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https://api.github.com/repos/materialsproject/pymatgen/issues/801
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| 252,371,190
|
MDU6SXNzdWUyNTIzNzExOTA=
| 801
|
Pathological error in VoronoiCoordFinder for slabs
|
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[] | null |
[
"How to use the `allow_pathological`?",
"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 2017-08-23T18:16:09
| 2023-08-08T21:20:31
|
2023-08-08T21:20:30Z
|
CONTRIBUTOR
|
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There is an issue for some slab structures where a `RunTimeError` occurs stating the structure is pathological. I think this may be due to the code being unable to properly create a convex hull for surface sites where there are neighboring atoms in the vacuum. There is a tag called `allow_pathological` that bypasses this error with an exception, but a more robust solution tackling the source of the problem would be preferred.
## Example code
```python
from pymatgen.core.surface import SlabGenerator, Lattice, Structure
lattice = Lattice.cubic(3.149000)
Mo = Structure(lattice, ["Mo", "Mo"], [[0,0,0], [0.5,0.5,0.5]])
slabgen = SlabGenerator(Mo, (1,0,0), 10, 20)
slab = slabgen.get_slabs()[0]
from pymatgen.analysis.structure_analyzer import VoronoiCoordFinder
v = VoronoiCoordFinder(slab)
for i, site in enumerate(slab):
cn = v.get_coordination_number(i)
```
raises
```py
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-18-ec5ec645f8df> in <module>()
8 v = VoronoiCoordFinder(slab)
9 for i, site in enumerate(slab):
---> 10 cn = v.get_coordination_number(i)
/repos/pymatgen/pymatgen/analysis/structure_analyzer.py in get_coordination_number(self, n)
121 n (int): Site index
122 """
--> 123 return sum(self.get_voronoi_polyhedra(n).values())
124
125 def get_coordinated_sites(self, n, tol=0, target=None):
/repos/pymatgen/pymatgen/analysis/structure_analyzer.py in get_voronoi_polyhedra(self, n)
91 continue
92 else:
---> 93 raise RuntimeError("This structure is pathological,"
94 " infinite vertex in the voronoi "
95 "construction")
RuntimeError: This structure is pathological, infinite vertex in the voronoi construction
```
|
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| 252,398,492
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MDU6SXNzdWUyNTIzOTg0OTI=
| 802
|
Rename LammpsData.write_data_file
|
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[] | 2017-08-23T19:58:34
| 2017-08-24T02:47:06
|
2017-08-24T02:47:06Z
|
MEMBER
|
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Suggest just calling it write_file to be consistent with other io.
Not sure if backwards compatibility needs to be maintained since I have no idea where this object is used in MP.
@matk86
|
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MDExOlB1bGxSZXF1ZXN0MTM3MzIzMzU4
| 803
|
write_data_file --> write_file
|
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[] | 2017-08-23T21:33:27
| 2017-08-23T21:48:08
|
2017-08-23T21:48:08Z
|
CONTRIBUTOR
|
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* addresses issue #802
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MDExOlB1bGxSZXF1ZXN0MTM3MzM0OTA4
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|
Added missing unit tests to local_env.py
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[] | 2017-08-23T22:48:08
| 2017-08-23T23:12:47
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2017-08-23T23:12:47Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MTM3NDcxODkz
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|
I modified two lines in "get_projected_plots_dots_patom_pmorb" method…
|
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[
"I already fixed this last time. But tests are still failing on Py27. ",
"@shyuep Could you accept my pull request and check it again. Actually, I did a simple fix and it works for both python 2.x and python 3.x (I checked).",
"I already fixed the map problem. Your pull req has merge conflicts with the main pymatgen branch because you are not up to date. Update your fork, and if there are other changes, resubmit another pr."
] | 2017-08-24T14:43:45
| 2017-08-24T15:03:40
|
2017-08-24T14:46:16Z
|
CONTRIBUTOR
|
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… in plotter.py file.
These changes make the usage of "map" function suitable with both python 2.x and python 3.x
## 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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| 252,688,241
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MDExOlB1bGxSZXF1ZXN0MTM3NTE5NjI3
| 806
|
Bug fix min_freq() in phonon/bandstructure.py
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[
"Thanks!"
] | 2017-08-24T18:22:01
| 2017-12-14T04:17:39
|
2017-08-24T18:49:25Z
|
NONE
|
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## Summary
The method min_freq in the PhononBandStructure object returns the wrong q-point. In its current form, the method would return the q-point with the index of the band that contains the minimum instead of using the index of the minimum frequency.
Fix: Change self.qpoints[i[0]] in line 106 to self.qpoints[i[1]]
|
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| 252,724,020
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MDExOlB1bGxSZXF1ZXN0MTM3NTQ2MDg3
| 807
|
Function to adsorb both surfaces in adsorption.py
|
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[] | 2017-08-24T20:37:56
| 2017-08-25T03:31:49
|
2017-08-25T03:31:49Z
|
CONTRIBUTOR
|
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## Summary
The AdsorbateSiteFinder class now has a new parameter "top_surface=True" which will adsorb molecules on the top surface if True and bottom surface if False. This is useful for studying the adsorption of nonsymmetric surfaces. A new function that utilizes this is adsorb_both_surfaces. A new parameter called "reorient_lattice=True" will automatically reorient the lattice parameter of the slab such that the c vector is parallel to the Miller index if set to True (default).
* top_surface parameter in AdsorbateSiteFinder
* adsorb_both_surfaces function in adsorption.py
* reorient_lattice parameter in SlabGenerator and Slab
## TODO (if any)
Allow adsorption on both sites with any molecules.
Incorporate adsorb_both_surfaces into AdsorbateSiteFinder class.
* adsorb_both_surfaces supports single atom adsorption, but not molecules due to the symmetry of the molecule.
|
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| 252,751,912
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MDExOlB1bGxSZXF1ZXN0MTM3NTY3NDcw
| 808
|
fix parsing BSE vasprun error
|
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[
"There is a test error. You need to check your tests and fix.",
"I am not sure how to deal with this situation in a pythonic way. The fix I wrote looks not professional. You may improve it. Thanks."
] | 2017-08-24T22:44:03
| 2017-08-25T00:14:50
|
2017-08-25T00:13:30Z
|
CONTRIBUTOR
|
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|
## Summary
When Vasprun() parses vasprun.xml , it generally first checks the convergence status (electronic and ionic). However, there is no electronic or ionic step in BSE calc. This fix is to ignore the convergence checking of BSE vasprun.xml.
|
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MDExOlB1bGxSZXF1ZXN0MTM3NTczMzgy
| 809
|
Converting LMPDATA to POSCAR
|
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[
"The code should not convert LAMMPS to POSCAR. It should just allow a person to get a structure.",
"There is never a reason to write code to convert one file format to another. If you are able to get a structure from LAMMPSDAta, you can already pass the structure to the Poscar class to get the Poscar object. The Structure object is the thing that links everything.",
"I understand. I just found that the lammps data file is closed to the POSCAR format. Thus it is easier to transform it to POSCAR first, and then use Poscar class to get the structure, which can link to everything. I have already obtained the POSCAR. Just use Poscar class to get the structure. Can I do it this way?",
"No,you should not convert to poscar first. It is straightforward to parse the lammps input data to a structure.",
"Thanks.",
"@ucsdlxg See the version that I wrote. You should not be introducing a new method and reparse the Data file. There is already a LAMMPData.from_file to parse the data file. All you need is to convert the LAMMPSData to a structure. See the `@structure` property in the latest pymatgen. \r\n\r\nHowever, for some reason, I cannot retrieve even the Li2O structure. Pls debug.",
"Nvm, I think the new code I wrote works fine. It is just that the Li2O structure in pymatgen is odd for some reason."
] | 2017-08-24T23:33:33
| 2017-08-25T15:33:59
|
2017-08-25T13:54:15Z
|
CONTRIBUTOR
|
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## Summary
Add the code to transform from the format of the lammps Data to vasp POSCAR.
* 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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MDExOlB1bGxSZXF1ZXN0MTM3NTc4NTY5
| 810
|
fix parsing BSE vasprun error
|
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[] | 2017-08-25T00:27:25
| 2017-08-25T00:33:18
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2017-08-25T00:33:18Z
|
CONTRIBUTOR
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## Summary
fix parsing BSE vasprun error
|
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MDExOlB1bGxSZXF1ZXN0MTM3NzU2ODQ3
| 811
|
Bug fix for LMPDATA to Structure object
|
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[
"Pls run Pycharm -> Reformat code first. Your code does not conform to Python PEP8."
] | 2017-08-25T21:04:16
| 2017-08-25T22:43:35
|
2017-08-25T22:43:35Z
|
CONTRIBUTOR
|
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## Summary
I add a variable "atom_style" to tell the LammpsData format.
The difference of atomic mass for some elements is small, e.g. Pt, Ce. Now set the criteria to 0.05.
* 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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MDExOlB1bGxSZXF1ZXN0MTM3Nzk5NDI0
| 812
|
surface_analysis.py ver1
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[] | 2017-08-26T14:19:35
| 2017-08-26T17:32:56
|
2017-08-26T17:32:56Z
|
CONTRIBUTOR
|
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## Summary
surface_analysis.py and its corresponding test file test_surface_analysis.py has been added. This is to partially address Issue #767 . The current version contains a class called SurfaceEnergyAnalyzer, which takes in a dictionary of a list of Vasprun objects for a set of slab calculations. The key is the Miller index while the value is a list cotaining Vaspruns for calculations of facets with the same Miller index, but different terminations/stoichiometries. The chemical potential obtained from querying Materials Project with the MPRester is used to calculate the surface energy. As such, surface energy can be calculated as a function of chemical potential, leading to a wide range of analysis that can be done. This also works for pure elemental systems.
* Feature 1: SurfaceEnergyAnalyzer class (works with elemental and binary systems).
1. class method calculate_gamma(): calculates surface energy using pymatgen-db type entries to get the chemical potential range.
2. class method wulff_shape_from_chempot(): Takes in a value of chemical potential and calculates the Wulff shape.
3. class method wulff_shape_dict(): Creates a dictionary of Wulff shapes. The key is the chemical potential and the value is a Wulff shape. The Wulff shapes generated corresponds to points in the surface energy vs chemical potential plot where a facet transitions to a different state.
4. class method get_slope_and_intercept(): Get the slope and intercept for a surface energy vs chemical potential line for a specific facet.
5. class method get_intersections(): Finds the chemical potential where a facet transitions from one configuration to another.
6. class method area_frac_vs_chempot_plot(): Plots the area fraction of each facet on the Wulff shape as a function of chemical potential.
7. class method chempot_vs_gamma_plot(): Plots the surface energy of each facet as a function of chemical potential.
* Fix 1: Added parameters for AdsorbateSiteFinder to adsorb_both_surfaces()
## TODO (if any)
1. Add analysis for adsorption
2. Analysis for work function
3. Function to get surface environment (to be implemented in slab)
4. Allows for labelling of termination types in the chempot_vs_gamma() method. Temporarily just label sites as either nonstoichiometric or Term 1, Term 2 etc.
5. General equation for mutliple components
6. Does this work for GBs?
7. SlabAnalyzer class
8. Contain surface coordination analyzer
9. Combine with SurfaceEnergyAnalyzer to get a surface energy modeler
10. Option to hide unstable facets
11. Will test on nonstoichiometric or adsorbed systems in the future. This is where this surface_analysis code will really shine.
|
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MDExOlB1bGxSZXF1ZXN0MTM3ODExODg0
| 813
|
Documentation of spectrum module
|
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[] | 2017-08-26T20:59:29
| 2017-08-27T20:24:12
|
2017-08-27T20:24:12Z
|
CONTRIBUTOR
|
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|
## Summary
Add document to functions in core/spectrum module
|
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MDU6SXNzdWUyNTM0ODIyMzM=
| 814
|
enumlib_caller: makestr.x deprecated
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[
"Ok. If you can fix these, it would be great. In general, I use only latest enumlib since that has significant speed advantages with the latest symmetry handling.",
"Hello,\r\n\r\nThe supporting files provided indeed work, thank you.\r\nHowever, please update the error message in pymatgen that is misleading.\r\n\r\nError message gotten\r\nRuntimeError: EnumlibAdaptor requires the executables 'enum.x' or 'multienum.x' and 'makestr.x' or 'makeStr.py' to be in the path. Please download the library at http://enum.sourceforge.net/ and follow the instructions in the README to compile these two executables accordingly.\r\n\r\nFile to be updated \r\npymatgen.command_line.enumlib_caller line 71\r\n\r\nIt should instead redirect to this link.\r\nhttps://github.com/materialsproject/pymatgen/tree/master/cmd_line/enum\r\n\r\nkind regard"
] | 2017-08-28T23:09:48
| 2019-07-08T13:29:02
|
2017-10-13T22:23:25Z
|
MEMBER
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An FYI: I noticed that makestr.x has been deprecated in enumlib, replaced by [makeStr.py](https://github.com/msg-byu/enumlib/tree/master/aux_src). I don't know if these are interchangeable, but we should probably update `enumlib_caller` at some point in case the code diverges more in future. (Also, I think [this test](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/command_line/tests/test_enumlib_caller.py#L31) is being incorrectly skipped if `enum.x` is present, even if `multienum.x` is not.)
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MDExOlB1bGxSZXF1ZXN0MTM4MDYwNDQx
| 815
|
add self.ref_energy which is useful for combining neb plots
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[
"I don't see a unit test."
] | 2017-08-28T23:38:01
| 2017-08-30T00:08:19
|
2017-08-30T00:08:19Z
|
NONE
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add self.ref_energy which is useful for combining neb plots
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MDExOlB1bGxSZXF1ZXN0MTM4MDg2MTgy
| 816
|
add max_sites parameter to oxi_state_guesses
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[] | 2017-08-29T04:03:50
| 2017-08-29T04:53:44
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2017-08-29T04:53:43Z
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MEMBER
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## Summary
oxi_state_guesses could take a long time for Compositions with large numbers of sites and many degrees of freedom (oxidation states) per site. If enabled, this feature allows one to try to limit the number of sites used by reducing the formula to at most max_sites before the analysis.
Notes:
* although having the max_sites feature is useful, after coding it I realized that in 99.9% of cases it's probably good enough to just reduce the composition before analysis. An exception is if your oxidation state table uses non-consecutive oxidation states, e.g. 4+ and 6+ but not 5+.
* I added a special value of max_sites=-1 to mean simply reduce the composition before analysis. This is not really needed if you know what you are doing. Starting with a composition ```comp```, one could easily just do ```comp.reduced_composition.oxi_state_guesses()``` which would have the same effect. So the -1 setting is more to guide people to that possibility. Feel free to remove it if you find it ugly.
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MDExOlB1bGxSZXF1ZXN0MTM4MTIzMjIx
| 817
|
MAINT: Numerical stability for symmetrise + finer control over tolerance
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[
"Thanks. However, there seems to be a test error? You can click on the travis-ci above to see the error.",
"Thanks as well for accepting ;)"
] | 2017-08-29T08:55:39
| 2017-08-29T16:43:34
|
2017-08-29T15:23:54Z
|
CONTRIBUTOR
|
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## Summary
Followup to #760
* Improved numerical stability in the symmetrise code. Previously if *O(i, j)* denotes the the symmetry operation to map atom *i* unto *j* it could end up with a chain of *O(3, 4) O(2, 3) O(1, 2)* even if *O(1, 4)* was already available. Mathematically this does not matter, but in longer chains of matrix multiplications the errors could accumulate.
* Iterative symmetrize supports two keywords now. epsilon and tolerance. The tolerance is the same as in the other functions in the same module and epsilon is the maximum allowed difference between two subsequently symmetrized molecules. Before tolerance was used in both cases.
* A second test was added
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| 818
|
Parsing energies from gen_scfman module in Qchem 5
|
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[
"Thanks!"
] | 2017-08-31T02:38:26
| 2017-08-31T03:51:57
|
2017-08-31T03:51:57Z
|
CONTRIBUTOR
|
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## Summary
In Qchem 5 there is new scf module called gen_scfman, unfortunately the scf output is slightly different from the default module. Also, I added .eggs/ to the git ignore file. I saw a few egg related ignore so hopefully that is alright.
* parse energies from gen_scfman output
*unittest added
## TODO (if any)
There are other incompatibilities with the new output. I'm unsure how many exists but for instance the scf_iter_pattern no longer matches.
* find and fix other incompatibilities
|
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MDExOlB1bGxSZXF1ZXN0MTM4OTY4ODA1
| 819
|
Bug fix for Hubbard-U in Vasprun, and added basic vdW support
|
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[
"Thanks! However, I don't think the use_vdw and del_vdw should eb within the Incar object. In general, the Incar etc. input files are generically defined to support any functional or calculation type. For actual settings, these should be implemented in the vasp input sets (in pymatgen.io.vasp.sets.py). Can you implement a VDWSet using your proposed paramters? Thanks.",
"Yes, I can do that instead.",
"I have another question before I implement this: van-der-Waals interactions can also make a lot of sense for some slab calculations, but implementing an additional VDWSlabSet class seems a little excessive.\r\n\r\nI could instead add the kwarg vdw=None to the existing MVLSlabSet and add the parameters to slab_incar if vdw is not None. If you don't think that's a good idea, I will just implement the VDWSet class.",
"I would suggest this - given that vdw is a relatively basic parameter, you can add that to DictSet. Based on the vdw, you can modify the self._config_dict[\"INCAR\"] to include the vdw settings.\r\n\r\nBecause all sets inherit from DictSet, the vdw = \"XXX\" will work on all input sets immediately without further mods. ",
"Okay, that should do it. Thank you for your patience, and please let me know if you want me to change anything else.",
"Great thanks!. I will merge and make a few minor changes. Generally the user_incar_settings should not be modified. Whatever is specified by the user is the paramount setting, regardless of the defaults."
] | 2017-09-01T20:34:01
| 2017-09-01T23:40:50
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2017-09-01T23:40:50Z
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NONE
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## Summary
Fixed a bug for Hubbard calculations in Vasprun, and added basic van-der-Waals support.
* Hubbard: If LDAUJ is not specified in INCAR, Vasprun.as_dict() will raise a VaspParserError because the lengths of the LDAUU and LDAUJ lists are different. This problem has already been resolved in Vasprun.hubbards, but hasn't been ported to the as_dict() methods. An easy way to fix this is to just set d["hubbards"] = self.hubbards, which does the same thing as what the current code intends to do.
* vdW: VASP supports a lot of vdW functionals with different flags. I added a convenient way to add these parameters to an Incar object. For the vdW-DF functionals, VASP adds the information to the vasprun.xml file, so I updated Vasprun.run_type() to detect them. run_type now also detects PBEsol, and LDA calculations.
## TODO (if any)
* The way Vasprun checks if the calculation is DFT or DFT+U is not completely fool-proof. If a user has LDAUJ parameters in the INCAR file with less elements than in the LDAUU tag, VASP won't abort the calculation. Instead, it will do a standard DFT calculation but still write all the U parameters into vasprun.xml. The only place to see whether DFT or DFT+U is used is the OUTCAR file. Maybe there's a clever way to determine that and warn the user?
* Vasprun cannot read vdW functionals that use the IVDW tag because it's not written in the vasprun.xml file. Besides reading the OUTCAR file, I don't know how to determine the vdW functional.
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fix slab set as_dict issue and add unittest
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[] | 2017-09-01T23:49:44
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2017-09-01T23:50:48Z
|
CONTRIBUTOR
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## Summary
MVLSlabSet.as_dict was failing due to a change in __init__ argument name without the corresponding assignment of attribute. I'm not sure this is the best way to do it, but this seems to fix the issue. Might want to check, @richardtran415. Also added a unittest.
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| 821
|
Add critic2 command line caller for topological analysis, includes new graph class
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[
"I've updated `StructureGraph` this morning to remove some of the rough edges. I'm a lot happier with it now.\r\n\r\nEven though it's quite minimal, I've submitted this PR to (a) solicit feedback and make it easier for people to test and (b) signal my intent to work on this, so that if anyone intends to work on something similar we can collaborate to prevent duplication of effort. I didn't want to carry on with this and implement a lot of extra features only to conflict with someone else's work a few months down the road.",
"Closed this for now, there are a few bugs + tests need to be improved. Will do this and rebase with a new PR."
] | 2017-09-02T00:17:31
| 2017-09-07T05:25:16
|
2017-09-06T22:47:13Z
|
MEMBER
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# Add critic2 command line caller
Critic2 provides a more advanced Bader analysis, giving information on critical points present in the charge density and connections between these critical points. This allows us to obtain bonding information directly from the charge density, but also provides a whole range of additional information that may be uesful for other purposes.
This PR contains:
* `Critic2Caller` and `Critic2Output` for interfacing with critic2
* a very general `StructureGraph` class that presents the bonding information provided by critic2 in a user-friendly way (`Critic2Output.structure_graph` gives an instance of this class)
* `StructureGraph` interfaces nicely with local_envs.py that @nisse3000 has been working on
* this class isn't only for storing bonds, I'm also using in another context to store exchange interactions between atom pairs in magnetic materials ... it's really for storing any kind of 'connection' information between PeriodicSites, we have other applications in mind here too
* happy to change this class or discuss the design further
* I suspect it might change significantly in future, but the current version does at least work and is fully tested, so is useful to have for the time being
## Dependencies
Rather than re-invent the wheel, `StructureGraph` uses [NetworkX](https://networkx.github.io) to store and process graph information: this is a widely-used, pure Python graph library, so is very easy to install via pip. It also allows `StructureGraph` to be easily MSONable.
For visualization, GraphViz and pygraphviz are also required (visualization presents the graphs using the VESTA color schema by default).
Critic2 itself is also a dependency, obviously :) For homebrew users, `brew install https://raw.githubusercontent.com/mkhorton/homebrew-science/patch-2/critic2.rb` should work for anyone who wants to test this (I have a PR submitted to homebrew-science, so `brew install critic2` will work once it's merged). Alternatively, critic2 can be [compiled manually](https://github.com/aoterodelaroza/critic2) quite easily.
## To Do
This critic2 interface is complete and ready to merge, but only supports crystals at present (with charge densities from VASP) -- it could be extended to support molecules too if there's interest.
The `StructureGraph` class is quite minimal at the moment, and will probably be developed further in future. Consider it in beta for now.
## Examples
This is an MoS2 `StructureGraph` obtained via critic2:
```Structure Graph
Structure:
Full Formula (Mo1 S2)
Reduced Formula: MoS2
abc : 3.190316 3.190315 17.439502
angles: 90.000000 90.000000 120.000006
Sites (3)
# SP a b c
--- ---- -------- -------- --------
0 Mo 0.333333 0.666667 0.213295
1 S 0.666667 0.333333 0.303027
2 S 0.666667 0.333333 0.123562
Graph: bonds
from to to_image bond_length (Å)
---- ---- ------------ ---------------
1 0 (1, 0, 0) 2.4169E+00
1 0 (0, 0, 0) 2.4169E+00
1 0 (0, -1, 0) 2.4169E+00
2 0 (0, -1, 0) 2.4169E+00
2 0 (1, 0, 0) 2.4169E+00
2 0 (0, 0, 0) 2.4169E+00
```
You can also obtain a StructureGraph from `StructureGraph.with_local_env_strategy(structure, strategy)` where `strategy` is an instance of a `NearNeighbor` class in `local_env.py`.
Two examples of `StructureGraph` are shown visualized: one MoS2 from above (image shows the graph multiplied by (9,9,1) just to make it a bit clearer what's going on), and another showing a simple square graph (multiplied by (3,3,1)) which demonstrates how periodic edges work (note that the periodic edges shown are then re-connected to the appropriate atoms on the opposite side, and the edge attribute information shows the periodic image associated with that edge).
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Kpath fix
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[
"Pls fix the failing tests.",
"Sorry, I have found a few problems in this PR.\r\n\r\n- Simply adding the test for the presence of \"A\" in the spg symbol does not guarantee to give a proper standard primitive cell for the face centered orthorhombic spacegroups:\r\n```\r\nfrom pymatgen import MPRester\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\n\r\ns = MPRester().get_structure_by_material_id('mp-4587')\r\n\r\nprint len(s)\r\n#out: 4\r\n\r\nspga = SpacegroupAnalyzer(s, symprec=1e-2)\r\n\r\nprint spga.get_space_group_number()\r\n# out: 38\r\n\r\nprint spga.get_space_group_symbol()\r\n#out: Amm2\r\n\r\nstd_prim = spga.get_primitive_standard_structure()\r\n\r\nprint len(std_prim)\r\n#out: 8 --> Not a primitive\r\n\r\nprint len(std_prim.get_primitive_structure())\r\n#out: 4\r\n\r\n```\r\n\r\n- Is there any reason to remove all the comments and warnings indicating that a primitive standard structure should be passed to the HighSymmKpath object? It doesn't seem that this PR changes this point.\r\n\r\n- According to its docstring the method _symmetrize_molecule_ should return a dict with a specific set of keys. However a check has been added so that the method may return a list of other objects instead. ",
"@gpetretto \r\nI think @katherinelatimer2013 forgot to rebase before she made this PR. I'll help her fix that. I don't believe she actually changed most of the warnings, etc. The primary purpose of this PR was to fix the 'C'/'A' issue and add in unit tests so that we are not blind-sided in the future, while she works on a more general method of finding the HighSymmKpath based on the spacegroup operations. ",
"Sorry for the errors; I am going to close this and resubmit after fixing my local configuration.",
"Thanks. I will expand a bit on the previous comment, hoping that this can be of some help. In case you are going to add the unit tests for the primitive structures as well, pay attention that both the current implementation and the one checking on the presence of the 'A' in the symbol will likely give you the wrong structure. The spacegroups 38 to 41 are all affected from this issue, as now in spglib the preferred notation is A-centered rather than C-centered for these spacegroups. (see https://arxiv.org/pdf/1506.01455.pdf)",
"@gpetretto Yes; the confusion arose because I didn't realize that the call to \"get_refined_structure\" in \"get_conventional_standard_structure\" uses the spglib convention (which you reference). I will make that fix, which should be sufficient for everything else for now as \"get_primitive_standard_structure\" and the initializer for HighSymmKpath both call the get_conventional method.\r\n\r\nI think the mixing of conventions could be confusing for general users, since there is not much explicit documentation that I've been able to find on the various MP sites regarding which one we are using for which purposes..."
] | 2017-09-03T21:09:11
| 2017-09-04T16:49:43
|
2017-09-04T16:06:35Z
|
CONTRIBUTOR
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## Summary
Modifications to account for space group naming conventions changes in spglib
* Fix in pymatgen.symmetry.bandstructure.HighSymmKpath class
* Fix in pymatgen.symmetry.analyzer.SpacegroupAnalyzer class
* Tests for both modifications
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MDExOlB1bGxSZXF1ZXN0MTM5MTk2NjEx
| 823
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Kpath fix: rebased to pymatgen master and centering issue fixed
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[
"Thanks. But while I appreciate the extremely comprehensive tests, this is adding 230 files (one for each structure), and each file is not exactly small. Any chance the structures can be generated usinng code on the fly? It should be a simple matter to pass a crystal lattice and use Structure.from_spacegroup to generate a test structure for each spacegroup.",
"Sure, I'll make those changes."
] | 2017-09-04T17:53:25
| 2017-09-16T03:39:45
|
2017-09-16T03:39:45Z
|
CONTRIBUTOR
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## Summary
Modifications to account for space group naming conventions changes in spglib.
* Fix in pymatgen.symmetry.bandstructure.HighSymmKpath class
* Fix in pymatgen.symmetry.analyzer.SpacegroupAnalyzer class
* Tests for both modifications
## Centering convention fix
```
from pymatgen import MPRester
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
struct = MPRester().get_structure_by_material_id('mp-4587')
print len(struct)
#out: 4
sga = SpacegroupAnalyzer(struct, symprec=1e-2)
print sga.get_space_group_number()
# out: 38
print sga.get_space_group_symbol()
#out: Amm2
std_prim = sga.get_primitive_standard_structure()
print len(std_prim)
#out: 4
print(std_prim.lattice.abc)
#out: (3.7566910450291151, 3.7566910450291155, 3.5941917999999999)
#Shows that it has been converted to Setyawan/Curtarolo convention with C-centering.
print len(std_prim.get_primitive_structure())
#out: 4
```
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| 824
|
Is get_primitive_structure has bug?
|
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[
"get primitive just returns a primitive cell, typically the niggli or LLL reduced version. This is not always the same as the rhom version. They are nevertheless the same structure.",
"@shyuep OK, I understand. Thank you for explanation"
] | 2017-09-05T03:00:20
| 2017-09-05T11:23:57
|
2017-09-05T11:20:34Z
|
NONE
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I am just pip installed the latest pymatgen, the python version is 2.7
I want to do primitive cell conversion on Bi2Se3 structure. The cif file is space group 166 in hexagonal mode, while the primitive cell should be rhombohedral. So I do the following
```
import pymatgen as mp
structure = mg.Structure.from_file("Bi2Se3.cif")
structure.get_primitive_structure()
```
and this is what I got
```
Structure Summary
Lattice
abc : 4.1380000000000017 4.1379999999999999 9.841063244272835
angles : 77.863494260448405 77.863494260448405 59.999999999999986
volume : 141.56743497851997
A : -2.0690000000000017 -3.5836131208600084 0.0
B : -4.1379999999999999 -4.4408920985006262e-16 0.0
C : -2.0690000000000004 -1.1945377069533363 -9.5466666666666669
PeriodicSite: Bi (-4.1380, -2.3891, -7.6660) [0.3990, 0.3990, 0.8030]
PeriodicSite: Bi (-4.1380, -2.3891, -1.8807) [0.6010, 0.6010, 0.1970]
PeriodicSite: Se (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
PeriodicSite: Se (-2.0690, -1.1945, -3.6468) [0.2060, 0.2060, 0.3820]
PeriodicSite: Se (-6.2070, -3.5836, -5.8998) [0.7940, 0.7940, 0.6180]
```
This is no rhombohedral. I also tried to set different tolerance and use_site_props, all get the same wrong result.
However, I tried spglib.find_primitive directly on structure parameter, I got right rhombohedral.
So what is wrong here for pymatgen?
best regards
below is the cif structure
```
data_Bi2Se3
_audit_creation_method 'generated by CrystalMaker 9.1.4'
_cell_length_a 4.1380(0)
_cell_length_b 4.1380(0)
_cell_length_c 28.6400(0)
_cell_angle_alpha 90.0000(0)
_cell_angle_beta 90.0000(0)
_cell_angle_gamma 120.0000(0)
_symmetry_space_group_name_H-M 'R -3 m'
_symmetry_Int_Tables_number 166
_symmetry_cell_setting trigonal
loop_
_symmetry_equiv_pos_as_xyz
'+x,+y,+z'
'2/3+x,1/3+y,1/3+z'
'1/3+x,2/3+y,2/3+z'
'-y,+x-y,+z'
'2/3-y,1/3+x-y,1/3+z'
'1/3-y,2/3+x-y,2/3+z'
'-x+y,-x,+z'
'2/3-x+y,1/3-x,1/3+z'
'1/3-x+y,2/3-x,2/3+z'
'+y,+x,-z'
'2/3+y,1/3+x,1/3-z'
'1/3+y,2/3+x,2/3-z'
'+x-y,-y,-z'
'2/3+x-y,1/3-y,1/3-z'
'1/3+x-y,2/3-y,2/3-z'
'-x,-x+y,-z'
'2/3-x,1/3-x+y,1/3-z'
'1/3-x,2/3-x+y,2/3-z'
'-x,-y,-z'
'2/3-x,1/3-y,1/3-z'
'1/3-x,2/3-y,2/3-z'
'+y,-x+y,-z'
'2/3+y,1/3-x+y,1/3-z'
'1/3+y,2/3-x+y,2/3-z'
'+x-y,+x,-z'
'2/3+x-y,1/3+x,1/3-z'
'1/3+x-y,2/3+x,2/3-z'
'-y,-x,+z'
'2/3-y,1/3-x,1/3+z'
'1/3-y,2/3-x,2/3+z'
'-x+y,+y,+z'
'2/3-x+y,1/3+y,1/3+z'
'1/3-x+y,2/3+y,2/3+z'
'+x,+x-y,+z'
'2/3+x,1/3+x-y,1/3+z'
'1/3+x,2/3+x-y,2/3+z'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Bi Bi 1.0000 0.0000 0.0000 0.3990
Se1 Se 1.0000 0.0000 0.0000 0.0000
Se2 Se 1.0000 0.0000 0.0000 0.2060
```
|
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FloatWithUnit does not play nicely with numpy arrays
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"Use arraywithunit\n\nOn Wed, Sep 6, 2017, 00:06 Brandon Bocklund <notifications@github.com>\nwrote:\n\n> from pymatgen.core.units import FloatWithUnitimport numpy as np\n>\n> scaling_array = np.array([0.5, 1, 2, 4])\n> one_ev = FloatWithUnit(1, 'eV')\n> # does not raise, drops unit (should be eV)# see the first\n> scaling_array*one_ev\n> # raises\n> one_ev*scaling_array\n>\n> from pymatgen.core.units import ArrayWithUnit\n> scaling_array_unit = ArrayWithUnit(scaling_array, '')\n> # does not raise, keeps unit (eV)\n> scaling_array_unit*one_ev\n> # raises\n> one_ev*scaling_array_unit\n>\n>\n> scaling_array_unit = ArrayWithUnit(scaling_array, 'm')\n> # does not raise, keeps units (eV-m)\n> scaling_array_unit*one_ev\n> # raises\n> one_ev*scaling_array_unit\n>\n> They all raise the same error:\n>\n> ---------------------------------------------------------------------------TypeError Traceback (most recent call last)<ipython-input-23-a8dd98862e48> in <module>()\n> 1 # raises----> 2 one_ev*scaling_array_unit\n> /Users/brandon/.virtualenvs/prlworkflows/lib/python3.6/site-packages/pymatgen/core/units.py in __mul__(self, other)\n> 408 return FloatWithUnit(float(self) * other,\n> 409 unit_type=self._unit_type,--> 410 unit=self._unit)\n> 411 return FloatWithUnit(float(self) * other, unit_type=None,\n> 412 unit=self._unit * other._unit)\n> /Users/brandon/.virtualenvs/prlworkflows/lib/python3.6/site-packages/pymatgen/core/units.py in __new__(cls, val, unit, unit_type)\n> 355\n> 356 def __new__(cls, val, unit, unit_type=None):--> 357 new = float.__new__(cls, val)\n> 358 new._unit = Unit(unit)\n> 359 new._unit_type = unit_type\n> TypeError: only length-1 arrays can be converted to Python scalars\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/825>, or mute the\n> thread\n> <https://github.com/notifications/unsubscribe-auth/AAjOU1E_fqaRZS4UX-TSI3q-8M6QP252ks5sfZSfgaJpZM4PNWYX>\n> .\n>\n",
"I have tried this. See the end of the example I supplied. Am I using this correctly? It fails both when I use a unit and when there is no unit (`unit=''`)",
"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 2017-09-05T18:36:14
| 2023-08-08T21:20:46
|
2023-08-08T21:20:46Z
|
CONTRIBUTOR
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``` python
from pymatgen.core.units import FloatWithUnit
import numpy as np
scaling_array = np.array([0.5, 1, 2, 4])
one_ev = FloatWithUnit(1, 'eV')
# does not raise, drops unit (should be eV)
# see the first
scaling_array*one_ev
# raises
one_ev*scaling_array
from pymatgen.core.units import ArrayWithUnit
scaling_array_unit = ArrayWithUnit(scaling_array, '')
# does not raise, keeps unit (eV)
scaling_array_unit*one_ev
# raises
one_ev*scaling_array_unit
scaling_array_unit = ArrayWithUnit(scaling_array, 'm')
# does not raise, keeps units (eV-m)
scaling_array_unit*one_ev
# raises
one_ev*scaling_array_unit
```
They all raise the same error:
``` python
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-23-a8dd98862e48> in <module>()
1 # raises
----> 2 one_ev*scaling_array_unit
/Users/brandon/.virtualenvs/prlworkflows/lib/python3.6/site-packages/pymatgen/core/units.py in __mul__(self, other)
408 return FloatWithUnit(float(self) * other,
409 unit_type=self._unit_type,
--> 410 unit=self._unit)
411 return FloatWithUnit(float(self) * other, unit_type=None,
412 unit=self._unit * other._unit)
/Users/brandon/.virtualenvs/prlworkflows/lib/python3.6/site-packages/pymatgen/core/units.py in __new__(cls, val, unit, unit_type)
355
356 def __new__(cls, val, unit, unit_type=None):
--> 357 new = float.__new__(cls, val)
358 new._unit = Unit(unit)
359 new._unit_type = unit_type
TypeError: only length-1 arrays can be converted to Python scalars
```
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| 255,412,266
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MDExOlB1bGxSZXF1ZXN0MTM5NDIzNzIy
| 826
|
resolving two small issues with periodic table data
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[
"Pls fix the values not in the json, but rather the yaml version in pymatgen/dev. That is supposed to be \"base data\" that we edit on. We then convert that yaml to json using the scipt in pymatgen/dev.",
"ok I just changed this value inside pymatgen/dev_scripts/periodic_table.yaml",
"@shyuep The script does not seem to fix the issue when working with `Element`, which uses the `pymatgen/core/periodic_table.json`. The file in `pymatgen/dev_scripts` is updated but the one in `pymatgen/core` is not.\r\n\r\nFor example, both @albalu and I notice that `Element(\"Se\").electrical_resistivity` returns `u'about 10000010<sup>-8</sup> Ω m'`, not `1e-08`.\r\n\r\nShould we change `pymatgen/core/periodic_table.json` file or the script?\r\n",
"You need to copy the generated json to the core folder. I just did that."
] | 2017-09-05T21:19:21
| 2017-11-01T13:52:50
|
2017-09-06T01:04:06Z
|
CONTRIBUTOR
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## Summary
both changes are very small:
* Electrical resistivity for Te is 1000010<sup>-8</sup> in periodic_table.json but it should be 10000 10<sup>-8</sup> equal to 1e-4 ohm.m consistent with here ( http://periodictable.com/Elements/052/data.html ) for example
* to have every Element property as float, I set the ">" to its lower bound.
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MDU6SXNzdWUyNTU0MTQ1NzA=
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|
Possible bug in local_env.py or PeriodicSite/Lattice, incorrect jimage?
|
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[
"It's a numerical issue because the third cell angle is 120 degrees. Does that make sense?\r\n\r\n\r\n",
"Hi Nils -- from your attached image, the neighbor from 1 (0,0) to 2' (0,1) makes sense to me, but isn't the code suggesting a neighbor to (1,1) too? Maybe I'm not looking at it right, but the (1,1,0) image just doesn't make sense to me.",
"I am pretty sure the PeriodicSite jimage is correct.",
"Okay, thanks both. I've attached a sketch to illustrate the behavior I was expecting, which might help show where I'm getting confused ...\r\n\r\n<img width=\"943\" alt=\"mos2_sketch\" src=\"https://user-images.githubusercontent.com/2976580/30093948-91393c32-927d-11e7-88ac-6868940d6b1d.png\">",
"I think I see what's happening here. The problem is that in the MinNN code, the image is defined relative to Mo. Since there are 6 S atoms that are at degenerate distance to Mo, any of the images are likely to be returned based on slight numerical perturbations. \r\n\r\nBased on your supplied structure, the NN to MO are:\r\n```\r\n[(PeriodicSite: S (-1.5952, 0.9210, 5.2846) [-0.3333, 0.3333, 0.3030],\r\n 2.4169302746952126,\r\n 1),\r\n (PeriodicSite: S (1.5952, 0.9210, 5.2846) [0.6667, 0.3333, 0.3030],\r\n 2.4169344853367503,\r\n 1),\r\n (PeriodicSite: S (0.0000, 3.6839, 5.2846) [0.6667, 1.3333, 0.3030],\r\n 2.4169300062989856,\r\n 1),\r\n (PeriodicSite: S (-1.5952, 0.9210, 2.1549) [-0.3333, 0.3333, 0.1236],\r\n 2.4169415662251317,\r\n 2),\r\n (PeriodicSite: S (1.5952, 0.9210, 2.1549) [0.6667, 0.3333, 0.1236],\r\n 2.4169457768469989,\r\n 2),\r\n (PeriodicSite: S (0.0000, 3.6839, 2.1549) [0.6667, 1.3333, 0.1236],\r\n 2.4169412978301592,\r\n 2)]\r\n```\r\nIf you look at the above, the third site has a slightly smaller distance than the first and second site. So when you do a jimage calculation, the algo maps site 1 and 2 to site 3. Site 3 is therefore the (0,0,0) image reference [the (010) site in your figure). When the algo tries to find the shortest distance for site 1 for example, it needs to move your (-1, 0, 0) site to (0, 1, 0). Hence the jimage is (110).\r\n\r\nMakes sense?",
"Ah, that explains it, thank you! Do you think the behavior in local_env should be changed to account for this then? Though the returned jimages are technically correct, this seems fairly non-intuitive, especially since it's fundamentally a precision issue.\r\n\r\nI think I'd be inclined just to get the jimages by subtracting the frac coords of the corresponding original PeriodicSite in the origin lattice from the PeriodicSite returned by the NN class. In the list you've provided this would give` [[-1, 0, 0], [0, 0, 0], [0, 1, 0], ...]`.",
"I agree your definition is probably more intuitive. In that case, I would carefully explain what the \"image\" means in the context of local_env to avoid confusion with the `distance_and_image` definition of jimage. The former really tells you what mappings from an existing site within the cell gives you another neighbor. The latter really is aiming to give you the shortest distance between two points, and what image mapping needs to be added to give that. ",
"Thank you @mkhorton and @shyuep for raising this issue.\r\n\r\nI agree that Matt's definition is more intuitive. But I had in mind that it is important to keep track of lattice displacement vectors when you do 2nd-nearest neighbor analysis. So, I think the best course of action is to update the documentation to clearly state that these are lattice displacement vectors, not image locations.\r\n\r\nDo you guys agree, or do you see a more important use of the image locations over the lattice displacement vectors? In that case, we should go for Matt's suggestion, I guess.",
"I don't have strong opinions on this -- if you think it's useful to keep the original definition for other reasons, then let's do that. I wouldn't be surprised if people might mis-use it though.\r\n\r\nI more just wanted to understand what was going on because it was causing an issue in my graph class, obtaining incorrect topology. However, now I know, it was just a one-line fix and it works fine now, regardless of what definition ends up being used in local_env.",
"I would think using Matt's suggestion is better. It does not make sense for the local_env to map vectors to just the absolute nearest image. The whole idea is to identify multiple NN, which have different distances to the center atom."
] | 2017-09-05T21:28:46
| 2017-09-12T22:07:34
|
2017-09-12T22:07:34Z
|
MEMBER
|
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## System
* Pymatgen version: 2017.9.1 (development)
* Python version: 3.6.0
* OS version: macOS 10.12.6
## Summary
Would appreciate a sanity check here. I'm looking at a single layer of MoS2 from a .cif file ([attached](https://raw.githubusercontent.com/mkhorton/pymatgen/e807247f43153a71b6f3389120c623c3d7e13c25/test_files/critic2/MoS2.cif)), where site 0 is Mo, site 1 is S, site 2 is S. From a visual inspection in VESTA, I see the Mo site has the following neighbors in the periodic images specified:
0 -> 1, (0, 0, 0)
0 -> 1, (0, 1, 0)
0 -> 1, (-1, 0, 0)
0 -> 2, (0, 0, 0)
0 -> 2, (0, 1, 0)
0 -> 2, (-1, 0, 0)
However, using `MinimumDistanceNN()` (which is very straight-forward, most logic comes from `PeriodicSite`/`Lattice`), I get:
0 -> 1, (0, 0, 0)
0 -> 1, (0, 1, 0)
0 -> 1, (1, 1, 0) # this line is different
0 -> 2, (0, 0, 0)
0 -> 2, (0, 1, 0)
0 -> 2, (1, 1, 0) # this line is different
This seems wrong to me, but I'm having difficulty tracking down the bug, I get the same results with `MinimumOKeeffeNN` too ... @nisse3000 do you have any ideas?
## Example code
```python
from pymatgen.core import Structure
from pymatgen.analysis.local_env import MinimumDistanceNN
s = Structure.from_file('MoS2.cif')
nn = MinimumDistanceNN()
nn.get_nn_info(s, 0) # neighbors of Mo site
```
## Files (if any)
MoS2 CIF file [here](https://raw.githubusercontent.com/mkhorton/pymatgen/e807247f43153a71b6f3389120c623c3d7e13c25/test_files/critic2/MoS2.cif).
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MDExOlB1bGxSZXF1ZXN0MTM5NDY4ODg2
| 828
|
Code style fix
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[
"Thanks!"
] | 2017-09-06T04:16:02
| 2017-09-11T05:06:58
|
2017-09-11T05:06:54Z
|
CONTRIBUTOR
|
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## Summary
Fixed code style in interface_reaction module.
* Modified docstring to conform to pymatgen standard.
* Modified code style to conform to PEP 8 requirements.
|
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| 255,835,829
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MDExOlB1bGxSZXF1ZXN0MTM5NzMwNjE2
| 829
|
Fix the bug for str conversion with tilted box
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[] | 2017-09-07T07:06:10
| 2017-09-07T07:09:07
|
2017-09-07T07:09:07Z
|
CONTRIBUTOR
|
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## Summary
For lammpsData,
1), The lattice vector a should be along x direction.
2), The plane formed by lattice vectors a, b should be perpendicular with z direction.
Thus we need to rotate input structure's lattice so that it conforms to the above requirements, from which we can get the new lattice. The atomic coordinate should be also rotated according to the new lattice.
The previous code did not consider this. The new version adds this part.
In addition, The new version also adds a formal_float control to the output. The atomic mass cannot be formatted, since Lammps cannot read the formatted atomic mass.
* 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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| 830
|
Adding two volume predicting schemes
|
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[] | 2017-09-07T07:29:39
| 2017-09-08T00:06:11
|
2017-09-08T00:06:11Z
|
NONE
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## Summary
* Reference lattice scaling scheme (RLS) improved on top of ConditionalVolumePredictor in MatMiner.
* Data-mined lattice scaling scheme (DLS) improved on top of VolumePredictor in MatMiner (Sayan Roychowdhury and Anubhav Jain).
* Unittests are also provided.
|
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MDExOlB1bGxSZXF1ZXN0MTM5OTE1ODU2
| 831
|
Add critic2 command line caller for topological analysis
|
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[
"09/12: Updated to account for changes due to #827, added method to extract molecules from periodic crystals for #833",
"can you fix the merge conflicts? I will then merge the pull req.",
"Great, thanks. The graph library this uses (networkx) just had a big 2.0 release, so I'm going to update to that/run some tests to make sure everything still works, then I'll resolve the merge conflicts and it should be good to go."
] | 2017-09-07T22:07:39
| 2017-09-29T17:21:17
|
2017-09-29T17:21:17Z
|
MEMBER
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This is an update of a [previous pull request](https://github.com/materialsproject/pymatgen/pull/821), fixing a few bugs and adding some new features (e.g. `StructureGraph.diff()` to, for example, easily compare two different neighbor-detection strategies).
From a technical point of view it's ready to merge, unless there's an issue with the class on principle, in which case I'm happy to discuss + change as appropriate.
# Add critic2 command line caller
Critic2 provides a more advanced Bader analysis, giving information on critical points present in the charge density and connections between these critical points. This allows us to obtain bonding information directly from the charge density, but also provides a whole range of additional information that may be uesful for other purposes.
This PR contains:
* `Critic2Caller` and `Critic2Output` for interfacing with critic2
* a very general `StructureGraph` class that presents the bonding information provided by critic2 in a user-friendly way (`Critic2Output.structure_graph` gives an instance of this class)
* `StructureGraph` interfaces nicely with local_envs.py that @nisse3000 has been working on
* this class isn't only for storing bonds, I'm also using in another context to store exchange interactions between atom pairs in magnetic materials ... it's really for storing any kind of 'connection' information between PeriodicSites, we have other applications in mind here too
* there were a few different ways to implement this class, I'm happy with the current implementation for now, but it could probably be improved at a later date -- I have a few ideas if anyone wants to discuss/collaborate
## Dependencies
Rather than re-invent the wheel, `StructureGraph` uses [NetworkX](https://networkx.github.io) to store and process graph information: this is a widely-used, pure Python graph library, so is very easy to install via pip. It also allows `StructureGraph` to be easily MSONable.
For visualization, GraphViz and pygraphviz are also required (visualization presents the graphs using the VESTA color schema by default).
Critic2 itself is also a dependency, obviously :) For homebrew users, `brew install https://raw.githubusercontent.com/mkhorton/homebrew-science/patch-2/critic2.rb` should work for anyone who wants to test this (I have a PR submitted to homebrew-science, so `brew install critic2` will work once it's merged). Alternatively, critic2 can be [compiled manually](https://github.com/aoterodelaroza/critic2) quite easily.
## To Do
This critic2 interface is complete and ready to merge, but only supports crystals at present (with charge densities from VASP) -- it could be extended to support molecules too if there's interest.
The `StructureGraph` class is in beta and will have new features added at a later date.
## Examples
This is an MoS2 `StructureGraph` obtained via critic2:
```
Structure Graph
Structure:
Full Formula (Mo1 S2)
Reduced Formula: MoS2
abc : 3.190316 3.190315 17.439502
angles: 90.000000 90.000000 120.000006
Sites (3)
# SP a b c
--- ---- -------- -------- --------
0 Mo 0.333333 0.666667 0.213295
1 S 0.666667 0.333333 0.303027
2 S 0.666667 0.333333 0.123562
Graph: bonds
from to to_image bond_length (A)
---- ---- ------------ ------------------
0 1 (-1, 0, 0) 2.416930006299E+00
0 1 (0, 0, 0) 2.416930006299E+00
0 1 (0, 1, 0) 2.416930006299E+00
0 2 (0, 1, 0) 2.416941297830E+00
0 2 (-1, 0, 0) 2.416941297830E+00
0 2 (0, 0, 0) 2.416941297830E+00
```
You can also obtain a StructureGraph from `StructureGraph.with_local_env_strategy(structure, strategy)` where `strategy` is an instance of a `NearNeighbor` class in `local_env.py`.
Figure shows a MoS2 StructureGraph (multiplied by (9,9,1) to make it easier to visualize).
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MDU6SXNzdWUyNTYxNjA2NDA=
| 832
|
How to vary slab thickness when creating slab?
|
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[
"Hi, everyone. no one help?",
"The min_slab_thickness and min_vacuum_thickness arguments to the SlabGenerator?\r\n\r\nBTW, for questions on usage, please us the Google groups. Github issues is meant for reporting bugs and feature requests."
] | 2017-09-08T07:08:37
| 2017-09-11T05:03:36
|
2017-09-11T05:03:36Z
|
NONE
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Dear developers,
I am trying to use pymatgen to create slab structure. I want to create a single and a double quintuple layer of Bi2Se3.
Bi2Se3 has spacegroup 166, and the conventional cell of hexagonal setting has 15 atom layers along c axis which is 3 quintuple layer (as show in [this picture](https://www.researchgate.net/profile/Xi_Dai/publication/232748137/figure/fig3/AS:267706196820008@1440837539369/Figure-1-Crystal-structurea-Crystal-structure-of-Bi2Se3-with-three-primitive-lattice.png) . But I want to make a single quintuple layer.
I can use SlabGenerator to easily create 3 quintuple layer Bi2Se3
```
cif_file=r'r:\Bi2Se3.cif'
structure=pymatgen.Structure.from_file(cif_file)
slabgen = SlabGenerator(structure, (0,0,1), 10, 10)
all_slabs = slabgen.get_slabs()
cif_file_obj=pymatgen.io.cif.CifWriter(all_slabs[2],symprec=1e-4) # all_slabs[2] gives the correct surface
cif_file_obj.write_file(r'r:\Bi2Se3_layer.cif')
```
But the problem is how to make 1 quintuple layer or double layer, or even 1.5 layer of Bi2Se3?
I didn't find an option to control this. Is this possible with pymatgen?
best regards
------------
below is Bi2Se3 cif file :
data_Bi2Se3_zhanghaijun
_audit_creation_method 'generated by CrystalMaker 9.1.4'
_cell_length_a 4.1380(0)
_cell_length_b 4.1380(0)
_cell_length_c 28.6400(0)
_cell_angle_alpha 90.0000(0)
_cell_angle_beta 90.0000(0)
_cell_angle_gamma 120.0000(0)
_symmetry_space_group_name_H-M 'R -3 m'
_symmetry_Int_Tables_number 166
_symmetry_cell_setting trigonal
loop_
_symmetry_equiv_pos_as_xyz
'+x,+y,+z'
'2/3+x,1/3+y,1/3+z'
'1/3+x,2/3+y,2/3+z'
'-y,+x-y,+z'
'2/3-y,1/3+x-y,1/3+z'
'1/3-y,2/3+x-y,2/3+z'
'-x+y,-x,+z'
'2/3-x+y,1/3-x,1/3+z'
'1/3-x+y,2/3-x,2/3+z'
'+y,+x,-z'
'2/3+y,1/3+x,1/3-z'
'1/3+y,2/3+x,2/3-z'
'+x-y,-y,-z'
'2/3+x-y,1/3-y,1/3-z'
'1/3+x-y,2/3-y,2/3-z'
'-x,-x+y,-z'
'2/3-x,1/3-x+y,1/3-z'
'1/3-x,2/3-x+y,2/3-z'
'-x,-y,-z'
'2/3-x,1/3-y,1/3-z'
'1/3-x,2/3-y,2/3-z'
'+y,-x+y,-z'
'2/3+y,1/3-x+y,1/3-z'
'1/3+y,2/3-x+y,2/3-z'
'+x-y,+x,-z'
'2/3+x-y,1/3+x,1/3-z'
'1/3+x-y,2/3+x,2/3-z'
'-y,-x,+z'
'2/3-y,1/3-x,1/3+z'
'1/3-y,2/3-x,2/3+z'
'-x+y,+y,+z'
'2/3-x+y,1/3+y,1/3+z'
'1/3-x+y,2/3+y,2/3+z'
'+x,+x-y,+z'
'2/3+x,1/3+x-y,1/3+z'
'1/3+x,2/3+x-y,2/3+z'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Bi Bi 1.0000 0.0000 0.0000 0.3990
Se1 Se 1.0000 0.0000 0.0000 0.0000
Se2 Se 1.0000 0.0000 0.0000 0.2060
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MDU6SXNzdWUyNTYyMjMxMjc=
| 833
|
extract molecules from organic crystal
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[
"I don't believe this is currently implemented (perhaps others can correct me) -- but I may be able to help implement something that does this. I think you're right that the closest we currently have is a nearest neighbour algorithm.\r\n\r\nDo you have any constraints on your inputs? Do they just contain molecules, or are they organic-inorganic hybrids? Do you have any sample files to share?",
"Thank you, @mkhorton ! In my case they're just molecules, and a sample of my cif file could be found in [https://gist.github.com/liwt31/cecfb19145e152f96d47702c817fd4da](https://gist.github.com/liwt31/cecfb19145e152f96d47702c817fd4da) . \r\n\r\nThe cif file was downloaded from CCDC and I think it''s illegal to publish it online. So I'll delete the gist in one day. If anyone's still interested to it maybe I can share it by email.",
"Great, thanks! I should have time to implement this mid-week sometime.\r\n\r\nThe thing that makes this trickier is when the molecules go across the unit cell boundaries, if your cell only contains a single molecule it'd be easy to extract (just use structure.coords), or if it had multiple molecules, but again not across the unit cell boundary, you could use a clustering approach similar to what's in the break_bonds function. Hopefully we can get a fully general solution to this however.",
"Hi @liwt31 ,\r\n\r\nSome basic functionality has been added for this. It should work, but might be a little slow.\r\n\r\n```\r\nfrom pymatgen.analysis.graphs import StructureGraph\r\nfrom pymatgen.analysis.local_env import JMolNN # used for deciding which atoms are bonded\r\nsg = StructureGraph.with_local_env_strategy(my_structure, JMolNN())\r\nmy_molecules = sg.get_subgraphs_as_molecules()\r\n```\r\n\r\n(Code above assumes you've already loaded your organic crystal CIF as `my_structure`, and you'll need to `pip install networkx` to use the StructureGraph module.)\r\n\r\nI might wrap this up as a convenience method somewhere once it's been tested more. If you find any bugs, let me know!",
"Thanks! I think it's working. I'll report if I found any bugs in furture usage. ",
"Hi @mkhorton \r\n\r\nI'm wondering which release of pymatgen contains your JMolNN addition to the code, because I have upgraded my pymatgen using pip, but I still don't seem to have it in my local_env.py file.\r\n\r\nThe error is:\r\n\r\n```\r\nfrom pymatgen.analysis.local_env import JMolNN # used for deciding which atoms are bonded\r\nImportError: cannot import name 'JMolNN' from 'pymatgen.analysis.local_env' \r\n```\r\n\r\nThanks.\r\n",
"Hi @misterblonde, try `JmolNN` with a lower-case `m`",
"If I call \"JmolNN\" with lower-case m, I don't get an error anymore, but I feel there is something wrong with the function, some infinite loop or something, because I have been waiting for >6 mins and nothing happens and the function is still running. ",
"That definitely does seem suspicious. JmolNN is actually one of the fastest\nsince it’s a simple cut-off distance based approach. What version of\npymatgen are you running? I can confirm JmolNN definitely works so we’d\nneed some more info to track down the issue you’re seeing.\n\nOn Sun, May 9, 2021 at 23:04, misterblonde ***@***.***> wrote:\n\n> If I call \"JmolNN\" with lower-case m, I don't get an error anymore, but I\n> feel there is something wrong with the function, some infinite loop or\n> something, because I have been waiting for >6 mins and nothing happens and\n> the function is still running.\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/833#issuecomment-836434937>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRAPTQ43Q7TSHFNWRNDTM6OSZANCNFSM4D2EGADQ>\n> .\n>\n",
"[I have a similar to question to the above: I have a cif file of molecules, and I'm creating a supercell and I want to be able to access the coordinates of the molecules of the original cell (each molecule individually), so that I can calculate distance distributions to other molecules (e.g., within minimum image convention). How can I do this? \r\n\r\nstruct = Structure.from_file(\"227799.cif\")\r\nprint(struct)\r\nnew_molecule = Molecule.from_sites(sorted(molecules[0], key=lambda site: site.species))\r\nsg = StructureGraph.with_local_env_strategy(struct, JmolNN())\r\nmolecules = sg.get_subgraphs_as_molecules()\r\n\r\nThis only gives a single unique molecule (I want the central molecules in their original positions in the unit cell as molecular objects that I can [manipulate).](url)\r\nThanks,\r\nDan](url)\r\n",
"> That definitely does seem suspicious. JmolNN is actually one of the fastest since it’s a simple cut-off distance based approach. What version of pymatgen are you running? I can confirm JmolNN definitely works so we’d need some more info to track down the issue you’re seeing.\r\n> […](#)\r\n\r\nHi @mkhorton and @misterblonde. \r\nI am actually wondering if it is possible to get a single molecule with labels of their corresponding atoms (C1, C2, S3...) not only string of atoms (C, C, S)?"
] | 2017-09-08T11:20:55
| 2023-01-24T16:00:59
|
2018-09-07T18:42:55Z
|
CONTRIBUTOR
|
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If I've got a cif file for a small organic molecule crystal, how could I convert it to a Molecule object?
I've looked through the document but my closest match is some nearest neighbor algorithm... Maybe I've missed something?
If the feature is not yet implemented, I hope I can be of help. I plan to:
1. build a supercell according to cif file
2. find all possible molecules from that supercell
3. delete invalid and redundant ones
Any suggestions? Thank you all in advance.
|
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| 256,383,175
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MDExOlB1bGxSZXF1ZXN0MTQwMTM0NDIx
| 834
|
fixed spacing for Electrical resistivity of Si and Ge (very small change)
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[] | 2017-09-08T22:05:38
| 2017-09-09T02:23:24
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2017-09-09T02:23:24Z
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CONTRIBUTOR
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## Summary
fixed spacing for Electrical resistivity of Si and Ge. For example in Ge the resistivity was 5000010... rather than 50000 10... and that would prevent correct parsing.
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MDExOlB1bGxSZXF1ZXN0MTQwNDQ5MzI5
| 835
|
Corrected image location computation in local_env.py
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[
"Can we have a few unittests confirming the new definition pls? @mkhorton example of MoSi2 would be a good one."
] | 2017-09-11T22:26:12
| 2017-09-11T23:29:31
|
2017-09-11T23:29:31Z
|
CONTRIBUTOR
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I've changed the way the images locations are computed in local_env.py according to @mkhorton and @shyuep's comments in issue #827
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MDU6SXNzdWUyNTczNzQxNzc=
| 836
|
Bug in io.gaussian.GaussianOutput
|
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[] | 2017-09-13T13:08:09
| 2017-09-13T13:25:05
|
2017-09-13T13:25:05Z
|
CONTRIBUTOR
|
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Hi, all! I belive I've found a bug in io.gaussian module at line 1301. Luckily I think it's easy to fix.
```
if not charge:
charge = self.charge
```
When a user tries to set the charge of the generated input file to 0, i.e., the parameter `charge = 0`, the statement `not charge` will be considered as `True`, and thus `charge` will not be changed.
I personally think using `not isinstance(charge, int)` here might be a better idea. :)
|
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MDExOlB1bGxSZXF1ZXN0MTQwOTU5NDM0
| 837
|
New argument max_row in periodic heating map
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[] | 2017-09-14T00:35:55
| 2017-09-14T15:37:56
|
2017-09-14T15:37:56Z
|
NONE
|
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## Summary
- Add argument "max_row" in period table heat map. That way one can control the number of rows shown in the heat map.
- Add unittests
|
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MDExOlB1bGxSZXF1ZXN0MTQxNDMxMTE3
| 838
|
Kpath fix with on-the-fly structures for tests and some comments
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[
"There are two test errors (see travis). The errors are:\r\n\r\n```\r\n======================================================================\r\nERROR: test_kpath_acentered (pymatgen.symmetry.tests.test_kpaths.HighSymmKpathTest)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n File \"/home/travis/build/materialsproject/pymatgen/pymatgen/symmetry/tests/test_kpaths.py\", line 57, in test_kpath_acentered\r\n lattice = Lattice.orthorhombic(2, 9, 1)\r\nNameError: name 'Lattice' is not defined\r\n\r\n======================================================================\r\nERROR: test_kpath_generation (pymatgen.symmetry.tests.test_kpaths.HighSymmKpathTest)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n File \"/home/travis/build/materialsproject/pymatgen/pymatgen/symmetry/tests/test_kpaths.py\", line 36, in test_kpath_generation\r\n if sg_num in triclinic:\r\nNameError: name 'triclinic' is not defined\r\n\r\n----------------------------------------------------------------------\r\n```\r\n\r\nSeems to be just import and quotes error. Can you fix pls? Thanks."
] | 2017-09-16T03:41:54
| 2017-09-16T22:38:35
|
2017-09-16T22:38:35Z
|
CONTRIBUTOR
|
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## Summary
Modifications to account for space group naming conventions changes in spglib.
* Fix in pymatgen.symmetry.bandstructure.HighSymmKpath class
* Fix in pymatgen.symmetry.analyzer.SpacegroupAnalyzer class
* Tests for both modifications, this time generating structures within tests
* A few comments to explain modifications
## Centering convention fix
```
from pymatgen import MPRester
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
struct = MPRester().get_structure_by_material_id('mp-4587')
print len(struct)
#out: 4
sga = SpacegroupAnalyzer(struct, symprec=1e-2)
print sga.get_space_group_number()
# out: 38
print sga.get_space_group_symbol()
#out: Amm2
std_prim = sga.get_primitive_standard_structure()
print len(std_prim)
#out: 4
print(std_prim.lattice.abc)
#out: (3.7566910450291151, 3.7566910450291155, 3.5941917999999999)
#Shows that it has been converted to Setyawan/Curtarolo convention with C-centering.
print len(std_prim.get_primitive_structure())
#out: 4
```
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MDExOlB1bGxSZXF1ZXN0MTQxNjU5OTYw
| 839
|
Gibbs free energy of a material with respect to Pourbaix stable domains
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[
"I am not sure the __eq__ test for phase diagrams is a good idea. In fact, I am not even sure tehre should be an __eq__ implementation for a PD. When would such a function be used?",
"It's not for the pd itself, it's just for a single PDEntry. We use it primarily to test if a list of entries contains a specific entry (e. g. `if entry in list_of_entries`), which is an integral part of the multi-entry processing that's in the current pourbaix diagram implementation. We could isolate it to the PourbaixEntry object, if it's a problem for the general case.",
"The problem here is that the current `__eq__` makes no sense to me even for PDEntry. Generally, any sort or search algo computes the hash first. Here, your hash is the id. The No. 1 rule in programming is that all equal objects must have the same hash, though objects with the same hash need not be equal. Your code violates the construct used in things like sets and dicts. For example,\r\n\r\n```python\r\nclass Val:\r\n\r\n def __init__(self, val):\r\n self.val = val\r\n\r\n def __eq__(self, other):\r\n return self.val == other.val\r\n\r\n def __hash__(self):\r\n return id(self)\r\n\r\n def __repr__(self):\r\n return \"Val: %s\" % self.val\r\n\r\na1 = Val(1)\r\nb1 = Val(1)\r\n\r\nprint(a1 == b1) # This is True.\r\nprint(set([a1, b1])) # This set contains two items!!\r\n```\r\n\r\nThe final set contains two items, not one. That is wrong behavior. Similarly, if you use the PDEntry in a set or dict, it will lead to very strange behavior.",
"Ah, I understand the problem now. I've just tested it after deleting the new eq and hash and it doesn't seem to break the new unittests, so we can just scrap it. I'm not sure why I thought it was necessary in the first place."
] | 2017-09-18T17:29:18
| 2017-09-19T02:26:43
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2017-09-19T02:26:43Z
|
MEMBER
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Added functions related to computation of Gibbs free energy of a material with respect to Pourbaix stable domains.
Some revisions and simplification to existing routines.
|
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| 258,577,813
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MDExOlB1bGxSZXF1ZXN0MTQxNjcyNzQy
| 840
|
avoid importing palettable
|
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[] | 2017-09-18T18:32:47
| 2017-09-18T18:47:38
|
2017-09-18T18:39:20Z
|
CONTRIBUTOR
|
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## Summary
Fixes a performance regression that has caused the time taken by `import pymatgen` to rise by about 50%.
In short, palettable imports matplotlib, undoing all of pymatgen's hard work to avoid exactly that.
|
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MDExOlB1bGxSZXF1ZXN0MTQxNjkxMjI2
| 841
|
use significant_digits in poscar lattice str
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[
"Thanks."
] | 2017-09-18T20:03:31
| 2017-09-18T20:25:32
|
2017-09-18T20:25:27Z
|
CONTRIBUTOR
|
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## Summary
* Fix formatting of lattice in `Poscar.get_string` to respect the `significant_digits` argument
|
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| 259,131,223
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MDU6SXNzdWUyNTkxMzEyMjM=
| 842
|
BoltztrapRunner discards bands with no warning
|
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[] | null |
[
"I agree, and I would say a parameter should be set to allow people to choose to discard a certain % or none at all. I will leave @hautierg and @computron to comment and implement.",
"I think the relevant person here is @fraricci to implement and @hautierg to comment on the procedure (as per the explicit comment that Geoffroy suggests throwing out the top 10% of bands)",
"I will implement what @shyuep suggested: a parameter to choose the % of the band cut, with 10% as default.",
"This was fixed by #850 "
] | 2017-09-20T11:32:53
| 2017-09-29T13:14:49
|
2017-09-29T13:14:49Z
|
MEMBER
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The `BoltztrapRunner` class discards the top 10% of bands when writing the eigenvalues to the input files needed by BoltzTraP. In some cases this can cause the valence band maximum and conduction band minimum to be discarded, leading to BoltzTraP errors. I understand the rationale for discarding these bands (i.e. that often they are not very well converged) but I think it is presumptuous to discard them. For example, calculations performed using different codes, or with `ALGO = Exact` in VASP, will not suffer from the same problems.
## Example code
On lines 254-257 of `pymatgen/electronic_structure/boltztrap.py`:
```python
# use 90% of bottom bands since highest eigenvalues
# are usually incorrect
# ask Geoffroy Hautier for more details
nb_bands = int(math.floor(self._bs.nb_bands * 0.9))
```
## Error message
If the valence band maximum and conduction band minimum are both discarded, the `BANDANA` section of the `boltztrap.outputtrans` file will read:
```
============== OUTPUT from BANDANA ================
Egap: 0.000000 Energy range: -0.176310 - -0.049760. Bands range: 47 - 57
VBM: 0.000000 CBM: 0.000000 Efermi: 0.000000
```
BoltzTraP will also warn the user with the message:
```
Error - Fermi level was not found for doping
```
## Suggested solution
Either remove this code, or check to see if the bands removed include the VBM/CBM+2/3, in which case don't scrap these bands. At the minimum a warning should be thrown.
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MDExOlB1bGxSZXF1ZXN0MTQyMDkzNjE3
| 843
|
Import pymatgen.util.serialization
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[] | 2017-09-20T13:03:42
| 2017-09-20T13:19:17
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2017-09-20T13:19:17Z
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CONTRIBUTOR
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More general algo to avoid breaking of specific bonds for SlabGenerator
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[] | 2017-09-21T00:09:37
| 2017-09-22T00:26:12
|
2017-09-22T00:26:12Z
|
CONTRIBUTOR
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The get_slabs() method of the SlabGenerator class has a parameter called bonds that allow the users to specify which terminations to avoid based on whether this specific bond is broken (e.g. PO4 or PS4 bonds). However, this leads to many missing possible terminations in more complicated structures such as LiFePO4. A more general implementation for avoiding break of specific bonds would be to allow all terminations and then repair any specific broken specified bonds.
Note that will always return at least one viable termination for any orientation provided that the specified bonds are noncontiguous.
|
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MDExOlB1bGxSZXF1ZXN0MTQyNDE2NTYy
| 845
|
Add MVLNPTMDSet with unittest
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[] | 2017-09-21T18:43:02
| 2017-09-21T19:02:25
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2017-09-21T19:02:25Z
|
CONTRIBUTOR
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## Summary
Add `MVLNPTMDSet` class
* Add MVLNPTMDSet for AIMD input set in NpT ensemble
* Add unittest
* Minor docstring change
|
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Not all relevant species in a facet are reported by Pourbaix Plotter
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[
"@kristinpersson Maybe get one of your folks working on the Pourbaix stuff to look into this?",
"@ashtonmv Hey Michael, using the pymatgen.analysis.pourbaix.plotter functions you can enable the labeling of all the entries in a Pourbaix domain. I think the problem in this specific case is due to the way the Pourbaix entries are generated for doing the Pourbaix analysis. In this example I can only find “Pourbaix Entry”. \r\n\r\nHowever, for more than 1 non H and O elements considered for the Pourbaix analysis, the pymatgen.analysis.pourbaix.maker creates multi-entries, or “Multiple Pourbaix Entry”, which are combination of the “Pourbaix Entry”. These multi-entries can have # of Pourbaix Entry < = # of non H and O elements considered in your Pourbaix analysis. This is based on the Gibbs phase rule. You can see an example of this for the case of a ternary Ag, Te, N system in the pymatgen.analysis.pourbaix.tests.test_analyzer. Please use the latest version since we added the ternary test recently. \r\n",
"Hi Arunima,\r\n\r\nThanks so much! I am surprised the solution was so simple- I just needed to add a `comp_dict` as an argument when I created the PourbaixGiagram object (I also had a few bugs in the above code).\r\n\r\nAs far as I can tell, the actual values in `comp_dict` do not affect the Pourbaix diagram, so maybe `comp_dict` can just be automatically generated based on the entries used and should not need to be specified as an argument? Have I misunderstood that?",
"@ashtonmv, Hi Michael, It is great that you were able to generate the PourbaixDiagram object for multi-element systems. Since only those multi-entries which have the ratio of elements same as in the comp_dict are retained in the Pourbaix diagram, the Pourbaix diagrams should be affected quite a bit by the comp dict. Note that the individual entries in the multi-entries have weights. These weights are not available through the MP website Pourbaix app, but are easy to get from pymatgen.\r\n\r\nFor example, for the V: Co Pourbaix diagram you will see that the Pourbaix stable domain at potential < -2 V changes when a {‘V’: 0.8,’Co’: 0.2} comp_dict is used instead of the default {‘V’: 0.5, ‘Co’: 0.5}. In both cases though, the Pourbaix stable entries satisfy the comp_dict with certain weights for each entry in the “Multi Entry”. It is possible that for the cases you examined the Pourbaix diagram does not change since the comp_dict is satisfied by the same set of multi-entries in the entire composition range. However, the weights of the entries in each multi-entry should be changing as you change the comp_dict. \r\n\r\n",
"Ah okay, that makes a lot of sense. I was not seeing the weights for each entry. Thanks!"
] | 2017-09-21T20:44:29
| 2023-05-29T15:46:38
|
2023-05-29T15:46:38Z
|
NONE
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## Summary
* This is a feature request. I would like to be able to report *all* stable species in each facet of a Pourbaix diagram, much like what happens on the MaterialsProject website Pourbaix app. Instead, what currently shows up is a single species.
## Example code
```python
from pymatgen.analysis.pourbaix.analyzer import PourbaixAnalyzer
from pymatgen.analysis.pourbaix.entry import PourbaixEntry, IonEntry
from pymatgen.analysis.pourbaix.maker import PourbaixDiagram
from pymatgen.analysis.pourbaix.plotter import PourbaixPlotter
from pymatgen.entries.computed_entries import ComputedEntry
from pymatgen.phasediagram.maker import PhaseDiagram
from pymatgen import Composition, Element
from pymatgen.core.ion import Ion
import matplotlib.pyplot as plt
from matplotlib.patches import Polygon
import seaborn as sb
elements = ["Zn", "Cu"]
ion_concentration = 1e-6 # Molar concentration of all ions in solution.
DFT_DATA = {'Cr': {'Cr1': -9.63855526, 'Cr2': -18.46059112, 'Cr8': -76.55796371, 'Cr6 O16': -173.41734137, 'Cr12 O24': -301.39540709, 'Cr4 O8': -101.87982108, 'Cr8 O16': -203.64870131, 'Cr4 O10': -111.70017197, 'Cr6 O18': -164.37043378, 'Cr16 O32': -402.10647713000003, 'Cr3 O8': -85.90411586, 'Cr2 O6': -61.196047279999995, 'Cr2 O4': -50.19744204, 'Cr12 O28': -322.89517198, 'Cr8 O12': -182.54916321, 'Cr10 O14': -213.79653814, 'Cr1 O2': -25.09149781, 'Cr8 O18': -210.1552443, 'Cr9 O13': -195.66151579, 'Cr1 O3': -30.36372084, 'Cr4 O12': -121.53645591, 'Cr19 O48': -532.97091756, 'Cr16 O24': -365.28992538999995, 'Cr8 O8': -145.63123877, 'Cr8 O21': -230.13747106, 'Cr6 O2': -61.35854639, 'Cr20 O48': -553.54453296, 'Cr4 O6': -91.05921984, 'Cr6 O8': -127.23524215, 'Cr1 O1': -17.81872604, 'Cr2 O2': -36.64706484, 'Cr6 O6': -109.10354077, 'Cr1 H1': -12.98096354, 'Cr2 H2': -25.302549, 'Cr1 H2': -16.21170315, 'H1 O2 Cr1': -30.832740790000003, 'H2 O4 Cr2': -61.561420770000005, 'Cr2 O4 H1': -56.300474460000004, 'Cr6 O16 H2': -180.83487127, 'Cr4 O8 H4': -123.31355353000001}, 'Fe': {'Fe2': -16.7278538, 'Fe1': -8.31266428, 'Fe6': -46.05347314, 'Fe4 O8': -89.66020753, 'Fe8 O16': -175.93366871, 'Fe12 O24': -265.23717575, 'Fe2 O4': -45.26742012, 'Fe1 O2': -22.30417569, 'Fe16 O32': -353.710741, 'Fe8 O12': -163.50194596, 'Fe10 O14': -193.70198301, 'Fe43 O64': -871.6942494699999, 'Fe64 O96': -1286.15875187, 'Fe32 O35': -556.6097124199999, 'Fe16 O24': -322.42751699, 'Fe35 O36': -587.79564685, 'Fe9 O13': -177.31327963, 'Fe38 O39': -643.29935963, 'Fe15 O16': -257.18807836, 'Fe2 O2': -33.16405348, 'Fe12 O18': -233.17108267999998, 'Fe24 O32': -456.84616745999995, 'Fe6 O8': -112.48629374999999, 'Fe23 O25': -399.2480867, 'Fe21 O27': -388.42010648999997, 'Fe2 O6': -55.2428685, 'Fe41 O56': -782.1973546199999, 'Fe13 O14': -216.26811935, 'Fe11 O12': -191.26877137000002, 'Fe12 O16': -230.13741406999998, 'Fe17 O18': -291.71916361, 'Fe21 O32': -396.67246079, 'Fe9 O10': -158.08496116999999, 'Fe21 O23': -365.95350949, 'Fe20 O32': -398.5544822, 'Fe12 O13': -207.25752108, 'Fe13 O15': -227.98661347, 'Fe4 O6': -82.31106048000001, 'Fe10 O11': -174.45994504, 'Fe14 O15': -237.19155325000003, 'Fe8 O9': -141.00985131, 'Fe14 O16': -248.88203259, 'Fe4 O4': -66.32824289, 'Fe16 O18': -281.14962684, 'Fe23 O32': -442.50592830999994, 'Fe1 O1': -15.90710818, 'Fe12 O12': -198.97163238, 'Fe20 O22': -349.46194576000005, 'Fe7 O8': -123.85862518, 'H2 Fe6': -52.61762353, 'H3 Fe1': -17.52759945, 'H1 Fe1': -11.8135345, 'H2 Fe42 O64': -866.61665873, 'H16 Fe16 O32': -443.93843547, 'H2 Fe2 O4': -56.41867967, 'H4 Fe4 O8': -112.29883521, 'H2 Fe1 O2': -32.29983393, 'H20 Fe16 O34': -475.36958252, 'H14 Fe4 O13': -188.33015303, 'H1 Fe1 O2': -28.08261191}, 'Ni': {'Ni2': -11.50759993, 'Ni1': -5.77713619, 'Ni4': -20.7238843, 'Ni2 O4': -34.55866155, 'Ni9 O13': -128.96431095, 'Ni12 O24': -205.06196917, 'Ni8 O12': -115.86613666, 'Ni10 O14': -141.27277680999998, 'Ni4 O8': -69.0414111, 'Ni1 O2': -17.29577084, 'Ni16 O32': -265.37076793, 'Ni8 O16': -136.28786271, 'Ni12 O14': -160.04721952, 'Ni3 O4': -42.685898910000006, 'Ni6 O8': -85.01586619000001, 'Ni15 O16': -190.61065495, 'Ni5 O6': -67.43739237999999, 'Ni2 O2': -25.16227672, 'Ni9 O10': -117.30897441, 'Ni1 O1': -12.499247910000001, 'H6 Ni2': -29.60708342, 'H1 Ni1': -9.24218458, 'H1 Ni2': -14.9537264, 'H1 Ni3': -18.62541446, 'H2 Ni6': -37.46048501, 'H1 O2 Ni1': -22.53897943, 'H2 O2 Ni1': -28.00920867}, 'Cu': {'Cu2': -8.18695876, 'Cu1': -4.09881235, 'Cu4': -16.38209642, 'Cu9 O13': -115.95764487, 'Cu8 O12': -110.91936536, 'Cu10 O14': -126.71951978, 'Cu2 O4': -31.17387195, 'Cu8 O7': -79.72144566, 'Cu16 O16': -178.25853609, 'Cu8 O1': -38.06555083, 'Cu2 O2': -21.88310477, 'Cu1 O2': -15.22022848, 'Cu1 O1': -10.6034845, 'Cu16 O24': -217.44930975, 'Cu4 O2': -30.16371667, 'Cu8 O6': -72.41523587, 'Cu4 O8': -62.21381766, 'Cu4 O4': -39.06145244, 'Cu4 O6': -54.35408565, 'Cu3 O2': -25.216271029999998, 'Cu8 O8': -85.01700835, 'H2 Cu2': -14.43186655, 'H2 Cu2 O4': -42.431307329999996, 'H1 Cu1 O2': -21.315096479999998, 'H4 Cu2 O4': -51.87450708}, 'Zn': {'H12 Zn6 O12': -150.9611988, 'H2 Zn1 O2': -24.89819783, 'H2 Zn2': -7.63904814, 'H4 Zn24 O24': -244.29155522, 'H8 Zn4 O8': -101.30155395999999, 'Zn1 O1': -8.37152477, 'Zn12 O12': -113.49470373, 'Zn2': -2.54433504, 'Zn2 O2': -18.39817112, 'Zn4 O8': -57.23496385}, 'Si': {'Si2': -10.85073298, 'Si1': -4.88861001, 'Si8': -39.91456936, 'Si46': -246.67712539, 'Si23': -122.90686896, 'Si4': -21.6584824, 'Si34': -172.91580555, 'Si30 O60': -718.52508282, 'Si16 O32': -397.67820858, 'Si6 O12': -146.25622408, 'Si8 O16': -197.14199162, 'Si4 O8': -96.95159471, 'Si12 O24': -284.33501127, 'Si18 O36': -451.1797014, 'Si2 O4': -47.78844694, 'Si3 O6': -75.35639395, 'Si1 O2': -21.33645897, 'Si36 O72': -904.02894055, 'Si32 O64': -803.47951011, 'Si28 O56': -702.91911153, 'Si24 O48': -602.30151028, 'Si22 O44': -552.46013027, 'Si48 O96': -1081.17829571, 'Si40 O80': -1002.5353485799999, 'Si6 O14': -142.53195331, 'Si56 O112': -1405.6819772400002, 'Si14 O28': -351.41483736000004, 'Si46 O92': -1155.73584262, 'Si5 O10': -125.37082849000001, 'Si34 O68': -854.04674275, 'Si10 O20': -250.74134930000002, 'Si12 O4': -97.5628526, 'Si17 O34': -426.87216217, 'Si64 O128': -1584.6848330799999, 'Si24 O52': -581.08321702, 'Si20 O40': -501.02898387000005, 'Si6 O6': -86.89641169000001, 'Si4 O10': -107.63911160999999, 'Si60 O120': -1504.78068369, 'Si3 O12': -99.43645066, 'Si54 O108': -1356.59379433, 'H1 Si3': -17.19631432, 'H2 Si6': -38.95277657, 'H2 Si2': -17.49653262, 'H16 Si4': -75.66880693, 'H8 Si1': -32.38367938, 'H20 Si20 O30': -430.36439077999995, 'H8 Si8 O12': -188.17013374, 'H24 Si8 O4': -162.28364717, 'H4 Si4 O10': -130.94868235, 'H8 Si16 O36': -461.16932584, 'H2 Si1 O1': -19.41968791}}
OH = {'H1': -3.2397366613799994, 'H11 O8': -96.59891012, 'H14 O8': -97.73905279, 'H16 O8': -101.99091727999999, 'H2': -6.479473322759999, 'H24 O12': -187.01891262, 'H28 O14': -199.20391543000002, 'H4': -27.367, 'H4 O2': -30.77041763, 'H8 O4': -61.103031009999995, 'H8 O8': -80.14937463, 'O2': -10.8}
# Create a phase diagram to determine which solid phases are most stable.
# These will be used in the Pourbaix diagram.
for element in elements:
entries = [ComputedEntry(composition=k, energy=DFT_DATA[element][k]) for k in DFT_DATA[element]]
entries += [ComputedEntry(composition=k, energy=OH[k]) for k in OH]
pd = PhaseDiagram(entries)
stable_solids = [entry for entry in pd.stable_entries if
entry.composition.reduced_formula not in ["H2", "O2", "H2O", "H2O2"]]
pbx_solid_entries = list()
for entry in stable_solids:
pbx_entry = PourbaixEntry(entry)
pbx_entry.g0_replace(pd.get_form_energy(entry))
pbx_entry.reduced_entry()
pbx_solid_entries.append(pbx_entry)
ION_FORMATION_ENERGIES = {'Li': {'Li[+]': -3.04, 'Li2O2': -6.886, 'LiOH': -4.682}, 'Be': {'Be[2+]': -3.936, 'BeO2[2-]': -6.634, 'Be3(OH)3[3+]': -18.672}, 'B': {'BO2[-]': -7.036, 'B4O7[2-]': -26.996, 'BH4[-]': 1.185, 'H3BO3': -10.04, 'B(OH)4[-]': -11.951, 'H2BO3(H2O2)[-]': -10.961, 'H5(BO3)2(H2O2)2[-]': -22.38, 'HB4O7[-]': -27.828, 'H2B4O7': -28.189}, 'C': {'CO2': -4.0, 'CH4': -0.355, 'HCO3[-]': -6.08, 'CO3[2-]': -5.47}, 'N': {'HNO3': -1.153, 'N2': 0.19, 'NO3[-]': -1.15, 'NH3': -0.275, 'NH4[+]': -0.822}, 'F': {'F[-]': -2.8655592000000003, 'HF': -3.0533296500000002}, 'Na': {'Na[+]': -2.714, 'NaOH': -4.344, 'NaHO2': -3.412}, 'Mg': {'Mg[2+]': -4.714, 'MgOH[+]': -6.495, 'Mg(OH)2': -7.974}, 'Al': {'AlO2[-]': -8.70378915, 'Al[3+]': -4.986975}, 'Si': {'H2SiO3': -10.49433, 'SiO3[2-]': -9.193380000000001, 'HSiO3[-]': -9.9028314, 'H4SiO4': -13.814, 'HSi(OH)6[-]': -17.98}, 'P': {'H3PO3': 8.881152, 'H3PO2': -5.4249615, 'H3PO4': 11.890683000000001, 'PO4[3-]': -10.628761500000001, 'HPO3[2-]': 8.41281, 'H2PO4[2-]': 11.764924500000001, 'H4P2O6': 16.99908, 'H3P2O6[-]': 16.868985000000002, 'HPO4[2-]': 11.339947500000001, 'HPO3': -9.358167, 'H2PO2[-]': 5.307876, 'P2O6[4-]': 15.6851205, 'HP2O6[3-]': 16.274884500000002, 'H2PO3[-]': 8.77490775, 'H2P2O6[2-]': 16.704198}, 'S': {'S3O6[2-]': -9.930585, 'SO3[2-]': -5.034676500000001, 'H2S2O3': 5.6331135, 'S5O6[2-]': -9.9089025, 'S2O4[2-]': -5.98437, 'HS[-]': 0.13052865, 'H2SO3': -5.58064185, 'S5[2-]': 0.680353485, 'S2O8[2-]': -11.36163, 'S2O6[2-]': -10.017315, 'S4[2-]': 0.7205094750000001, 'HS2O3[-]': -5.6157675000000005, 'S[2-]': 0.9522086700000001, 'HSO3[-]': -5.46399, 'HSO4[-]': -7.803098100000001, 'S4O6[2-]': -10.5940695, 'SO4[2-]': -7.690349100000001, 'S3[2-]': 0.7791823200000001, 'HS2O4[-]': -6.13215792, 'H2SO4': -7.690349100000001, 'H2S': -0.2836071, 'S2[2-]': 0.856415385, 'S2O3[2-]': -5.516028}, 'Cl': {'Cl[-]': -1.36, 'Cl2': 0.072, 'Cl3[-]': -1.248, 'ClO[-]': -0.381, 'ClO2': 1.245, 'ClO2[-]': 0.178, 'ClO3[-]': -0.096, 'ClO4[-]': -0.088, 'HCl': -1.36, 'HClO': -0.828, 'HClO2': 0.061, 'HClO3': -0.082, 'HClO4': -0.088}, 'K': {'K[+]': -2.936, 'KOH': -4.565}, 'Ca': {'Ca[2+]': -5.737, 'CaOH[+]': -7.445, 'Ca(OH)2': -8.997}, 'Sc': {'ScOH[2+]': -8.3036, 'Sc[3+]': -6.079}, 'Ti': {'Ti[2+]': -3.2567115, 'Ti[3+]': -3.6253140000000004, 'TiO2[2+]': -4.84256955}, 'V': {'VO4[3-]': -9.545720625000001, 'HVO4[2-]': -10.1028272, 'VO[2+]': -4.626785000000001, 'VO3[-]': -8.1212304, 'VO2[+]': -6.08168075, 'HVO2[+]': -6.868148700000001, 'VO4[-]': -8.842123500000001}, 'Cr': {'CrOH[2+]': -4.466595, 'CrO4[2-]': -7.6365765, 'HCrO4[-]': -8.0181885, 'Cr[2+]': -1.8256665, 'Cr[3+]': -2.2332975}, 'Mn': {'Mn[2+]': -2.364, 'MnO4[-]': -4.365, 'MnO4[2-]': -5.189, 'MnOH[+]': -4.197, 'Mn(OH)3[-]': -7.713}, 'Fe': {'Fe[2+]': -0.818, 'Fe[3+]': -0.049, 'FeO2[2-]': -3.06, 'FeOH[+]': -2.875, 'FeOH[2+]': -2.378, 'HFeO2[-]': -3.914, 'Fe(OH)2[+]': -4.539, 'Fe(OH)3': -5.833, 'Fe(OH)3[-]': -6.373, 'Fe(OH)4[2-]': -7.977, 'Fe2(OH)2[4+]': -4.843}, 'Co': {'Co[2+]': -0.564, 'Co[3+]': 1.389, 'HCoO2[-]': -4.223, 'Co(OH)2': 4.37}, 'Ni': {'Ni[2+]': -0.472, 'NiOH[+]': -2.359, 'Ni(OH)2': -3.733}, 'Cu': {'Cu[+]': 0.518, 'Cu[2+]': 0.679, 'CuO2[2-]': -1.903, 'HCuO2[-]': -2.679, 'Cu(OH)2': -2.581}, 'Zn': {'Zn[2+]': -1.524, 'ZnO2[2-]': -3.982, 'ZnOH[+]': -3.421, 'HZnO2[-]': -4.737, 'Zn(OH)2': -5.418, 'Zn(OH)3[-]': -7.195, 'Zn(OH)4[2-]': -8.898}, 'Ga': {'Ga[3+]': -1.587159, 'Ga[2+]': -0.9106650000000001, 'HGaO3[2-]': -7.11186, 'GaO2[-]': -5.260174500000001, 'Ga(OH)3': -9.884184450000001, 'GaO[+]': -3.703371, 'GaOH[2+]': -3.894177, 'GaO3[3-]': -6.41802}, 'Ge': {'HGeO2[-]': -3.998253, 'H2GeO3': -8.100582000000001, 'GeO3[2-]': -6.8473335, 'HGeO3[-]': -7.597548000000001}, 'As': {'AsO[+]': -1.6955715, 'H3AsO4': -7.970487, 'HAsO2': -4.17388125, 'H2AsO3[-]': -6.088446, 'AsO2[-]': -3.6296505000000003, 'AsO4[3-]': -6.591480000000001, 'H3AsO3': -6.6322431, 'H2AsO4[-]': -7.7579985, 'HAsO4[2-]': -7.328685}, 'Se': {'H2Se': 0.2300808, 'H2SeO3': -4.41651496, 'HSeO3[-]': -4.26437144, 'HSeO4[-]': -4.6866008, 'HSe[-]': 0.456016, 'SeO2': -2.2969733199999998, 'SeO3[2-]': -3.8326072, 'SeO4[2-]': -4.5736332, 'Se[2-]': 1.3400652000000002}, 'Br': {'Br[-]': -1.26, 'Br2': -0.027, 'Br3[-]': -1.352, 'Br5[-]': -1.475, 'BrO[-]': -0.975, 'BrO3[-]': -0.695, 'HBrO': -1.171, 'HBrO3': -0.695}, 'Rb': {'Rb': -2.943, 'RbOH': -4.573, 'RbHO2': -3.642}, 'Sr': {'Sr[2+]': -5.798, 'SrOH[+]': -7.476}, 'Y': {'Y[3+]': -7.191, 'Y(OH)[2+]': -9.111, 'Y2(OH)2[4+]': -18.451}, 'Zr': {'Zr[4+]': -5.774, 'ZrOH[3+]': -8.25, 'ZrO[2+]': -8.128, 'ZrO2': -10.113, 'HZrO2[2+]': -10.386, 'HZrO3[3-]': -12.197}, 'Nb': {'NbO3[-]': -9.6602844, 'Nb(OH)5': -15.0101812, 'Nb(OH)4[+]': -12.525930399999998}, 'Mo': {'MoO4[2-]': -8.6641, 'Mo[3+]': -0.5982}, 'Tc': {'HTcO4': -7.504}, 'Ru': {'RuO4': -1.526, 'RuO4[-]': -2.544, 'RuO4[2-]': -3.148, 'Ru(OH)2[2+]': -2.208}, 'Rh': None, 'Pd': {'Pd[2+]': 1.829}, 'Ag': {'Ag[+]': 0.799, 'AgOH': -0.953, 'Ag(OH)2[-]': -2.697}, 'Cd': {'Cd[2+]': -0.8057217000000001, 'HCdO2[-]': -3.7510725000000003, 'Cd(OH)2': -2.4475206000000003}, 'In': {'In[2+]': -0.537726, 'InOH[2+]': -3.2567115, 'In[+]': -0.138768, 'InO2[-]': 4.50996, 'In(OH)3': -8.40977445, 'In[3+]': -1.0277505}, 'Sn': {'Sn[4+]': 0.02818725, 'Sn[2+]': -0.272115375, 'SnO3[2-]': -5.959218300000001, 'Sn(OH)4': -4.9488138, 'Sn2O3[2-]': -6.1179342000000005, 'SnOH[+]': -2.6279190000000003, 'SnO(OH)[+]': -4.913, 'HSnO2[-]': -4.24977, 'Sn(OH)2': -2.64136215}, 'Sb': {'H3SbO4': -9.4011844, 'HSb(OH)6': -15.324210399999998, 'HSbO2': -4.22333, 'Sb(OH)3': -6.6816708, 'Sb2O3': -7.1501236, 'Sb2O5': -9.9173116, 'SbO2[-]': -3.52572916, 'SbO[+]': -1.83556804}, 'Te': {'H2TeO3': -4.934300400000001, 'H4TeO6[2-]': -12.6658444, 'H5TeO6[-]': -13.074186, 'H6TeO6': -13.307376, 'Te(OH)3[+]': -5.1415804000000005, 'TeO3[2-]': -5.6463072}, 'I': {'I[-]': -0.572, 'I3[-]': -0.534, 'IO[-]': -1.114, 'IO3[-]': -2.294, 'IO4[-]': -0.606, 'I2O[2-]': -0.854, 'HIO': -1.431, 'HIO3': -2.19, 'H2OI[+]': -1.106, 'H3IO6[2-]': -7.835, 'H4IO6[-]': -7.87, 'H5IO6': -7.87, 'I2OH[-]': -2.385}, 'Cs': {'Cs[+]': -3.026, 'CsOH': -4.656, 'CsHO2': -3.725}, 'Ba': {'Ba[2+]': -5.812, 'BaOH[+]': -7.571}, 'La': {'La[3+]': -7.328}, 'Hf': {'Hf[4+]': -6.799632000000001, 'HfO[2+]': -9.3538305}, 'Ta': {'TaO2[+]': -8.7327064}, 'W': {'WO4[2-]': -11.149, 'HW6O21[5-]': -60.517}, 'Re': {'Re[+]': -0.342, 'Re[-]': 0.105, 'ReO4[-]': -7.198, 'HReO4': -7.198}, 'Os': {'OsO4': -301.85, 'HOsO5[-]': -470.2, 'H2OsO5': -538.95}, 'Ir': None, 'Pt': {'Pt[2+]': 2.641}, 'Au': {'AuO3[3-]': -0.537, 'HAuO3[2-]': -1.474, 'H2AuO3[-]': -2.262, 'Au(OH)3': -2.937}, 'Hg': {'Hg': 0.407, 'Hg[2+]': 1.704, 'Hg2[2+]': 1.591, 'HgOH[+]': -0.542, 'HHgO2[-]': -1.972, 'Hg(OH)2[-]': -2.848}, 'Tl': {'TlOH': -1.48785315, 'Tl[3+]': 2.16825, 'Tl[+]': -0.336295575, 'Tl(OH)3': -3.29270445}, 'Pb': {'PbO3[2-]': -2.8768341, 'PbO4[4-]': -2.9237116650000003, 'HPbO2[-]': -3.5125650000000004, 'Pb[2+]': -0.25195065, 'Pb[4+]': 3.1352895000000003, 'Pb(OH)2': -1.90415715}, 'Bi': None}
# These corrections are the difference in formation energy
# (in eV/atom) of reference oxides between DFT and experiment.
ION_CORRECTIONS = {'Cr': -0.093, 'Fe': -0.608, 'Ni': 0.630, 'Cu': -0.230, 'Zn': 0.0, 'Si': -0.573}
# Add all relevant ions to a list.
pbx_ion_entries = list()
for element in elements:
for key in ION_FORMATION_ENERGIES[element]:
comp = Ion.from_formula(key)
if comp.composition[element] != 0:
factor = comp.composition[element]
energy = ION_FORMATION_ENERGIES[element][key]
pbx_entry_ion = PourbaixEntry(IonEntry(comp, energy))
pbx_entry_ion.correction = (
ION_CORRECTIONS[element] * factor
)
pbx_entry_ion.conc = ion_concentration
pbx_entry_ion.name = key
pbx_ion_entries.append(pbx_entry_ion)
all_entries = pbx_solid_entries + pbx_ion_entries
pourbaix_diagram = PourbaixDiagram(all_entries)
plotter = PourbaixPlotter(pourbaix_diagram)
# Plotting details...
font = "serif"
fig = plt.figure(figsize=(14, 9))
ax1 = fig.gca()
ax1.set_xlim([0, 14])
ax1.set_xticklabels([int(t) for t in ax1.get_xticks()], fontname=font, fontsize=18)
ax1.set_ylim(-2, 2)
ax1.set_yticklabels(ax1.get_yticks(), fontname=font, fontsize=18)
ax1.set_xlabel("pH", fontname=font, fontsize=18)
ax1.set_ylabel("Potential vs. SHE (V)", fontname=font, fontsize=18)
# Outline water's stability range.
ax1.plot([0, 14], [0, -0.829], color="gray", linestyle="--", alpha=0.7, linewidth=2)
ax1.plot([0, 14], [1.229, 0.401], color="gray", linestyle="--", alpha=0.7, linewidth=2)
stable_entries = plotter.pourbaix_plot_data(
limits=[[0, 14], [-2, 2]])[0]
# Add coloring.
colors = sb.color_palette("Set2", len(stable_entries))
i = 0
for entry in stable_entries:
col = colors[i]
i += 1
vertices = plotter.domain_vertices(entry)
center_x = sum([v[0] for v in vertices])/len(vertices)
center_y = sum([v[1] for v in vertices])/len(vertices)
patch = Polygon(vertices, closed=True, fill=True, facecolor=col, linewidth=2, edgecolor="w")
ax1.text(center_x, center_y, plotter.print_name(entry),
verticalalignment="center", horizontalalignment="center", fontname=font, fontsize=18)
ax1.add_patch(patch)
# Display plot
plt.show()
```
## Suggested solution (if any)
* I guess whatever code is running for MaterialsProject's backend would work.
## Files (if any)
* [Plot generated by above code](https://s3.amazonaws.com/mashton/Zn-Cu.png)
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| 259,663,062
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MDExOlB1bGxSZXF1ZXN0MTQyNDY5MTE2
| 847
|
repair_broken_bonds method for SlabGenerator
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[] | 2017-09-21T23:38:57
| 2017-09-22T00:25:56
|
2017-09-22T00:25:56Z
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CONTRIBUTOR
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This pull request will address issue #844
This method of generating slabs will repair slabs with more broken bonds than the allotted max_broken_bonds parameter instead of omitting them. Because this can lead to a large number of possible terminations, for now, I’ve made the repair of broken bonds optional. Default repair=False: omit terminations that break bonds.
* Feature 1: repair_broken_bonds(slab, bonds) method for SlabGenerator takes in a slab and specified bonds, returns the slab with all specified bonds intact.
* Feature 2: move_to_other_side(init_slab, index_of_sites, to_top=True) method for SlabGenerator move sites based on site index to the opposite surface.
* Feature 3: Added unit testing to ensure that for LiFePO4, at least one slab exists per distinct Miller index.
* Feature 4: Also tests to ensure that all P sites are coordinated with 4 O sites
* Feature 5: Also tests to ensure move_to_other_side will actually move a surface site to the other side
|
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MDExOlB1bGxSZXF1ZXN0MTQyNDk2MTQw
| 848
|
add combine_neb_plots method
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[
"When is this going to be done?",
"This might be merged. The error of ModuleNotFoundError: No module named 'pip._vendor.requests.adapters' seems not related to this code."
] | 2017-09-22T04:45:21
| 2017-10-10T20:52:40
|
2017-10-10T20:52:40Z
|
NONE
|
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add combine_neb_plots method.
Due to this method:
move test_files/neb_analysis/neb1/start/OUTCAR to test_files/neb_analysis/neb1/neb/00/
move test_files/neb_analysis/neb1/end/OUTCAR to test_files/neb_analysis/neb1/neb/04/
Finally, remove test_files/neb_analysis/neb1/start and test_files/neb_analysis/neb1/end
|
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| 849
|
Adding phonopy-related functions
|
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[] | 2017-09-22T05:48:16
| 2017-09-22T13:06:55
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2017-09-22T13:06:55Z
|
NONE
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## Summary
- Basic functions that convert structure objects between pymatgen and phonopy.
- Function that generates a list of atomic displaced pmg structures (for phonon calculations).
## Additional dependencies introduced (if any)
* phonopy
## TODO (if any)
Implement functions that extract modulated pmg structures.
|
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MDExOlB1bGxSZXF1ZXN0MTQzMDk0Nzc4
| 850
|
fix issue #842
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[] | 2017-09-26T10:22:30
| 2017-09-26T15:39:29
|
2017-09-26T15:39:29Z
|
CONTRIBUTOR
|
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added: parameter cb_cut to the BoltztrapRunner to tune the percentage of the highest bands
to remove in the calculation of transport properties
|
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MDExOlB1bGxSZXF1ZXN0MTQzMjU4Nzcz
| 851
|
Added many more OPs and made normalization procedure more robust
|
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[] | null |
[
"At this juncture, I think you need to rethink your approach. Basically, there is far too many permutations of order parameters to just hard code them into if statements. I suggest storing the parameters in some sensible json/yaml file, and the *short* code then uses the data from the file without the many if statements. @computron comment pls. ",
"From casual inspection of the code I agree with @shyuep . It seems possible to:\r\n\r\n- group together order parameters that have the same functional form, but different parameters, into a single code block. If the functional forms are similar but not exactly the same, it might still be possible to combine.\r\n- The parameters can then be read from a file. I would suggest JSON (for speed). Also, make sure the file is read only ONCE and the data is cached. We don't want to be reading the parameter file every time the OrderParameter class is instantiated, just the first time. e.g., you can look at ``periodic_table.py`` which loads the data at the top of the module so that it's available upon import.\r\n\r\nYou should also use Google-style docstrings - i.e., clearly explain the parameters and their expected type (array, dict, etc) and also the return type. There is a lot of description of the order parameters themselves but not much \"programmer\" information about what kind of format is expected for the various parameters.\r\n",
"@computron & @shyuep, I think I have addressed all your concerns regarding the OP class restructuring. The one failing build test doesn't seem to have to do anything with pymatgen-related things, right? Pull request \"Molecular Orbitals Functionality #863\" by @dyllamt seems to have the same issue.",
"Thanks!"
] | 2017-09-26T22:32:21
| 2017-10-16T20:38:52
|
2017-10-16T20:38:49Z
|
CONTRIBUTOR
|
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Added order parameters for:
- single-bond case
- trigonal planar
- square planar
- pentagonal planar
- square pyramid (previous one (sq_pyr_legacy) recognizes any pyramidal motif with neighbors on the basal plane being on a circle)
- trigonal pyramid
- pentagonal pyramid
- hexagonal pyramid
- T-shape
- cuboctahedron
- see-saw
Also changed normalizations to a numerical procedure via a counter because the trigonal bipyramid OP could become >1 before that (which is not desirable).
Rewrote parameter assignment section (more concise now).
|
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| 261,507,107
|
MDExOlB1bGxSZXF1ZXN0MTQzNzkwMzA3
| 852
|
Reverted slab argument to structure in MVLSlabSet
|
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[
"This is fine with me."
] | 2017-09-29T01:31:22
| 2017-09-29T02:11:11
|
2017-09-29T02:11:03Z
|
CONTRIBUTOR
|
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Can we revert the constructor syntax of MVLSlabSet such that it takes a "structure" kwarg instead of a "slab"? My reasoning for this is twofold:
* Input structures to MVLSlabSet aren't always slabs, e.g. when doing reference bulk calculations, but they are always structures
* Having "slab" as the input argument name changes the structure of the dictionary resultant from as_dict() such that it's different from every other input set, which makes it unwieldy when trying to do some db operations or modifications on the serialized object, for example.
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| 261,913,329
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MDExOlB1bGxSZXF1ZXN0MTQ0MDY4ODQw
| 853
|
Correct attribute used in example for generating a Structure object
|
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[] | 2017-10-01T12:39:30
| 2017-10-01T14:36:29
|
2017-10-01T14:36:29Z
|
CONTRIBUTOR
|
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from a VASP POSCAR
The docs previously had this example for generating a
Structure object from a VASP POSCAR file:
```python
from pymatgen.io.vasp import Poscar
poscar = Poscar.from_file("POSCAR")
struct = poscar.struct
```
The correct attribute is `poscar.structure`.
This pull request updates the `usage` documentation file to reflect this.
|
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| 262,266,922
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MDExOlB1bGxSZXF1ZXN0MTQ0MzEyMTc5
| 854
|
typo: gas<-->anion in docstrings
|
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[] | 2017-10-03T00:11:23
| 2017-10-03T00:14:46
|
2017-10-03T00:14:46Z
|
MEMBER
|
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SImple typo fix.
|
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| 262,271,143
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MDU6SXNzdWUyNjIyNzExNDM=
| 855
|
Adsorption finder: AttributeError: 'Structure' object has no attribute 'center_of_mass'
|
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[
"Right, the center_of_mass is a property that was added to the slab object\nrecently as a property. I added it to the adsorption code so that it would\nbe able to adsorb one surface or the other or both. Changing the structure\nto a slab object should work, but @montoyjh@lbl.gov do you think I should\njust change it back to just taking in Structures for simplicity?\n\nThanks,\nRichard\n\nOn Mon, Oct 2, 2017 at 5:39 PM, Andrew S. Rosen <notifications@github.com>\nwrote:\n\n> System\n>\n> - Pymatgen version: 2017.9.23\n> - Python version: 3.6.2\n> - OS version: Windows 10 (not an OS issue)\n>\n> Summary\n>\n> When using the AdsorptionSiteFinder, I get a center_of_mass issue when\n> reading a structure from a CONTCAR or other VASP file.\n> Example code\n>\n> from pymatgen import Structurefrom pymatgen.analysis.adsorption import *\n> structure = Structure.from_file(\"CONTCAR\")\n> asf = AdsorbateSiteFinder(structure)\n> ads_sites = asf.find_adsorption_sites()\n>\n> Error message\n>\n> Traceback (most recent call last):\n> File \"<stdin>\", line 1, in <module>\n> File \"C:\\Users\\andre\\Anaconda3\\lib\\site-packages\\pymatgen\\analysis\\adsorption.py\", line 320, in find_adsorption_sites\n> self.slab.center_of_mass)\n> AttributeError: 'Structure' object has no attribute 'center_of_mass'\n>\n> Suggested solution (if any)\n>\n> Switching to the old branch\n> <https://github.com/montoyjh/pymatgen/tree/adsorption_new> of the code\n> solves the issue because it doesn't use the center_of_mass object. That's\n> not a solution though.\n> Files (if any)\n>\n> See here for example file: CONTCAR.txt\n> <https://github.com/materialsproject/pymatgen/files/1350820/CONTCAR.txt>.\n> Make sure to delete the .txt extension!\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/855>, or mute the\n> thread\n> <https://github.com/notifications/unsubscribe-auth/AHqe1uOAezYhpFCVmU_TeuNbN8RmGjpJks5soYJagaJpZM4PrcIF>\n> .\n>\n\n\n\n-- \n\nRichard Tran\nPhone: (415) 425-7660\nEmail: rit001@eng.ucsd.edu\n<https://acs-webmail.ucsd.edu/squirrelmail/src/compose.php?send_to=rit001%40ucsd.edu>\n",
"I just added the COM determination explicitly in the adsorption code, since it's only two lines. I'm not sure it really makes sense on periodic structures anyway, and we're really only using it in this case to find a sensible average c coordinate. I've got a PR ready, I'm just waiting on CircleCI to finish up before submitting.",
"COM makes zero sense on periodic structures.",
"Should be fixed via #856. Let us know if you have any further issues @arosen93.",
"Great, thanks for the prompt replies!"
] | 2017-10-03T00:39:52
| 2017-10-03T23:20:46
|
2017-10-03T23:20:46Z
|
MEMBER
|
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## System
* Pymatgen version: 2017.9.23
* Python version: 3.6.2
* OS version: Windows 10 (not an OS issue)
## Summary
When using the `AdsorptionSiteFinder`, I get a `center_of_mass` issue when reading a structure from a `CONTCAR` or other VASP file.
## Example code
```python
from pymatgen import Structure
from pymatgen.analysis.adsorption import *
structure = Structure.from_file("CONTCAR")
asf = AdsorbateSiteFinder(structure)
ads_sites = asf.find_adsorption_sites()
```
## Error message
```
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\andre\Anaconda3\lib\site-packages\pymatgen\analysis\adsorption.py", line 320, in find_adsorption_sites
self.slab.center_of_mass)
AttributeError: 'Structure' object has no attribute 'center_of_mass'
```
## Suggested solution (if any)
Switching to the [old branch](https://github.com/montoyjh/pymatgen/tree/adsorption_new) of the code solves the issue because it doesn't use the `center_of_mass` object. That's not a solution though.
## Files (if any)
See here for example file: [CONTCAR.txt](https://github.com/materialsproject/pymatgen/files/1350820/CONTCAR.txt). Make sure to delete the `.txt` extension!
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| 262,561,333
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MDExOlB1bGxSZXF1ZXN0MTQ0NTExMTkx
| 856
|
Asf fix
|
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[
"\n[](https://coveralls.io/builds/28491945)\n\nCoverage decreased (-38.6%) to 38.141% when pulling **e6694758020c46e2cfc8db9ccc47ff4a28679bc7 on montoyjh:asf_fix** into **482ee1dea30aa940da8c736b1f146efdedb507ff on materialsproject:master**.\n"
] | 2017-10-03T19:45:42
| 2020-02-03T09:25:26
|
2017-10-03T20:36:37Z
|
CONTRIBUTOR
|
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## Summary
Fix for issue #855 and a few things cleaning up cartesian conversion to fractional coords and vice versa.
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MDExOlB1bGxSZXF1ZXN0MTQ0NTc0MjYy
| 857
|
Add OccupancyComparator
|
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[] | 2017-10-04T03:13:43
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2017-10-04T03:55:16Z
|
MEMBER
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## Summary
Couldn't find this in pymatgen already. Patch to add a comparator which matches occupancies in StructureMatcher. Used for SQS generation, to match a disordered pymatgen Structure to its appropriate SQS template file.
(Also included another commit to delete a stray print statement in my previous PR...)
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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MDExOlB1bGxSZXF1ZXN0MTQ0Nzg2NzY1
| 858
|
Drift in Outcar
|
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[] | 2017-10-04T22:02:50
| 2017-10-04T23:49:41
|
2017-10-04T23:49:41Z
|
NONE
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Added parsing of drift from the OUTCAR
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MDExOlB1bGxSZXF1ZXN0MTQ1MDI1NzY2
| 859
|
Add I/O for ATAT’s mcsqs lattice format
|
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[] | 2017-10-05T21:28:46
| 2017-10-05T21:30:17
|
2017-10-05T21:30:17Z
|
MEMBER
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## Summary
Input/output for [ATAT](https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/), for use with the mcsqs tool.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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MDExOlB1bGxSZXF1ZXN0MTQ1MDM5MjIw
| 860
|
Made adsorb_both_surfaces() into a class method and more flexible
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[
"Pls do not keep adding to the same pull request. merge the current origin to your fork properly and submit NEW pull requests in future."
] | 2017-10-05T22:49:31
| 2017-10-08T00:02:21
|
2017-10-07T23:17:05Z
|
CONTRIBUTOR
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## Summary
This pull request removes the need for differentiating two surfaces when building an adsorbed slab with adsorbates on both sides. Therefore the use of COM in the AdsorbateSiteFinder() class as well as the option to adsorb at the bottom or top is also remove. The algorithm will rollback to Joseph Montoya's previous method as the new method for adsorb_both_surfaces() will not require any edits to the original algorithm.
* adsorb_both_surfaces() is now a class method of AdsorbateSiteFinder()
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Error: Connection must be made over secure https.
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[
"Materials project is down right now because of maintenance. This is not an\nerror in the code.\n\nOn Sat, Oct 7, 2017, 5:09 PM Bruno Abreu Calfa <notifications@github.com>\nwrote:\n\n> System\n>\n> - Pymatgen version: pymatgen==2017.9.23\n> - Python version: 3.6.3\n> - OS version: Mac OS X 10.12.6\n>\n> Summary\n>\n> Something wrong (apparently related to secure https) is happening in the\n> call to requests.post. The same script I'm running used to work a while\n> ago.\n> Example code\n>\n> You may consider the one in this\n> <https://discuss.materialsproject.org/t/mprester-query-crashing/519>\n> discussion.\n>\n> m = MPRester(my_api_key)\n> basic_properties = ['task_id','pretty_formula','reduced_cell_formula','unit_cell_formula','spacegroup.number','energy','formation_energy_per_atom','density']\n> electronic_properties = ['band_gap','efermi','total_magnetization']\n> elasticity_properties_prefix = ['elasticity']\n> all_properties = basic_properties + electronic_properties + elasticity_properties_prefix\n>\n> # Query options\n> criteria = {\"nelements\": {\"$lte\": 3}, \"elasticity\": {\"$exists\": True}, \"spacegroup.number\": {\"$exists\": True}, \"band_gap\": {\"$exists\": True}}\n>\n> # All properties: query response\n> results = m.query(criteria=criteria, properties=all_properties)\n>\n> Error message\n>\n> Traceback (most recent call last):\n> File \"/usr/local/lib/python3.6/site-packages/pymatgen/ext/matproj.py\", line 150, in _make_request\n> .format(response.status_code))\n> pymatgen.ext.matproj.MPRestError: REST query returned with error status code 403\n>\n> During handling of the above exception, another exception occurred:\n>\n> Traceback (most recent call last):\n> File \"/Users/bacalfa/Documents/test.py\", line 55, in <module>\n> results = m.query(criteria=criteria, properties=all_properties)\n> File \"/usr/local/lib/python3.6/site-packages/pymatgen/ext/matproj.py\", line 581, in query\n> mp_decode=mp_decode)\n> File \"/usr/local/lib/python3.6/site-packages/pymatgen/ext/matproj.py\", line 155, in _make_request\n> raise MPRestError(msg)\n> pymatgen.ext.matproj.MPRestError: REST query returned with error status code 403. Content: b'Connection must be made over secure https.'\n>\n> Process finished with exit code 1\n>\n> This message about secure https also occurs when I access the example link\n> on the Materials Project API website:\n> https://www.materialsproject.org/rest/v1/materials/Fe2O3/vasp?API_KEY=MyKey,\n> where MyKey is my personal key.\n> Suggested solution (if any)\n>\n> Sorry, don't know what to suggest. The url variable in the method\n> _make_request does have \"https\" in it. Same thing via the website.\n> Files (if any)\n>\n> None.\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/861>, or mute the\n> thread\n> <https://github.com/notifications/unsubscribe-auth/AAjOU6qgG6dxeJWN4rgk0_1N45CjV3bSks5sqBLBgaJpZM4Pxiih>\n> .\n>\n",
"Makes sense! Thanks! :) When do you estimate it'll be up and running again?",
"It should be back by Wednesday 11th, this is related to the NERSC maintenance detailed at http://www.nersc.gov/users/live-status/\r\n\r\nIf you're on materialsproject.org and logged in, you should see a status message about the outage.",
"Ok thanks, I saw the message, which was clear on the topics mentioned. The python error message was a bit cryptic… :-) \n\n\n> On 09 Oct 2017, at 20:15, Matthew Horton <notifications@github.com> wrote:\n> \n> It should be back by Wednesday 11th, this is related to the NERSC maintenance detailed at http://www.nersc.gov/users/live-status/ <http://www.nersc.gov/users/live-status/>\n> If you're on materialsproject.org and logged in, you should see a status message about the outage.\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/861#issuecomment-335243075>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AF0i-BarHaN4rV6Y_Te2CVNP7NP3h7TXks5sqmLAgaJpZM4Pxiih>.\n> \n\n",
"It's back up! :)"
] | 2017-10-08T00:09:37
| 2023-05-29T15:44:22
|
2023-05-29T15:44:22Z
|
NONE
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## System
* Pymatgen version: `pymatgen==2017.9.23`
* Python version: 3.6.3
* OS version: Mac OS X 10.12.6
## Summary
Something wrong (apparently related to secure https) is happening in the call to `requests.post`. The same script I'm running used to work a while ago.
## Example code
You may consider the one in [this](https://discuss.materialsproject.org/t/mprester-query-crashing/519) discussion.
```
m = MPRester(my_api_key)
basic_properties = ['task_id','pretty_formula','reduced_cell_formula','unit_cell_formula','spacegroup.number','energy','formation_energy_per_atom','density']
electronic_properties = ['band_gap','efermi','total_magnetization']
elasticity_properties_prefix = ['elasticity']
all_properties = basic_properties + electronic_properties + elasticity_properties_prefix
# Query options
criteria = {"nelements": {"$lte": 3}, "elasticity": {"$exists": True}, "spacegroup.number": {"$exists": True}, "band_gap": {"$exists": True}}
# All properties: query response
results = m.query(criteria=criteria, properties=all_properties)
```
## Error message
```
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/pymatgen/ext/matproj.py", line 150, in _make_request
.format(response.status_code))
pymatgen.ext.matproj.MPRestError: REST query returned with error status code 403
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/bacalfa/Documents/test.py", line 55, in <module>
results = m.query(criteria=criteria, properties=all_properties)
File "/usr/local/lib/python3.6/site-packages/pymatgen/ext/matproj.py", line 581, in query
mp_decode=mp_decode)
File "/usr/local/lib/python3.6/site-packages/pymatgen/ext/matproj.py", line 155, in _make_request
raise MPRestError(msg)
pymatgen.ext.matproj.MPRestError: REST query returned with error status code 403. Content: b'Connection must be made over secure https.'
Process finished with exit code 1
```
This message about secure https also occurs when I access the example link on the Materials Project API website: `https://www.materialsproject.org/rest/v1/materials/Fe2O3/vasp?API_KEY=MyKey`, where `MyKey` is my personal key.
## Suggested solution (if any)
Sorry, don't know what to suggest. The `url` variable in the method `_make_request` does have "https" in it. Same thing via the website.
## Files (if any)
None.
|
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MDExOlB1bGxSZXF1ZXN0MTQ1NjI4MTk3
| 862
|
Improvements in chemenv + minor changes
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[
"Sorry, but I have to insist on more comprehensive unittests of the functionality before I merge. If you look at https://coveralls.io/github/materialsproject/pymatgen, a lot of modules in the chemenv package have some of the lowest coverages. You just need to sort by the \"Missed\" category.\r\n\r\nPls add proper unit tests for almost all functions that are implemented.",
"Yup I figured out that afterwards. There was an old file from a previous\nversion lying there for some obscure reason ...\n\nThanks for the update.\n\nDavid\n\nOn Wed, Oct 11, 2017 at 9:10 PM, Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> *@shyuep* commented on this pull request.\n>\n> I m pretty sure the changes on structure_matcher are wrong. The methods\n> have already been renamed. Pls pull the latest version of pymatgen from the\n> origin and merge first. You may also need to run python setup.py develop.\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/862#pullrequestreview-68718700>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/ADdRUIkJWyc9t07mQQxk6rVdI97MXKhaks5srRKLgaJpZM4Pzjgh>\n> .\n>\n",
"Thanks,"
] | 2017-10-10T08:30:01
| 2017-10-13T22:22:57
|
2017-10-13T22:22:48Z
|
CONTRIBUTOR
|
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## Summary
* Radial distribution and angular distribution figures in chemenv
* Clear environments
* Added citation for chemenv
* Minor addition in memory policy in io.abinit.qadapters
|
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MDExOlB1bGxSZXF1ZXN0MTQ2MDE3OTI3
| 863
|
Molecular Orbitals Functionality
|
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[
"Pls fix failing tests.",
"Fixed failed composition test"
] | 2017-10-11T17:49:53
| 2017-10-16T20:36:57
|
2017-10-16T20:36:57Z
|
CONTRIBUTOR
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## Summary
* Feature 1: added atomic orbital energies to periodic table data
* Feature 2: collect atomic orbitals for all elements in a composition to predict band character with MolecularOrbitals class
## TODO (if any)
* Feature 2 has no concept of covalent bonding or the orbital energies of ions
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MDExOlB1bGxSZXF1ZXN0MTQ2MDUwMDQy
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ATAT ordering fix
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2017-10-11T20:14:32Z
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Hopefully this should fix it. I wrote a bad test though really, because it was failing even with a correct output...
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Improvements needed for io.lammps.data
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[
"Go ahead and make the changes.",
"After struggling for weeks, here I will list a few upcoming major changes to the entire `io.lammps` package. Yes it will certainly break some code, but I don't see many API usage depending on methods or attributes of `LammpsData` or `LammpsForceFieldData`. \r\n\r\n1. `LammpsData` and `LammpsForceFieldData` will be merged into one class `LammpsData`, where force field and topology sections are optional. `write_file` and `from_file` will be the only methods of `LammpsData`, and it will have no dependency on any subclass of `SiteCollection`. As LAMMPS data file may carry a lot more information than other geometry input files (like POSCAR), it might not be suitable for `LammpsData` to take in or export any types of molecule or structure directly.\r\n2. Though `LammpsData` will become kinda independent, there would be supporting classes/methods to help generate all kinds of data. For instance, getting Atoms section data from any `SiteCollection`, labeling atoms or topologies from `ForceField`, and automatically determining bonding topologies. These would be in module `io.lammps.data` or a separate module, say `io.lammps.data_utils`. `ForceField` and `Topology` are now in separate modules, though both of them only serve `LammpsForceFieldData`.\r\n\r\nI would like to hear some feedbacks from users of this package, especially @matk86 \r\n",
"Just go ahead and make the changes."
] | 2017-10-13T08:39:08
| 2017-11-08T04:46:03
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2017-11-08T04:46:03Z
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CONTRIBUTOR
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A few issues with the current implementation I would like to discuss with whoever involved in this module.
* A list of lists of floats is now used as the data structure for each long section like "atoms", "bonds", etc. Since each column has its specific meaning, can we store the data using a list of dicts instead? Though this means more efforts in refactoring the parser, it will make formatting (e.g., float rounding) a lot easier. The current code after last time fix will output integers with 6 digits after the decimal point as well, which is ridiculous.
* With the dict setting above, the "atoms" section can be formatted according to an external variable `atom_style`.
* Is it possible to merge the two objects? The parent class `LammpsData` is a special case where only "atoms" is required.
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Request for enumlib tester (PR is to add makeStr.py support)
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[] | 2017-10-13T20:55:58
| 2017-10-13T22:22:32
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2017-10-13T22:22:32Z
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MEMBER
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## Summary
Tests for enumlib have been incorrectly skipped for a while if `enum.x` was present (they only ran if `multienum.x` was present, which is an old version).
When running these tests myself on current pymatgen, I get test failures -- `self.assertEqual(len(structures), 10)` will fail with `len(structures)==16` instead. I'm having trouble tracking down the reason for this test failure, I'm not sure if it's an issue with my enum install or whether it's a bug.
This PR fixes the test skip issue, and also adds initial support for makeStr.py (#814) -- makeStr.x is still used by default however. My sense is that makeStr.py is still a bit rough around the edges, so even though makeStr.x has been deprecated, I suggest we keep it as the default for the near future.
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Correction in io/abinit/qadapters
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[] | 2017-10-16T08:22:53
| 2017-10-16T14:04:03
|
2017-10-16T14:04:03Z
|
CONTRIBUTOR
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## Summary
Correction of io/abinit/qadapters (mem is now the default behavior)
|
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CIF reading error
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[
"This CIF file is bad. atom_site_label is defined twice. Just change the last atom_site_label to something like atom_site_lbl and pymatgen parses it correctly."
] | 2017-10-18T04:24:39
| 2017-10-18T04:30:10
|
2017-10-18T04:30:10Z
|
MEMBER
|
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## System
* Pymatgen version: 2017.10.16
* Python version: 3.x
## Summary
Reading certain CIF files leads to error even though it can be read in VESTA, ChemCraft, or other visualizers.
## Example code
```python
import pymatgen as pm
mof = pm.Structure.from_file('mof.cif')
```
## Error message
```
~\Anaconda3\lib\site-packages\pymatgen\core\structure.py in from_file(cls, filename, primitive, sort, merge_tol)
1570 return cls.from_str(contents, fmt="cif",
1571 primitive=primitive, sort=sort,
-> 1572 merge_tol=merge_tol)
1573 elif fnmatch(fname, "*POSCAR*") or fnmatch(fname, "*CONTCAR*"):
1574 s = cls.from_str(contents, fmt="poscar",
~\Anaconda3\lib\site-packages\pymatgen\core\structure.py in from_str(cls, input_string, fmt, primitive, sort, merge_tol)
1509 if fmt == "cif":
1510 parser = CifParser.from_string(input_string)
-> 1511 s = parser.get_structures(primitive=primitive)[0]
1512 elif fmt == "poscar":
1513 s = Poscar.from_string(input_string, False).structure
~\Anaconda3\lib\site-packages\pymatgen\io\cif.py in get_structures(self, primitive)
978 for d in self._cif.data.values():
979 try:
--> 980 s = self._get_structure(d, primitive)
981 if s:
982 structures.append(s)
~\Anaconda3\lib\site-packages\pymatgen\io\cif.py in _get_structure(self, data, primitive)
861 el = get_el_sp(symbol)
862
--> 863 x = str2float(data["_atom_site_fract_x"][i])
864 y = str2float(data["_atom_site_fract_y"][i])
865 z = str2float(data["_atom_site_fract_z"][i])
IndexError: list index out of range
```
## Suggested solution (if any)
Workaround is to read the CIF in VESTA and export it.
## Files (if any)
See attached. Change the extension to .cif.
[mof.txt](https://github.com/materialsproject/pymatgen/files/1393417/mof.txt)
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| 267,772,841
|
MDExOlB1bGxSZXF1ZXN0MTQ4MjA3Nzg1
| 869
|
Fix bug in POSCAR parsing
|
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[
"This fix seems to be causing a lot of existing tests to fail? https://travis-ci.org/materialsproject/pymatgen/builds/291690908\r\n\r\nThe test file [here](https://github.com/materialsproject/pymatgen/blob/master/test_files/POSCAR) claims it's LiFePO4 but it's actually Fe4P4O16, I'm not sure if that's intentional or not, but I think that's where the failures are coming from.",
"This seems to be a Py3 vs Py2 issue. The Py3 test has a failure that is not related to this change. But the Py2 test has a huge number of failures. I am reverting this pull requset. Pls fix it properly first."
] | 2017-10-23T18:36:56
| 2017-10-24T15:27:09
|
2017-10-23T18:42:15Z
|
NONE
|
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Bug in POSCAR parsing from file looking for POTCAR by name only
Misses extensions such as .gz .orig, .relax1.gz , etc.
Fixed by looking for POTCAR in filename
|
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| 268,071,380
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MDExOlB1bGxSZXF1ZXN0MTQ4NDI2ODU5
| 870
|
Magnetic analysis module + improvements to MagOrderingTransformation
|
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[
"Thanks!"
] | 2017-10-24T15:11:39
| 2017-10-27T23:45:24
|
2017-10-27T23:45:01Z
|
MEMBER
|
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|
## Summary
A magnetic analysis module with some helpful methods + backwards-compatible improvements to MagOrderingTransformation to handle more complex cases + tests for same. Also a few general bugfixes.
More features will be added to the module in future, but it'd be useful to merge this now.
## Additional dependencies introduced (if any)
None
## TODO (if any)
I'll be adding a Jupyter notebook to go over the new functionality at some point.
|
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MDExOlB1bGxSZXF1ZXN0MTQ4NDMxNTM4
| 871
|
Revert "Fix bug in POSCAR parsing"
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[] | 2017-10-24T15:27:17
| 2018-03-25T13:28:55
|
2017-10-24T15:27:23Z
|
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Reverts materialsproject/pymatgen#869
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| 268,164,388
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MDExOlB1bGxSZXF1ZXN0MTQ4NDk2Njc4
| 872
|
Add some additional filename wildcards for mcsqs input
|
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[] | 2017-10-24T19:53:38
| 2017-10-24T22:30:22
|
2017-10-24T22:30:22Z
|
MEMBER
|
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## Summary
Add some additional filename wildcards for mcsqs input
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
* Feature 1 supports a, but not b.
|
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| 268,197,990
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MDExOlB1bGxSZXF1ZXN0MTQ4NTIxOTY1
| 873
|
fix jhu issue
|
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[
"Thanks\r\n"
] | 2017-10-24T21:49:25
| 2017-10-24T21:50:27
|
2017-10-24T21:50:21Z
|
CONTRIBUTOR
|
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Should fix JHU servlet issue. Was using a static INCAR from the test files, rather than generating it on the fly, and JHU updated their system to parse magmoms for symmetry.
|
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MDExOlB1bGxSZXF1ZXN0MTQ4NTI5ODc1
| 874
|
Add more filename wildcards for mcsqs input
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[] | 2017-10-24T22:34:49
| 2017-10-27T23:45:20
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2017-10-27T23:45:20Z
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MEMBER
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## Summary
Add more filename wildcards for mcsqs input
## Additional dependencies introduced (if any)
## TODO (if any)
|
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MDExOlB1bGxSZXF1ZXN0MTQ5MjcyNzMw
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|
Feff io DirectoryInput
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[
"This is not a good name. SEe how VaspInput is defined.",
"I renamed the class name to PostFEFFSet to make the name more specific about the class' function, similar to the class names defined in the VaspInput. "
] | 2017-10-27T19:53:40
| 2017-10-30T21:05:39
|
2017-10-30T21:05:39Z
|
CONTRIBUTOR
|
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## Summary
Add PostFEFFSet class to pymatgen.io.feff that allows post-processing of FEFF input files from an existing FEFF input files directory. Unittest files have been added accordingly
|
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MDExOlB1bGxSZXF1ZXN0MTQ5MzAxNzQx
| 876
|
Bandstructure fix
|
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[] | 2017-10-27T22:56:29
| 2017-10-27T23:44:05
|
2017-10-27T23:44:05Z
|
CONTRIBUTOR
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@rwoodsrobinson noticed that bandstructures for a number of materials were returning negative values from `Bandstructure.get_direct_band_gap()`, which was because the sampling over the bands didn't consistently account for the spin down bands when determining the valence band maxima.
This PR should fix that, and adds an extra function `Bandstructure.get_direct_band_gap_dict()` that returns some additional detail about the direct band gap (i. e. the k-point and band indices) and returns the direct gap for both spins (requested by @mkhorton). Also added a metallic bandstructure and a few unittests.
|
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| 877
|
surface_analysis.py update
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[
"I said this before - merge the origin with your fork and submit a new pull request. This pull request contains all the code from previous pull requests.",
"Will do, sorry about that"
] | 2017-10-27T23:07:49
| 2017-10-28T05:02:02
|
2017-10-28T05:02:02Z
|
CONTRIBUTOR
|
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## Summary
Removed import of MPRester to calculate chemical potential range. Temporarily set chemical potential range for a nonstoichiometric slab as an optional parameter. A future release will handle the calculation of the chemical potential range automatically. Added class method to plot binding energy vs clean surface energy for class SurfaceEnergyPlotter(). Added more unit tests, specifically for the case of adsorption (credits to Joseph Montoya for providing the files).
* gbind_vs_gamma() class method to plot binding energy vs clean surface energy
* class WulffShape() method get_plot() parameter color_set can now be the name for a color set or a dictionary of user specified rgb list for each facet (hkl).
## TODO (if any)
-Only works for monatomic adsorbates
-Only works for 1 reference element if we are dealing
with non-stoichiometric slabs.
-Need a method to automatically get chempot range when
dealing with non-stoichiometric slabs
-Simplify or clean the stable_u_range_dict() method
for the SurfaceEnergyPlotter class
-Combine chempot_vs_gamma_clean(), chempot_vs_gamma_plot_one()
and chempot_vs_gamma_facet() into one class method.
-Annotations for which configuration is on a plot
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MDExOlB1bGxSZXF1ZXN0MTQ5MzA5NzE1
| 878
|
Parsing Updates and Bug Squashing
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[] | 2017-10-28T00:28:50
| 2017-10-28T00:31:51
|
2017-10-28T00:30:40Z
|
NONE
|
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- Fixed the POTCAR parsing bug in POSCAR again
- Updated the tests so they are appropriate conditioned for a test folder with multiple POSCARs and POTCARs
- Added in electrostatic potential parsing at each atom in OUTCAR
- Moved drift to an Outcar attribute
- Used a more sensible regex for parsing the drift
|
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MDExOlB1bGxSZXF1ZXN0MTQ5NjY5MTIy
| 879
|
Adding PostFEFFSet class
|
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[] | 2017-10-31T00:23:16
| 2017-10-31T01:09:10
|
2017-10-31T01:09:10Z
|
CONTRIBUTOR
|
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## Summary
Add PostFEFFSet class to pymatgen FEFF io used for post-processing of FEFF input files, with modified FEFF set test files.
|
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MDExOlB1bGxSZXF1ZXN0MTQ5OTM1MTIy
| 880
|
Order-disorder transformation tools
|
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[] | null |
[
"Should wait for tests ... for some reason py2 tests were failing when I created the branch - even before I made any changes. Could not figure out the reason for this."
] | 2017-11-01T00:00:11
| 2018-04-04T19:40:23
|
2017-11-01T13:49:18Z
|
MEMBER
|
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|
## Summary
Adds some new features for order-disorder transformation
* A new DiscretizeOccupanciesTransformation that will discretize the site occupancies in a structure, e.g., 0.62, 0.19, 0.19 to 0.6, 0.2, 0.2 - according to tunable tolerances.
* Test for above
* A new option for EnumerateStructureTransformation that lets you set max_disordered_sites instead of max_cell_size. The former can iterate over multiple max_cell_size values until either finding a solution or hitting the max number of disordered sites.
* Test for above
## Additional dependencies introduced (if any)
None
|
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MDExOlB1bGxSZXF1ZXN0MTUwMTQ2OTI4
| 881
|
Add two functions to Bandstructure to get k-points degeneracy
|
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[] | 2017-11-01T21:09:11
| 2017-11-01T21:50:02
|
2017-11-01T21:50:02Z
|
CONTRIBUTOR
|
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|
## Summary
added a function to get symmetrically equivalent k-points to a given k-point to then be used to obtain band degeneracies via get_kpoint_degeneracy. I did not define degeneracy as default properties of cbm and vbm since they will be None most of the time as usually bs.structure is None. Also, I did not define get_sym_eq_kpoints inside SpacegroupAnalyzer as it seemed like everything else there is in direct lattice rather than reciprocal lattice where the Bandstructure is defined.
I also added tests for these two functions based on CaO band structure and crystal structure.
|
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| 270,698,530
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MDExOlB1bGxSZXF1ZXN0MTUwMzI0NzQy
| 882
|
Fix a bug in is_element in computed entry
|
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[
"Can you also add a test to ensure this doesn't happen again."
] | 2017-11-02T15:32:44
| 2017-11-02T16:29:28
|
2017-11-02T15:36:36Z
|
NONE
|
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This bug causes problems in evaluating if an elemental composition is an element.
Fixed by switching to the logic used in PDEntry.
|
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| 270,796,697
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MDExOlB1bGxSZXF1ZXN0MTUwMzk1OTYy
| 883
|
Added Test for is_element
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[] | 2017-11-02T20:29:18
| 2017-11-21T20:57:32
|
2017-11-06T21:05:40Z
|
NONE
|
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Should have included this with the previous PR #882
* Added a test for is_element in computed entry
|
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| 271,199,405
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MDExOlB1bGxSZXF1ZXN0MTUwNjgwNjU0
| 884
|
get_symmetry_operations API convenience method for PointGroupAnalyzer
|
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[] | 2017-11-04T15:17:22
| 2017-11-06T21:05:21
|
2017-11-06T21:05:21Z
|
CONTRIBUTOR
|
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The APIs for dealing with symmetry operations from `SpacegroupAnalyzer` and `PointGroupAnalyzer` objects have a lot of differences. This pull request adds a `PointGroupAnalyzer.get_symmetry_operations()` method, that mirrors the `SpacegroupAnalyzer.get_symmetry_operatsion()` method.
|
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MDU6SXNzdWUyNzEyMjYwNDI=
| 885
|
broad exception catching EnumlibAdapter making writing some code impossible
|
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[] | 2017-11-04T21:07:28
| 2017-11-05T15:04:08
|
2017-11-05T15:04:08Z
|
MEMBER
|
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I am trying to run the EnumlibAdapter code, but wrap that code with a monty timeout
e.g.,
```
with timeout(4):
try:
# run EnumlibAdapter
except TimeoutError:
# handle timeout
```
But this doesn't work because EnumlibAdapter catches all exceptions that might occur inside of it in two places - within the run() function as well as within the _get_structures() function.
This exception handling should be made more specific
|
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MDU6SXNzdWUyNzEyNDk1NTA=
| 886
|
problem when reading magnetic cif files
|
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[] | null |
[
"@mkhorton Pls handle this. Thanks.",
"Will do, thanks for the report.\r\n\r\n@cyz11 do you have a test file to share please?",
"Regarding the first issue, it should work regardless of if an underscore or period is used as the delimiter -- this was because the magCIF standard changed during development, but there are already files out there in the wild using the older format. However, there may be a bug, so I'll check up on this.\r\n\r\nRegarding the co-ordinate system, we want them in Cartesian in the generated structure, since I believe this is the format VASP expects for non-collinear calculations, though I think relative would make more sense generally. We could well be changing co-ordinate systems at the wrong point however, so I'll investigate -- again, any specific example is very helpful.",
"Ok, the first issue should be fixed. The best reference I have for magCIF right now is http://comcifs.github.io/magCIF.dic.html -- this claims that both `_atom_site_moment.crystalaxis_x` and `_atom_site_moment_crystalaxis_x` are correct (the latter is an alias). I've updated the parser to support both.",
"I have attached a cif file I am working on. It report an error for the first issue if I use get_structures. Even if I fixed the first issue, I found it did not give the correct magnetic moment for symmetry related points(You can check it with the image in VESTA).\r\nThanks!\r\n\r\nOn Nov 6, 2017, at 1:08 PM, Matthew Horton <notifications@github.com<mailto:notifications@github.com>> wrote:\r\n\r\n\r\nRegarding the first issue, it should work regardless of if an underscore or period is used as the delimiter -- this was because the magCIF standard changed during development, but there are already files out there in the wild using the older format. However, there may be a bug, so I'll check up on this.\r\n\r\nRegarding the co-ordinate system, we want them in Cartesian in the generated structure, since I believe this is the format VASP expects for non-collinear calculations, though I think relative would make more sense generally. We could well be changing co-ordinate systems at the wrong point however, so I'll investigate -- again, any specific example is very helpful.\r\n\r\n—\r\nYou are receiving this because you were mentioned.\r\nReply to this email directly, view it on GitHub<https://github.com/materialsproject/pymatgen/issues/886#issuecomment-342234990>, or mute the thread<https://github.com/notifications/unsubscribe-auth/Afy9XX8L6HSJbczwZMTWlrHAKzl0jTu4ks5sz0skgaJpZM4QSRD->.\r\n\r\n",
"I don't think the attachment came through on GitHub via your email reply. If you log in on the GitHub website, you should be able to add the attachment manually. Thanks!",
"Here is an example in txt\r\n[Mn3Ge_IR2.cif.txt](https://github.com/materialsproject/pymatgen/files/1447618/Mn3Ge_IR2.cif.txt)\r\n\r\nSorry, it is my first time using github",
"No problem, worked fine that time.",
"Hi @cyz11, this should be fixed now. Thanks for bringing this to our attention! Your summary of the error was spot-on. \r\n\r\nThe fixed code should be merged into pymatgen shortly, but until then you can retrieve the fixed code from here https://github.com/materialsproject/pymatgen/pull/887\r\n\r\nIf you're still having issues with the updated code, please do report back!",
"New version of pymatgen released which includes all these fixes."
] | 2017-11-05T05:16:57
| 2017-11-06T21:58:21
|
2017-11-06T21:58:21Z
|
NONE
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I had problems when reading a magnetic cif file generated by ISOCIF.
It seems the 'parse_magmoms' method in cif.py have some problems.
First, the keys in data
'_atom_site_moment_crystalaxis_x'
'_atom_site_moment_crystalaxis_y'
'_atom_site_moment_crystalaxis_z'
'_atom_site_moment_label'
should be changed into
'_atom_site_moment.crystalaxis_x'
'_atom_site_moment.crystalaxis_y'
'_atom_site_moment.crystalaxis_z'
'_atom_site_moment.label'
to support the new standard magnetic cif files.
Secondly, it parse_magmom gets the magnetic moments in Cartesian coordinates, which turns out to be a problem in _get_structure method. Because the symmetry operation in _get_structure is done in relative units, using Cartesian coordinates first will give the wrong moment for symmetry related sites. I think the correct order is first do the symmetry operation to get all the sites and then transfer into Cartesian coordinates, or you can just leave it as relative units.
Hope the bugs could be fixed soon.
|
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https://github.com/materialsproject/pymatgen/pull/887
| 271,574,261
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MDExOlB1bGxSZXF1ZXN0MTUwOTI1MDg2
| 887
|
Adds aliases for common keys in magCIF standard
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[
"Pls add tests for the new fixes.",
"Will add the test file from @cyz11",
"Both issues should be fixed now, tests added."
] | 2017-11-06T18:26:28
| 2017-11-06T21:46:43
|
2017-11-06T21:46:43Z
|
MEMBER
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See http://comcifs.github.io/magCIF.dic.html for more information
Fixes issue 1 of 2 in #886
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| 888
|
move two functions to BandStructure instead of BandStructureSymmLine
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[
"If this is merged, could you please release a new version of pymatgen so that I can use this updated feature in matminer?"
] | 2017-11-07T18:39:03
| 2017-11-09T04:14:38
|
2017-11-09T04:14:38Z
|
CONTRIBUTOR
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I mistakenly defined get_sym_eq_kpoints and get_kpoint_degeneracy under BandStructureSymmLine but they work with any BandStructure object so I moved them under BandStructure.
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|
Bugfix for PointGroupAnalyzer get_symmetry_operations
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[] | 2017-11-08T00:33:08
| 2017-11-08T00:36:41
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2017-11-08T00:34:30Z
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CONTRIBUTOR
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Commit 42df22fe0d2488c539914f58ed90961411eaec46 added a `get_symmetry_operations` method to the `PointGroupAnalyzer` class.
It also introduced a bug, where the symmetry operations returned only included those found from the initial analysis of a molecule, instead of the complete set of symmetry operations for the corresponding point group.
This commit fixes this bug, and adds a more detailed test that checks a full set of symmetry operations is returned.
|
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|
LAMMPS data rewritten
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[
"I will merge now. BUut go ahead and introduce pandas as a dependency. I foresee we will be doing so soon enough given that there are clear advantages to using pandas for many types of analysis."
] | 2017-11-08T04:36:06
| 2017-11-08T04:46:03
|
2017-11-08T04:46:03Z
|
CONTRIBUTOR
|
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## Summary
`io.lammps.data` has been completely rewritten to fix the formatting issue. Closes #865
* `LammpsForceFieldData` has been merged into `LammpsData`, with `force_field` and `topology` as optional args.
* Data in each line is now stored in a dict rather than a plain list in order to distinguish floats from intergers. Will be of great help for handling a mixture of data, especially in Atoms section.
* For the format of Atoms section, `atom_style` can be set to control the output or the way a file is parsed. Implementing a new supported style should be easy-peasy.
* Code tuning box for either molecule or structure has been completely REMOVED.
* Moved `ForceField` and `Topology` into `io.lammps.data` as they only serve `LammpsData`.
* `Topology.from_molecule` is now `Topology.from_bonding`. Angle and dihedral searching in the latter method is index-based, 10x faster than before. Also fixed an incomplete bug in dihedral searching.
## Additional dependencies introduced (if any)
No
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* (optional) It would be even more beneficial to use `pandas.DataFrame` for 2d arrays in a LAMMPS data file. This would make breaking down `LammpsData` to `ForceField` and `Topology` much more efficient (code with similar spirit in `io.lammps.output.LammpsRun`). The price to pay is introducing pandas as a new dependency.
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|
Fix empty file for Structure.to(filename=) for fmt='mcsqs'
|
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[] | 2017-11-08T19:33:13
| 2017-11-09T04:14:22
|
2017-11-09T04:14:22Z
|
MEMBER
|
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Was previously just returning the string instead of writing to file. Thanks @josuav1 for the report.
|
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| 272,352,551
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MDExOlB1bGxSZXF1ZXN0MTUxNDk3NzM5
| 892
|
Add PostFEFFSet
|
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[
"This is truly a nonsensical class name and approach. It even violates what an \"InputSet\" as defined by pymatgen is. An InputSet is not a collection of input; it is a collection of RULES that create input. \r\n\r\nDo you see the equivalent class in pymatgen.io.vasp.sets? Of course not. If you just want to collect the input files, you use the pymatgen.io.vasp.inputs.VaspInput class. Only if you have new rules (e.g., to generate a BandStructure set of inputs) that you have a MPBSSet with corresponding from_prev_calc.\r\n\r\nI am rejecting this PR. Rethink the approach."
] | 2017-11-08T21:17:20
| 2017-11-09T01:04:31
|
2017-11-09T01:04:31Z
|
CONTRIBUTOR
|
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## Summary
Add PostFEFFSet used for post-processing of FEFF input from a directory contains FEFF input files. Useful when existing FEFF input needs some adjustment.
|
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| 272,783,772
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MDExOlB1bGxSZXF1ZXN0MTUxODAxNDQw
| 893
|
DiscretizeOccupanciesTransformation: fix_denominator
|
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[] | null |
[
"Thanks for the fixes.",
"There are failed tests on Py2 or 3. Pls fix.\r\n\r\nhttps://circleci.com/gh/materialsproject/pymatgen/7263?utm_campaign=build-failed&utm_medium=email&utm_source=notification"
] | 2017-11-10T00:49:20
| 2017-11-12T22:55:13
|
2017-11-12T22:02:35Z
|
CONTRIBUTOR
|
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added fix_denominator (bool) to DiscretizeOccupanciesTransformation:
if True, will enforce a common denominator for all species. This prevents a mix of denominators (for example, 1/3, 1/4) that might require large cell sizes to perform an enumeration.
added Test; successful
|
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MDExOlB1bGxSZXF1ZXN0MTUyMDMzMzk0
| 894
|
Fix Structure.remove_spin() when applied to elements not species
|
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[] | 2017-11-11T01:13:35
| 2017-11-11T15:09:47
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2017-11-11T15:09:47Z
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MEMBER
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Minor bug fix + updated test
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MDU6SXNzdWUyNzMxMTQyMzA=
| 895
|
Is it possible to convert symmetrized cif file to discard symmetry cif file while retaining the original inequivalent labels?
|
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[
"You can write a script to do it.",
"Also the `SpacegroupAnalyzer.get_symmetrized_structure()` method can help with this by grouping equivalent sites, but there's no guarantee it'll get the same grouping as the original CIF (this depends on what tolerances you use for the symmetry analysis)."
] | 2017-11-11T03:20:30
| 2017-11-11T16:23:35
|
2017-11-11T15:09:06Z
|
NONE
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Dear developers,
For example, I have a symmetrized cif file called "sym.cif" with spacegroup 31 and atom info like below
Te Te1 2 0.0000000000000 0.2072200000000 0.6463300000000 1
Te Te2 2 0.0000000000000 0.2984500000000 0.1022900000000 1
Te Te3 2 0.0000000000000 0.6463100000000 0.3535800000000 1
Te Te4 2 0.0000000000000 0.8576100000000 0.8977100000000 1
W W5 2 0.0000000000000 0.0398000000000 0.2576800000000 1
W W6 2 0.0000000000000 0.6006200000000 0.7424600000000 1
So there is totally 6 inequivalent atoms labeled Te1, Te2, Te3, Te4, W5, W6
However, if I discard symmetry of this cif file with below method
```
cif_file=r'r:\sym.cif'
struct=pymatgen.Structure.from_file(cif_file)
cif_file_obj=pymatgen.io.cif.CifWriter(struct)
print(cif_file_obj)
```
then I got this atom info
Te Te1 1 0.0000000000000 0.2072200000000 0.6463300000000 1.0
Te Te2 1 0.5000000000000 0.7927800000000 0.1463300000000 1.0
Te Te3 1 0.0000000000000 0.2984500000000 0.1022900000000 1.0
Te Te4 1 0.5000000000000 0.7015500000000 0.6022900000000 1.0
Te Te5 1 0.0000000000000 0.6463100000000 0.3535800000000 1.0
Te Te6 1 0.5000000000000 0.3536900000000 0.8535800000000 1.0
Te Te7 1 0.0000000000000 0.8576100000000 0.8977100000000 1.0
Te Te8 1 0.5000000000000 0.1423900000000 0.3977100000000 1.0
W W9 1 0.0000000000000 0.0398000000000 0.2576800000000 1.0
W W10 1 0.5000000000000 0.9602000000000 0.7576800000000 1.0
W W11 1 0.0000000000000 0.6006200000000 0.7424600000000 1.0
W W12 1 0.5000000000000 0.3993800000000 0.2424600000000 1.0
So all atom got relabeled, and I lost the inequvalent atom infomation
What I want is a discard cif with labels to indicate inequivalent atoms like this
Te Te1 1.0 0.0 0.20722 0.64633
Te Te1 1.0 0.5 0.79278 0.14633
Te Te2 1.0 0.0 0.29845 0.10229
Te Te2 1.0 0.5 0.70155 0.60229
Te Te3 1.0 0.0 0.64631 0.35358
Te Te3 1.0 0.5 0.35369 0.85358
Te Te4 1.0 0.0 0.85761 0.89771
Te Te4 1.0 0.5 0.14239 0.39771
W W5 1.0 0.0 0.0398 0.25768
W W5 1.0 0.5 0.9602 0.75768
W W6 1.0 0.0 0.60062 0.74246
W W6 1.0 0.5 0.39938 0.24246
How to achieve this using pymatgen? Thank you very much
best regards
|
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| 273,128,231
|
MDExOlB1bGxSZXF1ZXN0MTUyMDQ3NDA1
| 896
|
handle NoneType entries
|
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[] | 2017-11-11T08:02:43
| 2017-11-11T15:08:30
|
2017-11-11T15:08:30Z
|
CONTRIBUTOR
|
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## Summary
Mute MPRestError if the given criteria have no corresponding entries.
* `rester.get_entries_in_chemsys` throws MPRestError if no entry matches the given criteria. For example, a query in chemical system C-O-N:
```python
from pymatgen.ext.matproj import MPRester
rester = MPRester()
mp_entries = rester.get_entries_in_chemsys(["C", "O", "N"])
```
Error message:
`MPRestError: local variable 'first' referenced before assignment. Content: b'{"valid_response": false, "version": {"pymatgen": "2017.11.9", "db": "2.0.0", "rest": "2.0"}, "traceback": "Traceback (most recent call last):\\n File \\"/var/www/python/matgen/materials_django/rest/rest.py\\", line 91, in wrapped\\n d = func(*args, **kwargs)\\n File \\"/var/www/python/matgen/materials_django/rest/rest.py\\", line 182, in query\\n raise RESTError(str(ex))\\nRESTError: local variable \'first\' referenced before assignment\\n", "created_at": "2017-11-10T23:40:33.356887", "error": "local variable \'first\' referenced before assignment"}'`
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| 273,531,051
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MDExOlB1bGxSZXF1ZXN0MTUyMzEyNjY4
| 897
|
Fix rounding errors in py2
|
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[] | 2017-11-13T18:29:02
| 2017-11-13T18:45:32
|
2017-11-13T18:45:31Z
|
CONTRIBUTOR
|
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Replaced "round" by around in DiscretizeOccupanciesTransformation
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| 273,559,429
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MDExOlB1bGxSZXF1ZXN0MTUyMzMzNzM3
| 898
|
Make the conversion battery module useful for multivalent cations
|
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[] | null |
[
"Pls add a test first. I do not merge things without tests.",
"I will close this pull request and send off a new pull request with unittest."
] | 2017-11-13T20:03:23
| 2018-01-06T08:25:40
|
2018-01-06T08:25:40Z
|
CONTRIBUTOR
|
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|
Applied the same treatment as we did for insertion electrodes. When the ion oxidation state is 2+, the voltage reduced to half, and the capacity multiplied by 2.
## Summary
* Previously, the code works for LIB. However, it ignores the valence state of multivalent cations such as Mg and Ca, and treat it like Li. The fixed code, take the oxidation state of the working ion into account.
## Additional dependencies introduced (if any)
* N/A
## TODO (if any)
* someone may add nosetest for it
|
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| 273,765,923
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MDExOlB1bGxSZXF1ZXN0MTUyNDg0OTYx
| 899
|
fix pmg plot --xrd
|
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[] | 2017-11-14T11:55:27
| 2017-11-14T12:33:57
|
2017-11-14T12:33:57Z
|
CONTRIBUTOR
|
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## Summary
fix `pmg plot --xrd POSCAR`
error message:
```plain
AttributeError: 'Namespace' object has no attribute 'xrd'
```
|
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MDU6SXNzdWUyNzQwMjc2Mzc=
| 900
|
what happened to LammpsData.from_structure classmethod?
|
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[
"Sorry it was removed in the recent PR because\r\n\r\n1. A LAMMPS data file usually contains more information than a structure does. \r\n2. There is no reason to place the molecule in the center of the simulation box, or alter the simulation box size simply based the size of input molecule. \r\n\r\nTo work with pmg objects like structure or molecule, use the new `Topology` and `ForceField` objects.",
"I agree with @matk86 that it is probably useful to have a convenience method to construct Lammpsdata from a structure/molecule. But I also agree with @adengz that the LAMMPS data file require more information. I suggest you just include a from_structure method, which will simply construct a topology from the sites and set up the cell with additional parameters. \r\n\r\nI would suggest we do not allow construct from molecule. Instead, someone will have to go through get_boxed_structure to construct the simulation cell before passing it into Lammpsdata.",
"I will bring back a standalone method building `LammpsData` from structure soon, instead of a classmethod associated with `LammpsData` since this will ignore topologies and their force field parameters.",
"Thanks.\r\n The use case I had in mind was not just simple boxed molecule but actual periodic structures with tilt etc computed from the given structures lattice and simple 'atomic' or molecule style (no need for topologies and forcefields, the reason why I had a separate lammpsforcefield class that inherited from lammpsdata)"
] | 2017-11-15T04:01:17
| 2017-11-15T19:56:38
|
2017-11-15T19:56:38Z
|
CONTRIBUTOR
|
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it used to be there until the recent PR. @adengz why did you remove it? it is very useful to have it in there for generating data files for general structure objects.
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