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fixes in the get_environment script
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[] | 2018-01-18T12:30:37
| 2018-01-18T14:09:11
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2018-01-18T14:09:11Z
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MEMBER
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Fixed the access to the materials project in a more thorough way and adapted the test accordingly. Moreover, a small bug in the reading in of the chemenv strategy was fixed.
I introduced an additional dependency on SETTINGS in chemenv_strategies.py and its test test_chemenv_config.py.
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Standalone function for d_hkl to define size of structures
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[
"Don't think there is right now. By all means implement it in the Slab class. ",
"A function to go from three PeriodicSites to output a (h,k,l) tuple would be nice to have too.",
"@mkhorton Just to clarify, do you mean something that would generate a plane with any 3 PeriodicSites and then return the hkl of that plane?",
"@richardtran415 yes, that's exactly what I meant -- to my knowledge this isn't in pymatgen currently?",
"@shyuep \r\nActually I think a function for getting d_hkl might be more at home as a method of the Lattice class, its not standalone, but at least its accessible outside xrd.py, but I agree the function to describe slab thickness in terms of nlayers should be part of class Slab().",
"that's fine. Implement then."
] | 2018-01-19T08:50:16
| 2018-02-06T03:33:54
|
2018-02-06T03:33:54Z
|
CONTRIBUTOR
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Is there a stand alone function that returns d_hkl given a structure and a Miller index? I know the class XRDPattern() has something that gets d_hkl, but I don't that can be used outside the class right? This would be useful for things like if we wanted a standard nlayer of atoms of slab thickness or gb thickness thats not defined by length scale where the number atoms would vary across different systems (e.g. a 10 Angstrom slab/gb of Cs would only have n layer of atoms while the same size slab/gb for Fe would have a larger number of layer of atoms.
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MDU6SXNzdWUyOTAwNjU2NjA=
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BoltzTrap2
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[
"No objections. Are you volunteering to do the rewrite?",
"Nope. Should probably be some of the thermoelectrics people since they will be using the new code anyways and will need the secondary analysis currently implemented in our boltztrap module. \r\n\r\nI'm relying on your authority to assign them this task :)",
"@computron can I ask you to suggest who is the best candidate to do this (not asking your esteemed self to do it)? It does not have to be someone from your group. ",
"I had a look at the new implementation of Boltztrap and I find it could be great to interface pymatgen with it, both solving different problems and having a much smoother boltztrap module.\r\nI think I could spend sometime on it.\r\nOne thing that could be limiting is that bzt2 is only python3.\r\nThis means that the user will be forced to upgrade to use the boltztrap.\r\nProbably not a big deal because it is just matter of time, as also pymatgen will \r\nstop supporting py2 soon (right?)",
"pmg already abandoned Py2 support from 2018. New code does not have to support Py2.\r\n\r\nThank you in advance for volunteering to implement. I am sure it would be a good help to the research community.",
"Update:\r\nI've been working on a new module to interface pymatgen and BoltzTraP2.\r\nI pushed a first version in my fork:\r\n[boltztrap2](https://github.com/fraricci/pymatgen/tree/boltztrap2)\r\n\r\nIn the example folder, you can find a ipynb:\r\n[How to use Boltztra2 interface](https://github.com/fraricci/pymatgen/blob/boltztrap2/examples/How%20to%20use%20Boltztra2%20interface.ipynb)\r\nthat explain roughly how it works.\r\nThere, PbTe case has been considered and the results shown are comparable \r\nwith results from BZT1.\r\n\r\nThe module is still under development, no documentation is provided, so\r\nfor the moment I won't do any pull request to the master.\r\n\r\nIf someone (thinking about @computron, @albalu, @hautierg,... ) want to \r\nhave a look and have comments, it would be great.",
"From our side I think @albalu and @ardunn should take a look, they will likely be the most heavy users (Alireza in short term, Alex in long term)",
"FYI: the development of BoltzTraP2 is now on gitlab\r\nhttps://gitlab.com/sousaw/BoltzTraP2",
"Hi @fraricci \r\nthanks for the new BoltzTrap2 interface. \r\nDo you plan to implement a read/load function for Boltztrap2 calculations? \r\nSo you load the .btj and can run your Plotter than? This would avoid a subsequent boltztrap run for each plot. \r\nOr did you implement it and I just do not find it. ",
"Hi @ziechys , boltztrap2 has already such function. \r\nI have to see if it's better to implement it in a different way or the native one is good enough. \r\nIt's an important function so I'll put it higher in the todo list.\r\nThanks.",
"@fraricci \r\nIs it JSON? If not, it might still be usefull to have something that is JSON or atleast BSON compliant. ",
"Taken care of in #1307 "
] | 2018-01-19T18:25:58
| 2018-12-17T16:20:20
|
2018-12-17T16:20:19Z
|
NONE
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## Summary
It looks like Madsen group has released a new major version upgrade of BoltzTrap that is written in python/cython/C++ : https://arxiv.org/abs/1712.07946
The current BoltzTrap module is very hairy. It would be good to get it rewritten to wrap the new BoltzTrap2 module and in the process improve the code quality and documentation.
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MDExOlB1bGxSZXF1ZXN0MTY0MTA3NDk4
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Add term symbol related properties
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[] | 2018-01-20T03:02:52
| 2018-01-25T23:57:01
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2018-01-25T23:57:01Z
|
CONTRIBUTOR
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## Summary
Add termsymbol related properties to Element class
Specifically, these three are the added properties
* Add valence property:
Find the total number of valence electrons from full_electron_configuration of the Element
Do not work for those with two unfilled subshells
* Add term_symbols property:
All possible Russell-Saunders term symbol of the Element (J included)
* Add ground_state_term_symbol property:
Based on Hund's rule, give the ground state term symbol
Also, small fix for the method get_shannon_radius
* The self._oxi_state returns a float value, however, the keys in radii{dict} are int. So change self._oxi_state to int
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MDExOlB1bGxSZXF1ZXN0MTY0MzExMDU2
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Addtional change on get_environment script
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[
"Pls fix the Code Quality Review issues. These are valid concerns.",
"Thanks."
] | 2018-01-22T13:49:43
| 2018-01-22T17:38:54
|
2018-01-22T17:38:45Z
|
MEMBER
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## Summary
For now, I excluded two strategies to interpret the structure environments from the get_environment script because they are not fully implemented and cause errors if they are chosen by the user. Moreover, I included some error handling for reading in the sites to visualize the coordination environment as a function of distance and angle parameters. Thereby, also a bug was resolved (one could not give one site as an input, it had to be 2) Also, some error handling was introduced when reading in the multiplicity to construct the supercell that will be visualized.
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Interface
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[] | 2018-01-24T03:23:44
| 2018-01-24T05:19:14
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2018-01-24T05:19:13Z
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CONTRIBUTOR
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## Summary
Modified interface_reaction.py and add a Jupyter notebook as the tutorial of this interface_reactions module.
* Add the option to use convex hull energy for reactants for reaction energy calculation.
* For reactants with no matching entry, always use the convex hull energy as reactant energy.
* Add a Jupyter notebook Interface Reactions.ipynb as the tutorial of using interface_reactions module.
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MDExOlB1bGxSZXF1ZXN0MTY1MTc3MjYz
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Added several new OPs and optimized parameters involved in OP computation.
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[
"Can you do a rebase before sending a PR? This contains commits from Aug.",
"Also, the tests failed.",
"I did rebase. It's this weird github behavior that the entire PR history would pop up again. We had this discussion before (in December) I think.\r\n\r\nI know that the tests failed. I'm working on that. It takes a little longer because I take the opportunity to clean up all the warnings that some classes would be shuffled around with pymatgen >= 2018.",
"@shyuep, do you think you can merge this? All tests passed successfully.",
"I will merge it this time. But I am not going to next time unless the commits properly tell me what is being changed. There are others who have submitted PRs and they don't seem to encounter this issue.",
"@shyuep, I know that you can avoid that if you always get a new fork. But is that really sensible that you'd require that people do that every time---when you really want people to participate and contribute in as easy a way as possible? On the long run, I fear that we'd just make people walk away from pymatgen if we'd require them to always make new forks. Don't you agree that that could hurt us as an active developer community that tries to make this library as attractive, because as open and welcoming to new people as possible?",
"I am not insisting on new forks. But I don't think that's the only way to sync the fork. I never had these issues on other repos that I contribute to (e.g., FireWorks). https://help.github.com/articles/syncing-a-fork/ almost always works for me.\r\n\r\nI cannot believe your claim that creating new forks is the only way to do this. Surely Github cannot be that badly designed that the only alternative is for the lead maintainer to tolerate looking through > 100 and growing commits from every developer.",
"@nisse3000 I have ascertain the issues with why the commits are showing up. Essentially, it is a difference between using \"Squash and merge\" vs \"Merge commits\". For future PRs, I will do a merge commit and that should avoid duplicate commits. What I would suggest you do now is to do a trivial change (e.g., some minor doc fix), and resubmit a PR for that trivial change. I will then do a proper merge commit and that should resolve all these issues with the commit hisotry.",
"@shyuep, OK. Just made a test pull request."
] | 2018-01-25T17:13:57
| 2018-01-29T17:49:54
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2018-01-26T18:44:18Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MTY1MjA2NjEx
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Add timeout kwarg to enumlib + test
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[
"Py2 tests fail because TimeoutError is apparently new to Py3, but given the new Py2 deprecation policy I'll leave this as-is unless asked otherwise.",
"That's fine. We are not going to care about py2."
] | 2018-01-25T19:26:23
| 2018-01-25T21:46:51
|
2018-01-25T21:46:51Z
|
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## Summary
Adds a timeout kwarg to enumlib to automatically terminate if no enumerations are found within a specified length of time.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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Algorithm to convert Miller index to Somorjai microfacet/step notation for surfaces
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[
"I would say this is not of the highest priority unless you have a clear idea of the generalization approach."
] | 2018-01-25T20:35:56
| 2018-01-25T23:09:36
|
2018-01-25T23:09:36Z
|
CONTRIBUTOR
|
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|
The microfacet/step notation for Miller indices is a convention used to define the step and terraces of higher Miller index surfaces based on low Miller index surfaces. E.g. the (331) facet of an fcc crystal can be defined by the (111) facet.
For fcc system, an exmaple would be:
(hkl) = (n+1, n+1, n-1)
Microfacet notation: n_n(111) + 1_1(11-1)
Step notation: (n+1)(111)x(111)
This can be useful in catalytic studies where steps play an important role in surface energy and can also be used in studies involving modelling surface energy or work function relative to the values of low miller index facets.
However Somorjai has only developed this for cubic systems, it make take a little bit of further investigation to generalize this beyond cubic systems....
See:
Van Hove, M. A., & Somorjai, G. A. (1980). A new microfacet notation for high-Miller-index surfaces of cubic materials with terrace, step and kink structures. Surface Science, 92(2-3), 489–518. https://doi.org/10.1016/0039-6028(80)90219-8
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MDExOlB1bGxSZXF1ZXN0MTY1MjYwMDYz
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Add term symbol related properties
|
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[] | 2018-01-25T23:58:58
| 2018-01-26T00:13:06
|
2018-01-26T00:13:06Z
|
CONTRIBUTOR
|
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Add termsymbol related properties to Element class
Specifically, these three are the added properties
Add valence property:
Find the total number of valence electrons from full_electron_configuration of the Element
Do not work for those with two unfilled subshells
Add term_symbols property:
All possible Russell-Saunders term symbol of the Element (J included)
Add ground_state_term_symbol property:
Based on Hund's rule, give the ground state term symbol
Also, small fix for the method get_shannon_radius
The self._oxi_state returns a float value, however, the keys in radii{dict} are int. So change self._oxi_state to int
|
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MDExOlB1bGxSZXF1ZXN0MTY1MjYzMzk1
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Add term symbol related properties
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[] | 2018-01-26T00:24:30
| 2018-01-26T03:44:16
|
2018-01-26T03:44:16Z
|
CONTRIBUTOR
|
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Add termsymbol related properties to Element class
Specifically, these three are the added properties
Add valence property:
Find the total number of valence electrons from full_electron_configuration of the Element
Do not work for those with two unfilled subshells for now
Add term_symbols property:
All possible Russell-Saunders term symbol of the Element (J included)
Add ground_state_term_symbol property:
Based on Hund's rule, give the ground state term symbol
Also, small fix for the method get_shannon_radius
The self._oxi_state returns a float value, however, the keys in radii{dict} are int. So change self._oxi_state to int
|
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MDExOlB1bGxSZXF1ZXN0MTY1MzgzOTg3
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Moved import matplotlib inside the plotting function in interface_reactions.py
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[] | 2018-01-26T15:05:19
| 2018-01-26T15:08:21
|
2018-01-26T15:08:21Z
|
CONTRIBUTOR
|
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import matplotlib can cause problems in headless systems.
I moved the import to inside the plot function, this way the import problem only shows if plotting is required.
|
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MDExOlB1bGxSZXF1ZXN0MTY1NDc5NTQ3
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|
Clean up tasks.py
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[] | 2018-01-26T22:55:18
| 2018-01-26T22:55:26
|
2018-01-26T22:55:26Z
|
MEMBER
|
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## Summary
Short few sentences, and summary of the major changes in bullet
points
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. Provide a justification why that dependency is needed.
Especially frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* Feature 1 supports a, but not b.
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Trivial commit for testing.
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dhkl method and in_unit_planes parameter to SlabGenerator
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2018-01-27T04:56:46Z
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CONTRIBUTOR
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This pull request will add a new class method to the Lattice class, d_hkl which takes in a Miler index and returns the distance of the hkl plane from the origin.
Using the new d_hkl method, there is now an optional parameter in SlabGenerator called in_unit_planes=False, which if set to True, will measure the min_vac/slab_size in oriented unit cell height per dhkl instead of Angstroms. This has the advantage of building a slab based on a standard number of layer of atoms instead of an absolute length, especially for situations where you want a slab of Fe and Cs to have the same number of atoms for example. A 10Ang slab of Fe will have more atoms than Cs, but using in_unit_planes=True will give slabs with the same number of atoms.
* Fix 1 Only return reduced ouc if primitive=True
* Fix 2 Change EDIFFG of MVLSlabSet from -0.01 to -0.02
* Fix 3 When using get_entries in MPRester and setting conventional_unit_cell=True, the total energy (and therefore energy_per_atom) will be consistent with the new number of atoms in the cell.
## TODO (if any)
Algorithm to get Miller index from three PeriodicSites, will implement very soon
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[] | 2018-01-29T17:48:16
| 2018-01-29T17:49:14
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2018-01-29T17:49:14Z
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| 292,932,158
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MDExOlB1bGxSZXF1ZXN0MTY2MDkzNDUy
| 1,019
|
Fix small bug in MinimumVIRENN get_nn_info
|
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[] | 2018-01-30T20:48:45
| 2018-01-31T01:09:36
|
2018-01-31T01:09:36Z
|
MEMBER
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## Summary
VIRENN adds oxidation states to the input structure, causing a subtle bug in .get_periodic_image which was referencing the input structure instead of the oxi-state decorated structure.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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| 292,995,983
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MDExOlB1bGxSZXF1ZXN0MTY2MTQxMTE4
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|
Added a order parameter-computing function to StructureGraph
|
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[] | 2018-01-31T01:07:36
| 2018-01-31T03:08:26
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2018-01-31T03:08:26Z
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MDExOlB1bGxSZXF1ZXN0MTY2MzI4NDU0
| 1,021
|
Update structure_analyzer.py
|
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[] | 2018-01-31T17:37:30
| 2018-01-31T18:32:45
|
2018-01-31T18:32:45Z
|
CONTRIBUTOR
|
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Change initialization of coordination number dictionary keys to species rather than elements to match with species_string use later on. This avoids a key error when dealing with ions like 'Ba2+'
## Summary
Short few sentences, and summary of the major changes in bullet
points
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. Provide a justification why that dependency is needed.
Especially frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* Feature 1 supports a, but not b.
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MDExOlB1bGxSZXF1ZXN0MTY2MzQ2MDg2
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Removed bug from point_defects.py
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2018-01-31T19:50:49Z
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CONTRIBUTOR
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Interface
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[] | 2018-01-31T23:18:25
| 2018-02-01T00:22:16
|
2018-02-01T00:22:16Z
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CONTRIBUTOR
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## Summary
Fix bug in _get_grand_potential method.
* Fix the bug in get_grand_potential method, occurred when setting use_hull_energy=True for InterfacialReactivity class.
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| 293,365,862
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MDExOlB1bGxSZXF1ZXN0MTY2NDE2OTA5
| 1,024
|
Added decorate_structure_with_ce_info function to StructureGraph and corresponding unit test.
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[] | 2018-02-01T00:50:31
| 2018-02-01T03:22:26
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2018-02-01T03:22:26Z
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MDU6SXNzdWUyOTMzOTkyMDY=
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miller_index.py in util folder
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[] | null |
[
"No. Miller indices are not a util package thing. It is specific to planes in crystals. Leave it in surface.py.",
"OK"
] | 2018-02-01T04:22:09
| 2018-02-01T05:43:15
|
2018-02-01T04:56:27Z
|
CONTRIBUTOR
|
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For organization, I would suggest a python module in the utils folder for containing functions and classes related to Miller indices. Functions such as get_symmetrically_distinct_miller_indices in the surface.py module can be moved here along with other related functions such as a function to get_symmerically_equivalent_miller_indices, miller_index_from_sites, convert from hkl to hkil for hexagonal systems, parse to a latex format (e.g. (1,-2,3) would be ($1 \bar{2} 3$)), etc.
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MDU6SXNzdWUyOTM2NzE4MTQ=
| 1,026
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Structure objects changed during serialization/deserialization
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[] | 2018-02-01T20:26:03
| 2018-02-01T21:05:45
|
2018-02-01T21:05:45Z
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CONTRIBUTOR
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## System
* Pymatgen version: 2018.1.29
* Python version: 3.6.2
## Summary
* Structure and IStructure objects' compositions and sites are corrupted during pickle serialization
* Only occurs when sites have oxidation numbers
## Example code
```python
cscl = Structure(
Lattice([[4.209, 0, 0], [0, 4.209, 0], [0, 0, 4.209]]),
["Cl1-", "Cs1+"], [[2.105, 2.105, 2.105], [0, 0, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
print("Before:", cscl)
pickle.dump(cscl, open('cscl.pickle', 'wb'))
print("After:", pickle.load(open('cscl.pickle', 'rb')))
```
## Error
After serialization, the composition is no longer CsCl, and all the sites have been changed to Cs+.
```
Before: Full Formula (Cs1 Cl1)
Reduced Formula: CsCl
abc : 4.209000 4.209000 4.209000
angles: 90.000000 90.000000 90.000000
Sites (2)
# SP a b c
--- ---- -------- -------- --------
0 Cl- 0.500119 0.500119 0.500119
1 Cs+ 0 0 0
After: Full Formula (Cs1)
Reduced Formula: Cs
abc : 4.209000 4.209000 4.209000
angles: 90.000000 90.000000 90.000000
Sites (2)
# SP a b c
--- ---- -------- -------- --------
0 Cs+ 0.500119 0.500119 0.500119
1 Cs+ 0 0 0
```
If a structure object is used with no oxidation states as species, i.e. all species as elements, this corruption does not occur.
## Suggested solution (if any)
* N/A
## Files (if any)
N/A
|
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MDExOlB1bGxSZXF1ZXN0MTY2Njc0NTM4
| 1,027
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Function to get Miller index from three sites
|
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[
"Thanks for adding `miller_index_from_sites`, will be useful!"
] | 2018-02-01T22:53:23
| 2018-02-06T05:08:01
|
2018-02-05T20:58:50Z
|
CONTRIBUTOR
|
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New function in surface.py called miller_index_from_sites() that takes in the supercell_matrix and three Cartesian coordinates to return a Miller index associated with the plane formed by the three points (credits to @wenhaosun ). This concludes issue #1002
* Minor fixes to surface_analysis.py
* Added unittesting for miller_index_from_sites
|
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MDExOlB1bGxSZXF1ZXN0MTY2Njc0NzI2
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Removed bug in _get_image function of NearNeighbor class.
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| 2018-02-05T20:58:24
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Add htmilify, unicodify to string utils for formula formatting + tests
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[] | 2018-02-02T19:49:46
| 2018-02-02T20:21:16
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2018-02-02T20:21:16Z
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MEMBER
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## Summary
Add htmilify, unicodify to string utils for formula formatting + tests
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
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MDU6SXNzdWUyOTQwOTIxMDU=
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Madelung constant calculator
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[
"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 2018-02-03T07:38:13
| 2023-08-08T21:21:44
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2023-08-08T21:21:43Z
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CONTRIBUTOR
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A function to calculate the Madelung constant of a ionic crystal. It measures the electrostatic potential of an ion in a crystal. Takes in a structure (only works if structure is decorated with oxidation states?) as the input along with a convergence tolerance.
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MDU6SXNzdWUyOTQxNDc3MTA=
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Bandstructures from database have incorrect reciprocal lattices stored.
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[
"@dwinston Pls fix in the Database?",
"FYI @mfkoerner, you have your private API key in the example code. There's also a `reciprocal_lattice` method on `Lattice`, so `structure.lattice.reciprocal_lattice` should give the reciprocal lattice directly -- this seems to agree with your `reciprocal()` function, but mentioning in case it's useful in future.\r\n\r\nRegarding the error itself, I'm just noting `mp-764505` as an example to investigate further.",
"Responding to @mkhorton , I fixed up my report a bit to fix the API issue and include some results I found. Most notably, I have percentages of the type of error and example materials for each style of error.\r\n\r\nSo, as far as I can tell, the order of the reciprocal vectors in `bandstructure.lattice_rec` are different than those from my `reciprocal()` function and I don't know a consistent way to properly match the lattice vectors in `bandstructure.lattice_rec` to the locations of the covalent band minimum (CBM) and valence band maximums (VMB) in the bandstructure itself.\r\n\r\nIt would be extremely useful to me if anyone has a way to get the cartesian reciprocal space coordinates of the CBM and VBM correctly while this error persists. The proper way to do this if the error is fixed is `BandStructure.get_cbm()['kpoint'].cart_coords`, but this is unfortunately impacted by the error.",
"Thanks very much for the extra detail @mfkoerner, this is very useful. Unfortunately, I don't (personally) know a way to get the information you want via the API until we've tracked down the root cause, but we will investigate the issue asap.",
"I'd like to echo this issue. The information about the reciprocal lattice seems to quite frequently be materially different between the reciprocal lattice stored/calculated in the \"structure\" object and the reciprocal lattice stored/calculated in the \"band structure\" object of the electronic structure module. Like, @mfkoerner above, I've conducted a number of tests, including calculating the reciprocal lattice on my end from the real lattice stored in the \"structure\" object, the result of which always properly matches the reciprocal lattice from the \"structure\" object.\r\n\r\nWe are doing some analysis of the electronic structure which involves looking at absolute crystal momentum differences between various points in the BZ, so resolving these issues is essential for us. The issues are 2-fold:\r\n\r\n1. Many of the reciprocal lattices stored in the \"band structure\" objects have lattice vector lengths off by a factor of 2pi, a few other \"round\" numbers, or (less commonly) arbitrary numbers. This is quickly illustrated in the two plots I've attached below, which show that for many materials, the reciprocal lattice unit cell volume from the \"band structure\" object is 8pi^3 times too large, while the volume from the \"structure\" object is correct. As a quick sanity check, something like bcc-Li should have roughly the largest Brillouin zone possible, and indeed nothing has a much larger BZ in the seemingly correct entries from the \"structure\" object (volume roughly 12 A^-3).\r\n -> Examples of materials with BZ volume too big by 8pi^3 include LiAlSi (mp-3161), fcc-Al (mp-134), FeOF (mp-763221) and YSiNi (mp-20557).\r\n -> A particularly simple example is that of Si (mp-149) versus LiAlSi (mp-3161), where the latter has reciprocal lattice vectors each too long by a factor of 2pi in the \"band structure\" object, though the two materials have nearly identical electronic structures and should have nearly identical Brillouin zones.\r\n -> Examples of materials with BZ volume too big by 64pi^3 include UB2Ru3 (mp-10137), TmNi2 (mp-1576), MgZn (mp-583266), and CrTe2 (mp-685055).\r\n ->This issue results, for instance, in a gross overestimate of carrier effective masses or of the crystal momentum change of indirect optical transitions.\r\n2. Independently or in addition to issue (1) above, the reciprocal lattice from the \"band structure\" object is sometimes a different choice of vectors/angles than the one in the \"structure\" object. This means that we can't simply use the correct reciprocal lattice from the \"structure\" object to calculate things related to the band structure. Is this just an application of the rules in Setyawan & Curtarolo (https://doi.org/10.1016/j.commatsci.2010.05.010) for standardizing high symmetry paths through the BZ?\r\n -> Examples of BZ volume correct, but different choice of vectors / angles: Y(Al2Cr)4 (mp-30177), Bi2AuO5 (mp-618309), Y13Ho19O48 (mp-758033)\r\n -> Example of each reciprocal lattice vector off by 2pi AND reciprocal lattice vectors chosen differently (leading to, among other things, a different monoclinic angle) for FeOF (mp-7631230)\r\n\r\nThere are additionally many examples where the reciprocal lattices from the two database modules (\"structure\" and \"band structure\" objects) are rotated in cartesian space relative to one another, though this presents no problem as it is essentially just a choice of coordinates, and only differences in crystal momentum should matter for most analyses.\r\n\r\nIt seems that were it not for issue (2), a workaround for issue (1) would be easy, by simply querying the \"correct\" reciprocal lattice from the \"structure\" object. However, if the lattice vectors are cycled, or for lower symmetry crystal systems, a different choice of angles is made, it's unclear how to correctly map points from the band structure k-point path to the correct absolute crystal momentum. If we are correct about these issues, I also suspect it would be better to fix the issues in the database, rather than make a bespoke workaround on our end.\r\n\r\nAs a quick illustration of issue (1), plots of the BZ volumes from the two different locations in the database are below. [Note that these plots are only for the ~20k semiconductors (E_g < 2.5 eV) for which the database has a calculated bandstructure.]\r\n\r\n\r\n\r\n\r\n\r\nAny help you can offer is greatly appreciated.\r\n\r\nThanks,\r\nDoug",
"Just to update, we believe we've identified (or partly identified) the issue, but the fix is going to take some time to address. Once this has been resolved, we'll write up a full description here of what happened and what's been changed as a result to ensure consistency in future. Many thanks both for the detailed bug report and for your patience while we address this.",
"@mkhorton Thanks very much. Any information you can provide about the rough timeline for fixing this would be extremely helpful for our project planning purposes.",
"(Caveat: we're still investigating this issue, so the following is subject to change.)\r\n\r\nOk, to provide a little more detail... Essentially, the structure optimization calculation and the band structure calculation are essentially two separate (though related) calculations, and the 'structure' reported by the API is from the former and the band structure from the latter. While it should be the case that both structures should match each other, clearly in some instances this is not the case. This is due to a combination of issues, partly involving faulty logic, and partly involving some stale data. A robust fix needs to address this, and should also include new database validation logic to ensure any similar issues are caught in future. As such, it will take some time to address. We're actually in the process of moving to a new database build system in part to avoid issues such as this.\r\n\r\nHowever, as a stop-gap, it may be possible to extract the correct band structure object from the API. This is slightly convoluted since the API wasn't designed for this use, but the following code should work:\r\n\r\n```\r\nfrom pymatgen import MPRester, Structure\r\n\r\nmpid = 'mp-764505' # mpid of interest\r\nrun_type = 'GGA' # material-dependent, can also be 'GGA+U'\r\n\r\nmpr = MPRester()\r\n\r\ndata = mpr.query({'task_id':mpid},['band_structure'], mp_decode=False)\r\ntask_id = data[0]['band_structure'][run_type]['task_id']\r\ntask_data = mpr.get_task_data(task_id)\r\nband_structure_structure = Structure.from_str(task_data[0]['cif'], fmt='cif')\r\nband_structure_lattice = band_structure_structure.lattice\r\n```\r\n\r\nI believe this should work, and hope it's useful as an interim solution.",
"Hi Matthew,\n\nFrancesco (here in cc) could help on this if needed.\n\nGeoffroy\n\n> On 16 Feb 2018, at 20:38, Matthew Horton <notifications@github.com> wrote:\n> \n> (Caveat: we're still investigating this issue, so the following is subject to change.)\n> \n> Ok, to provide a little more detail... Essentially, the structure optimization calculation and the band structure calculation are essentially two separate (though related) calculations, and the 'structure' reported by the API is from the former and the band structure from the latter. While it should be the case that both structures should match each other, clearly in some instances this is not the case. This is due to a combination of issues, partly involving faulty logic, and partly involving some stale data. A robust fix needs to address this, and should also include new database validation logic to ensure any similar issues are caught in future. As such, it will take some time to address. We're actually in the process of moving to a new database build system in part to avoid issues such as this.\n> \n> However, as a stop-gap, it may be possible to extract the correct band structure object from the API. This is slightly convoluted since the API wasn't designed for use, but the following code should work:\n> \n> from pymatgen import MPRester, Structure\n> \n> mpid = 'mp-764505' # mpid of interest\n> run_type = 'GGA' # material-dependent\n> \n> mpr = MPRester()\n> \n> data = mpr.query({'task_id':mpid},['band_structure'], mp_decode=False)\n> task_id = data[0]['band_structure'][run_type]['task_id']\n> task_data = mpr.get_task_data(task_id)\n> band_structure_structure = Structure.from_str(task_data[0]['cif'], fmt='cif')\n> band_structure_lattice = band_structure_structure.lattice\n> I believe this should work, and hope it's useful as an interim solution.\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/1031#issuecomment-366337635>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA3l9_lGHjq6nohYlA_OU3MKDoWITQVoks5tVdlDgaJpZM4R4VsI>.\n> \n\n",
"Thanks, Matthew, this is very helpful. Just to give you a bit of additional information in case it helps on your end, the workaround certainly fixes the issue for many compounds. However, some are off by small but meaningful amounts, very small amounts (perhaps just different relaxation parameters?), or by a factor of 2 or 4. I haven't dug into the last issue much yet, my first thought was perhaps these were magnetically ordered supercells for the electronic structure calculations, but that would make the BZ smaller rather than larger...do you have any insight on this? The entries with this issue number only in the hundreds, but it would be nice not to have exclude them on this basis from our analysis.\r\n\r\nHere are two quick figures, again for ~19,000 semiconductors with E_g < 2.5 eV.\r\n\r\n\r\n\r\n\r\n",
"Hi again!\r\n\r\n@dhfabini, @mfkoerner and I have made a good deal of progress with the workaround offered by @mkhorton, but discovered this month (07/18) that it no longer seems to work. We have four computers with separately installed versions of python + pymatgen and the line:\r\n\r\n`task_data = mpr.get_task_data(task_id)`\r\n\r\nno longer seems to work on any of them. For example, when called on Si (mp-149), I get:\r\n\r\n`pymatgen.ext.matproj.MPRestError: 'NoneType' object is not iterable. Content: b'{\"valid_response\": false, \"error\": \"\\'NoneType\\' object is not iterable\", \"version\": {\"db\": \"3.0.0\", \"pymatgen\": \"2018.6.11\", \"rest\": \"2.0\"}, \"created_at\": \"2018-07-06T15:59:31.330706\", \"traceback\": \"Traceback (most recent call last):\\\\n File \\\\\"/var/www/python/matgen_prod/materials_django/rest/rest.py\\\\\", line 94, in wrapped\\\\n d = func(*args, **kwargs)\\\\n File \\\\\"/var/www/python/matgen_prod/materials_django/tasks/rest.py\\\\\", line 47, in get_property\\\\n entries = qe.get_entries(crit, False, supported_task_properties)\\\\n File \\\\\"/var/www/miniconda3/envs/mpprod3/lib/python3.6/site-packages/matgendb/query_engine.py\\\\\", line 305, in get_entries\\\\n symbols = [\\\\\"{} {}\\\\\".format(func, label) for label in labels]\\\\nTypeError: \\'NoneType\\' object is not iterable\\\\n\"}'`\r\n\r\nIs there an easy way around this? Thanks again!",
"Closing as stale."
] | 2018-02-03T21:45:42
| 2023-05-29T18:50:20
|
2023-05-29T18:50:20Z
|
NONE
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## System
* Pymatgen version: 4.6.2
* Python version: 3.5.3
* OS version: MacOS Sierra 10.12.6
## Summary
When using MPRester('API_key').get_bandstructure_by_material_id('mpid') to get BandStructureSymmLine objects from the database, many of them (~50%) have incorrect reciprocal lattices.
Of those incorrect, about half of the incorrect ones are off by a scalar factor of 2pi (as in b1 = 4pi^2 (a2 x a3) / (a1 . a2 x a3) instead of the correct 2pi term).
Some of them are off in angle but have the correct volume. Others are also off in volume.
## Example code
```python
import pymatgen as pmg
import numpy as np
mpr = pmg.MPRester("Your_API_Key")
mpidsdicts = mpr.query({'has_bandstructure': True}, ['material_id'])
mpids = [i['material_id'] for i in mpidsdicts]
def reciprocal(Lattice):
"""Returns the reciprocal of a lattice
Lattice: input as [[a1],[a2],[a3]]
Output: [[b1],[b2],[b3]]"""
tsprod = np.dot(Lattice[0], np.cross(Lattice[1], Lattice[2])) #Triple scalar product
rLattice = 2*np.pi * np.array([np.cross(Lattice[1], Lattice[2]),
np.cross(Lattice[2], Lattice[0]),
np.cross(Lattice[0], Lattice[1])]) / tsprod
return(rLattice)
N = 5
mpids = np.random.choice(mpids, N)
for mpid in mpids:
bs = mpr.get_bandstructure_by_material_id(mpid)
structure = mpr.query(mpid, ['structure'])[0]['structure']
lattice = structure.lattice.matrix
rec_lat = mmg.reciprocal(lattice)
np.set_printoptions(precision=3, suppress= True)
print('mpid\n', mpid)
print('volume from structure', np.linalg.det(rec_lat))
print('volume from bandstruct', np.linalg.det(bs.lattice_rec.matrix))
print('lattice\n', lattice) # real lattice from structure data
print('rec_lattice\n', rec_lat) # reciprocal lattice from structure data
print('rec_lattice_bs\n', bs.lattice_rec) # reciprocal lattice stored in band structure
realabc = np.sort(np.sum(rec_lat**2, axis=1)**(.5))
print('structure abc\n', realabc) # sanity check for structure data
bandabc = np.sort(np.array(bs.lattice_rec.abc))
print('band abc\n', bandabc) # sanity check for band data
print('quotient', bandabc/realabc) # quotient of them each (sometimes wrong order)
```
No error message, just wrong results about half the time
## Testing run on error
Ran a census on the database and found the following:
Good: 47.2%
Volume good: 18.4%
2pi per vector: 21.8%
other: 12.7%
These data are collected from a census on the materials project bandstructures
There are a total of 52857 materials considered here
The data were taken from the database on July 14 2017
"Good" means that all lattice vectors and angles are correct to within 0.1 inverse angstroms and 0.1 degrees
"Volume good" means that the lattice volume is correct to within 0.01 inverse angstroms cubed but the material is not "Good"
"2pi per vector" means that the vectors are off by a factor of 2pi but the angles are correct.
"Other" is any material that doesn't fit into the three previously mentioned categories.
Materials with different types of errors:
no materials are off by 4pi^2, 8pi^3, or 8pi per lattice vector
1 material is off by 2 (`mp-20557`)
4 materials were off by 4pi (`mp-10137`, `mp-1576`, `mp-583266`, `mp-685055`)
5 example materials for each category:
good:
`mp-13981`
`mp-1008280`
`mp-11022`
`mp-763833`
`mp-770501`
volume good:
`mp-989622`
`mp-754192`
`mp-643903`
`mp-1008601`
`mp-556356`
2pi per vector:
`mp-626542`
`mp-4308`
`mp-31412`
`mp-773060`
`mp-11271`
other:
`mp-773764`
`mp-705574`
`mp-772309`
`mp-505584`
`mp-767321`
(note that many of these are off by nearly 2pi per vector but not exactly)
## Files (if any)
no files
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| 294,539,545
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MDExOlB1bGxSZXF1ZXN0MTY3MjUyNDk5
| 1,032
|
Minor fix in lammps.output
|
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[
"Since you fixed the bug, then write a unittest for it so that it will not happen again.",
"Only a few simple logic tests were added. Honestly it is the developer's responsibility to write his/her own unit test.",
"@adengz This is not the right attitude. Of course it is the developer's responsibility to write tests. At the same time, people sometimes miss things. The code base only improves when people give time to write new functionality, including fixing bugs and writing missing tests. If you fix a bug that was not found before, you help write the test to prevent it from recurring.\r\n\r\nIf you really want to be that calculative on the time spent, how about you evaluate how much you have benefited from the code of other developers of pymatgen? ",
"I think there is a misunderstanding. I am more than happy to fix something and ensure it never happens again. But for a piece of code with no test at all, it makes this kind of contribution difficult, and takes extra amount of time. \r\n\r\nThis bug is not totally avoidable at the first time if there are failing tests at the beginning. Unfortunately, there are not. "
] | 2018-02-05T20:57:09
| 2018-02-06T00:49:49
|
2018-02-06T00:48:42Z
|
CONTRIBUTOR
|
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## Summary
Fix `unique_atomic_masses` in two methods.
## Additional dependencies introduced (if any)
None
## TODO (if any)
This bug was reported in a user post in pmg google group. It was caused by rewriting `lammps.data`, but I would not take the blame because it would have been found if there were unit tests for those methods. So, if the developer/user is still using them, can you update your code and add comprehensive tests, please? Thank you.
|
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| 295,646,848
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MDExOlB1bGxSZXF1ZXN0MTY4MDcyNzE5
| 1,033
|
Print cif in COD.get_structure_by_formula if exc and re-raise
|
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[
"Hi @gmatteo , saw your COD commit -- not sure if you're interested but I compiled a mapping of mp-ids to COD IDs recently. Drop me an email if this is of interest, I think this will be added to MP alongside ICSD IDs in due course."
] | 2018-02-08T20:02:07
| 2018-02-09T05:30:45
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2018-02-08T21:24:15Z
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CONTRIBUTOR
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Optimization of chemenv
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[] | 2018-02-09T09:59:21
| 2018-02-09T13:03:55
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2018-02-09T13:03:55Z
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## Summary
* Optimization of the chemenv code
* Faster presets for chemenv
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MDExOlB1bGxSZXF1ZXN0MTY4MzQ0Mjk2
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Updated some parameters for some OPs & structure of cn_opt_paras.yaml
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[] | 2018-02-09T21:16:58
| 2018-02-09T22:00:02
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2018-02-09T22:00:01Z
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Miscellaneous bug fixes for graph, magnetic analysis modules
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[] | 2018-02-11T23:23:45
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MEMBER
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## Summary
Nothing major here.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
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new Q-Chem IO Module
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[
"Failing tests. Pls fix.\r\n"
] | 2018-02-12T18:27:04
| 2018-02-12T23:07:48
|
2018-02-12T23:07:48Z
|
NONE
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## Summary
Developing a new Q-Chem IO module to replace the old one with something that is easier to update/maintain. This is a basic module that others can add onto.
- Basic functionality has been implemented using regex/read_pattern/read_table_pattern
- Current parsing routines are robust with respect to most of the IO changes in Q-Chem
- Includes parser for Q-Chem's latest GenSCFMan module
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[
"@shyuep, if the checks pass successfully, can you release the next stable version soon? Would be greatly appreciated because I'm currently changing/completing matminer site-fingerprint classes that depend however on the most recent changes to the LocalStructOrderParas classes and associated yaml files."
] | 2018-02-12T18:27:14
| 2018-02-12T19:33:15
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2018-02-12T19:33:14Z
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MDExOlB1bGxSZXF1ZXN0MTY4NjYzNTI2
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Implement Nscf task from external files with paral_kgb
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[
"Pls remove assert."
] | 2018-02-12T19:12:27
| 2018-02-15T14:41:44
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2018-02-15T14:41:44Z
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CONTRIBUTOR
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## Summary
* NscfTask can now be initialized from external DEN files and executed in parallel with paral_kgb
* Added new methods to produce graphs in the DOT language for flows/works/tasks
(graphviz module is optional)
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New ChemEnv Tutorial
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2018-02-13T13:27:03Z
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We created a new ChemEnv Tutorial that replaces the old one. There is also an additional graphic. If I should store it somewhere else, please let me know.
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2018-02-14T13:03:15Z
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Fixed the broken picture. If there is a better way to do this, please let me know.
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Moved ValenceIonicRadiusEvaluator to local_env and cleaned up some naming inconsistencies
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2018-02-26T14:59:18Z
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MDExOlB1bGxSZXF1ZXN0MTY5NjkwMTUy
| 1,044
|
added BrunnerNN class that uses Brunner's method to calculate near neighbors
|
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[] | 2018-02-16T18:07:49
| 2018-02-20T20:43:49
|
2018-02-20T20:43:48Z
|
NONE
|
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## Summary
Short few sentences, and summary of the major changes in bullet
points
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. Provide a justification why that dependency is needed.
Especially frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* Feature 1 supports a, but not b.
|
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MDExOlB1bGxSZXF1ZXN0MTY5OTk0MzE4
| 1,045
|
bugfix in get_axarray_fig_plt
|
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[] | 2018-02-19T15:46:12
| 2018-02-19T16:56:02
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2018-02-19T16:56:02Z
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CONTRIBUTOR
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MDU6SXNzdWUyOTk1NDM2NjA=
| 1,046
|
FEFF EXAFS Output parsing
|
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[
"Go ahead."
] | 2018-02-22T23:14:19
| 2018-03-22T21:32:31
|
2018-03-22T21:32:31Z
|
CONTRIBUTOR
|
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Current FEFF modules only support parsing outputs of Xmu, LDos files. More class needs to be added for the processing of FEFF output files like feffpath, phase shifts, and scattering amplitude, etc.
|
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MDU6SXNzdWUyOTk1OTIzNzE=
| 1,047
|
Vasprun.from_dict() error
|
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[] | null |
[
"No one uses the from_dict for Vasprun as far as I know. Under what circumstances would you want to do this?",
"Hi. I came across this problem as well. My use case was for saving very long MD trajectories where vasp is run several times in series. I would feed the Vaspruns into the DiffusionAnalyzer in series to monitor the mean square displacement after each vasp run, and do another subsequent vasp MD run if the MSD doesn't seem to be equilibrated enough. ",
"You need to be more specific on what is the exact error you seen. The DiffusionAnalyzer for MD calculations do not use from_dict at all.",
"Sorry for being unclear. That was just explaining why I would want to save a Vasprun as_dict for later use with from_dict. The code snippet and error are as follows:\r\n\r\nfrom pymatgen.io.vasp import Vasprun\r\nfrom pymatgen import MontyEncoder,MontyDecoder\r\nimport json\r\n\r\nmyvasprun = Vasprun(\"vasprun.xml\",parse_dos=False,parse_eigen=False,ionic_step_skip=5)\r\n\r\nwith open('vasprun.json','w') as f:\r\n json.dump(myvasprun, cls=MontyEncoder, fp=f)\r\n\r\nwith open(\"vasprun.json\",\"r\") as f:\r\n vasprun = json.load(f, cls=MontyDecoder)\r\n\r\n\r\nand the error:\r\n\r\nTraceback (most recent call last):\r\n File \"vasprun_json.py\", line 11, in <module>\r\n vasprun = json.load(f, cls=MontyDecoder)\r\n File \"/home/k0306/k030600/.pyenv/versions/anaconda3-5.3.1/lib/python3.7/json/__init__.py\", line 296, in load\r\n parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)\r\n File \"/home/k0306/k030600/.pyenv/versions/anaconda3-5.3.1/lib/python3.7/json/__init__.py\", line 361, in loads\r\n return cls(**kw).decode(s)\r\n File \"/home/k0306/k030600/.pyenv/versions/anaconda3-5.3.1/lib/python3.7/site-packages/monty/json.py\", line 228, in decode\r\n return self.process_decoded(d)\r\n File \"/home/k0306/k030600/.pyenv/versions/anaconda3-5.3.1/lib/python3.7/site-packages/monty/json.py\", line 210, in process_decoded\r\n return cls_.from_dict(data)\r\n File \"/home/k0306/k030600/.pyenv/versions/anaconda3-5.3.1/lib/python3.7/site-packages/monty/json.py\", line 105, in from_dict\r\n return cls(**decoded)\r\nTypeError: __init__() got an unexpected keyword argument 'vasp_version'`"
] | 2018-02-23T04:03:23
| 2019-01-08T01:45:56
|
2018-02-23T04:04:21Z
|
NONE
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When trying to create a Vasprun object from Vasprun.from_dict(d), the following error happens:
TypeError: __init__() got an unexpected keyword argument 'vasp_version'
This deserves a fix for users that need Vasprun object to be in a dict format for later uses.
|
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User friendly surface analysis
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[] | 2018-02-23T06:41:50
| 2018-02-27T23:15:15
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2018-02-26T14:59:04Z
|
CONTRIBUTOR
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## Summary
Pull request to make the SurfaceEnergyPlotter slightly easier to use. Also added a WorkfunctionAnalyzer class.
Features:
-WorkfFunctionAnalysis: Not much to analyze for now, just calculates the work function or gives a neat plot of the local potential along c.
-SurfaceEnergyPlotter can now take either a dictionary of Slabentries or a list. If entries contain adsorbate, you must have the adsorbates and clean_entry fields filled in.
-Correct oriented unit cell for reconstructed slabs based on the slab_scale_factor and the transformation matrix for reconstruction
-MVLSlabSet can generate the LVTOT by setting get_locpot=True. This is for calculating the work function.
-Also added normalization (bool) by volume to nanoscalibilty plot.
TODO:
-Ideas for work function analysis
-Plot the slab structure along side the locpot plot as a visual aid?
-chempot_range calculator for slabs
|
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MDExOlB1bGxSZXF1ZXN0MTcxMjQ4ODc4
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A few small feature additions to magnetic analysis + tests
|
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[] | 2018-02-25T20:17:33
| 2018-02-26T14:58:48
|
2018-02-26T14:58:48Z
|
MEMBER
|
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## Summary
* Adds spin polarization to DOS + test (e.g. see 10.1126/sciadv.1602241)
* Adds magnetic deformation + test (see 10.1021/acs.chemmater.6b04729)
* Adds a Jahn-Teller heuristic + tests, which attempts to classify if a structure may be Jahn-Teller active -- this is going into the magnetic analysis module I'm working on, it's fairly old code / may be improved at a later date
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* None
|
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| 300,672,219
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MDExOlB1bGxSZXF1ZXN0MTcxNjkzNDgx
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|
Small doc fixes pertaining return types in electronic_structure.plotter
|
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[
"Many thanks."
] | 2018-02-27T15:19:45
| 2018-02-27T16:34:10
|
2018-02-27T16:33:55Z
|
CONTRIBUTOR
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In the online documentation for [pymatgen.electronic_structure.plotter](http://pymatgen.org/pymatgen.electronic_structure.plotter.html), the "**Returns**" and "**Return type**" sections of some methods (cf. below) which return complicated ``dict``s are pretty much unreadable because [Sphinx's napoleon extension](http://www.sphinx-doc.org/en/stable/ext/napoleon.html) parses whatever precedes the first colon after ``Returns:`` as the method's return type. This PR aims to fix this by explicitly adding the return type as ``dict:`` and making some cosmetic changes to the rest of the ``Returns:`` description.
Affected methods:
- [BSPlotter.bs_plot_data](http://pymatgen.org/pymatgen.electronic_structure.plotter.html#pymatgen.electronic_structure.plotter.BSPlotter.bs_plot_data)
- [BSPlotter.get_ticks](http://pymatgen.org/pymatgen.electronic_structure.plotter.html#pymatgen.electronic_structure.plotter.BSPlotter.get_ticks)
- [CohpPlotter.get_cohp_dict](http://pymatgen.org/pymatgen.electronic_structure.plotter.html#pymatgen.electronic_structure.plotter.CohpPlotter.get_cohp_dict)
- [DosPlotter.get_dos_dict](http://pymatgen.org/pymatgen.electronic_structure.plotter.html#pymatgen.electronic_structure.plotter.DosPlotter.get_dos_dict)
I think this issue also appears in documentation for some of the other modules, so perhaps you have another, more general plan for how to circumvent it (e.g. patching the *napoleon* extension)? If so, sorry for wasting your time.
|
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MDExOlB1bGxSZXF1ZXN0MTcxNzEwMjEx
| 1,051
|
jupyter notebook example
|
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[
"Many thanks."
] | 2018-02-27T16:13:20
| 2018-02-27T16:33:42
|
2018-02-27T16:33:32Z
|
CONTRIBUTOR
|
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## Summary
This is a jupyter notebook example to show how to extract data from a band structure and how to plot a band structure or a DOS with elements projected contributions to the bands or the DOS.
|
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MDExOlB1bGxSZXF1ZXN0MTcyMDcxNTA5
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added EconNN algo and unit test
|
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[] | 2018-02-28T21:01:56
| 2018-02-28T23:01:45
|
2018-02-28T23:01:45Z
|
NONE
|
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## Summary
Short few sentences, and summary of the major changes in bullet
points
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. Provide a justification why that dependency is needed.
Especially frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* Feature 1 supports a, but not b.
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MDU6SXNzdWUzMDEzNjM5Mzc=
| 1,053
|
In pymatgen, is it possible to partially substitute atoms?
|
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[
"Github issues should only be used for reporting problems. For help, pls post on the Google groups.\r\n\r\nLook at the examples. For example: http://pymatgen.org/_static/Ordering%20Disordered%20Structures.html "
] | 2018-03-01T11:05:53
| 2018-03-01T12:52:09
|
2018-03-01T12:52:09Z
|
NONE
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What I would like to do is the following:
For a given POSCAR file I would like to select some atoms and substitute them partially. I know I can remove them partially with PartialRemoveSitesTransformation module in pymatgen.transformations.site_transformations. You provide a list of positions and a fraction to be removed and the program returns a list of electrostatically most stables vacancy configurations. I would like to know if there is any posibility of doing the same but instead of removing atoms substituing them with another atom.
Thanks in advanced
Jon
|
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MDExOlB1bGxSZXF1ZXN0MTcyMzE1ODQ1
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modified version of VoronoiNN
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[] | 2018-03-01T18:26:02
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2018-03-01T19:53:47Z
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NONE
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Modified VoronoiNN that only considers neighbors with at least 50% weight of max(weight).
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MDExOlB1bGxSZXF1ZXN0MTcyNjE4NDM2
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|
fix documentation wording.
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[] | 2018-03-02T22:17:23
| 2018-03-03T00:01:30
|
2018-03-03T00:01:30Z
|
CONTRIBUTOR
|
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## Summary
Fix documentation wording for parameter use_hull_energy.
|
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Gau
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[] | 2018-03-08T14:47:33
| 2018-03-08T18:59:26
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2018-03-08T18:59:26Z
|
CONTRIBUTOR
|
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## Summary
Update `GaussianOutput` class
* If nosymm is used, input orientation is read instead of standard orientation
* Read bond orders in the output file if a NBO calculation is done
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MDExOlB1bGxSZXF1ZXN0MTc0MjY2ODA1
| 1,057
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An alternative matrix in Lattice.from_parameters
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[
"Thank you very much for the contribution."
] | 2018-03-12T03:46:49
| 2018-03-12T04:55:24
|
2018-03-12T04:55:24Z
|
CONTRIBUTOR
|
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|
## Summary
* An alternative Cartesian lattice matrix compatible with VESTA, GULP, and cif2cell.
* Useful for processing Cartesian trajectories of molecular simulations under periodic boundary conditions.
* The alternative matrix is off by default, but can pass most of the unittests.
Unittests are added to ensure:
* The conventional matrix cannot handle the xyz file exported by VESTA, while the alternative one can correctly interpret it.
* If `alpha == 90` and `beta == 90`, the alternative matrix and the conventional matrix are identical.
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| 1,058
|
Patch 3
|
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[] | 2018-03-12T07:45:34
| 2018-03-12T13:27:19
|
2018-03-12T13:27:19Z
|
CONTRIBUTOR
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## Summary
Changed `MITMDSet` and `MVLNPTMDSet` default "PREC" from "Normal" to "Low".
Note that we already set "ENCUT" = 1.5*"ENMAX" in `MVLNPTMDSet`, which address the main concern that not using "PREC" = "Low" for NPT-MD (more details can be found in [VASP-MDALGO](https://cms.mpi.univie.ac.at/wiki/index.php/MDALGO)).
* Changed "PREC" for both `MITMDSet` and `MVLNPTMDSet`.
* Update the unittest.
|
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MDExOlB1bGxSZXF1ZXN0MTc0NDQ1ODcx
| 1,059
|
Removed a n-dash.
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[] | 2018-03-12T17:48:55
| 2018-03-13T04:42:25
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2018-03-13T04:42:25Z
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MDExOlB1bGxSZXF1ZXN0MTc0NTIxMjU0
| 1,060
|
Bug fix for phonon
|
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[] | 2018-03-12T23:23:56
| 2018-03-13T04:42:11
|
2018-03-13T04:42:11Z
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CONTRIBUTOR
|
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## Summary
This PR fixes a few minor bugs in the phonon module
|
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MDExOlB1bGxSZXF1ZXN0MTc0NTI0NDYx
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|
Add Node.get_vars_dataframe
|
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[
"Hi Shyue,\r\n\r\nIs it possible to release a new version of pmg in the forthcoming days?\r\nThere's a school next week and I would like to use the last pmg version that includes\r\nthe bug fix in #1060 and other minor changes merged in this PR.\r\n\r\nThanks\r\n\r\n ",
"Done",
"Thank you"
] | 2018-03-12T23:46:32
| 2018-03-14T00:44:00
|
2018-03-13T04:42:00Z
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MDExOlB1bGxSZXF1ZXN0MTc0NzM1NTAy
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Update MagOrderingTransformation error handling
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[] | 2018-03-13T17:32:39
| 2018-03-14T00:37:14
|
2018-03-14T00:37:14Z
|
MEMBER
|
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## Summary
Previously transformation would fail if max cell size was set too small, now it will give a warning and increase max cell size instead.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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| 1,063
|
Several issues with EnumlibAdaptor
|
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[
"1. I don't actually quite understand the situation where the first error will occur. If the ordered sites list is empty, then the disordered symmetry should be equal to the full symmetry. I can put in a break, but I am confused when such an issue would occur.\r\n2. Also not clear why this will occur. The sites are not modified as far as I can tell....\r\n3. Removed.\r\n4. What version of enumlib are you running? My machine, which is running latest enumlib, returns 10.\r\n\r\nI addressed 1 and 3. See https://github.com/materialsproject/pymatgen/commit/a73c0967b42c67450d800693094c9fdba681f240",
"For 4., I re-compiled using the latest version from their repo to double check it wasn't an issue with a faulty compilation. Previously, I was using 1.0.8.",
"@mkhorton can you do a structure matcher of the 16 structures you get to check if any of them are similar?",
"Will do ... perhaps that part could actually be an spglib issue, will try reinstalling that too.",
"Ok, StructureMatcher reports 7 to be equivalent, which accounts for the discrepancy. I've attached all 16: [enumlib_structures.txt](https://github.com/materialsproject/pymatgen/files/1813154/enumlib_structures.txt)\r\n\r\nMy understanding is that EnumerateStructureTransformation filters out equivalent structures, so this issue would probably not be encountered in production unless someone uses EnumlibAdaptor directly.",
"Ok, I have a fix for 1. and a partial fix for 2., PR pending. Still no idea on the 16 vs 10.",
"I already fixed 1?",
"Your fix stopped the crash, but didn't stop the underlying reason for why the list was becoming empty to start with.",
"1 is now fully fixed.\r\n\r\nRegarding 2, the missing site properties issue is simply because any sites that go through enumblib lose their site properties in the round trip. There's no easy way to solve this, so I'm leaving it for now.\r\n\r\n2 was only an issue because it was leading to a secondary bug where a Structure was initalized and the `len(species)` != `len(site_properties)` ... I lost the original bug so haven't been able to track down where this was happening exactly, I think somewhere in `get_primitive_structure()`. Will keep an eye on that one.",
"Closing, also noting in case others find this that the newer enumlib is much better and more stable, but should be compiled from source (the version on conda is out of date)."
] | 2018-03-14T16:24:54
| 2020-07-11T02:44:01
|
2020-07-11T02:44:01Z
|
MEMBER
|
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## System
* Pymatgen version: affects several versions, using 2018.3.13
* Python version: 3.6
* OS version: macOS 10.13.3
## Summary
* [This line](https://github.com/materialsproject/pymatgen/blob/f9d984d25b550ff04e534a4a67f18a52799dee68/pymatgen/command_line/enumlib_caller.py#L227) causes a crash in a small percentage of disordered structures (~5%), where it tries to pop from an empty list
* When `check_ordered_symmetry` is True, some site properties are not propagated correctly in the enumerated structure. This leads to exceptions elsewhere in pymatgen, e.g. anywhere a new structure object is initialized from the enumerated structure, as the site property key is only present on some sites of the enumerated structure
* [This line](https://github.com/materialsproject/pymatgen/blob/f9d984d25b550ff04e534a4a67f18a52799dee68/pymatgen/command_line/enumlib_caller.py#L245) seems like it doesn't do anything
* [This test](https://github.com/materialsproject/pymatgen/blob/f9d984d25b550ff04e534a4a67f18a52799dee68/pymatgen/command_line/tests/test_enumlib_caller.py#L94) expects to return 10, but reliably returns 16 for me and for a colleague too. This may be related to `check_ordered_symmetry`, but I'm not sure. I'm also not sure why the CI hasn't caught this.
* I'm still investigating this, if I find a good minimal example or a fix I'll post it here.
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MDExOlB1bGxSZXF1ZXN0MTc1MTA5ODIx
| 1,064
|
EnumlibAdaptor: fix for trying to pop empty list
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[] | 2018-03-14T23:13:02
| 2018-03-14T23:14:55
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2018-03-14T23:14:55Z
|
MEMBER
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## Summary
The `curr_sites` variable needed to be extended by `sites` during each
iteration of the loop. This meant that the wrong spacegroup number was being calculated which is why, in some instances, the target spacegroup number was never reached.
Fixes one issue in #1063
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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| 1,065
|
modifications for ReactionDiagram
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[
"The test is terrible. Write a proper test that checks the compounds formed."
] | 2018-03-15T01:24:06
| 2018-03-15T03:54:21
|
2018-03-15T03:54:08Z
|
NONE
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* change entry_id to attribute in ReactionDiagram
* add ReactionDiagramTest
* debug PDEntry.to_csv
* add reaction_entries_test.csv
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Qchem needs to be refactored.
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[] | null |
[
"I don't use Qchem, but I'll ask the people that do. This shouldn't be a problem though.",
"@shyuep we (myself, @samblau, @shyamd) can refactor the new qchem io to pymatgen.io.qchem. We didn't do that from the start because of the old qchem.py file (which we are still not ready to completely phase out).",
"FYI, just about to submit a pull request that includes the refactor. I'm ready to submit similar pull requests for Custodian and then Atomate as well.",
"This can now be closed"
] | 2018-03-15T06:03:13
| 2018-09-09T20:47:45
|
2018-09-09T20:47:45Z
|
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pymatgen.io.qchem_io should be refactored to pymatgen.io.qchem to be consistent with all the other io packages.
I do not want to undertake this task because if I do it, it may break code on MP end of things.
@mkhorton @montoyjh ? I know Xiaohui is the original author. I am not sure who took over his duties.
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MDExOlB1bGxSZXF1ZXN0MTc1MzEwNzMz
| 1,067
|
EnumlibAdaptor: fix missing site properties
|
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[] | 2018-03-15T16:40:23
| 2018-03-15T18:07:12
|
2018-03-15T18:07:12Z
|
MEMBER
|
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## Summary
As a temporary fix, missing site properties are now set to None when they’re not available, so at least the site property dictionary has the correct keys. This fixes the crashes that were observed in #1063
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* A longer-term fix would be to map the ordered sites back onto the original disordered structure and pull the appropriate site properties from there. I don't need to do this right now, but if someone wants to improve EnumlibAdaptor in the future they can do this.
|
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MDExOlB1bGxSZXF1ZXN0MTc1MzM2MTYy
| 1,068
|
MagneticStructureAnalyzer updates + tests
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[] | 2018-03-15T18:10:55
| 2018-03-21T03:48:27
|
2018-03-21T03:48:27Z
|
MEMBER
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## Summary
Smarter magmom rounding, normalization option + tests
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* None
|
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| 305,729,482
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MDExOlB1bGxSZXF1ZXN0MTc1Mzg2NzYw
| 1,069
|
add test_formed_formula in ReactionDiagramTest
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[] | 2018-03-15T21:42:06
| 2018-03-15T22:29:17
|
2018-03-15T22:29:17Z
|
NONE
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add test_formed_formula in ReactionDiagramTest
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| 305,842,274
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MDU6SXNzdWUzMDU4NDIyNzQ=
| 1,070
|
Neutron diffraction pattern calculator
|
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[] | null |
[
"Hi, yes we are very interested. Pls submit a pull request when you are ready, and thank you in advance for your contributions!",
"Hi @resnant, if it's helpful at all, note we have magnetic symmetry groups in pymatgen, available at pymatgen.symmetry.maggroups",
"Thank you @mkhorton, I'll check it.",
"Hi. The work was almost finished, and I'm preparing the unit test.\r\nHowever, when I set a Debye-Waller B factor, I encountered intensity mismatch with other software and textbook. I'll recheck this.\r\n\r\nBy the way, should I fill the credit? (i.e., copyright, version, maintainer, etc.)",
"Yes pls provide the credit information. If you have a publication you would like users to cite, pls provide it as well. We will make sure to acknowledge this contribution in the documentation as well ",
"Ok, I will fill and update the credit.\r\nSince my code to calculate neutron diffraction pattern is a slight modification of pymatgen.analysis.diffraction.xrd, may I fill the \\_\\_copyright__ as \"Copyright 2018, The Materials Project\"?\r\n[https://github.com/resnant/pymatgen/blob/00ae1075000b7dc7bcf23b1791fa52403d96540d/pymatgen/analysis/diffraction/neutron.py](https://github.com/resnant/pymatgen/blob/00ae1075000b7dc7bcf23b1791fa52403d96540d/pymatgen/analysis/diffraction/neutron.py)\r\n\r\nThe publication is not published yet, I will contact you later."
] | 2018-03-16T08:37:14
| 2018-04-19T04:29:50
|
2018-04-19T04:29:50Z
|
CONTRIBUTOR
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Hi, now I research magnetic materials using neutron beam.
I am writing a program to calculate the neutron diffraction pattern based on pymatgen.analysis.diffraction.xrd, for the case of nuclear scattering.
I will prepare the code according to the contribution guidelines, so please consider merge it.
Do you have an interest?
|
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added get_cn_dict function
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[] | 2018-03-20T17:31:37
| 2018-03-21T03:48:15
|
2018-03-21T03:48:15Z
|
NONE
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Instead of just returning a coordination number total (as with get_cn), returns a dictionary of elements and the coordination of the elements to the central site.
Using NaCl as an example --
Na is bonded to 6 Cl atoms. get_cn would return 6.0, whereas get_cn_dict would return {'Na': 0.0, 'Cl': 6.0}.
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MDU6SXNzdWUzMDY5OTE5NzI=
| 1,072
|
Adding Functional Group substitution to periodic crystals
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[
"You can add this. If you can think of a general enough way to add it to SiteCollection, that would be good. But I think the Site vs PeriodicSite might be tricky.\r\n\r\nThe other thing we may want in future for both Mol and Structure is to be able to replace a functional group (e.g., -CH3) with a functional group (-NH2). Conceptually it isn't hard. There is already a method for bond breaking in Molecule. But doing it in a way that is robust is not easy. ",
"I've been thinking of ways to do this also -- using the bond graph should make this relatively tractable, and this works with periodicity, might be overkill though. Will have a think about how to do this gracefully (i.e. integrating a common solution into SiteCollection). @espottesmith do you have any thoughts on this?",
"Warning: since I've been working pretty much exclusively with non-periodic Molecules, I'm not sure I have a complete understanding of the differences that would be involved with Structures.\r\n\r\nSo, I think that there are a couple of different levels of complexity here, and I'm not sure there's a single solution that elegantly addresses all of them.\r\n\r\n- For simple functional group substitution, I agree with @mkhorton that using the StructureGraph/MoleculeGraph classes is a bit overkill. I haven't read the SiteCollection class that closely, but I think it should be possible to extend & generalize Molecule.substitute().\r\n- For swapping functional groups, as @shyuep mentioned, we could also stay at the level of Molecule.substitute() for simple functional groups. But, if you want to do more complicated substitutions - for instance, changing a functional group that is attached to the larger molecule in more than one place - then the graph representation simplifies things significantly. I already have a somewhat more robust molecule-splitting function in MoleculeGraph that could allow for this (MoleculeGraph.split_molecule_subgraphs()).\r\n- For my workflows, I've been simultaneously substituting functional groups into reactant and product molecules. This use case requires the graph representation (which reduces the problem to a search for subgraph isomorphisms) to be at all reasonable. But, I don't know if that use case of mapping substitutions to multiple related Structures would be needed.\r\n\r\nIn summary, it's probably best to have functional group substitution both at the level of Molecule/Structure (bundled into SiteCollection or otherwise) and MoleculeGraph/StructureGraph. This wasn't at all what the original Issue was about, but if we're going to be adding even more similar functionality between the two Graph functions than what already exists, we might also want to refactor (again) and make some sort of base class for the two."
] | 2018-03-20T18:43:12
| 2023-08-08T21:22:23
|
2023-08-08T21:22:23Z
|
MEMBER
|
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## System
* Pymatgen version: master
## Summary
* Currently, one can only add a functional group to a site for a Molecule object (substitute() method)
* Sometimes, you want to do functional group replacement for molecular crystals (i.e. Structure objects)
* From what I can tell, this is easy to do. The substitute method essentially works out of the box, you just have to change:
```py
del self[index]
for site in func_grp[1:]:
self._sites.append(site)
```
to
```py
del self[index]
for site in func_grp[1:]:
s_new = PeriodicSite(site.species_and_occu, site.coords, self.lattice, coords_are_cartesian=True)
self._sites.append(s_new)
```
Thoughts on:
* do you want to add this?
* what's the best way to do it to avoid code repetition, e.g. putting it in SiteCollection, etc.
|
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MDU6SXNzdWUzMDc0MDY4NzU=
| 1,073
|
Documentation misleadingly indicates structure coords can be fractions
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[
"fractional coordinates does not mean Fractions, but rather direct coordinates. Nevertheless, I have pushed a fix."
] | 2018-03-21T20:31:21
| 2018-03-21T20:39:11
|
2018-03-21T20:39:07Z
|
CONTRIBUTOR
|
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## Summary
The documentation for Structure.from_spacegroup states
> coords (Nx3 array): list of fractional/cartesian coordinates of
> each species.
This sounds like it should be possible to initialise them with a list of fractions from the built-in fractions module.
## Example code
```python
from pymatgen.core import Structure
import numpy as np
from fractions import Fraction
Structure.from_spacegroup(139, np.eye(3), ["H"], [[Fraction(1,2), Fraction(1,4), Fraction(0)]])
```
## Error message
```
Traceback (most recent call last):
File "test.py", line 35, in <module>
print run.primitive_lattice.reciprocal_lattice.matrix
File "/home/mueslo/Nextcloud/tmp/fplore/fplore/loader.py", line 306, in primitive_lattice
return self.primitive_structure.lattice
File "/home/mueslo/Nextcloud/tmp/fplore/fplore/loader.py", line 302, in primitive_structure
return self.structure.get_primitive_structure()
File "/home/mueslo/Nextcloud/tmp/fplore/fplore/loader.py", line 296, in structure
self.spacegroup_number, self.lattice, elements, coords)
File "/home/mueslo/.virtualenvs/fplore/lib/python2.7/site-packages/pymatgen/core/structure.py", line 533, in from_spacegroup
cc = sgp.get_orbit(c, tol=tol)
File "/home/mueslo/.virtualenvs/fplore/lib/python2.7/site-packages/pymatgen/symmetry/groups.py", line 356, in get_orbit
pp = np.mod(np.round(pp, decimals=10), 1)
File "/home/mueslo/.virtualenvs/fplore/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2851, in round_
return around(a, decimals=decimals, out=out)
File "/home/mueslo/.virtualenvs/fplore/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2837, in around
return _wrapfunc(a, 'round', decimals=decimals, out=out)
File "/home/mueslo/.virtualenvs/fplore/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 62, in _wrapfunc
return _wrapit(obj, method, *args, **kwds)
File "/home/mueslo/.virtualenvs/fplore/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 42, in _wrapit
result = getattr(asarray(obj), method)(*args, **kwds)
AttributeError: 'float' object has no attribute 'rint'
```
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MDExOlB1bGxSZXF1ZXN0MTc2Njc1ODgx
| 1,074
|
Surf analysis
|
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[] | 2018-03-22T05:00:23
| 2018-03-22T18:02:04
|
2018-03-22T18:02:04Z
|
CONTRIBUTOR
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## Summary
A few miscellaneous changes to the surface related codes.
* WorkFunctionAnalyzer now takes a structure, list of locpot along c and fermi energy. There is a from_files method still available to build the analyzer from paths to the COTNCAR, LOCPOT and OUTCAR instead.
* ReconstructionGenerator will apply operations to all possible terminations instead of determining which one before hand.
* For each reconstruction type, check exact structure is generated in unittest
* There is no reason not to generate the LOCPOT at the end of each slab calculation to get the workfunction, as such LVTOT is set to True by default in MVLSlabSet
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MDExOlB1bGxSZXF1ZXN0MTc2NjgwODI4
| 1,075
|
Fix incar list_key parse error
|
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[
"Write a test.",
"Unittests have been added."
] | 2018-03-22T05:42:17
| 2018-03-22T12:58:01
|
2018-03-22T12:58:01Z
|
CONTRIBUTOR
|
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## Summary
This commit fixes incar write error and one example is shown below. This error is triggered if a structure contains elements in ["F", "O", "S"] but the most electro-negative element is not within the list.
Example:
```python
>>> from pymatgen.ext.matproj import MPRester
>>> from pymatgen.io.vasp.sets import MITRelaxSet
>>> rest = MPRester()
>>> SCl = rest.get_structures("SCl")[0]
>>> vis = MITRelaxSet(SCl)
>>> print(vis.incar)
TypeError
~/repos/pymatgen/pymatgen/io/vasp/sets.py in incar(self)
--> 341 has_u = hubbard_u and sum(incar['LDAUU']) > 0
TypeError: unsupported operand type(s) for +: 'int' and 'dict'
```
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MDExOlB1bGxSZXF1ZXN0MTc2ODMzMjYz
| 1,076
|
Bug handling 0 during writing VolumetricData
|
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[
"Thanks."
] | 2018-03-22T16:19:22
| 2018-03-22T16:25:03
|
2018-03-22T16:24:59Z
|
CONTRIBUTOR
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## Summary
* Fix the Bug handling 0 during writing VolumetricData
before fix
-..000000000EE+01
after fix
0.00000000000E+01
|
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MDU6SXNzdWUzMDc4MjM4NzU=
| 1,077
|
Drone for FEFF output
|
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[
"How long will this take?"
] | 2018-03-22T21:37:14
| 2023-08-08T21:22:33
|
2023-08-08T21:22:33Z
|
CONTRIBUTOR
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Instead of creating individual methods for output parsing, creating a drone specified for FEFF output parsing seems like a more reasonable idea. A "FeffToEntryDrone" will be implemented and includes all output file parsing and entry construction functions.
|
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MDU6SXNzdWUzMDgxNDA5NjI=
| 1,078
|
Issue with Outputting Symmetrized CIFs
|
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[
"Hi Gerry, try\n\nCifWriter(struct=material, *symprec=1e-5*).write_file('Li_Test.cif')\n\nAlso, just FYI, be a bit careful when interpreting the elastic constants of\nmaterials with non-empty \"warnings\" fields. The elastic analysis of this\nparticularly material strongly suggests it is mechanically unstable, which\nmay mean that its suggested predicted auxetic behavior is the consequence\nof a bad linear fit.\n\nBest,\nJoey\n\nOn Fri, Mar 23, 2018 at 11:45 AM, GerardMattei <notifications@github.com>\nwrote:\n\n> System\n>\n> - Pymatgen version: 2017.8.21\n> - Python version: 3.6\n>\n> Summary\n>\n> Hello, I'm currently searching through the Materials Project's auxetic\n> materials and I'm having difficulty ensuring that pymatgen generates cif\n> files with the correct structures/properties. I have an example below using\n> lithium metal. mp-567337 is the lithium polymorph I'm interested in with a\n> Poisson's ratio of 0.\n>\n> I'm using the MPRester method to load mp-567337 as a pymatgen structure\n> object from its material ID which appears to produce the correct space\n> group, sites, etc. However when I output the structure object with\n> CifWriter and symprec, the output is of the corresponding Li subcell,\n> mp-135, which exhibits a positive Poisson's ratio of 0.36. Is there a way\n> to ensure that pymatgen outputs a Cif file using the exact structure object\n> I'm observing in my code?\n> Example code\n>\n> import json\n> from pymatgen.matproj.rest import MPRester\n> from pymatgen.io.cif import CifWriter\n>\n> with MPRester(matproj_key) as m:\n> mat_id = 'mp-567337'\n> material = m.get_structure_by_material_id(mat_id)\n> print(mat_id, material.composition, material.get_space_group_info(),\n> material.sites)\n> # This outputs the correct material ID and spacegroup of mp-567337 lithium\n> with a negative poisson's ratio.\n>\n> CifWriter(struct=material, symprec=True).write_file('Li_Test.cif')\n> #This instead appears to output the subcell of the desired structure,\n> mp-135 lithium with a positive poisson's ratio.\n>\n> Thank you,\n> -Gerry\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1078>, or mute the\n> thread\n> <https://github.com/notifications/unsubscribe-auth/AGMZNNEzVNv0rd4_BLnR6aTqGMH-BI7uks5thULQgaJpZM4S5NZS>\n> .\n>\n",
"Hi Joey,\r\nI just tested it out - it worked perfectly - thanks for the help!\r\nI'll definitely keep that in mind, we're probably going to focus on other predicted auxetic materials. The Li polymorph just happened to be where we first noticed the CIFs were outputting incorrectly.\r\nCheers and thanks again!\r\n-Gerry"
] | 2018-03-23T18:45:30
| 2018-03-23T19:52:16
|
2018-03-23T19:52:15Z
|
NONE
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## System
* Pymatgen version: 2017.8.21
* Python version: 3.6
## Summary
Hello, I'm currently searching through the Materials Project's auxetic materials and I'm having difficulty ensuring that pymatgen generates cif files with the correct structures/properties. I have an example below using lithium metal. mp-567337 is the lithium polymorph I'm interested in with a Poisson's ratio of 0.
I'm using the MPRester method to load mp-567337 as a pymatgen structure object from its material ID which appears to produce the correct space group, sites, etc. However when I output the structure object with CifWriter and symprec, the output is of the corresponding Li subcell, mp-135, which exhibits a positive Poisson's ratio of 0.36. Is there a way to ensure that pymatgen outputs a Cif file using the exact structure object I'm observing in my code?
## Example code
import json
from pymatgen.matproj.rest import MPRester
from pymatgen.io.cif import CifWriter
with MPRester(matproj_key) as m:
mat_id = 'mp-567337'
material = m.get_structure_by_material_id(mat_id)
print(mat_id, material.composition, material.get_space_group_info(), material.sites)
# This outputs the correct material ID and spacegroup of mp-567337 lithium with a negative poisson's ratio.
CifWriter(struct=material, symprec=True).write_file('Li_Test.cif')
#This instead appears to output the subcell of the desired structure, mp-135 lithium with a positive poisson's ratio.
Thank you,
-Gerry
|
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MDExOlB1bGxSZXF1ZXN0MTc3MjUwMjYx
| 1,079
|
Added additional statistics to VoronoiNN calculation
|
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[] | 2018-03-24T18:00:26
| 2018-03-24T19:13:33
|
2018-03-24T19:13:33Z
|
CONTRIBUTOR
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## Summary
Adds additional information about each facet to the `get_voronoi_polyhedra` method of `VoronoiNN`.
- Altered `get_voronoi_polyhedra` to compute a few other statistics
- Added option to `VoronoiNN` that changes whether solid angle is used to weigh neighbors, or one of these other statistics
## Additional dependencies introduced (if any)
None
## TODO (if any)
I'm not sure whether these changes make the most sense here, or in one of the other Voronoi-related classes. It was just easiest for me to build it here.
PS. Borrowed code from @qi-max, who wrote similar methods into matminer.
|
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Added ability to compute Nth nearest neighbors
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[] | 2018-03-26T13:20:45
| 2018-03-26T14:14:15
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2018-03-26T14:14:15Z
|
CONTRIBUTOR
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## Summary
Added a method for computing information about arbitrary nearest-neighbor shells of a particular site.
- Also added utility method for computing neighbors for all sites in a structure
## Additional dependencies introduced (if any)
None
## TODO (if any)
None.
Tagging @Qi-max, who I discussed this PR with and might use this operation for matminer.
|
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LocalStructOrderParas -> LocalStructOrderParams (with an 'm')
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[
"@computron, addressed in PR #1083. Can be closed once the tests ran successfully.",
"@computron, can be closed.",
"Thanks!"
] | 2018-03-27T18:27:34
| 2018-04-02T22:29:55
|
2018-04-02T22:29:55Z
|
MEMBER
|
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@nisse3000 to have better consistency in naming, ditch the "paras" and move to "params"
This refactor should be maybe 30 seconds of work with PyCharm, or even a simple find/replace across files
|
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|
surface_chempot_range_map()
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[
"Pls resolve the codacy issues.",
"Fix failing tests.",
"All checks have been fixed"
] | 2018-03-27T21:13:50
| 2018-06-15T20:39:50
|
2018-06-15T12:07:17Z
|
CONTRIBUTOR
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WorkFunctionAnalyzer now takes a structure, list of locpot along c and fermi energy. There is a from_files method still available to build the analyzer from paths to the CONTCAR, LOCPOT and OUTCAR instead.
ReconstructionGenerator will apply operations to all possible terminations instead of determining which one before hand.
For each reconstruction type, check exact structure is generated in unittest
There is no reason not to generate the LOCPOT at the end of each slab calculation to get the workfunction, as such LVTOT is set to True by default in MVLSlabSet
Fix the scaling of Wulff shapes with a user given effective radius in the NanoscaleStability class. Also added option to scale the formation energy of the particle with number of atoms.
A method to check if the work function is converged based on its electrostatic potential along the c direction of the slab is added to the WorkFunctionAnalysis class.
Added a surface_chempot_range_map() method to the SurfaceEnergyPlotter. Provides a 2D map similar to that of the PDPlotter except the "phases" shown are different terminations, adsorption coverages, segregation etc. with stability determined by their surface energy.
TODO:
-ReconstructionGenerator() with simpler methods of building reconstructions
-morphology_evolution_chempot_range_map for analyzing change in Wulff shape
-Make surface_chempot_range_map() more efficient by solving up to three system of eqns.
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Changed LocalStructOrderParas to LocalStructOrderParams
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[] | 2018-03-27T22:59:51
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2018-03-27T23:39:43Z
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| 309,830,516
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MDExOlB1bGxSZXF1ZXN0MTc4Mzg1Nzcz
| 1,084
|
add scattering coefficient of deuterium
|
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[
"Thanks!"
] | 2018-03-29T16:57:35
| 2018-03-29T20:48:42
|
2018-03-29T20:48:42Z
|
CONTRIBUTOR
|
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## Summary
Add X-ray scattering coefficient of deuterium (D).
The value was copied from hydrogen (H).
This change enables us to calculate XRD of deuterium-substituted materials.
|
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MDU6SXNzdWUzMDk4NTY0MDE=
| 1,085
|
Unable to Determine CN # For Mixed Site Occupancies
|
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[] | null |
[
"Hi @GerardMattei,\r\n\r\nthanks for indicating this issue. A couple of quick questions.\r\n\r\nI'm trying to reproduce that the previous pymatgen version that you used would indeed give expected results. I tried one pymatgen version from August 20 (5e6f0f755a41016975c8e1137fd11c6810c39766) and one from August 21 (764da43fca24ba71978c331c9ecdf1e77a4cd13e). With neither of these, I got it to work. Have you used exactly this testing code in the past, too? Or, is there a possibility that the partial occupancy was actually not set so that the previous pymatgen version didn't complain at that point. I'm just trying to understand the problem completely.\r\n\r\nIn any event, the NearNeighbor class should be able to successfully deal with partial occupancies, and I'm working on getting that fixed.",
"It also looks like being specifically a problem of the VoronoiNN because the MinimumDistanceNN works perfectly.\r\n\r\nprint(Pt, PtPd)\r\nprint('Pt Coordination: ', MinimumDistanceNN().get_cn(Pt, 0))\r\nprint('PtPd Alloy Coordination: ', MinimumDistanceNN().get_cn(PtPd, 0))\r\n\r\n-->\r\n\r\n('Pt Coordination: ', 12)\r\n('PtPd Alloy Coordination: ', 12)",
"Hi Nils, \r\nThanks for the response: in the previous version of pymatgen, I had used the VoronoiCoordFinder class in pymatgen.analysis.structure_analyzer, which (I assume) became the new VoronoiNN class in the latest release. I used the get_coordination_number() and get_coordinated_sites() methods to extract coordination number and atom-atom distances for the sites of interest.\r\n\r\nI'm pretty sure the problem is related to the new VoronoiNN class because I had tested the code using the PtPd mixed occupancy (as seen above), along with another material which had only partial sodium occupancies, in the old version of the code. When I updated to pymatgen 2018, I used the same structures/code as before, only updating to the new VoronoiNN class. \r\n\r\nWould it help if I were to send you the old code I had used, which I can verify worked without any issues? ",
"Hi @GerardMattei,\r\ncan you pull the latest pymatgen version and test whether your issue is resolved by the changes I made to VoronoiNN in PR #1182?",
"Hi Nils,\r\n\r\nTentatively it looks like that took care of the problem - I still want to test a few things, but I tried the original test code above using both mixed PtPd occupancies and partial Pt occupancies and the VoronoiNN returns the same coordination number as the original pristine Pt structure, which is exactly what I was hoping to see. \r\n\r\nThank you again for your help on this,\r\n-Gerry",
"Hi @GerardMattei,\r\n\r\nthat sounds great. I'd then suggest that @shyuep closes the issue. You can still reopen it later, but the problem that you described seems to be dealt with. "
] | 2018-03-29T18:24:36
| 2018-07-02T17:58:38
|
2018-07-02T17:58:38Z
|
NONE
|
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## System
* Pymatgen version: 2018.2.13
* Python version: 3
## Summary
Hello,
I am running into an error message when attempting to determine the CN # of mixed occupancies using the Voronoi NN class (sample code attached below). If I attempt to determine the CN # around an pymatgen periodic site with a single species, the .get_cn() method successfully returns a CN # of 12.
But if I then use the same structure, but replace the Pt site with Pt0.5Pd0.5, the method instead returns an error message. Since the structures for both are the same, this should also return a CN # of 12. A similar issue is encountered when using the .get_nn() method for mixed site occupancies.
If it helps, I just updated to the newest version of pymatgen (2/13/18). The VoronoiCoordFinder from Version 2017.8.21 was able to successfully return CN #'s, for either single or mixed occupancies.
Cheers and thank you for the help,
-Gerry
## Example code
from pymatgen.analysis.local_env import VoronoiNN
from pymatgen.ext.matproj import MPRester
from pymatgen.core.structure import Structure
with MPRester() as m:
Pt = m.get_structure_by_material_id('mp-126')
PtPd = m.get_structure_by_material_id('mp-126')
PtPd['Pt'] = {'Pt': 0.5, 'Pd': 0.5}
print(Pt, PtPd)
print('Pt Coordination: ', VoronoiNN().get_cn(Pt, 0))
#This successfully returns a CN # of 12 around Pt[0].
print('PtPd Alloy Coordination: ', VoronoiNN().get_cn(PtPd, 0)) # This should also return a CN # of 12, but instead produces an attribute error.
|
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MDExOlB1bGxSZXF1ZXN0MTc4NjU2NDY3
| 1,086
|
Amend API method to specify use of hull energy for interface rxn calc
|
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[] | 2018-03-31T00:22:53
| 2018-03-31T11:51:32
|
2018-03-31T11:51:32Z
|
MEMBER
|
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## Summary
For `MPRester.get_interface_reactions`, extend method signature to allow toggling of whether to use the convex hull energy for a given composition for the reaction energy calculation. If false (default), the energy of the ground state structure will be preferred; if a ground state cannot be found for a composition, the convex hull energy will be used with a warning message. Add a test for this.
## TODO
@yihanxiao92 will amend [the example `matgenb` notebook](https://github.com/materialsvirtuallab/matgenb/blob/eb5b67bc1064cd96211117b23403c27fc36b7f6b/notebooks/2018-01-29-Interface%20Reactions.ipynb) to include this functionality. However, this does not block merging -- this is only to notify Yihan that this PR is done and that the notebook no longer lives in the pymatgen repo).
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MDExOlB1bGxSZXF1ZXN0MTc4NzM4ODU1
| 1,087
|
Removed use of deep copy
|
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[] | 2018-04-01T17:24:50
| 2018-04-01T17:28:00
|
2018-04-01T17:27:09Z
|
CONTRIBUTOR
|
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## Summary
Removed use of `deepcopy` in nearest neighbor calculation.
Aside: Turns out that this one line was 50% of the execution time of getting Nth nearest neighbor shells. I've learned my lesson.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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| 310,372,673
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MDExOlB1bGxSZXF1ZXN0MTc4NzU4Nzc2
| 1,088
|
Changes to accelerate Voronoi-tessellation based features
|
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[] | null |
[] | 2018-04-02T01:45:26
| 2018-04-02T03:38:22
|
2018-04-02T03:38:22Z
|
CONTRIBUTOR
|
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|
## Summary
A series of changes to make the calculation of Voronoi-tessellation-based features in matminer faster.
* Optimization of `get_nn_shell_info`
* Optimization of `get_voronoi_polyhedra`. No longer returns a dict indexed by `PeriodicSite`, which is very slow to modify.
* Implemented `__hash__` and `__eq__` for NearNeighbors. Makes it easier to use LRU caches with these tools
* Faster implementation of `solid_angle`
* VoronoiNN now can return all polyhedron information as part of `get_nn_info`. Used to improve usefulness of cached results in matminer
## Additional dependencies introduced (if any)
None
## TODO (if any)
Optional: Index output of `get_voronoi_polyhedron` by "site index" and "image". Right now, the key of the output dict is the facet number, which is not useful.
|
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MDExOlB1bGxSZXF1ZXN0MTc4OTI4OTg0
| 1,089
|
add FermiDos for convenient fermi and doping calculations
|
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[] | null |
[] | 2018-04-02T20:47:44
| 2018-04-02T22:19:07
|
2018-04-02T22:19:07Z
|
CONTRIBUTOR
|
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|
## Summary
added FermiDos class that makes it very easy to calculate the fermi level at a given concentration (get_fermi) or the concentration (doping) at a given fermi level (get_doping). Also added tests for both methods.
|
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MDExOlB1bGxSZXF1ZXN0MTc5MTk5NzQ5
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|
Pourbaix revision 2
|
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[] | null |
[] | 2018-04-03T19:41:51
| 2018-04-04T03:27:06
|
2018-04-04T03:27:06Z
|
CONTRIBUTOR
|
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## Summary
Major overhaul to pourbaix diagram code. Makes it more in-line with the phase-diagram refactor and more transparent to use.
* module and submodules of `pymatgen.analysis.pourbaix` moved to a single module: `pymatgen.analysis.pourbaix_diagram` and the analyzer and maker functionalities are now in a single `PourbaixDiagram` class. `PourbaixPlotter` is still included.
* Cleanup and simplification of PourbaixEntry and multi-entry. No more in-place modification, a number of attributes are now properties, and solid filtering can be applied to single as well as multi-entry pourbaix diagrams.
* Hull energy finding uses operations performed on the pourbaix entry itself, rather than locating matching entries in the diagram, which means that hull energies can be determined using entries other than those included in the pbx diagram.
* Hull energy finding of a single entry will find its stability with multiple ion-pairings, if relevant, and is implicitly vectorized (you can supply vectors or meshes of pH/V to PourbaixDiagram.get_decomposition_energy directly)
* All of the hull-finding code in pH-V-E0 space has been removed, since it wasn't being used to find pourbaix domains.
## TODO (if any)
* I've marked a number of things I'd like to change eventually in the code. Specifically, I think treatment of ions could be cleaned up a bit, PourbaixEntries could be refactored to resemble the design patterns of PDEntries a bit more closely. Also, I suspect there might be a way to find valid MultiEntries without resorting to testing every possible k-nary combination of PourbaixEntries using the reaction calculator.
* The "solids_filter" that is currently the default on the MP website and is optionally conducted here has a few nuances to its thermodynamic interpretation that might be worth discussing.
* The example on matgenb should be updated.
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MDExOlB1bGxSZXF1ZXN0MTc5MjU2OTM5
| 1,091
|
Use future numpy default for rcond
|
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[] | null |
[] | 2018-04-04T00:57:35
| 2018-04-04T03:26:13
|
2018-04-04T03:26:12Z
|
MEMBER
|
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Uses machine precision times the largest of the input array dimensions rather
than simply the machine precision as the `rcond` parameter to `numpy.linalg.lstsq`.
## Summary
Adds `rcond=None` to all calls to `numpy.linalg.lstsq`.
* This suppresses a `FutureWarning` for numpy>=1.14 (pmg dep)
* The future default is [apparently](https://stackoverflow.com/a/44678023) more consistent with `scipy` and is "a good and robust default threshold."
However, I don't know if any current code _depends_ on the old default. I would hope not, and that code would break anyway with numpy 1.15.
|
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MDU6SXNzdWUzMTExMDU3MTg=
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|
PyThreadState_Get: no current thread when exporting Molecule to xyz
|
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[
"The error comes from a conflict version with openbabel. Actually the script crashes when it tries to import openbabel in `pymatgen.io.babel.py` this last module being imported in the `IMolecule.to()` mehtod.\r\n\r\nThe error is fixed after an openbabel update : \r\n\r\n``` \r\n--> conda install -c openbabel openbabel\r\nFetching package metadata .................\r\nSolving package specifications: .\r\n\r\nPackage plan for installation in environment /Users/gvallver/anaconda:\r\n\r\nThe following packages will be UPDATED:\r\n\r\n openbabel: 2.4.1-py36_3 openbabel --> 2.4.1-py36_5 openbabel\r\n```"
] | 2018-04-04T06:51:49
| 2018-04-04T13:02:57
|
2018-04-04T13:02:57Z
|
CONTRIBUTOR
|
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When I try to export a Molecule to a xyz file I got a PyThreadState error that I do not understand.
## System
* Pymatgen version: 2018.3.14
* Python version: Python 3.6.4 |Anaconda custom (64-bit)| (default, Jan 16 2018, 12:04:33)
* OS version: MacOSX 10.13.3
## Example code
```python
import pymatgen as mg
xyz = """4
BF3
B 0.0000 0.0000 0.0000
F 1.5000 0.0000 0.0000
F -0.7500 1.2990 0.0000
F -0.7500 -1.2990 0.0000
"""
with open("amol.xyz", "w") as f:
f.write(xyz)
mol = mg.Molecule.from_file("amol.xyz")
print(mol)
mol.to("xyz", "t.xyz")
```
## Error message
```
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6
```
|
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| 311,365,207
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MDExOlB1bGxSZXF1ZXN0MTc5NDkyNTkw
| 1,093
|
allow kwargs in ASE atoms converter
|
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[] | 2018-04-04T19:43:55
| 2018-04-04T19:48:11
|
2018-04-04T19:48:11Z
|
MEMBER
|
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## Summary
When translating PMG structures to ASE atoms, sometimes you want to use additional ASE Atoms kwargs. e.g., for myself I want to add a calculator in the ASE Atoms object when creating it from a PMG structure.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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MDExOlB1bGxSZXF1ZXN0MTc5NTMwMjE5
| 1,094
|
add bandgap option for FermiDos
|
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[
"Thanks @shyuep, Would it be possible for you to release a new pymatgen version that reflect these changes?"
] | 2018-04-04T22:34:07
| 2018-04-05T22:54:09
|
2018-04-05T21:57:58Z
|
CONTRIBUTOR
|
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add bandgap option for FermiDos enabling scissoring of the gap + testing. No scissoring by default.
|
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MDU6SXNzdWUzMTE3Nzk0MjE=
| 1,095
|
2D topographical chempot map for surface stability.
|
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[
"Go ahead.",
"Addressed in #1082 \r\nFuture improvements to be made to optimize efficiency but issue will be closed now"
] | 2018-04-05T21:42:17
| 2018-06-15T20:32:25
|
2018-06-15T20:32:25Z
|
CONTRIBUTOR
|
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The grand surface potential (ie surface energy) determines the stability of a surface and is a function of chemical potential. In ternary systems and systems of greater complexity of different species, the surface energy is a function of 2 or more chemical potentials. It is more convenient to visualize which terminations (stoichiometric, nonstoichiometric, adsorbed, segregated, reconstructed, etc) are most stable at specific chemical potentials using a 2D topographical map then a chempot vs surface energy plot. This will also look better in publication.
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MDExOlB1bGxSZXF1ZXN0MTc5ODA2OTg1
| 1,096
|
setup.py: add DLS_bond_params for VolumePredictor
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[] | 2018-04-05T21:53:36
| 2018-08-10T11:12:33
|
2018-04-05T21:57:45Z
|
MEMBER
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`DLS_bond_params.yaml` isn't included in the package files. The VolumePredictor thus break when pymatgen is `pip install`'ed.
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| 311,839,686
|
MDExOlB1bGxSZXF1ZXN0MTc5ODQ4NTE4
| 1,097
|
updated debye temperature formulation
|
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[] | 2018-04-06T03:47:23
| 2019-04-04T02:44:59
|
2018-04-06T09:31:52Z
|
CONTRIBUTOR
|
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|
## Summary
I've found that estimating the debye temperature of solids from the elastic tensor using the formulation from the longitudinal and transverse speed of sound is significantly more accurate than that of the isotropic young's modulus, so I've moved that to the default function and deleted both the old one and the GIBBS formulation, which is both somewhat unstable and very inaccurate as implemented. Also cleaned up some trailing whitespace and codacy issues in the elasticity module.
|
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| 312,243,323
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MDExOlB1bGxSZXF1ZXN0MTgwMTI1MjY0
| 1,098
|
Locate lowest density of charge
|
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[] | 2018-04-07T21:09:08
| 2018-04-08T13:17:54
|
2018-04-08T13:17:54Z
|
CONTRIBUTOR
|
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|
## Summary
Analyzer to find potential interstitial sites based on charge density.
* Locate the minimum density of charge in a crystal using CHGCAR-type file
* unittest
## Additional dependencies introduced (if any)
* Optional: External function `skimage.feature.peak_local_max` is required to find extreama.
|
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| 312,581,920
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MDExOlB1bGxSZXF1ZXN0MTgwMzQ4NzAw
| 1,099
|
NMR Updates
|
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[
"Pls fix codacy issues and check the other failing tests.",
"I fixed all the issues related to the NMR code. For some reason Hanmei's fixes that i merged in are showing up as changes and Codacy is complaining about them. They are structural, e.g. the use of asserts and random, so I don't think changing them is a good idea. "
] | 2018-04-09T15:39:34
| 2018-04-10T21:21:56
|
2018-04-09T22:53:19Z
|
NONE
|
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|
## Summary
Refactored the NMR tensor and added a NMR InputSet for VASP
- Updated periodic table to have NMR quadrupolar moments for isotopes
- Added an MPNMRSet for chemical shielding and EFG calculations
- Fixed inheritance issues in from_prev for various InputSets
- Updating parsing of chemical shielding and electric field gradient tensors in Outcar
- Switch the NMRChemicalShiftNotation class to an actual tensor class
- Updated nomenclature to reflect the fact that VASP actually calculates chemical shielding even though it says shift in several places in its own output
- Added in parsing of EFG tensors and a class for them
|
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MDExOlB1bGxSZXF1ZXN0MTgwNjMyMjcz
| 1,100
|
Small bug in tetragonal conventional structure method when a = c
|
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[
"I would suggest you add a test to make sure this is done correctly."
] | 2018-04-10T15:00:26
| 2018-04-10T16:00:32
|
2018-04-10T16:00:14Z
|
CONTRIBUTOR
|
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|
## Summary
The `get_conventional_standard_structure` method currently unexpectedly switches a and c for tetragonal space groups if a = b = c. This is obviously not desirable and so has been removed, while still allowing for switching a and c if a != b = c (the original intention).
## Additional dependencies introduced (if any)
None
## TODO (if any)
This only removes unexpected behaviour for a = b = c, but doesn't determine which is the conventional c axis in that case.
|
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