and fixed a bug preventing plot_compare from ever succeeding.
In BSPlotter.plot_compare(other_plotter), the indentation level of the block regarding the spin-down channel was incorrect, and the content ... | {
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} | Ensure SNL references is a string rather than any falsy value. Prevents downstream surprises for users who e.g. submit SNLs in bulk to Materials Project. Thank you @shyamd for discovering this.
* Type-check on SNL construction
* Add unit tests for "empty" references | {
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"Two additional comments: (1) my CircleCI isn't working yet, so hope this one's okay! tests pass locally though, (2) what's the desired behavior of `occupancy_tolerance` in `CifParser`? It doesn't seem to do anything at present, the line `if 1 < totaloccu <= self._occupancy_tolerance:` looks like it'll always evalu... | 2017-05-24T05:55:30 | 2017-05-24T13:36:29 | 2017-05-24T13:36:23Z | MEMBER | {
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} | ## Summary
* Adds read support and partial write support for the magCIF standard (preliminary v1 dictionary available [here](http://comcifs.github.io/magCIF.dic.html)).
* This was developed as a separate class based on `CifParser`, but given that `CifParser` itself has seen recent changes, it seemed sensible to c... | {
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] | 2017-05-24T09:16:36 | 2017-05-24T22:20:13 | 2017-05-24T13:33:14Z | NONE | {
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} | ## Summary
* Added method from_file to PWInput.
* Enabled PWInput type list.
* Enabled to read tags shown like "list(index) = val"
* PWInput changes
* pseudo (dict) not required.
* For spin polarization calculation
(nspin=2), Site.properties for each site in Structure class will be needed.
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} | - fix in read_cube_file to read correctly the fort.30 (a cube formate file)
- added the possibility to plot arrows in the plot_ellipsoid function of plotter.py
- new functions in BoltztrapPlotter object to plot Seebeck, PF, zT, effective mass, and conductivity
as function of temperature and doping levels | {
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} | ## Summary
Unit tests for ieee conversion were failing because the 'transformation_matrix' from spglib's symmetry dataset changes for one of the test structures between version 1.9.9.18 and 1.9.9.3. I'm not able to determine what in spglib caused the change, but the distinct transformation matrices are symmetricall... | {
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Fixed a bug in PWInput.from_string() | {
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Can't evaluate truth of an array in py2 directly
Fixed by testing if list and ensuring list size greater than 0 | {
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} | ## Summary
* Adds `JonesFaithfulTransformation` class to easily transform between different crystallographic settings.
* Should initialize using `from_transformation_string` in Jones faithful notation, given by a string specifying both a transformation matrix and an origin shift, with parts delimited by a semi-colo... | {
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} | From using plot_slab in the adsorption module, I was getting a
`TypeError: 'zip' object is not subscriptable`
This error came from `lim[0]` where `lim` is a zip object. This was okay in Python 2, but in Python 3, the zip object cannot be indexed like this anymore.
Therefore, I have made a simple change by usi... | {
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"This is not the way to modify the config of an input set. The CONFIG is an internal class variable that should not be changed. It merely provides a reference. If changes are needed, you should be modifying the self.config_dict instance or supply user_incar_settings if you are modifying the INCAR."
] | 2017-06-06T00:56:31 | 2017-06-06T02:43:42 | 2017-06-06T02:43:42Z | CONTRIBUTOR | {
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this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: 4.7.7
* Python version: 2.7
* OS version: macOS
## Summary
* Modifying the CONFIG dict instance of a VaspInputSet class instance ch... | {
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"Can you please provide the POTCAR that is being parsed?",
"I just pushed a changed which will try to ignore Unicode decoding errors in Potcar. Can you pull the latest changes and see if it solves your problems?",
"@shyuep regarding your changes, is there an advantage in using `codecs` over `zopen(filename, \"r... | 2017-06-06T21:10:25 | 2017-06-07T21:04:48 | 2017-06-07T21:04:48Z | NONE | {
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} | ## System
* Pymatgen version: v4.7.7
* Python version: 2.7.12
* OS version: Linux Ubuntu 14.04
## Summary
* Trying to parse POTCAR I get:
UnicodeDecodeError: 'utf8' codec can't decode byte 0x97 in position 37: invalid start byte
## Example code
```python
from pymatgen.io.vasp import Vasprun
v = Vasp... | {
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"It appears that it is not just substituting bromine twice, instead, once bromine has been substituted in, I can't substitute anything else in. E.g.:\r\n\r\n```python\r\nfrom pymatgen.core.structure import Molecule, FunctionalGroups\r\n\r\nspecies = ['C', 'C', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H']\r\npo... | 2017-06-07T10:25:38 | 2017-06-07T13:00:00 | 2017-06-07T12:57:33Z | MEMBER | {
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} | ## System
* Pymatgen version: 4.7.7
* Python version: 2.7.12
## Summary
Substituting a bromo group into a molecule more than once causes an error. Substituting multiple chloro or fluoro groups works fine.
## Example code
```python
from pymatgen.core.structure import Molecule, FunctionalGroups
specie... | {
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"Note: returning \"None\" for undefined electronegativity (like He) would also work for me",
"Returning None is an issue. That means that code that averages electronegativity needs to specially take into account None as a possible value. I can fix the values that have them. But for those without Pauling electrone... | 2017-06-07T20:08:41 | 2017-06-07T21:52:25 | 2017-06-07T21:17:28Z | MEMBER | {
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this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: master
## Summary
* pymatgen is missing electronegativity data for the following elements:
-He
-Ne
-Ar
-Pm
-Eu
-Tb
-Yb
-Rn
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} | Fixed the from_dict function which was previously passing variables to the constructor in order and was garbling up variables after DOS due to intrans being in the middle.
Fixed the linalg inversion in get_average_eff_mass to try and catch the linalg exception. This can be caused by a matrix of zeros, which can't be... | {
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Fixes equality operator | {
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"Sorry, there is an error on testing. I am working on fixing it. "
] | 2017-06-09T01:06:36 | 2017-06-09T05:38:42 | 2017-06-09T05:38:42Z | CONTRIBUTOR | {
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} | ## Summary
In VASP 5.4.4, there are two datasets given in OUTCAR for dielectric function (LOPTICS=True). One is "density-density" and the other is "current-current". The first data set has values of IMAGINARY and REAL as the old VASP version (e.g vasp.5.4.1). This push adds the feature of extracting the first datase... | {
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2) Added chemical shift G0 contribution parsing
3) Added chemical shift core contribution parsing
4) Improvements on Pourbaix color domain plotting | {
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"Both the POSCAR and CIF open just fine on my VESTA.",
"Thank you so much. I will check it again.\nOn Sun, Jun 11, 2017 at 3:24 PM Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> Closed #693 <https://github.com/materialsproject/pymatgen/issues/693>.\n>\n> —\n> You are receiving this because you authored th... | 2017-06-11T18:00:35 | 2017-06-11T20:53:40 | 2017-06-11T19:24:25Z | NONE | {
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I am able to download CIF files from material project and convert them to POSCAR. When I drag them to VESTA, original CIF file shows the structure but I cannot see the structure by using transformed POSCAR. I have attached both files.
[NO2.zip](https://github.com/materialsproject/pymatgen/files/1066648/NO2.zip... | {
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## Summary
PWscf gives an error if the namelists are out of order. ATOMIC_SPECIES should come before ATOMIC_POSITIONS. | {
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"Pls make the method a classmethod, rather than a static method, and also rename the method to follow the convention used in other classes. It should be from_file. ",
"I consolidated the JSON and lammps style input parsers in the from_file method and changed it from a staticmethod to classmethod. ",
"Test files... | 2017-06-12T08:04:56 | 2017-06-12T22:18:23 | 2017-06-12T22:18:17Z | CONTRIBUTOR | {
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I added a parser to read lammps style input files directly. This is useful if input files do not need to be generated.
* read a lammps style input file
## TODO
More comprehensive unittest. Check if total number of atom, bonds, diheadrals ... etc. are added to DictLammpsInput | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/697 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/697/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/697/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/697/events | https://github.com/materialsproject/pymatgen/pull/697 | 235,402,432 | MDExOlB1bGxSZXF1ZXN0MTI1MjU2NTUy | 697 | Enable k-point generation from JHU servlet | {
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"Thanks. But I am not sure I want this method in the Kpoint class. In general, I want to keep the core classes and io classes free of entanglements to external sources etc. The idea is that I may want to refactor all the core classes out to a pymatgen-core at some later date. \r\n\r\nCan you create a new package ca... | 2017-06-13T00:26:33 | 2017-06-22T16:40:44 | 2017-06-22T16:40:43Z | CONTRIBUTOR | {
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This PR enables retrieval of a Kpoint object via retrieval from the JHU servlet via a static method from the Kpoints object.
See http://muellergroup.jhu.edu/K-Points.html and Wisesa, McGill, Mueller, PRB 93, 155109 (2017).
* Usage: Kpoints.get_from_wmm(structure, min_distance=29) | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/698 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/698/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/698/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/698/events | https://github.com/materialsproject/pymatgen/issues/698 | 235,740,325 | MDU6SXNzdWUyMzU3NDAzMjU= | 698 | Extraneous backslash in latex label in plotter.py from pymatgen.electronic_structure.plotter | {
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"Thanks. I pushed a fix. The odd thing about matplotlib is why it is so sensitve to this kind of errors. I would have thought that the easier way is to ignore such rendering issues."
] | 2017-06-14T01:52:38 | 2017-06-14T02:30:49 | 2017-06-14T02:30:01Z | NONE | {
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this is a feature request, please simply state the requested feature.>
## System
Python version: 2.7
OS Version: CentOS Linux release 7.3.1611 (Core)
pymatgen version: pymatgen-2017.6.8-py2.7
## Summary
The plotter.py code contai... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/699 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/699/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/699/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/699/events | https://github.com/materialsproject/pymatgen/issues/699 | 235,747,931 | MDU6SXNzdWUyMzU3NDc5MzE= | 699 | plotter.get_projected_plots_dots_patom_pmorb will not accept a single orbital | {
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"I suspect this has nothing to do with the orbital, but the fact that you are passing a range into the method. Can you try putting it as list(range(9, 17))?",
"actually the same statement without the range statements has the same problem:\r\n\r\nplot = plotter.get_projected_plots_dots_patom_pmorb({'N':['px']},{'N... | 2017-06-14T02:51:32 | 2023-08-16T07:45:24 | 2017-06-15T18:37:28Z | NONE | {
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this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: pymatgen-2017.6.8-py2.7
* Python version: 2.7
* OS version: CentOS Linux release 7.3.1611 (Core)
## Summary
plotter.get_projected... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/700 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/700/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/700/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/700/events | https://github.com/materialsproject/pymatgen/pull/700 | 235,942,214 | MDExOlB1bGxSZXF1ZXN0MTI1NjQyNTUz | 700 | bug fixing for get_projected_plots_dots_patom_pmorb | {
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I update the get_projected_plots_dots_patom_pmorb method in plotter.py file in order to fix the bug "plotter.get_projected_plots_dots_patom_pmorb will not accept a single orbital #699" complained by "paulfons". Would you like to check and merge my changes to the official pymatgen.
Thank you v... | {
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