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https://api.github.com/repos/materialsproject/pymatgen/issues/1001 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1001/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1001/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1001/events | https://github.com/materialsproject/pymatgen/pull/1001 | 289,611,996 | MDExOlB1bGxSZXF1ZXN0MTYzNjk5MjI5 | 1,001 | fixes in the get_environment script | {
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} | Fixed the access to the materials project in a more thorough way and adapted the test accordingly. Moreover, a small bug in the reading in of the chemenv strategy was fixed.
I introduced an additional dependency on SETTINGS in chemenv_strategies.py and its test test_chemenv_config.py. | {
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"Don't think there is right now. By all means implement it in the Slab class. ",
"A function to go from three PeriodicSites to output a (h,k,l) tuple would be nice to have too.",
"@mkhorton Just to clarify, do you mean something that would generate a plane with any 3 PeriodicSites and then return the hkl of th... | 2018-01-19T08:50:16 | 2018-02-06T03:33:54 | 2018-02-06T03:33:54Z | CONTRIBUTOR | {
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} | Is there a stand alone function that returns d_hkl given a structure and a Miller index? I know the class XRDPattern() has something that gets d_hkl, but I don't that can be used outside the class right? This would be useful for things like if we wanted a standard nlayer of atoms of slab thickness or gb thickness thats... | {
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"No objections. Are you volunteering to do the rewrite?",
"Nope. Should probably be some of the thermoelectrics people since they will be using the new code anyways and will need the secondary analysis currently implemented in our boltztrap module. \r\n\r\nI'm relying on your authority to assign them this task :)... | 2018-01-19T18:25:58 | 2018-12-17T16:20:20 | 2018-12-17T16:20:19Z | NONE | {
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} | ## Summary
It looks like Madsen group has released a new major version upgrade of BoltzTrap that is written in python/cython/C++ : https://arxiv.org/abs/1712.07946
The current BoltzTrap module is very hairy. It would be good to get it rewritten to wrap the new BoltzTrap2 module and in the process improve the code q... | {
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} | ## Summary
Add termsymbol related properties to Element class
Specifically, these three are the added properties
* Add valence property:
Find the total number of valence electrons from full_electron_configuration of the Element
Do not work for those with two unfilled subshells
* Add term_symbols property:
A... | {
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"Pls fix the Code Quality Review issues. These are valid concerns.",
"Thanks."
] | 2018-01-22T13:49:43 | 2018-01-22T17:38:54 | 2018-01-22T17:38:45Z | MEMBER | {
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} | ## Summary
For now, I excluded two strategies to interpret the structure environments from the get_environment script because they are not fully implemented and cause errors if they are chosen by the user. Moreover, I included some error handling for reading in the sites to visualize the coordination environment as ... | {
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} | ## Summary
Modified interface_reaction.py and add a Jupyter notebook as the tutorial of this interface_reactions module.
* Add the option to use convex hull energy for reactants for reaction energy calculation.
* For reactants with no matching entry, always use the convex hull energy as reactant energy.
* Add a... | {
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"Can you do a rebase before sending a PR? This contains commits from Aug.",
"Also, the tests failed.",
"I did rebase. It's this weird github behavior that the entire PR history would pop up again. We had this discussion before (in December) I think.\r\n\r\nI know that the tests failed. I'm working on that. It... | 2018-01-25T17:13:57 | 2018-01-29T17:49:54 | 2018-01-26T18:44:18Z | CONTRIBUTOR | {
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"Py2 tests fail because TimeoutError is apparently new to Py3, but given the new Py2 deprecation policy I'll leave this as-is unless asked otherwise.",
"That's fine. We are not going to care about py2."
] | 2018-01-25T19:26:23 | 2018-01-25T21:46:51 | 2018-01-25T21:46:51Z | MEMBER | {
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Adds a timeout kwarg to enumlib to automatically terminate if no enumerations are found within a specified length of time.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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"I would say this is not of the highest priority unless you have a clear idea of the generalization approach."
] | 2018-01-25T20:35:56 | 2018-01-25T23:09:36 | 2018-01-25T23:09:36Z | CONTRIBUTOR | {
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} | The microfacet/step notation for Miller indices is a convention used to define the step and terraces of higher Miller index surfaces based on low Miller index surfaces. E.g. the (331) facet of an fcc crystal can be defined by the (111) facet.
For fcc system, an exmaple would be:
(hkl) = (n+1, n+1, n-1)
Microfacet n... | {
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Specifically, these three are the added properties
Add valence property:
Find the total number of valence electrons from full_electron_configuration of the Element
Do not work for those with two unfilled subshells
Add term_symbols property:
All possible Russell... | {
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Specifically, these three are the added properties
Add valence property:
Find the total number of valence electrons from full_electron_configuration of the Element
Do not work for those with two unfilled subshells for now
Add term_symbols property:
All possib... | {
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I moved the import to inside the plot function, this way the import problem only shows if plotting is required.
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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... | {
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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... | {
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Short few sentences, and summary of the major changes in bullet
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* Feature 1
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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... | {
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} | This pull request will add a new class method to the Lattice class, d_hkl which takes in a Miler index and returns the distance of the hkl plane from the origin.
Using the new d_hkl method, there is now an optional parameter in SlabGenerator called in_unit_planes=False, which if set to True, will measure the min_va... | {
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} | ## Summary
VIRENN adds oxidation states to the input structure, causing a subtle bug in .get_periodic_image which was referencing the input structure instead of the oxi-state decorated structure.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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} | Change initialization of coordination number dictionary keys to species rather than elements to match with species_string use later on. This avoids a key error when dealing with ions like 'Ba2+'
## Summary
Short few sentences, and summary of the major changes in bullet
points
* Feature 1
* Feature 2
* Fix ... | {
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} | ## Summary
Fix bug in _get_grand_potential method.
* Fix the bug in get_grand_potential method, occurred when setting use_hull_energy=True for InterfacialReactivity class. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1025 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1025/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1025/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1025/events | https://github.com/materialsproject/pymatgen/issues/1025 | 293,399,206 | MDU6SXNzdWUyOTMzOTkyMDY= | 1,025 | miller_index.py in util folder | {
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"No. Miller indices are not a util package thing. It is specific to planes in crystals. Leave it in surface.py.",
"OK"
] | 2018-02-01T04:22:09 | 2018-02-01T05:43:15 | 2018-02-01T04:56:27Z | CONTRIBUTOR | {
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} | For organization, I would suggest a python module in the utils folder for containing functions and classes related to Miller indices. Functions such as get_symmetrically_distinct_miller_indices in the surface.py module can be moved here along with other related functions such as a function to get_symmerically_equivalen... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1026 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1026/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1026/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1026/events | https://github.com/materialsproject/pymatgen/issues/1026 | 293,671,814 | MDU6SXNzdWUyOTM2NzE4MTQ= | 1,026 | Structure objects changed during serialization/deserialization | {
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} | ## System
* Pymatgen version: 2018.1.29
* Python version: 3.6.2
## Summary
* Structure and IStructure objects' compositions and sites are corrupted during pickle serialization
* Only occurs when sites have oxidation numbers
## Example code
```python
cscl = Structure(
Lattice([[4.209, 0, 0], [0, 4... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1027 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1027/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1027/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1027/events | https://github.com/materialsproject/pymatgen/pull/1027 | 293,713,135 | MDExOlB1bGxSZXF1ZXN0MTY2Njc0NTM4 | 1,027 | Function to get Miller index from three sites | {
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"Thanks for adding `miller_index_from_sites`, will be useful!"
] | 2018-02-01T22:53:23 | 2018-02-06T05:08:01 | 2018-02-05T20:58:50Z | CONTRIBUTOR | {
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} | New function in surface.py called miller_index_from_sites() that takes in the supercell_matrix and three Cartesian coordinates to return a Miller index associated with the plane formed by the three points (credits to @wenhaosun ). This concludes issue #1002
* Minor fixes to surface_analysis.py
* Added unittesting f... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1028 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1028/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1028/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1028/events | https://github.com/materialsproject/pymatgen/pull/1028 | 293,713,376 | MDExOlB1bGxSZXF1ZXN0MTY2Njc0NzI2 | 1,028 | Removed bug in _get_image function of NearNeighbor class. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1029 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1029/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1029/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1029/events | https://github.com/materialsproject/pymatgen/pull/1029 | 294,003,111 | MDExOlB1bGxSZXF1ZXN0MTY2ODg4NTU4 | 1,029 | Add htmilify, unicodify to string utils for formula formatting + tests | {
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} | ## Summary
Add htmilify, unicodify to string utils for formula formatting + tests
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1030 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1030/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1030/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1030/events | https://github.com/materialsproject/pymatgen/issues/1030 | 294,092,105 | MDU6SXNzdWUyOTQwOTIxMDU= | 1,030 | Madelung constant calculator | {
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"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 2018-02-03T07:38:13 | 2023-08-08T21:21:44 | 2023-08-08T21:21:43Z | CONTRIBUTOR | {
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} | A function to calculate the Madelung constant of a ionic crystal. It measures the electrostatic potential of an ion in a crystal. Takes in a structure (only works if structure is decorated with oxidation states?) as the input along with a convergence tolerance. | {
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"@dwinston Pls fix in the Database?",
"FYI @mfkoerner, you have your private API key in the example code. There's also a `reciprocal_lattice` method on `Lattice`, so `structure.lattice.reciprocal_lattice` should give the reciprocal lattice directly -- this seems to agree with your `reciprocal()` function, but men... | 2018-02-03T21:45:42 | 2023-05-29T18:50:20 | 2023-05-29T18:50:20Z | NONE | {
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} | ## System
* Pymatgen version: 4.6.2
* Python version: 3.5.3
* OS version: MacOS Sierra 10.12.6
## Summary
When using MPRester('API_key').get_bandstructure_by_material_id('mpid') to get BandStructureSymmLine objects from the database, many of them (~50%) have incorrect reciprocal lattices.
Of those incorrect, ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1032 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1032/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1032/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1032/events | https://github.com/materialsproject/pymatgen/pull/1032 | 294,539,545 | MDExOlB1bGxSZXF1ZXN0MTY3MjUyNDk5 | 1,032 | Minor fix in lammps.output | {
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"Since you fixed the bug, then write a unittest for it so that it will not happen again.",
"Only a few simple logic tests were added. Honestly it is the developer's responsibility to write his/her own unit test.",
"@adengz This is not the right attitude. Of course it is the developer's responsibility to write t... | 2018-02-05T20:57:09 | 2018-02-06T00:49:49 | 2018-02-06T00:48:42Z | CONTRIBUTOR | {
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Fix `unique_atomic_masses` in two methods.
## Additional dependencies introduced (if any)
None
## TODO (if any)
This bug was reported in a user post in pmg google group. It was caused by rewriting `lammps.data`, but I would not take the blame because it would have been found if there were unit... | {
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"Hi @gmatteo , saw your COD commit -- not sure if you're interested but I compiled a mapping of mp-ids to COD IDs recently. Drop me an email if this is of interest, I think this will be added to MP alongside ICSD IDs in due course."
] | 2018-02-08T20:02:07 | 2018-02-09T05:30:45 | 2018-02-08T21:24:15Z | CONTRIBUTOR | {
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* Optimization of the chemenv code
* Faster presets for chemenv | {
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} | ## Summary
Nothing major here.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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"Failing tests. Pls fix.\r\n"
] | 2018-02-12T18:27:04 | 2018-02-12T23:07:48 | 2018-02-12T23:07:48Z | NONE | {
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} | ## Summary
Developing a new Q-Chem IO module to replace the old one with something that is easier to update/maintain. This is a basic module that others can add onto.
- Basic functionality has been implemented using regex/read_pattern/read_table_pattern
- Current parsing routines are robust with respect to most o... | {
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"@shyuep, if the checks pass successfully, can you release the next stable version soon? Would be greatly appreciated because I'm currently changing/completing matminer site-fingerprint classes that depend however on the most recent changes to the LocalStructOrderParas classes and associated yaml files."
] | 2018-02-12T18:27:14 | 2018-02-12T19:33:15 | 2018-02-12T19:33:14Z | CONTRIBUTOR | {
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"Pls remove assert."
] | 2018-02-12T19:12:27 | 2018-02-15T14:41:44 | 2018-02-15T14:41:44Z | CONTRIBUTOR | {
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} | ## Summary
* NscfTask can now be initialized from external DEN files and executed in parallel with paral_kgb
* Added new methods to produce graphs in the DOT language for flows/works/tasks
(graphviz module is optional) | {
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} | ## 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... | {
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"Go ahead."
] | 2018-02-22T23:14:19 | 2018-03-22T21:32:31 | 2018-03-22T21:32:31Z | CONTRIBUTOR | {
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"No one uses the from_dict for Vasprun as far as I know. Under what circumstances would you want to do this?",
"Hi. I came across this problem as well. My use case was for saving very long MD trajectories where vasp is run several times in series. I would feed the Vaspruns into the DiffusionAnalyzer in series to ... | 2018-02-23T04:03:23 | 2019-01-08T01:45:56 | 2018-02-23T04:04:21Z | NONE | {
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} | When trying to create a Vasprun object from Vasprun.from_dict(d), the following error happens:
TypeError: __init__() got an unexpected keyword argument 'vasp_version'
This deserves a fix for users that need Vasprun object to be in a dict format for later uses.
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} | ## Summary
Pull request to make the SurfaceEnergyPlotter slightly easier to use. Also added a WorkfunctionAnalyzer class.
Features:
-WorkfFunctionAnalysis: Not much to analyze for now, just calculates the work function or gives a neat plot of the local potential along c.
-SurfaceEnergyPlotter can now take eith... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1049 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1049/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1049/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1049/events | https://github.com/materialsproject/pymatgen/pull/1049 | 300,057,209 | MDExOlB1bGxSZXF1ZXN0MTcxMjQ4ODc4 | 1,049 | A few small feature additions to magnetic analysis + tests | {
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} | ## Summary
* Adds spin polarization to DOS + test (e.g. see 10.1126/sciadv.1602241)
* Adds magnetic deformation + test (see 10.1021/acs.chemmater.6b04729)
* Adds a Jahn-Teller heuristic + tests, which attempts to classify if a structure may be Jahn-Teller active -- this is going into the magnetic analysis module ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1050 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1050/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1050/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1050/events | https://github.com/materialsproject/pymatgen/pull/1050 | 300,672,219 | MDExOlB1bGxSZXF1ZXN0MTcxNjkzNDgx | 1,050 | Small doc fixes pertaining return types in electronic_structure.plotter | {
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"Many thanks."
] | 2018-02-27T15:19:45 | 2018-02-27T16:34:10 | 2018-02-27T16:33:55Z | CONTRIBUTOR | {
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} | In the online documentation for [pymatgen.electronic_structure.plotter](http://pymatgen.org/pymatgen.electronic_structure.plotter.html), the "**Returns**" and "**Return type**" sections of some methods (cf. below) which return complicated ``dict``s are pretty much unreadable because [Sphinx's napoleon extension](http:/... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1051 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1051/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1051/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1051/events | https://github.com/materialsproject/pymatgen/pull/1051 | 300,694,558 | MDExOlB1bGxSZXF1ZXN0MTcxNzEwMjEx | 1,051 | jupyter notebook example | {
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"Many thanks."
] | 2018-02-27T16:13:20 | 2018-02-27T16:33:42 | 2018-02-27T16:33:32Z | CONTRIBUTOR | {
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} | ## Summary
This is a jupyter notebook example to show how to extract data from a band structure and how to plot a band structure or a DOS with elements projected contributions to the bands or the DOS.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1052 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1052/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1052/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1052/events | https://github.com/materialsproject/pymatgen/pull/1052 | 301,181,780 | MDExOlB1bGxSZXF1ZXN0MTcyMDcxNTA5 | 1,052 | added EconNN algo and unit test | {
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} | ## Summary
Short few sentences, and summary of the major changes in bullet
points
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1053 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1053/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1053/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1053/events | https://github.com/materialsproject/pymatgen/issues/1053 | 301,363,937 | MDU6SXNzdWUzMDEzNjM5Mzc= | 1,053 | In pymatgen, is it possible to partially substitute atoms? | {
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"Github issues should only be used for reporting problems. For help, pls post on the Google groups.\r\n\r\nLook at the examples. For example: http://pymatgen.org/_static/Ordering%20Disordered%20Structures.html "
] | 2018-03-01T11:05:53 | 2018-03-01T12:52:09 | 2018-03-01T12:52:09Z | NONE | {
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} | What I would like to do is the following:
For a given POSCAR file I would like to select some atoms and substitute them partially. I know I can remove them partially with PartialRemoveSitesTransformation module in pymatgen.transformations.site_transformations. You provide a list of positions and a fraction to be remo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1054 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1054/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1054/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1054/events | https://github.com/materialsproject/pymatgen/pull/1054 | 301,509,992 | MDExOlB1bGxSZXF1ZXN0MTcyMzE1ODQ1 | 1,054 | modified version of VoronoiNN | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1055 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1055/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1055/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1055/events | https://github.com/materialsproject/pymatgen/pull/1055 | 301,922,876 | MDExOlB1bGxSZXF1ZXN0MTcyNjE4NDM2 | 1,055 | fix documentation wording. | {
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} | ## Summary
Fix documentation wording for parameter use_hull_energy. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1056 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1056/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1056/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1056/events | https://github.com/materialsproject/pymatgen/pull/1056 | 303,505,263 | MDExOlB1bGxSZXF1ZXN0MTczNzU1MDM1 | 1,056 | Gau | {
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} | ## Summary
Update `GaussianOutput` class
* If nosymm is used, input orientation is read instead of standard orientation
* Read bond orders in the output file if a NBO calculation is done | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1057 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1057/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1057/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1057/events | https://github.com/materialsproject/pymatgen/pull/1057 | 304,232,801 | MDExOlB1bGxSZXF1ZXN0MTc0MjY2ODA1 | 1,057 | An alternative matrix in Lattice.from_parameters | {
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"Thank you very much for the contribution."
] | 2018-03-12T03:46:49 | 2018-03-12T04:55:24 | 2018-03-12T04:55:24Z | CONTRIBUTOR | {
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} | ## Summary
* An alternative Cartesian lattice matrix compatible with VESTA, GULP, and cif2cell.
* Useful for processing Cartesian trajectories of molecular simulations under periodic boundary conditions.
* The alternative matrix is off by default, but can pass most of the unittests.
Unittests are added to ensur... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1058 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1058/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1058/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1058/events | https://github.com/materialsproject/pymatgen/pull/1058 | 304,268,442 | MDExOlB1bGxSZXF1ZXN0MTc0MjkyMjkz | 1,058 | Patch 3 | {
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} | ## Summary
Changed `MITMDSet` and `MVLNPTMDSet` default "PREC" from "Normal" to "Low".
Note that we already set "ENCUT" = 1.5*"ENMAX" in `MVLNPTMDSet`, which address the main concern that not using "PREC" = "Low" for NPT-MD (more details can be found in [VASP-MDALGO](https://cms.mpi.univie.ac.at/wiki/index.php/M... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1059 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1059/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1059/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1059/events | https://github.com/materialsproject/pymatgen/pull/1059 | 304,475,331 | MDExOlB1bGxSZXF1ZXN0MTc0NDQ1ODcx | 1,059 | Removed a n-dash. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1060 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1060/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1060/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1060/events | https://github.com/materialsproject/pymatgen/pull/1060 | 304,575,728 | MDExOlB1bGxSZXF1ZXN0MTc0NTIxMjU0 | 1,060 | Bug fix for phonon | {
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This PR fixes a few minor bugs in the phonon module | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1061 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1061/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1061/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1061/events | https://github.com/materialsproject/pymatgen/pull/1061 | 304,580,061 | MDExOlB1bGxSZXF1ZXN0MTc0NTI0NDYx | 1,061 | Add Node.get_vars_dataframe | {
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"Hi Shyue,\r\n\r\nIs it possible to release a new version of pmg in the forthcoming days?\r\nThere's a school next week and I would like to use the last pmg version that includes\r\nthe bug fix in #1060 and other minor changes merged in this PR.\r\n\r\nThanks\r\n\r\n ",
"Done",
"Thank you"
] | 2018-03-12T23:46:32 | 2018-03-14T00:44:00 | 2018-03-13T04:42:00Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1062 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1062/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1062/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1062/events | https://github.com/materialsproject/pymatgen/pull/1062 | 304,864,211 | MDExOlB1bGxSZXF1ZXN0MTc0NzM1NTAy | 1,062 | Update MagOrderingTransformation error handling | {
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} | ## Summary
Previously transformation would fail if max cell size was set too small, now it will give a warning and increase max cell size instead.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1063 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1063/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1063/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1063/events | https://github.com/materialsproject/pymatgen/issues/1063 | 305,232,545 | MDU6SXNzdWUzMDUyMzI1NDU= | 1,063 | Several issues with EnumlibAdaptor | {
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"1. I don't actually quite understand the situation where the first error will occur. If the ordered sites list is empty, then the disordered symmetry should be equal to the full symmetry. I can put in a break, but I am confused when such an issue would occur.\r\n2. Also not clear why this will occur. The sites are... | 2018-03-14T16:24:54 | 2020-07-11T02:44:01 | 2020-07-11T02:44:01Z | MEMBER | {
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} | ## System
* Pymatgen version: affects several versions, using 2018.3.13
* Python version: 3.6
* OS version: macOS 10.13.3
## Summary
* [This line](https://github.com/materialsproject/pymatgen/blob/f9d984d25b550ff04e534a4a67f18a52799dee68/pymatgen/command_line/enumlib_caller.py#L227) causes a crash in a small... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1064 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1064/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1064/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1064/events | https://github.com/materialsproject/pymatgen/pull/1064 | 305,361,409 | MDExOlB1bGxSZXF1ZXN0MTc1MTA5ODIx | 1,064 | EnumlibAdaptor: fix for trying to pop empty list | {
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} | ## Summary
The `curr_sites` variable needed to be extended by `sites` during each
iteration of the loop. This meant that the wrong spacegroup number was being calculated which is why, in some instances, the target spacegroup number was never reached.
Fixes one issue in #1063
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"The test is terrible. Write a proper test that checks the compounds formed."
] | 2018-03-15T01:24:06 | 2018-03-15T03:54:21 | 2018-03-15T03:54:08Z | NONE | {
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} | * change entry_id to attribute in ReactionDiagram
* add ReactionDiagramTest
* debug PDEntry.to_csv
* add reaction_entries_test.csv | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1066 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1066/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1066/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1066/events | https://github.com/materialsproject/pymatgen/issues/1066 | 305,425,905 | MDU6SXNzdWUzMDU0MjU5MDU= | 1,066 | Qchem needs to be refactored. | {
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"I don't use Qchem, but I'll ask the people that do. This shouldn't be a problem though.",
"@shyuep we (myself, @samblau, @shyamd) can refactor the new qchem io to pymatgen.io.qchem. We didn't do that from the start because of the old qchem.py file (which we are still not ready to completely phase out).",
"FYI,... | 2018-03-15T06:03:13 | 2018-09-09T20:47:45 | 2018-09-09T20:47:45Z | MEMBER | {
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} | pymatgen.io.qchem_io should be refactored to pymatgen.io.qchem to be consistent with all the other io packages.
I do not want to undertake this task because if I do it, it may break code on MP end of things.
@mkhorton @montoyjh ? I know Xiaohui is the original author. I am not sure who took over his duties. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1067 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1067/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1067/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1067/events | https://github.com/materialsproject/pymatgen/pull/1067 | 305,630,855 | MDExOlB1bGxSZXF1ZXN0MTc1MzEwNzMz | 1,067 | EnumlibAdaptor: fix missing site properties | {
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} | ## Summary
As a temporary fix, missing site properties are now set to None when they’re not available, so at least the site property dictionary has the correct keys. This fixes the crashes that were observed in #1063
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* A longer-term ... | {
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} | ## Summary
Smarter magmom rounding, normalization option + tests
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* None | {
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"Hi, yes we are very interested. Pls submit a pull request when you are ready, and thank you in advance for your contributions!",
"Hi @resnant, if it's helpful at all, note we have magnetic symmetry groups in pymatgen, available at pymatgen.symmetry.maggroups",
"Thank you @mkhorton, I'll check it.",
"Hi. The ... | 2018-03-16T08:37:14 | 2018-04-19T04:29:50 | 2018-04-19T04:29:50Z | CONTRIBUTOR | {
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} | Hi, now I research magnetic materials using neutron beam.
I am writing a program to calculate the neutron diffraction pattern based on pymatgen.analysis.diffraction.xrd, for the case of nuclear scattering.
I will prepare the code according to the contribution guidelines, so please consider merge it.
Do you have an i... | {
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} | Instead of just returning a coordination number total (as with get_cn), returns a dictionary of elements and the coordination of the elements to the central site.
Using NaCl as an example --
Na is bonded to 6 Cl atoms. get_cn would return 6.0, whereas get_cn_dict would return {'Na': 0.0, 'Cl': 6.0}. | {
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"You can add this. If you can think of a general enough way to add it to SiteCollection, that would be good. But I think the Site vs PeriodicSite might be tricky.\r\n\r\nThe other thing we may want in future for both Mol and Structure is to be able to replace a functional group (e.g., -CH3) with a functional group ... | 2018-03-20T18:43:12 | 2023-08-08T21:22:23 | 2023-08-08T21:22:23Z | MEMBER | {
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} | ## System
* Pymatgen version: master
## Summary
* Currently, one can only add a functional group to a site for a Molecule object (substitute() method)
* Sometimes, you want to do functional group replacement for molecular crystals (i.e. Structure objects)
* From what I can tell, this is easy to do. The subst... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1073 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1073/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1073/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1073/events | https://github.com/materialsproject/pymatgen/issues/1073 | 307,406,875 | MDU6SXNzdWUzMDc0MDY4NzU= | 1,073 | Documentation misleadingly indicates structure coords can be fractions | {
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"fractional coordinates does not mean Fractions, but rather direct coordinates. Nevertheless, I have pushed a fix."
] | 2018-03-21T20:31:21 | 2018-03-21T20:39:11 | 2018-03-21T20:39:07Z | CONTRIBUTOR | {
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} | ## Summary
The documentation for Structure.from_spacegroup states
> coords (Nx3 array): list of fractional/cartesian coordinates of
> each species.
This sounds like it should be possible to initialise them with a list of fractions from the built-in fractions module.
## Example code
```pyth... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1074 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1074/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1074/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1074/events | https://github.com/materialsproject/pymatgen/pull/1074 | 307,506,829 | MDExOlB1bGxSZXF1ZXN0MTc2Njc1ODgx | 1,074 | Surf analysis | {
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} | ## Summary
A few miscellaneous changes to the surface related codes.
* WorkFunctionAnalyzer now takes a structure, list of locpot along c and fermi energy. There is a from_files method still available to build the analyzer from paths to the COTNCAR, LOCPOT and OUTCAR instead.
* ReconstructionGenerator will appl... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1075 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1075/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1075/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1075/events | https://github.com/materialsproject/pymatgen/pull/1075 | 307,513,467 | MDExOlB1bGxSZXF1ZXN0MTc2NjgwODI4 | 1,075 | Fix incar list_key parse error | {
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"Write a test.",
"Unittests have been added."
] | 2018-03-22T05:42:17 | 2018-03-22T12:58:01 | 2018-03-22T12:58:01Z | CONTRIBUTOR | {
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} | ## Summary
This commit fixes incar write error and one example is shown below. This error is triggered if a structure contains elements in ["F", "O", "S"] but the most electro-negative element is not within the list.
Example:
```python
>>> from pymatgen.ext.matproj import MPRester
>>> from pymatgen.io.vasp.set... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1076 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1076/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1076/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1076/events | https://github.com/materialsproject/pymatgen/pull/1076 | 307,715,447 | MDExOlB1bGxSZXF1ZXN0MTc2ODMzMjYz | 1,076 | Bug handling 0 during writing VolumetricData | {
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"Thanks."
] | 2018-03-22T16:19:22 | 2018-03-22T16:25:03 | 2018-03-22T16:24:59Z | CONTRIBUTOR | {
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} | ## Summary
* Fix the Bug handling 0 during writing VolumetricData
before fix
-..000000000EE+01
after fix
0.00000000000E+01
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https://api.github.com/repos/materialsproject/pymatgen/issues/1077 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1077/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1077/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1077/events | https://github.com/materialsproject/pymatgen/issues/1077 | 307,823,875 | MDU6SXNzdWUzMDc4MjM4NzU= | 1,077 | Drone for FEFF output | {
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"How long will this take?"
] | 2018-03-22T21:37:14 | 2023-08-08T21:22:33 | 2023-08-08T21:22:33Z | CONTRIBUTOR | {
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} | Instead of creating individual methods for output parsing, creating a drone specified for FEFF output parsing seems like a more reasonable idea. A "FeffToEntryDrone" will be implemented and includes all output file parsing and entry construction functions. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1078 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1078/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1078/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1078/events | https://github.com/materialsproject/pymatgen/issues/1078 | 308,140,962 | MDU6SXNzdWUzMDgxNDA5NjI= | 1,078 | Issue with Outputting Symmetrized CIFs | {
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"Hi Gerry, try\n\nCifWriter(struct=material, *symprec=1e-5*).write_file('Li_Test.cif')\n\nAlso, just FYI, be a bit careful when interpreting the elastic constants of\nmaterials with non-empty \"warnings\" fields. The elastic analysis of this\nparticularly material strongly suggests it is mechanically unstable, whi... | 2018-03-23T18:45:30 | 2018-03-23T19:52:16 | 2018-03-23T19:52:15Z | NONE | {
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} | ## System
* Pymatgen version: 2017.8.21
* Python version: 3.6
## Summary
Hello, I'm currently searching through the Materials Project's auxetic materials and I'm having difficulty ensuring that pymatgen generates cif files with the correct structures/properties. I have an example below using lithium metal. mp-56... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1079 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1079/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1079/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1079/events | https://github.com/materialsproject/pymatgen/pull/1079 | 308,284,819 | MDExOlB1bGxSZXF1ZXN0MTc3MjUwMjYx | 1,079 | Added additional statistics to VoronoiNN calculation | {
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} | ## Summary
Adds additional information about each facet to the `get_voronoi_polyhedra` method of `VoronoiNN`.
- Altered `get_voronoi_polyhedra` to compute a few other statistics
- Added option to `VoronoiNN` that changes whether solid angle is used to weigh neighbors, or one of these other statistics
## Addit... | {
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} | ## Summary
Added a method for computing information about arbitrary nearest-neighbor shells of a particular site.
- Also added utility method for computing neighbors for all sites in a structure
## Additional dependencies introduced (if any)
None
## TODO (if any)
None.
Tagging @Qi-max, who I discu... | {
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"@computron, addressed in PR #1083. Can be closed once the tests ran successfully.",
"@computron, can be closed.",
"Thanks!"
] | 2018-03-27T18:27:34 | 2018-04-02T22:29:55 | 2018-04-02T22:29:55Z | MEMBER | {
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} | @nisse3000 to have better consistency in naming, ditch the "paras" and move to "params"
This refactor should be maybe 30 seconds of work with PyCharm, or even a simple find/replace across files | {
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"Pls resolve the codacy issues.",
"Fix failing tests.",
"All checks have been fixed"
] | 2018-03-27T21:13:50 | 2018-06-15T20:39:50 | 2018-06-15T12:07:17Z | CONTRIBUTOR | {
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} | WorkFunctionAnalyzer now takes a structure, list of locpot along c and fermi energy. There is a from_files method still available to build the analyzer from paths to the CONTCAR, LOCPOT and OUTCAR instead.
ReconstructionGenerator will apply operations to all possible terminations instead of determining which one bef... | {
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"Thanks!"
] | 2018-03-29T16:57:35 | 2018-03-29T20:48:42 | 2018-03-29T20:48:42Z | CONTRIBUTOR | {
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} | ## Summary
Add X-ray scattering coefficient of deuterium (D).
The value was copied from hydrogen (H).
This change enables us to calculate XRD of deuterium-substituted materials. | {
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"Hi @GerardMattei,\r\n\r\nthanks for indicating this issue. A couple of quick questions.\r\n\r\nI'm trying to reproduce that the previous pymatgen version that you used would indeed give expected results. I tried one pymatgen version from August 20 (5e6f0f755a41016975c8e1137fd11c6810c39766) and one from August 21 ... | 2018-03-29T18:24:36 | 2018-07-02T17:58:38 | 2018-07-02T17:58:38Z | NONE | {
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} | ## System
* Pymatgen version: 2018.2.13
* Python version: 3
## Summary
Hello,
I am running into an error message when attempting to determine the CN # of mixed occupancies using the Voronoi NN class (sample code attached below). If I attempt to determine the CN # around an pymatgen periodic site with a single sp... | {
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} | ## Summary
For `MPRester.get_interface_reactions`, extend method signature to allow toggling of whether to use the convex hull energy for a given composition for the reaction energy calculation. If false (default), the energy of the ground state structure will be preferred; if a ground state cannot be found for a co... | {
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} | ## Summary
Removed use of `deepcopy` in nearest neighbor calculation.
Aside: Turns out that this one line was 50% of the execution time of getting Nth nearest neighbor shells. I've learned my lesson.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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} | ## Summary
A series of changes to make the calculation of Voronoi-tessellation-based features in matminer faster.
* Optimization of `get_nn_shell_info`
* Optimization of `get_voronoi_polyhedra`. No longer returns a dict indexed by `PeriodicSite`, which is very slow to modify.
* Implemented `__hash__` and `__e... | {
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} | ## Summary
added FermiDos class that makes it very easy to calculate the fermi level at a given concentration (get_fermi) or the concentration (doping) at a given fermi level (get_doping). Also added tests for both methods. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1090 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1090/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1090/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1090/events | https://github.com/materialsproject/pymatgen/pull/1090 | 310,970,952 | MDExOlB1bGxSZXF1ZXN0MTc5MTk5NzQ5 | 1,090 | Pourbaix revision 2 | {
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} | ## Summary
Major overhaul to pourbaix diagram code. Makes it more in-line with the phase-diagram refactor and more transparent to use.
* module and submodules of `pymatgen.analysis.pourbaix` moved to a single module: `pymatgen.analysis.pourbaix_diagram` and the analyzer and maker functionalities are now in a sin... | {
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} | Uses machine precision times the largest of the input array dimensions rather
than simply the machine precision as the `rcond` parameter to `numpy.linalg.lstsq`.
## Summary
Adds `rcond=None` to all calls to `numpy.linalg.lstsq`.
* This suppresses a `FutureWarning` for numpy>=1.14 (pmg dep)
* The future defau... | {
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"The error comes from a conflict version with openbabel. Actually the script crashes when it tries to import openbabel in `pymatgen.io.babel.py` this last module being imported in the `IMolecule.to()` mehtod.\r\n\r\nThe error is fixed after an openbabel update : \r\n\r\n``` \r\n--> conda install -c openbabel openba... | 2018-04-04T06:51:49 | 2018-04-04T13:02:57 | 2018-04-04T13:02:57Z | CONTRIBUTOR | {
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} | When I try to export a Molecule to a xyz file I got a PyThreadState error that I do not understand.
## System
* Pymatgen version: 2018.3.14
* Python version: Python 3.6.4 |Anaconda custom (64-bit)| (default, Jan 16 2018, 12:04:33)
* OS version: MacOSX 10.13.3
## Example code
```python
import pymatgen as ... | {
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} | ## Summary
When translating PMG structures to ASE atoms, sometimes you want to use additional ASE Atoms kwargs. e.g., for myself I want to add a calculator in the ASE Atoms object when creating it from a PMG structure.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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"Thanks @shyuep, Would it be possible for you to release a new pymatgen version that reflect these changes?"
] | 2018-04-04T22:34:07 | 2018-04-05T22:54:09 | 2018-04-05T21:57:58Z | CONTRIBUTOR | {
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"Go ahead.",
"Addressed in #1082 \r\nFuture improvements to be made to optimize efficiency but issue will be closed now"
] | 2018-04-05T21:42:17 | 2018-06-15T20:32:25 | 2018-06-15T20:32:25Z | CONTRIBUTOR | {
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} | The grand surface potential (ie surface energy) determines the stability of a surface and is a function of chemical potential. In ternary systems and systems of greater complexity of different species, the surface energy is a function of 2 or more chemical potentials. It is more convenient to visualize which terminatio... | {
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} | `DLS_bond_params.yaml` isn't included in the package files. The VolumePredictor thus break when pymatgen is `pip install`'ed. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1097 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1097/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1097/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1097/events | https://github.com/materialsproject/pymatgen/pull/1097 | 311,839,686 | MDExOlB1bGxSZXF1ZXN0MTc5ODQ4NTE4 | 1,097 | updated debye temperature formulation | {
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} | ## Summary
I've found that estimating the debye temperature of solids from the elastic tensor using the formulation from the longitudinal and transverse speed of sound is significantly more accurate than that of the isotropic young's modulus, so I've moved that to the default function and deleted both the old one an... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1098 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1098/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1098/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1098/events | https://github.com/materialsproject/pymatgen/pull/1098 | 312,243,323 | MDExOlB1bGxSZXF1ZXN0MTgwMTI1MjY0 | 1,098 | Locate lowest density of charge | {
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} | ## Summary
Analyzer to find potential interstitial sites based on charge density.
* Locate the minimum density of charge in a crystal using CHGCAR-type file
* unittest
## Additional dependencies introduced (if any)
* Optional: External function `skimage.feature.peak_local_max` is required to find extreama. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1099 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1099/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1099/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1099/events | https://github.com/materialsproject/pymatgen/pull/1099 | 312,581,920 | MDExOlB1bGxSZXF1ZXN0MTgwMzQ4NzAw | 1,099 | NMR Updates | {
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"Pls fix codacy issues and check the other failing tests.",
"I fixed all the issues related to the NMR code. For some reason Hanmei's fixes that i merged in are showing up as changes and Codacy is complaining about them. They are structural, e.g. the use of asserts and random, so I don't think changing them is a ... | 2018-04-09T15:39:34 | 2018-04-10T21:21:56 | 2018-04-09T22:53:19Z | NONE | {
"total": 0,
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} | ## Summary
Refactored the NMR tensor and added a NMR InputSet for VASP
- Updated periodic table to have NMR quadrupolar moments for isotopes
- Added an MPNMRSet for chemical shielding and EFG calculations
- Fixed inheritance issues in from_prev for various InputSets
- Updating parsing of chemical shielding and... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1100 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1100/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1100/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1100/events | https://github.com/materialsproject/pymatgen/pull/1100 | 312,963,158 | MDExOlB1bGxSZXF1ZXN0MTgwNjMyMjcz | 1,100 | Small bug in tetragonal conventional structure method when a = c | {
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"I would suggest you add a test to make sure this is done correctly."
] | 2018-04-10T15:00:26 | 2018-04-10T16:00:32 | 2018-04-10T16:00:14Z | CONTRIBUTOR | {
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} | ## Summary
The `get_conventional_standard_structure` method currently unexpectedly switches a and c for tetragonal space groups if a = b = c. This is obviously not desirable and so has been removed, while still allowing for switching a and c if a != b = c (the original intention).
## Additional dependencies introd... | {
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