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MDExOlB1bGxSZXF1ZXN0MTUyODM3Mjk2
| 901
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LammpsData is now powered by pandas.DataFrame
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[
"This PR contains too many unrelated commits, including those from previous PRs. Pls merge your fork with origin and resubmit a NEW PR."
] | 2017-11-15T17:25:55
| 2017-11-15T19:24:36
|
2017-11-15T19:24:36Z
|
CONTRIBUTOR
|
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## Summary
LammpsData is now powered by pandas.DataFrame.
* `get_string` method can set Nos. of significant digits for distance (coordinates), velocities and charges separately.
* Two more attributes added to `ForceField`. They can serve as the input args for the new `LammpsData` directly.
* The old `LammpsData.from_structure` is partly back as `structure_2_lmpdata`. Closes #900
* Fix checking duplicated force field labels.
## Additional dependencies introduced (if any)
* pandas 0.21.0
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* A method for `LammpsData` that can break it down to `ForceField` and a series of `Topology`. Certain restrictions apply. For instance, no intermolecular bondings, force field parameters only based on atom types with no duplications.
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MDExOlB1bGxSZXF1ZXN0MTUyODU4MjUx
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|
add timeout option to BoltztrapRunner
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[
"This PR contains too many unrelated commits because you did not sync your fork with the origin. Pls do so and resubmit a new PR."
] | 2017-11-15T19:02:36
| 2017-11-15T19:23:37
|
2017-11-15T19:23:37Z
|
CONTRIBUTOR
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add timeout option to BoltztrapRunner (default 7200 seconds) to avoid infinite loop and wasting CPU time.
|
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MDExOlB1bGxSZXF1ZXN0MTUyODY5ODk3
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LammpsData powered by pd.DataFrame
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[] | 2017-11-15T19:55:45
| 2017-11-15T19:56:38
|
2017-11-15T19:56:38Z
|
CONTRIBUTOR
|
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## Summary
LammpsData is now powered by pandas.DataFrame.
* `get_string` method can set Nos. of significant digits for distance (coordinates), velocities and charges separately.
* Two more attributes added to `ForceField`. They can serve as the input args for the new `LammpsData` directly.
* The old `LammpsData.from_structure` is partly back as `structure_2_lmpdata`. Closes #900
* Fix checking duplicated force field labels.
## Additional dependencies introduced (if any)
* pandas 0.21.0
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* A method for `LammpsData` that can break it down to `ForceField` and a series of `Topology`. Certain restrictions apply. For instance, no intermolecular bondings, force field parameters only based on atom types with no duplications.
|
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MDExOlB1bGxSZXF1ZXN0MTUyODczNDkx
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|
add timeout for BoltztrapRunner default to 7200 seconds
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[] | 2017-11-15T20:12:28
| 2017-11-15T20:20:06
|
2017-11-15T20:20:06Z
|
CONTRIBUTOR
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to avoid wasting CPU hours when finding Fermi level is not converging (specially at high concentrations), I introduced a timeout option defaulting to 2 hours.
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MDExOlB1bGxSZXF1ZXN0MTUyOTE3ODcy
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Redefine DiscretizeOccupanciesTransformations
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[] | null |
[] | 2017-11-15T23:59:29
| 2017-11-16T00:24:58
|
2017-11-16T00:24:58Z
|
CONTRIBUTOR
|
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## Summary
The current version of DiscretizeOccupanciesTransformations fails in some cases, because a total occupancy other than 1.00 is reached per lattice site. Moreover, the definition of the tolerance requires that different values are used in different cases to get equally good discretizations for different structures.
This new version uses a completely different approach for discretization, which should work well for the vast majority of structures.
* all denominators from 2 to max_denominator are tried until the difference between discretized and original occupancy is smaller than the tolerance, which is now an absolute value and 0.05 by default
* in each iteration, all possible nominators which result in a total occupancy of 1.00 per site are tried
* the combination of nominators with the smallest absolute difference between discretized and original occupancies per species is selected
* if there are two or more equally good discretizations, one of them will be randomly chosen if rnd=True
* occupancies of zero (i.e. removal of species with very small occupancies) are enabled if zerocc = True
* errors are only produced if no discretization can be found for a given max_denominator with difference between discretized and original occupancy is smaller than the tolerance
See comments in the code/docstring and testfile for further explanations.
## Additional dependencies introduced (all part of the standard python packages in py2.3 or higher)
* numpy
* itertools
* random
## TODO
Structures with empty lattice sites, i.e. vacancies, are not supported. The discretization method will force an occupation of 1.00 per lattice site in all cases. Input files should therefore contain the vacancies as a dummy species.
Automatic addition of these dummy species in the input files would be a plus for future versions.
|
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| 275,001,481
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MDExOlB1bGxSZXF1ZXN0MTUzMzk3NzUw
| 906
|
LammpsData.disassemble
|
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[] | 2017-11-17T21:27:46
| 2017-11-17T23:26:21
|
2017-11-17T23:26:21Z
|
CONTRIBUTOR
|
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## Summary
Added a method to break down `LammpsData` to `ForceField` and a series of `Topology`.
## Additional dependencies introduced (if any)
No
## TODO (if any)
No
|
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MDU6SXNzdWUyNzUwMTUwNTc=
| 907
|
/lib64/libc.so.6: version `GLIBC_2.14' not found
|
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[
"HOw are you installing pymatgen? Conda or pip?",
"Standard conda instructions. I've installed on other machines without\nissue. I'm just not sure where to go from here.\n\nOn Fri, Nov 17, 2017, 5:14 PM Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> HOw are you installing pymatgen? Conda or pip?\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/907#issuecomment-345391138>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AIRbGIqHLSOp4xO8iWVCTb9PraMEQNq_ks5s3hNqgaJpZM4QitDH>\n> .\n>\n",
"Try pip install pymatgen.",
"Well, that seemed to fix that issue but introduced another. The full traceback:\r\n\r\n```\r\nTraceback (most recent call last):\r\n File \"<stdin>\", line 1, in <module>\r\n File \"/home/arosen/software/anaconda2/lib/python2.7/site-packages/pymatgen/__init__.py\", line 54, in <module>\r\n from pymatgen.core import *\r\n File \"/home/arosen/software/anaconda2/lib/python2.7/site-packages/pymatgen/core/__init__.py\", line 9, in <module>\r\n from .structure import Structure, IStructure, Molecule, IMolecule\r\n File \"/home/arosen/software/anaconda2/lib/python2.7/site-packages/pymatgen/core/structure.py\", line 30, in <module>\r\n from pymatgen.core.lattice import Lattice\r\n File \"/home/arosen/software/anaconda2/lib/python2.7/site-packages/pymatgen/core/lattice.py\", line 18, in <module>\r\n from pymatgen.util.coord import pbc_shortest_vectors\r\n File \"/home/arosen/software/anaconda2/lib/python2.7/site-packages/pymatgen/util/coord.py\", line 11, in <module>\r\n from . import coord_cython as cuc\r\nImportError: /home/arosen/software/anaconda2/lib/python2.7/site-packages/pymatgen/util/coord_cython.so: undefined symbol: _intel_fast_memcpy\r\n>>>\r\n```",
"I was able to fix it. Here is what I did:\r\n1) Uninstalled Anaconda2\r\n2) Installed Anaconda3\r\n3) pip installed Pymatgen\r\n\r\nI don't know if it was specifically switching to Python3 that fixed it or if it was uninstall Anaconda and starting fresh.",
"No idea. In any case, I recommend you use Py3 going forward. It has definite speed (and coding) advantages.",
"Me either, but at least it's fixed. I'll definitely stick with Py3 going forward. It's time."
] | 2017-11-17T22:26:55
| 2017-11-18T04:31:59
|
2017-11-18T04:26:56Z
|
MEMBER
|
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|
I'm running into the following issue. Any ideas what I need to do to resolve the issue? I'm using a remote supercomputer so can't do anything to the central OS or anything like that.
## System
* Pymatgen version: 2017.11.6
* Python version: python 2.7.14
* OS version: SUSE Linux Enterprise Server 11
## Summary
Running into gcc issue
## Example code
```python
import pymatgen as pm
```
## Error message
```
ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/arosen/software/anaconda2/lib/python2.7/site-packages/pymatgen/util/coord_cython.so)```
```
|
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MDExOlB1bGxSZXF1ZXN0MTUzNDE2NDYz
| 908
|
Method in PhononBandStructure class to write json to phononwebsite
|
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[] | 2017-11-17T23:27:46
| 2017-12-01T00:30:30
|
2017-12-01T00:30:30Z
|
CONTRIBUTOR
|
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## Summary
* Implemented as_phononwebsite and write_phononwebsite functions to export the phonon dispersion to the phononwebsite: http://henriquemiranda.github.io/phononwebsite/
* Implemented band_reorder to order the eigenvalues and according to the similarity of the eigenvectors using the estimate_band_connection from phonopy by Atsushi Togo:
https://atztogo.github.io/phonopy/
|
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MDExOlB1bGxSZXF1ZXN0MTUzNDQzMDM4
| 909
|
method to symmetrically edit both sides of a slab
|
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[] | 2017-11-18T09:35:36
| 2017-11-20T06:44:57
|
2017-11-18T13:37:05Z
|
CONTRIBUTOR
|
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## Summary
* class method of AdsorbateSiteFinder, adsorb_both_surfaces() now uses symmetry operators to find a position on the other side of the slab for an adsorbate. This more generalized method will allow for adsorption of molecules on both surfaces. The method is also much more simplified compared to the previous version. This is useful for anyone trying to calculate an adsorbed slab without having slab polarity or if one wants to calculate surface energy (where both surfaces must be equivalent).
* class method of Slab, get_symmetric_site() finds a symmetrically equivalent point on the other side of the slab given a point.
|
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| 275,872,228
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MDExOlB1bGxSZXF1ZXN0MTU0MDEwNTU5
| 910
|
Add MPRester methods for surface data and Wulff construction
|
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[] | 2017-11-21T21:52:41
| 2017-11-21T22:13:11
|
2017-11-21T22:13:10Z
|
MEMBER
|
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## Summary
Provides methods to retrieve MP surface data and to construct a Wulff shape given a material ID. Addresses #768.
|
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MDExOlB1bGxSZXF1ZXN0MTU0MzAyMDQw
| 911
|
Minor changes to magnetic structure analyzer + new tests
|
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[] | 2017-11-23T05:39:36
| 2017-11-23T05:51:23
|
2017-11-23T05:51:23Z
|
MEMBER
|
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## Summary
Some minor changes (convenience properties, docstring changes) to the magnetic structure analyzer + a few more tests.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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MDExOlB1bGxSZXF1ZXN0MTU0NDIzNzI2
| 912
|
ReconstructionGenerator()
|
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[] | 2017-11-23T17:13:49
| 2017-11-27T19:12:57
|
2017-11-24T01:10:43Z
|
CONTRIBUTOR
|
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## Summary
A new class has been added to surface.py: ReconstructionGenerator().
* ReconstructionGenerator takes in an initial structure (conventional ucell), a slab and vacuum size and a string for the name of the type of reconstruction the user desires to create and the index of termination (some reconstructions such as for the (111) diamond will only work for a specific termination).
* The user can select from a set of reconstructions each with a unique name available in the reconstructions_archive.json file. This file contains a dictionary with the name being the key and the value being a dictionary containing information pertaining to creating a reconstruction. Anyone is encourage to continue adding on more reconstruction types given that they follow the format specified in the docs in order to ensure compatibility with the ReconstructionGenerator class. A set of unittests has been added.
## TODO (if any)
Still need to find a way to identify surface sites belonging to a atom of a certain basis and element in order for this to work on non-elemental systems (e.g. the rocksalt (halite) (111) 2x2 octopolar and alpha type reconstructions). Also need a better way to handle terminations so the user does not have to randomly pick one.
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MDExOlB1bGxSZXF1ZXN0MTU0NjAyNTcw
| 913
|
Feff input
|
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[] | 2017-11-24T19:56:46
| 2018-02-14T21:53:53
|
2017-11-27T20:47:41Z
|
CONTRIBUTOR
|
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## Summary
Add from_directory method to existed FEFFDictSet for post-processing of FEFF input files. Unittest has been added accordingly.
|
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MDExOlB1bGxSZXF1ZXN0MTU0OTE0NDI0
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Add method to generate FEFF input from directory
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[] | 2017-11-27T20:56:31
| 2018-02-14T21:53:53
|
2017-11-28T05:18:30Z
|
CONTRIBUTOR
|
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## Summary
Add from_directory method to existed FEFFDictSet for post-processing of FEFF input files. Unittest has been added accordingly.
|
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MDExOlB1bGxSZXF1ZXN0MTU1MjQ4ODEz
| 915
|
More reconstructions and fix bug in adsorb_both_sides
|
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[] | 2017-11-29T04:46:29
| 2017-11-29T23:12:28
|
2017-11-29T04:48:09Z
|
CONTRIBUTOR
|
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## Summary
* Added instructions for generating the fcc_100_missing_row_1x2 and fcc_100_missing_row_1x1 slabs.
* Return slabs after adsorbing both sides
|
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MDU6SXNzdWUyNzgyMTYwMjk=
| 916
|
Updating subspacematrix error handling with VASP
|
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[
"Sorry. I posted this on the wrong MaterialsProject project. I'm so used to using Pymatgen."
] | 2017-11-30T18:03:51
| 2017-11-30T18:25:24
|
2017-11-30T18:24:50Z
|
MEMBER
|
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In the custodian.vasp.handlers.py script, there is an error-handling method for the "subspacematrix" (i.e. "WARNING: Sub-Space-Matrix is not hermitian in DAV") error. As it stands right now, the custodian file tries to change LREAL when this error occurs. I have found that in systems I have studied, this error often occurs when PREC is not set to Accurate. I have attached an example set of input files. It runs with PREC = Accurate but has the subspace error when PREC = Normal. It therefore may be desirable to add a PREC switch for this error message. Note that this may be dependent on the particular VASP build.
[INCAR.txt](https://github.com/materialsproject/pymatgen/files/1518937/INCAR.txt)
[KPOINTS.txt](https://github.com/materialsproject/pymatgen/files/1518938/KPOINTS.txt)
[POSCAR.txt](https://github.com/materialsproject/pymatgen/files/1518939/POSCAR.txt)
[POTCAR.txt](https://github.com/materialsproject/pymatgen/files/1518940/POTCAR.txt)
|
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MDExOlB1bGxSZXF1ZXN0MTU1Njg4NDY4
| 917
|
Recover functions of old LammpsData
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[] | 2017-11-30T18:45:51
| 2017-11-30T19:11:23
|
2017-11-30T19:11:22Z
|
CONTRIBUTOR
|
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## Summary
Thank Zhi for the new version of LammpsData.
The new version lost some functions compared to the old one, e.g. converting LammpsData to Structure object. It is better to rewrite those parts according to the new version and add them back.
|
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[] | 2017-11-30T19:15:09
| 2017-12-16T17:54:58
|
2017-12-16T17:54:58Z
|
CONTRIBUTOR
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Thank Zhi for the new version of LammpsData.
The new version lost some functions compared to the old one, e.g. converting LammpsData to Structure Object. It is better to rewrite those parts based on the new version and add them back.
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MDU6SXNzdWUyNzgzMTc5MzI=
| 919
|
Fix FEFF EXAFS input file generation for small system
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[] | 2017-12-01T00:28:02
| 2017-12-01T18:26:18
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2017-12-01T18:26:18Z
|
CONTRIBUTOR
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Fixed EXAFS input file generation for the small system. The EXAFS calculation for the small system should be done in real space. Currently, the EXAFS input file generated for small system includes reciprocal tag
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MDExOlB1bGxSZXF1ZXN0MTU1NzU4NTY1
| 920
|
added more unittests for reconstruction
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[
"I don't think having is_reconstructed having dual meanings of boolean and string is a good idea. Fundamentally, \"is_reconstructed\" implies just a boolean type variable. No one would think it can contain a string. I think it is better to have a property called \"reconstruction\", which is a string. If it is None, it means it is not reconstructed.",
"Understood, I will make this change in my next pull request instead."
] | 2017-12-01T00:56:53
| 2017-12-20T22:50:00
|
2017-12-04T00:06:52Z
|
CONTRIBUTOR
|
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## Summary
* Added option to include reconstructions when using generate_all_slabs
* Slab class has property called is_reconstructed. Can be a bool or a str (i.e. the name of the reconstruction).
* Made sure reconstructions that inherit from another base_reconstruction will properly be built.
* Added unittest for generate_all_slabs to make sure it includes existing reconstructions.
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MDU6SXNzdWUyNzgzMjg2NjA=
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Nanoscale stabilization analyzer
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[
"Ok. Go ahead."
] | 2017-12-01T01:30:38
| 2018-01-11T04:43:09
|
2018-01-11T04:43:09Z
|
CONTRIBUTOR
|
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Analyze the stability of nanoparticles of different polymorphs with respect to size. The Wulff shape will be the model for the nanoparticle. Stability will be determined by an energetic competition between the weighted surface energy (surface energy of the Wulff shape) and the bulk energy. A future release will include a 2D phase diagram (e.g. wrt size vs chempot for adsorbed or nonstoichiometric surfaces). Based on the work done here:
Kang, S., Mo, Y., Ong, S. P., & Ceder, G. (2014). Nanoscale stabilization of sodium oxides: Implications for Na-O2 batteries. Nano Letters, 14(2), 1016–1020. https://doi.org/10.1021/nl404557w
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Small system EXAFS input set generation fix
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[] | 2017-12-01T18:24:26
| 2018-02-14T21:53:51
|
2017-12-01T18:26:18Z
|
CONTRIBUTOR
|
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## Summary
Fixed FEFF EXAFS input set generation for the small system (atoms < 14). For EXAFS calculation, all FEFF calculations will be done in the real space. Resolves #919
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| 278,576,633
|
MDExOlB1bGxSZXF1ZXN0MTU1OTQyODU4
| 923
|
fix voltage sign for anion voltage profile
|
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[
"Pls add a test using a hypothetical compound."
] | 2017-12-01T19:49:22
| 2017-12-01T20:16:34
|
2017-12-01T20:16:34Z
|
CONTRIBUTOR
|
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## Summary
Fixed the sign of calculated voltage of `InsertionVoltagePair` when anion is intercalated.
* Fix the wrong sign of the calculated voltage (revised script, line 431)
* Minor formatting.
|
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| 278,592,044
|
MDExOlB1bGxSZXF1ZXN0MTU1OTU0MTc4
| 924
|
Add structure property for LammpsData
|
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[
"Pls pull the latest changes and submit a clean pull request. This includes commits from previous PRs."
] | 2017-12-01T20:48:57
| 2017-12-01T20:49:49
|
2017-12-01T20:49:49Z
|
CONTRIBUTOR
|
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## Summary
Add a property method for LammpsData object, which returns the pmg Structure object of the corresponding LammpsData.
This will allow us to analyze the LammpsData geometry and make it easy to transform the structures between lammps and other DFT codes (e.g. VASP POSCAR).
|
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| 278,600,532
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MDExOlB1bGxSZXF1ZXN0MTU1OTYwNTU4
| 925
|
Convert LammpsData to pmg Structure
|
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[] | 2017-12-01T21:22:55
| 2017-12-01T21:23:41
|
2017-12-01T21:23:40Z
|
CONTRIBUTOR
|
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## Summary
Add a property method for LammpsData, which returns the pmg Structure object.
It will allow us to analyze the geometry of the LammpsData and make it convenient transform structures between Lammps and other DFT code (e.g. VASP POSCAR).
|
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MDExOlB1bGxSZXF1ZXN0MTU1OTkzODk1
| 926
|
Optical add vasprun
|
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[] | 2017-12-02T02:18:37
| 2017-12-03T05:20:28
|
2017-12-03T05:20:28Z
|
NONE
|
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## Summary
Added a new Vasprun parser to parse opticaltransitions tags printed in vasprun.xml after a BSE calculation. The new parser will output both the oscillator strength in (eV) and the probability of transition (dimensionless)
## Additional dependencies introduced (if any)
None
## TODO (if any)
N/A
|
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Pourbaix rest
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[] | 2017-12-03T17:34:08
| 2017-12-03T21:02:27
|
2017-12-03T21:02:27Z
|
CONTRIBUTOR
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## Pourbaix Rest and Plotter Refactoring
This PR adds functionality to the MP Rester to retrieve entries and perform the necessary preprocessing of both solids and aqueous species to make entries suitable for constructing a pourbaix diagram. The plotter/analyzer have also been modified for easier plotting of stability heatmaps for individual entries, and the example notebook has been completely rewritten based on these changes.
* `MPRester.get_pourbaix_entries` added, returns ion and solid pourbaix entries that can be used directly as arguments to `PourbaixDiagram`.
* `MPRester.get_entries_in_chemsys` was refactored slightly to improve efficiency of `compatible_only=False` setting.
* `PourbaixAnalyzer` includes a method `get_entry_stability` to get the stability of an entry with respect to the most stable decomposition product at a given pH/V condition.
* `PourbaixPlotter` includes a method `plot_entry_stability` to plot heatmaps of individual entries a la the website. Added unittest for `PourbaixPlotter` including new functionality.
* Rewrote example notebook for pourbaix diagram plotting from scratch.
## TODO (if any)
It's very difficult to follow the logic of both the PourbaixDiagram and PourbaixAnalyzer. I think it can be considerably simplified, but unravelling everything and deciding how best to refactor will take some time (for me at least). Also, might be consolidated like recent refactors to `PhaseDiagram`.
Also, as a final note, occasionally materials will appear on these pourbaix diagrams that aren't on the website, particularly hydrides. I'm almost certain this is due to a bug on the web side in preprocessing of solid entries, so we'll be addressing that on that end sometime in the near future.
|
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MDExOlB1bGxSZXF1ZXN0MTU2Mzg3NzI1
| 928
|
Crystal Orbital Hamilton Populations (COHPs)
|
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[] | null |
[
"Thanks! There seems to be some failing tests (you just need to check the Travis-CI one). It is related to the plotter tests, and seems probably like some form of a numerical or dict sorting issue. Can you fix them pls? Thanks.",
"I found the issues with the code and solved them. The AppVeyor test failures are not because of my code.\r\n\r\nThe biggest issues were incompatibilities between python2 and python3 (I forgot to test with python3 - lesson learned). For example, the error with the keys are not because of sorting but because I needed to convert the keys into a list whereas python2 lets me get away without doing that.\r\n\r\nThere were also some numerical issues with the LMTO COHPs, so I needed to make the test a little more detailed. Maybe we (or I) need to add \"assertDictAlmostEqual\" to the PymatgenTest class?\r\n\r\n"
] | 2017-12-05T07:15:37
| 2017-12-06T03:53:33
|
2017-12-06T03:47:13Z
|
NONE
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## Summary
This pull request introduces a new module for Crystal Orbital Hamilton Populations (COHPs). It can also be applied to Crystal Orbital Overlap Populations (COOPs). The objects are roughly modeled after DOS objects in order to be more intuitive for pymatgen users. It also creates modules to read the output files of the two codes that I used to calculate them (Stuttgart LMTO-ASA and LOBSTER).
* **electronic_structure.cohp** introduces a Cohp and a CompleteCohp object, similar to Dos and CompleteDos. The big differences are that the Cohp objects also include the integrated populations, and that CompleteCohp objects can be directly loaded from an output file. Cohp objects can also be used for COOPs via the Boolean attribute cls.are_coops
* **electronic_structure.plotter** got an additional CohpPlotter class, which works similar to a DosPlotter object. The main difference is that COHPs can be positive and negative, so Spin.up and Spin.down are plotted using solid and dashed lines, respectively. Additionally, it is common to plot -COHPs instead of COHPs, so the plotter needs to be fairly flexible. The user can adjust all that with Booleans.
* **io.lobster** contains a Cohpcar and a Icohplist class that read COHPCAR.lobster and ICOHPLIST.lobster files, respectively (and of course COOPCAR.lobster and ICOOPLIST.lobster files).
* **io.lmto** contains the classes LMTOCtrl, which handles the CTRL files for the LMTO code. It currently only contains the tokens for the structure, so it is mostly used to read the structure for a CompleteCohp object. It can also be used to write a new bare-bones CTRL file, but see caveat in the TODO! It also contains a class (LMTOCopl) to read a COPL file, which contains all the COHP data.
* **core.structure** has been updated to recognize LMTO CTRL files and read the structure.
* Of course, I also added unit tests and plenty of test files. Since this is a new module, I may have gone a little overboard though. The tests files be found under test_files/cohp.
## TODO (if any)
* Orbital-resolved COHPs are not supported yet. I will implement those when I have more time.
* Stacked COHP plots are not implemented yet.
* The COOP files in the Stuttgart LMTO-ASA code are written in binary format, so I haven't implented COOPs for LMTO yet.
* This one is lower priority: the CTRL files written with the LMTOCtrl object aren't always interpreted correctly by the LMTO-ASA code, mainly because LMTO isn't particularly tolerant when it comes to the precision of atomic positions. For example, even though the CTRL file contains the correct structure, LMTO may assign the wrong spacegroup. Fixing this requires more knowledge of the LMTO code and its symmetrizers than I currently have, so use that feature with caution. Reading CTRL files works reliably though.
### Additional comment
I think the unit tests I wrote for the CohpPlotter object could be easily applied to other plotter objects. That way, we'd have tests that are a little more solid than the current bare-bones tests.
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| 929
|
Overall charge for structures
|
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[] | 2017-12-05T17:06:50
| 2018-01-03T16:51:30
|
2017-12-05T20:28:16Z
|
NONE
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## Summary
Added the ability for a structure to have an overall charge. This will default to the behavior in SiteCollection when overall charge is not specified: the structure's charge is the sum of the oxidation state of its sites.
- IStructure and Structure contain an overall charge
- The generator functions such as make_supercell/__mul__ properly account for overall charge
- Vasp input sets will modify NELECT in INCAR when an overall charge is specified.
- Vasprun compares nelect against potcars when available and sets charge if they are different.
|
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MDExOlB1bGxSZXF1ZXN0MTU2NjY0Nzgy
| 930
|
Bug fix for DiffusionAnalyzer with NPT runs
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[
"THanks."
] | 2017-12-06T08:09:35
| 2017-12-06T21:47:33
|
2017-12-06T17:55:07Z
|
CONTRIBUTOR
|
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The `DiffusionAnalyzer` `from_structures()` method calculates cartesian displacements using
c_disp = [np.dot(d, m) for d, m in zip(f_disp, l)]
`f_disp` has dimensions `[site, time step, axis]`.
`l` has dimensions `[time step, axis, axis]`
This means the lattice used for calculating the cartesian displacements is selected based on site number, not on time step.
Displacements calculated for NPT simulations therefore contain errors (equivalent to assuming NVT, and then taking a different lattice for each site).
This commit fixes this, by replacing the calculation of `c_disp` with
c_disp = []
for i in f_disp:
c_disp.append([np.dot(d, m) for d, m in zip(i, l[1:])])
The new calculation also addresses an off-by-one error, where the displacement at time step t was calculated using the lattice at time step t-1.
This commit includes a test to check `self.disp` is correct after initialising using `from_structures()`.
|
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MDExOlB1bGxSZXF1ZXN0MTU2ODE3MTY0
| 931
|
do not read_velocities for Poscar input to Structure.from_file
|
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[] | 2017-12-06T19:23:36
| 2017-12-06T19:28:15
|
2017-12-06T19:28:15Z
|
CONTRIBUTOR
|
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## Summary
When trying to load a Structure from a Poscar file format, there is no need to read_velocities. However, if the Poscar file has an incomplete velocities list then the from_file method previously broke. This has caused issues for users within the PyCDT package for point defects in non-metals - which inspired this pull request.
|
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| 279,890,972
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MDExOlB1bGxSZXF1ZXN0MTU2ODI4NDIz
| 932
|
Add MPRester method to get interface reaction kinks
|
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[] | 2017-12-06T20:14:02
| 2017-12-07T15:04:33
|
2017-12-07T15:04:33Z
|
MEMBER
|
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## Summary
Get critical reactions ("kinks" in the mixing ratio where reaction products change) between two reactants. See the `pymatgen.analysis.interface_reactions` module for more info. Useful to generate pseudo-binary phase diagrams of two reactants. Also allows elemental reservoir open to system with _relative_ chemical potential with respect to pure substance. Work done with @yihanxiao92.
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MDExOlB1bGxSZXF1ZXN0MTU2ODY2MTEx
| 933
|
Remove pyhull
|
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[] | 2017-12-06T23:20:29
| 2019-04-04T02:41:33
|
2017-12-07T15:04:08Z
|
CONTRIBUTOR
|
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## Remove pyhull dependency in PourbaixAnalyzer
Replaces pyhull halfspace usage with scipy.spatial.HalfspaceIntersection usage in pourbaix analysis module. Also adds a few more unittests to the plotter and fleshes out the docstring in PourbaixAnalyzer.
Addresses #283.
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MDExOlB1bGxSZXF1ZXN0MTU2ODc1NjA3
| 934
|
Fixed bcc OP normalization issue
|
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[
"This contains many past commits. Pls merge properly with pymatgen origin first and submit a new PR. Thanks."
] | 2017-12-07T00:27:47
| 2017-12-07T01:24:32
|
2017-12-07T01:24:32Z
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MDExOlB1bGxSZXF1ZXN0MTU3MzA3MTY4
| 935
|
Add relax input set using SCAN
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[] | 2017-12-08T18:39:10
| 2017-12-08T19:04:45
|
2017-12-08T19:04:45Z
|
CONTRIBUTOR
|
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## Summary
Relax input set using SCAN and unittests have been added.
* Add `MVLScanRelaxSet`
* Enable van-der-Waals functional rVV10
* unittests
* minor reformatting
|
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| 936
|
Moved OP class
|
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[
"@shyuep, the build errors are not due to my changes. Any chance to merge?"
] | 2017-12-08T19:46:08
| 2017-12-08T21:52:01
|
2017-12-08T21:52:00Z
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CONTRIBUTOR
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| 280,651,304
|
MDExOlB1bGxSZXF1ZXN0MTU3MzU4MjI4
| 937
|
Added non-Zeo++ dependent Voronoi interstitial finder.
|
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[
"There seems to be failing tests which are related to this PR.",
"I will close this pull request and issue a new one once I'm done."
] | 2017-12-08T23:53:49
| 2018-01-03T00:17:27
|
2018-01-03T00:17:27Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MTU3MzYwNjYw
| 938
|
SCAN input set
|
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[
"Erm, what's the difference with the MVLSCANSet?",
"What MVLSCANSet? I don't see it.",
"NVM. found it. That works too!",
"Quick question. I'm not a big fan of the ISYM, EDIFFG, nor NELM parameters. I'm running SCAN for MP using ISYM on, EDIFFG ~ -0.05, and NELEM at default of 100 with decent success. Can i just go ahead and change these parameters or do you want a separate MP input inherited from MPRelaxSet?",
"You can remove ISYM. EDIFFG is necessary, and I am fine with changing it to 0.05. I have no view on NELEM. Go ahead and change those. ",
"ISYM = 0 is default anyway if you don't specify anything. @HanmeiTang \r\n",
"Will do.\n\nOn Dec 8, 2017, 16:34 -0800, Shyue Ping Ong <notifications@github.com>, wrote:\n> ISYM = 0 is default anyway if you don't specify anything. @HanmeiTang\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub, or mute the thread.\n"
] | 2017-12-09T00:18:16
| 2017-12-09T00:49:02
|
2017-12-09T00:24:20Z
|
NONE
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This a simple SCAN input set. All potentials have been benchmarked to work with SCAN. The key here is the default to PBE_52 potcars. I'm not sure if this is the best way to go about this?
|
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| 939
|
Updates to MVLScanSet
|
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[] | 2017-12-09T00:57:29
| 2018-01-03T16:51:42
|
2017-12-12T15:37:37Z
|
NONE
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Updates to MVLScanSet
- compromised on NELM
- ensure LDAU is False
|
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| 940
|
density-density and velocity-velocity dielectric functions in VASP 5.4.4
|
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[
"YEs, these should be stored in the Vasprun object.",
"Proposed solution:\r\n\r\nIn `Vasprun._parse()` first initialise `self.dielectric=None`.\r\n\r\nThe dielectric function parser can then become:\r\n```\r\nelif tag == \"dielectricfunction\":\r\n if (\"comment\" not in elem.attrib) or \\\r\n elem.attrib[\"comment\"] == \"INVERSE MACROSCOPIC DIELECTRIC TENSOR (including local field effects in RPA (Hartree))\":\r\n if not self.dielectric:\r\n self.dielectric = self._parse_diel(elem)\r\n elif not 'current-current' in self.other_dielectric: \r\n self.other_dielectric['current-current'] = self._parse_diel(elem)\r\n else:\r\n raise NotImplementedError('This vasprun.xml has >2 unlabelled dielectric functions')\r\n else:\r\n comment = elem.attrib[\"comment\"]\r\n self.other_dielectric[comment] = self._parse_diel(elem)\r\n```\r\n\r\nNow the first dielectric response function in the `vasprun.xml` is stored as `self.dielectric`. This is the \"density–density\" linear response. The \"current-current\" linear response is stored as `self.other_dielectric['current-current']`.\r\n\r\nThis keeps the old behaviour for vasp versions < 5.4.4 (there is only one dielectric function in `vasprun.xml`, and this is stored in `self.dielectric`).\r\n\r\n`vasprun.xml` does not label the two dielectric response functions, so this solution relies on the order they are written out not changing."
] | 2017-12-12T22:23:49
| 2017-12-16T17:54:43
|
2017-12-16T17:54:43Z
|
CONTRIBUTOR
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VASP 5.4.4 calculates the frequency dependent dielectric response in two ways, using a "density-density" response function, and using a "velocity-velocity" response function (see the comments in `linear_optics.F`. The latter is marked in `OUTCAR` as `current-current (2nd set in vasprun.xml)`, but is not labelled in `vasprun.xml`.
These two dielectric functions can have different imaginary components (in my tests, this appears as omega → 0.)
The present XML parser for `Vasprun` objects overwrites the first set of data with the second.
If both data sets are present in `vasprun.xml`, should these both be stored in the `Vasprun` object?
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| 281,609,440
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MDExOlB1bGxSZXF1ZXN0MTU3OTkyNjg5
| 941
|
Pourbaix binary fix
|
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[] | 2017-12-13T02:59:50
| 2019-04-04T02:41:30
|
2017-12-13T04:26:09Z
|
CONTRIBUTOR
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## Fixes a few issues with binary/ternary pourbaix diagrams and makes plotting a bit more robust.
* Binary/ternary pourbaix diagrams fix a default composition of equivalent parts of each non-OH element.
* Cases where multiple binary solid-ion phases exist are handled more robustly
* Example notebook is updated with a binary example for the Bi-V system.
* Misc cleanup and small cosmetic improvements
|
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MDU6SXNzdWUyODE4MTQwMDI=
| 942
|
Infinite recursion in DummySpecie::__getattr_ when applying interstitial transformation leading to unpredictable behaviour.
|
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[
"Thanks for the detailed bug report. Since `DummySpecie` doesn't have `._el` defined, I can't see why the try:\r\n\r\n```\r\n try:\r\n return getattr(self._el, a)\r\n```\r\n\r\nshould even be there, because it seems like this would never return anything useful for `DummySpecie`. I'll try removing it and see if any tests fail, and if not then submit a PR.\r\n\r\nIn the longer term, I think a conversation about the relationship between Element-Specie-DummySpecie and specie properties vs site properties might be useful. I think there's a historical reason why e.g. Specie doesn't inherit from Element, but overriding getattr is problematic, if only because it causes confusion with new users since it breaks autocomplete (and can lead to other bugs like this).",
"Thanks for the bug report. I just pushed a fix. I think someone simply copied the getattr from Specie to DummySpecie. self._el is valid for Specie. \r\n\r\nThe reason why Element, Specie and DummySpecie are not subclasses is mainly because Element is an Enum, which cannot be extended. Previously, Element is a singleton-like, which also cannot be inherited. It is actually important for efficiency reasons to keep Element as an Enum type.\r\n\r\nSo the approach pymatgen uses is to rely on duck-typing to make Specie and DummySpecie behave like Element where possible, e.g., inheriting things such as atomic numbers, masses, etc. "
] | 2017-12-13T16:33:00
| 2017-12-13T21:49:40
|
2017-12-13T21:42:24Z
|
NONE
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## System
* Pymatgen version: 2017.12.8
* Python version: 2.7.
* OS version: Ubuntu 15.04LTS
## Summary
- Pymatgen returns an error when trying to apply interstitial transformation with some structure. Issue has been tracked down to the DummeSpecie::getattr function which has an undefined behaviour in this context due to it infinitely calling itself and running out of stack space.
## Example code
(see below for cif files)
import pymatgen as pmg
s = pmg.Structure.from_file('Li10Ge(PS6)2_mp-696128_computed.cif')
from pymatgen.transformations.defect_transformations import InterstitialTransformation
transfo = InterstitialTransformation('Li+',[1,1,1])
s.add_oxidation_state_by_element({"Li":1,"Ge":4,"P":5,"S":-2})
trans_list = transfo.apply_transformation(s, return_ranked_list=200) ----> works fine
s2 = pmg.Structure.from_file('LiFeV2O7_prim.cif')
s2.add_oxidation_state_by_element({'Li':1,'Fe':3,'O':-2,'V':5})
trans_list = transfo.apply_transformation(s2, return_ranked_list=200) ---> crash
## Error message
```
_<ipython-input-10-7b1d34264ebe> in <module>()
----> 1 trans_list = transfo.apply_transformation(s2, return_ranked_list=200)
/usr/local/lib/python2.7/dist-packages/pymatgen/transformations/defect_transformations.pyc in apply_transformation(self, structure, return_ranked_list)
282 val = valrad_eval.valences
283 rad = valrad_eval.radii
--> 284 inter = Interstitial(s,val,rad,oxi_state=True)
285
286 scs = inter.make_supercells_with_defects(
/usr/local/lib/python2.7/dist-packages/pymatgen/analysis/defects/point_defects.pyc in __init__(self, structure, valences, radii, site_type, accuracy, symmetry_flag, oxi_state)
639 vor_node_sites, vor_edgecenter_sites, vor_facecenter_sites = \
640 symmetry_reduced_voronoi_nodes(self._structure, self._rad_dict,
--> 641 high_accuracy_flag, symmetry_flag)
642
643 if site_type == 'voronoi_vertex':
/usr/local/lib/python2.7/dist-packages/pymatgen/analysis/defects/point_defects.pyc in symmetry_reduced_voronoi_nodes(structure, rad_dict, high_accuracy_flag, symm_flag)
1463
1464 node_dist_sites = get_dist_sites(vor_node_struct)
-> 1465 edgecenter_dist_sites = get_dist_sites(vor_edgecenter_struct)
1466 facecenter_dist_sites = get_dist_sites(vor_facecenter_struct)
1467
/usr/local/lib/python2.7/dist-packages/pymatgen/analysis/defects/point_defects.pyc in get_dist_sites(vor_struct)
1448 vor_struct.merge_sites(0.1, 'delete')
1449 symmetry_finder = SpgA(vor_struct, symprec=1e-1)
-> 1450 symm_struct = symmetry_finder.get_symmetrized_structure()
1451 equiv_sites_list = symm_struct.equivalent_sites
1452
/usr/local/lib/python2.7/dist-packages/pymatgen/symmetry/analyzer.pyc in get_symmetrized_structure(self)
337 """
338 ds = self.get_symmetry_dataset()
--> 339 sg = SpacegroupOperations(self.get_space_group_symbol(),
340 self.get_space_group_number(),
341 self.get_symmetry_operations())
/usr/local/lib/python2.7/dist-packages/pymatgen/symmetry/analyzer.pyc in get_space_group_symbol(self)
155 (str): Spacegroup symbol for structure.
156 """
--> 157 return self._space_group_data["international"]
158
159 def get_space_group_number(self):
TypeError: 'NoneType' object has no attribute '__getitem__'_
```
## Suggested solution (if any)
The issue is coming from that fact that when reading result from Zeo++, all atoms are of Dummyspecie type 'X0+'. The code then tries to initialize the space group analyser with this structure, and tries to assign the magmom property. It then encounters this line :
` elif site.is_ordered and hasattr(site.specie, 'spin'):`
which calls to the __getattr function of DummySpecie with 'spin' as argument a:
```
def __ getattr __(self, a):
p = object.__getattribute__(self, '_properties')
if a in p:
return p[a]
try:
return getattr(self._el, a)
except:
raise AttributeError(a)
```
Since DummySpecie has no properties, p is an empty dict, we therefore enter the try with "spin" as argument a. The issue then is the _getattr(self._el,a)_ . Since DummySpecie has no '_el' attribute, the self._el calls again __getattr__ and infinite recursion occurs.
In some cases (as the example with the first file) it is not an issue and python recovers correctly (as to how, I have no idea), in others, this cause python to skip the rest of the space group analyser initialisation, which results in its _space_groupe_data not being initialised, leading to the subsequent crash.
Note that due to the unpredictable aspect, it might be that this behaviour is machine dependent.
An obvious fix would be to immediately raise an AttributeError after the 'return p[a]' line, but I don't know what ripple effects it can have on the rest of the code base.
## Files (if any)
Li10Ge(PS6)2_mp-696128_computed.cif :
generated using pymatgen
data_Li10Ge(PS6)2
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 8.78764647
_cell_length_b 8.78764647
_cell_length_c 12.65754627
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural Li10Ge(PS6)2
_chemical_formula_sum 'Li20 Ge2 P4 S24'
_cell_volume 977.450284168
_cell_formula_units_Z 2
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Li Li1 1 0.228698 0.772950 0.294563 1
Li Li2 1 0.771302 0.227050 0.294563 1
Li Li3 1 0.272950 0.271302 0.794563 1
Li Li4 1 0.727050 0.728698 0.794563 1
Li Li5 1 0.228698 0.227050 0.294563 1
Li Li6 1 0.771302 0.772950 0.294563 1
Li Li7 1 0.272950 0.728698 0.794563 1
Li Li8 1 0.727050 0.271302 0.794563 1
Li Li9 1 0.000000 0.500000 0.939730 1
Li Li10 1 0.000000 0.500000 0.439730 1
Li Li11 1 0.500000 0.000000 0.548020 1
Li Li12 1 0.500000 0.000000 0.048020 1
Li Li13 1 0.256318 0.224772 0.036663 1
Li Li14 1 0.743682 0.775228 0.036663 1
Li Li15 1 0.275228 0.756318 0.536663 1
Li Li16 1 0.724772 0.243682 0.536663 1
Li Li17 1 0.275228 0.243682 0.536663 1
Li Li18 1 0.724772 0.756318 0.536663 1
Li Li19 1 0.256318 0.775228 0.036663 1
Li Li20 1 0.743682 0.224772 0.036663 1
Ge Ge21 1 0.500000 0.000000 0.801028 1
Ge Ge22 1 0.500000 0.000000 0.301028 1
P P23 1 0.000000 0.500000 0.686051 1
P P24 1 0.000000 0.500000 0.186051 1
P P25 1 0.000000 0.000000 0.504073 1
P P26 1 0.500000 0.500000 0.004073 1
S S27 1 0.000000 0.194431 0.412071 1
S S28 1 0.000000 0.805569 0.412071 1
S S29 1 0.305569 0.500000 0.912071 1
S S30 1 0.694431 0.500000 0.912071 1
S S31 1 0.500000 0.689848 0.097057 1
S S32 1 0.500000 0.310152 0.097057 1
S S33 1 0.189848 0.000000 0.597057 1
S S34 1 0.810152 0.000000 0.597057 1
S S35 1 0.000000 0.304708 0.094096 1
S S36 1 0.000000 0.695292 0.094096 1
S S37 1 0.195292 0.500000 0.594096 1
S S38 1 0.804708 0.500000 0.594096 1
S S39 1 0.500000 0.790002 0.403242 1
S S40 1 0.500000 0.209998 0.403242 1
S S41 1 0.290002 0.000000 0.903242 1
S S42 1 0.709998 0.000000 0.903242 1
S S43 1 0.000000 0.691950 0.777069 1
S S44 1 0.000000 0.308050 0.777069 1
S S45 1 0.808050 0.500000 0.277069 1
S S46 1 0.191950 0.500000 0.277069 1
S S47 1 0.500000 0.207378 0.698166 1
S S48 1 0.500000 0.792622 0.698166 1
S S49 1 0.707378 0.000000 0.198166 1
S S50 1 0.292622 0.000000 0.198166 1
LiFeV2O7_prim.cif :
generated using pymatgen
data_LiV2FeO7
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 7.87875289
_cell_length_b 7.87875289
_cell_length_c 14.38600000
_cell_angle_alpha 84.40963056
_cell_angle_beta 84.40963056
_cell_angle_gamma 62.61595511
_symmetry_Int_Tables_number 1
_chemical_formula_structural LiV2FeO7
_chemical_formula_sum 'Li6 V12 Fe6 O42'
_cell_volume 787.769007978
_cell_formula_units_Z 6
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Fe Fe1 1 0.444800 0.094600 0.524500 1.0
Fe Fe2 1 0.094600 0.444800 0.024500 1.0
Fe Fe3 1 0.717400 0.116200 0.198100 1.0
Fe Fe4 1 0.116200 0.717400 0.698100 1.0
Fe Fe5 1 0.423400 0.811600 0.854500 1.0
Fe Fe6 1 0.811600 0.423400 0.354500 1.0
Li Li7 1 0.731400 0.378600 0.857200 1.0
Li Li8 1 0.378600 0.731400 0.357200 1.0
Li Li9 1 0.128500 0.753300 0.189400 1.0
Li Li10 1 0.753300 0.128500 0.689400 1.0
Li Li11 1 0.066000 0.456800 0.535100 1.0
Li Li12 1 0.456800 0.066000 0.035100 1.0
O O13 1 0.317800 0.953000 0.468700 1.0
O O14 1 0.953000 0.317800 0.968700 1.0
O O15 1 0.264700 0.577300 0.292200 1.0
O O16 1 0.577300 0.264700 0.792200 1.0
O O17 1 0.662800 0.647000 0.778300 1.0
O O18 1 0.647000 0.662800 0.278300 1.0
O O19 1 0.943400 0.215800 0.457100 1.0
O O20 1 0.215800 0.943400 0.957100 1.0
O O21 1 0.298800 0.326400 0.446000 1.0
O O22 1 0.326400 0.298800 0.946000 1.0
O O23 1 0.665300 0.980100 0.436100 1.0
O O24 1 0.980100 0.665300 0.936100 1.0
O O25 1 0.940600 0.647600 0.631800 1.0
O O26 1 0.647600 0.940600 0.131800 1.0
O O27 1 0.341900 0.080100 0.787200 1.0
O O28 1 0.080100 0.341900 0.287200 1.0
O O29 1 0.041000 0.979000 0.623500 1.0
O O30 1 0.979000 0.041000 0.123500 1.0
O O31 1 0.709900 0.473500 0.608800 1.0
O O32 1 0.473500 0.709900 0.108800 1.0
O O33 1 0.553600 0.872800 0.616600 1.0
O O34 1 0.872800 0.553600 0.116600 1.0
O O35 1 0.890600 0.592200 0.419200 1.0
O O36 1 0.592200 0.890600 0.919200 1.0
O O37 1 0.061900 0.827700 0.441900 1.0
O O38 1 0.827700 0.061900 0.941900 1.0
O O39 1 0.875300 0.869700 0.272400 1.0
O O40 1 0.869700 0.875300 0.772400 1.0
O O41 1 0.569300 0.495300 0.433500 1.0
O O42 1 0.495300 0.569300 0.933500 1.0
O O43 1 0.956600 0.230000 0.758900 1.0
O O44 1 0.230000 0.956600 0.258900 1.0
O O45 1 0.315700 0.603500 0.592000 1.0
O O46 1 0.603500 0.315700 0.092000 1.0
O O47 1 0.481100 0.199100 0.272800 1.0
O O48 1 0.199100 0.481100 0.772800 1.0
O O49 1 0.249100 0.827300 0.762500 1.0
O O50 1 0.827300 0.249100 0.262500 1.0
O O51 1 0.206300 0.207300 0.612700 1.0
O O52 1 0.207300 0.206300 0.112700 1.0
O O53 1 0.573200 0.220000 0.580600 1.0
O O54 1 0.220000 0.573200 0.080600 1.0
V V55 1 0.868600 0.815200 0.389900 1.0
V V56 1 0.815200 0.868600 0.889900 1.0
V V57 1 0.534200 0.450200 0.550900 1.0
V V58 1 0.450200 0.534200 0.050900 1.0
V V59 1 0.159100 0.085900 0.709000 1.0
V V60 1 0.085900 0.159100 0.209000 1.0
V V61 1 0.717800 0.666400 0.661700 1.0
V V62 1 0.666400 0.717800 0.161700 1.0
V V63 1 0.283700 0.364500 0.325800 1.0
V V64 1 0.364500 0.283700 0.825800 1.0
V V65 1 0.090300 0.999100 0.499100 1.0
V V66 1 0.999100 0.090300 0.999100 1.0
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MDU6SXNzdWUyODE4NzYwNDU=
| 943
|
Gamma-point grid even when structure is not hexagonal
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[
"Never mind (sort of). On the [Pymatgen](http://pymatgen.org/pymatgen.io.vasp.inputs.html) webpage, I now see that `automatic_density` uses a gamma-centered grid for hexagonal cells *and* for odd meshes. The mesh is 2x1x1, so I suppose that's odd then. I was looking at [the source code](http://pymatgen.org/_modules/pymatgen/io/vasp/inputs.html#Kpoints.automatic_density), which says \" Returns an automatic Kpoint object based on a structure and a kpoint density. Uses Gamma centered meshes for hexagonal cells and Monkhorst-Pack grids otherwise.\" I didn't see below that the `force_gamma` flag considers odd meshes as well.\r\n\r\nI am not sure why you'd want to use a gamma-centered mesh on odd grids though. I'm looking at the part of the VASP manual [here](https://cms.mpi.univie.ac.at/vasp/vasp/Number_k_points_method_smearing.html) but am finding it very unclear.",
"For the purposes of convergence, the choice between Gamma vs Monk is critical only when it is a hexagonal crystal. In general, we use Gamma on odd meshes so that a 1x1x1 will be centered on the Gamma point, which is usually what is desired for larger cells.\r\n\r\nIn any case, the mesh density calculated using the input sets are usually fairly dense to give good results on insulators. However, if you are running metals, you might want to crank up the grid. ",
"Thanks for the helpful reply. Fortunately, all the materials I am studying are insulators, so that comment is particularly reassuring!"
] | 2017-12-13T19:56:46
| 2017-12-13T21:48:38
|
2017-12-13T21:37:28Z
|
MEMBER
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## System
* Pymatgen version: 2017.10.16
* Python version: 3.6.3 (and 2.x)
* OS version: Windows 10 and Linux
## Summary
When using the vasp Kpoints generator, I am getting a gamma-centered grid even when the unit cell is not hexagonal.
## Example code
```python
from pymatgen.io.vasp.inputs import Kpoints
from pymatgen.io.cif import CifParser
parser = CifParser('test.cif')
struct = parser.get_structures()[0]
kpts = Kpoints.automatic_density(struct,1000)
print(kpts.style.name)
```
It then shows a gamma-centered k-point mesh despite the fact that the cell is not hexagonal. The lattice parameters are:
abc : 12.825999999999999 19.634 23.413
angles : 91.529000000000011 89.598000000000013 89.795000000000002
## Files (if any)
Here is the CIF file: [test.zip](https://github.com/materialsproject/pymatgen/files/1556865/test.zip)
In text form, please find it below:
```
# generated using pymatgen
data_Ag3P2H12C8S6(OF)4
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 23.41300000
_cell_length_b 12.82600000
_cell_length_c 19.63400000
_cell_angle_alpha 89.79500000
_cell_angle_beta 88.47100000
_cell_angle_gamma 90.40200000
_symmetry_Int_Tables_number 1
_chemical_formula_structural Ag3P2H12C8S6(OF)4
_chemical_formula_sum 'Ag24 P16 H96 C64 S48 O32 F32'
_cell_volume 5893.70857891
_cell_formula_units_Z 8
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Ag Ag1 1 0.266930 0.274533 0.582053 1.0
Ag Ag2 1 0.744925 0.324801 0.546753 1.0
Ag Ag3 1 0.099273 0.380864 0.890377 1.0
Ag Ag4 1 0.594996 0.379379 0.879681 1.0
Ag Ag5 1 0.265942 0.735095 0.673196 1.0
Ag Ag6 1 0.762603 0.732101 0.667025 1.0
Ag Ag7 1 0.018685 0.231020 0.923453 1.0
Ag Ag8 1 0.515427 0.230165 0.917688 1.0
Ag Ag9 1 0.348087 0.130270 0.617156 1.0
Ag Ag10 1 0.795524 0.143523 0.576532 1.0
Ag Ag11 1 0.513864 0.770608 0.829696 1.0
Ag Ag12 1 0.000000 0.758452 0.844363 1.0
Ag Ag13 1 0.231126 0.740296 0.371543 1.0
Ag Ag14 1 0.731968 0.750037 0.369474 1.0
Ag Ag15 1 0.393887 0.463623 0.164296 1.0
Ag Ag16 1 0.890085 0.469376 0.163778 1.0
Ag Ag17 1 0.313327 0.146723 0.486657 1.0
Ag Ag18 1 0.785827 0.198720 0.445919 1.0
Ag Ag19 1 0.480264 0.761088 0.131262 1.0
Ag Ag20 1 0.982322 0.766544 0.141950 1.0
Ag Ag21 1 0.146782 0.000000 0.338401 1.0
Ag Ag22 1 0.639524 0.000000 0.331526 1.0
Ag Ag23 1 0.061663 0.353011 0.021775 1.0
Ag Ag24 1 0.560792 0.356856 0.012182 1.0
P P25 1 0.142413 0.174645 0.488269 1.0
P P26 1 0.622196 0.180160 0.485775 1.0
P P27 1 0.234470 0.991565 0.693520 1.0
P P28 1 0.728762 0.985003 0.685987 1.0
P P29 1 0.391041 0.334470 0.012316 1.0
P P30 1 0.890381 0.339939 0.010711 1.0
P P31 1 0.483390 0.517556 0.807661 1.0
P P32 1 0.981950 0.511780 0.809308 1.0
P P33 1 0.313750 0.778965 0.508617 1.0
P P34 1 0.818103 0.792873 0.507214 1.0
P P35 1 0.280875 0.987687 0.335284 1.0
P P36 1 0.775205 0.997043 0.319873 1.0
P P37 1 0.069563 0.710112 0.000000 1.0
P P38 1 0.566424 0.723001 0.989215 1.0
P P39 1 0.024632 0.516832 0.172578 1.0
P P40 1 0.529883 0.516346 0.164137 1.0
H H41 1 0.355263 0.426988 0.623263 1.0
H H42 1 0.846720 0.429590 0.610346 1.0
H H43 1 0.378471 0.499770 0.695225 1.0
H H44 1 0.873802 0.492394 0.684344 1.0
H H45 1 0.345549 0.565265 0.626028 1.0
H H46 1 0.841820 0.568225 0.619063 1.0
H H47 1 0.179137 0.221477 0.840323 1.0
H H48 1 0.669460 0.223544 0.825441 1.0
H H49 1 0.251804 0.248462 0.859780 1.0
H H50 1 0.743828 0.238437 0.841393 1.0
H H51 1 0.236120 0.175250 0.785004 1.0
H H52 1 0.721963 0.175936 0.765172 1.0
H H53 1 0.221346 0.658076 0.871211 1.0
H H54 1 0.726002 0.647191 0.874006 1.0
H H55 1 0.146929 0.641114 0.858277 1.0
H H56 1 0.650836 0.644402 0.860256 1.0
H H57 1 0.188016 0.725238 0.803225 1.0
H H58 1 0.696074 0.727095 0.809471 1.0
H H59 1 0.079632 0.431913 0.640531 1.0
H H60 1 0.570948 0.465253 0.640898 1.0
H H61 1 0.130021 0.375959 0.580464 1.0
H H62 1 0.616416 0.407583 0.576571 1.0
H H63 1 0.121702 0.514529 0.585313 1.0
H H64 1 0.613860 0.546861 0.585877 1.0
H H65 1 0.108010 0.067321 0.906232 1.0
H H66 1 0.602241 0.076719 0.871888 1.0
H H67 1 0.138806 0.996116 0.836286 1.0
H H68 1 0.624936 0.000000 0.798880 1.0
H H69 1 0.097993 0.928786 0.901124 1.0
H H70 1 0.590858 0.938701 0.870106 1.0
H H71 1 0.430768 0.283421 0.662799 1.0
H H72 1 0.958191 0.269380 0.671001 1.0
H H73 1 0.032239 0.241479 0.657122 1.0
H H74 1 0.503406 0.255500 0.640148 1.0
H H75 1 0.009840 0.318571 0.729049 1.0
H H76 1 0.487484 0.329609 0.715449 1.0
H H77 1 0.996704 0.835906 0.647099 1.0
H H78 1 0.464947 0.846721 0.631856 1.0
H H79 1 0.390884 0.864966 0.650929 1.0
H H80 1 0.921374 0.854976 0.656591 1.0
H H81 1 0.431729 0.780260 0.702613 1.0
H H82 1 0.957150 0.770080 0.713583 1.0
H H83 1 0.326972 0.081526 0.869617 1.0
H H84 1 0.836884 0.072698 0.865593 1.0
H H85 1 0.378289 0.133548 0.927347 1.0
H H86 1 0.882800 0.125906 0.928858 1.0
H H87 1 0.366332 0.995732 0.922398 1.0
H H88 1 0.871262 0.987767 0.923740 1.0
H H89 1 0.186930 0.544768 0.450597 1.0
H H90 1 0.676141 0.555768 0.444198 1.0
H H91 1 0.140984 0.465366 0.400309 1.0
H H92 1 0.630898 0.481703 0.389930 1.0
H H93 1 0.193260 0.405338 0.451021 1.0
H H94 1 0.679377 0.416037 0.442752 1.0
H H95 1 0.267767 0.685066 0.142827 1.0
H H96 1 0.769696 0.698809 0.141494 1.0
H H97 1 0.194683 0.663427 0.167552 1.0
H H98 1 0.695649 0.680496 0.162792 1.0
H H99 1 0.237174 0.754566 0.213472 1.0
H H100 1 0.737988 0.768731 0.211193 1.0
H H101 1 0.234230 0.252884 0.190309 1.0
H H102 1 0.727919 0.267912 0.183104 1.0
H H103 1 0.306644 0.276798 0.162972 1.0
H H104 1 0.801498 0.287808 0.159612 1.0
H H105 1 0.291205 0.208987 0.241675 1.0
H H106 1 0.782100 0.219387 0.237209 1.0
H H107 1 0.433695 0.552309 0.305264 1.0
H H108 1 0.927910 0.553156 0.310602 1.0
H H109 1 0.401436 0.617967 0.376970 1.0
H H110 1 0.894398 0.619201 0.381274 1.0
H H111 1 0.415990 0.481756 0.381644 1.0
H H112 1 0.906408 0.482047 0.385420 1.0
H H113 1 0.437181 0.956033 0.051867 1.0
H H114 1 0.943734 0.964453 0.059790 1.0
H H115 1 0.389943 0.032751 0.104357 1.0
H H116 1 0.899272 0.046892 0.111948 1.0
H H117 1 0.442739 0.095822 0.051935 1.0
H H118 1 0.953216 0.103332 0.058124 1.0
H H119 1 0.017158 0.829868 0.367105 1.0
H H120 1 0.512392 0.819924 0.357811 1.0
H H121 1 0.439703 0.838994 0.335718 1.0
H H122 1 0.945032 0.854900 0.345051 1.0
H H123 1 0.483216 0.748812 0.288579 1.0
H H124 1 0.985719 0.759227 0.299165 1.0
H H125 1 0.478992 0.250700 0.309648 1.0
H H126 1 0.996846 0.261755 0.313344 1.0
H H127 1 0.068591 0.234904 0.336800 1.0
H H128 1 0.550965 0.229733 0.334469 1.0
H H129 1 0.054736 0.299718 0.257534 1.0
H H130 1 0.536880 0.295821 0.255837 1.0
H H131 1 0.188668 0.944511 0.193778 1.0
H H132 1 0.681202 0.955467 0.188375 1.0
H H133 1 0.155022 0.877489 0.125276 1.0
H H134 1 0.650179 0.889038 0.117974 1.0
H H135 1 0.173372 0.012379 0.116949 1.0
H H136 1 0.664825 0.025575 0.112673 1.0
C C137 1 0.345454 0.493427 0.656831 1.0
C C138 1 0.839846 0.493542 0.646803 1.0
C C139 1 0.286874 0.475624 0.691219 1.0
C C140 1 0.781546 0.478786 0.682603 1.0
C C141 1 0.221723 0.239331 0.818133 1.0
C C142 1 0.711776 0.238169 0.801509 1.0
C C143 1 0.219821 0.340557 0.776839 1.0
C C144 1 0.712382 0.343443 0.764679 1.0
C C145 1 0.188672 0.651786 0.832263 1.0
C C146 1 0.693202 0.650797 0.835099 1.0
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C C151 1 0.167581 0.447513 0.668809 1.0
C C152 1 0.660065 0.467677 0.664690 1.0
C C153 1 0.101739 0.000000 0.871369 1.0
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C C157 1 0.998447 0.252650 0.696301 1.0
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C C163 1 0.447706 0.944759 0.719676 1.0
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C C167 1 0.414622 0.060712 0.836688 1.0
C C168 1 0.926818 0.051238 0.843800 1.0
C C169 1 0.184493 0.474010 0.419302 1.0
C C170 1 0.673643 0.486474 0.411567 1.0
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C C174 1 0.738082 0.694140 0.183797 1.0
C C175 1 0.255693 0.592431 0.234543 1.0
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C C179 1 0.276057 0.375037 0.246026 1.0
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C C181 1 0.402527 0.545002 0.347890 1.0
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S S234 1 0.752325 0.487359 0.180679 1.0
S S235 1 0.326334 0.629474 0.264403 1.0
S S236 1 0.823363 0.637607 0.265385 1.0
S S237 1 0.472280 0.145283 0.184653 1.0
S S238 1 0.985557 0.153342 0.189712 1.0
S S239 1 0.053151 0.991514 0.109279 1.0
S S240 1 0.545165 0.992555 0.102764 1.0
S S241 1 0.108950 0.106854 0.225562 1.0
S S242 1 0.596469 0.110160 0.220959 1.0
S S243 1 0.448607 0.912467 0.198104 1.0
S S244 1 0.955190 0.923333 0.206527 1.0
S S245 1 0.500300 0.030536 0.315962 1.0
S S246 1 0.000000 0.039930 0.322170 1.0
S S247 1 0.078719 0.876065 0.241572 1.0
S S248 1 0.573129 0.876175 0.233849 1.0
O O249 1 0.172864 0.266767 0.516196 1.0
O O250 1 0.642922 0.282933 0.510685 1.0
O O251 1 0.127385 0.169346 0.414419 1.0
O O252 1 0.609867 0.164286 0.411836 1.0
O O253 1 0.240280 0.896615 0.649909 1.0
O O254 1 0.719750 0.884229 0.649957 1.0
O O255 1 0.281938 0.066005 0.706346 1.0
O O256 1 0.780119 0.053219 0.675071 1.0
O O257 1 0.422866 0.239154 0.991366 1.0
O O258 1 0.922192 0.243528 0.992276 1.0
O O259 1 0.367394 0.346659 0.083676 1.0
O O260 1 0.865334 0.355567 0.081288 1.0
O O261 1 0.490007 0.607103 0.855548 1.0
O O262 1 0.982238 0.604089 0.855676 1.0
O O263 1 0.029398 0.435656 0.803945 1.0
O O264 1 0.528720 0.439761 0.792460 1.0
O O265 1 0.258405 0.742124 0.480595 1.0
O O266 1 0.762703 0.765576 0.475356 1.0
O O267 1 0.332183 0.746639 0.577643 1.0
O O268 1 0.832119 0.754647 0.576599 1.0
O O269 1 0.297505 0.083276 0.372021 1.0
O O270 1 0.785078 0.106692 0.340655 1.0
O O271 1 0.227284 0.925095 0.352554 1.0
O O272 1 0.721258 0.937159 0.339023 1.0
O O273 1 0.017178 0.759066 0.034313 1.0
O O274 1 0.510395 0.750728 0.022298 1.0
O O275 1 0.089598 0.736477 0.933125 1.0
O O276 1 0.582423 0.760488 0.919193 1.0
O O277 1 0.039759 0.417820 0.138338 1.0
O O278 1 0.544916 0.418616 0.128177 1.0
O O279 1 0.474943 0.574840 0.152773 1.0
O O280 1 0.972532 0.580494 0.155698 1.0
F F281 1 0.174940 0.070704 0.506079 1.0
F F282 1 0.662655 0.088711 0.508609 1.0
F F283 1 0.085359 0.155407 0.532932 1.0
F F284 1 0.567235 0.146842 0.530191 1.0
F F285 1 0.209784 0.954987 0.766999 1.0
F F286 1 0.722508 0.964393 0.766438 1.0
F F287 1 0.180097 0.053088 0.669577 1.0
F F288 1 0.672696 0.052670 0.677949 1.0
F F289 1 0.427467 0.435780 0.994142 1.0
F F290 1 0.927446 0.440115 0.991509 1.0
F F291 1 0.340095 0.351218 0.961386 1.0
F F292 1 0.840153 0.355582 0.958608 1.0
F F293 1 0.464603 0.564652 0.735640 1.0
F F294 1 0.969872 0.551619 0.733269 1.0
F F295 1 0.425305 0.458641 0.827411 1.0
F F296 1 0.922687 0.453170 0.822174 1.0
F F297 1 0.317707 0.901882 0.500225 1.0
F F298 1 0.827575 0.915306 0.502801 1.0
F F299 1 0.364785 0.751144 0.455616 1.0
F F300 1 0.869581 0.760328 0.455990 1.0
F F301 1 0.277796 0.000000 0.255569 1.0
F F302 1 0.782604 0.990997 0.238875 1.0
F F303 1 0.332165 0.907083 0.330727 1.0
F F304 1 0.827334 0.925008 0.338770 1.0
F F305 1 0.065144 0.587486 0.013639 1.0
F F306 1 0.575097 0.600616 0.994312 1.0
F F307 1 0.122310 0.729149 0.052834 1.0
F F308 1 0.617119 0.755604 0.038564 1.0
F F309 1 0.020219 0.497548 0.253150 1.0
F F310 1 0.532550 0.497464 0.244536 1.0
F F311 1 0.077385 0.595448 0.172198 1.0
F F312 1 0.580065 0.599967 0.158122 1.0
```
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| 281,945,317
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MDExOlB1bGxSZXF1ZXN0MTU4MjQyNDA3
| 944
|
Orbital-resolved COHPs and small changes to COHP modules
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[] | 2017-12-14T00:41:37
| 2017-12-14T03:54:04
|
2017-12-14T03:54:04Z
|
NONE
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## Summary
This pull request adds orbitals-resolved COHPs to the lobster and cohp modules. Currently, only LOBSTER outputs orbital-resolved COHPs that can be read in a convenient way.
* I changed the io.lobster and electronic_structure.cohp modules to handle orbital-resolved COHPs with a separate attribute. I added the appropriate output files for the tests as well.
* I also changed the existing json files to accommodate the new format of the structure dictionaries (especially the total charge).
* CompleteCohp.get_cohp will now try to reverse the label if the enetered label is not found (i.e. tries "Fe7-Fe8" if "Fe8-Fe7" is not in the COHP labels) before raising a KeyError.
* I also added a round_to_sigfigs function to util.num. LMTO rounds everything to 5 significant figures (instead of using a precision of 5), but converting energies from Ry to eV adds additional digits. So far, I used string formatters to round, which looks kind of ugly. Since this is done in multiple places, I figured defining a function is better. Maybe someone else will find it useful as well.
## Note
There is a bug in LOBSTER, which causes it to sometimes output orbital-resolved COHPs without the total COHP. The total COHPs are calculated in electronic_structure.cohp if these totals are missing. According to the developers, this will be resolved in the next version of LOBSTER, so once the current version is obsolete, this part can be removed.
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| 281,973,627
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| 945
|
PDPlotter.plot_element_profile
|
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[
"Done with the implementation as a method in PDPlotter. The result of testing case (Na3PS4 under different Na chemical potential) is shown below (selected profile step products are annotated in the plot):\r\n\r\nindex= 0, -Δμ=-0.0000(eV), 2 Na3PS4 + 16 Na -> 2 Na3P + 8 Na2S\r\nindex= 1, -Δμ=0.2945(eV), 2 Na3PS4 + 12 Na -> 8 Na2S + 2 NaP\r\nindex= 2, -Δμ=0.6391(eV), 2 Na3PS4 + 10.55 Na -> 0.1818 Na3P11 + 8 Na2S\r\nindex= 3, -Δμ=1.1448(eV), 2 Na3PS4 + 10 Na -> 2 P + 8 Na2S\r\nindex= 4, -Δμ=1.1623(eV), 2 Na3PS4 -> 2 Na3PS4\r\nindex= 5, -Δμ=2.4944(eV), 2 Na3PS4 -> P2S5 + 3 S + 6 Na\r\n\r\n"
] | 2017-12-14T03:52:01
| 2017-12-16T17:54:27
|
2017-12-16T17:54:27Z
|
MEMBER
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Right now, someone has to manually plot the element profile from pd.get_element_profile. A simple PDPlotter.plot_element_profile should be added.
@Zhuoying to implement
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MDExOlB1bGxSZXF1ZXN0MTU4MzMxMzk2
| 946
|
Dielectric 5.4.4
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[
"I would suggest we be explicit and we keep all dielectric data in self.dielectric_data[\"density\"] and self.dielectric_data[\"velocity\"]. And then map self.dielectric to self.dielectric_data[\"density\"].",
"That makes sense. What should be the behaviour for older VASP versions? Read directly into `self.dielectric` or into `self.dielectric_data[“density”]` and map?",
"Yes, old and new should have the same behavior. Only that newer VASP versions have an additional self.dielectric_data[\"velocity\"]. That way, people can write code for both VASP versions transparently.",
"Hi @bjmorgan, this is useful, thank you! I just came across this myself. However I read the `linear_optics.F` comment and was none-the-wiser. I read that both methods should be equivalent and agree, but read elsewhere they can differ practically and especially in the low frequency limit. Do you have a reference on the difference between these, and when one is preferred over the other?",
"@mkhorton I don't think the discussion with @shyuep was that these two methods in VASP should give the same output when processed. Rather that `pymatgen` should give the same result for VASP versions pre and post 5.4.4. when `self.dielectric` is used (which now is a mapping of `self.dielectric_data[\"density\"]`).\r\n\r\nAs to the difference in the physics of how these two are calculated, I am not able to help, and it has been a while since I looked into this.",
"No worries, but thanks for the context!"
] | 2017-12-14T11:21:55
| 2021-05-12T18:31:09
|
2017-12-14T23:32:07Z
|
CONTRIBUTOR
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Addresses issue https://github.com/materialsproject/pymatgen/issues/940.
VASP 5.4.4 calculates the frequency dependent dielectric response in two ways, using a "density-density" response function, and using a "velocity-velocity" response function (see the comments in `linear_optics.F` in the vasp source code). The latter is marked in OUTCAR as `current-current (2nd set in vasprun.xml)`, but is not labelled in `vasprun.xml`.
This commit addresses an issue where the second unlabelled dielectric function would overwrite the first.
For consistency with older versions of vasp, the "density-density" linear response function
is read into `self.dielectric`.
The "velocity-velocity" linear response function (described as "current-current" in OUTCAR)
is read into `self.other_dielectric['current-current']`.
This commit includes a test that if `vasprun.xml` contains a second unlabelled set of dielectric
repsonse data, this is read into `self.other_dielectric['current-current']`.
If a third unlablled set of dielectric data is present in the `vasprun.xml`, a `NotImplementedError`
is raise (also tested).
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MDExOlB1bGxSZXF1ZXN0MTU4Mzk3MjU3
| 947
|
Add py2k support for electronic_structure.cohp
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[] | 2017-12-14T16:08:29
| 2017-12-14T16:39:21
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2017-12-14T16:39:21Z
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NONE
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## Summary
Adds string handling support for py2k in electronic_structure.cohp using the six library.
|
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MDExOlB1bGxSZXF1ZXN0MTU4NDkwOTkx
| 948
|
add plot_element_profile method in PDPlotter
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[
"Write a proper PR summary.",
"@shyuep Done with the summary editing",
"@Zhuoying This is not good enough. Why do you make people supply an evolution instead of the same parameters as pd.get_element_profile and just call that method to get the evolution? How does anyone know what \"evolution\" means? Why are the profile steps not labelled at all? Surely this is not what we publish in our papers?\r\n\r\nYou have been in the group for several years. Surely you understand the importance of proper functional argument and code design. Fix all these problems by today. I need it for a demo next week."
] | 2017-12-14T23:40:50
| 2017-12-15T15:27:07
|
2017-12-14T23:51:39Z
|
CONTRIBUTOR
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## Summary
* Add a method in PDPlotter to draw plot using data from Phasediagram.get_element_profile
* Unittest added
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MDU6SXNzdWUyODIyNzYxMDY=
| 949
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Generalize surface_analysis.py
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[] | 2017-12-14T23:46:45
| 2018-01-11T04:43:20
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2018-01-11T04:43:20Z
|
CONTRIBUTOR
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The surface_analysis.py as of now is limited to the number of parameters (chemical potentials) that can be used as a free variable, primarily because the equation it uses is not generalized and because current plots implemented are for single variables. The surface_analysis.py code can be rewritten to incorporate the generalize equation which can calculate the surface energy of any slab regardless of stoichiometry and number/types of adsorbates.
General surface energy:
\gamma = (E_surf-\Sigma N_i * \mu_i)/(2A)
Using this equation will also significantly simplify much of the code and number of parameters needed for some functions, making it much easier to use.
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MDU6SXNzdWUyODIyNzgxNTY=
| 950
|
Reduced oriented_unit_cell
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[
"Ok. But I don't think you need to artificially add a vacuum to reduce the unit cell. That would work, but it is an inelegant approach. \r\n\r\nAll you need to do is to modify the get_primitive of the structure method to provide an option to only search in certain directions and disallow modification of the c direction. ",
"In that case, then perhaps an optional parameter for get_primitive_structure() to say \"limit reduction to these particular directions\" could be useful. And by default it would just work normally as it does now."
] | 2017-12-14T23:57:44
| 2018-01-11T04:42:55
|
2018-01-11T04:42:55Z
|
CONTRIBUTOR
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To ensure that the surface energy does not diverge wrt slab size for some systems, we need to calculate an oriented unit cell with a kpoint grid consistent with the slab to sample the Brillouin zone of the slab. So both the OUC and slab have to be calculated.
Right now when generating an OUC and reduced slab, the lattice vectors in the a and b direction are sometimes inconsistent with the OUC and so sometimes, we are stuck with calculating a larger slab size to keep the kpoints consistent with the OUC instead of just significantly smaller reduced slab.
We can actually reduced the OUC further in order to make it consistent with the reduced slab. This will make surface calculations much faster, as long as the c lattice vector is maintained (i.e. we want to reduce the OUC along the a and b vector only).
1. Get the OUC
2. Break the symmetry along the c direction by adding a vacuum.
3. Use get_primitive cell() on the new system (because symmetry is broken along c, only the a and b vectors are reduced)
4. Remove the vacuum from this reduced system.
The resulting OUC should now have a consistent a and b lattice vector with the slab. Now not only are the slab calculations cheaper, but the OUC calculations as well.
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MDU6SXNzdWUyODIyODI3NTY=
| 951
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add absorption coefficient method
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[
"@zbwang to implement.",
"I have code that does this, using `Vasprun.dielectric`. I’d be happy to contribute it. What would be the preferred way to access this? A `Vasprun.optical_absorption` property? Or some kind of `Optics` analysis class?",
"Hi bjmorgan, thanks for your contribution. This is a topic I come up with for our biweekly hackathon held in MAVRL group. I have placed a PR to fix this issue. ,\r\n\r\nAlso, I have a question to seek advice from you. Do you know what is the difference btw dielectric functions calculated with \"density-density\" and \"velocity-velocity\" linear response functions?\r\nIn the VASP source code, they state these are \"two equivalent ways\". The values in vasprun.xml of these two methods, however, are totally different. The dielectric constants calc by \"density-density\" in OUTCAR is called \"current-current (2nd set in vasprun.xml)\", though they have the same meaning. ",
"Hi @zbwang. I would need to do a lot more reading to follow the difference between the two methods. In my limited tests they give the same result at high frequencies, but diverge as w goes to zero, with the “velocity-velocity” looking unphysical. From looking at the VASP source code, the “density-density” function appears to be the same as in earlier versions. The “velocity-velocity” function is called “current-current” in OUTCAR, which confuses things."
] | 2017-12-15T00:25:08
| 2017-12-15T21:40:37
|
2017-12-15T21:40:37Z
|
CONTRIBUTOR
|
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The optical absorption coefficient can be calculated from dielectric tensors. The dielectric tensors have been well processed with pymatgen. It will be more user-friendly if pymatgen could directly produce this optical property.
|
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MDU6SXNzdWUyODIyODUzMTI=
| 952
|
MVLCDFTSet for constrained DFT calc
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[
"OK. Mahdi to implement.",
"Not planned."
] | 2017-12-15T00:40:07
| 2023-08-08T21:21:13
|
2023-08-08T21:21:04Z
|
CONTRIBUTOR
|
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The constrained DFT(CDFT) is valuable for excited state calculations. A VASP input set for CDFT calc will be implemented in pymatgen.
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| 282,288,820
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MDU6SXNzdWUyODIyODg4MjA=
| 953
|
FEFF LDos creating using Reciprocal calculation file
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[
"OK go ahead and implement."
] | 2017-12-15T01:03:15
| 2017-12-16T12:32:08
|
2017-12-16T12:32:08Z
|
CONTRIBUTOR
|
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Currently, the LDos class of pymatgen.io.feff.outputs only supports generating Dos object from real-space calculated output files. Modification of the LDos class methods and allows the generation of Dos object from Reciprocal space calculated FEFF output files will be useful.
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MDExOlB1bGxSZXF1ZXN0MTU4NjgwNDU4
| 954
|
Minor updates to lammps.data
|
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[] | 2017-12-15T19:50:23
| 2017-12-15T19:51:50
|
2017-12-15T19:51:50Z
|
CONTRIBUTOR
|
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## Summary
Minor updates to lammps.data
* Added an option to have additional elements (defined in force field but not present in a structure).
* Fix box bounds issue in structure property.
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MDExOlB1bGxSZXF1ZXN0MTU4Njg1MDYw
| 955
|
Add optical absorption coefficient method
|
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[] | 2017-12-15T20:15:33
| 2017-12-15T21:40:37
|
2017-12-15T21:40:37Z
|
CONTRIBUTOR
|
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This PR is to fix #951. Also, fix a bug in Vasprun when it parses vasprun.xml files of GW/BSE calc, where the structure is not available.
|
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MDExOlB1bGxSZXF1ZXN0MTU4Njk4ODMw
| 956
|
improve plot_element_profile
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[] | 2017-12-15T21:38:09
| 2017-12-15T21:40:03
|
2017-12-15T21:40:03Z
|
CONTRIBUTOR
|
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## Summary
* Change input parameters as the same with pd.get_element_profile
* Add show_label option to annotate reaction products in profile steps as users want
* Modify unittest.
|
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| 282,605,169
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MDExOlB1bGxSZXF1ZXN0MTU4NzMzNjIw
| 957
|
Update MAGMOM setting for Ln3+ ions
|
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[
"And finally, why no unittests at all for these? You are in my group long enough to know what needs to be done.",
"@w6ye It should not take this long to write a few tests and push them.",
"1. From VASP default is usually the experimental magnetic moment multiplied by 1.2 or 1.5. I followed it by multiplying the experimental ground state magnetic moment (No. of unpaired spin) by 1.5. I think it's fine to have non-integer MAGMOM\r\n2. I have added test ",
"No, use the actual integer values. There is no need to multiply by 1.2 or 1.5. Even if we wanted to do that, we will make it an operation that is applied across all MAGMOMs, not hard code it in the yaml file. Use some sense in writing code. The other magmom values do not have 1.2 or 1.5 x. Why would the Ln be treated differently?",
"Updated. Use the true number of unpaired spin instead of x1.5 for all Ln3+."
] | 2017-12-16T07:00:09
| 2017-12-29T13:26:01
|
2017-12-29T13:26:01Z
|
CONTRIBUTOR
|
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## Summary
* Feature 1 Update MAGMOM setting for Ln3+ ions, the values are calculated as
number of ground state unpaired electrons of Ln3+ * 1.5
|
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MDExOlB1bGxSZXF1ZXN0MTU4NzM0OTYy
| 958
|
Enable creation of LDos using FEFF reciprocal calculation files
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[] | 2017-12-16T07:46:11
| 2017-12-16T12:32:08
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2017-12-16T12:32:08Z
|
CONTRIBUTOR
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## Summary
Enable creation of LDos using FEFF reciprocal calculation files and fixes #953 . Unittest has been implemented accordingly.
|
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An Odd ImportError
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[
"This is clearly an issue with your `scipy` installation\r\n",
"Thanks for the quick reply.\nI am aware of that. I reinstalled it, but still couldn’t fix it.\nUninstall:\npip uninstall scipy\nInstall:\npip install scipy\n\nShould I try some other ways to reinstall scipy?\n\n> On Dec 16, 2017, at 12:57 PM, Shyue Ping Ong <notifications@github.com> wrote:\n> \n> This is clearly an issue with your scipy installation\n> \n> Shyue Ping\n> ________________________________\n> From: jic198 <notifications@github.com>\n> Sent: Saturday, December 16, 2017 12:55:20 PM\n> To: materialsproject/pymatgen\n> Cc: Subscribed\n> Subject: [materialsproject/pymatgen] An Odd ImportError (#959)\n> \n> \n> I have been trying to run pymatgen in Python 3 but always getting an odd ImportError. I also installed pymatgen in Python 2, but that one is fine. I have tried:\n> \n> 1. pip install pymatgen\n> 2. git clone pymatgen and pip install .\n> 3. reinstall scipy\n> But none of the above fix the error. Any idea why it happens?\n> Thanks\n> \n> System\n> \n> * Pymatgen version: 2017.12.8\n> * Python version: 3.6\n> * OS version: OS X EI Capitan\n> \n> Example code\n> \n> pmg -h\n> \n> Error message\n> \n> Traceback (most recent call last):\n> File \"/Library/Frameworks/Python.framework/Versions/3.6/bin/pmg\", line 11, in <module>\n> load_entry_point('pymatgen', 'console_scripts', 'pmg')()\n> File \"/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 565, in load_entry_point\n> return get_distribution(dist).load_entry_point(group, name)\n> File \"/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 2631, in load_entry_point\n> return ep.load()\n> File \"/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 2291, in load\n> return self.resolve()\n> File \"/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 2297, in resolve\n> module = __import__(self.module_name, fromlist=['__name__'], level=0)\n> File \"/Users/Jianli/GDrive/repos/pymatgen/pymatgen/__init__.py\", line 54, in <module>\n> from pymatgen.core import *\n> File \"/Users/Jianli/GDrive/repos/pymatgen/pymatgen/core/__init__.py\", line 7, in <module>\n> from .periodic_table import Element, Specie, DummySpecie\n> File \"/Users/Jianli/GDrive/repos/pymatgen/pymatgen/core/periodic_table.py\", line 14, in <module>\n> from pymatgen.core.units import Mass, Length, unitized, FloatWithUnit, Unit, \\\n> File \"/Users/Jianli/GDrive/repos/pymatgen/pymatgen/core/units.py\", line 16, in <module>\n> import scipy.constants as const\n> File \"/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/__init__.py\", line 118, in <module>\n> from scipy._lib._ccallback import LowLevelCallable\n> File \"/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/_lib/_ccallback.py\", line 1, in <module>\n> from . import _ccallback_c\n> ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/_lib/_ccallback_c.cpython-36m-darwin.so, 2): no suitable image found. Did find:\n> /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/_lib/_ccallback_c.cpython-36m-darwin.so: mach-o, but wrong architecture\n> \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/959>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AAjOU_3c4pWM2lOTNNAtyz64XZ5LfahFks5tBC44gaJpZM4REdJJ>.\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/959#issuecomment-352211319>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ARnz1OpX_uKqDUovs6UG-k_4aQ1vN27oks5tBC63gaJpZM4REdJJ>.\n> \n\n",
"Try using the conda way of installing.",
"That got it to work. Thanks:)"
] | 2017-12-16T20:55:19
| 2023-05-27T19:46:42
|
2023-05-27T19:46:38Z
|
NONE
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I have been trying to run pymatgen in Python 3 but always getting an odd ImportError. I also installed pymatgen in Python 2, but that one is fine. I have tried:
1. pip install pymatgen
2. git clone pymatgen and pip install .
3. reinstall scipy
But none of the above fix the error. Any idea why it happens?
Thanks
## System
* Pymatgen version: 2017.12.8
* Python version: 3.6
* OS version: OS X EI Capitan
## Example code
```python
pmg -h
```
## Error message
```
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.6/bin/pmg", line 11, in <module>
load_entry_point('pymatgen', 'console_scripts', 'pmg')()
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pkg_resources/__init__.py", line 565, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2631, in load_entry_point
return ep.load()
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2291, in load
return self.resolve()
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2297, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/Users/Jianli/GDrive/repos/pymatgen/pymatgen/__init__.py", line 54, in <module>
from pymatgen.core import *
File "/Users/Jianli/GDrive/repos/pymatgen/pymatgen/core/__init__.py", line 7, in <module>
from .periodic_table import Element, Specie, DummySpecie
File "/Users/Jianli/GDrive/repos/pymatgen/pymatgen/core/periodic_table.py", line 14, in <module>
from pymatgen.core.units import Mass, Length, unitized, FloatWithUnit, Unit, \
File "/Users/Jianli/GDrive/repos/pymatgen/pymatgen/core/units.py", line 16, in <module>
import scipy.constants as const
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/__init__.py", line 118, in <module>
from scipy._lib._ccallback import LowLevelCallable
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/_lib/_ccallback.py", line 1, in <module>
from . import _ccallback_c
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/_lib/_ccallback_c.cpython-36m-darwin.so, 2): no suitable image found. Did find:
/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/_lib/_ccallback_c.cpython-36m-darwin.so: mach-o, but wrong architecture
```
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MDExOlB1bGxSZXF1ZXN0MTU4Nzc2Mjg4
| 960
|
Generalized surface analysis and NanoscaleStability
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[] | 2017-12-17T08:27:03
| 2017-12-18T23:38:08
|
2017-12-18T23:38:08Z
|
CONTRIBUTOR
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## Summary
This pull request resolves issue #921 and #949 .
The surface_analysis.py code has been drastically modified. A class for analyzing nanoscale stability of particles among different polymorphs has also been added. It now contains two primary classes, the
* SlabEntry class (a child of ComputedStructureEntry) which contains methods for calculating surface energy, binding energy of adsorbates, adsorption energy, and other surface thermodynamic quantities. The surface energy now uses the general formula for surface energy:
$\gamma = E_{slab}-\Sigma \mu_i N_i$
This will work for anything from clean slabs, non-stoichiometric systems, adsorption, substitution, etc. The returned surface energy is actually a Sympy Add object.
* SurfaceEnergyPlotter class works similarly to the SurfaceEnergyCalculator class. It still takes in a dictionary of SlabEntries. It also provides gamma vs chempot plots with the option of only showing stable plots along the chempot. New plotting methods added are the following:
* chempot_vs_gamma: plots surface energy vs chemical potential
* monolayer_vs_BE: plots the monolayer of the adsorbed slab against the binding energy (adsorption energy).
* BE_vs_clean_SE: plots the binding energy (or adsorption energy) against the clean surface energy.
* Unittesting now uses json files containing dictionary representations of entries instead of vasprun files.
* Added reconstruction property to Slab object, None if not reconstructed, str (name of reconstruction) if reconstructed.
* NanoscaleStability class takes in a list of SurfaceEnergyPlotter objects to build plots showing nanoscale stability of different polymorphs. Models the particle either as a Wulff shape or a perfect sphere.
* solve_equilibrium_point: finds the particle radius where two particles are stable at the same time.
* plot_all_stability_map: plots an arbitrary radius against the particle formation energy for all polymorphs.
* Particle formation energy is calculate as such:
$\Delta G_{form} = \Delta G^{bulk}_{form} * V + \Sigma_{i} \gamma_{i} \A_{i}$
$A_{i}$ is the area of the facet on a particle (Wulff shape), $\gamma_{i}$ is the surface energy of a particular facet, V is the volume of the particle, $\Delta G^{bulk}_{form}$ is the bulk formation energy and is $(N_{atoms in ucell}/V_{ucell})*E_{bulk energy per atom}$. If the particle were approximated as a sphere then $V=4/3 \pi r^3$ and $\Sigma_{i} \gamma_{i} \A_{i}$ would simply be $\bar{\gamma} * 4\pi r^2$.
* Now uses the general formula for surface energy.
* User can now choose to have as many free variables (chempots) in their surface energy as they want, or just calculate the surface energy at specific chempots.
Removed:
*The chempot range is now user provided.
## TODO (if any)
-Still assumes individual elements have their own chempots
in a molecular adsorbate instead of considering a single
chempot for a single molecular adsorbate. E.g. for an OH
adsorbate, the surface energy is a function of delu_O and
delu_H instead of delu_OH
-Need a method to automatically get chempot range when
dealing with non-stoichiometric slabs
-Simplify the input for SurfaceEnergyPlotter such that the
user does not need to generate a dict
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UCL contributions
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[] | 2017-12-17T23:25:05
| 2017-12-18T23:38:26
|
2017-12-18T23:38:26Z
|
CONTRIBUTOR
|
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## Summary
* Fix minor bugs and py3k portability issues in io.abinit modules
* Add `mpi_runner_options` and `shell_runnner_options` to qadapter
* NscfTasks now use the same FFT mesh (ngfft) as the one employed by the ScfTask
* Remove deprecated code
|
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MDExOlB1bGxSZXF1ZXN0MTU5MDUwNTc3
| 962
|
Revert "Generalized surface analysis and NanoscaleStability"
|
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[] | 2017-12-19T00:20:33
| 2018-03-25T13:29:49
|
2017-12-27T09:55:22Z
|
MEMBER
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Reverts materialsproject/pymatgen#960
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MDU6SXNzdWUyODMxNTAzOTY=
| 963
|
Element.name returns the symbol but not the long name of element
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[
"This was a bug introduced when we switched Element to a Enum type. Basically, \"name\" is a reserved attribute for Enums. \r\n\r\nSince no one else seems to be missing this feature, I have renamed Element.name to Element.long_name and added a unittest to make sure it does not disappear again.",
"@shyuep thanks."
] | 2017-12-19T09:04:34
| 2017-12-20T07:28:46
|
2017-12-19T20:13:50Z
|
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: 2017.12.16
* Python version: python 3.6.3 (anaconda)
* OS version: macOS 10.13.2
## Summary
Element.name returns the symbol but not the long name
## Example code
```python
from pymatgen.core.periodic_table import Element
Element("H").name
Element("H").symbol
```
all return with "H"
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| 283,422,419
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MDU6SXNzdWUyODM0MjI0MTk=
| 964
|
Regression in pourbaix analyzer - pourbaix_domain_vertices
|
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[] | 2017-12-20T01:34:28
| 2023-08-08T21:21:28
|
2023-08-08T21:21:28Z
|
MEMBER
|
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In removing pyhull dependency via 5445e6de90090424da9c6e906e203272eeffe291, the `pourbaix_domain_vertices` instance attribute of `PourbaixAnalyzer` was removed. This attribute is used by the `PourbaixPlotter.domain_vertices` method and thus for plot serialization.
## System
* Pymatgen version: "master"
* Python version: 3.5.0
* OS version: OSX
## Summary
* In removing pyhull dependency via 5445e6de90090424da9c6e906e203272eeffe291, the `pourbaix_domain_vertices` instance attribute of `PourbaixAnalyzer` was removed. This attribute is used by the `PourbaixPlotter.domain_vertices` method and thus for plot serialization.
## Example code
```python
from pymatgen import MPRester
from pymatgen.analysis.pourbaix.maker import PourbaixDiagram
from pymatgen.analysis.pourbaix.plotter import PourbaixPlotter
mpr = MPRester()
entries = mpr.get_pourbaix_entries(["Cu"])
pd = PourbaixDiagram(entries)
plotter = PourbaixPlotter(pd)
plotter.get_pourbaix_plot()
plotter.domain_vertices(entries[0])
```
## Error message
```
...pymatgen/pymatgen/analysis/pourbaix/plotter.py in domain_vertices(self, entry)
537 list of vertices
538 """
--> 539 if entry not in self._analyzer.pourbaix_domain_vertices.keys():
540 return []
541 return self._analyzer.pourbaix_domain_vertices[entry]
AttributeError: 'PourbaixAnalyzer' object has no attribute 'pourbaix_domain_vertices'
```
## Suggested solution (if any)
* restore `pourbaix_domain_vertices` as an instance attribute of `PourbaixAnalyzer`.
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| 283,484,618
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MDExOlB1bGxSZXF1ZXN0MTU5MzU2OTc3
| 965
|
Surf substitution
|
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[] | null |
[] | 2017-12-20T08:28:55
| 2017-12-20T22:49:29
|
2017-12-20T19:24:51Z
|
CONTRIBUTOR
|
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## Summary
Fixed tests for surface_analysis and added generate_substitution_structures() option to AdsorbateSiteFinder.
* Fixed test_surface_analysis.py, the chemical potential used in the test led to surface energy values that were too small. Had to change to a chemical potential that would result in a larger surface energy.
* In addition to performing adsorption, AdsorbateSiteFinder can also perform simple surface substitution operations with .generate_substitution_structures().
|
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| 283,622,919
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MDU6SXNzdWUyODM2MjI5MTk=
| 966
|
error:"No module named 'pymatgen.io.vaspio'"
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[
"You are using an ancient pymatgen. pymatgen.io.vaspio has been deprecated for quite a long time and now renamed as pymatgen.io.vasp. Pls update your pymatgen to the latest and then try\r\n```from pymatgen.io.vasp.outputs import Vasprun```"
] | 2017-12-20T16:35:29
| 2023-05-29T15:45:07
|
2023-05-29T15:45:07Z
|
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: 2017.12.16-py36_0
python 3
* OS version: 10.13.2
## Summary
Cannot load vaspio:
## Example code
```python
from pymatgen.io.vaspio.vasp_output import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter
v = Vasprun("TiS2-band/vasprun.xml")
bs = v.get_band_structure(line_mode=True)
BSPlotter(bs).get_plot()
#BSPlotter(bs).save_plot(filename= "TiS2_band.eps")
```
## Error message
```
from pymatgen.io.vaspio.vasp_output import Vasprun
Traceback (most recent call last):
File "<ipython-input-6-f8fc65c2cc65>", line 1, in <module>
from pymatgen.io.vaspio.vasp_output import Vasprun
ModuleNotFoundError: No module named 'pymatgen.io.vaspio'
```
## 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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MDU6SXNzdWUyODM2NjE3NTU=
| 967
|
Cannot find get_projections_on_elts_and_orbitals
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[
"The tutorials you are referring to use an ancient pymatgen. This functionality has actually been implemented into pymatgen by Dr Anubhav Jain. Pls take a look at the class BSDOSPlotter in pymatgen.electronic_structure.plotter module.\r\n```from pymatgen.electronic_structure.plotter import BSDOSPlotter```",
"if I use from pymatgen.electronic_structure.plotter import BSDOSPlotter, how can I edit the detials in the plot? such as number font, line color, to plot better figures like Dr Jain did? from you example, BSDOSPlotter only can give very simple and rough plot (http://pymatgen.org/_static/Analyze%20and%20plot%20band%20structures.html) "
] | 2017-12-20T18:54:09
| 2023-05-29T18:48:03
|
2023-05-29T18:48:03Z
|
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: 2017.12.16-py36_0
* Python version: python3.6
* OS version: 10.13.2
## Summary
I run the band plot code from https://github.com/gVallverdu/bandstructureplots/tree/master/Cu_bands. But cannot run this command:
pbands = bands.get_projections_on_elts_and_orbitals({name: ["s", "p", "d"]})
## Example code
```python
# Example code generating error
```
bands = run.get_band_structure("./Bandes/KPOINTS",
line_mode=True,
efermi=dosrun.efermi)
pbands = bands.get_projections_on_elts_and_orbitals({name: ["s", "p", "d"]})
```
AttributeError: 'BandStructureSymmLine' object has no attribute 'get_projections_on_elts_and_orbitals'
```
## 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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| 283,716,664
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MDExOlB1bGxSZXF1ZXN0MTU5NTM0Mjg0
| 968
|
updated analyzer to restore pourbaix_domain_vertices and added unittest
|
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[] | 2017-12-20T22:36:20
| 2019-04-04T02:41:31
|
2017-12-21T20:39:13Z
|
CONTRIBUTOR
|
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## Summary
Returns pourbaix_domain_vertices attribute to PourbaixAnalyzer. Addresses #964.
* Adds the pourbaix_domain_vertices attribute back
* provides a more stable sort of the points bounding the pourbaix region to ensure consistency
* Adds test of functionality
|
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| 284,036,932
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MDExOlB1bGxSZXF1ZXN0MTU5Nzc0NzU5
| 969
|
fix minor bug in generating k path in monoclinic#462
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[] | 2017-12-21T23:52:08
| 2017-12-27T09:54:59
|
2017-12-27T09:54:59Z
|
CONTRIBUTOR
|
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## Summary
Transform degree to radian as argument of sine function
1. add a test cif file under test_files/space_group_struct/ directory
2. add a unittest for the fix in test_kpath.py
|
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| 970
|
Chemenv tests
|
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[] | 2017-12-27T09:18:08
| 2017-12-27T10:04:50
|
2017-12-27T10:04:50Z
|
CONTRIBUTOR
|
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## Summary
Added tests in chemenv.
Added timing info in chemenv.
Small bug fixes in chemenv.
|
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MDExOlB1bGxSZXF1ZXN0MTYwMzAxNzg0
| 971
|
Ewald site energy
|
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[] | 2017-12-27T20:57:21
| 2017-12-27T22:04:25
|
2017-12-27T22:04:25Z
|
CONTRIBUTOR
|
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## Summary
Added a function to EwaldSummation that returns the energy of a single site. Adds the values along the columns of the `total_energy` matrix.
## Additional dependencies introduced
None
|
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MDU6SXNzdWUyODQ3OTczNTQ=
| 972
|
Charged Structures and Ewald Summation
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[] | null |
[
"I am not sure how LAMMPS and GULP deals with charged structures. In pymatgen, the implementation using a jellum background to maintain neutrality. One way to check is to comment out the jellum interaction and sees if it leads to the same answer.",
"Are you sure that pymatgen uses a Jellium correction? I don't see it implemented in the code, but could certainly be mistaken. \r\n\r\nGULP uses a charged cell correction. When I add the same correction to EwaldSummation, I get the same answer as GULP and LAMMPS.\r\n\r\nI will soon open a PR with the code that adds the charged-cell correction to EwaldSummation."
] | 2017-12-27T21:15:50
| 2017-12-28T21:43:16
|
2017-12-28T21:43:16Z
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CONTRIBUTOR
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I am unable to reproduce the Ewald summation result from `test_ewald.py`. For the same structure file, I get an energy of -1123 eV using LAMMPS, GULP, and [mint](http://github.com/materials/mint), yet the Ewald summation value listed in the unit test is -1116 eV/atom.
Am I correct in assuming that this difference between pymatgen and these codes is the result of pymatgen not supporting charged cells? I am basing this assumption based on the warning listed in `total_energy`.
## System
* Pymatgen version: master
* Python version: 3.6
* OS version: Windows
## Summary
* Ewald Summation returns different results than other codes
* Documentation unclear about whether it supports charged structures
## Suggested solution
* Add explanation about charged structures and pymatgen in documentation
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https://github.com/materialsproject/pymatgen/pull/973
| 284,829,453
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MDExOlB1bGxSZXF1ZXN0MTYwMzI1Njk2
| 973
|
Added charged cell correction to EwaldSummation
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[
"I see that this fails some unit tests. Sorry for not catching it. I'll clean that up soon.",
"Thanks!"
] | 2017-12-28T02:35:27
| 2017-12-28T21:19:54
|
2017-12-28T21:19:46Z
|
CONTRIBUTOR
|
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## Summary
Added charge cell correction to Ewald summation method. Ewald summation now exactly matches results for Ewald calculations from LAMMPS and GULP.
See discussion in #972
## Additional dependencies introduced
None
|
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|
Add charges to Composition based on oxidation state guesses
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[
"Thanks."
] | 2017-12-28T16:46:21
| 2017-12-28T23:08:40
|
2017-12-28T23:08:35Z
|
CONTRIBUTOR
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Added a function that returns a copy of a Composition decorated using oxidation states determined from `oxi_state_guesses`. Also refactored the `oxi_state_guesses` to move the computation of likely oxidation states to a private utility function so that the guessing logic could return both the average oxidation states for each element and the oxidation states for each site.
As part of this modification, the `oxi_state_guesses` function now returns a tuple of operations rather than a list but is otherwise unchanged. I could easily modify the code to still return a list, but decided it was unnecessary since both collections are iterable and addressable.
## Summary
* Added operation for adding guessed charges to Composition object
## Additional dependencies introduced (if any)
None
|
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MDExOlB1bGxSZXF1ZXN0MTYwNTk5ODc2
| 975
|
Some bug fixes for Gaussian
|
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[
"Would it also be possible to squash-merge so that my old commits don't keep appearing? Thanks!",
"Thanks. I actually do squash and merge. But you need to merge latest changes from origin before submitting a PR in order for the old commits not to appear.\r\n\r\nAs for Zmatrix, I agree. I suggest you start a core.molecule module and put it in there. I have wanted to separate MOlecule and Structure for some time. I can easily do this in a backwards compatible manner.",
"Also, pls look at the codacy review. There seems to be new issues introduced.",
"I like the idea of creating a new Molecule class. I will get to that when I have time.\r\n\r\nI may be wrong, but I think Codacy only flagged the issue as new because I modified the line during the PEP8 clean-up. The issue it was complaining about is still present in the original code. I found a way to fix the issue, so Codacy should be happy now either way.",
"Oh you misunderstood. I am not asking to create a new molecule class. I am merely asking for you to create the zmatrix class in a molecule module. We will move the existing Molecule class there later.",
"That's what I meant. I have no idea why I wrote \"class\" instead of \"module\"..."
] | 2017-12-30T20:21:21
| 2017-12-31T05:36:20
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2017-12-31T05:36:20Z
|
NONE
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## Summary
The current Gaussian module cannot handle multi-parameter keywords and multi-line route cards in input and output files (see the l-cysteine test files for examples). This pull request fixes these bugs and has some minor changes.
* Fixed the multi-parameter keyword issue. Multi-parameter keywords such as opt=(tight, maxcycles=20) are now of the form {"opt": {"tight": None, "maxcycles": 20}}.
* Fixed the multi-line issue for input and output files.
* Fixed another bug that raised a KeyError when there was no space between a z-matrix variable name and the equal sign.
* Added test files (l-cysteine.inp and l-cysteine.out) and unit tests for these cases.
* Implemented a way to recognize the title of a Gaussian run from its output file.
* The method to_input was changed to not force the user to write the returned object to file. If the user wants to write the input file, they can always do it with the write_file method of the returned input object. Also, the default title is not "restart" anymore, but the title of the output file.
* Added an underscore to all the helper functions and regex patterns that shouldn't be used by the user, but would otherwise appear as methods/attributes when e.g. using ipython.
* Established more consistency between the attribute names of input and output objects. E.g. the route card is "route_parameters" for GaussianInput and "route" for GaussianOutput, which is less intuitive to users than having the same names.
* Some PEP8 clean-up.
EDIT: After running codacy, I fixed an old issue where a dictionary was called "dict". There is one more old issue, but I'd have to go through a lot of code to figure out how to fix it. I'll do it in a later PR.
## TODO
This is only semi-related to this PR, but I would like to get feedback before coding. The GaussianInput has a method get_zmatrix(). However, I think the z-matrix is important enough that it should actually be a method for the molecule and not just limited to GaussianInput. I think the best way to do this would be to actually have a Zmatrix(MSONable) class to allow for greater flexibility. What would be the best place for it? core.structure, core.site, or a new module core.zmatrix?
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Minor COHP clean-up
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[] | 2017-12-31T06:53:00
| 2018-01-02T16:41:55
|
2018-01-01T01:03:06Z
|
NONE
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## Summary
Minor clean-up for COHP-related modules.
* Removed unnecessary imports and variables.
* Replaced type with isinstance methods.
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| 285,362,958
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MDExOlB1bGxSZXF1ZXN0MTYwNjgwMjQ3
| 977
|
Wavecar
|
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[
"Many thanks for your contributions!"
] | 2018-01-02T06:31:26
| 2018-01-02T17:59:48
|
2018-01-02T09:48:58Z
|
CONTRIBUTOR
|
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## Summary
This pull request adds support for reading WAVECAR output files from VASP. It is essentially a python version of [WaveTrans](https://www.andrew.cmu.edu/user/feenstra/wavetrans/) by Feenstra and Widom with some added functionality.
* adds a Wavecar class to pymatgen.io.vasp.outputs
* 100% test coverage of the added code
## Additional dependencies introduced (if any)
* N/A
## TODO (if any)
While I don't consider this a work in progress, the following may be desired (and I would be willing to look into upon request):
* spin-polarization support
* partial charge density plotting from the wavefunctions
|
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MDU6SXNzdWUyODU3NDkyMjU=
| 978
|
Cann't find get_environments.py) in the pymatgen/scripts directory
|
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[
"@davidwaroquiers Pls handle.",
"A tutorial is currently being written. Be patient it should be out in a few weeks.\r\nThe get_environments.py script has been moved to pymatgen/cli",
"The tutorial can now be accessed via http://matgenb.materialsvirtuallab.org/2018/01/01/ChemEnv-How-to-automatically-identify-coordination-environments-in-a-structure.html . "
] | 2018-01-03T17:07:30
| 2018-04-24T16:04:09
|
2018-04-24T16:04:09Z
|
NONE
|
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|
## System
* Pymatgen version: 2017.9.23
* Python version: 3.5
## Summary
* Cann't find get_environments.py and pymatgen/scripts directory
* Please provide some examples about analyzing chemical environments and coordination geometries
|
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MDExOlB1bGxSZXF1ZXN0MTYwOTg3NTQ2
| 979
|
Fix access to materials project
|
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[] | 2018-01-03T19:54:33
| 2018-01-05T17:12:47
|
2018-01-05T17:12:47Z
|
MEMBER
|
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## Summary
Fixed access to materials project for get_environment.
* Excluded the setup of the access to the materials project data base (not necessary)
* removed chemenv_configuration.has_materials_project_access because it is not defined
## TODO
If the API_KEY is not supplied it raises an error. A treatment might be necessary.
|
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MDExOlB1bGxSZXF1ZXN0MTYxMDE4MDI3
| 980
|
Pourbaix rev
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[] | 2018-01-03T22:50:26
| 2019-04-04T02:41:36
|
2018-01-04T05:03:31Z
|
CONTRIBUTOR
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## Summary
Small bug fix that affects region shading for pourbaix stable domains.
|
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MDExOlB1bGxSZXF1ZXN0MTYxMjIzOTYz
| 981
|
modify barrier label for get_plot and change criteria to connect end …
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[] | 2018-01-04T21:44:06
| 2018-01-04T21:48:01
|
2018-01-04T21:48:01Z
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NONE
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* modify barrier label for get_plot
* change criteria to connect end points for combine_neb_plots
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| 286,177,548
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MDExOlB1bGxSZXF1ZXN0MTYxMjYyNjUz
| 982
|
Add site finder using Voronoi Tessellation algorithm
|
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[
"Pls look at the codacy reviews and at least try to fix the red warnings.",
"Red warnings are fixed."
] | 2018-01-05T02:58:35
| 2018-01-05T17:12:27
|
2018-01-05T17:12:27Z
|
CONTRIBUTOR
|
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|
## Summary
Add site finder using Voronoi Tessellation algorithm
* Added `TopographyAnalyzer` class
* Added `VoronoiPolyhedron` class and `calculate_vol` method.
* Unittest for LiFePO4 case
* Minor formatting
## TODO (if any)
None
|
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MDExOlB1bGxSZXF1ZXN0MTYxNDI0MTM1
| 983
|
bug fix in FEFFDictSet from_directory method
|
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[] | 2018-01-05T20:46:47
| 2018-02-14T21:53:48
|
2018-01-06T00:07:56Z
|
CONTRIBUTOR
|
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|
## Summary
Fixed a bug in the FEFFDictSet.from_directory method, allows shell distance matrix comparison between absorbing atoms with different distance matrix shape when determining the absorbing index.
|
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MDExOlB1bGxSZXF1ZXN0MTYxNDQ3MjY2
| 984
|
Bug fix in lammps data
|
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[] | 2018-01-05T23:16:03
| 2018-01-06T00:07:32
|
2018-01-06T00:07:32Z
|
CONTRIBUTOR
|
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|
## Summary
Fix a bug where the molecule-ID column is edited when calling `LammpsData.structure` attribute.
|
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MDExOlB1bGxSZXF1ZXN0MTYxNDcyODI1
| 985
|
Make the conversion battery module useful for multivalent cations
|
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[] | 2018-01-06T09:08:48
| 2018-01-06T16:02:54
|
2018-01-06T16:02:54Z
|
CONTRIBUTOR
|
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|
## Summary
Applied the same treatment as we did for insertion electrodes. e.g., When the ion oxidation state is 2+, the voltage reduced to half, and the capacity multiplied by 2.
This new pull request is to add additional test for previous pull request #898
* added unittest to /pymatgen/apps/battery/tests/conversion_battery.py
* added test_file to /test_files/MnO2_batt.json; using Mg-MnO2 system
## Additional dependencies introduced (if any)
* N/A
## TODO (if any)
*N/A
|
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MDExOlB1bGxSZXF1ZXN0MTYxNDc3MjU4
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Avoid `inspect.getfullargspec` to maintain compatibility with py2.7
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[
"This PR contains far too many commits. Also, we are cutting Py2.7 support from 2018.",
"The majority of the commits have been already merged in #961 \r\nand indeed the changes introduced by this PR are minimal as can be seen in https://github.com/materialsproject/pymatgen/pull/986/files\r\nPerhaps github reports 65 commits because you have reverted the merge in\r\n4a6db8133d35f6ed2349d9ac3cc8baed31146853\r\n\r\nFor what concerns py2.7 support:\r\nThe PR address a regression introduced in 38122517b13e0e039254977d6cdaab132f8df451\r\nas `inspect.getargspec` is deprecated in py3.6 while `inspect.getfullargspec` is not \r\navailable in py2.7. \r\nSo we have refactored the code to avoid using introspection at run time and \r\nwe consider the new approach much safer.\r\n\r\n The pymatgen documentations explicitly states:\r\n\r\n>From v2018.1.1, new features implemented in pymatgen no longer need to support Py2k (i.e., unittests do not need to pass Py2k testing), though existing features will still be Py2k > compatible.`\r\n\r\nHere we are not adding a new feature, we are just refactoring a preexisting API that \r\nstopped working after the recent modifications.\r\nThis piece of code is being used in production with py2.7 and py3.6 and we need to maintain\r\npy2k compatibility for this existing feature. \r\n",
"Fine, I will merge this time. But note that we will not support Py2 going forward. This means that it is entirely possible that some features will be introduced in core classes that will break Py27 compatibility. I would suggest you move to Py3k. We have given ample notice since 2017 that we will be making this move. And in fact, future versions of numpy and scipy will be py3k only."
] | 2018-01-06T11:46:45
| 2018-01-06T17:49:30
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2018-01-06T17:49:30Z
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CONTRIBUTOR
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Bug fix for DiffusionAnalyzer.from_vasprun()
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[] | 2018-01-09T11:11:05
| 2018-01-09T13:59:34
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2018-01-09T13:59:33Z
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CONTRIBUTOR
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Commit c99dba04ebba648909ab5f71a7593f26cb388f11 introduces a bug in the `from_structures()` method if this is called from the `from_vaspruns()` method. This commit reverts this change.
In `from_vasprun()`, structures are collected as a generator function, using `get_structures()`. The `from_structures()` method, however, expects a list of structures, and tries to access `structures[0]`. This fails if a constructor has been passed in, instead of a list (as is the case with `from_vasprun()`).
This commit:
a) reverts the behaviour of `from_structures()` to explicitly store the first structure passed in.
b) generates a list of structures in `from_vaspruns()` before calling `from_structures()`, for
consistency with the argument types in the `from_structures()` docstring.
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Miscellaneous updates and additional functionalities
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[] | 2018-01-11T01:54:19
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2018-01-11T03:22:29Z
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CONTRIBUTOR
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## Summary
A set of some small, but nonetheless useful commits.
* MPRester now has the conventional_unit_cell option (False by default) for methods of querying entries to return the standard conventional unit cell instead of the primitive unit cell by using SpacegroupAnlayzer. Prior, the user can just get the cif of the conventional unit cell using the key "cifs.conventional_standard" when querying the MAPI, however the user would then have to convert the cif to a Structure object if they wanted to use it in pymatgen. This alternative is a quicker way to get the conventional unit cell.
* The get_plot() method in the WulffShape class now has a custom_color optional parameter, a dict with the keys being the Miller index and value being the color. Allows the user to edit the facet colors of their Wulff shape.
* The get_primitive_structure method of the Structure class now has a new optional parameter called constrain_latt, a list of 6 bools corresponding to a list of lattice parameters as such: [a, b, c, alpha, beta, gamma]. If one of these bools are True, the get_primitive_structure will limit its search for reduced structures that retain the lattice parameter corresponding to the bool that was set to True. e.g.: constrain_latt=[False, False, True, False, False, False] means that only a reduced structure with the same c lattice parameter as the initial structure will be considered as a primitive structure. The usual behavior of get_primitive_structure is retained for default parameters (constrain_latt=[False, False, False, False, False, False]).
*The oriented_unit_cell of the Slab class now corresponds to the reduced oriented unit cell (the smallest possible oriented unit cell) using the new constrain_latt parameter. For anyone who wants to get accurate (converged) surface energies that require consistent kpoints among the bulk and slab calculations, this will significantly reduced the cost of calculations. This concludes issue #950 .
* Reduced EDIFF from 1e-6 to 1e-4 for MVLSlabSet, the former is way too strict and costly.
* Several methods in SurfaceEnergyPlotter now have the option of omitting clean surfaces or doped surfaces.
* Fixed bug in nonstoichiometric_symmetrized_slab for SlabGenerator
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MDU6SXNzdWUyODc5MzczNDE=
| 989
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Surface energy predictor web app
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[
"This is fine, but it is not a pymatgen Issue. Also, I need to be convinced of the fact that broken bond extrapolation will lead to reasonable estimates. "
] | 2018-01-11T21:54:53
| 2018-01-11T23:22:50
|
2018-01-11T23:22:50Z
|
CONTRIBUTOR
|
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A Materials Project web app that allows the user to enter in an MPID or element and a Miller index and in return, will get a surface energy.
With the addition of the surface data into the MAPI, we can use simple broken bond rules to extrapolate a cohesive energy term and use that cohesive energy to predict surface energy of facets that are not present in the database. The app will do this every time a user enters in a Miller index not present in the MAPI and the app will also return statistical data such as how accurate the prediction is based on R2 and standard error of estimate of existing data.
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fit_to_structure() not giving the required symmetry in elastic tensor
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"Hi azheeshan, I think the problem is here:\r\n\r\n```\r\nelastic_mat_sym = (elastic_tensor.fit_to_structure(structure=st)).voigt\r\n```\r\n\r\nwhere the tensor is being fit to the primitive cell, rather than the conventional cell. The cartesian basis vectors aren't the same for these two crystal settings, and the axes of symmetry aren't aligned with the cartesian axes in the primitive case. You can either rotate the primitive structure so that it has the same basis as the conventional cell or just symmetrize with respect to the conventional cell and the expected equivalences in the tensor should result.",
"Thanks for the quick reply @montoyjh. I fitted to the conventional structure which gave me the symmetrized elastic tensor within numerical precision:\r\n```\r\nimport pymatgen as pmg\r\nfrom pymatgen import MPRester\r\nfrom pymatgen.analysis.structure_analyzer import *\r\nimport json\r\nfrom pymatgen.analysis.elasticity.tensors import Tensor\r\n\r\n(print(pmg.__version__))\r\nm = MPRester()\r\ndata = m.query(criteria={\"pretty_formula\":\"NaCl\"},\r\n properties=[\"pretty_formula\",\r\n \"cif\",\r\n \"elasticity\",\r\n \"task_id\"])\r\nprint(data[0]['pretty_formula'])\r\nelem_data = data[0]\r\nst = pmg.Structure.from_str(elem_data['cif'], fmt = \"cif\")\r\nanalyzer = pmg.symmetry.analyzer.SpacegroupAnalyzer(st)\r\nstconv = analyzer.get_conventional_standard_structure()\r\n#analyzer_conv = pymatgen.symmetry.analyzer.SpacegroupAnalyzer(stconv)\r\nprint((stconv.lattice.matrix))\r\nprint(analyzer.get_crystal_system())\r\nprint(analyzer.get_point_group_symbol())\r\nelastic_mat = elem_data['elasticity']['elastic_tensor_original']\r\nelastic_tensor = Tensor.from_voigt(elastic_mat)\r\nelastic_mat_sym = (elastic_tensor.fit_to_structure(structure=stconv)).voigt\r\nprint('Printing original elastic tensor')\r\nprint('\\n'.join([''.join(['{:15.6}'.format(item) for item in row]) for row in elastic_mat]))\r\nprint('Printing symmetrized elastic tensor')\r\nprint('\\n'.join([''.join(['{:15.6}'.format(item) for item in row]) for row in elastic_mat_sym.tolist()]))\r\n```\r\nproduces:\r\n```\r\n2017.12.30\r\nNaCl\r\n[[ 5.69169356e+00 0.00000000e+00 3.48515715e-16]\r\n [-3.48515715e-16 5.69169356e+00 3.48515715e-16]\r\n [ 0.00000000e+00 0.00000000e+00 5.69169356e+00]]\r\ncubic\r\nm-3m\r\nPrinting original elastic tensor\r\n 46.3494 10.711 10.7109 0.0 0.0 0.0\r\n 10.7109 46.3499 10.7109 0.0 0.0 0.0\r\n 10.7109 10.711 46.3496 0.0 0.0 0.0\r\n 0.0 0.0 0.0 12.3016 0.0 0.0\r\n 0.0 0.0 0.0 0.0 12.3016 0.0\r\n 0.0 0.0 0.0 0.0 0.0 12.3016\r\nPrinting symmetrized elastic tensor\r\n 46.3496 10.7109 10.7109 6.55855e-16 2.8381e-15 -2.16236e-15\r\n 10.7109 46.3496 10.7109 2.8381e-15 6.55855e-16 -2.8381e-15\r\n 10.7109 10.7109 46.3496 2.16236e-15 2.16236e-15 -6.55855e-16\r\n 6.55855e-16 2.8381e-15 2.16236e-15 12.3016 -7.53255e-16 7.53255e-16\r\n 2.8381e-15 6.55855e-16 2.16236e-15 -7.53255e-16 12.3016 7.53255e-16\r\n -2.16236e-15 -2.8381e-15 -6.55855e-16 7.53255e-16 7.53255e-16 12.3016\r\n```\r\nPS: My code in the earlier post had some mistakes (some variables already defined in my notebook workspace, so I corrected them here)."
] | 2018-01-12T05:09:00
| 2018-01-29T18:16:41
|
2018-01-12T07:20:46Z
|
NONE
|
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## System
* Pymatgen version: 2017.12.30
* Python version: 3.6
* OS version: OS X 10.11.6
## Summary
* The fit_to_structure() function inside [tensors.py](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/elasticity/tensors.py) is supposed to return a tensor that is invariant with respect to symmetry operations corresponding to a structure. I tried to use this function to symmetrize the elastic_tensor_original (obtained from the materials project API) according to the crystal symmetry (since the elastic_tensor_original sometimes does not obey the symmetry requirements, see example). For a cubic structure, this means the elastic tensor should have only three independent components and should be of the form given in, for instance, Eq (5) of [this paper](https://arxiv.org/pdf/1410.0065.pdf). However, after applying this function to the elastic tensor of cubic crystal, I don't get the required form. Am I interpreting the use of the function wrong or are there some symmetry operations that the function does not use?
## Code
```
import pymatgen as pmg
from pymatgen import MPRester
from pymatgen.analysis.structure_analyzer import *
import json
from pymatgen.analysis.elasticity.tensors import Tensor
(print(pmg.__version__))
m = MPRester()
data = m.query(criteria={"pretty_formula":"NaCl"},
properties=["pretty_formula",
"cif",
"elasticity",
"task_id"])
print(data[0]['pretty_formula'])
elem_data = data[0]
st = pymatgen.Structure.from_str(elem_data['cif'], fmt = "cif")
stconv = analyzer.get_conventional_standard_structure()
print((stconv.lattice.matrix))
analyzer = pymatgen.symmetry.analyzer.SpacegroupAnalyzer(st)
print(analyzer.get_crystal_system())
print(analyzer.get_point_group_symbol())
elastic_mat = elem_data['elasticity']['elastic_tensor_original']
elastic_tensor = Tensor.from_voigt(elastic_mat)
elastic_mat_sym = (elastic_tensor.fit_to_structure(structure=st)).voigt
print('Printing original elastic tensor')
print('\n'.join([''.join(['{:15.6}'.format(item) for item in row]) for row in elastic_mat]))
print('Printing symmetrized elastic tensor')
print('\n'.join([''.join(['{:15.6}'.format(item) for item in row]) for row in elastic_mat_sym.tolist()]))
```
## Output
```
2017.12.30
NaCl
[[ 5.69169356e+00 0.00000000e+00 3.48515715e-16]
[-3.48515715e-16 5.69169356e+00 3.48515715e-16]
[ 0.00000000e+00 0.00000000e+00 5.69169356e+00]]
cubic
m-3m
Printing original elastic tensor
46.3494 10.711 10.7109 0.0 0.0 0.0
10.7109 46.3499 10.7109 0.0 0.0 0.0
10.7109 10.711 46.3496 0.0 0.0 0.0
0.0 0.0 0.0 12.3016 0.0 0.0
0.0 0.0 0.0 0.0 12.3016 0.0
0.0 0.0 0.0 0.0 0.0 12.3016
Printing symmetrized elastic tensor
42.3646 12.3458 13.0611 -1.01727e-08 2.29721e-08 -1.01155
12.3458 43.0799 12.3458 -3.36488e-08 6.46425e-09 -7.46792e-08
13.0611 12.3458 42.3646 -2.98251e-08 1.98117e-08 1.01155
-1.01727e-08 -3.36488e-08 -2.98251e-08 13.9365 1.01155 7.29712e-09
2.29721e-08 6.46425e-09 1.98117e-08 1.01155 14.6518 -1.14151e-08
-1.01155 -7.46792e-08 1.01155 7.29712e-09 -1.14151e-08 13.9365
```
## Comments
Clearly, both the elastic_tensor_original and symmetrized version don't have the required symmetry of cubic elastic tensor (for example, C11 is not equal to C22).
|
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| 288,114,240
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MDExOlB1bGxSZXF1ZXN0MTYyNjI2NzY4
| 991
|
Fix parsing of vasprun containing *
|
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[] | 2018-01-12T13:10:01
| 2018-01-12T13:57:41
|
2018-01-12T13:57:41Z
|
MEMBER
|
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VASP 5.4.4 introduced calculation of the dielectric constant based on the current-current response.
When using small values of the `CSHIFT` parameter (necessary to produce optical spectra with no broadening), this can result in anomalously large values of the current-current response, which VASP writes to the vasprun.xml files as `***********`.
I've updated the `Vasprun` parser to use the specific parsing method that can detect this bad behaviour.
|
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| 288,198,278
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MDExOlB1bGxSZXF1ZXN0MTYyNjg5NTc3
| 992
|
Fix get_reconstructed_band_structure method
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[] | null |
[
"There are failing tests due to tabs. Pls fix. Thanks.",
"Ok, this has been fixed.\r\n\r\nApologies for the messy commit history."
] | 2018-01-12T17:53:04
| 2018-01-15T13:42:22
|
2018-01-15T13:42:22Z
|
MEMBER
|
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Use numpy concatenate function to fix the `pymatgen.electronic_structure.bandstructure.get_reconstructed_band_structure()` function.
Fixes #543
I've also added a basic test to ensure this method is not broken in the future.
|
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| 288,280,007
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MDExOlB1bGxSZXF1ZXN0MTYyNzUwNTAw
| 993
|
Small fix to speed up primitive structure search under specific lattice constraints
|
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[] | 2018-01-12T23:57:19
| 2018-01-12T23:59:38
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2018-01-12T23:59:38Z
|
CONTRIBUTOR
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Structure.get_primitive_structure() previous uses .lattice instead of ._lattice when searching for primitive cells with certain lattice constraints. Switching to the latter will make it 17x faster.
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| 994
|
Fix bug in task.reset
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"Pls submit a PR that does not include past commits. it is impossible to know what is happening with this PR."
] | 2018-01-14T00:27:58
| 2018-01-14T00:48:33
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2018-01-14T00:48:33Z
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|
Bug fix in task.reset
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[] | 2018-01-14T18:34:06
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2018-01-15T16:11:18Z
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CONTRIBUTOR
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I had to rebase my origin/master to make it based on upstream/master
followed by a force-push to get rid of the old commits.
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|
Thermodynamic properties from phonon DOS
|
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[] | 2018-01-15T12:41:54
| 2018-01-15T16:11:06
|
2018-01-15T16:11:06Z
|
CONTRIBUTOR
|
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## Summary
* Extract thermodynamic properties from the integration on a phonon DOS
* Plotter of the thermodynamic properties
* option to change units in phonon BS and DOS plotters
* tests
|
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| 997
|
Minor bug fixes
|
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[] | 2018-01-16T11:38:41
| 2018-01-16T14:13:06
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2018-01-16T14:13:06Z
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|
Minor update to extract references from CIF files + test
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[
"Pybtex is an optional req. I would prefer to keep it that way given that it is not very Py3 friendly.",
"Ok, have updated the import accordingly."
] | 2018-01-17T20:58:53
| 2018-01-18T16:58:16
|
2018-01-18T16:58:16Z
|
MEMBER
|
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## Summary
Now uses pybtex, more robust. Updated test.
## Additional dependencies introduced (if any)
None (pybtex already requirement).
## TODO (if any)
None
|
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units for phonon BS
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[] | 2018-01-18T00:48:41
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2018-01-18T01:13:24Z
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CONTRIBUTOR
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This PR completes the PR #996 about the units in the PhononBSPlotter.
A few lines were missing in the previous one. Sorry for the bothering.
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MDU6SXNzdWUyODk1OTEyNTQ=
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|
Plotting phase diagrams for more than 4 elements
|
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[
"There is no way to plot a phase diagram in more than 4 terminals in 3D space."
] | 2018-01-18T11:13:00
| 2018-01-18T13:22:41
|
2018-01-18T13:22:41Z
|
NONE
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Hello,
I would like to plot the phase diagram of a metal composition with more than 4 elements but now it's possible just for 1-4 elements. It says: `ValueError: Only 1-4 components supported!`
Would you please guide me if there is any possibility to solve the problem?
|
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