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https://api.github.com/repos/materialsproject/pymatgen/issues/401 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/401/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/401/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/401/events | https://github.com/materialsproject/pymatgen/pull/401 | 158,275,009 | MDExOlB1bGxSZXF1ZXN0NzI0NDMwOTE= | 401 | fix rotational symmetry operations check in pointgroupanalyzer | {
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- addresses issue #400
- split the the conditional statements
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} | ## System
- Pymatgen version: master
- Python version:2.7.11
- OS version: Red Hat Enterprise Linux Server release 6.3
## Summary
FireWorks, MPWorks can't import MPGGAVaspInputSet
## Example code
many FireWorks commend, such as `qlaunch` `lpad get_fws`
## Error message
error message of `lpad get_fws -i 9686`
```
k... | {
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"(this also pertains to a few others like MITVaspInputSet, MPHSEVaspInputSet)\n",
"The new input sets are called MPRelaxSet.yaml. And it retains EDIFF_PER_ATOM of the old MPVaspInputSet..\n",
"The old MPVaspInputSet.yaml is only used by the old deprecated sets.\n",
"I know ... that's also what my message says... | 2016-06-03T23:28:21 | 2016-06-04T00:35:16 | 2016-06-03T23:35:34Z | MEMBER | {
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} | I think that MPVaspInputSet.yaml should use EDIFF_PER_ATOM (not EDIFF) to maintain the old behavior of deprecated sets. Just confirming this is true rather than pushing the change directly.
I don't think this affects any of the new input sets either way...
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"Hi,\n\nAbinit supports different set of variables for the specification of the crystal structure.\nThat section is supposed to handle the case in which the dictionary specifies the lattice in terms of \nangles and vector lengths.\nThere's obviously an issue when `geomode == \"angdeg\"`. I will fix it.\nThanks for ... | 2016-06-06T23:24:59 | 2017-07-12T16:01:03 | 2017-07-12T16:01:03Z | MEMBER | {
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```
elif geomode == "angdeg":
d.update(dict(
acell=3 * [1.0],
angdeg=angdeg))
```
But in the last line, it looks like angdeg is never defined (at least, it is underlined in red in my IDE). So if this code were to be run, it would... | {
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"I have no objection, but I will leave the rest to comment. My suspicion is that you set ISYM to 0 to avoid symmetrization of the charge density. Does it really matter? This is a one step run. I doubt the cost is very much different.\n",
"Ok I am going to leave it as is for now. In some (static scf) HSE runs I ha... | 2016-06-07T21:57:31 | 2016-06-08T18:04:03 | 2016-06-08T17:35:57Z | MEMBER | {
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I am thinking to change this so that ISYM is left alone, i.e., if the scf run was done with ISYM=1, to leave that setting the same for the nscf run. It is trivial to implement but I want to make sure this procedure is correct, hence the ticket.
Any objections / comment... | {
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} | ## Summary
Adds a method to TensorBase that allows conversion to the IEEE standard, and a small fix to TensorBase.transform
- IEEE conversion based on rules from 1987 standard
- TensorBase.transform now returns the class of the instance
## TODO (if any)
IEEE conversion should be generalized to allow conversion based ... | {
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Adds test data.
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- set topology directly from the molecule
- set forcefield from file
- add/update unittests
- minor cleanup
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- read pair and improper dihedral forcefield coefficients
- set site charges in topology
- more unittests
- cleanup and minor refactoring
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} | ## Summary
If the `core.physical_constants` module will be removed in pmg 4.0 as the module warns, this change or similar is necessary. Currently, a deprecation warning is given with as little as `from pymatgen import __version__`.
- `pymatgen.core.physical_constants` --> `scipy.constants`
- define `HARTREE_TO_ELECTRO... | {
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"I am experiencing this same issue. I have also posted to the pymatgen google group. Any updates here?",
"I am the developer of the Zeo++ python extension. I wrote it with python\n2.7 in mind. I stopped working on Zeo++ more than a year ago.\nDue to the many requests, I will make this a high priority.\n\nBharat\... | 2016-06-14T20:58:44 | 2017-02-24T14:15:11 | 2017-02-24T14:12:57Z | NONE | {
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} | ## System
- Pymatgen version: "master"
- Python version: 3.5
- OS version: Linux - Ubuntu 16
## Summary
The Zeo++ extension io/zeopp.py has some python2 -> 3 problems regarding str vs. bytes. I did some simple fixes to the calls by applying `encode('utf-8')` to all the string input arguments to cython. However the pr... | {
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"Thanks!\n"
] | 2016-06-14T22:41:53 | 2016-06-14T23:08:33 | 2016-06-14T22:49:18Z | MEMBER | {
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- Pymatgen version: "master" vs. 3.6.1
- Python version: 2.7.10
- OS version: OSX 10.11
## Summary
- New `pymatgen.io.vasp.sets` class `MPRelaxSet` has no `name` attribute, so breaks `get_explanation_dict` for `MaterialsProjectCompatibility` instance.
- Not sure if this is a bug or a pmg4 change. If the latte... | {
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"Can you make sure you pull the latest pymatgen master and resolve all conflict first? There are merge conflicts according to Github. Thanks,\n",
"That is True, I did not work on the last pymatgen version.\nI did a new pull request with no merge conflict\nGermain\n\nLe mer. 15 juin 2016 à 14:30, Shyue Ping Ong no... | 2016-06-15T07:16:12 | 2016-06-16T22:47:06 | 2016-06-16T22:47:06Z | CONTRIBUTOR | {
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} | ## Summary
- major bug fixes in setting lammps data from molecular forcefield and topology
- update unittests: replace simple testscase with more complex ones
- refactoring/cleanup/doc updates
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} | ## Summary
- disable reading pair coeffs for i!=j atom pairs in forcefield
- generate polymer chains via random walk
- wrapper for [packmol](https://github.com/leandromartinez98/packmol) software
- unittests
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} | ## Summary
Support for "universal" conversion of tensors to IEEE standard format.
- TensorBase.convert_to_ieee can convert tensors without restrictions to the input structure (previously, only conventional was supported). Thanks to Atsushi Togo for assistance via the spglib mailing list.
- Applies to ElasticTensor an... | {
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} | ## System
- Pymatgen version: 3.7.0
- Python version: 2.7
- OS version: CentOS
## Summary
When LDAUJ is not specified, the band gap cann not be determined
## Example code
``` python
v = Vasprun('vasprun.xml')
bs = v.get_band_structure()
print bs.get_band_gap() #<-- crash
```
## Error message
```
Traceback (most rec... | {
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"Python `long` values are not cast to String values in MongoDB. They are stored as [NumberLong](https://docs.mongodb.com/manual/core/shell-types/#numberlong)s in MongoDB, i.e. 64-bit integers.\n\nI tried to reproduce your issue, but I could not. I tried MongoDB 3.2 and 2.6, and I'm using pymongo 3.2 and pymatgen 3.... | 2016-06-22T17:12:50 | 2016-06-26T21:29:24 | 2016-06-26T21:29:24Z | MEMBER | {
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} | Spacegroup analyzer returns spacegroup number as "_long_" type, e.g.:
```
sga = SpacegroupAnalyzer(structure)
print(type(sga.get_spacegroup_number()))
```
This is not a problem when working purely in Python, but inserting _long_ types into MongoDB causes them to be cast to String - so that spacegroup numbers are stri... | {
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} | ## Summary
_spacegroup_data["number"] is `long`. Can safely cast to `int` and match method signature.
Closes #421
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} | ## Summary
<Short few sentences, and summary of the major changes in bullet
points>
- Feature 1
- Feature 2
- Fix 1
- Fix 2
## Additional dependencies introduced (if any)
<List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
ad... | {
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} | ## Summary
Method for sulfide type determination based on crystal structure by checking the oxidation states from coordinated atoms of S. Output str listed below:
- "None" if it is an element, or it does not contain S, or S is coordinated by anions.
- "polysulfide" if any S is found to be bonded by S.
- "sulfide" fo... | {
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Fix anion correction when S and O are both anions. No corrections on polysulfides for now, which means they are destabilized.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
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- add LammpsRunner wrapper
- py3k bug fix
- other minor bug fixes and cleanup
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- Pymatgen version: 3.7.1
- Python version: 2.7
- OS version: Windows 10
## Summary
- The directory pymatgen-3.7.1\pymatgen\analysis\chemenv\coordination_environments\coordination_geometries_files contains filenames with the '?' character. This is not valid on windows. Trying install on windows produces:
co... | {
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Misc NMR code updates
<Short few sentences, and summary of the major changes in bullet
points>
- Parsing both "core only" and "valence and core" NMR chemical shift values
- Fix parsing of NMR vapsrun.xml SC step energy, which actually consists of several ionic steps but shown as single one.
- Organiza NMR ... | {
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- Add support for Abinit8, drop support for Abinit7
- Remove from_abivars and to_abivars methods
- Add enumerator for libxc XC functionals and XcFunc object
- Move dojo_report object to pseudo_dojo
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Added Christoffel tensor and acoustic wave velocities
Added Born elastic stability criterion
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"Is this working? It looks like there are still bugs in both the test and the new method. Also, should it really be called \"rotate_tensor\"? We have a \"rotate\" method already which takes a rotation matrix and transforms the tensor based on that. I think the new method should have a more descriptive name.\n\n... | 2016-06-30T17:51:06 | 2016-09-25T20:09:56 | 2016-09-25T20:09:55Z | CONTRIBUTOR | {
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} | ## Summary
Fixed a few bugs in get_ieee_tensor that caused problems in structures with lattice vectors that are close. Thanks to @dmrdjenovich for feedback and a pretty extensive test dataset.
- Removes atol/ltol from TensorBase.convert_to_ieee, they shouldn't be necessary.
- Fixes some bugs in comparison procedures ... | {
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} | This line of pymatgen requires unittest2:
pymatgen/util/testing.py:15
Since this could be considered a "core" test, unittest2 should be a required installation library for pymatgen.
Currently I get CircleCI failures for a derived library (MatMiner) that reuses PymatgenTest to get some structures for testing. The Cir... | {
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} | ## System
- Pymatgen version: 4.0.0
- Python version: 2.7.9
- OS version: Linux
## Summary
- Changing the "reciprocal_density" argument of MPStaticSet doesn't seem to have an effect on the generated k-point grid
## Example code
``` python
from pymatgen.io.vasp.sets import MPStaticSet
from pymatgen.util.testing import ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/437 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/437/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/437/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/437/events | https://github.com/materialsproject/pymatgen/pull/437 | 164,661,871 | MDExOlB1bGxSZXF1ZXN0NzY4NDQyNjU= | 437 | Fixed absolute path installation issue | {
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} | ## Summary
Removed os.path.abspath because this was preventing installation from the extracted tar.gz source when running setup.py install under Windows OS (not sure if it manifests on Linux). The setup() function should only need relative paths.
## Note
Please test this under Mac OS X / Linux to confirm the changes ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/438 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/438/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/438/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/438/events | https://github.com/materialsproject/pymatgen/issues/438 | 165,303,463 | MDU6SXNzdWUxNjUzMDM0NjM= | 438 | Different tolerance values for same site detection are used while reading CIF files | {
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"Many thanks, @shyuep!\n"
] | 2016-07-13T11:59:01 | 2016-07-13T13:13:40 | 2016-07-13T12:36:07Z | CONTRIBUTOR | {
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} | Different tolerance values for same site detection are used here:
- https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/cif.py#L469, modifiable, 1e-5 by default
- https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/cif.py#L308, hard-coded, 1e-3
I suggest using the same variable `self.... | {
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} | ## Summary
minor bug fixes and refactoring in the lammps subpackage
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} | ## Summary
While parsing 225k CIF files from the Springer materials/Pauling file DBs using CifParser, numerous errors were faced, which were earlier fixed at my end, but now I have tried to introduce those capabilities directly in CifParser.
Here's a summary of changes made. They passed all the tests in test_cif.py ... | {
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"Is this the new behavior of GULP or is the output specific to your input file?",
"It's specific to this input file. I have since run GULP on different systems/input files, and the outputs did contain the string:\r\n\r\n\"Final fractional coordinates of atoms\"",
"Seems like this issue has been defunct for 7 ye... | 2016-07-18T20:48:39 | 2023-08-08T21:17:33 | 2023-08-08T21:17:33Z | NONE | {
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} | <When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
- Pymatgen version: 3.7.1
- Python version: 2.7.8
- OS version: Linux Fedora, release 21
- GULP version: 4.4
## Summary
The pymatgen.command_line.gulp_caller.GulpIO... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/442 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/442/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/442/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/442/events | https://github.com/materialsproject/pymatgen/pull/442 | 166,440,187 | MDExOlB1bGxSZXF1ZXN0NzgwNTI0Nzg= | 442 | Update to REST Api for the substrate analyzer | {
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"You need to provide a proper description. I do not merge unless there is one.\n",
"@shyamd `orient` should default to `None` (avoid mutable values like `[]`), and if so, elide the \"orient\" field in the query string.\n\nAlso, let's thicken up the docstring. Include that `n=0` means \"no limit\" (perhaps this sh... | 2016-07-19T21:28:55 | 2016-07-20T16:21:16 | 2016-07-20T16:21:16Z | NONE | {
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} | ## Summary
get_structure_from_prev_run used to pop LDAU parameters in incar of the passed vasprun object in place. This resulted in missing LDAUU, LDAUJ and LDAUL parameters (all become empty lists) for all input sets created (e.g. MPStaticSet) with from_prev_calc methods.
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"@sdacek can you fix this?\nThis implementation breaks when the input lattice is a rotation. See commit 2f60449\n"
] | 2016-07-23T02:41:34 | 2016-07-25T22:36:55 | 2016-07-23T04:25:41Z | CONTRIBUTOR | {
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} | ## Summary
Change the implementation of interpolate_lattices. Previously, the
parameters for the lattice (a, b, c, alpha, beta, gamma) were all
linearly interpolated to the parameters of the second structure.
However, this can lead to various issues, including
that the interpolated volumes are not guarenteed monotoni... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/445 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/445/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/445/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/445/events | https://github.com/materialsproject/pymatgen/issues/445 | 167,497,684 | MDU6SXNzdWUxNjc0OTc2ODQ= | 445 | Key Error when parsing projected band structure for spin-orbit coupling VASP runs | {
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"Can you post an example SOC file?\n",
"Hi Shyue Ping, \n\n[Here are example vasprun.xml and KPOINTS files for a SOC band structure run. (The vasprun.xml is bigger than github allows for posts)](https://www.dropbox.com/sh/esiw6o6rao3w2c4/AAA0ezVqpkEMpCGAp6horVGVa?dl=0)\n\nI made a temporary fix of the key error t... | 2016-07-26T00:47:17 | 2016-08-03T03:39:15 | 2016-08-03T03:39:15Z | CONTRIBUTOR | {
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} | A Key Error is returned when BSVasprun(parse_projected_eigen=True).get_band_structure() is used to read spin-orbit coupling VASP runs.
## Example code
``` python
# while this works:
vasp_run = BSVasprun('vasprun.xml')
bs = vasp_run.get_band_structure(line_mode=True)
# this throws a key error:
vasp_run = BSVasprun('va... | {
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"The tests seems to be failing?\n",
"Hi Shyue,\n\nI think its a compatibility problem with python 3. I'm running with python\n2.7, I'll test with python on my machine and make the necessary changes.\n\nDavid\n\nOn Wed, Jul 27, 2016 at 3:01 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> The tests seems t... | 2016-07-27T11:19:30 | 2016-07-27T15:36:30 | 2016-07-27T15:36:30Z | CONTRIBUTOR | {
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} | ## Summary
- New strategy to identify coordination environments
- More convenient way to store and retrieve neighbors (NeighborsSets in StructureEnvironments and LightStructureEnvironments
- Tests are now much faster
- Added new tests for the new strategy and for the LightStructureEnvironments
- Fixed miscellaneous bug... | {
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"Thanks. Can you submit a pull request?\n"
] | 2016-07-31T19:15:27 | 2016-08-12T04:14:49 | 2016-08-12T04:14:49Z | MEMBER | {
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} | ## System
- Pymatgen version: 4.2.0
- Python version: 3.5.2
- OS version: OS X 10.11.6
## Summary
Parsing of core state eigenenergies fails, I suspect because it assumes that the number of lines equals the number of atoms: it's not handling entries for atoms which use multiple lines correctly (for example, because the... | {
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Fix PDEntry.from_dict to accommodate no-name entry dicts. Add a test for this.
I encountered this issue when using `monty.json.MontyEncoder` to `json.dumps` Pourbaix entries. I could ensure this dumps 'name's for each entry, but `PDEntry.from_dict` should also just accommodate no-name entries as `PDEntry._... | {
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"Don't think this is a bug? Band gap determination is ultimately a exercise in tolerances. The DOS and BS classes use different methods of determining the gap. In general, I would argue the DOS gives a much better band gap than the BS estimate.\n",
"the default tolerance for dos is 0.001. also the indirect gap re... | 2016-08-08T15:46:23 | 2017-06-03T14:32:24 | 2017-06-03T14:32:24Z | CONTRIBUTOR | {
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} | ## System
- Pymatgen version: master branch
- Python version: 3.5
- OS version: ubuntu 16.04
## Summary
- difference in gap of about 0.27 for Silicon(NEDOS=601 in INCAR)
- the value reported by Bandstructure object matches the value reported on the materialsproject(mp-149)
## Example code
``` python
from pymatgen.i... | {
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} | This is a suggestion. I was using the format material_name_POSCAR for several of my materials and I needed to read them via Structure.from_file but I couldn't. With _POSCAR_ file naming is more flexible than just POSCAR\* which was previously.
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} | Added a fix for the core state eigenenergies parsing, and also an additional test and an associated OUTCAR (GaAs from mp-2534 with ICORELEVEL=1) since none of the existing OUTCARs in test_files have core state eigenenergies with d-levels.
Fixes #447
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https://api.github.com/repos/materialsproject/pymatgen/issues/452 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/452/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/452/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/452/events | https://github.com/materialsproject/pymatgen/issues/452 | 171,453,018 | MDU6SXNzdWUxNzE0NTMwMTg= | 452 | vasprun.get_band_structure(line_mode=True) causes occasional mislabeling high symmetry k-point as 'None'. | {
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} | ## System
- Pymatgen version: 3.6.1
- Python version: 3.5.1
- OS version: OS X El Capitan
## Summary
- vasprun.get_band_structure(line_mode=True) constructs labels_dict with 'None' as a key, resulting in occasional mislabeling if 'None's value is a high symmetry k-point.
## Example code
``` python
# line 745 in pymatg... | {
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} | ## Summary
- add capability to translate each site separately: example:- displacing sites along normal modes
- add and update corresponding unittests
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https://api.github.com/repos/materialsproject/pymatgen/issues/454 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/454/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/454/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/454/events | https://github.com/materialsproject/pymatgen/issues/454 | 174,403,597 | MDU6SXNzdWUxNzQ0MDM1OTc= | 454 | Spacegroup 165 should have hexagonal lattice system? | {
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"Space Group 165 should not be hexagonal, it is indeed trigonal\n(rhombohedral). http://img.chem.ucl.ac.uk/sgp/large/sgp.htm\n\nBest,\nWenhao Sun\n\nOn Wed, Aug 31, 2016 at 4:33 PM, Tess notifications@github.com wrote:\n\n> Hello,\n> \n> I believe spacegroup 165 should have a hexagonal rather than a\n> rhombohedral... | 2016-08-31T23:33:45 | 2017-06-03T14:29:07 | 2017-06-03T14:28:35Z | CONTRIBUTOR | {
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I believe spacegroup 165 should have a hexagonal rather than a rhombohedral lattice system.
For example, see ICSD Collection Code 3 -- a crystal structure with this spacegroup. Using the lattice information for this structure:
``` python
lattice = Lattice.from_lengths_and_angles((7.1849999999999996, 7.185000... | {
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"Note - i don't think the vbm is listed in the above output, but it was above the Fermi level (I think something on the order of 1.85?)\n",
"Assigned to @hautierg \n",
"The two methods define differently what is the band gap.\nThe eigenvalue_band_properties looks at occupations. Here there are partial occupatio... | 2016-09-02T19:32:25 | 2016-09-26T04:33:44 | 2016-09-25T16:01:55Z | CONTRIBUTOR | {
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I get very different band gaps from Vasprun.eigenvalue_band_properties and Bandstructure.get_band_gap(). The former gives a gap of 1.3011 while the other 0. This seems to be because the maximum valence band is above the fermi level but still has some electron occupation.
```
vrun = Vasprun('vasprun.xml')
(gap,... | {
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"I ran this exact code nd I did not have any error. I suspect you have a problem with your numpy setup because that sounds like a compile error. Maybe your python version and numpy compile version is not compatible.\n",
"Hi Shyue Ping,\n\nThanks for your time. I am getting this error when switching between differ... | 2016-09-04T02:39:19 | 2016-09-04T20:11:09 | 2016-09-04T04:19:24Z | CONTRIBUTOR | {
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I get a "ValueError: ndarray is not C-contiguous" when running the following script:
```
from pymatgen.matproj.rest import MPRester
a = MPRester()
Si = a.query({'material_id':'mp-149'},['structure']).pop()['structure']
Si.get_distance(0,1)
```
Thanks!
Tess
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"Thanks Tess. Can you implement a few unit tests? Also, the clustering code should use scipy hierarchical clustering using the distance matrix. See the point group analyzer for an example of how it is done.\n",
"I would suggest that it use the same tolerance and clustering code as Structure.merge_sites()\n",
"H... | 2016-09-04T20:19:47 | 2016-09-06T03:02:04 | 2016-09-06T02:07:38Z | CONTRIBUTOR | {
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} | The Structure.remove_duplicates method can be used for deleting PeriodicSites that are within a tolerance of each other and have identical species_and_occu property. This is useful for deleting degenerate atoms that are generated when creating a Structure.from_spacegroup where the desired structure is to be in a lower ... | {
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"Did you run python setup.py install or develop and there were no errors? This seems like you did not install pymatgen correctly.\n",
"Oh, sorry. I didn't. It's working now. Thank you, Prof Ong!\n"
] | 2016-09-06T22:01:52 | 2016-09-08T21:12:48 | 2016-09-08T21:12:48Z | NONE | {
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} | <When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
- Pymatgen version: <Write "branch_name" if it is development version.>
- Python version: 2.7.9
- OS version: <If you are writing Windows here, you are on your own.> ... | {
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"The tests are failing. Pls fix the tests before I merge.\n",
"Dear Prof. Ong\n\nCan you please have a try commit 6df01df, commit 4086da3 was trying to use git-lfs tracker for the big CHGCAR file and as I found out I didn't have access to do that to a public forked repo.\n\nOnce you think it passed the test, p... | 2016-09-07T05:10:34 | 2016-09-11T01:51:16 | 2016-09-11T01:51:16Z | CONTRIBUTOR | {
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} | ## Summary
Added PathFinder module under pymatgen.analysis, added unit test cases for PathFinder module as well.
## TODO
In order to write unit test codes for PathFinder module, I had to include a CHGCAR file under test_files/path_finder, this file is very large (around 80MB), thus system suggests using git-lfs. Howe... | {
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"I just pushed a fix, and also released v4.2.5 which should fix this problem. THis was due to some refactoring of the bandstructure classes.\n",
"Thank you so much. Is working back again!\n"
] | 2016-09-08T21:03:23 | 2016-09-08T21:24:30 | 2016-09-08T21:06:31Z | NONE | {
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from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter, BSPlotterProjected
from pymatgen.electronic_structure.core import Spin, OrbitalType
emin = -2.0
emax = 2.0
v = Vasprun("./vasprun.xml", parse_projected_eigen=... | {
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"There is a reciprocal density arg already?\n",
"Does this work for MPRelaxSet? I'm getting an error:\n\n```\n>>> from pymatgen.io.vasp.sets import MPRelaxSet\n>>> from pymatgen.util.testing import PymatgenTest\n>>> struct = PymatgenTest.get_structure(\"Si\")\n>>> mpr = MPRelaxSet(struct, reciprocal_density=1000... | 2016-09-10T00:38:10 | 2016-09-10T02:47:56 | 2016-09-10T02:47:56Z | CONTRIBUTOR | {
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} | For some of the MP workflows, the initial optimization step needs a higher k-point density than what's standard in the MPRelaxSet. I can customize the input set by modifying the config_dict, but then when it's serialized via as_dict, my changes are lost. I'm thinking it might be worthwhile to add a parameter to custo... | {
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"@hautierg Can you look into this? This seems a rather huge bug?\n",
"@hautierg Any updates?",
"Closing, non-bug (thanks @munrojm for taking a sanity check!)"
] | 2016-09-10T15:14:38 | 2020-07-13T04:35:08 | 2020-07-13T04:35:07Z | CONTRIBUTOR | {
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} | ## System
- Pymatgen version: 4.2.5
- Python version: 2.7.11
## Summary
It seems that in generating the high symmetry K points for bandstructure calculations for the definite lattice system, the developer forgot to transfer the parameters of the sine function from degree to radian, thus may leading an error in generat... | {
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"Thanks for fix.\n\nBut it still puzzles me.\n\nSince there's a `get_point_group()` method which claims to return a `Pointgroup` object( actually it returns a `String`, another issue) and a `get_point_group_operations()` method which returns a `PointgroupOperations` object, it's kind of weird that there's only a `g... | 2016-09-10T15:21:13 | 2016-09-11T14:15:37 | 2016-09-10T17:49:04Z | NONE | {
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Line 102 in analyzer.py reads
``` python
"""
Get the Spacegroup for the Structure.
Returns:
Spacgroup object.
"""
```
however, the SpacegroupAnalyzer.get_spacegroup() method actually returns a SpacegroupOperations object as Line 109 reads
``` python
return SpacegroupOperations(self.get_spacegroup_symbol(),
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"There seems to be failing tests. Pls fix before I merge.\n",
"Should pass the tests now, forgot to update the unit tests when I renamed one of the methods.\n"
] | 2016-09-10T20:37:19 | 2016-09-11T01:50:22 | 2016-09-11T01:50:22Z | CONTRIBUTOR | {
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} | ## Major update to elasticity analysis package
Major update to the elasticity analysis package, including a significant refactoring of voigt-notation tensors and addition of properties to elastic tensor class. Thanks to @saurabh02 for the initial import of the thermal properties and to Ian Winter for sharing his meth... | {
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} | ## Summary
- split the classes into inputs and outputs
- complete overahul of sets module to enable custom xanes and exafs runs
- update/cleanup the unittests
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} | ## Summary
- feff io: major cleanup in feff.io.inputs. make cluster radius a controllable parameter. some other minor cleanups
- fix the sign issue in the phonon example notebook.
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} | Added effective total strain calculated by the von Mises equivalent strain criterion. This is useful for correlating to interfacial defects such as in microelectronics.
- Added von Misses strain to strain class
- Added output of effective total strain to substrate analyzer output
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- critical bug fixes
- refactor and cleanup outputs.
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"Can you also as the same time change the use of Pyhull's Voronoi class to the scipy.spatial Voronoi class in chemenv? I would like to start systematically remove use of pyhull. Note that scipy's implementation is faster.\n"
] | 2016-09-15T10:05:36 | 2016-09-21T12:03:23 | 2016-09-21T12:03:23Z | CONTRIBUTOR | {
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} | ## Summary
- Switch from pyhull.VoronoiTess to scipy.spatial.Voronoi
- Fixed small bugs in chemenv
- Added classmethod to MultiWeightsChemenvStrategy in order to ease it's use
- Added self.structures in NEBAnalysis
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"@mbkumar Can you look into this pls?\n",
"The problem seems to be in SpacegroupAnalyzer. Within **init** method there is a loop which checks for magnetic moment of each site of voronoi polyhedral. \n\n```\n for site in structure:\n if hasattr(site, 'magmom'):\n magmoms.append(site... | 2016-09-15T10:46:07 | 2017-06-07T13:07:22 | 2017-06-07T13:07:22Z | NONE | {
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} | ## System
- Pymatgen version: pymatgen (4.3.0)
- Python version: Python 2.7.6
- OS version: Ubuntu 14.04.4 LTS
## Summary
- I am trying to find possible non-equivalent interstitial positions in TiBe12 (intermetallic of ThMn12-type) structure using pymatgen.analysis.defects.point_defects. In fact I do need neither radii... | {
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"Sure I can revert Eos.py. I used the unittests as the reference for refactoring. In future please make sure that the unittests actually test the important API so that these sort of issues won't happen. Also I noticed that the original Eos.py module looks almost exactly the same as the one in ase python package(jus... | 2016-09-16T14:10:56 | 2016-09-20T22:55:04 | 2016-09-16T14:18:30Z | CONTRIBUTOR | {
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- feff io: add api to parse the atomic luster as molecule, some cleanup
- refactor and cleanup analysis.eos.py
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- add phonon dos to the example notebook and rename it
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"Thanks for reporting this. I have pushed a fix.\n",
"Thanks, @shyuep!\n"
] | 2016-09-19T08:04:57 | 2016-09-20T06:48:39 | 2016-09-19T12:51:46Z | CONTRIBUTOR | {
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} | ## System
- Pymatgen version: 4.3.1
- Python version: 2.7.3
- OS version: Ubuntu 12.04
## Summary
- value of CIF tag `_symmetry_equiv_pos_as_xyz` may be single and unlooped (basically for P1 space group, when it's `x,y,z`);
- CIF construction `_symmetry_equiv_pos_as_xyz x,y,z` results in incorrect list of symmetry oper... | {
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"at-mentioning to track discussion: @tschaume @montoyjh @kristinpersson \n",
"The hegemon does not need to be involved in this discussion right?\n",
"It is impossible to code review something that has 758 changed files. Pls copy your repo, refork the code, and then make only the changes that are on top of the e... | 2016-09-19T22:12:34 | 2016-09-21T17:37:11 | 2016-09-21T17:37:11Z | NONE | {
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} | Pull request for review of equation of state thermal properties code for Materials Project.
FAO: Patrick Huck, Donny Winston, Joey Montoya, Kristin Persson
Code is in pymatgen/analysis/eqn_of_state_thermal
Branch eos_thermal_pmg4 is implemented in pytmatgen 4
Fits E(V) data to equations of state and Debye-Gruenei... | {
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"Note: the files in the above Dropbox link are all you need to reproduce the error. But, if you want to look at the entire run, it is available here:\n\nhttps://www.dropbox.com/sh/a0j604ek0pacjml/AABVyg7xL3HAvpN8j5TLWf8Va?dl=0\n",
"Fixed, but if you have a file that is much smaller that can be used for testing, i... | 2016-09-19T22:54:54 | 2016-09-20T20:55:12 | 2016-09-20T02:31:10Z | MEMBER | {
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} | ## System
- Pymatgen version: master
- Python version: 2.7
- OS version: both Mac + Linux
## Summary
- Type the example code below
- You will get an error in parsing the vasprun.xml file
- This error seems to affect many high-throughput jobs
## Example code
``` python
from pymatgen.io.vasp.outputs import Vasprun
vr = ... | {
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"@shyuep recent PRs are failing checks due to a missing MAPI_KEY env var. Perhaps this is related to the introduction of .pmgrc.yaml?\n",
"Looks good Donny. \n\nCan we add not in:\n\n``` python\nif '$nin' in val:\n elt_list = [e for e in elt_list\n if getattr(e, field) not in val['$nin']]\n```\n... | 2016-09-21T00:14:59 | 2016-09-25T20:09:56 | 2016-09-25T20:09:56Z | MEMBER | {
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} | Please do not merge. This PR, though a working implementation, is for discussion/review. Please comment (esp. @shyamd).
## Summary
Allow filtering on `pymatgen.core.periodic_table.Element` attributes, using a subset of MongoDB filter syntax, in order to specify element sets as part of `MPRester.query` calls. Enables ... | {
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} | Pull request for review of equation of state thermal properties code for Materials Project.
FAO: Patrick Huck, Donny Winston, Joey Montoya, Kristin Persson
Code is in pymatgen/analysis/eqn_of_state_thermal
Branch eos_thermal_pmg4 is implemented in pytmatgen 4
Fits E(V) data to equations of state and Debye-Grueneise... | {
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"Your input is wrong. The [\"Be\", \"Ti\"] should be [\"Be\", \"Ti\", \"Ti\", \"Ti\"] I think.\n",
"Thank you! Now it works.\nThe correct input should be other way round: [\"Be\",\"Be\",\"Be\",\"Ti\"].\n"
] | 2016-09-21T07:31:50 | 2016-09-21T12:28:14 | 2016-09-21T12:17:23Z | NONE | {
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} | ## System
- Pymatgen version: pymatgen (4.3.0)
- Python version: Python 2.7.6
- OS version: Ubuntu 14.04.4 LTS
## Summary
- The following code should generate structure of Be12Ti. For both spacegroup "I4/mmm" or its number "139" (as in example below) the code generate POSCAR file with 8 Ti and 8 Be atoms, which is obvi... | {
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"I think it’s your symprec, your probably forcing a higher or lower symmetry in writing the gif.\n\nbest,\nMichiel\n\n> On 22 Sep 2016, at 08:10, Guoqiang Lan notifications@github.com wrote:\n> \n> this is a feature request, please simply state the requested feature.>\n> \n> System\n> \n> Pymatgen version: 4.3.2\n>... | 2016-09-22T06:10:13 | 2016-09-25T22:30:03 | 2016-09-25T22:30:02Z | NONE | {
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} | <When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
- Pymatgen version: 4.3.2
- Python version: 2.7
- OS version: Linux
## Summary
1. Some structures (e. g. Fe2O3, mp-19306) generated from "CIF" files are incorrect
##... | {
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- Added property ce_symbol in CoordinationGeometry (same as mp_symbol) in chemenv
- Fixed NEBAnalysis's piecewise polynomial construction for scipy versions > 0.18.
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"Hi Shyue,\n\nI made the changes that you suggested and reopened a pull request but the\ncircleCI failed for some tests. The thing is I checked which tests failed\nand I never touched these files or anything related to that. The tests that\nare failing are related to the MPRester so maybe the MaterialsProject was\n... | 2016-09-23T13:54:23 | 2016-09-29T08:32:39 | 2016-09-25T20:09:59Z | CONTRIBUTOR | {
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- Removed old and commented code from chemenv.
- Made NEBAnalysis MSONable.
- Made NEBAnalysis's **init** method independent from vasp (NEB structures and energies could come from any other code).
- Created from_outcars method for NEBAnalysis (to replace old **init**).
- Created test for NEBAnalysis.
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- Added method compute_coordination_environments in LocalGeometryFinder (now, a one-line command gets the environment of a given structure for a given "strategy").
- Removed old and commented code from chemenv.
- Made NEBAnalysis MSONable (as_dict() method has to be implemented because structures is a list o... | {
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"While this can certainly be done, I do not think it is something that is useful. The problem with taking the symmetry operations from the spacegroups is that many spacegroups have different settings. Without explicit statement of the operations, it is impossible to be sure what setting the atomic positions are giv... | 2016-09-28T11:01:49 | 2016-09-30T06:58:02 | 2016-09-29T18:21:44Z | CONTRIBUTOR | {
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this is a feature request, please simply state the requested feature.>
## System
- Pymatgen version: 4.3.2
- Python version: 2.7.3
- OS version: Ubuntu 12.04
## Summary
- if CIF file does not contain the list of symmetry operators (`_symmetry_equi... | {
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- add more unittests
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"I have just briefly skimmed this and I have a few questions.\n\n1) Why did you implement a class for an isotropic strain on your structure? Your class does one thing, which is running the `apply_strain()` method and you that transformation in one place. Why didn't you just use the `apply_strain()` method in the fi... | 2016-09-28T23:42:05 | 2017-02-23T20:59:19 | 2017-02-23T20:58:58Z | NONE | {
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} | Pull request for review of equation of state thermal properties code for Materials Project. Updated to re-clone pymatgen source and update fork after changes to pymatgen repo.
FAO: Patrick Huck, Donny Winston, Joey Montoya, Kristin Persson
Code is in pymatgen/analysis/eqn_of_state_thermal
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"Thanks!\n"
] | 2016-09-30T23:05:34 | 2016-09-30T23:37:51 | 2016-09-30T23:12:10Z | MEMBER | {
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## System
- Pymatgen version: 4.4.0
- Python version: 2.7.*
- OS version: OS... | {
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- EELS(near edge and extended spectrum) input sets
- added and updated unittests
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"I do not understand the mymul method for structure. How is that different from structure \\* [2, 2, 2]?\n",
"Hi Shyue,\n\nIt just allows to disable the fallback to the unit cell. I wasnt sure\nwhether I could add an optional parameter to the __mul__method but I\nthought not as it is a \"built-in\" method.\n\nDav... | 2016-10-04T16:09:25 | 2016-10-06T15:35:18 | 2016-10-06T15:35:18Z | CONTRIBUTOR | {
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} | ## Summary
Added a MultiStructuresVis to visualize series of structures (used to visualize from e.g. NEB or MD simulations)
- Visualization of multiple structures with vtk (using "n" and "p" keys to go from one structure to another)
- Possibility to have an "animated" movie of the structures (using the "m" key).
- Pos... | {
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"Thanks. I cannot merge this request as you are adding back 5 files. I think the only thing that was changed in structure.py? Pls make a copy, refork, and clone, and move structure,py over. Also, for all new functionality, pls implement unittests.\n"
] | 2016-10-04T20:36:12 | 2016-10-05T02:58:41 | 2016-10-05T02:58:41Z | CONTRIBUTOR | {
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"Recently, we hit the limit for Github repo sizes on pymatgen because of all the large test files. I had to do a history cleanup. Please make a copy of your existing pyamtgen repo, refork pymatgen, reclone pymatgen, and copy your new changes (I am guessing only files in the pymatgen package directory) over to the n... | 2016-10-05T14:49:26 | 2016-10-05T15:34:03 | 2016-10-05T15:34:03Z | CONTRIBUTOR | {
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} | We are trying to merge merge pymatgen/master
in our branches but git refuses to merge with the following error:
- branch master -> FETCH_HEAD
fatal: refusing to merge unrelated histories
If I look at the history, I see that the commits before Sep 25, 2016 now
have two different ids e.g.
```
Merge b... | {
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- added unittests
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"I'm not sure as to why the checks have failed. I modified only one class that doesn't seem to be imported elsewhere (except for two test cases (i) pymatgen/io/vasp/tests/test_outputs.py and (ii) pymatgen/analysis/tests/test_structure_analyzer.py). I also have not changed the default behavior.\n\n**Update-1:** I... | 2016-10-08T04:20:00 | 2016-10-08T18:31:44 | 2016-10-08T18:20:33Z | NONE | {
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} | ## Summary
<Incorporated options to select structures, concatenate new structures with existing one and write the Xdatcar class into a file>
- Added functionality to provide the starting and ending ionic step, to enable removal of structures in NVT AIMD before equilibration.
- Created a function concatenate new struc... | {
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} | - support for size dependent feff runs(real v reciprocal)
- add unittest
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"This is not a bug. In v4.4.0, the format of the projections and eigenvalues objects are changed to a ndarray. THis is much more memory and computationally efficient. All serializations has to work with the new formats.\n",
"but bs.as_dict() fails with \"IndexError: arrays used as indices must be of integer (or b... | 2016-10-13T07:14:37 | 2016-10-13T15:11:15 | 2016-10-13T15:03:58Z | CONTRIBUTOR | {
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} | vrun = Vasprun(vasprun.xml.gz, parse_eigen=True, parse_projected_eigen=True)
bs = vrun.get_band_structure(line_mode=True)
before version 4.4.0 bs.get_vbm()['projections'] returned:
{Spin.up: 1: {Orbital.py: 1: array([ 0.1277, 0.1277]),
Orbital.dxy: 4: array([ 0., 0.]),
Orbital.dyz: 5: array([ 0., 0.]),
Orbit... | {
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