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| 211,497,411
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MDExOlB1bGxSZXF1ZXN0MTA4ODM2NDI2
| 601
|
BSDOSPlotter figure size option
|
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[] | 2017-03-02T19:48:34
| 2017-03-02T19:49:04
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2017-03-02T19:49:04Z
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CONTRIBUTOR
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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
## TODO (if any)
N/A
* Feature 1 supports a, but not b.
|
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| 602
|
Incorrect handling of projections in Vasprun.get_band_structure
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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@github.com> wrote:\n> \n> Thanks. Yes, if you can fix it, it would be great.\n> \n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub <https://github.com/materialsproject/pymatgen/issues/602#issuecomment-284060860>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA3l9-cGxO-MDsdZMISynd5vF6EQDlirks5riHa8gaJpZM4MSfg1>.\n> \n\n"
] | 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 output. However, when running the `get_band_structure` method, the projections for all k-points are returned, regardless of their k-point weighting.
This means the projections for kpoint_x (e.g. `bandstructure.projections[Spin.up][band_n][kpoint_x]`) are actually referring to the projections for a different kpoint than the bands at kpoint_x (e.g. `bandstructure.bands[Spin.up][band_n][kpoint_x]`).
I presume this isn't the correct behaviour?
|
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| 211,753,436
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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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MDExOlB1bGxSZXF1ZXN0MTA5MDg1MTE3
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|
Proposal for Magmom class
|
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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 to simplify the implementation a little. I understand the rationale for making it immutable, but for now, let's just let it flow a little.",
"If you really want to make it immutable, you probably should subclass a namedtuple and add the relevant functions needed.",
"Okay, that sounds good, thanks for the clean-up! I'm completely fine with it being mutable, I don't have strong feelings either way in that regard.\r\n\r\n(The write-only numpy arrays were probably a bit heavier than necessary anyway, I tried using them to simplify performing vector operations elsewhere, but maybe named tuples would have been better.)\r\n\r\n"
] | 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 documentation.
Should give unsurprising results:
* if you want to use it as a scalar Magmom, e.g. `m = Magmom(5.0)`, this will work as expected with `float(m)` giving `5.0`
* if you want to use it as a list-type Magmom, e.g. `m = Magmom([1.0, 2.0, 3.0])`, this should also work as expected with `m[0]` giving `1.0`
* if you want to use a custom `SAXIS`, you can either use `m = Magmom([1, 2, 3], saxis=[1,1,1])` or you can use `m = Magmom([1,2,3])` and `m.get_moment(saxis=[1,1,1])`.
There also exist static helper methods such as:
* `Magmom.are_collinear(magmoms)` to check if a list of magmoms are collinear
* `Magmom.get_consistent_set_and_saxis(magmoms)` to return a list of magmoms with the same spin axis, and the spin axis itself to be used with VASP's `SAXIS` tag
For existing structures, can update `magmoms` with `[Magmom(m) for m in magmoms]` if any of the new functionality is required.
Would also simplify use and implementation of `MagCifParser` (#508). In particular, `MagCifParser` will always output a Structure with vector magmoms. However, for those structures which have collinear spin, a collinear approximation can be used with scalar magmoms, and `[float(m) for m in magmoms]` will give the correct values in this instance even in the case of e.g. antiferromagnetic structures. Additionally, `MagCifParser` and `MagCifWriter` need to read/write magmoms in terms of crystal axes, which is made possible by this new class.
PR is submitted for comments / code review. Feedback appreciated!
## Additional dependencies introduced (if any)
None
## TODO (if any)
* ~~Further testing.~~
* ~~Implement `get_moments_relative_to_crystal_axes` method used by `MagCifWriter`.~~
* Code review.
* (Future) If/when `Magmom` class is more mature, could change `io.vasp` to use it by default.
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Fix more edge cases in Reaction
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Reconciled normalization issues in order parameter class.
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Correct handling of band structure projections for hybrid calculations.
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[] | 2017-03-07T11:54:33
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2017-03-07T14:21:59Z
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MEMBER
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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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MDU6SXNzdWUyMTI1MjI1NzM=
| 608
|
Possible bug in core/surface.py
|
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[] | 2017-03-07T18:43:24
| 2017-03-07T21:19:40
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2017-03-07T21:19:40Z
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CONTRIBUTOR
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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[1], -x[2]))```
Or even (which should give the same result since x[2] is vector length, always positive):
```uvw, cosine, l = max(candidates, key=lambda x: (x[1], 1.0/x[2]))```
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MDU6SXNzdWUyMTI1MjY0MTg=
| 609
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possible bug in HighSymmKpath
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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 https://arxiv.org/pdf/1506.01455.pdf section 3 for more details. The init in HighSymmKpath, that checks the space group symbol expecting a c-centered orthorhombic symbol, fails to recognize the space group.\r\n\r\nIt should also be noted that, since the same kind of check is used in the SpaceGroupAnalyzer (i.e. if \"C\" in self.get_space_group_symbol()), also the primitive and conventional standard structures can have some problems in these cases.",
"Hi Guido,\n\nThanks for the follow-up. Maybe we should at least return an error or warning then?\n\nCould you implement this?\n\nThanks!\n\nGeoffroy\n\n> On 08 Mar 2017, at 12:22, Guido Petretto <notifications@github.com> wrote:\n> \n> Hi,\n> I want to point out that this is related to the issue #374 <https://github.com/materialsproject/pymatgen/issues/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 https://arxiv.org/pdf/1506.01455.pdf <https://arxiv.org/pdf/1506.01455.pdf> section 3 for more details. The init in HighSymmKpath, that checks the space group symbol expecting a c-centered orthorhombic symbol, fails to recognize the space group.\n> \n> It should also be noted that, since the same kind of check is used in the SpaceGroupAnalyzer (i.e. if \"C\" in self.get_space_group_symbol()), also the primitive and conventional standard structures can have some problems in these cases.\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub <https://github.com/materialsproject/pymatgen/issues/609#issuecomment-285016103>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA3l92L-DB_8p-9U2IDhknj_5mb0tI6Gks5rjo-IgaJpZM4MV4wA>.\n> \n\n",
"Hi Geoffroy,\r\n\r\nactually the warning is already present in the HighSymmKpath, when it cannot determine the path. When running the example I get the following warning:\r\n\r\n> warnings.warn(\"The input structure does not match the expected standard primitive! \"\r\npymatgen/pymatgen/symmetry/bandstructure.py:112: UserWarning: Unexpected value for spg_symbol: Ama2\r\n\r\nOn the other hand, adding a warning or an error on the SpacegroupAnalyzer would require first to check explicitly in which cases the problem will show up. It should be for the spacegroups that I mentioned, but I didn't do any extensive test. \r\n\r\nI believe that the a proper solution of the problem will require the analysis of the output produced by spglib in order to update the SpaceggroupAnalyzer and the HighSymmKpath objects. This is probably not so straightforward though.",
"In my opinion, the way to determine the path shouldn't depend on the crystal being in a specific setting - C or B or A. I would very much prefer a robust solution that will handle all crystal structures properly based on the symmetry operations that exist, rather than to have special case handling for A setting, C setting, B setting....",
"I have the same problem with space group 169 for FePS3 (ICSD 633085).",
"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 2017-03-07T18:58:50
| 2023-08-08T21:18:43
|
2023-08-08T21:18:43Z
|
CONTRIBUTOR
|
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## System
* 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.symmetry.bandstructure import HighSymmKpath
api = MPRester()
s = api.get_structure_by_material_id('mp-773965', final=True)
ibz = HighSymmKpath(s)
print ibz.kpath["path"]
```
## Error message
```
print ibz.kpath["path"]
TypeError: 'NoneType' object has no attribute '__getitem__'
```
|
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| 212,793,794
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MDU6SXNzdWUyMTI3OTM3OTQ=
| 610
|
suggested speedup for pymatgen.analysis.path_finder
|
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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 realized and let me know that in NEBPathfinder's string_relax method, the line:
dV = np.gradient(V)
could be moved outside of the loop, since "the potential never changes in this approximation so re-evaluating the gradient every step is not necessary."
Moving this line speeds up the code a lot and produces the same results.
## Example code
see suggested solution
## Error message
No error.
## Suggested solution (if any)
(near line 160)
```
dV = np.gradient(V) #line moved here
# Evolve string
for step in range(0, max_iter):
if step > min_iter:
h = h0 * np.exp(-2.0 * (step - min_iter)/max_iter) # Gradually decay step size to prevent oscillations
else:
h = h0
# Calculate forces acting on string
d = V.shape
s0 = s
```
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MDExOlB1bGxSZXF1ZXN0MTA5NzU0NzQ4
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|
pathfinder speedup
|
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[] | 2017-03-08T18:25:55
| 2017-03-08T20:00:05
|
2017-03-08T20:00:05Z
|
CONTRIBUTOR
|
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Implement Daniil's speedup suggestion
See issue #610
|
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MDExOlB1bGxSZXF1ZXN0MTA5ODczNDQ2
| 612
|
Fix bug in get_band_structure()
|
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[] | 2017-03-09T09:40:36
| 2017-03-09T13:10:39
|
2017-03-09T13:10:39Z
|
MEMBER
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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 proper testing of the band structure functionality in pymatgen.
|
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Huge size of fonts and objects in any plots
|
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[] | 2017-03-09T09:49:20
| 2017-03-09T14:56:12
|
2017-03-09T14:56:12Z
|
CONTRIBUTOR
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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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MDU6SXNzdWUyMTMyMjcwOTk=
| 614
|
conda warning of dependency installation
|
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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 Thanks in advance!",
"@shyuep I think `tqdm` have the same issue when use python2.7, sorry to find all of them yesterday."
] | 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`.
It will lead conda can't choose the right version.
## Example code
```
#~/.condarc
channels:
- defaults
- matsci
```
```
conda install flask-paginate
```
## Error message
```
conda install flask-paginate
Fetching package metadata ...........
Solving package specifications: .
Warning: 2 possible package resolutions (only showing differing packages):
- matsci::flask-paginate-0.4.5-py_0
- matsci::flask-paginate-0.4.5-py27_0
Package plan for installation in environment /lustre/home/acct-umjzhh/umjzhh-1/.conda/envs/kl_mpw:
The following NEW packages will be INSTALLED:
flask-paginate: 0.4.5-py_0 matsci
Proceed ([y]/n)? y
/lustre/usr/anaconda/2.4.3.0/lib/python2.7/site-packages/conda/core/link.py:446: UserWarning: Package matsci::flask-paginate-0.4.5-py_0 uses a pre-link script. Pre-link scripts are potentially dangerous.
This is because pre-link scripts have the ability to change the package contents in the
package cache, and therefore modify the underlying files for already-created conda
environments. Future versions of conda may deprecate and ignore pre-link scripts.
""" % dist))
```
then `flask-paginate` will be installed by `pip` again, finally there are 2 `flask-paginate` in `conda list`.
## Suggested solution (if any)
* I think the dependency with name `py_0` should be removed.
|
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MDExOlB1bGxSZXF1ZXN0MTEwMjM3MzM4
| 615
|
Minor refactoring of elasticity
|
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[] | 2017-03-11T00:53:02
| 2017-03-11T23:29:36
|
2017-03-11T23:29:36Z
|
CONTRIBUTOR
|
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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 returns a dictionary with keys of symmetrically distinct tensors and values of symmetry operations to generate any tensors which have been removed.
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Faster cif parsing
|
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[] | 2017-03-12T01:25:32
| 2017-03-12T03:45:11
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2017-03-12T03:45:11Z
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CONTRIBUTOR
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minor bug fix
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[] | 2017-03-12T06:16:06
| 2017-03-12T14:48:59
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2017-03-12T14:48:59Z
|
CONTRIBUTOR
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## Summary
* Minor bug fix for fraction coordinates and Cartesian coordinates conversion.
|
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MDExOlB1bGxSZXF1ZXN0MTEwMzIxODk5
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Minor bug fix on TOEC fitting
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[] | 2017-03-12T23:51:49
| 2017-03-13T02:28:28
|
2017-03-13T02:28:28Z
|
CONTRIBUTOR
|
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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 function
* For IEEE conversion, changes the default rotation matrix verification tolerance to align with what SpacegroupAnalyzer uses for determination of crystal symmetry (certain cubic structures weren't producing a valid rotation matrix).
|
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MDExOlB1bGxSZXF1ZXN0MTEwNjMyODY2
| 619
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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\nthe site properties will change.\n\n—\nYou are receiving this because you authored the thread.\nReply to this email directly, view it on GitHub\n<https://github.com/materialsproject/pymatgen/pull/619#issuecomment-286472130>,\nor mute the thread\n<https://github.com/notifications/unsubscribe-auth/AIXMDIZ6NuFvfkgwUm6x1oatbYnhjzEuks5rlrw7gaJpZM4McpcV>\n.\n"
] | 2017-03-14T14:26:26
| 2017-03-15T13:28:29
|
2017-03-15T13:28:29Z
|
CONTRIBUTOR
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## Summary
remain site_properties if exist when replace Element
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MDExOlB1bGxSZXF1ZXN0MTEwOTU5MDg2
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|
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 uses a tolerance criteria, rather than a strict non-zero criteria
* Updated unit tests
|
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MDU6SXNzdWUyMTQ2NDAyOTA=
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|
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 error. Fundamentally, you are not changing an attribute of Site itself, but rather the copy of coords you obtain."
] | 2017-03-16T09:17:48
| 2017-03-16T13:05:13
|
2017-03-16T13:05:13Z
|
CONTRIBUTOR
|
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|
Hi
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
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-51-f47d04af060a> in <module>()
----> 1 site.x = 2
AttributeError: can't set attribute
````
If you try to change the value in the coords array there is not any error message, but nothing is done. Again if you try to change the whole array, as `coords` is a property you get again the error message.
```
In [4]: site.coords[2] = 3
In [5]: site.coords
Out[5]: array([0, 0, 0])
In [6]: site.coords = [0, 0, 3]
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-50-37feefce5458> in <module>()
----> 1 site.coords = [0, 0, 3]
AttributeError: can't set attribute
```
I think the line `In[4]` in the example above should raise a warning. The main danger here is that it does not raise an exception AND it does not do what you want. In the Site class, all attributes (or almost all) are Properties, that is why you get an exception if you try to set the coords array. I do not know exactly how to fix it, it is may be above my OOP skills.
|
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MDExOlB1bGxSZXF1ZXN0MTExNDA4ODcy
| 622
|
quasi-harmonic debye approximation
|
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[] | 2017-03-18T12:36:03
| 2017-03-18T13:19:33
|
2017-03-18T13:19:33Z
|
CONTRIBUTOR
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* compute debye temperature, gruneisen paramter, thermal conductivity
* added tests
|
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MDExOlB1bGxSZXF1ZXN0MTExNjQxNDkz
| 623
|
Removed mutable default parameters.
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[] | 2017-03-20T20:18:55
| 2017-03-21T01:55:43
|
2017-03-21T01:55:43Z
|
CONTRIBUTOR
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Removed mutable default parameters in class OrderParameters and class StructureMotifInterstitial.
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MDExOlB1bGxSZXF1ZXN0MTEyMjczOTg0
| 624
|
add logging to boltztrap
|
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[] | 2017-03-23T15:59:24
| 2017-03-23T16:00:32
|
2017-03-23T16:00:32Z
|
CONTRIBUTOR
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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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MDExOlB1bGxSZXF1ZXN0MTEyMzU2NTAy
| 625
|
Fix cbm edge case at Fermi level
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[] | 2017-03-23T23:00:31
| 2017-03-24T00:09:59
|
2017-03-24T00:09:59Z
|
MEMBER
|
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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 regression
Thank you @miaoliu for solving this.
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|
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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|
This should fix FileExistsError on Win
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[] | 2017-03-24T16:31:39
| 2017-03-24T16:31:58
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2017-03-24T16:31:58Z
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MDExOlB1bGxSZXF1ZXN0MTEyNTEzNzky
| 628
|
Test if self.__name exists
|
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[] | 2017-03-24T18:10:16
| 2017-03-24T18:14:50
|
2017-03-24T18:14:50Z
|
CONTRIBUTOR
|
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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, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. If you are putting anything here, you should
provide a justification why that dependency is needed. Especially
frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.>
## TODO (if any)
<If this is a work-in-progress, write something about what else needs
to be done>
* Feature 1 supports a, but not b.
|
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MDExOlB1bGxSZXF1ZXN0MTEyNTY1ODI5
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|
Handle c1=c2 in PDAnalyzer.get_critical_compositions
|
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[] | 2017-03-25T00:43:27
| 2017-03-25T02:09:36
|
2017-03-25T02:09:36Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MTEzMjgxNDc5
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|
Fix typo in generating string representation of transformation
|
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[] | 2017-03-29T19:58:34
| 2017-04-01T22:54:23
|
2017-04-01T22:54:23Z
|
MEMBER
|
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Fix typo in generating string representation of transformation.
* Fix typo
* Add unit test
|
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MDExOlB1bGxSZXF1ZXN0MTEzMzI2Mjkx
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|
Refactor of elasticity package
|
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[] | 2017-03-30T01:01:03
| 2017-03-30T02:30:57
|
2017-03-30T02:30:57Z
|
CONTRIBUTOR
|
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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 stress/energy density
* Fitting functions for higher order elastic tensors are agnostic to stencils used to find derivatives (used to require odd central-difference stencils)
## TODO (if any)
* Working on a notebook of examples
* Additional functionality for the higher order elastic tensor expansions (yield surfaces, gruneisen parameters)
* Planning on getting rid of some of the legacy functionality, old fitting functions should be able to be replaced with the new ones
|
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Fixes and additional unit tests for higher order elastic tensors
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[] | 2017-03-31T05:19:25
| 2017-03-31T12:05:13
|
2017-03-31T12:05:13Z
|
CONTRIBUTOR
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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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MDU6SXNzdWUyMTg1ODI1MDk=
| 633
|
bug in latest pymatgen
|
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[] | null |
[
"(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 <notifications@github.com>\nwrote:\n\n> System\n>\n> - Pymatgen version: master\n> - Python version: 2.7\n> - OS version: mac\n>\n> Summary\n>\n> - See example code\n>\n> Example code\n>\n> from pymatgen.analysis.elasticity.elastic import *\n>\n> Error message\n>\n> Traceback (most recent call last):\n> File \"<stdin>\", line 1, in <module>\n> File \"/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/analysis/elasticity/__init__.py\", line 7, in <module>\n> from .elastic import *\n> File \"/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/analysis/elasticity/elastic.py\", line 747, in <module>\n> v_diff = np.vectorize(sp.diff)\n> NameError: name 'sp' is not defined\n>\n> Suggested solution (if any)\n>\n> - not sure what the intention is of the error-creating code, so no\n> suggestions\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/633>, or mute the\n> thread\n> <https://github.com/notifications/unsubscribe-auth/AGMZNHCSIeh_opp1aoGHVuxdjhfVA4-2ks5rrUedgaJpZM4MwAqk>\n> .\n>\n",
"Why is there a dependence on sympy?",
"If sympy is really needed, we can just add it to dependency. It is not that large.",
"Just FYI, sympy is being used to determine the pseudoinverse expression in\nthe higher order fitting scheme, which requires a symbolic derivative (this\nenables a lot more flexibility in handling different stress/strain inputs\nfor fitting). I'm working on a refactor that doesn't require sympy, since\nit's by far the slowest piece of the procudure, but it's convenient to have\nthe symbolic option.\n\nOn Mar 31, 2017 12:12 PM, \"Shyue Ping Ong\" <notifications@github.com> wrote:\n\n> Closed #633 <https://github.com/materialsproject/pymatgen/issues/633> via\n> b482fe2\n> <https://github.com/materialsproject/pymatgen/commit/b482fe2ef81b72dab9d0bb570f58de4808eb938e>\n> .\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/633#event-1024623415>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AGMZNDx71DclwoovlQnelKZF7rMmjX67ks5rrVAfgaJpZM4MwAqk>\n> .\n>\n"
] | 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 "/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/analysis/elasticity/__init__.py", line 7, in <module>
from .elastic import *
File "/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/analysis/elasticity/elastic.py", line 747, in <module>
v_diff = np.vectorize(sp.diff)
NameError: name 'sp' is not defined
```
## Suggested solution (if any)
* not sure what the intention is of the error-creating code, so no suggestions
|
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MDExOlB1bGxSZXF1ZXN0MTEzNzU0OTA1
| 634
|
major changes for computing weights of multi-entries
|
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[] | 2017-04-01T00:44:26
| 2017-04-01T02:23:26
|
2017-04-01T02:23:26Z
|
MEMBER
|
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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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MDExOlB1bGxSZXF1ZXN0MTEzNzk3ODgz
| 635
|
Cif and MITRelaxSEt changes.
|
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[] | 2017-04-01T22:56:29
| 2017-05-18T13:16:25
|
2017-04-01T22:56:34Z
|
MEMBER
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MDU6SXNzdWUyMTkzNDk4MTc=
| 636
|
Gascorrection sets the Ehull/energy_per_atom to the same value for gases
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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 filtering bad structures (e.g., to build a model such as for volume prediction) or even ranking good vs. bad structures more difficult since one cannot just use an e_above_hull filter and call it a day. Instead, you need to explicitly exclude all gas phase compositions, or do some more manual work to figure out which structures are the more reasonable ones (e.g., by examining raw energies).",
"I don't know if there is a good solution for this. Remember that the Compatibility operate on an individual entry, not a list of entries (process_entries is merely repeatedly calling process_entry). The solutions proposed here would make the correction depend on not just the entry being corrected, but also other entries (especially, the lowest energy entry). This \"non-local\" behavior is generally not a good programming practice. \r\n\r\nIs there a practical problem that we need this for? Volume predictor is nice in theory, but surely predicting the volume of a gas is futile? ",
"I think it's mainly because people expect an \"e above hull\" filter to remove most unstable compounds, but it (unexpectedly) won't remove very bad structures for H2, F2, etc.\r\n\r\ne.g., @montoyjh and others accidentally computed a lot of elastic tensors for these structures because they passed through the e above hull filter.\r\n\r\nEven if we keep this in mind for ourselves, others are likely to make the same mistake.",
"Ok. I can suggest a way out. We leave GasCorrection as is. But for Compatibility.process_entries, we can find some way to readjust the corrections for the remaining entries upwards.\r\n\r\nIn any case, accidentally running elastic constants for CO2 gas really shouldn't be a problem resolved by compatibility. In this case, the initial query criteria to select structures to do computations was wrong. ",
"After reviewing the code carefully, my conclusion is that there is no way to implement this in a clean manner in the current framework. Basically, what is required is for process_entries to specially treat entries that have formulas that have GasCorrections and adjust the corrections for affected entry to the lowest value. While the actual coding of this will take a mere few minutes, the result is that Compatibility will now have a special treatment for one of the correction schemes (GasCorrection). That is extremely bad code design. And the purpose of this is merely to treat a very strange edge case of gas atoms that have no place in a solid-state world.\r\n\r\nFor MP's purposes, if it really bothers you that multiple O2 atoms have ehull=0, I would suggest you implement the workaround in the builders in the pre-processing of entries before phase diagram construction to compute ehull. You merely need to reset the corrections to the minimum correction found for all O2, CO2, etc. molecules.\r\n\r\nI am closing this issue unless anyone has better ideas. Reopen if you have."
] | 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 to the same value, even though the total energies per atom from calculations are not the same.
## Example code
```python
from pymatgen import MPRester
from pandas import DataFrame
a = MPRester(api_key="API_KEY")
entries = a.get_entries_in_chemsys(['H'])
import collections
data = collections.defaultdict(list)
for e in entries:
data["Materials ID"].append(e.entry_id)
data["Composition"].append(e.composition.reduced_formula)
data["energy_per_atom"].append(e.energy_per_atom)
data["correction"].append(e.correction)
data["uncorrected_energy"].append(e.uncorrected_energy)
df = DataFrame(data, columns=["Materials ID", "Composition", "energy_per_atom", "correction","uncorrected_energy"])
print(df)
```
## Error message
Please note that the energy_per_atom is the same, so does the E^hull which is always equal to *ZERO* for all the calculations.
```
Materials ID Composition energy_per_atom correction uncorrected_energy
0 mp-570752 H2 -3.239737 -4.255533 -2.223940
1 mp-24504 H2 -3.239737 0.609450 -13.568397
2 mp-1001570 H2 -3.239737 0.303425 -6.782898
3 mp-973783 H2 -3.239737 0.572690 -13.531636
4 mp-634659 H2 -3.239737 -2.123957 -1.115780
5 mp-632250 H2 -3.239737 -2.118332 -1.121405
6 mp-632172 H2 -3.239737 0.303412 -6.782886
7 mp-632291 H2 -3.239737 0.301908 -6.781381
8 mp-754417 H2 -3.239737 -0.248806 -2.990931
9 mp-850274 H2 -3.239737 0.296408 -6.775881
10 mp-23907 H2 -3.239737 -4.244749 -2.234724
```
It can also be seen from website:
[https://materialsproject.org/#search/materials/{"reduced_cell_formula"%3A"H"}](url)
## Suggested solution (if any)
line around 188 in pymatgen/pymatgen/entries/compatibility.py is responsible for this:
```python
def get_correction(self, entry):
comp = entry.composition
rform = entry.composition.reduced_formula
if rform in self.cpd_energies:
return self.cpd_energies[rform] * comp.num_atoms \
- entry.uncorrected_energy
return 0
```
* Would suggest to use similar treatment of "O2" or chose the lowest energy compound as the stable compound.
* Should also considering the case that: when a new lower energy compound is added, the correct should able to recognized the new hull and readjust value accordingly.
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
```
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| 219,761,453
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MDU6SXNzdWUyMTk3NjE0NTM=
| 637
|
CIF files not parsed correctly
|
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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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<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: 4.3.16-py27_0
* Python version: Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15)
IPython 5.1.0
* OS version: CentOS Linux release 7.3.1611 (Core)
## Summary
* CIF files are currently parsed for composition data using the label field
* CIF files should be parsed using the composition field with the information stored as occupancy data
## Example code
A CIF file can specify site occupancy. For example, the structure of the cubic phase of Ge2Sb2Te5 is cubic with one Wyckoff site occupied by Te while the other site is occupied by 40% Sb, 40% Ge, and 20% vacancies. The appropriate bit of the (correct) CIF file for this structure reads
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Ge Ge 0.4000 0.5000 0.5000 0.5000
Ge Sb 0.4000 0.5000 0.5000 0.5000
Te Te 1.0000 0.0000 0.0000 0.0000
The first column is a label, while the second represents the occupancy. Below are the results of reading in the CIF file of which a clip is shown above.
In [50]: gst = mg.Structure.from_file('Ge2Sb2Te5_Fm3m.cif')
In [51]: gst
Out[51]:
Structure Summary
Lattice
abc : 6.0309999999999997 6.0309999999999997 6.0309999999999997
angles : 90.0 90.0 90.0
volume : 219.36532779099997
A : 6.0309999999999997 0.0 3.6929224228288435e-16
B : 9.6985877001997945e-16 6.0309999999999997 3.6929224228288435e-16
C : 0.0 0.0 6.0309999999999997
PeriodicSite: Ge:0.800 (3.0155, 3.0155, 3.0155) [0.5000, 0.5000, 0.5000]
PeriodicSite: Ge:0.800 (3.0155, 0.0000, 0.0000) [0.5000, 0.0000, 0.0000]
PeriodicSite: Ge:0.800 (0.0000, 0.0000, 3.0155) [0.0000, 0.0000, 0.5000]
PeriodicSite: Ge:0.800 (0.0000, 3.0155, 0.0000) [0.0000, 0.5000, 0.0000]
PeriodicSite: Te (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
PeriodicSite: Te (0.0000, 3.0155, 3.0155) [0.0000, 0.5000, 0.5000]
PeriodicSite: Te (3.0155, 3.0155, 0.0000) [0.5000, 0.5000, 0.0000]
PeriodicSite: Te (3.0155, 0.0000, 3.0155) [0.5000, 0.0000, 0.5000]
Note that there is no evidence of Sb in the structure at all! It would appear that the Structure.from_file method simply parses the labels as if they were composition and this is clearly incorrect. I came across this when I received a (different) CIF file exported from Materials Studio (CASTEP among other codes) and found the user had changed the composition, but not the labels. Materials Studio had no trouble with this as it correctly used the composition for calculations based upon the structure, but the CIF file maintained the older labels and included the correct compositions, which strictly speaking is still correct.
Correct behavior:
The Structure.from_file method should use the occupancy field to determine the atom type of the site, not the label field. I have included the CIF file of which I showed a clip above for reference.
## Suggested solution (if any)
The Structure.from_file() method should parse the composition fields and not the label fields to determine the contents of a given site in a structure.
## Files (if any)
Ge2Sb2Te5_(Fm3m).cif
```
data_Ge2Sb2Te5_(Fm3m)
_audit_creation_method 'generated by CrystalMaker 9.2.9'
_publ_section_comment
;
Ge2.005Sb2.095Te5,RT,Vb=40.1Ge41.9Sb,Yamada&Matsunaga(2000)R=2.3%(XPD) Ge
2.005Sb2.095Te5,RT,Vb=40.1Ge41.9Sb,Yamada&Matsunaga(2000)R=2.3%(XPD)
;
_cell_length_a 6.0310(0)
_cell_length_b 6.0310(0)
_cell_length_c 6.0310(0)
_cell_angle_alpha 90.0000(0)
_cell_angle_beta 90.0000(0)
_cell_angle_gamma 90.0000(0)
_symmetry_space_group_name_H-M 'F m -3 m'
_symmetry_Int_Tables_number 225
_symmetry_cell_setting cubic
loop_
_symmetry_equiv_pos_as_xyz
'+x,+y,+z'
'+x,1/2+y,1/2+z'
'1/2+x,1/2+y,+z'
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'-x,+y,+z'
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loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Ge Ge 0.4000 0.5000 0.5000 0.5000
Ge Sb 0.4000 0.5000 0.5000 0.5000
Te Te 1.0000 0.0000 0.0000 0.0000
```
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MDU6SXNzdWUyMjAyMjU2ODY=
| 638
|
Bandstructure handling
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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 object. If you are feeding in a non symm-line BS to the BSDOSPlotter, that's your fault.\r\n\r\nOf course the points about auto-detecting symm line, etc. are valid, but I'm just chiming in on the band structure plotting which is the part I was involved with\r\n",
"Note that I am not saying that I do not have the responsibility to pass the right object to the plotter (whether the new one or old one). My point is merely that *default parameters* do not result in a plot. Instead, I have to figure out there is a BS and a BSSymmLine (the differences are not entirely clear to me, when do we actually use the Non Symm Line version?), one of which is going to work, and to get that, I have to specify myriad options over multiple methods, and there are absolutely no examples.\r\n\r\nAll I am asking for is a \"it just works\" option for the majority of users. Right now, that is not the case.",
"As far as I can tell, the changes you are suggesting are:\r\n\r\n1. Vasprun.get_band_structure() should just ditch the line_mode parameter. Instead it should auto-detect whether we have a line mode and return a BandStructureSymmLine object if that's the case, or regular BandStructure object if not. Note that the latter is a subclass of the former so you get a BandStructure object no matter what.\r\n2. The default symmetry in BandStructure should be 0.1(?)\r\n3. There should be some examples of usage. e.g., starting from a VASP output dir and giving you a band structure plot\r\n\r\nIs that correct?",
"Yes for a start. Also, why is there a BS and a BSSymmLine. When is the former used?",
"Anywhere you want to compute something from band structure (let say some electronic transport properties) you should use a band structure on an uniform band structure.\nThe band structures along symmetry lines are basically mainly for plotting.\n\n\n\n> On 07 Apr 2017, at 21:01, Shyue Ping Ong <notifications@github.com> wrote:\n> \n> Yes for a start. Also, why is there a BS and a BSSymmLine. When is the former used?\n> \n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub <https://github.com/materialsproject/pymatgen/issues/638#issuecomment-292624117>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA3l9-VWacX1dNzsNVA23u0zM0QnNdejks5rtofvgaJpZM4M28pc>.\n> \n\n",
"From a code (rather than science) perspective\r\n\r\n- If you have k-points and energies, you have a BandStructure object. This is true both for symmetry line band structures as well as uniform mesh band structures.",
"sorry I didn't finish the last comment, let me try again shortly...",
"From a code (rather than science) perspective\r\n\r\n* If you have k-points and energies, you (essentially) have a BandStructure object. This is true both for symmetry line band structures as well as uniform mesh band structures.\r\n* If you can label certain k-points with names, and can define a sequential path through those k-points with distances, then you have special powers that are associated only with a line mode band structure.\r\n\r\nThere are multiple ways to structure that in code. The way that was chosen (not by me, although I don't think it's so bad) is to have BandStructure be the base class and BandStructureSymmLine be a subclass that inherits from it.\r\n\r\nOf course, other code designs are possible. e.g., we could put everything in a single BandStructureClass and have certain variables like labels and distances be set to None if those didn't exist. And there can be an attribute called \"is_line_mode\" or something that automatically returns T/F depending on whether those variables were initialized or not. This would be useful for certain codes to be able to check what style of band structure was run (e.g., you often want to enforce either a uniform mesh or line mode mesh for a certain analysis). I am certainly OK doing it either way - e.g. class/subclass or all in one class.",
"Ok. I see the code and science use cases now. For now, let's just simplify the usage of these by having some form of auto-detection and examples. I am fine with the class structure as it is for now."
] | 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 of Bandstructures, only one (SymmLine) of which BSPlotter would take. To get a SymmLine, I had to specify both kpoints file and line_mode=True. For some reason, supplying the Kpoints file itself is insufficient to get it to detect it is a symm line version, even though all the labels have been generated from MPNonSCFSet.
2. Why can't the get_band_structure method autodetect whether kpoints are along symmetry lines, whether the labels are specified or not? The labels should be generated from symmetry analysis right?
3. In the pymatgen example notebooks, there are no examples of how you would go about running a BS calculation and plotting that band structure. There is only an example of getting a pre-computed BS from MP and plotting this. I think the former is very important for users.
4. BS reading still gives a "Structure is not standard primitive", even though the structure was generated using get_primitive_standard. My conclusion is that the symprec default used in the symmetry.Bandstructure is 0.01, which is different from the defaults in other cases.
@hautierg @computron Can you guys comment and can some improvements be made?
|
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| 220,450,404
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MDExOlB1bGxSZXF1ZXN0MTE0OTc0MTQ3
| 639
|
Added to Outcar and MPStaticSet to support LCALCPOL VASP flag
|
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[] | 2017-04-09T05:56:12
| 2017-04-09T12:54:14
|
2017-04-09T12:54:14Z
|
CONTRIBUTOR
|
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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 properties p_sp1 and p_sp2
Added tests to vasp.tests.test_outputs for changes to Outcar under test_polarization
Added tests to MPStaticSet for LCALCPOL flag.
Added test_files/OUTCAR.BaTiO3.polar for Outcar polarization test
More polarization related pull requests that use these functions coming soon.
|
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MDExOlB1bGxSZXF1ZXN0MTE1MjEzNzE0
| 640
|
Multiple Changes to QChem Module
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[] | 2017-04-10T23:38:05
| 2017-04-11T00:06:01
|
2017-04-11T00:06:01Z
|
CONTRIBUTOR
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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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MDU6SXNzdWUyMjExNjI0NDk=
| 641
|
dict vs array issue in get_projected_plots_dots_patom_pmorb
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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[Spin][i][j] to then be a *dict* by orbital, rather than an array
* This is caused by `edict[elt + str(anum)][morb] = proj[Spin.up][i][j][Orbital(setos[morb])][anum-1]`
## Example code
```python
dosrun = Vasprun("vasprun.xml", parse_projected_eigen=True)
bp = BSPlotterProjected(dosrun.get_band_structure(line_mode=True))
bp.get_projected_plots_dots_patom_pmorb({"Mn" : ['dxy', 'dxz', 'dyz'], "Ru" : ['dxy', 'dxz', 'dyz']}, {"Mn" : [1,2], "Ru": [3,4,5,6]}, sum_morbs={"Mn" : ['dxy', 'dxz', 'dyz'], "Ru" : ['dxy', 'dxz', 'dyz']}, sum_atoms={"Mn" : [1,2], "Ru" : [3,4,5,6]})
```
## Error message
```
In [7]: bp.get_projected_plots_dots_patom_pmorb({"Mn" : ['dxy', 'dxz', 'dyz'], "Ru" : ['dxy', 'dxz', 'dyz']}, {"Mn" : [1,2], "Ru": [3,4,5,6]}, sum_morbs={"Mn" : ['dxy', 'dxz', 'dyz'], "Ru" : ['dxy', 'dxz', 'dyz']}, sum_atoms={"Mn" : [1,2], "Ru" : [3,4,5,6]})
Number of subfigures: 2
{u'name': u'Gamma-X', u'start_index': 0, u'end_index': 9}
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-7-a35d59aaa56f> in <module>()
----> 1 bp.get_projected_plots_dots_patom_pmorb({"Mn" : ['dxy', 'dxz', 'dyz'], "Ru" : ['dxy', 'dxz', 'dyz']}, {"Mn" : [1,2], "Ru": [3,4,5,6]}, sum_morbs={"Mn" : ['dxy', 'dxz', 'dyz'], "Ru" : ['dxy', 'dxz', 'dyz']}, sum_atoms={"Mn" : [1,2], "Ru" : [3,4,5,6]})
/home/liz/.local/lib/python2.7/site-packages/pymatgen/electronic_structure/plotter.py in get_projected_plots_dots_patom_pmorb(self, dictio, dictpa, sum_atoms, sum_morbs, zero_to_efermi, ylim, vbm_cbm_marker, selected_branches, w_h_size, num_column)
1318 plt = pretty_plot(w_h_size[0], w_h_size[1])
1319 proj_br_d, dictio_d, dictpa_d, branches = self._get_projections_by_branches_patom_pmorb(dictio, dictpa,
-> 1320 sum_atoms, sum_morbs, selected_branches)
1321 data = self.bs_plot_data(zero_to_efermi)
1322 e_min = -4
/home/liz/.local/lib/python2.7/site-packages/pymatgen/electronic_structure/plotter.py in _get_projections_by_branches_patom_pmorb(self, dictio, dictpa, sum_atoms, sum_morbs, selected_branches)
1030 edict[elt + str(anum)] = {}
1031 for morb in dictio[elt]:
-> 1032 edict[elt + str(anum)][morb] = proj[Spin.down][i][j][Orbital(setos[morb])][anum-1]
1033 proj_br[-1][str(Spin.down)][i].append(edict)
1034
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices
```
## Suggested solution (if any)
* On lines 1020 and 1032 of electronic_structure/plotter.py, modify `edict[elt + str(anum)][morb] = proj[Spin.up][i][j][Orbital(setos[morb])][anum-1]` to `edict[elt + str(anum)][morb] = proj[Spin.up][i][j][setos[morb]][anum-1]`
* This fixes the problem for *my specific case* but I do not know enough about pymatgen to know if 'this was specifically broken for VASP' (and thus implementing this fix would break the method for other projection sources) or 'this was broken overall'
|
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https://github.com/materialsproject/pymatgen/pull/642
| 221,431,835
|
MDExOlB1bGxSZXF1ZXN0MTE1NjY2MTUy
| 642
|
Proposal to add MagSymmOp class
|
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[] | null |
[] | 2017-04-13T01:10:26
| 2017-05-18T17:12:28
|
2017-04-13T20:40:34Z
|
MEMBER
|
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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 `MagneticSpaceGroup` class for a magnetic version of `symmetry/groups.py`, currently in development.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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| 221,675,502
|
MDExOlB1bGxSZXF1ZXN0MTE1ODM4MDg1
| 643
|
Add Na-H bond length from CCCBDB to bond_lengths.json
|
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[] | null |
[] | 2017-04-13T20:38:16
| 2017-04-13T20:40:20
|
2017-04-13T20:40:20Z
|
MEMBER
|
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|
## Summary
<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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| 221,877,002
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MDExOlB1bGxSZXF1ZXN0MTE1OTc5NTYx
| 644
|
Make it easier for user to submit custom LDAUU
|
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[] | null |
[] | 2017-04-14T19:43:57
| 2017-05-18T17:12:15
|
2017-04-16T22:45:36Z
|
MEMBER
|
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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, they would need to see if their structure is (e.g.) an oxide and then supply `user_incar_settings={'LDAUU':{'O':{'Fe':5}}}`. This seems non-obvious, and also would mean that `user_incar_settings` needs to be customized for every structure. The only other way I can see to do this is to add a `LDAUU` site_property but, again, this would require modification of every input structure.
This PR would add a fallback option, so that e.g. `user_incar_settings={'LDAUU':{'Fe':5}}` would work as expected in the general case.
## Additional dependencies introduced (if any)
None
## TODO (if any)
I'm not sure the best way to fix this, PR has my suggestion which should work.
|
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| 221,969,589
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MDExOlB1bGxSZXF1ZXN0MTE2MDM3MjY5
| 645
|
pymatgen.analysis.ferroelecticity module
|
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[] | null |
[] | 2017-04-15T20:04:19
| 2017-04-16T22:57:17
|
2017-04-16T22:57:17Z
|
CONTRIBUTOR
|
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This pull request contains the Polarization and EnergyTrend classes useful for evaluating the spontaneous polarization and energy trends of a candidate ferroelectric using polarization calculations for several structures sampled from along a nonpolar-polar distortion.
|
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MDExOlB1bGxSZXF1ZXN0MTE2MjA4NTI1
| 646
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Fix CONTRAINT stre bug in QChem Input
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2017-04-17T21:37:51Z
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Fix CONTRAINT stre bug in QChem Input
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Make AbinitTimerParser work with abinitv8.3
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| 648
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Should efermi from Vasprun be rounded to the 4th decimal place?
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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
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2017-04-25T23:17:43Z
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CONTRIBUTOR
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In vasprun.xml, the Fermi level is reported to 8 decimal places, while the band energies are only reported to 4 decimal places (and thus rounded to 4 decimal places).
Excerpt from vasprun.xml:
```
...
<i name="efermi"> 2.71196589 </i>
<total>
<array>
<dimension dim="1">gridpoints</dimension>
<dimension dim="2">spin</dimension>
<field>energy</field>
<field>total</field>
<field>integrated</field>
<set>
<set comment="spin 1">
<r> -31.9226 0.0000 0.0000 </r>
<r> -31.7774 0.0000 0.0000 </r>
<r> -31.6322 0.0000 0.0000 </r>
...
```
However, this can cause errors in determining whether a material is metallic if the valence band maximum is close to this value. I'm attaching the vasprun.xml and EIGENVAL files for such an example (BaTiO3 in space group 160 which is known to have a PBE band gap of ~2.5 eV).
```python
from pymatgen.io.vasp.outputs import Vasprun
import numpy as np
vrun = Vasprun('bto_vasprun.xml')
bs = vrun.get_band_structure()
print bs.efermi
print bs.is_metal()
bs.efermi = np.round(bs.efermi,4)
print bs.efermi
print bs.is_metal()
>> 2.71196589
>> True
>> 2.712
>> False
```
Should the efermi property be rounded to the same number of decimal places by default to avoid this issue?
[bto_example.zip](https://github.com/materialsproject/pymatgen/files/935823/bto_example.zip)
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added 1e-4 tolerance to is_metal method of BandStructure to account f…
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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, then it is a metal. Otherwise, it is not. So why would allowing for a +ve numerical error in the first instance and a -ve numerical error second instance lead to a wrong classification?\r\n\r\nMore importantly, why is this code not simply ```not np.all(values[i, :] - self.efermi < 1e-4)```?",
"I think you are right that one tolerance should be negative, but it should be the first one:\r\n`np.any(values[i, :] - self.efermi < -1e-4) and np.any(values[i, :] - self.efermi > 1e-4)`\r\n\r\nThis ensures that only energies outside the tolerance on efermi are used to determine if the material is a metal."
] | 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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update info format for bolztrap.out
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[] | 2017-04-20T14:15:06
| 2017-04-20T14:22:44
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2017-04-20T14:22:43Z
|
CONTRIBUTOR
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## Summary
the default type of p.communicate() is bytes in python3, the log info will not display as we wish.
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MDExOlB1bGxSZXF1ZXN0MTE3MzMwNzY0
| 651
|
Fix for dielectric tensors read from OUTCAR not being symmetric
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[] | 2017-04-24T18:42:10
| 2017-04-24T19:37:39
|
2017-04-24T19:37:39Z
|
CONTRIBUTOR
|
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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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| 223,979,504
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MDExOlB1bGxSZXF1ZXN0MTE3Mzc4MjYx
| 652
|
Warn MPRester user about need to install matproj.snl extras
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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`
* Gives one-liner `pip install` command to ensure matproj.snl dependencies.
|
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MDU6SXNzdWUyMjQzMDAzMTQ=
| 653
|
Adding trigonal bipyramid to OrderParameters in pymatgen.analysis.structure_analyzer?
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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 was implemented several months ago.\r\nAgreed, @blondegeek?"
] | 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://materialsproject.org/materials/mp-19385/)
|
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Support Multiple Frame XYZ; Minor Changes to QChem
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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 either a list of molecule or just a molecule, but the user will need to test wether it is a list.",
"An alternative would be to have both molecule and molecules properties. molecule returns the last frame in case multiple frame XYZ. Please let me know what is your preference."
] | 2017-04-26T22:26:49
| 2017-04-28T00:17:35
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2017-04-28T00:17:35Z
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CONTRIBUTOR
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* Added class MXYZ to support multiple frame xyz (e.g. MD trajectory)
* Add support for "velocity" section to QChem module to AIMD setup.
* Add class QcNucVeloc to parse QChem AIMD velocity output.
|
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| 655
|
Fix INCAR QUAD_EFG tag parsing
|
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[] | 2017-04-28T06:04:58
| 2017-04-28T13:32:40
|
2017-04-28T13:32:40Z
|
CONTRIBUTOR
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Fix INCAR QUAD_EFG tag parsing
|
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MDExOlB1bGxSZXF1ZXN0MTE5MDMxNDA0
| 656
|
Fixes to elasticity
|
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[] | 2017-05-04T17:58:19
| 2017-05-04T20:48:53
|
2017-05-04T20:48:53Z
|
CONTRIBUTOR
|
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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 third-order elastic constants is in the pipeline
|
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MDExOlB1bGxSZXF1ZXN0MTE5MjU2MjQy
| 657
|
2 structure analysis tools - Jmol coord finder and dimensionality
|
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[] | 2017-05-05T20:51:51
| 2017-05-05T20:59:10
|
2017-05-05T20:59:10Z
|
MEMBER
|
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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
+ tests for both
## Additional dependencies introduced (if any)
None
## TODO (if any)
JMol has additional autoBond features for things like hydrogen bonds and also valence-specific bonding algorithms if the oxidation state is known. Maybe I will implement some of those features at a later time if I get the chance / it becomes important. However the commits above are fully self-sufficient and useful.
|
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MDU6SXNzdWUyMjY5Mjc0Mjc=
| 658
|
UnicodeDecodeError: 'utf8' codec can't decode byte 0xb0
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[] | null |
[
"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 \"hard to install\" comment? I expect that it is more difficult for Windows users, but I have seldom heard complaints from Mac users and certainly not from Linux users. Also, pymatgen is already available on conda and that is the first recommended installation method in the documentation for people who have not done python packages before.",
"if I use `pmg -h `then `Author: Shyue Ping Ong Version: 5.0 Last updated: Sep 19 2016` appears, that's the version I meant. \r\n\r\nIt was hard because fedora didn't have the dependences needed, specifically, `redhat-rpm-config`, `python-devel`, `libxstl-devel`, `gcc-c++`, and more that I installed because they were dependencies for those that I think were the key to making it work. \r\n\r\nHave played around more and is just one vasprun.xml file that has the problem when importing it with Vasprun(), if the file is imported fine then everything else works. Note that all the files I am trying to import were imported just fine in Debian. Tried to compare the different vaspruns and I see no difference in the structure.\r\n",
"I see. If Fedora does not come with gcc and python-devel installed by default, that is a very bad practice by Fedora. Most Linux distributions come with them properly installed. THis is especially since anything within the SCipy package definitely requires these packages and those are pretty standard.\r\n\r\nUnfortunately I have no way to looking at a file that somehow does nto parse on Fedora but parses properly on Debian. That suggests that there is something wrong either with the python compilation itself or the system. You can check the python version with `python --version`. If it is somehow failing on Python 2 rather than Python 3 or vice versa, I can look at that. Reopen this issue if this issue persists."
] | 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`
Pymatgen was hard to install but was able to install it fine after some time with pip.
## Error message
Entire error code is:
```
Traceback (most recent call last):
File "an.py", line 199, in <module>
vasprun = Vasprun("/vasprun.xml")
File "/usr/lib64/python2.7/site-packages/pymatgen/io/vasp/outputs.py", line 383, in __init__
self.update_potcar_spec(parse_potcar_file)
File "/usr/lib64/python2.7/site-packages/pymatgen/io/vasp/outputs.py", line 829, in update_potcar_spec
potcar = get_potcar_in_path(os.path.split(self.filename)[0])
File "/usr/lib64/python2.7/site-packages/pymatgen/io/vasp/outputs.py", line 813, in get_potcar_in_path
pc = Potcar.from_file(os.path.join(p, fn))
File "/usr/lib64/python2.7/site-packages/pymatgen/io/vasp/inputs.py", line 1704, in from_file
fdata = reader.read()
File "/usr/lib64/python2.7/codecs.py", line 314, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf8' codec can't decode byte 0xb0 in position 37: invalid start byte
```
I am sure more errors would appear if I fix just the above one since that is the first time pymatgen is actually implemented in the code.
|
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MDExOlB1bGxSZXF1ZXN0MTE5NTAyODc2
| 659
|
Added a trigonal bipyramidal order parameter.
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Addressed numerical inconsistency in order parameter unit tests.
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Simplified structure motif-based interstitial finding tool (InFiT).
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MDU6SXNzdWUyMjc1MTUzNTI=
| 662
|
DeformedStructureSet returns dict_keys object in python 3
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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 additional functionality that you think would be useful there, feel free to implement and submit a PR."
] | 2017-05-09T22:21:51
| 2017-05-09T23:12:42
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2017-05-09T23:12:42Z
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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 python 2)
* this is harder to understand as the default argument `symmetry=False` returns a list rather than a dictionary view object (even in python 3).
* returning different objects makes it difficult to determine how to use the object
## Example code
```python
poscar = Poscar.from_file('POSCAR_orig')
structure = poscar.structure
dss = elasticity.strain.DeformedStructureSet(structure, symmetry=True)
for i, st_deformed in enumerate(dss.def_structs):
runvasp()
vasprun = Vasprun('vasprun.xml')
deformation_matrix = dss.deformations[i].tolist()
sm = elasticity.strain.IndependentStrain(deformation_matrix)
st = elasticity.stress.Stress(vasprun.ionic_steps[-1]['stress'])
ss_dict[sm] = st
```
## Error message
```
Traceback (most recent call last):
File "holy-potatoes-a-bug.py", line 28, in <module>
deformation_matrix = dss.deformations[i].tolist()
TypeError: 'dict_keys' object does not support indexing
```
## Suggested solution (if any)
* From DeformedStructureSet(), could we get the same functionality from
```python
self.deformations = list(self.sym_dict)
```
as opposed to
```python
self.deformations = self.sym_dict.keys()
```
* Alternatively, I'd be okay with returning a dict_keys object if it also returned the same type **with symmetry=False**
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MDExOlB1bGxSZXF1ZXN0MTE5NzcxMzA5
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Minor bugfix - ensure deformations is a list
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[] | 2017-05-09T22:55:59
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2017-05-09T23:12:34Z
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CONTRIBUTOR
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Minor bugfix
* Ensures deformations attribute of deformed structure set is a list
|
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| 227,725,974
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MDU6SXNzdWUyMjc3MjU5NzQ=
| 664
|
Pointgroup analyzer returns wrong point group
|
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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 classification of a cube as a symmetric top instead of a spherical top due to the fact that the center of mass is not at the origin during calculation of the inertia tensor). I have released v4.7.6 which contains this fix as well as other minor fixes and improvements."
] | 2017-05-10T15:47:34
| 2017-05-14T16:41:42
|
2017-05-14T16:31:22Z
|
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: <4.7.2>
* Python version: <3.6.1>
* OS version: <OpenSUSE 13.1>
## Summary
* <If you pass 8 carbon atoms at the corners of a cube to the point group analyzer it does not detect the 4 fold rotation axes and returns the incorrect point group. >
## Example code
```python
<Example code generating error>
```
## Error message
```
<Error message>
```
## Suggested solution (if any)
* <If you have a suggestion on how to solve the issue, you may write it
here.>
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
```
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| 665
|
Proposal for new k-point generation scheme
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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 with almost the same lattice parameters. One of them, after doing the various operations, shows that we should have 2.9 kpoints per vector. The other shows 3.1 kpoints. These materials are almost the same, yet one is run with 2x2x2 and the other as 4x4x4 (8X as many reducible kpoints!) That kind of huge discontinuity doesn't feel right to me. This is also because I don't fully understand the reasoning behind VASP's \"even for n<=8 rule\", which makes me question how seriously we should be taking this rule.",
"It might be useful to a have a legacy_scheme flag or something to that effect that retains the old generator method until the effect of this new kpt scheme can be determined. I wonder what it will do for things like NMR and Piezo which generally have very stringent convergence criteria. ",
"@shyamd I would say for convergence, MP has bigger issues to worry about than the kpoints. Most of the problems for NMR and Piezo has to do with proper force convergence. To me, the solution for those is for separately adapted input sets that crank up the density parameter for kpt generation, as well as add the necessary EDIFFG, etc. ",
"@shyuep I believe you've also brought up the suggestion in the past to just use VASP's fully automatic scheme, in which a single number is specified and VASP does all the various subdivisions.\r\n\r\nhttps://cms.mpi.univie.ac.at/vasp/vasp/Automatic_k_mesh_generation.html\r\n\r\nA couple of notes on this:\r\n- Nothing in their own scheme seems to really enforce the even/odd rule. Thus, they don't seem to be taking that rule too seriously themselves.\r\n- It's possible (although not guaranteed or tested) that the fully automatic method (i.e., single parameter automatic) might have fewer convergence problems than our semi-automatic (3 parameters) scheme. Our justification in the past for doing the latter was that our algorithm would take into account non-orthogonal lattice vectors better. But apart from possibly more stable behavior from VASP, another reason to do fully automatic might be because this generates \"gamma-centered Monkhorst Pack\" grids which might be better than the original MP scheme for estimating (rough) band gaps. \r\n\r\nI guess I don't really have issues with your changes vs what was there before but still want to know if we can do better if we are going to change anyway.",
"@computron I have no issues with moving to fully-automatic. My only concern is that such a move requires someone to benchmark the system to determine the proper grid parameter, and whether a robust value can be determined. I seem to recall we had some early attempts to do this benchmarking but can't remember the result.\r\n\r\nMy current changes is mainly to solve an immediate problem without causing too much impact on MP. For the most part, typical experimental cells are ~4-8 A, which will result in basically a 6x6x6 or 4x4x4 grid. Only at 8A does it transition to a 2x2x2 (which I think is reasonable). The immediate problem is for supercell calculations (e.g., defect studies, NEB calculations, AIMD simulations). There, something like 2x2x2 for a 15A cell is pretty ridiculous and makes what is already an expensive calculation much more expensive. ",
"Ok I won't let the perfect be the enemy of the good\r\n\r\nBut for the future I'd still think about:\r\n- removing even/odd rule\r\n- going fully automatic",
"@computron Ok, I have done some very basic testing of the VASP full auto mode. They basically ignore the even/odd rule. So I have removed that rule. Now the corresponding grids are:\r\n\r\n```\r\nFor a = 3.0, k = Monkhorst 8 x 8 x 8\r\nFor a = 4.0, k = Monkhorst 6 x 6 x 6\r\nFor a = 5.0, k = Gamma 5 x 5 x 5\r\nFor a = 6.0, k = Monkhorst 4 x 4 x 4\r\nFor a = 7.0, k = Gamma 3 x 3 x 3\r\nFor a = 8.0, k = Gamma 3 x 3 x 3\r\nFor a = 9.0, k = Gamma 3 x 3 x 3\r\nFor a = 10.0, k = Monkhorst 2 x 2 x 2\r\nFor a = 11.0, k = Monkhorst 2 x 2 x 2\r\nFor a = 12.0, k = Gamma 1 x 1 x 1\r\nFor a = 13.0, k = Gamma 1 x 1 x 1\r\nFor a = 14.0, k = Gamma 1 x 1 x 1\r\nFor a = 15.0, k = Gamma 1 x 1 x 1\r\nFor a = 16.0, k = Gamma 1 x 1 x 1\r\n```\r\n\r\nThe main affected grids are the ones at 7-9A, which now gives a Gamma 3x3x3.",
"Ok - I like the smoothness of the changes better; not sure if switching between Gamma and Monkhorst may lead to issues (hence the VASP fully automatic saying something about \"Gamma-centered Monkhorst-Pack\" for everything, which I don't fully understand since I never really looked into k-point integration schemes). In any case I am OK with it unless someone else sees a problem.",
"@computron In general, the so-called Gamma-Center MonkHorst just simply means you specify Gamma for all grids. Personally, I think the VASP people are just too lazy to figure out whether MH or Gamma and just use Gamma, since that is the most robust scheme (you do not care about whether the cell is hexagonal or not).",
"So at some point, we have to consider the fact that this is for the MPRelaxSet, which suggests it reflects MP as is. ",
"@shyuep FYI - this can change grids quite a bit\r\n\r\nSi structure relaxation was 8x8x8 (old) and 6x6x6 (new). Note that the new scheme seems to more closely resemble the desired grid (6.02 -> 6 instead 6.02 -> 8)\r\n\r\nSi uniform run was 220 explicit kpoints (old) and is now 145 explicit kpoints - this should have been the \"per volume\" scheme rather than \"per atom\". This is a huge reduction(!)\r\n\r\nThe new algorithm is probably more stable, but I don't know whether the tests of k-point convergence need to be re-run and some of the default k-point densities cranked up. e.g., if we were previously having 220 kpoints for the Si uniform run, I am not sure that 145 is going to cut it",
"Also the NEB runs in atomate tests used to 8x8x8. Now they are 3x3x3.\r\n\r\nThese are pretty big differences; I'm not sure this new k-mesh is well tested enough for atomate. Previously I was going to update all the k-point tests in atomate for new pymatgen, but for now I am just going to roll back the req pymatgen to 4.7.5 in atomate until we sort this out.",
"Which NEB test are you referring to?\r\n\r\nSi is a semiconductor. I am pretty sure a 6x6x6 grid is more than enough, even for the primitive cell. The number of kpoints, even without taking into account symmetry, drops from 512 to 256. So I am not surprised the uniform unique kpts drop from 220 to 145.",
"The NEB test in atomate:\r\n\r\natomate/vasp/workflows/tests/test_neb_workflow.py:40\r\n\r\nwhich appears to be for Li2O",
"Well, it is for a 2x2x2 of the primitive cell of Li2O, which puts it at 6.7 A in each direction. I *highly doubt* you need a 8x8x8 kpoint grid for that cell. A 3x3x3 grid sounds reasonable to me. \r\n\r\n@johnson1228 @HanmeiTang Comment?",
"Sorry - slight modification (some better, some worse)\r\n\r\nFor the NEB workflow, the endpoint calcs look to have been 4x4x4 in the past and 3x3x3 revised (=no big deal).\r\n\r\nFor the actual image calcs (i.e., multiple POSCAR, same INCAR/KPOINTS/etc) - the calcs look to be 8x8x8 in the past and 1x1x1 (!!) in the revised scheme. This is the major difference - i.e., not in the endpoints but rather the actual images.\r\n",
"I see. I am pretty sure the image calculations are wrong. You cannot possibly be using a 8x8x8 for image calculations. That NEB calculation will never finish. The image calculations should be <= the grid of end points.",
"I might be misinterpreting the NEB tests then. Looks like there are multiple \"configurations\" being tested and I can't make sense of it.\r\n\r\nThe reference files for the old kpoints are here:\r\natomate/atomate/vasp/test_files/neb_wf\r\n\r\nThere are 5 directories in there. I thought some of these were endpoints and others were the images, but it looks likes these are 5 different configurations of NEB runs as documented in:\r\n\r\natomate/vasp/workflows/tests/test_neb_workflow.py\r\n\r\nThe first 3 of these configurations show a rough match between previous and current kpoints (4x4x4 vs 3x3x3). The next two (configs 4 + 5) have 8x8x8 in the KPOINTS file - which change to 1x1x1 in the new scheme.",
"Ok. @HanmeiTang @johnson1228 Pls fix the tests in atomate PROPERLY.",
"Note that for configs 4 and 5, the KPOINTS file itself documents that the previously the grid points per atom were 1000, whereas in the new file it says 100 (an order of magnitude less).\r\n\r\nOLD\r\n---\r\npymatgen generated KPOINTS with grid density = 1000 / atom\r\n0\r\nMonkhorst\r\n8 8 8\r\n---\r\n\r\n\r\nNEW\r\n---\r\npymatgen 4.7.6+ generated KPOINTS with grid density = 100 / atom\r\n0\r\nGamma\r\n1 1 1\r\n---",
"Okay, we will fix the unittests soon.",
"We have fixed the unittests issue. \r\n\r\nBasically, the tests that we wrote before only check if file transfer using the RunNEBVaspFake class works properly in the NEB workflow, i.e. actual NEB calculations are not performed. The different KPOINTS settings from 1000/atom to 100/atom are just to make sure that KPOINTS file can be modified by the users. \r\n\r\nIn the KPOINTS file for perfect cell relaxations as well as endpoint relaxations, we have changed the k-mesh to Gamma 3x3x3, and Gamma 1x1x1 for NEB calculations.",
"Ok I am going to close this again for now. At some point I might try to do a test of \"new vs old\" k-point meshes. I am still a little nervous because we benchmarked the old scheme, and now it seems we are almost always reducing the k-point mesh from that.",
"also @HanmeiTang please push a PR to atomate when you have the chance",
"@computron Will do.",
"@computron I have already done tests for Li2O and NaCl kpoint meshes. Generally, large band gap insulators are not going to be an issue. These meshes are almost certainly too small for metals. It is more the intermediate semiconductor cases that might be of concern.\r\n\r\nCertainly the new scheme will always reduce the mesh. The idea was that the rounding and even/odd rules of the old mesh algo always rounds up, and sometimes by a significant amount. I highly doubt there is a major effect for structural relaxations.\r\n\r\nFor static and uniform calculations, I would certainly recommend upping the grid by 1.5x or even 2x if you feel uncomfortable. Those are cheap single SCF calculations. \r\n\r\nQuite frankly, we should not be worrying about kpoint meshes for relaxations when MP is still using EDIFF * # of atoms, which sometimes result in EDIFF > 0.005 eV, and correspondingly large EDIFFGs. The error of those washes out the small errors you are likely to get with the kpoints. Many structures in MP, especially those with a large # of atoms, are actually poorly converged in terms of structure.",
"@computron Final update - I have cranked up the reciprocal density for relaxation to 64 instead of 50. This results in a 7x7x7 grid for Si. \r\n\r\nNote that the VASP examples themselves show a grid of 11x11x11 for fcc Si. (https://cms.mpi.univie.ac.at/wiki/index.php/Fcc_Si) Recp density = 50 gives a 9x9x9 grid, which is not far off. Recp density = 64 gives 10x10x10, which I think is pretty reasonable for HT. \r\n\r\nThe correct behavior at high lattice lengths is maintained, i.e., after about 12 A, the gamma grid is obtained. I still think that 2x2x2 mesh for a 10Ax10Ax10A structure is a bit too much, but I will live with this."
] | 2017-05-10T19:42:36
| 2017-05-17T04:06:08
|
2017-05-15T23:39:38Z
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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 inefficient, with rounding to integers occurring at multiple steps along the way.
* The major problem is that even for lattices where you have lattice lengths of 13 A or more, the code assigns a 2x2x2 grid with the MPRelaxSet. This makes calculations of such large cells extremely expensive. The following code gives
```python
from pymatgen import Structure
from pymatgen.io.vasp.sets import MPRelaxSet
import numpy as np
for a in np.arange(3, 17, 1):
s = Structure.from_spacegroup("Pm-3m", np.eye(3) * a, ["Fe"], [[0, 0, 0]])
v = MPRelaxSet(s)
kpts = v.kpoints.kpts[0]
print("For a = %.1f, k = %d x %d x %d" % (a, *kpts))
```
```
For a = 3.0, k = 8 x 8 x 8
For a = 4.0, k = 6 x 6 x 6
For a = 5.0, k = 6 x 6 x 6
For a = 6.0, k = 4 x 4 x 4
For a = 7.0, k = 4 x 4 x 4
For a = 8.0, k = 4 x 4 x 4
For a = 9.0, k = 4 x 4 x 4
For a = 10.0, k = 2 x 2 x 2
For a = 11.0, k = 2 x 2 x 2
For a = 12.0, k = 2 x 2 x 2
For a = 13.0, k = 2 x 2 x 2
For a = 14.0, k = 2 x 2 x 2
For a = 15.0, k = 2 x 2 x 2
For a = 16.0, k = 1 x 1 x 1
```
Obviously, a 2x2x2 grid for a 15 A cell is ludicrous, especially for insulators (this is the main class of materials the MPRelaxSet handles - metals are a separate class we deal with separately). We have grids of 4x4x4 all the way up to a 9A cell.
## New proposal
* We will fix this in several areas.
* In the Kpoints.automatic_density_by_vol method, kppa will no longer be rounded to an integer.
* In the Kpoints.automatic_density method, we will retain non-integer num_div, followed by an improved rounding scheme that rounds something like 2.9 x 2.9 x 2.9 to a MH 2x2x2 grid, a 3.2x3.2x3.2 to a MH 4x4x4 grid, and for n = 1 and n > 8, the current scheme of rounding to an odd Gamma grid is retained. Revised code is below.
```python
num_div = [max(mult / l, 1) for l in lengths]
if all([k < 2 for k in num_div]):
return Kpoints(comment, 0, Kpoints.supported_modes.Gamma, [[1, 1, 1]], [0, 0, 0])
is_hexagonal = latt.is_hexagonal()
# VASP documentation recommends to use even grids for n <= 8 and odd
# grids for n > 8.
num_div = [int(round(i - i % 2 + 2 * math.floor(i % 2))) if i <= 8 else int(round(i - i % 2 + 1)) for i in num_div]
```
The new grids generated using the same test code is as follows:
```
For a = 3.0, k = 8 x 8 x 8
For a = 4.0, k = 6 x 6 x 6
For a = 5.0, k = 4 x 4 x 4
For a = 6.0, k = 4 x 4 x 4
For a = 7.0, k = 4 x 4 x 4
For a = 8.0, k = 2 x 2 x 2
For a = 9.0, k = 2 x 2 x 2
For a = 10.0, k = 2 x 2 x 2
For a = 11.0, k = 2 x 2 x 2
For a = 12.0, k = 1 x 1 x 1
For a = 13.0, k = 1 x 1 x 1
For a = 14.0, k = 1 x 1 x 1
For a = 15.0, k = 1 x 1 x 1
For a = 16.0, k = 1 x 1 x 1
```
Which is a lot more reasonable, especially for an 8x8x8 A sized cell (pretty large by most standards) onwards.
This new scheme has been implemented in the kpts branch.
|
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| 228,085,505
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MDExOlB1bGxSZXF1ZXN0MTIwMTc1MDc0
| 666
|
Avoid force calculation error when printing
|
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[] | 2017-05-11T18:45:45
| 2017-05-11T18:46:47
|
2017-05-11T18:46:47Z
|
CONTRIBUTOR
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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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Kpts
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[] | 2017-05-12T04:19:52
| 2018-03-25T13:29:08
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2017-05-12T04:19:59Z
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Closes #665
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problem on installing pymatgen
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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 recommends that you use conda to install pymatgen if you have no experience in installing python packages.",
"Thank you for your reply. I will try using conda to install pymatgen"
] | 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_vectors ' I don't know how to solve this problem. I would like to know how to solve it, please help me.
|
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|
modify KPOINTS file comment to more clearly indicate runs w/new kpoin…
|
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[
"(just look at the diff)"
] | 2017-05-15T19:59:19
| 2017-05-15T20:21:38
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2017-05-15T20:21:38Z
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MDExOlB1bGxSZXF1ZXN0MTIwOTcxMTM3
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|
MagneticSpaceGroup class and Structure.from_magnetic_spacegroup method
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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 sqlite, though I agree the complexity of the query may necessitate the use of sqlite.",
"Hi, there are a number of test failures. See https://circleci.com/gh/materialsproject/pymatgen/6335 . These have nothing to do with the MAPI key but are related to the new mag symmetry changes.\r\n\r\nCan you fix them and submit a PR? ",
"Sure, thanks, I see them. Looks like it may be a Python 2.x issue. Will submit a PR asap.",
"There is still one failure. https://circleci.com/gh/materialsproject/pymatgen/6336?utm_campaign=build-failed&utm_medium=email&utm_source=notification \r\n\r\nThink it is a Py2.7 issue.",
"Hmm, weird. It works in the console but not in the nosetests.\r\n\r\nFor some reason `Structure.from_magnetic_spacegroup(id, ...)` fails when `id` is a str/label but only in the tests (e.g. `Structure.from_magnetic_spacegroup(\"Pn'ma'\", ...)` fails in the nosetests, but works in the console for 2.7). Will look into this.\r\n\r\nEdit: fixed, will submit PR",
"Sorry, this should hopefully be fixed once and for all now in #673. Have used `six` to fix. Will make to test Py2.7 robustly before future PRs to make sure this doesn't happen again! (Have also now set up my own CircleCI to perform tests before submitting future PRs)"
] | 2017-05-17T04:09:07
| 2017-05-17T18:38:19
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2017-05-17T05:02:46Z
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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 found in the docstrings.
* Subclasses `SymmetryGroup` and, as much as possible, has methods equivalent to those in `SpaceGroup` have been used, and implementations re-used where appropriate.
* Incorporates data from [ISO-MAG, ISOTROPY Software Suite](http://stokes.byu.edu/iso/isotropy.php) with kind permission of Prof. Branton Campbell, BYU. The way the space group data is stored and loaded in the class is based on this data file.
* Example, to create antiferromagnetic MnF2:
```
Structure.from_magnetic_spacegroup("P4_2'/mnm'", Lattice.tetragonal(4.87, 3.30),
["Mn", "F"], [[0, 0, 0], [0.30, 0.30, 0.0]],
{'magmom': [4, 0]})
```
## Additional dependencies introduced (if any)
It's in the Python standard library, but this does use `sqlite3`. A JSON data file was also tried, but loading times were really slow (19 MB), and look-ups were awkward (since the class needs to look up by one of BNS label, BNS number, OG label and OG number). Therefore a small sqlite database was used instead.
## TODO (if any)
* An additional class allowing transformations between arbitrary settings is being developed. This is slightly different from origin shifts in `groups.py`, but follows a standard specification provided by IUCr used in various CIF formats (which specifies transformations in Jones faithful notation). However, bugs are still being worked out with this.
* Not implemented are `is_supergroup()`, `is_subgroup()`
* Data file includes Wyckoff sites. These are currently parsed and printed, but nothing else is done with them.
|
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| 229,387,646
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MDExOlB1bGxSZXF1ZXN0MTIxMDgzMDEx
| 671
|
Fix MagneticSpaceGroup for Python 2.7
|
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[] | 2017-05-17T15:12:47
| 2017-05-17T15:42:05
|
2017-05-17T15:42:05Z
|
MEMBER
|
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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.
Apologies for this! Have set up proper Python 2.7 testing locally to catch this in future.
|
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| 229,430,192
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MDExOlB1bGxSZXF1ZXN0MTIxMTEwNTYw
| 672
|
Fix MagneticSymmteryGroup for unicode arguments in Python 2.7
|
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[] | 2017-05-17T17:22:22
| 2017-05-17T18:03:00
|
2017-05-17T18:03:00Z
|
MEMBER
|
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Nosetests supply label string as `unicode` type, which wasn’t being
caught by `if isinstance(…, str)` statement leading to no SQL query
being generated.
|
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| 229,443,423
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MDExOlB1bGxSZXF1ZXN0MTIxMTIwMjIw
| 673
|
Fix MagneticSymmetryGroup for unicode arguments in Python 2.7 (v2)
|
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[] | null |
[] | 2017-05-17T18:14:20
| 2017-05-18T17:12:05
|
2017-05-17T20:24:12Z
|
MEMBER
|
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|
Now using `six` to fix compatibility issues.
|
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| 229,536,629
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MDExOlB1bGxSZXF1ZXN0MTIxMTg4Mzc3
| 674
|
Glitch in BSPlotter.plot_compare
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[] | 2017-05-18T02:18:42
| 2017-05-18T03:26:07
|
2017-05-18T03:26:07Z
|
CONTRIBUTOR
|
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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 of the block itself was incorrect, causing:
1. Spin-down BS to be evaluated only in one branch
2. The band number being used in-place of the k-point branch
Point 1 was merely incorrect, while point 2 would lead to an index-out-of-range error, and the plot to fail. This pull request fixes the syntax so that plot_compare works properly.
|
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MDExOlB1bGxSZXF1ZXN0MTIxODc5ODIz
| 675
|
Introduced variants of tetrahedral and octahedral order parameter
|
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[] | 2017-05-22T22:39:23
| 2017-05-23T01:41:25
|
2017-05-23T01:41:25Z
|
CONTRIBUTOR
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The alternative tetrahedral (tetalt) and octahedral (octalt) order parameter cannot become negative by construction and are therefore preferable to the original ones.
|
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MDExOlB1bGxSZXF1ZXN0MTIyMDY1NTQ3
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|
Ensure SNL references is a string rather than any falsy value
|
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[] | 2017-05-23T18:31:06
| 2017-05-23T21:07:00
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2017-05-23T21:07:00Z
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MEMBER
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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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MDExOlB1bGxSZXF1ZXN0MTIyMTQ5ODY0
| 677
|
Add magCIF support to CifParser and CifWriter
|
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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 evaluate as `True` ... I haven't submitted a fix because I wasn't sure what the desired behavior was. Maybe could replace it with a `rescale_occupancies` (bool) kwarg instead, that will just rescale occupancies to sum 1.0 if True?",
"GReat. Thanks!"
] | 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 combine them now before they diverge too much.
* CifParser changes:
* Includes a new CIF `feature_flags` dictionary (extensible for other non-core CIF features), checks to see if a file is magCIF
* If magCIF, will try to place atoms:
* First by magnetic symmetry operations, if provided (most common case)
* If not, then by BNS symmetry group, if provided
* Will output a Structure with magnetic moments on site properties
* Note that this means disordered magnetic structures not currently supported
* Includes refactor of Pauling/Springer correction code, putting it into a `_sanitize_data()` function – *all current tests pass, but I'm not familiar with the Pauling files, so I'm cautious about this.* The refactor was done to introduce a logical separation between correction code and parsing code, so that parsing code can assume the data conforms to specification, and will make it easier to make changes to the parser in the future
* Adds simple `get_bibtex_strings()` function to extract reference from CIF file, I found it useful for constructing SNLs
* CifWriter changes:
* Adds `write_magmoms` kwarg
* If moments are written, will not perform symmetry analysis
* Scalar moments are arbitrarily aligned along z (note that magnetic symmetry not well defined with scalar moments), this comes directly from the `Magmom` class
* Useful for visualization of magnetic moments (works with VESTA, JMOL etc.)
* Tested on Py3.6 and Py2.7 locally
* Closes #508
## Additional dependencies introduced (if any)
None
## TODO (if any)
Core functionality is all present, but there are some features to add (these raise NotImplementedErrors for now):
* Add code to parse an arbitrary change of setting, which is included in the spec
* Add support for disordered magnetic structures
* I don't think there's currently a good way to do this in pymatgen, was going to implement this by adding a `Magmom` to a `Specie` 'spin' property, but this would likely be confusing to the end user (would introduce a fictitious oxidation state, and misuses the spin property) ... open to suggestions here
additionally,
* More graceful handing of `get_primitive_structure()` for magnetic structures, which often gives the wrong results for complex magnetic structures. Will address this with `get_primitive_magnetic_structure()` in a `MagneticStructureAnalyzer` in a future PR, until then advise using `primitive=False` in `CifParser` for magCIF files.
* (Future) Add magnetic symmetry detection support to output full-featured magCIF files containing appropriate symmetry information
|
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|
Add from_file method to PWInput
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[
"Thanks!"
] | 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.
However, for non-polarization calculation, pseudo(dict) is also OK.
* Added test file for PWInput
* test_files/sio2.pw.in
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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|
Bug fix and new functions for Boltztrap classes:
|
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[] | null |
[] | 2017-05-26T18:53:47
| 2017-05-26T18:56:43
|
2017-05-26T18:56:43Z
|
CONTRIBUTOR
|
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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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| 231,802,597
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MDExOlB1bGxSZXF1ZXN0MTIyNzYxODkx
| 680
|
Minor fix for ieee conversion based on symmetry
|
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[] | null |
[] | 2017-05-27T13:51:14
| 2017-05-27T13:52:52
|
2017-05-27T13:52:52Z
|
CONTRIBUTOR
|
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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 symmetrically equivalent. In general, if someone wants to convert the tensor to ieee (which requires recognition of the symmetry to ensure a conventional setting) they should probably be fitting the tensor to the structure symmetry anyway, so I've added an option for this that defaults to true. I've updated the tests accordingly.
* Tensor.convert_to_ieee now takes an `initial_fit` keyword argument that defaults to True, which indicates whether or not to fit the tensor to the symmetry of the structure prior to conversion.
* Fixes unit test failure.
|
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| 231,996,812
|
MDExOlB1bGxSZXF1ZXN0MTIyODc2NDU4
| 681
|
Fixed a bug in PWInput.from_string()
|
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[] | null |
[] | 2017-05-29T11:25:35
| 2017-05-29T12:56:03
|
2017-05-29T12:56:03Z
|
NONE
|
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## Summary
Fixed a bug in PWInput.from_string()
|
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| 232,085,088
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MDExOlB1bGxSZXF1ZXN0MTIyOTM2NjEz
| 682
|
Fixed bug in boltztrap runner with alternate dopings
|
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[] | null |
[] | 2017-05-29T19:26:24
| 2017-05-29T19:32:52
|
2017-05-29T19:32:52Z
|
NONE
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Boltztrap runner tried to evaluate truth of doping variable to test if None or array.
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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MDExOlB1bGxSZXF1ZXN0MTIzMTYyMDYy
| 683
|
Proposal for class to enable arbitrary change of crystallographic setting
|
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[] | null |
[] | 2017-05-30T23:05:10
| 2017-05-30T23:23:47
|
2017-05-30T23:23:47Z
|
MEMBER
|
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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-colon. Best shown by example:
* `a,b,c;0,0,0` is the identity
* `-b+c,a+c,-a+b+c;0,0,0` is R3:r to R3:h (rhombohedral to hexagonal setting)
* `a,b,c;-1/4,-1/4,-1/4` is Pnnn:1 to Pnnn:2 (change in origin choice)
* `b,c,a;-1/2,-1/2,-1/2` is Bbab:1 to Ccca:2 (change setting and origin)
* Can also be initialized from transformation matrix `P` and translation vector `p` directly
* IUCr uses this directly in a few different CIF standards (symCIF, magCIF)
* Has methods `transform_coords`, `transform_lattice` and `transform_symmop` and properties `transformation_string` and `inverse`
Key reference:
* [H. Wondratschek, M.I. Aroyo, B. Souvignier, and G. Chapuis, Transformations of Coordinate Systems, 2nd ed. (International Union of Crystallography, Chester, England, 2016), pp. 75–106.](http://dx.doi.org/10.1107/97809553602060000923)
### Other changes
* Transformations sometimes lead to valid non-integer rotation matrices, so the`ValueError` in `core.operations` has been changed to a warning instead, and `as_xyz_string()` is also updated since it was giving incorrect strings in these cases (a more general `transformation_to_string` is used instead, and this has been added to `util.string`). The test case for this uses transformed symmetry operations directly from [GENPOS](http://cryst.ehu.es/cryst/get_gen.html), which are assumed to be correct.
## Additional dependencies introduced (if any)
None
## TODO (if any)
* Wait for CI results
* This class correctly transforms individual symmetry operations but it does *not* yet transform the full list of general positions of a given space group. This is because I don't know how to generate the new list of centering operations...
For example, take space group Im-3m, transformed by (a-b,a+b,2c;0,0,1/2). Fm-3m has 48 symmetry operations, which are then further combined with centering (1/2, 1/2, 1/2)+. Comparing to [GENPOS](http://cryst.ehu.es/cryst/get_gen.html), this new class correctly generates all 48 (uncentered) transformed symmetry operations. *However*, the centerings also change under the transformation to: (1/2, 1/2, 0)+, (1, 0, 0)+ and (3/2, 1/2, 1/2)+, (0, 0, 1)+ and (1/2, 1/2, 3/2)+, (1, 0, 1)+ and (3/2, 1/2, 3/2)+, but I'm not sure where these new centerings come from? It seems like it should be straight-forward, but I can't see it.
* This will be used used in `CifParser`, but could also integrate into `groups.py` in future.
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| 232,697,251
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MDExOlB1bGxSZXF1ZXN0MTIzMzY5Njk0
| 684
|
Debug plot_slab from adsorption module
|
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[] | 2017-05-31T21:10:21
| 2017-05-31T21:11:33
|
2017-05-31T21:11:33Z
|
CONTRIBUTOR
|
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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 using putting them into a list and use list comprehensions instead. This change was tested and it works in my development environment.
|
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MDU6SXNzdWUyMzM3NTA2ODk=
| 685
|
Modifying the CONFIG dict instance of a VaspInputSet class instance changes the base class
|
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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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<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: 4.7.7
* Python version: 2.7
* OS version: macOS
## Summary
* Modifying the CONFIG dict instance of a VaspInputSet class instance changes the base class
## Example code
```python
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen import Structure
# load your structure, e.g. from a POSCAR
struct = Structure.from_file('POSCAR')
# create a custom input set
my_custom_input_set = MPRelaxSet(struct)
print('Base class config dict before: {}\n'.format(MPRelaxSet.CONFIG))
print('Instance before change: {}'.format(my_custom_input_set.CONFIG['POTCAR']['Mg']))
my_custom_input_set.CONFIG['POTCAR']['Mg'] = 'Mg'
print('Instance after change: {}'.format(my_custom_input_set.CONFIG['POTCAR']['Mg']))
print('Base class after change: {}'.format(MPRelaxSet.CONFIG['POTCAR']['Mg']))
```
results in
```
Base class config dict before: {'INCAR': ... *'Mg': 'Mg_pv'*, ...'Er': 'Er_3'}}
Instance before change: Mg_pv
Instance after change: Mg
Base class after change: Mg
```
## Suggested solution (if any)
* Dictionaries of instances should be copied from the one passed in the __init__ constructor
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MDU6SXNzdWUyMzQwMjU2NDM=
| 686
|
Parsing POTCAR: 'utf8' codec can't decode byte 0x97 in position 37: invalid start byte
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[] | null |
[
"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, \"rt\", errors=\"replace\")`? I ran into a similar issue in cif.py with unknown characters, usually in author names",
"@mkhorton I am not sure if there are any advantages per se. I would say ignoring errors probably result in a higher likelihood of success. In general, I am not too worried about POTCAR parsing since the information in the POTCAR is seldom used for final analysis (except in very specialized cases such as counting electrons, etc.). So I would bias the code toward a more successful parse rather than an absolutely accurate parse.\r\n\r\nI am not able to reproduce the same error either in Py36 or Py27 using all VASP PSPs from the old 2012 version all the way to the newest 54 version. Cycling through all the PSPs resulted in a successful read even before I made the codec change, though there are some PSPs, especially the H PSPs that did not have description and other fields which caused a failed read. I have fixed those.",
"Hi,\n\nI tracked down the problem:\nIn the directory where my vasprun.xml and POTCAR file reside there was a file called ._POTCAR present.\nThis useless file is created by this horrible Mac Finder. Probably this happened when I mounted my partition on our fileserver on my macbook at some point …\nAnyway: the pymatgen input scripts where trying to read from ._POTCAR instead of POTCAR.\nI removed all ._* files and now everything runs without trouble (without you latest change as well).\n\nSorry to have waisted your time!\nMany thanks for your efforts!\n\nCheers,\nMartijn\n\n> On 07 Jun 2017, at 00:34, Shyue Ping Ong <notifications@github.com> wrote:\n> \n> 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?\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub <https://github.com/materialsproject/pymatgen/issues/686#issuecomment-306636633>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGPizRT0wOcg93cZdlumMYOrgKEA34t7ks5sBdPlgaJpZM4Nx60D>.\n> \n\n"
] | 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 = Vasprun("./vasprun.xml")
print(v.final_energy)
```
## Error message
/fs/home/mmars/matgen/local/lib/python2.7/site-packages/pymatgen/io/vasp/outputs.py in __init__(self, filename, ionic_step_skip, ionic_step_offset, parse_dos, parse_eigen, parse_projected_eigen, parse_potcar_file, occu_tol, exception_on_bad_xml)
381
382 if parse_potcar_file:
--> 383 self.update_potcar_spec(parse_potcar_file)
384
385 if not self.converged:
/fs/home/mmars/matgen/local/lib/python2.7/site-packages/pymatgen/io/vasp/outputs.py in update_potcar_spec(self, path)
827 potcar = get_potcar_in_path(path)
828 elif isinstance(path, bool) and path:
--> 829 potcar = get_potcar_in_path(os.path.split(self.filename)[0])
830 else:
831 potcar = None
/fs/home/mmars/matgen/local/lib/python2.7/site-packages/pymatgen/io/vasp/outputs.py in get_potcar_in_path(p)
811 for fn in os.listdir(os.path.abspath(p)):
812 if 'POTCAR' in fn:
--> 813 pc = Potcar.from_file(os.path.join(p, fn))
814 if {d.header for d in pc} == \
815 {sym for sym in self.potcar_symbols}:
/fs/home/mmars/matgen/local/lib/python2.7/site-packages/pymatgen/io/vasp/inputs.pyc in from_file(filename)
1711 def from_file(filename):
1712 with zopen(filename, "rt") as reader:
-> 1713 fdata = reader.read()
1714 potcar = Potcar()
1715 potcar_strings = re.compile(r"\n?(\s*.*?End of Dataset)",
/fs/home/mmars/matgen/lib/python2.7/codecs.pyc in decode(self, input, final)
312 # decode input (taking the buffer into account)
313 data = self.buffer + input
--> 314 (result, consumed) = self._buffer_decode(data, self.errors, final)
315 # keep undecoded input until the next call
316 self.buffer = data[consumed:]
UnicodeDecodeError: 'utf8' codec can't decode byte 0x97 in position 37: invalid start byte
|
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MDU6SXNzdWUyMzQxNjI5MjY=
| 687
|
Inconsistent behaviour in Molecule substitution causing Error
|
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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\npositions = [[0.0, 1.396, 0.0], [1.209, 0.698, 0.0], [1.209, -0.698, 0.0], \r\n\t\t\t [0.0, -1.396, 0.0], [-1.209, -0.698, 0.0], [-1.209, 0.698, 0.0], \r\n\t\t\t [0.0, 2.479, 0.0], [2.147, 1.24, 0.0], [2.147, -1.24, 0.0], \r\n\t\t\t [0.0, -2.479, 0.0], [-2.147, -1.24, 0.0], [-2.147, 1.24, 0.0]]\r\n\r\nbenzene = Molecule(species, positions)\r\nbromo = FunctionalGroups['fluoro']\r\nbromo.replace_species({'F': 'Br'})\r\nbenzene.substitute(11, bromo)\r\nbenzene.substitute(10, 'amine')\r\n\r\n# > TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'\r\n```\r\n\r\nFurthermore, this seems to occur even if bromine is introduced without using the substitute function:\r\n\r\n```python\r\nfrom pymatgen import Composition\r\nfrom pymatgen.core.structure import Molecule\r\n\r\nspecies = ['C', 'C', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H']\r\npositions = [[0.0, 1.396, 0.0], [1.209, 0.698, 0.0], [1.209, -0.698, 0.0], \r\n\t\t\t [0.0, -1.396, 0.0], [-1.209, -0.698, 0.0], [-1.209, 0.698, 0.0], \r\n\t\t\t [0.0, 2.479, 0.0], [2.147, 1.24, 0.0], [2.147, -1.24, 0.0], \r\n\t\t\t [0.0, -2.479, 0.0], [-2.147, -1.24, 0.0], [-2.147, 1.24, 0.0]]\r\nbenzene = Molecule(species, positions)\r\nbenzene[11]._species = Composition('Br')\r\nbenzene.substitute(10, 'amine')\r\n\r\n# > TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'\r\n```\r\n",
"I just pushed a fix. The main reason is that the C-Br bond length is not defined within the internal bond length database, causing a None to be returned. I have fixed this by defaulting to the sum of atomic radii as the bond length.",
"Thanks for pushing the fix so quickly."
] | 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
species = ['C', 'C', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H']
positions = [[0.0, 1.396, 0.0], [1.209, 0.698, 0.0], [1.209, -0.698, 0.0],
[0.0, -1.396, 0.0], [-1.209, -0.698, 0.0], [-1.209, 0.698, 0.0],
[0.0, 2.479, 0.0], [2.147, 1.24, 0.0], [2.147, -1.24, 0.0],
[0.0, -2.479, 0.0], [-2.147, -1.24, 0.0], [-2.147, 1.24, 0.0]]
benzene = Molecule(species, positions)
fluoro = FunctionalGroups['fluoro']
benzene.substitute(10, fluoro)
benzene.substitute(11, fluoro)
print(fluoro[1])
# > [0.0, 0.0, 1.11] F
# substitution works without error
# fluoro group unchaged
benzene = Molecule(species, positions)
fluoro.replace_species({'F': 'Br'})
benzene.substitute(11, fluoro)
benzene.substitute(10, fluoro)
# > TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'
print(fluoro[1])
# > [-2.1700905 1.25334227 0. ] Br
# atomic position seems to have changed
# error still occurs if you use a deep copy of the functional group
```
## Error message
```
TypeError Traceback (most recent call last)
<ipython-input-19-c69c63aca90a> in <module>()
----> 1 benzene.substitute(10, fluoro)
/home/alex/dev/pymatgen/pymatgen/core/structure.pyc in substitute(self, index, func_grp, bond_order)
3132 if inn != self[index] and \
3133 dist2 < 1.2 * get_bond_length(nn.specie,
-> 3134 inn.specie):
3135 all_non_terminal_nn.append((nn, dist))
3136 break
TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'
```
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| 234,327,195
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MDU6SXNzdWUyMzQzMjcxOTU=
| 688
|
missing electronegativities and default behavior for missing electronegativities
|
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[] | null |
[
"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 electronegativities, it is very bad for a code to expect a float and then get a None.",
"@shyuep I don't understand - it looks like you disagree with returning None, but the commit now seems to return None. I am satisfied in theory but perplexed at the decision.\r\n\r\nIf you don't agree with returning None, how about throwing an error - perhaps by creating a MissingDataError or using ValueError. e.g., throwing a negative number into math.log() throws a ValueError",
"@computron The answer is simple. BHFL changed his mind. :-)\r\nAnyway, since the only three elements from Z=1-103 that do not have electroneg are He, Ne and Ar, we can live with it for now. There might be sorting issues though. If anything, I think we should assign a *high* X to He, Ne and Ar. Probably float(\"inf\") or something like 4.0, which is more electroneg than even F.",
"Anyway, I just set it to infinite in the latest commit."
] | 2017-06-07T20:08:41
| 2017-06-07T21:52:25
|
2017-06-07T21:17:28Z
|
MEMBER
|
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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: master
## Summary
* pymatgen is missing electronegativity data for the following elements:
-He
-Ne
-Ar
-Pm
-Eu
-Tb
-Yb
-Rn
-Lr
* First, the default behavior of returning zero for missing electronegativities can cause downstream problems. For example, we wrote a straightforward code to get the average electronegativity of elements in a composition for use in data mining. If the composition includes an element like "Eu", we get back an answer that is completely wrong for average electronegativity (due to Eu being assigned an electronegativity of zero) without any indication that something improper happened. I suggest throwing an error if the electronegativity can't be found. At the very least, to throw a clear warning.
* Second, some of these elements do have Pauling electronegativity reported:
https://en.wikipedia.org/wiki/Electronegativity
Eu=1.2
Tb=1.1
Yb=1.1
Lr=1.3
The above electronegativities might not be 100% consistent with your version of Pauling electronegativity table for elements common to both Wikipedia and pymatgen but at least should be in the right ballpark, e.g., maybe off by 0.1.
I can provide more information, examples, etc. if needed
|
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| 234,340,261
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MDExOlB1bGxSZXF1ZXN0MTI0NTE2Mzc3
| 689
|
More boltztrap fixes
|
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[] | 2017-06-07T20:57:48
| 2017-06-07T21:17:58
|
2017-06-07T21:17:58Z
|
NONE
|
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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 inverted. Why boltztrap spits this out, I don't know.
|
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MDExOlB1bGxSZXF1ZXN0MTI0Njk0Nzg0
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|
Bug fix for Magmom class + tests for same
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[] | 2017-06-08T16:40:12
| 2017-06-08T18:14:53
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2017-06-08T18:14:53Z
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MEMBER
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## Summary
Fixes equality operator
|
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MDExOlB1bGxSZXF1ZXN0MTI0NzczNzc3
| 691
|
add dielectric function parser for vasp5.4.4
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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 dataset of VASP5.4.4 while keeping the functionality of old read_freq_dielectric.
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MDExOlB1bGxSZXF1ZXN0MTI0OTU3Mjgy
| 692
|
Added CIF Implicit Hydrogen Parsing
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[] | 2017-06-09T21:55:53
| 2017-06-10T13:47:38
|
2017-06-10T13:47:38Z
|
CONTRIBUTOR
|
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1) Added CIF Implicit Hydrogen Parsing
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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MDU6SXNzdWUyMzUwODE0NDk=
| 693
|
CIF to POSCAR
|
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[] | null |
[
"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 the thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/693#event-1118620133>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/ATsfHJ4LC4JfhgviSycnLVwL9jhu3wvtks5sDD7rgaJpZM4N2dsm>\n> .\n>\n"
] | 2017-06-11T18:00:35
| 2017-06-11T20:53:40
|
2017-06-11T19:24:25Z
|
NONE
|
{
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|
Hi,
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)
The following is the script I used.
import json
import re
from fnmatch import fnmatch
from pymatgen.io.cif import CifParser, CifWriter
output = open("POSCAR", "w")
def read_structure(filename, primitive = True, sort = False):
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.cif*"):
parser = CifParser(filename)
s = parser.get_structures(primitive=primitive)[0]
print s
output.write(str(s))
st = read_structure('N2O3.cif')
Thank you in advance.
<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 here, you are on your own.>
## Summary
* <Short 1-2 bullet points stating the problem.>
## Example code
```python
<Example code generating error>
```
## Error message
```
<Error message>
```
## Suggested solution (if any)
* <If you have a suggestion on how to solve the issue, you may write it
here.>
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
```
|
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MDExOlB1bGxSZXF1ZXN0MTI1MDQyNTc4
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|
Fix ordering of ATOMIC_SPECIES and ATOMIC_POSITIONS
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[] | 2017-06-11T22:10:20
| 2017-06-11T22:39:48
|
2017-06-11T22:39:48Z
|
CONTRIBUTOR
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See http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idm140629872670512
## Summary
PWscf gives an error if the namelists are out of order. ATOMIC_SPECIES should come before ATOMIC_POSITIONS.
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MDExOlB1bGxSZXF1ZXN0MTI1MDQ0MDQx
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Fix test for PWInput
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[] | 2017-06-11T23:00:39
| 2017-06-11T23:01:04
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2017-06-11T23:01:04Z
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CONTRIBUTOR
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| 235,152,777
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MDExOlB1bGxSZXF1ZXN0MTI1MDc5NDQ1
| 696
|
Parser to read lammps style input files
|
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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 moved to standard location, all related tests should pass.",
"Thanks."
] | 2017-06-12T08:04:56
| 2017-06-12T22:18:23
|
2017-06-12T22:18:17Z
|
CONTRIBUTOR
|
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## Summary
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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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 called pymatgen.ext.wmm and put your new method in there? At some point, I will move the matproj interface in there too. In future, we can build other interfaces to other web databases and REST APIs.",
"Yep, I agree and think that's a good plan. Will update later this week.",
"Got one of my branches crossed here, going to close and reopen."
] | 2017-06-13T00:26:33
| 2017-06-22T16:40:44
|
2017-06-22T16:40:43Z
|
CONTRIBUTOR
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## Summary
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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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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<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
OS Version: CentOS Linux release 7.3.1611 (Core)
pymatgen version: pymatgen-2017.6.8-py2.7
## Summary
The plotter.py code contains an extra backslash character that results in an error when plotting band structure with matplotlib
[error.txt](https://github.com/materialsproject/pymatgen/files/1073309/error.txt)
. I have included the output of the error in an attached file.
## Example code
The included file shows the text generated when attempting to plot a band structure, namely there is a statement "\\mathrm{Wave\ Vector}" in the plotting module which has an extra "\" that leads to an error in interpreting the latex in the matplotlib routines.
```python
```
## Error message
```
<Error message>
```
## Suggested solution (if any)
The original code in plotter.py reads
# Main X and Y Labels
plt.xlabel(r'$\\mathrm{Wave\ Vector}$', fontsize=30)
ylabel = r'$\\mathrm{E\ -\ E_f\ (eV)}$' if zero_to_efermi \
else r'$\\mathrm{Energy\ (eV)}$'
plt.ylabel(ylabel, fontsize=30)
Changing the code (I have done it locally) to remove the extra backslash allows plotting without any latex errors.
# Main X and Y Labels
plt.xlabel(r'$\mathrm{Wave\ Vector}$', fontsize=30)
ylabel = r'$\mathrm{E\ -\ E_f\ (eV)}$' if zero_to_efermi \
else r'$\mathrm{Energy\ (eV)}$'
plt.ylabel(ylabel, fontsize=30)
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
```
|
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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':[9,10,11,12,13,14,15,16]},{'N':[9,10,11,12,13,14,15,16]},ylim=(-0.5,2))\r\n\r\n/usr/lib64/python2.7/site-packages/pymatgen/electronic_structure/plotter.py in get_projected_plots_dots_patom_pmorb(self, dictio, dictpa, sum_atoms, sum_morbs, zero_to_efermi, ylim, vbm_cbm_marker, selected_branches, w_h_size, num_column)\r\n 1318 f_3 = 9 f_2 = 10 f_1 = 11 f0 = 12 f1 = 13 f2 = 14 f3 = 15\r\n 1319 \"\"\"\r\n-> 1320 dictio, sum_morbs = self._Orbitals_SumOrbitals(dictio, sum_morbs)\r\n 1321 dictpa, sum_atoms, number_figs = self._number_of_subfigures(dictio, dictpa, sum_atoms, sum_morbs)\r\n 1322 print('Number of subfigures: %s' % str(number_figs))\r\n\r\n/usr/lib64/python2.7/site-packages/pymatgen/electronic_structure/plotter.py in _Orbitals_SumOrbitals(self, dictio, sum_morbs)\r\n 1495 if len(dictio[elt]) == 1:\r\n 1496 if len(dictio[elt][0]) > 1:\r\n-> 1497 if elt in sum_morbs.keys():\r\n 1498 raise ValueError(\"You cannot sum projection over one individual orbital '%s' of '%s'.\" %\r\n 1499 (dictio[elt][0], elt))\r\n\r\nAttributeError: 'NoneType' object has no attribute 'keys'\r\n\r\n\r\n\r\n\r\nOn the other hand, if I specify more than one orbital, it runs as advertised:\r\n\r\n plot = plotter.get_projected_plots_dots_patom_pmorb({'N':['px','py','pz']},{'N':range(9,17)},{'N':range(9,17)},ylim=(-0.\r\n ...: 5,2))\r\nYou do not want to sum projection over orbitals.\r\nNumber of subfigures: 3\r\n{u'name': u'F-Q', u'start_index': 0, u'end_index': 19}\r\n{u'name': u'Q-Z', u'start_index': 20, u'end_index': 39}\r\n{u'name': u'Z-\\\\Gamma', u'start_index': 40, u'end_index': 59}\r\n{u'name': u'\\\\Gamma-F', u'start_index': 60, u'end_index': 79}\r\ndictio_d: {'N': ['px', 'py', 'pz']}\r\ndictpa_d: {'N': [u'all']}\r\n",
"I am sorry, but I will refer you to @computron and @hautierg to solve this. The code in question (that _Orbital_SumOrbitals) method contains many nested isinstance tests of whether something is a valid list or dict, which should almost never be done in a python code. Also, the method has no unittest, so I cannot debug any changes I make.",
"I don't have any experience with plotters other than BSDosPlotter (that's the only one I coded and worked with), so I'd leave it to @hautierg ",
"I think @anhhv coded that function",
"@paulfons I updated the \"get_projected_plots_dots_patom_pmorb\" method. Please wait until the administrators accept my changes and you can clone the newest pymatgen and retry again. If you still get some problems, please tell me.",
"I have accepted the pull request.",
"> @paulfons I updated the \"get_projected_plots_dots_patom_pmorb\" method. Please wait until the administrators accept my changes and you can clone the newest pymatgen and retry again. If you still get some problems, please tell me.\r\n\r\nHi anhhv, are you sure we can select only one orbital now? I stuck at `if elt in sum_morbs:` because by default sum_morbs is None and is not iterable.\r\n\r\npymatgen 2023.05.10 version\r\n\r\nThank you",
"@m3lab-zzl Can you share your script? I think you should not get this error because this if condition is always constrained by condition \"sum_morbs is not None\"",
"> @m3lab-zzl Can you share your script? I think you should not get this error because this if condition is always constrained by condition \"sum_morbs is not None\"\r\n\r\nSure, script:\r\n\r\n```py\r\nimport json\r\nfrom pymatgen.electronic_structure.plotter import BSPlotterProjected\r\nfrom pymatgen.electronic_structure.bandstructure import BandStructureSymmLine\r\n\r\nd = json.load(open(\"band_data.json\", \"r\"))\r\nbs = BandStructureSymmLine.from_dict(d)\r\nprint(bs)\r\n\r\nbsp = BSPlotterProjected(bs=bs)\r\ndict_elem_orbit = {\"Mo\": [\"px\"]}\r\ndict_elem_index = {\"Mo\": [1]}\r\n\r\nplt = bsp.get_projected_plots_dots_patom_pmorb(\r\n dictio=dict_elem_orbit, \r\n dictpa=dict_elem_index,\r\n sum_atoms=None, \r\n sum_morbs=None, \r\n zero_to_efermi=False, \r\n ylim=None,\r\n vbm_cbm_marker=False, \r\n selected_branches=None, \r\n w_h_size=(12, 8), \r\n num_column=None, \r\n)\r\n\r\nplt.savefig('band.png')\r\n```\r\n[band_data.zip](https://github.com/materialsproject/pymatgen/files/11997529/band_data.zip)\r\n\r\nExtract band_data.zip as band_data.json, and run it, you will probably get error message:\r\n\r\n```txt\r\n if elt in sum_morbs:\r\nTypeError: argument of type 'NoneType' is not iterable\r\n```",
"Hi, @anhhv \r\n\r\nIn debug mode, I found the if condition (in plotter.py 1809 line, 2023.05.10 version) may be the reason:\r\n\r\n```py\r\nif len(dictio[elt][0]) > 1 # length of 'px' str is 2 \r\n```\r\n\r\nIt may be better to determine the type before considering its length:\r\n\r\n```py\r\nif not isinstance(dictio[elt][0], str) and len(dictio[elt][0]) > 1:\r\n```",
"Hi, @anhhv\r\n\r\nIt has been a week, what do you think about the issue? Should we create a PR? ",
"@anhhv Two more weeks...",
"Hi @m3lab-zzl \r\n\r\nSorry that I'm super busy and currently not working in relevant Materials Project. Your can modify the code like this\r\n\r\n if len(dictio[elt]) == 1:\r\n if len(dictio[elt][0]) > 1:\r\n if sum_morbs is None:\r\n pass\r\n else:\r\n if elt in sum_morbs.keys():\r\n raise ValueError(\r\n \"You cannot sum projection over one individual orbital '%s' of '%s'.\" %\r\n (dictio[elt][0], elt))\r\n\r\nIf you want to contribute or open a PR for Pymatgen, don't hesitate to do it. It would be nice if you also prepare a test-suite for this part as well.\r\n\r\nBest regards,\r\nViet-Anh Ha",
"> Hi @m3lab-zzl \n> \n> \n> \n> Sorry that I'm super busy and currently not working in relevant Materials Project. Your can modify the code like this\n> \n> \n> \n> if len(dictio[elt]) == 1:\n> \n> if len(dictio[elt][0]) > 1:\n> \n> if sum_morbs is None:\n> \n> pass\n> \n> else:\n> \n> if elt in sum_morbs.keys():\n> \n> raise ValueError(\n> \n> \"You cannot sum projection over one individual orbital '%s' of '%s'.\" %\n> \n> (dictio[elt][0], elt))\n> \n> \n> \n> If you want to contribute or open a PR for Pymatgen, don't hesitate to do it. It would be nice if you also prepare a test-suite for this part as well.\n> \n> \n> \n> Best regards,\n> \n> Viet-Anh Ha\n\nI prefer not to open a new PR because I am not familiar with the test-suite"
] | 2017-06-14T02:51:32
| 2023-08-16T07:45:24
|
2017-06-15T18:37:28Z
|
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: pymatgen-2017.6.8-py2.7
* Python version: 2.7
* OS version: CentOS Linux release 7.3.1611 (Core)
## Summary
plotter.get_projected_plots_dots_patom_pmorb should accept a single orbital as a target instead it generates an error. This used to work previously.
## Example code
plot = plotter.get_projected_plots_dots_patom_pmorb({'N':['px']},{'N':range(9,17)},{'N':range(9,17)})
## Error message
```
<Error message>
You do not want to sum projection over orbitals.
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-29-955a7dd9ef4d> in <module>()
----> 1 plot = plotter.get_projected_plots_dots_patom_pmorb({'N':['px']},{'N':range(9,17)},{'N':range(9,17)})
/usr/lib64/python2.7/site-packages/pymatgen/electronic_structure/plotter.py in get_projected_plots_dots_patom_pmorb(self, dictio, dictpa, sum_atoms, sum_morbs, zero_to_efermi, ylim, vbm_cbm_marker, selected_branches, w_h_size, num_column)
1318 f_3 = 9 f_2 = 10 f_1 = 11 f0 = 12 f1 = 13 f2 = 14 f3 = 15
1319 """
-> 1320 dictio, sum_morbs = self._Orbitals_SumOrbitals(dictio, sum_morbs)
1321 dictpa, sum_atoms, number_figs = self._number_of_subfigures(dictio, dictpa, sum_atoms, sum_morbs)
1322 print('Number of subfigures: %s' % str(number_figs))
/usr/lib64/python2.7/site-packages/pymatgen/electronic_structure/plotter.py in _Orbitals_SumOrbitals(self, dictio, sum_morbs)
1495 if len(dictio[elt]) == 1:
1496 if len(dictio[elt][0]) > 1:
-> 1497 if elt in sum_morbs.keys():
1498 raise ValueError("You cannot sum projection over one individual orbital '%s' of '%s'." %
1499 (dictio[elt][0], elt))
AttributeError: 'NoneType' object has no attribute 'keys'
```
## Suggested solution (if any)
* <If you have a suggestion on how to solve the issue, you may write it
here.>
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
```
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| 235,942,214
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MDExOlB1bGxSZXF1ZXN0MTI1NjQyNTUz
| 700
|
bug fixing for get_projected_plots_dots_patom_pmorb
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[] | 2017-06-14T16:45:45
| 2017-06-14T17:03:37
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2017-06-14T17:03:36Z
|
CONTRIBUTOR
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Dear administrators,
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 very much.
Best regards,
Anh HA.
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