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https://api.github.com/repos/materialsproject/pymatgen/issues/901 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/901/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/901/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/901/events | https://github.com/materialsproject/pymatgen/pull/901 | 274,239,614 | MDExOlB1bGxSZXF1ZXN0MTUyODM3Mjk2 | 901 | LammpsData is now powered by pandas.DataFrame | {
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"This PR contains too many unrelated commits, including those from previous PRs. Pls merge your fork with origin and resubmit a NEW PR."
] | 2017-11-15T17:25:55 | 2017-11-15T19:24:36 | 2017-11-15T19:24:36Z | CONTRIBUTOR | {
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} | ## Summary
LammpsData is now powered by pandas.DataFrame.
* `get_string` method can set Nos. of significant digits for distance (coordinates), velocities and charges separately.
* Two more attributes added to `ForceField`. They can serve as the input args for the new `LammpsData` directly.
* The old `LammpsDat... | {
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"This PR contains too many unrelated commits because you did not sync your fork with the origin. Pls do so and resubmit a new PR."
] | 2017-11-15T19:02:36 | 2017-11-15T19:23:37 | 2017-11-15T19:23:37Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/903 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/903/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/903/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/903/events | https://github.com/materialsproject/pymatgen/pull/903 | 274,284,029 | MDExOlB1bGxSZXF1ZXN0MTUyODY5ODk3 | 903 | LammpsData powered by pd.DataFrame | {
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LammpsData is now powered by pandas.DataFrame.
* `get_string` method can set Nos. of significant digits for distance (coordinates), velocities and charges separately.
* Two more attributes added to `ForceField`. They can serve as the input args for the new `LammpsData` directly.
* The old `LammpsDat... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/904 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/904/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/904/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/904/events | https://github.com/materialsproject/pymatgen/pull/904 | 274,288,909 | MDExOlB1bGxSZXF1ZXN0MTUyODczNDkx | 904 | add timeout for BoltztrapRunner default to 7200 seconds | {
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} | to avoid wasting CPU hours when finding Fermi level is not converging (specially at high concentrations), I introduced a timeout option defaulting to 2 hours. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/905 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/905/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/905/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/905/events | https://github.com/materialsproject/pymatgen/pull/905 | 274,348,167 | MDExOlB1bGxSZXF1ZXN0MTUyOTE3ODcy | 905 | Redefine DiscretizeOccupanciesTransformations | {
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} | ## Summary
The current version of DiscretizeOccupanciesTransformations fails in some cases, because a total occupancy other than 1.00 is reached per lattice site. Moreover, the definition of the tolerance requires that different values are used in different cases to get equally good discretizations for different str... | {
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} | ## Summary
Added a method to break down `LammpsData` to `ForceField` and a series of `Topology`.
## Additional dependencies introduced (if any)
No
## TODO (if any)
No | {
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"HOw are you installing pymatgen? Conda or pip?",
"Standard conda instructions. I've installed on other machines without\nissue. I'm just not sure where to go from here.\n\nOn Fri, Nov 17, 2017, 5:14 PM Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> HOw are you installing pymatgen? Conda or pip?\n>\n> —\n... | 2017-11-17T22:26:55 | 2017-11-18T04:31:59 | 2017-11-18T04:26:56Z | MEMBER | {
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} | I'm running into the following issue. Any ideas what I need to do to resolve the issue? I'm using a remote supercomputer so can't do anything to the central OS or anything like that.
## System
* Pymatgen version: 2017.11.6
* Python version: python 2.7.14
* OS version: SUSE Linux Enterprise Server 11
## Summa... | {
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* Implemented as_phononwebsite and write_phononwebsite functions to export the phonon dispersion to the phononwebsite: http://henriquemiranda.github.io/phononwebsite/
* Implemented band_reorder to order the eigenvalues and according to the similarity of the eigenvectors using the estimate_band_connection... | {
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} | ## Summary
* class method of AdsorbateSiteFinder, adsorb_both_surfaces() now uses symmetry operators to find a position on the other side of the slab for an adsorbate. This more generalized method will allow for adsorption of molecules on both surfaces. The method is also much more simplified compared to the previou... | {
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Provides methods to retrieve MP surface data and to construct a Wulff shape given a material ID. Addresses #768. | {
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} | ## Summary
Some minor changes (convenience properties, docstring changes) to the magnetic structure analyzer + a few more tests.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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} | ## Summary
A new class has been added to surface.py: ReconstructionGenerator().
* ReconstructionGenerator takes in an initial structure (conventional ucell), a slab and vacuum size and a string for the name of the type of reconstruction the user desires to create and the index of termination (some reconstructions... | {
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Add from_directory method to existed FEFFDictSet for post-processing of FEFF input files. Unittest has been added accordingly. | {
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Add from_directory method to existed FEFFDictSet for post-processing of FEFF input files. Unittest has been added accordingly. | {
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} | ## Summary
* Added instructions for generating the fcc_100_missing_row_1x2 and fcc_100_missing_row_1x1 slabs.
* Return slabs after adsorbing both sides | {
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"Sorry. I posted this on the wrong MaterialsProject project. I'm so used to using Pymatgen."
] | 2017-11-30T18:03:51 | 2017-11-30T18:25:24 | 2017-11-30T18:24:50Z | MEMBER | {
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} | In the custodian.vasp.handlers.py script, there is an error-handling method for the "subspacematrix" (i.e. "WARNING: Sub-Space-Matrix is not hermitian in DAV") error. As it stands right now, the custodian file tries to change LREAL when this error occurs. I have found that in systems I have studied, this error often o... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/917 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/917/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/917/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/917/events | https://github.com/materialsproject/pymatgen/pull/917 | 278,228,331 | MDExOlB1bGxSZXF1ZXN0MTU1Njg4NDY4 | 917 | Recover functions of old LammpsData | {
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} | ## Summary
Thank Zhi for the new version of LammpsData.
The new version lost some functions compared to the old one, e.g. converting LammpsData to Structure object. It is better to rewrite those parts according to the new version and add them back.
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https://api.github.com/repos/materialsproject/pymatgen/issues/918 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/918/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/918/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/918/events | https://github.com/materialsproject/pymatgen/issues/918 | 278,237,160 | MDU6SXNzdWUyNzgyMzcxNjA= | 918 | Recover functions of old LammpsData | {
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} | Thank Zhi for the new version of LammpsData.
The new version lost some functions compared to the old one, e.g. converting LammpsData to Structure Object. It is better to rewrite those parts based on the new version and add them back. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/919 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/919/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/919/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/919/events | https://github.com/materialsproject/pymatgen/issues/919 | 278,317,932 | MDU6SXNzdWUyNzgzMTc5MzI= | 919 | Fix FEFF EXAFS input file generation for small system | {
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} | Fixed EXAFS input file generation for the small system. The EXAFS calculation for the small system should be done in real space. Currently, the EXAFS input file generated for small system includes reciprocal tag | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/920 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/920/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/920/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/920/events | https://github.com/materialsproject/pymatgen/pull/920 | 278,322,911 | MDExOlB1bGxSZXF1ZXN0MTU1NzU4NTY1 | 920 | added more unittests for reconstruction | {
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"I don't think having is_reconstructed having dual meanings of boolean and string is a good idea. Fundamentally, \"is_reconstructed\" implies just a boolean type variable. No one would think it can contain a string. I think it is better to have a property called \"reconstruction\", which is a string. If it is None,... | 2017-12-01T00:56:53 | 2017-12-20T22:50:00 | 2017-12-04T00:06:52Z | CONTRIBUTOR | {
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} | ## Summary
* Added option to include reconstructions when using generate_all_slabs
* Slab class has property called is_reconstructed. Can be a bool or a str (i.e. the name of the reconstruction).
* Made sure reconstructions that inherit from another base_reconstruction will properly be built.
* Added unittest for... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/921 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/921/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/921/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/921/events | https://github.com/materialsproject/pymatgen/issues/921 | 278,328,660 | MDU6SXNzdWUyNzgzMjg2NjA= | 921 | Nanoscale stabilization analyzer | {
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"Ok. Go ahead."
] | 2017-12-01T01:30:38 | 2018-01-11T04:43:09 | 2018-01-11T04:43:09Z | CONTRIBUTOR | {
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} | Analyze the stability of nanoparticles of different polymorphs with respect to size. The Wulff shape will be the model for the nanoparticle. Stability will be determined by an energetic competition between the weighted surface energy (surface energy of the Wulff shape) and the bulk energy. A future release will include... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/922 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/922/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/922/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/922/events | https://github.com/materialsproject/pymatgen/pull/922 | 278,553,264 | MDExOlB1bGxSZXF1ZXN0MTU1OTI2Mjk5 | 922 | Small system EXAFS input set generation fix | {
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} | ## Summary
Fixed FEFF EXAFS input set generation for the small system (atoms < 14). For EXAFS calculation, all FEFF calculations will be done in the real space. Resolves #919 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/923 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/923/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/923/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/923/events | https://github.com/materialsproject/pymatgen/pull/923 | 278,576,633 | MDExOlB1bGxSZXF1ZXN0MTU1OTQyODU4 | 923 | fix voltage sign for anion voltage profile | {
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"Pls add a test using a hypothetical compound."
] | 2017-12-01T19:49:22 | 2017-12-01T20:16:34 | 2017-12-01T20:16:34Z | CONTRIBUTOR | {
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} | ## Summary
Fixed the sign of calculated voltage of `InsertionVoltagePair` when anion is intercalated.
* Fix the wrong sign of the calculated voltage (revised script, line 431)
* Minor formatting. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/924 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/924/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/924/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/924/events | https://github.com/materialsproject/pymatgen/pull/924 | 278,592,044 | MDExOlB1bGxSZXF1ZXN0MTU1OTU0MTc4 | 924 | Add structure property for LammpsData | {
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"Pls pull the latest changes and submit a clean pull request. This includes commits from previous PRs."
] | 2017-12-01T20:48:57 | 2017-12-01T20:49:49 | 2017-12-01T20:49:49Z | CONTRIBUTOR | {
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} | ## Summary
Add a property method for LammpsData object, which returns the pmg Structure object of the corresponding LammpsData.
This will allow us to analyze the LammpsData geometry and make it easy to transform the structures between lammps and other DFT codes (e.g. VASP POSCAR).
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https://api.github.com/repos/materialsproject/pymatgen/issues/925 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/925/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/925/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/925/events | https://github.com/materialsproject/pymatgen/pull/925 | 278,600,532 | MDExOlB1bGxSZXF1ZXN0MTU1OTYwNTU4 | 925 | Convert LammpsData to pmg Structure | {
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} | ## Summary
Add a property method for LammpsData, which returns the pmg Structure object.
It will allow us to analyze the geometry of the LammpsData and make it convenient transform structures between Lammps and other DFT code (e.g. VASP POSCAR). | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/926 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/926/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/926/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/926/events | https://github.com/materialsproject/pymatgen/pull/926 | 278,646,246 | MDExOlB1bGxSZXF1ZXN0MTU1OTkzODk1 | 926 | Optical add vasprun | {
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} | ## Summary
Added a new Vasprun parser to parse opticaltransitions tags printed in vasprun.xml after a BSE calculation. The new parser will output both the oscillator strength in (eV) and the probability of transition (dimensionless)
## Additional dependencies introduced (if any)
None
## TODO (if any)
N/... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/927 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/927/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/927/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/927/events | https://github.com/materialsproject/pymatgen/pull/927 | 278,802,029 | MDExOlB1bGxSZXF1ZXN0MTU2MDcwOTU4 | 927 | Pourbaix rest | {
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} | ## Pourbaix Rest and Plotter Refactoring
This PR adds functionality to the MP Rester to retrieve entries and perform the necessary preprocessing of both solids and aqueous species to make entries suitable for constructing a pourbaix diagram. The plotter/analyzer have also been modified for easier plotting of stabil... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/928 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/928/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/928/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/928/events | https://github.com/materialsproject/pymatgen/pull/928 | 279,270,562 | MDExOlB1bGxSZXF1ZXN0MTU2Mzg3NzI1 | 928 | Crystal Orbital Hamilton Populations (COHPs) | {
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"Thanks! There seems to be some failing tests (you just need to check the Travis-CI one). It is related to the plotter tests, and seems probably like some form of a numerical or dict sorting issue. Can you fix them pls? Thanks.",
"I found the issues with the code and solved them. The AppVeyor test failures are no... | 2017-12-05T07:15:37 | 2017-12-06T03:53:33 | 2017-12-06T03:47:13Z | NONE | {
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} | ## Summary
This pull request introduces a new module for Crystal Orbital Hamilton Populations (COHPs). It can also be applied to Crystal Orbital Overlap Populations (COOPs). The objects are roughly modeled after DOS objects in order to be more intuitive for pymatgen users. It also creates modules to read the output ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/929 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/929/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/929/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/929/events | https://github.com/materialsproject/pymatgen/pull/929 | 279,454,795 | MDExOlB1bGxSZXF1ZXN0MTU2NTIwNDk2 | 929 | Overall charge for structures | {
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} | ## Summary
Added the ability for a structure to have an overall charge. This will default to the behavior in SiteCollection when overall charge is not specified: the structure's charge is the sum of the oxidation state of its sites.
- IStructure and Structure contain an overall charge
- The generator functions ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/930 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/930/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/930/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/930/events | https://github.com/materialsproject/pymatgen/pull/930 | 279,661,821 | MDExOlB1bGxSZXF1ZXN0MTU2NjY0Nzgy | 930 | Bug fix for DiffusionAnalyzer with NPT runs | {
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"THanks."
] | 2017-12-06T08:09:35 | 2017-12-06T21:47:33 | 2017-12-06T17:55:07Z | CONTRIBUTOR | {
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} | The `DiffusionAnalyzer` `from_structures()` method calculates cartesian displacements using
c_disp = [np.dot(d, m) for d, m in zip(f_disp, l)]
`f_disp` has dimensions `[site, time step, axis]`.
`l` has dimensions `[time step, axis, axis]`
This means the lattice used for calculating the cartesian displacem... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/931 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/931/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/931/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/931/events | https://github.com/materialsproject/pymatgen/pull/931 | 279,875,623 | MDExOlB1bGxSZXF1ZXN0MTU2ODE3MTY0 | 931 | do not read_velocities for Poscar input to Structure.from_file | {
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} | ## Summary
When trying to load a Structure from a Poscar file format, there is no need to read_velocities. However, if the Poscar file has an incomplete velocities list then the from_file method previously broke. This has caused issues for users within the PyCDT package for point defects in non-metals - which inspir... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/932 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/932/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/932/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/932/events | https://github.com/materialsproject/pymatgen/pull/932 | 279,890,972 | MDExOlB1bGxSZXF1ZXN0MTU2ODI4NDIz | 932 | Add MPRester method to get interface reaction kinks | {
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} | ## Summary
Get critical reactions ("kinks" in the mixing ratio where reaction products change) between two reactants. See the `pymatgen.analysis.interface_reactions` module for more info. Useful to generate pseudo-binary phase diagrams of two reactants. Also allows elemental reservoir open to system with _relative_ ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/933 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/933/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/933/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/933/events | https://github.com/materialsproject/pymatgen/pull/933 | 279,943,213 | MDExOlB1bGxSZXF1ZXN0MTU2ODY2MTEx | 933 | Remove pyhull | {
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} | ## Remove pyhull dependency in PourbaixAnalyzer
Replaces pyhull halfspace usage with scipy.spatial.HalfspaceIntersection usage in pourbaix analysis module. Also adds a few more unittests to the plotter and fleshes out the docstring in PourbaixAnalyzer.
Addresses #283. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/934 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/934/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/934/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/934/events | https://github.com/materialsproject/pymatgen/pull/934 | 279,956,243 | MDExOlB1bGxSZXF1ZXN0MTU2ODc1NjA3 | 934 | Fixed bcc OP normalization issue | {
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"This contains many past commits. Pls merge properly with pymatgen origin first and submit a new PR. Thanks."
] | 2017-12-07T00:27:47 | 2017-12-07T01:24:32 | 2017-12-07T01:24:32Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/935 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/935/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/935/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/935/events | https://github.com/materialsproject/pymatgen/pull/935 | 280,579,867 | MDExOlB1bGxSZXF1ZXN0MTU3MzA3MTY4 | 935 | Add relax input set using SCAN | {
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} | ## Summary
Relax input set using SCAN and unittests have been added.
* Add `MVLScanRelaxSet`
* Enable van-der-Waals functional rVV10
* unittests
* minor reformatting | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/936 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/936/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/936/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/936/events | https://github.com/materialsproject/pymatgen/pull/936 | 280,597,102 | MDExOlB1bGxSZXF1ZXN0MTU3MzE5Njkw | 936 | Moved OP class | {
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"@shyuep, the build errors are not due to my changes. Any chance to merge?"
] | 2017-12-08T19:46:08 | 2017-12-08T21:52:01 | 2017-12-08T21:52:00Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/937 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/937/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/937/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/937/events | https://github.com/materialsproject/pymatgen/pull/937 | 280,651,304 | MDExOlB1bGxSZXF1ZXN0MTU3MzU4MjI4 | 937 | Added non-Zeo++ dependent Voronoi interstitial finder. | {
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"There seems to be failing tests which are related to this PR.",
"I will close this pull request and issue a new one once I'm done."
] | 2017-12-08T23:53:49 | 2018-01-03T00:17:27 | 2018-01-03T00:17:27Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/938 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/938/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/938/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/938/events | https://github.com/materialsproject/pymatgen/pull/938 | 280,654,905 | MDExOlB1bGxSZXF1ZXN0MTU3MzYwNjYw | 938 | SCAN input set | {
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"Erm, what's the difference with the MVLSCANSet?",
"What MVLSCANSet? I don't see it.",
"NVM. found it. That works too!",
"Quick question. I'm not a big fan of the ISYM, EDIFFG, nor NELM parameters. I'm running SCAN for MP using ISYM on, EDIFFG ~ -0.05, and NELEM at default of 100 with decent success. Can i ju... | 2017-12-09T00:18:16 | 2017-12-09T00:49:02 | 2017-12-09T00:24:20Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/939 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/939/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/939/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/939/events | https://github.com/materialsproject/pymatgen/pull/939 | 280,659,855 | MDExOlB1bGxSZXF1ZXN0MTU3MzYzODc1 | 939 | Updates to MVLScanSet | {
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- compromised on NELM
- ensure LDAU is False | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/940 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/940/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/940/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/940/events | https://github.com/materialsproject/pymatgen/issues/940 | 281,558,735 | MDU6SXNzdWUyODE1NTg3MzU= | 940 | density-density and velocity-velocity dielectric functions in VASP 5.4.4 | {
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"YEs, these should be stored in the Vasprun object.",
"Proposed solution:\r\n\r\nIn `Vasprun._parse()` first initialise `self.dielectric=None`.\r\n\r\nThe dielectric function parser can then become:\r\n```\r\nelif tag == \"dielectricfunction\":\r\n if (\"comment\" not in elem.attrib) or \\\r\n elem.attr... | 2017-12-12T22:23:49 | 2017-12-16T17:54:43 | 2017-12-16T17:54:43Z | CONTRIBUTOR | {
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} | VASP 5.4.4 calculates the frequency dependent dielectric response in two ways, using a "density-density" response function, and using a "velocity-velocity" response function (see the comments in `linear_optics.F`. The latter is marked in `OUTCAR` as `current-current (2nd set in vasprun.xml)`, but is not labelled in `va... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/941 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/941/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/941/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/941/events | https://github.com/materialsproject/pymatgen/pull/941 | 281,609,440 | MDExOlB1bGxSZXF1ZXN0MTU3OTkyNjg5 | 941 | Pourbaix binary fix | {
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} | ## Fixes a few issues with binary/ternary pourbaix diagrams and makes plotting a bit more robust.
* Binary/ternary pourbaix diagrams fix a default composition of equivalent parts of each non-OH element.
* Cases where multiple binary solid-ion phases exist are handled more robustly
* Example notebook is updated w... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/942 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/942/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/942/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/942/events | https://github.com/materialsproject/pymatgen/issues/942 | 281,814,002 | MDU6SXNzdWUyODE4MTQwMDI= | 942 | Infinite recursion in DummySpecie::__getattr_ when applying interstitial transformation leading to unpredictable behaviour. | {
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"Thanks for the detailed bug report. Since `DummySpecie` doesn't have `._el` defined, I can't see why the try:\r\n\r\n```\r\n try:\r\n return getattr(self._el, a)\r\n```\r\n\r\nshould even be there, because it seems like this would never return anything useful for `DummySpecie`. I'll try removing ... | 2017-12-13T16:33:00 | 2017-12-13T21:49:40 | 2017-12-13T21:42:24Z | NONE | {
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## System
* Pymatgen version: 2017.12.8
* Python version: 2.7.
* OS version: Ubuntu 15.04LTS
## Summary
- Pymatgen returns an error when trying to apply interstitial transformation with some structure. Issue has been tracked down to the DummeSpecie::getattr function which has an undefined behaviour in this... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/943 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/943/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/943/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/943/events | https://github.com/materialsproject/pymatgen/issues/943 | 281,876,045 | MDU6SXNzdWUyODE4NzYwNDU= | 943 | Gamma-point grid even when structure is not hexagonal | {
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"Never mind (sort of). On the [Pymatgen](http://pymatgen.org/pymatgen.io.vasp.inputs.html) webpage, I now see that `automatic_density` uses a gamma-centered grid for hexagonal cells *and* for odd meshes. The mesh is 2x1x1, so I suppose that's odd then. I was looking at [the source code](http://pymatgen.org/_modules... | 2017-12-13T19:56:46 | 2017-12-13T21:48:38 | 2017-12-13T21:37:28Z | MEMBER | {
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} | ## System
* Pymatgen version: 2017.10.16
* Python version: 3.6.3 (and 2.x)
* OS version: Windows 10 and Linux
## Summary
When using the vasp Kpoints generator, I am getting a gamma-centered grid even when the unit cell is not hexagonal.
## Example code
```python
from pymatgen.io.vasp.inputs import K... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/944 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/944/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/944/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/944/events | https://github.com/materialsproject/pymatgen/pull/944 | 281,945,317 | MDExOlB1bGxSZXF1ZXN0MTU4MjQyNDA3 | 944 | Orbital-resolved COHPs and small changes to COHP modules | {
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} | ## Summary
This pull request adds orbitals-resolved COHPs to the lobster and cohp modules. Currently, only LOBSTER outputs orbital-resolved COHPs that can be read in a convenient way.
* I changed the io.lobster and electronic_structure.cohp modules to handle orbital-resolved COHPs with a separate attribute. I add... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/945 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/945/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/945/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/945/events | https://github.com/materialsproject/pymatgen/issues/945 | 281,973,627 | MDU6SXNzdWUyODE5NzM2Mjc= | 945 | PDPlotter.plot_element_profile | {
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"Done with the implementation as a method in PDPlotter. The result of testing case (Na3PS4 under different Na chemical potential) is shown below (selected profile step products are annotated in the plot):\r\n\r\nindex= 0, -Δμ=-0.0000(eV), 2 Na3PS4 + 16 Na -> 2 Na3P + 8 Na2S\r\nindex= 1, -Δμ=0.2945(eV), 2 Na3PS4 + 1... | 2017-12-14T03:52:01 | 2017-12-16T17:54:27 | 2017-12-16T17:54:27Z | MEMBER | {
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@Zhuoying to implement | {
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"I would suggest we be explicit and we keep all dielectric data in self.dielectric_data[\"density\"] and self.dielectric_data[\"velocity\"]. And then map self.dielectric to self.dielectric_data[\"density\"].",
"That makes sense. What should be the behaviour for older VASP versions? Read directly into `self.dielec... | 2017-12-14T11:21:55 | 2021-05-12T18:31:09 | 2017-12-14T23:32:07Z | CONTRIBUTOR | {
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} | Addresses issue https://github.com/materialsproject/pymatgen/issues/940.
VASP 5.4.4 calculates the frequency dependent dielectric response in two ways, using a "density-density" response function, and using a "velocity-velocity" response function (see the comments in `linear_optics.F` in the vasp source code). The l... | {
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Adds string handling support for py2k in electronic_structure.cohp using the six library. | {
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"Write a proper PR summary.",
"@shyuep Done with the summary editing",
"@Zhuoying This is not good enough. Why do you make people supply an evolution instead of the same parameters as pd.get_element_profile and just call that method to get the evolution? How does anyone know what \"evolution\" means? Why are th... | 2017-12-14T23:40:50 | 2017-12-15T15:27:07 | 2017-12-14T23:51:39Z | CONTRIBUTOR | {
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* Add a method in PDPlotter to draw plot using data from Phasediagram.get_element_profile
* Unittest added
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} | The surface_analysis.py as of now is limited to the number of parameters (chemical potentials) that can be used as a free variable, primarily because the equation it uses is not generalized and because current plots implemented are for single variables. The surface_analysis.py code can be rewritten to incorporate the g... | {
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"Ok. But I don't think you need to artificially add a vacuum to reduce the unit cell. That would work, but it is an inelegant approach. \r\n\r\nAll you need to do is to modify the get_primitive of the structure method to provide an option to only search in certain directions and disallow modification of the c direc... | 2017-12-14T23:57:44 | 2018-01-11T04:42:55 | 2018-01-11T04:42:55Z | CONTRIBUTOR | {
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} | To ensure that the surface energy does not diverge wrt slab size for some systems, we need to calculate an oriented unit cell with a kpoint grid consistent with the slab to sample the Brillouin zone of the slab. So both the OUC and slab have to be calculated.
Right now when generating an OUC and reduced slab, the l... | {
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"@zbwang to implement.",
"I have code that does this, using `Vasprun.dielectric`. I’d be happy to contribute it. What would be the preferred way to access this? A `Vasprun.optical_absorption` property? Or some kind of `Optics` analysis class?",
"Hi bjmorgan, thanks for your contribution. This is a topic I come ... | 2017-12-15T00:25:08 | 2017-12-15T21:40:37 | 2017-12-15T21:40:37Z | CONTRIBUTOR | {
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} | The optical absorption coefficient can be calculated from dielectric tensors. The dielectric tensors have been well processed with pymatgen. It will be more user-friendly if pymatgen could directly produce this optical property.
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"OK. Mahdi to implement.",
"Not planned."
] | 2017-12-15T00:40:07 | 2023-08-08T21:21:13 | 2023-08-08T21:21:04Z | CONTRIBUTOR | {
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"OK go ahead and implement."
] | 2017-12-15T01:03:15 | 2017-12-16T12:32:08 | 2017-12-16T12:32:08Z | CONTRIBUTOR | {
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} | Currently, the LDos class of pymatgen.io.feff.outputs only supports generating Dos object from real-space calculated output files. Modification of the LDos class methods and allows the generation of Dos object from Reciprocal space calculated FEFF output files will be useful. | {
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} | ## Summary
Minor updates to lammps.data
* Added an option to have additional elements (defined in force field but not present in a structure).
* Fix box bounds issue in structure property.
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} | This PR is to fix #951. Also, fix a bug in Vasprun when it parses vasprun.xml files of GW/BSE calc, where the structure is not available. | {
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} | ## Summary
* Change input parameters as the same with pd.get_element_profile
* Add show_label option to annotate reaction products in profile steps as users want
* Modify unittest.
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"And finally, why no unittests at all for these? You are in my group long enough to know what needs to be done.",
"@w6ye It should not take this long to write a few tests and push them.",
"1. From VASP default is usually the experimental magnetic moment multiplied by 1.2 or 1.5. I followed it by multiplying the... | 2017-12-16T07:00:09 | 2017-12-29T13:26:01 | 2017-12-29T13:26:01Z | CONTRIBUTOR | {
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## Summary
* Feature 1 Update MAGMOM setting for Ln3+ ions, the values are calculated as
number of ground state unpaired electrons of Ln3+ * 1.5
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Enable creation of LDos using FEFF reciprocal calculation files and fixes #953 . Unittest has been implemented accordingly. | {
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"This is clearly an issue with your `scipy` installation\r\n",
"Thanks for the quick reply.\nI am aware of that. I reinstalled it, but still couldn’t fix it.\nUninstall:\npip uninstall scipy\nInstall:\npip install scipy\n\nShould I try some other ways to reinstall scipy?\n\n> On Dec 16, 2017, at 12:57 PM, Shyue P... | 2017-12-16T20:55:19 | 2023-05-27T19:46:42 | 2023-05-27T19:46:38Z | NONE | {
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} | I have been trying to run pymatgen in Python 3 but always getting an odd ImportError. I also installed pymatgen in Python 2, but that one is fine. I have tried:
1. pip install pymatgen
2. git clone pymatgen and pip install .
3. reinstall scipy
But none of the above fix the error. Any idea why it happens?
Thanks
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} | ## Summary
This pull request resolves issue #921 and #949 .
The surface_analysis.py code has been drastically modified. A class for analyzing nanoscale stability of particles among different polymorphs has also been added. It now contains two primary classes, the
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} | ## Summary
* Fix minor bugs and py3k portability issues in io.abinit modules
* Add `mpi_runner_options` and `shell_runnner_options` to qadapter
* NscfTasks now use the same FFT mesh (ngfft) as the one employed by the ScfTask
* Remove deprecated code
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"This was a bug introduced when we switched Element to a Enum type. Basically, \"name\" is a reserved attribute for Enums. \r\n\r\nSince no one else seems to be missing this feature, I have renamed Element.name to Element.long_name and added a unittest to make sure it does not disappear again.",
"@shyuep thanks."... | 2017-12-19T09:04:34 | 2017-12-20T07:28:46 | 2017-12-19T20:13:50Z | CONTRIBUTOR | {
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} | When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
* Pymatgen version: 2017.12.16
* Python version: python 3.6.3 (anaconda)
* OS version: macOS 10.13.2
## Summary
Element.name returns the symbol but not t... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/964 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/964/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/964/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/964/events | https://github.com/materialsproject/pymatgen/issues/964 | 283,422,419 | MDU6SXNzdWUyODM0MjI0MTk= | 964 | Regression in pourbaix analyzer - pourbaix_domain_vertices | {
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} | In removing pyhull dependency via 5445e6de90090424da9c6e906e203272eeffe291, the `pourbaix_domain_vertices` instance attribute of `PourbaixAnalyzer` was removed. This attribute is used by the `PourbaixPlotter.domain_vertices` method and thus for plot serialization.
## System
* Pymatgen version: "master"
* Python ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/965 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/965/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/965/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/965/events | https://github.com/materialsproject/pymatgen/pull/965 | 283,484,618 | MDExOlB1bGxSZXF1ZXN0MTU5MzU2OTc3 | 965 | Surf substitution | {
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} | ## Summary
Fixed tests for surface_analysis and added generate_substitution_structures() option to AdsorbateSiteFinder.
* Fixed test_surface_analysis.py, the chemical potential used in the test led to surface energy values that were too small. Had to change to a chemical potential that would result in a larger su... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/966 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/966/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/966/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/966/events | https://github.com/materialsproject/pymatgen/issues/966 | 283,622,919 | MDU6SXNzdWUyODM2MjI5MTk= | 966 | error:"No module named 'pymatgen.io.vaspio'" | {
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"You are using an ancient pymatgen. pymatgen.io.vaspio has been deprecated for quite a long time and now renamed as pymatgen.io.vasp. Pls update your pymatgen to the latest and then try\r\n```from pymatgen.io.vasp.outputs import Vasprun```"
] | 2017-12-20T16:35:29 | 2023-05-29T15:45:07 | 2023-05-29T15:45:07Z | NONE | {
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} | When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
pymatgen: 2017.12.16-py36_0
python 3
* OS version: 10.13.2
## Summary
Cannot load vaspio:
## Example code
```python
from pymatgen.io.vaspio.... | {
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"The tutorials you are referring to use an ancient pymatgen. This functionality has actually been implemented into pymatgen by Dr Anubhav Jain. Pls take a look at the class BSDOSPlotter in pymatgen.electronic_structure.plotter module.\r\n```from pymatgen.electronic_structure.plotter import BSDOSPlotter```",
"if I... | 2017-12-20T18:54:09 | 2023-05-29T18:48:03 | 2023-05-29T18:48:03Z | NONE | {
"total": 0,
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} | When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
* Pymatgen version:pymatgen: 2017.12.16-py36_0
* Python version: python3.6
* OS version: 10.13.2
## Summary
I run the band plot code from https://git... | {
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} | ## Summary
Returns pourbaix_domain_vertices attribute to PourbaixAnalyzer. Addresses #964.
* Adds the pourbaix_domain_vertices attribute back
* provides a more stable sort of the points bounding the pourbaix region to ensure consistency
* Adds test of functionality | {
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} | ## Summary
Transform degree to radian as argument of sine function
1. add a test cif file under test_files/space_group_struct/ directory
2. add a unittest for the fix in test_kpath.py | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/970 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/970/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/970/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/970/events | https://github.com/materialsproject/pymatgen/pull/970 | 284,682,566 | MDExOlB1bGxSZXF1ZXN0MTYwMjE4MjA5 | 970 | Chemenv tests | {
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} | ## Summary
Added tests in chemenv.
Added timing info in chemenv.
Small bug fixes in chemenv. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/971 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/971/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/971/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/971/events | https://github.com/materialsproject/pymatgen/pull/971 | 284,794,755 | MDExOlB1bGxSZXF1ZXN0MTYwMzAxNzg0 | 971 | Ewald site energy | {
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} | ## Summary
Added a function to EwaldSummation that returns the energy of a single site. Adds the values along the columns of the `total_energy` matrix.
## Additional dependencies introduced
None | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/972 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/972/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/972/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/972/events | https://github.com/materialsproject/pymatgen/issues/972 | 284,797,354 | MDU6SXNzdWUyODQ3OTczNTQ= | 972 | Charged Structures and Ewald Summation | {
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"I am not sure how LAMMPS and GULP deals with charged structures. In pymatgen, the implementation using a jellum background to maintain neutrality. One way to check is to comment out the jellum interaction and sees if it leads to the same answer.",
"Are you sure that pymatgen uses a Jellium correction? I don't se... | 2017-12-27T21:15:50 | 2017-12-28T21:43:16 | 2017-12-28T21:43:16Z | CONTRIBUTOR | {
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} | I am unable to reproduce the Ewald summation result from `test_ewald.py`. For the same structure file, I get an energy of -1123 eV using LAMMPS, GULP, and [mint](http://github.com/materials/mint), yet the Ewald summation value listed in the unit test is -1116 eV/atom.
Am I correct in assuming that this difference ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/973 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/973/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/973/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/973/events | https://github.com/materialsproject/pymatgen/pull/973 | 284,829,453 | MDExOlB1bGxSZXF1ZXN0MTYwMzI1Njk2 | 973 | Added charged cell correction to EwaldSummation | {
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"I see that this fails some unit tests. Sorry for not catching it. I'll clean that up soon.",
"Thanks!"
] | 2017-12-28T02:35:27 | 2017-12-28T21:19:54 | 2017-12-28T21:19:46Z | CONTRIBUTOR | {
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} | ## Summary
Added charge cell correction to Ewald summation method. Ewald summation now exactly matches results for Ewald calculations from LAMMPS and GULP.
See discussion in #972
## Additional dependencies introduced
None | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/974 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/974/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/974/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/974/events | https://github.com/materialsproject/pymatgen/pull/974 | 284,950,584 | MDExOlB1bGxSZXF1ZXN0MTYwNDE0NTI0 | 974 | Add charges to Composition based on oxidation state guesses | {
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"Thanks."
] | 2017-12-28T16:46:21 | 2017-12-28T23:08:40 | 2017-12-28T23:08:35Z | CONTRIBUTOR | {
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} | Added a function that returns a copy of a Composition decorated using oxidation states determined from `oxi_state_guesses`. Also refactored the `oxi_state_guesses` to move the computation of likely oxidation states to a private utility function so that the guessing logic could return both the average oxidation states f... | {
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"Would it also be possible to squash-merge so that my old commits don't keep appearing? Thanks!",
"Thanks. I actually do squash and merge. But you need to merge latest changes from origin before submitting a PR in order for the old commits not to appear.\r\n\r\nAs for Zmatrix, I agree. I suggest you start a core.... | 2017-12-30T20:21:21 | 2017-12-31T05:36:20 | 2017-12-31T05:36:20Z | NONE | {
"total": 0,
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} | ## Summary
The current Gaussian module cannot handle multi-parameter keywords and multi-line route cards in input and output files (see the l-cysteine test files for examples). This pull request fixes these bugs and has some minor changes.
* Fixed the multi-parameter keyword issue. Multi-parameter keywords such a... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/976 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/976/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/976/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/976/events | https://github.com/materialsproject/pymatgen/pull/976 | 285,243,476 | MDExOlB1bGxSZXF1ZXN0MTYwNjExNzMz | 976 | Minor COHP clean-up | {
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} | ## Summary
Minor clean-up for COHP-related modules.
* Removed unnecessary imports and variables.
* Replaced type with isinstance methods. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/977 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/977/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/977/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/977/events | https://github.com/materialsproject/pymatgen/pull/977 | 285,362,958 | MDExOlB1bGxSZXF1ZXN0MTYwNjgwMjQ3 | 977 | Wavecar | {
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"Many thanks for your contributions!"
] | 2018-01-02T06:31:26 | 2018-01-02T17:59:48 | 2018-01-02T09:48:58Z | CONTRIBUTOR | {
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} | ## Summary
This pull request adds support for reading WAVECAR output files from VASP. It is essentially a python version of [WaveTrans](https://www.andrew.cmu.edu/user/feenstra/wavetrans/) by Feenstra and Widom with some added functionality.
* adds a Wavecar class to pymatgen.io.vasp.outputs
* 100% test coverage... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/978 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/978/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/978/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/978/events | https://github.com/materialsproject/pymatgen/issues/978 | 285,749,225 | MDU6SXNzdWUyODU3NDkyMjU= | 978 | Cann't find get_environments.py) in the pymatgen/scripts directory | {
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"@davidwaroquiers Pls handle.",
"A tutorial is currently being written. Be patient it should be out in a few weeks.\r\nThe get_environments.py script has been moved to pymatgen/cli",
"The tutorial can now be accessed via http://matgenb.materialsvirtuallab.org/2018/01/01/ChemEnv-How-to-automatically-identify-coo... | 2018-01-03T17:07:30 | 2018-04-24T16:04:09 | 2018-04-24T16:04:09Z | NONE | {
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} | ## System
* Pymatgen version: 2017.9.23
* Python version: 3.5
## Summary
* Cann't find get_environments.py and pymatgen/scripts directory
* Please provide some examples about analyzing chemical environments and coordination geometries | {
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} | ## Summary
Fixed access to materials project for get_environment.
* Excluded the setup of the access to the materials project data base (not necessary)
* removed chemenv_configuration.has_materials_project_access because it is not defined
## TODO
If the API_KEY is not supplied it raises an error. A treatm... | {
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Small bug fix that affects region shading for pourbaix stable domains. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/981 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/981/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/981/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/981/events | https://github.com/materialsproject/pymatgen/pull/981 | 286,122,355 | MDExOlB1bGxSZXF1ZXN0MTYxMjIzOTYz | 981 | modify barrier label for get_plot and change criteria to connect end … | {
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* change criteria to connect end points for combine_neb_plots | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/982 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/982/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/982/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/982/events | https://github.com/materialsproject/pymatgen/pull/982 | 286,177,548 | MDExOlB1bGxSZXF1ZXN0MTYxMjYyNjUz | 982 | Add site finder using Voronoi Tessellation algorithm | {
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"Pls look at the codacy reviews and at least try to fix the red warnings.",
"Red warnings are fixed."
] | 2018-01-05T02:58:35 | 2018-01-05T17:12:27 | 2018-01-05T17:12:27Z | CONTRIBUTOR | {
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} | ## Summary
Add site finder using Voronoi Tessellation algorithm
* Added `TopographyAnalyzer` class
* Added `VoronoiPolyhedron` class and `calculate_vol` method.
* Unittest for LiFePO4 case
* Minor formatting
## TODO (if any)
None | {
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Fixed a bug in the FEFFDictSet.from_directory method, allows shell distance matrix comparison between absorbing atoms with different distance matrix shape when determining the absorbing index. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/984 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/984/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/984/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/984/events | https://github.com/materialsproject/pymatgen/pull/984 | 286,431,815 | MDExOlB1bGxSZXF1ZXN0MTYxNDQ3MjY2 | 984 | Bug fix in lammps data | {
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Fix a bug where the molecule-ID column is edited when calling `LammpsData.structure` attribute.
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Applied the same treatment as we did for insertion electrodes. e.g., When the ion oxidation state is 2+, the voltage reduced to half, and the capacity multiplied by 2.
This new pull request is to add additional test for previous pull request #898
* added unittest to /pymatgen/apps/battery/tests/con... | {
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"This PR contains far too many commits. Also, we are cutting Py2.7 support from 2018.",
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In `from_vasprun()`, structures are collected as a generator function, using `get_structures()`. The `from_structures()` method, how... | {
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} | ## Summary
A set of some small, but nonetheless useful commits.
* MPRester now has the conventional_unit_cell option (False by default) for methods of querying entries to return the standard conventional unit cell instead of the primitive unit cell by using SpacegroupAnlayzer. Prior, the user can just get the cif... | {
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"This is fine, but it is not a pymatgen Issue. Also, I need to be convinced of the fact that broken bond extrapolation will lead to reasonable estimates. "
] | 2018-01-11T21:54:53 | 2018-01-11T23:22:50 | 2018-01-11T23:22:50Z | CONTRIBUTOR | {
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With the addition of the surface data into the MAPI, we can use simple broken bond rules to extrapolate a cohesive energy term and use that cohesive energy to predict surface ... | {
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"Hi azheeshan, I think the problem is here:\r\n\r\n```\r\nelastic_mat_sym = (elastic_tensor.fit_to_structure(structure=st)).voigt\r\n```\r\n\r\nwhere the tensor is being fit to the primitive cell, rather than the conventional cell. The cartesian basis vectors aren't the same for these two crystal settings, and the... | 2018-01-12T05:09:00 | 2018-01-29T18:16:41 | 2018-01-12T07:20:46Z | NONE | {
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} | ## System
* Pymatgen version: 2017.12.30
* Python version: 3.6
* OS version: OS X 10.11.6
## Summary
* The fit_to_structure() function inside [tensors.py](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/elasticity/tensors.py) is supposed to return a tensor that is invariant with r... | {
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} | VASP 5.4.4 introduced calculation of the dielectric constant based on the current-current response.
When using small values of the `CSHIFT` parameter (necessary to produce optical spectra with no broadening), this can result in anomalously large values of the current-current response, which VASP writes to the vaspru... | {
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"There are failing tests due to tabs. Pls fix. Thanks.",
"Ok, this has been fixed.\r\n\r\nApologies for the messy commit history."
] | 2018-01-12T17:53:04 | 2018-01-15T13:42:22 | 2018-01-15T13:42:22Z | MEMBER | {
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} | Use numpy concatenate function to fix the `pymatgen.electronic_structure.bandstructure.get_reconstructed_band_structure()` function.
Fixes #543
I've also added a basic test to ensure this method is not broken in the future. | {
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"Pls submit a PR that does not include past commits. it is impossible to know what is happening with this PR."
] | 2018-01-14T00:27:58 | 2018-01-14T00:48:33 | 2018-01-14T00:48:33Z | CONTRIBUTOR | {
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followed by a force-push to get rid of the old commits. | {
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} | ## Summary
* Extract thermodynamic properties from the integration on a phonon DOS
* Plotter of the thermodynamic properties
* option to change units in phonon BS and DOS plotters
* tests
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"Pybtex is an optional req. I would prefer to keep it that way given that it is not very Py3 friendly.",
"Ok, have updated the import accordingly."
] | 2018-01-17T20:58:53 | 2018-01-18T16:58:16 | 2018-01-18T16:58:16Z | MEMBER | {
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Now uses pybtex, more robust. Updated test.
## Additional dependencies introduced (if any)
None (pybtex already requirement).
## TODO (if any)
None | {
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A few lines were missing in the previous one. Sorry for the bothering. | {
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"There is no way to plot a phase diagram in more than 4 terminals in 3D space."
] | 2018-01-18T11:13:00 | 2018-01-18T13:22:41 | 2018-01-18T13:22:41Z | NONE | {
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I would like to plot the phase diagram of a metal composition with more than 4 elements but now it's possible just for 1-4 elements. It says: `ValueError: Only 1-4 components supported!`
Would you please guide me if there is any possibility to solve the problem? | {
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