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| 413,151,373
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MDU6SXNzdWU0MTMxNTEzNzM=
| 1,401
|
Unhelpful error message in BabelMolAdaptor
|
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[
"I found the helpful error message later. :)"
] | 2019-02-21T22:22:10
| 2019-02-21T23:18:51
|
2019-02-21T23:17:49Z
|
NONE
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**Describe the bug**
When I use BabelMolAdaptor.from_file() from pymatgen.io.babel, if I don't have OpenBabel installed, I get the following error:
```
312 BabelMolAdaptor object
313 """
--> 314 mols = list(pb.readfile(str(file_format), str(filename)))
315 return BabelMolAdaptor(mols[0].OBMol)
316
AttributeError: 'NoneType' object has no attribute 'readfile'
```
It'd be more useful if this could tell me I'm missing OpenBabel and maybe even give me the line I need to install it e.g.
```conda install -c openbabel openbabel```
**To Reproduce**
Use BabelMolAdaptor.from_file() from pymatgen.io.babel without OpenBabel installed.
**Expected behavior**
Either OpenBabel being listed as a dependency in conda or an error that gives me more information.
**Desktop (please complete the following information):**
- MacOS Mojave
- Firefox
- pymatgen-2019.2.4 build py36_0
|
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| 413,625,993
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MDExOlB1bGxSZXF1ZXN0MjU1NTY5ODYz
| 1,402
|
Fix NearNeighbors._get_image to work properly for sites not in unitcell
|
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[
"Thanks @lan496 !",
"(p.s. this fixed an unrelated issue I hadn't had chance to track down yet, so thanks again! saved me a lot of time)"
] | 2019-02-23T00:06:46
| 2020-08-14T13:16:42
|
2019-02-23T19:13:39Z
|
CONTRIBUTOR
|
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## Summary
- fix behavior of `NearNeighbors._get_image` to deal with cases such that initial sites are not in unitcell(fix https://github.com/materialsproject/pymatgen/issues/1321)
An image is defined as displacement from original site in structure to a given site.
For example, if structure has a site at (-0.1, 1.0, 0.3), then (0.9, 0, 2.3) -> jimage = (1, -1, 2).
Note that this definition returns the same result with the previous implementation of `NearNeighbors._get_image` for atoms in unit cell(i.e. when fractional coordinates are contained in [0, 1)^3)
|
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| 414,266,618
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MDExOlB1bGxSZXF1ZXN0MjU2MDE1ODI3
| 1,403
|
Various bug fixes (graphs, phase diagram, magnetism)
|
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[
"Note to self: tests can fail due to `muellergroup.jhu.edu:8080` being offline for `pymatgen.ext.tests.test_jhu.JhuTest`, will try to handle this more gracefully.",
"I suggest adding a pymatgen.util.typing module with the useful type hints like Vector.",
"That said, I would suggest no need to go overboard. Let's just do hints for the five core modules (periodic table, sites, compostion, lattice and structure). then we see how useful they are. And we can expand gradually to other modules as needed.",
"Agreed, I'd be happy to see hints just in core for now to see how useful they are.\r\n\r\nAdding comprehensive type hints to Lattice was already seemed helpful, both for live coding (PyCharm will highlight if you try to call a method with the wrong type), and also to highlight hidden complexity (eg very long type signatures are interesting). Personally, I've found it most useful so far just to know when a method is returning an np.ndarray vs a list/tuple.",
"Ok. I suggest you go ahead and merge first and just work on master. I already implemented a few hints here and there. It might be easier to deconflict. in general, the co-pymatgen dictator does not need to use pull requests for simple bug fixes or doc (though for big features, it is still a good practice).",
"Noted!\r\n\r\nAs mentioned, I will keep to PRs for larger features for record keeping/good practice. "
] | 2019-02-25T19:25:42
| 2019-02-26T18:14:08
|
2019-02-26T18:14:08Z
|
MEMBER
|
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## Summary
Fixes MSONable for PhaseDigram when non-PDEntries used. Fixes graph bug (thanks Jack Sundberg). See individual commit messages for more, includes code reformatting. Will merge once CI passes.
|
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MDU6SXNzdWU0MTYxNjUyNjA=
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|
Missing some radii & mistakes in commonness of some oxidation states
|
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[
"Thanks. I agree the ionic radii tabulation is incomplete. In the first place, only one ionic radius is assigned to each oxidation state. Some of the elements have multiple ionic radius depending on coordination environment, oxidation state as well as high/low spin. The source of the ionic radii is https://www.wikiwand.com/en/Ionic_radius . I believe the reason why some of these are missing is because they are not in the oct environment. For Ni, the problem is that there are high and low spins, which affect the ionic radii. We can try to correct it.",
"Actually I just realized that get_shannon_radius would already do what you want. Pls see that method for Elements."
] | 2019-03-01T15:54:39
| 2019-03-03T02:17:49
|
2019-03-03T02:17:49Z
|
NONE
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There are some mistakes in the common oxidation state of some elements and some radii are missing.
When I do the following :
from pymatgen.core.periodic_table import Element
for Elem in Element:
print(Elem)
print(Element(Elem).common_oxidation_states)
print(Element(Elem).ionic_radii)
I have the following
Ni
(2,)
{3: 0.74}
--> but in Shannon table oxidation state 3 is reported as well (--> common) and crystal radius of Ni2+ is 0.84 Å.
Sn
(-4, 2, 4)
{4: 0.83}
--> but in Shannon table crystal radius of Sn2+ is 1.36 Å.
Te
(-2, 2, 4, 6)
{-2: 2.07, 4: 1.11, 6: 0.7}
--> but in Shannon table Te2+ is not present (--> uncommon)
I am using pymatgen version from 2018.08.30 on python 3.6.6. with ubuntu 18.04.2 LTS
Kind regard
|
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| 416,907,149
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MDU6SXNzdWU0MTY5MDcxNDk=
| 1,405
|
Abandoning immutability for Site, PeriodicSite, Structure and Molecule
|
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[
"I'm on board with this change.\r\n\r\nIn general, I like immutable data structures, and think they lend themselves to better code. However, they're only useful if they are used. I think the majority of pymatgen/MP users (and probably devs) have never used or are not aware of IStructure or IMolecule, people assume structures are mutable by default, and code like `structure.copy()` is very common for this reason. I think it makes sense that the design of pymatgen reflects how it's actually used in practice, especially if making them mutable-by-default will make the code a lot simpler, easier to understand and faster.",
"IIRC, I think Hulk's original motivation for these was to have a safe object to use as dict keys.\r\n\r\nA quick Github search for \"pymatgen IStructure\" does reveal that there are a lot of code snippets that use IStructure. But, it's not clear which of these snippets actually require IStructures.\r\n\r\nFor us, the only thing I remember is that we actually use IStructures in matminer as a way to help with caching - although it's not clear to me whether IStructure is needed or simply makes things more safe. I think @utf or Alex Dunn (can't tag him for some reason) could comment more on this.\r\n\r\n",
"> IIRC, I think Hulk's original motivation for these was to have a safe object to use as dict keys.\r\n\r\nAlways useful to have historical context! I can certainly see cases where having a structure as a dict key might be useful, but in general this seems a little dubious (given that many equivalent structures are not bit-for-bit identical, and I'm not sure how well defined the structure hash is either, so this would be probably be quite slow?). In any case, if this functionality is still required, we could just adopt a frozendict library and use structure.as_dict() as the key -- I don't think this is sufficient motivation either way for whether to keep IStructure around or not. Caching purposes are more compelling, I'm not familiar with how it's used in matminer.",
"Yes, initially the idea is for IStructure to be hashable and usable as a dict key (or in a set). But given that it is basically near impossible to define structure equality outside the context of StructureMatcher, this is a theoretical, but not practically used feature.\r\n\r\nAs for caching, I am pretty sure immutability is not required.\r\n\r\nAnyway, we can leave it for now. Even with the recent changes, the code has been cleaned up significantly. ",
"Just to give examples of how this change has impacted overall code:\r\n\r\ni. Methods such as replace_species, etc. are now unified for both Molecule and Structure, instead of having duplicated methods for both (because originally, new Site/PeriodicSite had to be made). THis also makes it easier to maintain,.\r\nii. Many of the operations such as translate_sites can be done in place in the site, rather than making new sites.\r\niii. the pymatgen.core.structure module has lost ~100 lines of code with no loss in functionality.",
"> For us, the only thing I remember is that we actually use IStructures in matminer as a way to help with caching - although it's not clear to me whether IStructure is needed or simply makes things more safe.\r\n\r\nThis is correct. For something to be hashable it has to be immutable, so we always cast to an IStructure for caching in matminer. \r\n\r\n> In any case, if this functionality is still required, we could just adopt a frozendict library and use structure.as_dict() as the key.\r\n\r\nThis would work for matminer purposes.",
"The reason why Structure is not hashable is not because it is mutable, but because its `__hash__` is purposely set as None. We can of course just remove that and treat Structure like any other mutable object which always compare unequal and is therefore hashable.",
"AFAIK comparing as equal is different to being hashable?\r\n\r\nE.g.:\r\n\r\n```python\r\nx = [1, 2, 3]\r\n\r\nhash(x)\r\n> TypeError: unhashable type: 'list'\r\n\r\nx == x\r\nTrue\r\n```\r\n\r\nSimilarly,\r\n\r\n```python\r\n{x: 1} \r\n> TypeError: unhashable type: 'list'\r\n```\r\n\r\nThat said, we can just override the hash method using the frozendict idea that Matt suggested.",
"They are different. But equal objects must have same hash. From python doc.\r\n\r\n```An object is hashable if it has a hash value which never changes during its lifetime ```\r\n\r\nThe reason why mutable objects are usually not considered hashable is because you would typically use an invariant property as a hash. For IStructure, the hash value is simply derived from the composition. For Structure, composition can change over time. But there is really no problem with making Structure hashable simply by assuming all Structures are different and their hash is simply the default id(). AFAIK, there should be no serious practical consequences given that almost no one uses it as a dict key or expects Structure.__eq__ to mean anything significant. When we need to compare equality of structures, it is almost always with StructureMatcher."
] | 2019-03-04T17:19:17
| 2019-05-23T13:49:26
|
2019-05-23T13:49:26Z
|
MEMBER
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Historically, Site and PeriodicSite are considered immutable, as are IStructure and IMolecule. This is due to bad coding in the early days, which ports over the coding styles of Java to Python due to inexperience of @shyuep at that time.
These impositions are artificial, and indeed, have been violated in common practice. To simplify the code, I propose we abandon immutability for these core objects. Here are the things that need to be done:
1. I have already modified Site and PeriodicSite to allow setting of coordinates, lattice, species, etc. - all while maintaining consistency, using property.setters, with appropriate tests.
2. As a result of (1), many methods in Structure can be considerably simplified. I have done a few of these (e.g., Structure.delete_oxidation_states). This simplification has the added benefit that because we are not creating Site/PeriodicSites all the time, speed is improved by a lot.
3. We can simply a lot of other code as well, e.g., transformations, matchers, etc. By these can be done gradually.
4. I propose we completely deprecate IStructure and IMolecule, with a view of deleting these in pmg v2020. I do not know of any places where these are used in place of Structure/Molecule. Methods will be ported over where appropriate.
@mkhorton @computron Comments?
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MDU6SXNzdWU0MTcxMzE3NTg=
| 1,406
|
TypeError: invalid file pymatgen/core/periodic_table.json
|
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[
"Hi there, given that Python is now at 3.7 going to 3.8, v3.5 is rather old. Can you upgrade your Python version and see if it persists? ",
"I had the same problem with python 3.5 on one computer and updated to python 3.7. With python 3.7, it worked fine. ",
"Closing this issue. ",
"@shyuep THX! I will think about that."
] | 2019-03-05T06:01:25
| 2019-03-11T07:21:48
|
2019-03-05T14:31:04Z
|
NONE
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**Describe the bug**
import pymatgen in python3.5 will raise ``TypeError: invalid file pymatgen/core/periodic_table.json``
**To Reproduce**
Steps to reproduce the behavior:
1. pip install pymatgen=2019.2.28
2. import pymatgen
3. See error
**Logs**
```
tests/datatools/test_boxcox.py:10: in <module>
from xenonpy.datatools.transform import BoxCox
xenonpy/__init__.py:9: in <module>
from . import descriptor
xenonpy/descriptor/__init__.py:7: in <module>
from .composition import Compositions, WeightedAvgFeature, WeightedSumFeature, WeightedVarFeature, MaxFeature, \
xenonpy/descriptor/composition.py:6: in <module>
from pymatgen.core.composition import Composition as PMGComp
../../../miniconda/envs/xepy35/lib/python3.5/site-packages/pymatgen/__init__.py:55: in <module>
from pymatgen.core import *
../../../miniconda/envs/xepy35/lib/python3.5/site-packages/pymatgen/core/__init__.py:6: in <module>
from .periodic_table import Element, Specie, DummySpecie
../../../miniconda/envs/xepy35/lib/python3.5/site-packages/pymatgen/core/periodic_table.py:34: in <module>
with open(Path(__file__).absolute().parent / "periodic_table.json", "rt") as f:
E TypeError: invalid file: PosixPath('/home/travis/miniconda/envs/xepy35/lib/python3.5/site-packages/pymatgen/core/periodic_table.json')
```
**Additional context**
This error can be reproduced under Linux and OSX from version 2019.2.24. See link for details.
https://travis-ci.org/yoshida-lab/XenonPy/builds/501869381
|
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MDU6SXNzdWU0MTcxNjg3NzY=
| 1,407
|
Potential bug in `CifParser`
|
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[
"@sphuber in the example CIF the terminating `;` is missing in the line right after\r\n```\r\n 4 x-1/2,-y-1/2,z-1/2\r\n```\r\nas multiline CIF fields are expected to start and end with `;`.",
"@merkys thanks a lot, I have updated the example",
"Thanks. A fix has been pushed to master.",
"@shyuep thanks a lot, but I am afraid this only solves part of the problem. The [fix pushed to master](https://github.com/materialsproject/pymatgen/commit/c34a6c0b69a6654bc6b8e9164341d5b8d6769e18) addresses the initial problem that I described but the solution will lead to problems when calling `parser.get_structures`. This can be demonstrated with the following slightly adapted input file\r\n```\r\ndata_1526655\r\n_journal_name_full\r\n_space_group_IT_number 227\r\n_symmetry_space_group_name_Hall 'F 4d 2 3 -1d'\r\n_symmetry_space_group_name_H-M 'F d -3 m :1'\r\n_cell_angle_alpha 90\r\n_cell_angle_beta 90\r\n_cell_angle_gamma 90\r\n_cell_formula_units_Z 8\r\n_cell_length_a 5.381\r\n_cell_length_b 5.381\r\n_cell_length_c 5.381\r\n_cell_volume 155.808\r\n_iucr_refine_fcf_details\r\n;\r\ndata_symmetries\r\nloop_\r\n _space_group_symop_id\r\n _space_group_symop_operation_xyz\r\n 1 x,y,z\r\n 2 -x+1/2,y+1/2,-z+1/2\r\n 3 -x,-y,-z\r\n 4 x-1/2,-y-1/2,z-1/2\r\n;\r\nloop_\r\n_atom_site_label\r\n_atom_site_type_symbol\r\n_atom_site_fract_x\r\n_atom_site_fract_y\r\n_atom_site_fract_z\r\n_atom_site_occupancy\r\n_atom_site_U_iso_or_equiv\r\nSi1 Si 0 0 0 1 0.0\r\n```\r\nThe only thing I have done is move the `_iucr_refine_fcf_details` tag before the definition of the structure symmetries and sites. Constructing the `CifParser` for this file now works fine, however, calling `parser.get_structures` will yield the following exception:\r\n```\r\nValueError Traceback (most recent call last)\r\n<ipython-input-5-e2a0eb59b33a> in <module>()\r\n----> 1 parser.get_structures()\r\n\r\n/home/aiida/.virtualenvs/aiida_sdb/local/lib/python2.7/site-packages/pymatgen/io/cif.pyc in get_structures(self, primitive)\r\n 1072 warnings.warn(str(exc))\r\n 1073 if len(structures) == 0:\r\n-> 1074 raise ValueError(\"Invalid cif file with no structures!\")\r\n 1075 return structures\r\n 1076 \r\n\r\nValueError: Invalid cif file with no structures!\r\n```\r\nI will open a new issue for this"
] | 2019-03-05T08:11:58
| 2019-03-14T17:07:15
|
2019-03-13T19:04:17Z
|
NONE
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**Describe the bug**
Due to the logic in the detection of `CifBlocks` in the content of a CIF, the `CifParser` can fail for certain CIFs with valid structure and syntax
**To Reproduce**
Call `CifParser` on a file with the following content:
```
data_1526655
_journal_name_full
_space_group_IT_number 227
_symmetry_space_group_name_Hall 'F 4d 2 3 -1d'
_symmetry_space_group_name_H-M 'F d -3 m :1'
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_formula_units_Z 8
_cell_length_a 5.381
_cell_length_b 5.381
_cell_length_c 5.381
_cell_volume 155.808
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_U_iso_or_equiv
Si1 Si 0 0 0 1 0.0
_iucr_refine_fcf_details
;
data_symmetries
loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 x,y,z
2 -x+1/2,y+1/2,-z+1/2
3 -x,-y,-z
4 x-1/2,-y-1/2,z-1/2
;
```
Except we get an exception:
```
/home/sph/.virtualenvs/aiida_prov/local/lib/python2.7/site-packages/pymatgen/io/cif.pyc in __init__(self, filename, occupancy_tolerance, site_tolerance)
313 self._site_tolerance = site_tolerance
314 if isinstance(filename, six.string_types):
--> 315 self._cif = CifFile.from_file(filename)
316 else:
317 self._cif = CifFile.from_string(filename.read())
/home/sph/.virtualenvs/aiida_prov/local/lib/python2.7/site-packages/pymatgen/io/cif.pyc in from_file(cls, filename)
293 def from_file(cls, filename):
294 with zopen(filename, "rt", errors="replace") as f:
--> 295 return cls.from_string(f.read())
296
297
/home/sph/.virtualenvs/aiida_prov/local/lib/python2.7/site-packages/pymatgen/io/cif.pyc in from_string(cls, string)
286 if 'powder_pattern' in re.split(r"\n", x, 1)[0]:
287 continue
--> 288 c = CifBlock.from_string("data_" + x)
289 d[c.header] = c
290 return cls(d, string)
/home/sph/.virtualenvs/aiida_prov/local/lib/python2.7/site-packages/pymatgen/io/cif.pyc in from_string(cls, string)
227 break
228 if s[0].startswith("_"):
--> 229 data[s[0]] = "".join(q.popleft())
230 elif s[0].startswith("loop_"):
231 columns = []
IndexError: pop from an empty deque
```
**Expected behavior**
A successfully parsed structure
**Desktop (please complete the following information):**
- Ubuntu 16.04
- 2018.04.20
**Additional context**
The problem seems to arise when there are tags with multiline values, such as the tag `_iucr_refine_fcf_details`, where the value starts with the prefix `data_`. One of the first steps the parser seems to perform is to split the content on `data_` occurrences and treating those as individual CIF blocks. In this example, this will create a CIF block where the last tuple only contains the tag `_iucr_refine_fcf_details`. When the parser comes to that tag and tries to get its corresponding value by popping left from the dequeue, we hit the index error because there is no value to be popped.
As I understand it, it is perfectly valid for multiine values in the CIF spec to start with `data_` which makes this a bug in the parser I think
|
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MDU6SXNzdWU0MTcyNDIyNDY=
| 1,408
|
surface.py and symmetrized slabs / vacuumless slab
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[
"@richardtran415 Pls look into Case 1.\r\n\r\nFor case 2, what you want is not to give a 0 vacuum. You should just simply get the `oriented_unit_cell` property for each slab, which gives the oriented bulk structure. The slabs generator assumes you actually want a slab structure, and so imposes some minimum space.\r\n\r\nAs for dependencies, I suggest you use miniconda and create an environment to install everything. That isolates all installs into your own user directory and there should be no requirements for admin privileges. We install pymatgen and its dependencies on supercomputing clusters (which have strict security protocols) all the time.",
"@cpashartis \r\n\r\nFor Case 1. you should be using a.get_slabs() with the optional parameter \"symmetrize\" set to True instead of a.get_slab(). The latter is used by the former to generate slab objects but is typically not suppose to be called by the user. \r\n\r\n```\r\nfrom pymatgen.core.surface import SlabGenerator\r\nfrom pymatgen import Structure\r\nfrom pymatgen.io.cif import CifWriter\r\n```\r\n```\r\nst = Structure.from_file('Si_mp-149_conventional_standard.cif')\r\na = SlabGenerator(st, (1,0,0), 10, 15, center_slab=True)\r\nnew_st = a.get_slabs(symmetrize=True)\r\n```\r\n\r\nThis returns a list of slabs, but since there is only one SYMMETRIC termination for a diamond (100) structure, there should only be one slab in the list.\r\n\r\nYou can check whether or not the slab is symmetric using the following slab method:\r\n```\r\nprint(new_st[0].is_symmetric())\r\n>True\r\n```\r\n\r\nwhich just checks if the slab has inversion symmetry (Laue point group).",
"I will check this tomorrow, but then what you are telling me is that public\nmethods in the class yield different results... that is an issue I would\nthink no? Also did you try to print out the structure and visualize it?\nBecause I don't disagree it is Laue point group according to the symmetry\nanalyzer, *but* it clearly isn't inversion symmetric if you look at it.\n\nThanks,\n\nChristopher Pashartis\n\n\n\n\n\nOn Tue, Mar 5, 2019 at 8:05 PM Richard Tran <notifications@github.com>\nwrote:\n\n> @cpashartis <https://github.com/cpashartis>\n>\n> For Case 1. you should be using a.get_slabs() with the optional parameter\n> \"symmetrize\" set to True instead of a.get_slab(). The latter is used by the\n> former to generate slab objects but is typically not suppose to be called\n> by the user.\n>\n> from pymatgen.core.surface import SlabGenerator\n> from pymatgen import Structure\n> from pymatgen.io.cif import CifWriter\n>\n> st = Structure.from_file('Si_mp-149_conventional_standard.cif')\n> a = SlabGenerator(st, (1,0,0), 10, 15, center_slab=True)\n> new_st = a.get_slabs(symmetrize=True)\n>\n> This returns a list of slabs, but since there is only one termination for\n> a diamond (100) structure, there should only be one slab in the list.\n>\n> You can check whether or not the slab is symmetric using the following\n> slab method:\n>\n> print(new_st[0].is_symmetric())\n> >True\n>\n> which just checks if the slab has inversion symmetry (Laue point group).\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1408#issuecomment-469816916>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AHJUrwehV6sKfHOlVlMdd0Cg0n12pVmtks5vTsACgaJpZM4beWJ->\n> .\n>\n",
"@richardtran415 The solution you gave me is not symmetric with respect to inversion symmetry. It is symmetric in one axis, not the other. You'll notice one of the atoms on the top surface doesn't have an inversion equivalent on the bottom surface. \r\n\r\nAre our definitions different for symmetry? What am I missing here? Even your own comments designate symmetric as inversion symmetry and remove surfaces until they are equal.\r\n\r\n```\r\nfrom pymatgen.core.surface import SlabGenerator\r\nfrom pymatgen import Structure\r\nfrom pymatgen.io.cif import CifWriter\r\n\r\nst = Structure.from_file('Si_mp-149_conventional_standard.cif')\r\na = SlabGenerator(st, (1,0,0), 5, 10, center_slab=True, primitive=False)\r\n\r\nc = CifWriter(a.get_slab())\r\nc.write_file('standard.cif')\r\n\r\nnew_st = a.nonstoichiometric_symmetrized_slab(a.get_slab(),1E-1)\r\nprint(new_st[0].is_symmetric())\r\nc = CifWriter(new_st[0])\r\nc.write_file('symmetrized_by_function_call.cif')\r\n\r\na = SlabGenerator(st, (1,0,0), 5, 10, center_slab=True, primitive=False)\r\n\r\nsymmetrized_slab = a.get_slabs(symmetrize=True)\r\nprint(symmetrized_slab[0].is_symmetric())\r\nassert(len(symmetrized_slab)== 1)\r\nc = CifWriter(symmetrized_slab[0])\r\nc.write_file('symmetrized_get_slabs_with_symmetry.cif')\r\n```\r\n\r\nAll three results are the same (the one with the `symmetry = True` is just a pi/4 rotation). Note, both claim to have `slab_name.is_symmetric() = True`.\r\n\r\nP.S. @shyuep you probably shouldn't close the topic unless it is resolved ;).\r\n",
"These slabs are clearly symmetric. Valid slabs can have mirror, two told,\nfour fold, six fold, glide plane or inversion symmetry.\n\n\nOn Fri, Mar 8, 2019, 9:37 AM Christopher Pashartis <notifications@github.com>\nwrote:\n\n> @richardtran415 <https://github.com/richardtran415> The solution you gave\n> me is not symmetric with respect to inversion symmetry. It is symmetric in\n> one axis, not the other. You'll notice one of the atoms on the top surface\n> doesn't have an inversion equivalent on the bottom surface.\n>\n> Are our definitions different for symmetry? What am I missing here? Even\n> your own comments designate symmetric as inversion symmetry and remove\n> surfaces until they are equal.\n>\n> from pymatgen.core.surface import SlabGenerator\n> from pymatgen import Structure\n> from pymatgen.io.cif import CifWriter\n>\n> st = Structure.from_file('Si_mp-149_conventional_standard.cif')\n> a = SlabGenerator(st, (1,0,0), 5, 10, center_slab=True, primitive=False)\n>\n> c = CifWriter(a.get_slab())\n> c.write_file('standard.cif')\n>\n> new_st = a.nonstoichiometric_symmetrized_slab(a.get_slab(),1E-1)\n> print(new_st[0].is_symmetric())\n> c = CifWriter(new_st[0])\n> c.write_file('symmetrized_by_function_call.cif')\n>\n> a = SlabGenerator(st, (1,0,0), 5, 10, center_slab=True, primitive=False)\n>\n> symmetrized_slab = a.get_slabs(symmetrize=True)\n> print(symmetrized_slab[0].is_symmetric())\n> assert(len(symmetrized_slab)== 1)\n> c = CifWriter(symmetrized_slab[0])\n> c.write_file('symmetrized_get_slabs_with_symmetry.cif')\n>\n> All three results are the same (the one with the symmetry = True is just\n> a pi/4 rotation). Note, both claim to have slab_name.is_symmetric() = True\n> .\n>\n> P.S. @shyuep <https://github.com/shyuep> you probably shouldn't close the\n> topic unless it is resolved ;).\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1408#issuecomment-470949408>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/ABvGoxBp8eUT6TfvcGjGEn3WgA9fFN9sks5vUnV_gaJpZM4beWJ->\n> .\n>\n"
] | 2019-03-05T11:05:50
| 2019-03-08T16:01:33
|
2019-03-05T19:33:10Z
|
NONE
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1. SlabGenerator.nonstoichiometric_symmetrized_slab will not make a symmetrized surface of a conventional Silicon unit cell in the [1,0,0] direction. It returns a non symmetrized surface.
2. SlabGenerator() with 0 vacuum should return a crystal oriented in the direction of [h,k,l]?
A clear and concise description of what the bug is.
**To Reproduce**
```
from pymatgen.core.surface import SlabGenerator
from pymatgen import Structure
from pymatgen.io.cif import CifWriter
```
Case 1.
```
st = Structure.from_file('Si_mp-149_conventional_standard.cif')
a = SlabGenerator(st, (1,0,0), 10, 15, center_slab=True)
new_st = a.nonstoichiometric_symmetrized_slab(a.get_slab()) # varying tolerance to 1E-1 doesn't help
cif_w = CifWriter(new_st[0])
cif_w.write_file('test.cif')
```
Case 2.
```
st = Structure.from_file('Si_mp-149_conventional_standard.cif')
a = SlabGenerator(st, (1,1,0), 10, 0, center_slab=True, primitive=False) # can also use lll_reduce=True ?
new_st = a.get_slab()
cif_w = CifWriter(new_st)
cif_w.write_file('test.cif')
```
**Expected behavior**
For Case 1, expected a slab to be returned with one less row / plane of original slab. I expect it is being seen as a Laue group and hence returning the original structure. Note that you get the expected behaviour should you choose [1,1,0] direction.
For Case 2, expected an orthorhombic crystal or vacuum-less slab to be created. Instead, a sheared vector is made for one axis. This can also be seen if you add 1 Angstrom of vacuum that a orthorhombic structure should be made.
P.S. I would look into it but I am having issues without some admin commands at my institute with dependencies for install.
Let me know if something I did was wrong, or if you require more information.
**Version**
2018.9.12
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| 417,918,252
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MDU6SXNzdWU0MTc5MTgyNTI=
| 1,409
|
Structure.get_primitive_structure incredibly memory intensive
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[
"No to (a). I would say you can add an option to select the primitive finder for (b). Structure matching is meant to be symmetry independent. The Structure.get_primitive is also non-symmetry dependent. SpacegroupAnalyzer is symmetry dependent. \r\n\r\nIf you are getting structures from a expt database, by all means turn the tolerance down and use spglib to get a primitive version of the structure first. That is how we have always done this. \r\n\r\nAlso, ask @computron to buy you a better laptop. :-)"
] | 2019-03-06T17:15:37
| 2019-03-13T07:51:55
|
2019-03-13T07:51:55Z
|
MEMBER
|
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For certain structures, the `Structure.get_primitive_structure` can be incredibly memory intensive.
For example, for this structure (https://gist.github.com/utf/3982741b90a4fcb500998433e582d031), calling the function uses 20 GB of memory and takes ~2 min. Admittedly this structure has a very large unit cell (~800 atoms) but this memory usage is impractical.
Using the `SpacegroupAnalyzer.get_primitive_standard_structure` instead takes seconds with minimal memory use.
This is not a hypothetical structure and actually came from the Pearson crystal structure database.
This method is used by the `StructureMatcher.fit` function. When I originally tried to match several Pearson crystal structure database structures to Materials Project structures it crashed my computer due to memory use.
Can we:
a) Change `Structure.get_primitive_structure` to wrap `SpacegroupAnalyzer.get_primitive_standard_structure`.
or
b) Change `StructureMatcher` to instead use `SpacegroupAnalyzer`.
|
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MDU6SXNzdWU0MTk1Njc5NjI=
| 1,410
|
Wulffshape for hexagonal lattice
|
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[] | null |
[
"You do not have enough surface energies to generate a closed Wulff shape. Specifically, none of your surfaces contain the (001) direction. "
] | 2019-03-11T16:35:42
| 2019-03-13T07:54:03
|
2019-03-13T07:54:03Z
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NONE
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**Describe the bug**
When I try to construct a Wulff shape for a hexagonal lattice Qhull generates the error
QH6154 Qhull precision error: Initial simplex is flat (facet 1 is coplanar with the interior point
**To Reproduce**
Steps to reproduce the behavior:
Execute the following commands with python 3.6.7
from pymatgen.core.surface import Lattice
from pymatgen.analysis.wulff import WulffShape
lattice=Lattice.hexagonal(3.838,6.317)
surface_energies={(1, 1, 0): 79.1,
(0, 1, 0): 79.4}
miller_list = surface_energies.keys()
e_surf_list = surface_energies.values()
wulffshape = WulffShape(lattice, miller_list, e_surf_list)
**Desktop (please complete the following information):**
- OS: Ubuntu 18.04.2 LTS
- Version : 2018.11.6
**Additional context**
Add any other context about the problem here.
|
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MDU6SXNzdWU0MjAxNjk0Mjk=
| 1,411
|
Outcar class reads in elements for ZVAL dictionary non-robustly
|
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[
"This is not a bad idea, would be interested in implementing the change?",
"Not at this time. I expect to be very busy for the next while. Someone else\ncould almost certainly have it implemented before I would get around to it.\n\nOn Tue, Mar 12, 2019, 4:09 PM Matthew Horton <notifications@github.com>\nwrote:\n\n> This is not a bad idea, would be interested in implementing the change?\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1411#issuecomment-472161209>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AT9wCTnrwBKnb4qRlCMSs4edb2y5ybV1ks5vWAlegaJpZM4brt5w>\n> .\n>\n",
"I believe this was fixed by PR #1521 and so the issue can be closed",
"Thanks @sthartman "
] | 2019-03-12T19:36:16
| 2021-05-13T18:10:07
|
2021-05-13T18:10:07Z
|
NONE
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Hello,
The Outcar class in pymatgen.io.vasp reads in the atomic species by searching for the name of the POSCAR file in the OUTCAR. This is not required to have anything to do with the atomic species for VASP calculations and can cause errors importing OUTCARs made from POSCARS that were not produced with pymatgen. It may be better to search the OUTCAR for the POTCAR lines and pull the elements from the names of the pseudopotentials directly.
grepped POSCAR lines in OUTCAR example:
POSCAR: [literally any string could be here without changing calculation details]
POSCAR = [literally any string could be here without changing calculation details]
grepped POTCAR lines in OUTCAR example:
POTCAR: [pseudo type] [pseudo name #1 - starts with element] [date]
POTCAR: [pseudo type] [pseudo name #2 - starts with element] [date]
POTCAR: [pseudo type] [pseudo name #1 - starts with element] [date]
POTCAR: [pseudo type] [pseudo name #2 - starts with element] [date]
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MDExOlB1bGxSZXF1ZXN0MjYwNTA5NDA4
| 1,412
|
Fix Python 3.5 compatibility
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[
"Thanks. Though people should start moving to py36/37....",
"Btw: You are at TMS right? ",
"I was. Had to leave on Monday as I have to teach. "
] | 2019-03-12T19:40:42
| 2019-03-12T20:04:23
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2019-03-12T19:41:15Z
|
CONTRIBUTOR
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To prevent `TypeError: invalid file: PosixPath()`
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MDU6SXNzdWU0MjAyMTQ3NjQ=
| 1,413
|
Clarity on backwards compatibility given date-based versioning
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[
"In terms of backwards incompatibility, the most important thing is that v2019.x onwards is Python 3 only, which was announced both in the docs and in the mailing list.\r\n\r\nGenerally, I think pymatgen has been fairly good about backwards compatibility and deprecations. Have you noticed specific breaking changes that have caused problems, or have any been reported to you? Might be useful for discussion to have a specific example in mind.",
"Here's one strange example from the MP discussion forum: [https://discuss.materialsproject.org/t/get-entries-returns-empty-list-for-irru3/1976/3](https://discuss.materialsproject.org/t/get-entries-returns-empty-list-for-irru3/1976/3). I did not care to investigate what changed because the user's error was using the Nov 6, 2015 release of pymatgen.\r\n\r\nThe issue is that I *expected* breaking changes from e.g. `3.2.5` to `3.3.0` because @shyuep declared in #213 a license to break compatibility on minor version bumps. Now, I don't know what to expect going forward.",
"I would say that most changes are backwards compatible. It is fine if it is something that is understood to be a work in progress, e.g if you are coding a new analysis and is releasing a new version. We expect anyone using these bleeding edge features to adjust. But for the core, all changes are expected to be backwards compatible with a relatively long deprecation schedule (usually a year). That is why I took the step of warning people about 2019 py3 only from late 2017. \r\n\r\nNo one *needs* to upgrade as long as they are not using bleeding edge features. They can always install 2018 and we will support them all the same. ",
"I personally prefer semantic versioning precisely for the clarity of expectations. In `x.y.z`, if `x` changes expect backwards incompatible changes, if `y` changes expect new features, if `z` changes expect fixes.\r\n\r\nThat said, I don't see anything actionable in this issue so closing as completed.",
"I agree, I don't think there's anything imminently actionable here.\n\nThat said, I've come around a lot more strongly with regards to semantic versioning since the last time this thread was open. I realise it causes more overhead and work for us, but at a certain point when a package becomes important enough to other people's workflows, it becomes worth the investment.",
"I would challenge someone to find the last time that an actual backward-incompatible change occurred in pymatgen core classes. I get the *theoretical* argument for semantic versioning. But if the *practical* effect is negligible, then the choice is based on what is easiest for maintenance. I see too many proposals on ideal solutions but frequently, the execution is less than disciplined. I would rather spend the time ensuring things like unittest coverage, i.e., things that actually matter in terms of correctness of code.",
"> I would challenge someone to find the last time that an actual backward-incompatible change occurred in pymatgen core classes.\r\n\r\n[Today](https://github.com/materialsproject/pymatgen/commit/02dad560a1870473c28868f48c378c52ede1fc93#diff-5ea334b067925ce7079b569683cf7cc7ee088d0b19d62e4257f79cbb6aa73914R3300). I normalized the error messages which strictly speaking is a breaking change. If someone built a tool like `custodian` on top of pymatgen that reacts to certain error messages, that could be broken by [today's release](https://github.com/materialsproject/pymatgen/releases/tag/v2023.06.23). Very unlikely so I think it's fine but you asked. :)\r\n\r\nI agree tests are most important. Many of our tests were only checking the error class, not the error message. I found several tests where the expected error message was left as a comment but the actual error raised was not the one in the comment. `pymatgen`'s test coverage has a long ways still to go but at least I managed to test all messages on errors raised in `pymatgen.core` (https://github.com/materialsproject/pymatgen/commit/a9c3ca3fdfecbda890fb5e42c7a0fc5a908e71f9 https://github.com/materialsproject/pymatgen/commit/893cad7ca160cc302b09dbf8461f763b4118612b https://github.com/materialsproject/pymatgen/commit/0baff29897e0873021e79129517a4604cfe6d19d)",
"If you are suggesting that based on semantic versioning, you are going to increment the major version number for error messages, that is plainly ridiculous. ",
"If you take SV seriously, then yes. `numpy` or `pytorch` would not change error messages in a minor. I'm not that strict personally. I also don't see the connection between frequency of breaking changes and the discussion on what version scheme to use. SV is better for reasons mentioned above in any case."
] | 2019-03-12T21:30:17
| 2023-06-23T23:55:26
|
2023-06-23T22:38:27Z
|
MEMBER
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#213 clarified that backwards-incompatible changes used to be signaled with the bumping of the so-called minor version, e.g. someone upgrading pymatgen 3.3.x to 3.4.y should expect the possibility of breaking changes and should consult the [change log](http://pymatgen.org/change_log.html). However, since `v2017.6.8`, pymatgen has switched to date-based versioning. This is a problem because it makes every upgrade something for users to be cautious about. I am raising this issue now because a user asked me when they would "need" to upgrade next, and I don't know the answer.
Ideally, one release will have "long-term support" in that backwards-compatible bug fixes will be applied. Ubuntu handles this with date-based versioning by pledging long-term support of an April release each two years (e.g. 18.04 for the Apr 2018 release, 16.04 for the 2016 release, etc.).
I don't know the right path for pymatgen. Perhaps pymatgen could release backwards-incompatible changes only in each year's January release? Perhaps this is already the case, but I'd like this issue to be closed only on this being stated explicitly. Perhaps backwards-incompatible changes have already been introduced in released versions since v2019.1.13, in which case perhaps v2019.4 can be the version with only backwards-compatible changes until v2020.4.
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[WIP] Add user-agent header to MPRester session requests
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[
"Excellent idea!",
"Do you think it might be useful to add Python version also? It might also be a good idea to mention this in the docstring to ensure that users are appropriately informed that this information is being shared.",
"I'm on the fence for this from a user privacy perspective. In favor, I think this is very standard information that is included in, for example, any other kind of HTTP request in a user agent string (such as from a web browser). As long as it's disclosed appropriately in the docstring for MPRester I think this is ok, but I would welcome other input.\r\n\r\nFor a more expanded version, we could have:\r\n\r\n```\r\nimport sys\r\nimport platform\r\n\r\n... f\"pymatgen/{__version__} (Python {sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}) {platform.system()} {platform.release()}\"\r\n```\r\n\r\nWhich would give a user agent like `pymatgen/2019.2.28 (Python 3.7.0) Darwin 18.0.0`.\r\n\r\nI think this would be incredibly useful information in aggregate from a development perspective.",
"Sounds good to me. I amended your disclosure in the docstring to clarify the purpose and normalcy of user-agent headers.\r\n\r\nHowever, I'm not sure this is enough, and it gave me an additional idea that I believe could help tremendously for communicating important messages on pymatgen upgrades. This may be best done via a separate PR, but the idea is to store a flag e.g. `described_changes` in a user's `~/.pmg.rc` indicating whether a summary of this version's changes have been communicated to the user (I'd suggest via `warnings.warn`). We also want an e.g. `last_version` flag (default `None` on the first install). If `described_changes==False`, the relevant changelog sections are output, the flag is set to true, and `last_version` is updated. This way, we can e.g. clearly communicate the user-agent header addition in the case of users who do not consult the docstring, and in general, we can have more confidence that more users are aware of changes upon upgrade.\r\n\r\nI realize the above is not standard practice even the most important packages -- standard practice is to insist that users RTFM. So, I expect resistance, and I'd be okay with merging as is. However, in our case, many users may not even know to look for a changelog, releases are often packed with interesting new features that some users become aware of months/years later, and I think many contributors would love to know that their acknowledged contributions (via name- and @-mentions in the changelog) are announced to the entire userbase in what I feel is a suitable time and place.\r\n\r\nWow, that was long.",
"This will need tests also (to check that disabling the user agent does indeed delete it from the headers at least), for some reason `__version__` doesn't seem to be working on the AppVeyor tests.",
"Excellent, your case for being co-BDFL grows stronger by the day...",
"Thanks @dwinston, will merge once tests pass!"
] | 2019-03-12T22:26:15
| 2021-02-13T17:25:20
|
2019-03-27T23:43:30Z
|
MEMBER
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Add a user-agent header of [conventional syntax](https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/User-Agent) to identify pymatgen and its version to the MP server.
* Allows server, if it is running a later version of pymatgen than the user, to suggest upgrading (e.g. through adding a note in the response "warning" field).
* Allows server to collect statistics on pymatgen versions in active use for gathering MP data, and on what proportion of API use is via pymatgen.
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MDU6SXNzdWU0MjExNDQ1NjA=
| 1,415
|
Bug in `CifParser` for files with multiline blocks starting with `data_` prefix
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[
"I can certainly fix this problem, but as far as I know, this is bad CIF syntax. The ; is used as an indicator of a multiline string. Here, you have ; with `_iucr_refine_fcf_details`, which is not closed until after the data_symmetries loop.",
"@shyuep you are absolutely right, my mistake. I updated the example to a CIF syntax that should now be correct. Basically the problem lies in the fact that the multiline string contains a line that starts with `data_`. The parsing strategy of `CifParser` will split all blocks on that marker, however, in this case it is not the start of an actual data block but just an ordinary string, which is legal. The fix for #1407 merely \"fixes\" the `IndexError` being thrown because the `_iucr_refine_fcf_details` tag was without its accompanying value. But the rest of the parsing for structures will still fail because the `data_composition` is unjustly marked as a data block leading to later problems.",
"This is still incorrect. The data_symmetries have to be provided. Otherwise, the code cannot generate all the symmetrically equivalent positions.\r\n\r\nIn any case, I am closing this issue until an example can be provided from an actual public source that demonstrates the problem, rather than a hand-written CIF file. I prefer the CIF parsing code to be tested on real world data out there.",
"I tried to write a representative minimal working example because the real examples I have are pretty big. But [this is a real example from the COD](http://www.crystallography.net/cod/7045976.html) The COD has multiple CIFs like this that have the same problem and as far as I am aware, these have valid CIF syntax.",
"I downloaded the CIF. I opened it in VESTA, and I see nothing. ",
"Is data_symmetries in an official CIF dictionary? I understand there are a\nfew extensions to that also (I think there’s a symmetry CIF dictionary too)\n\nOn Fri, Mar 15, 2019 at 08:42, Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> I downloaded the CIF. I opened it in VESTA, and I see nothing.\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1415#issuecomment-473336025>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AC1rRDnqMtrAJR0m4cRANAZDjczh5Fp3ks5vW79PgaJpZM4b0x0g>\n> .\n>\n",
"For what it is worth, parsing it with `ase==3.12.0` manages to parse the cell:\r\n```\r\nimport ase.io\r\nIn [3]: ase.io.read('cif_problem_real.cif')\r\nOut[3]: Atoms(symbols='C144H176F48Fe4N48O16P8', pbc=[True, True, True], cell=[[15.8913, 0.0, 0.0], [9.730614839645167e-16, 15.8913, 0.0], [9.074510317001974e-16, 9.074510317001974e-16, 14.8198]], positions=...)\r\n```"
] | 2019-03-14T17:12:33
| 2019-03-15T15:53:11
|
2019-03-15T15:32:59Z
|
NONE
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**Describe the bug**
A bug in the `CifParser.from_string` method was reported in #1407 which was addressed in [this commit](https://github.com/materialsproject/pymatgen/commit/c34a6c0b69a6654bc6b8e9164341d5b8d6769e18). However, the solution does not actually solve the problem because now the `get_structures` method will fail to parse a valid structure.
**To Reproduce**
```
from pymatgen.cif.io import CifParser
cif = """
data_1526655
_journal_name_full
_space_group_IT_number 227
_symmetry_space_group_name_Hall 'F 4d 2 3 -1d'
_symmetry_space_group_name_H-M 'F d -3 m :1'
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_formula_units_Z 8
_cell_length_a 5.381
_cell_length_b 5.381
_cell_length_c 5.381
_cell_volume 155.808
_iucr_refine_fcf_details
;
data_symmetries
Some arbitrary multiline string
;
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_U_iso_or_equiv
Si1 Si 0 0 0 1 0.0
"""
parser = CifParser.from_string(cif)
parser.get_structures()
```
**Expected behavior**
A successfully parsed structure
**Desktop (please complete the following information):**
- Ubuntu 16.04
- On [unreleased commit](https://github.com/materialsproject/pymatgen/commit/c34a6c0b69a6654bc6b8e9164341d5b8d6769e18)
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MDU6SXNzdWU0MjE0MzI5NDc=
| 1,416
|
bug in work function plot
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[
"@richardtran415 Pls check and follow-up",
"What's more, the model I used is a surface slab model.",
"Looking into it"
] | 2019-03-15T09:45:27
| 2019-05-23T13:48:20
|
2019-05-23T13:48:20Z
|
NONE
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**Describe the bug**
if the slab contain any atom with very big frac_z (e.g. z = 0.99 which is supposed to be -0.01 due to the perodicity), the ave_bulk_p will be wrongly calculated because the the frac_z is not a right limitation of the bulk region.
**Expected behavior**
I think during the initiation, any site with such frac_z need to be converted to (frac_z -1) to avoid such thing.
**Screenshots**
the wrong calculation:
the right one after change the fra_z to fra_z -1 or just 0:
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| 1,417
|
[WIP] Piezo Sensitivity and Site symmetries packages added
|
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[
"Thanks for the contributions. Yes, you can add this to pymatgen.analysis. However, I would ask that you document the methods. Site symmetries should be put in the pymatgen.symmetry.analyzer module.",
"Are the site symmetry routines not uses in the PIezo sensitivity analysis?\r\n\r\nThings to do:\r\n- Write a Born Effective Charge (BEC), Internal Strain Tensor (IST), and Force Constant Matrix (FCM) tensor class; @shyuep Can we start collecting tensor quantities in a root level tensors module?\r\n- Add in the construction of the Piezo Tensor from BEC,IST, and FCM into the PiezoTensor Class\r\n- Add documentation\r\n- Make variable names more explicit so we don't have to guess what they are\r\n- We'll work on some algo clean up\r\n\r\n",
"Added documentation and classes for the separate tensors",
"Ok, fix the conflicts from the main branch. Then unit tests for all the functions. That will allow you to see what is still broken. Also expand out your abbreviations. It's better for public code to read almost like prose. ",
"Ooops, I don't think this was ready to be merged yet. @dongsenfo Can you make a new PR that addresses the outlined issues?"
] | 2019-03-15T22:56:08
| 2019-05-09T16:04:30
|
2019-05-09T02:34:48Z
|
CONTRIBUTOR
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WIP
## Summary
Added piezo_sensitivity and site_symmetry packages under analysis. Site_symmetries allow for users to get the point symmetries of atomic sites and symmetry operations relating sites. Piezo sensitivity allows for random generation of piezoelectric components and the calculation of the piezoelectric tensor from components
## TODO (if any)
Needs to be unit tested and style formatted. Not quite sure if this is the appropriate place for the packages but these are still heavily work in progress.
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MDU6SXNzdWU0MjE5MTQxNDg=
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I cant use the rotation function in the structure lib
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[
"`rotate_sites` is a function that is part of the Structure class, not the structure module.\r\nIn your code, use `structure1.rotate_sites`. The indices should be numbers.\r\nPls post such question at https://pymatgen.discourse.group in future. Github Issues is meant for bug reports and feature requests. "
] | 2019-03-17T12:03:36
| 2019-03-17T14:52:09
|
2019-03-17T14:52:09Z
|
CONTRIBUTOR
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Is there something wrong with my codes?
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MDExOlB1bGxSZXF1ZXN0MjYyMjE3OTI0
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|
Update to make new builder work
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[
"Thanks @jmmshn will merge once tests pass",
"There are some test errors related to the PR, `ERROR: test_as_dict_summary (pymatgen.apps.battery.tests.test_insertion_battery.InsertionElectrodeTest)`",
"oops, I forgot to check that before submitting",
"The checks all passed this time, I didn't account for the fact that the old test files did not have the muO2 data in the entries"
] | 2019-03-18T20:39:04
| 2019-03-20T21:08:47
|
2019-03-20T21:08:47Z
|
CONTRIBUTOR
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I updated some keys in the insertion_battery.py and added tests for muO2 data.
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MDExOlB1bGxSZXF1ZXN0MjYyMzg4ODg2
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Some bug fixes and binary van Arkel-Ketelaar triangle
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[] | 2019-03-19T10:14:11
| 2019-03-19T19:43:12
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2019-03-19T12:28:25Z
|
CONTRIBUTOR
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## Summary
Some fixes to the periodic boundary condition for plotting work function, new method for getting a primitive oriented unit cell, added binary van Arkel-Ketelaar triangle, temporary fix to ReconstructionGenerator tests, also new function to determine slab layer regions in a slab cell when the slab layer is not contiguous between 0 and 1.
* Temporary fix to ReconstructionGenerator test.
* van Arkel-Ketelaar triangle plots the electronegativity difference and mean for binary materials and categorizes their bonding type (ionic, covalent, metallic) based on these values and their position in the triangle. Available as a function in util/plotting.py
* Fixed the issue with WorkfunctionAnalyzer plotter where if the slab layer is not completely within 0 and 1 (periodic boundary condition problem), the average bulk potential is wrongly calculated. Fixed this problem by identifying the region of the slab layers regardless of pbc and then averaging the values again. This addresses issue #1416 . NOTE that due to the way the potentials in the slab region are sampled, you may get slightly different (0.04 eV) potetnials in the bulk. Just keep in mind this is an AVERAGED bulk potential in the slab cell.
* Added get_slab_region() function to surface.py, this function returns a list of ranges where the slab layer is. Values of these regions are alway between 0 and 1.
* Modified the lattice constraint behavior of get_primitive_structure() method for Structure class. Can now list the name of the parameter as well as a dict in order to limit your primitive cell search to specific lattice parameters.
* This will ensure that we always get the oriented unit cell corresponding to the primitive slab.
## TODO
* A better algorithm for generating a posteriori reconstructed surfaces.
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MDExOlB1bGxSZXF1ZXN0MjYyNDI0NzQy
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Update view_environment.py
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[] | 2019-03-19T11:56:54
| 2019-03-19T12:27:44
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2019-03-19T12:27:44Z
|
MEMBER
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## Summary
Updated the development script of ChemEnv to be compatible with Python 3.x
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Read WAVEDER file
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[
"Thanks for the contribution. However, please provide a unittest with an example input file of how this will be used. Thanks.",
"Hi @shyuep ,\r\n\r\nI guess I added a simple unittest in the test_outputs.py.\r\nCould you please check if its good enough?\r\n\r\nThanks\r\n",
"Thanks!"
] | 2019-03-20T15:04:58
| 2019-03-21T14:39:15
|
2019-03-21T14:39:10Z
|
CONTRIBUTOR
|
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Class for reading WAVEDER file. The WAVEDER file is produced invoking LOPTICS tag in VASP.
|
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MDExOlB1bGxSZXF1ZXN0MjYzMjQxODg3
| 1,423
|
New methods for COHP classes
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[] | 2019-03-21T13:47:38
| 2019-03-21T14:47:23
|
2019-03-21T14:47:22Z
|
MEMBER
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## Summary
Included a method which allows to get a summed orbital-resolved cohp and a method to assess whether there are antibonding contributions in a cohp below or at the Fermi level. I also included tests.
|
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MDU6SXNzdWU0MjQxNjg2MjM=
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Harmful standardize=True in MPNonSCF/MPStatic.from_prev_calc()
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[
"There are reasons why standardization is sometimes necessary.\r\nWhat I would suggest instead is that if standardize is True, the CHGCAR copy is not allowed and a warning is raised.",
"Yes, I think a warning is mandatory there.\r\nI am curious to know at least one case where is necessary to standardize at that point.\r\nI usually standardize at the very beginning...\r\n\r\nI would change also this notebook:\r\nhttp://matgenb.materialsvirtuallab.org/2017/04/14/Inputs-and-Analysis-of-VASP-runs.html\r\n\r\nin cell 5, a standardize=True appears to get a the input for bands calculation.",
"I would actually agree that standardize should be False by default for `from_prev_calc()`, though extra warnings sound sensible.",
"I am looking at pmg's sets and it seems that it is indeed standardize=False for from_prev_calc. Is there something we need to do here or can we close this issue.",
"As said, a warning if standardize=True is set would be very useful and, I would not copy the CHGCAR in that case.\r\nI'm still curious to know at least one case where is necessary to standardize at that point.\r\n\r\nI would change also this notebook:\r\nhttp://matgenb.materialsvirtuallab.org/2017/04/14/Inputs-and-Analysis-of-VASP-runs.html\r\nShall I open an issue in matgenb?",
"Added the warning and enforced copy_chgcar to be False. Pls modify the notebook in matgenb and submit a PR."
] | 2019-03-22T11:40:32
| 2019-04-01T14:27:35
|
2019-04-01T14:27:07Z
|
CONTRIBUTOR
|
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MPNonSCF/MPStatic.from_prev_calc(standardize=True) leads to have a CHGCAR from previous calculation and POSCAR with a NEW structure that does not match anymore with
the charge. This brings for example to a band structure completely wrong.
I think that the standardization of a structure should not be allowed in this function.
I got this problem with Ca2Si, but I guess the problem is not related to this particular material.
Note: even if the structure is already a standard primitive in the previous calculation,
sometime applying again the standardization leads to a different structure.
|
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MDU6SXNzdWU0MjQzMTQ4NTQ=
| 1,425
|
Pymatgen Slabs Not Json Serializable from .as_dict()
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[
"Generally, serialization is done using the MontyEncoder and MOntyDecoder. If you use that, the numpy array is automatically converted to a serializable form. The easiest way is to simply use the loadfn or dumpfn functions in monty.serialization.\r\n\r\n```python\r\nfrom monty.serialization import loadfn, dumpfn\r\ndumpfn(structure, \"structure.json\")\r\nstructure = loadfn(\"structure.json\")\r\n```\r\n\r\nOtherwise, you can use the MontyEncoder and MontyDecoder as the cls argument to json.load and json.dump.",
"hmmm, I thought the point of those functions was to just work in serialization. from the [usage](http://pymatgen.org/usage.html) page:\r\n\r\nThe output from an `as_dict` method is always json/yaml serializable. So if you want to save a structure, you may do the following:\r\n\r\n```\r\nwith open('structure.json','w') as f:\r\n json.dump(structure.as_dict(), f)\r\n```",
"If you look further down the usage page, there is a portion which says:\r\n\r\n```python\r\njson.dumps(object, cls=MontyEncoder)\r\n```\r\n\r\nWe can certainly make the dict completely json serializable. Given that the dict has more uses than simply being dumped into json, it is preferable to use the MontyEncoder to do the serialziation.\r\n"
] | 2019-03-22T17:14:01
| 2019-03-27T16:36:11
|
2019-03-22T17:15:53Z
|
NONE
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Currently pymatgen Structure objects are Json serializable from the `.as_dict()` but Slab objects are not Json serializable because the `scale_factor` variable is a numpy array.
This can be easily fixed by modifying the `as_dict` function to return it as a list like this:
d["scale_factor"] = self.scale_factor.tolist()
and the `from_dict` function to convert it back into a numpy array like this:
shift=d["shift"], scale_factor=np.array(d["scale_factor"]),
You guys may be able to think of a more elegant solution.
|
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Propagate site properties to orthogonal slab
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[
"CAn we have unittests pls? Thanks.",
"Unit tests added! :D"
] | 2019-03-22T20:11:30
| 2019-04-06T13:04:33
|
2019-04-06T13:04:33Z
|
CONTRIBUTOR
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## Summary
Previously site properties in slabs were not passed to the new slab when getting an orthogonal c slab.
|
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MDExOlB1bGxSZXF1ZXN0MjY0NjY3NTU0
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Allow user kpoints in NSCF calculations
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[
"Need unittests.",
"The tests failed.",
"THanks."
] | 2019-03-26T19:41:50
| 2019-03-26T22:09:03
|
2019-03-26T22:08:56Z
|
CONTRIBUTOR
|
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## Summary
Users were not able to supply their own kpoints settings in NSCF calculations. This pull request allows for a Kpoints object to override the Kpoints object generated by default by pymatgen.
This was an issue raised in atomate (https://github.com/hackingmaterials/atomate/issues/278)
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Add MagneticStructureEnumerator (moved from atomate)
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[] | 2019-03-27T20:13:21
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2019-03-27T20:13:36Z
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MEMBER
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Used to generate list of magnetic orderings from an input structure and MagOrderingTransformation by trying different enumeration strategies (eg antiferromagnetic, ferrimagnetic, afm/ferrimagnetic on different sub lattices, etc.)
Old code, moved from atomate. Works + tested, but subject to future improvements.
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MDExOlB1bGxSZXF1ZXN0MjY1MTM2NTc3
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|
Implement new OrderDisorderElementComparator
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[
"Thanks @utf! Will review and merge once tests pass",
"Can you think of any reason where the old behavior would be desirable? (I can't, just curious if this is an explicit bug or if there was a use case I wasn't considering)",
"I couldn't think of any scenarios where you'd want the old behavior. I think it is just an oversight.\r\n\r\nNote that this comparator won't allow matching disordered structures with partial occupancies (e.g. sum(site occupancies) != 1).\r\n\r\nI have an idea for a future PR to make this possible.",
"The old behavior is intentional. The reason was that disordered entries (for example in the ICSD) are often very approximate in their composition so you want to match partial occupancies with a lot of leeway. It is very easy to check the average composition either of the whole structure, or each individual site, after using StructureMatcher to check coordinates. It is hard to go the other way since StructureMatcher just returns no match.\r\n\r\nOne solution would be to add a tolerance on disordered composition, but this is so easy to do on a case-by-case basis after the fact that I personally very much prefer the old behavior.",
"Thanks for the input Daniil! We can certainly add an additional comparator\nwith fuzzy matching/with a tolerance. There’s also the discretize\noccupancies transformation as a preprocessor that might be suitable. It\nseems clear we do need a comparator that does compare occupancies as in\nthis fixed version however, and I would probably argue that’s its expected\nbehavior.\n\nOn Wed, Mar 27, 2019 at 18:25, Daniil Kitchaev <notifications@github.com>\nwrote:\n\n> The reason for the old behavior was that disordered entries (for example\n> in the ICSD) are often very approximate in their composition so you want to\n> match partial occupancies with a lot of leeway. It is very easy to check\n> the average composition either of the whole structure, or each individual\n> site, after using StructureMatcher to check coordinates. It is hard to go\n> the other way.\n>\n> One solution would be to add a tolerance on disordered composition, but\n> this is so easy to do on a case-by-case basis after the fact that I\n> personally very much prefer the old behavior.\n>\n> —\n> You are receiving this because you modified the open/close state.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1429#issuecomment-477407495>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AC1rRLl6xZ0vQmZdLD2OiUkcf7oTXI_Vks5vbBnsgaJpZM4cO-Z0>\n> .\n>\n",
"Fair enough, having a occupation fraction tolerance flag would make the behavior more transparent. I personally have a lot of code that relies on very loose occupation fraction matching as per the old behavior, but I'll just preserve the old comparator in my code internally. I agree that matching composition plus/minus a reasonable tolerance would be the expected behavior for a general user who is not relying on historical hacks.",
"Ok, that’s fair. Apologies for breaking backwards compatibility for your\ncode!\n\nOn Wed, Mar 27, 2019 at 20:28, Daniil Kitchaev <notifications@github.com>\nwrote:\n\n> Fair enough, having a occupation fraction tolerance flag would make the\n> behavior more transparent. I personally have a lot of code that relies on\n> very loose occupation fraction matching as per the old behavior, but I'll\n> just preserve the old comparator in my code internally. I agree that\n> matching composition plus/minus a reasonable tolerance would be the\n> expected behavior for a general user who is not relying on historical hacks.\n>\n> —\n> You are receiving this because you modified the open/close state.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1429#issuecomment-477433242>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AC1rRAte7fXS7NCWr3lVyGFEJr6_I3IMks5vbDb5gaJpZM4cO-Z0>\n> .\n>\n",
"@dkitch \r\nTo be clear are you talking about situations such as matching a Sn0.45 Pb0.55 O2 with SnPbO4 , ie the ordered counterpart only differs slightly from the disordered composition, or are you referring to something more extreme?",
"EDIT: I did originally misinterpret the behavior of the new code. It will still match different fractional compositions, so that's fine. The key difference is as I listed below. It still breaks my code but its for reasons that are probably too specific to my work to matter.\r\n\r\nThe difference in the two implementations is if we have a\r\n\r\nsite1: occupied by some combination of A and C\r\nsite2: occupied by some combination of A and D\r\n\r\nthey used to match while now they wont.\r\n\r\nThe situation where one might want the old behavior is if C and D are defect elements that don't matter for matching\r\n\r\nExample 1: Si p-doped with 0.1% B on the Si site should match to Si p-doped with 0.1% Al on the Si site, since they're both structurally Si. This issue comes up with processing experimental CIFs which often have defect elements listed as part of site occupancies. \r\n\r\nExample 2: Matching structural frameworks across different kinds of stabilizer elements. For example, you want to match prototypical yttria-stabilized zirconia to anything else that stabilizes cubic zirconia, since what you care about is the cubic zirconia not the stabilizer.\r\n\r\nWriting this up, I realize that whether or not you'd want this behavior depends entirely on whether or not you treat the dopant chemistry as important or just as \"there is some dopant\". In both cases, the alternative solution would be to round off low-concentration elements for the purposes of structure matching, or replace dopants with dummy species.\r\n",
"Ok,\r\n\r\nThis helps a lot as we're thinking about connecting the disordered ICSD entries to MP entries. I think there should be an explicit DisorderedWithDopantMatcher for these two cases, since it should only happen in the \"dilute\" limit which can be a user configurable parameter. ",
"Hi @dkitch, apologies for breaking your code.\r\n\r\nI agree with Shyam that there are two separate use cases here. I think the new behavior of OrderDisorderElementComparator makes sense and will be less confusing to users but I can see the utility of a more tolerant comparators that allows for dopant species."
] | 2019-03-27T23:30:09
| 2019-03-29T18:46:54
|
2019-03-28T00:06:55Z
|
MEMBER
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## Summary
The current OrderDisorderElementComparator will match in unexpected cases. E.g.,
1. A structure with the fractional composition Sn0.2 O0.8 will match a structure with the composition Sn0.5 O0.5.
2. A structure with a 50:50 Sn:Pb site would match with a structure with a 50:50 Sn:O site.
This PR fixes both scenarios and should allow proper matching of disordered structures to their ordered counterparts.
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MDU6SXNzdWU0MjY0ODM4MTA=
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Wigner Seitz cells appear too large in difficult cases
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[
"Do you have a suggested fix, would considering lattice points up to 2 unit cells away fix the edge cases?",
"I don't think it would cover _every_ case. In this example, the highlighted atom pair is three unit cells apart.\r\n\r\n\r\n\r\nA naive stab at an algorithm would be something like\r\n- get distances from origin to immediate periodic images, note the furthest distance (i.e. unit cell \"outer radius\") to use as threshold for search\r\n- add a shell of periodic images\r\n- repeat adding shells until a shell only adds points beyond the threshold.\r\n\r\nWould need a bit of pen and paper work to confirm if that is actually rigorous. It could certainly get expensive, which is why it would be very useful to have a geometric criterion (e.g. all angles greater than 30 degrees) to use the simpler routine. It does seem like the sort of problem that would have been solved a century ago, but all my textbooks have nice high-symmetry cases and avoid going near these \"bad primitives\".\r\n\r\nI also note that spglib is capable of generating a \"standard\" primitive cell with a more reasonable set of lattice angles. I'm not the crystallography expert that is needed to determine if that will always work!",
"Thanks @ajjackson, illustration is helpful!\r\n\r\nYes, you could definitely try the reduced cell (Structure.get_reduced_structure). Still, it would be nice to get this fixed.",
"Hi Adam!\r\n\r\nIf I'm following this properly, it seems like this function in pymatgen covers at least some of what you're suggesting.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/6a7a2c3442e0413affda32c3704895e9a5133b72/pymatgen/core/structure.py#L1020-L1048\r\n\r\n",
"Yes, I’m wondering if just getting sites in a sphere of radius (max lattice vector length) during Wigner Seitz construction would fix it?",
"Or not even sites, lattice points I should say.",
"Funnily enough the reason I was looking at the W-S construction was to get a radius for use with `get_sites_in_sphere`. That does seem like an approach that should work (or maybe with a radius equal to the maximum corner-to-corner distance in the unit cell?) but I'm not entirely confident with this kind of spatial reasoning.\r\n\r\nThe reduced structure approach could be more efficient. It does require a guarantee that a) the naive 1-cell-shell method always works with reduced structures and b) the rotational orientation does not change (so that the generated W-S cell matches your input lattice).",
"@dmrdjenovich has found a nice method for Wigner Seitz construction that is guaranteed to give the correct answer, and nicely side-steps the need to use the SciPy Voronoi too which has some stability issues in edge cases. I'll be working with him to integrate this method into pymatgen, stay tuned...",
"@mkhorton has there been any progress on this? ",
"Yes ... @dmrdjenovich wrote a method for this but we haven't checked in about it in a while. It still needed a SciPy Voronoi call at the end, so in that sense it's not the cleanest.",
"Hello All,\r\n\r\nI have implemented an algorithm that finds all 14 Voronoi vectors of a lattice in 3D space (some possibly non strict). This is a well-known algorithm from the lattice mathematical community.\r\n\r\nEach Voronoi vector is normal to a plane of the Voronoi envelope, and each plane is offset from the origin by half of a Voronoi vector translation. So together these 14 vectors define the Voronoi envelope. \r\n\r\npymatgen requires the output of the method to be a list of coordinates where the plane faces intersect. I’ve attempted to use the scipy.voronoi package to find these intersections; however, I’ve really struggled to understand how the package works. As of now that is the reason the code has not been fixed.\r\n\r\nIf anyone has any expertise on the package or has an alternative solution, I’d be happy to collaborate to finish the solution.\r\n\r\nBest,\r\nDavid",
"This issue has been outstanding for a number of years. So I am closing it. Feel free to reopen if still valid."
] | 2019-03-28T13:11:26
| 2023-08-10T14:59:05
|
2023-08-10T14:59:04Z
|
CONTRIBUTOR
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**Describe the bug**
The implementation of the Wigner-Seitz cell builder only considers lattice points up to one unit cell away
```python
for i, j, k in itertools.product([-1, 0, 1], [-1, 0, 1], [-1, 0, 1]):
list_k_points.append(i * vec1 + j * vec2 + k * vec3)
```
but this does not cover all possible crystal structures, and may lead to the construction of a cell that is too large.
**To Reproduce**
Calculating the distance from the origin to each surface of the WS cell
```
import numpy as np
from scipy.linalg import norm
from pymatgen import lattice
lat = lattice.Lattice.from_lengths_and_angles([5, 5, 3], [22, 90, 90])
def _distance_to_plane(facet):
# get a vector orthogonal to the plane
plane_vector = np.cross(facet[1] - facet[0], facet[2] - facet[0])
# project one of the plane points onto this vector
distance = abs(facet[0].dot(plane_vector)) / norm(plane_vector)
return distance
distances = map(_distance_to_plane, lat.get_wigner_seitz_cell())
print(list(distances))
```
which returns:
> [2.5, 1.4999999999999984, 1.2434311765228887, 2.5000000000000004, 1.2434311765228883, 1.4999999999999998]
**Expected behavior**
Expanding this lattice with the VESTA package we see that the nearest neighbour distance is 2.3171 Å. There should be a Wigner-Seitz cell surface running half-way through this line, giving a minimum distance from the origin to the cell boundary of 2.3171 / 2 = 1.15855
If the WS builder in Pymatgen is to be limited to "sensible" lattice vectors this should probably be mentioned in the docstring? Is there a way to detect problematic angles and raise a warning?
**Notes**
XCrySDen seems to have similar behaviour, here is its attempt at a W-S cell on the same lattice:
Clearly an atom-centered primitive cell should not contain any neighbouring atoms.
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MDU6SXNzdWU0Mjc1NzA5MDQ=
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io.phonopy.get_displaced_structures() calls for non-existent method
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[
"@mkhorton Can you look into this one",
"I’ll take a look. Phonopy changed a lot of their API recently, broke some workflows in atomate too.",
"Yeah, we're pinned to a pre-v2 version of phonopy, I'll update + see what else is broken. Looks like there also isn't a unit test with `yaml_fname` set in `get_displaced_structures` so I'll add one.",
"Fixed."
] | 2019-04-01T08:19:03
| 2019-04-12T04:34:03
|
2019-04-12T04:34:02Z
|
NONE
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**Describe the bug**
In the method _pymatgen.io.phonopy.get_displaced_structures()_,
the call to _phonon.get_displacement_directions()_ raises an error.
**To Reproduce**
Steps to reproduce the behavior:
**1**. import pymatgen.io.phonopy as pmg_phonopy
from pymatgen.core import Structure
**2** . s=Structure.from_file(your_structure_directory+"/POSCAR")
**3**. s_list = pmg_phonopy.get_displaced_structures(s,
yaml_fname="structure/phonopy/phonon.yaml")
**4**. See error :
/usr/local/lib/python3.6/dist-packages/pymatgen/io/phonopy.py in get_displaced_structures(pmg_structure, atom_disp, supercell_matrix, yaml_fname, **kwargs)
265 if yaml_fname is not None:
266 displacements = phonon.get_displacements()
--> 267 directions = phonon.get_displacement_directions()
268 write_disp_yaml(displacements=displacements,
269 supercell=phonon.get_supercell(),
270 directions=directions, filename=yaml_fname)
AttributeError: 'Phonopy' object has no attribute 'get_displacement_directions'
**Proposed fix**
The method phonon.get_displacement_directions() does not appear to exist anymore.
Luckily, the method phonopy.file_IO.write_disp_yaml() does not require direction anymore.
I think it should simply be updated in pmg :
In pymatgen the call is currently :
[write_disp_yaml(displacements=displacements, supercell=phonon.get_supercell(), directions=directions, filename=yaml_fname)](http://pymatgen.org/_modules/pymatgen/io/phonopy.html#get_displaced_structures)
The new syntax is :
[write_disp_yaml(displacements, supercell, filename='disp.yaml')](https://github.com/atztogo/phonopy/blob/master/phonopy/file_IO.py)
**Screenshots**
bug :
phonopy code :
pmg code :
**Desktop (please complete the following information):**
- OS: Ubuntu 18.04
- Browser Mozilla
**Additional context**
Using Jupyter Notebook on Emacs via ein.
|
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MDU6SXNzdWU0Mjc3MTI2NzI=
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pymatgen.io.aiida broken with aiida_core >= 1.0
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[
"I would say this depends entirely on the aiida developers. I would be fine with just deprecating this function and raising an error and pointing to the aiida package. Because there are no unittests written for pymatgen.io.aiida, we have no way of testing the functionality at all.\r\n\r\nI will just completely deprecate this module. I will push a change shortly.",
"I think this is fine, but I defer to @sphuber ."
] | 2019-04-01T13:42:09
| 2019-04-02T07:47:53
|
2019-04-01T14:08:49Z
|
NONE
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The [pymatgen.io.aiida](http://pymatgen.org/_modules/pymatgen/io/aiida.html) module is broken in AiiDA core v1.0 and onwards.
This is due to the refactoring of AiiDA which breaks the import line:
https://github.com/materialsproject/pymatgen/blob/5f652417aa3a03214e8dfe726fc9747ed71f13e2/pymatgen/io/aiida.py#L21
The code falls through into the except block, setting the `aiida_loaded` flag to false and preventing any of the methods from being used.
Should be straightforward to fix and happy to contribute a pull request, but it would be good to have some input as to whether it should be fixed.
Within AiiDA core, it is now straightforward to convert to and from Pymatgen structure objects. Any fix would need to support AiiDA before and after v1.0, in principle. So alternatively, as AiiDA does these things, does it make sense to simply deprecate this function and, if you have AiiDA > v1.0, print a warning to this effect?
Would be great to hear your thoughts!
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MDExOlB1bGxSZXF1ZXN0MjY2Nzk0ODkx
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Update LICENSE.rst
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[] | 2019-04-02T20:21:26
| 2021-02-13T17:25:53
|
2019-04-02T23:48:33Z
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MEMBER
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## Summary
Change institution for license from LBNL to UC Regents via LBNL
|
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MDExOlB1bGxSZXF1ZXN0MjY2ODA1MTYw
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Allow averaging of site_properties when merging sites
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[] | 2019-04-02T20:53:19
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2019-04-02T23:48:17Z
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CONTRIBUTOR
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## Summary
Added new mode for merge_sites and updated test_merge_sites
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MDExOlB1bGxSZXF1ZXN0MjY3OTIwNzkx
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Hops dev
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[
"Pls check the pymatgen-diffusion package and make sure it is not already implemented there.",
"Even if some parts of it is not implemented there, I would prefer if those portions be integrated there rather than having duplicate code. E.g., I think charge density is not implemented (though our experience is that the charge density actually does not work that well). But unique path enumeration is already there.",
"@shyuep there's already a path finder in pymatgen also? in pymatgen.analysis.path_finder, there's definitely already some charge density analysis in pymatgen\r\n\r\n@jmmshn maybe a more descriptive PR title? :)",
"@mkhorton The pathfinder in pymatgen does not do enumeration of paths. It merely finds a path based on given start and end points and a potential. Pymatgen-diffusion's pathfinder enumerates ALL points, and there are other potentials implemented like the IDPP relaxer (which we find to be a lot more reliable than the Static Potential). ",
" \n \n\n Thanks for the feedback. I think the path_finder in pymatgen is for getting the geometry of the individual hop. It can be incorporated into this workflow to come up with a better scalar descriptor for a given hop. \n \n\n \nI will look at pymatgen-diffusion more to see if there is a better place to put this.\n \n\n \n@shyuep can you elaborate on your experience with using the charge density?\n \nI had trouble using the charge density alone — so using the local minima as the initial and final positions. But using the relaxed positions seems to work much better but I’m still in the testing phase so any input will be greatly appreciated.\n \n \n \n -Jimmy \n \n\n \n \n> \n> On Apr 5, 2019 at 11:36 AM, <Matthew Horton (mailto:notifications@github.com)> wrote:\n> \n> \n> \n>\n> @shyuep (https://github.com/shyuep) there's already a path finder in pymatgen also? in pymatgen.analysis.path_finder, there's definitely already some charge density analysis in pymatgen\n>\n> \n>\n> @jmmshn (https://github.com/jmmshn) maybe a more descriptive PR title? :)\n>\n> \n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub (https://github.com/materialsproject/pymatgen/pull/1435#issuecomment-480380207), or mute the thread (https://github.com/notifications/unsubscribe-auth/ANWt7QiR7I89IxwfgWU1qE8NJCnnLM_Lks5vd5e0gaJpZM4cfevP).\n>\n> \n> \n \n \n ",
"Understood\n\nOn Fri, Apr 5, 2019 at 11:39, Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> The pathfinder in pymatgen does not do enumeration of paths. It merely\n> finds a path based on given start and end points and a potential.\n> Pymatgen-diffusion's pathfinder enumerates ALL points, and there are other\n> potentials implemented like the IDPP relaxer (which we find to be a lot\n> more reliable than the Static Potential).\n>\n> —\n> You are receiving this because you commented.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1435#issuecomment-480380988>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AC1rRA57hElFKd26y9MmdDM97E_EL6eJks5vd5hNgaJpZM4cfevP>\n> .\n>\n",
"@jmmshn In general, the charge density is tends to be very shallow. Even if you use local minima, that minima is spread across a large spatial region. Further, cation-cation repulsion plays a big role in stabilization of sites. While the method may work marginally for dilute limits, e.g., single Li in FePO4, it does not work well when you have non-dilute diffusion.\r\n\r\nAs a general schematic of how I think we can merge all these efforts, I suggest the following:\r\n\r\ni. Let's keep diffusion stuff in pymatgen-diffusion. I am happy to add you as a co-contributor. We have no plans of writing a paper based on that code base, but you will be recognized.\r\nii. I would prefer to keep the current schematic of how pymatgen-diffusion implements path enumeration, but with some changes. The path enumeration code should be modified to include both vacancy and species diffusion. The enumeration identifies start and end points. We can then implement an abstract Path maker class which can be subclassed to construct different paths. E.g., LinearInterpolationPath, IDPPPath, ChargeDensityPath, etc.",
"@shyuep \r\n\r\n> In general, the charge density is tends to be very shallow. Even if you use local minima, that minima is spread across a large spatial region. \r\n\r\nI was actually running into this exact problem. In my experience, the local minima is a good way to suggest initial positions to try but you really have to use the relaxed position to map out the migration path.\r\n\r\n> i. Let's keep diffusion stuff in pymatgen-diffusion. I am happy to add you as a co-contributor. We have no plans of writing a paper based on that code base, but you will be recognized.\r\n\r\nThanks!\r\n\r\n> ii. I would prefer to keep the current schematic of how pymatgen-diffusion implements path enumeration, but with some changes. The path enumeration code should be modified to include both vacancy and species diffusion. The enumeration identifies start and end points. We can then implement an abstract Path maker class which can be subclassed to construct different paths. E.g., LinearInterpolationPath, IDPPPath, ChargeDensityPath, etc.\r\n\r\nThis sounds like a good path forward. I will look at pymatgen-diffusion and figure out how to do this.\r\nI will close this PR for now."
] | 2019-04-05T18:22:18
| 2019-04-05T19:53:53
|
2019-04-05T19:53:53Z
|
CONTRIBUTOR
|
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## Summary
New methods for analyzing the migration path of a material using the following scheme:
1. start with an empty structure and multiple structures with a single cation
2. Map the positions of the relaxed structures back onto the empty host lattice
3. Apply symmetry operations of the empty lattice to obtain the other positions of the intercollated atom
4. Get the symmetry inequivalent hops
5. Get the total charge density that each inequivalent hop in the system has to move through
6. Map all the values obtained for these unique hops onto the full set of hops
The end results of this analysis a dataframe that contains all the hops in the lattice and total amount of charge density that each hop as to move through.
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MDU6SXNzdWU0MzAxMjg2NzU=
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GulpCaller crashes because cell input string too long
|
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[
"This workaround makes code above run without problem\r\n```\r\ndef prepare_input(bad_input):\r\n input = ''\r\n for n, line in enumerate(bad_input.split('\\n')):\r\n if n == 2:\r\n input += '{:.6f} {:.6f} {:.6f} {:.6f} {:.6f} {:.6f}'.format(*map(float, line.split())) + '\\n'\r\n else:\r\n input += line + '\\n'\r\n return input\r\n```"
] | 2019-04-07T10:31:28
| 2019-05-01T13:05:12
|
2019-05-01T13:05:12Z
|
NONE
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**Describe the bug**
Gulp cannot parse cell if it is too long
**To Reproduce**
Steps to reproduce the behavior:
`from pymatgen.command_line.gulp_caller import GulpCaller, BuckinghamPotential, GulpIO
from pymatgen import Structure
struct = Structure.from_str("""Mg2 Al4 O8
1.0
5.003532 0.000000 2.888790
1.667844 4.717375 2.888790
0.000000 0.000000 5.777581
O Mg Al
8 2 4
direct
0.736371 0.736371 0.736371 O
0.263629 0.263629 0.709114 O
0.263629 0.709114 0.263629 O
0.709114 0.263629 0.263629 O
0.736371 0.290886 0.736371 O
0.290886 0.736371 0.736371 O
0.263629 0.263629 0.263629 O
0.736371 0.736371 0.290886 O
0.125000 0.125000 0.125000 Mg
0.875000 0.875000 0.875000 Mg
0.500000 0.500000 0.000000 Al
0.500000 0.500000 0.500000 Al
0.000000 0.500000 0.500000 Al
0.500000 0.000000 0.500000 Al""", fmt='poscar')
bp = BuckinghamPotential(bush_lewis_flag="bush")
gio = GulpIO()
input = gio.buckingham_input(struct, ['relax conp'])
caller = GulpCaller()
gout = caller.run(input)`
**Expected behavior**
If I copy input generated by buckingham_input but cut cell parameters to reasonable amount of characters after . gulp runs without problems
Instead I got
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! ERROR : Insufficient cell parameters in input
!! : Error is apparently on line 3
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
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MDU6SXNzdWU0MzAxMzA2NTQ=
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GulpIO.get_energy cannot get enthalpy (under pressure)
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[] | null |
[
"```\r\ndef get_energy(self, gout):\r\n energy = None\r\n enthalpy = None\r\n for line in gout.split(\"\\n\"):\r\n if \"Total lattice energy\" in line and \"eV\" in line:\r\n energy = line.split()\r\n elif \"Non-primitive unit cell\" in line and \"eV\" in line:\r\n energy = line.split()\r\n elif \"Total lattice enthalpy\" in line and \"eV\" in line:\r\n enthalpy = line.split()\r\n if energy:\r\n return float(energy[4])\r\n elif enthalpy:\r\n return float(enthalpy[4])\r\n else:\r\n raise GulpError(\"Energy not found in Gulp output\")\r\n```\r\nfix can be like this",
"Thanks. Can you pls implement the fix in a fork and submit a PR?"
] | 2019-04-07T10:56:10
| 2023-08-13T16:32:53
|
2023-08-13T16:32:53Z
|
NONE
|
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**Describe the bug**
If pressure is not zero, gulp prints "Total lattice enthalpy" instead of "Total lattice energy"
and output cannot be parsed by GulpIO().get_energy()
**To Reproduce**
Steps to reproduce the behavior:
Try to read any gulp calculation with pressure
**Expected behavior**
A clear and concise description of what you expected to happen.
get_energy() returns enthalpy or energy
|
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MDU6SXNzdWU0MzA3OTQyMTE=
| 1,438
|
New constructor _BaderAnalysis.from_ACF()_
|
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[] | null |
[
"Sure. Pls go ahead and implement and submit a pull request. Thanks,",
"Ok :-) ",
"This issue has been outstanding for a number of years. So I am closing it. Feel free to reopen if still valid."
] | 2019-04-09T06:45:29
| 2023-08-10T14:58:05
|
2023-08-10T14:58:05Z
|
NONE
|
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**Is your feature request related to a problem? Please describe.**
In the module _pymatgen.command_line.bader_caller_
I would like to build an instance of _BaderAnalysis_ from an already calculated Bader data so as to avoid repeating the summation each time I study the run without the need to dump a json.
Consequently, I would also need an option in the method _bader_analysis_from_path_ to store the resulting ACF.dat (and CHGCAR_ref and CHGCAR_mag) in a permanent directory (and not a temp_dir which would instead be the default behavior).
**Describe the solution you'd like**
This would imply
**1)** to have a constructor _BaderAnalysis.from_ACF()_ , relying upon an isolated ACF_parsing method oustide of the _init_().
**2)** to have a flag "results_path" in bader_analysis_from_objects() with a default to None (current behavior with temp_dir) which would indicate the permanent parent directory if any.
**Describe alternatives you've considered**
The alternative of using JSON to dump only the results in the directory is fine but requires a specific workflow which impedes some users to access the very useful methods _get_charge_transfer()_ and _get_oxidation_state_decorated_structure()_ This feature will allow more flexibility at a minimal coding expense.
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MDExOlB1bGxSZXF1ZXN0MjY4NzIzNjMx
| 1,439
|
New lobsterout class plus tests
|
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[] | 2019-04-09T12:49:07
| 2019-04-09T14:46:19
|
2019-04-09T14:46:19Z
|
MEMBER
|
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## Summary
I included a class to read lobsterout files from Lobster (www.cohp.de). Regarding the design of the class, I am happy to do some adaptions. I have also included several tests to make sure that the files are read in correctly. This class might be extended in the future to cover newer features of Lobster.
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MDExOlB1bGxSZXF1ZXN0MjY5MjY4Mjkw
| 1,440
|
allow the MimimumDistanceNN class to only use the cutoff distance as …
|
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[
"Thanks @jmmshn, will merge once a test has been added"
] | 2019-04-10T18:00:46
| 2019-04-11T04:17:21
|
2019-04-11T04:17:21Z
|
CONTRIBUTOR
|
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## New option in MimimumDistanceNN
Allow the MimimumDistanceNN class to only use the cutoff distance as the filter.
So you can ignore the tolerance value.
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MDU6SXNzdWU0MzI5MzkyNDY=
| 1,441
|
dielectric function parsing in OUTCAR lists "frequencies" but it should be energies
|
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[] | 2019-04-14T06:49:21
| 2019-04-14T14:35:20
|
2019-04-14T14:35:20Z
|
MEMBER
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**Describe the bug**
The OUTCAR parsing in pymatgen can parse the dielectric function. The first column is the energies (in eV). Pymatgen lists this column as "frequencies". It should be called "energies".
This is what an OUTCAR looks like for dielectric function - note the first column is E in eV
```
frequency dependent IMAGINARY DIELECTRIC FUNCTION (independent particle, no local field effects)
E(ev) X Y Z XY YZ ZX
--------------------------------------------------------------------------------------
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.142760 20.788117 20.788117 20.788117 -0.000000 -0.000000 0.000000
0.285519 22.627524 22.627524 22.627524 0.000000 0.000000 0.000000
0.428279 22.343548 22.343548 22.343548 -0.000000 0.000000 0.000000
```
**Additional context**
See lines:
pymatgen/io/vasp/outputs.py:1843
```
if component == "IMAGINARY":
freq.append(float(toks[0]))
```
and:
pymatgen/io/vasp/outputs.py:1856
```
self.frequencies = np.array(freq)
```
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| 434,819,906
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MDU6SXNzdWU0MzQ4MTk5MDY=
| 1,442
|
waveder AttributeError: can't set attribute
|
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[
"This is also the case for the `nbands` and `nelect` attributes.",
"I am also a little confused about cder_data. Should it be a complex vector with x,y,z components for each spin? Then it should have 6 float numbers for each (band1, band2, kpoint, spin)? But from the code, we only get 3 float numbers. It should be similar to the data in wavederf, right? ",
"I was also having this issue, I believe the datatype for the cder should be \"complex64\". E.g. the data is composed of two 32 bit numbers (real and imaginary component). However, looking at the VASP code, it seems like the exact format of the data will depend on whether the wave function is complex or not. I don't know when the wave function is not complex but the code seems like this could happen (perhaps when using the Gamma only version of VASP).\r\n\r\nUnfortunately, even setting the dtype of cder to be complex, I couldn't get agreement between the WAVEDER and WAVEDERF file. \r\n\r\nAnother thing to note is that `nelect` is incorrectly named. It is not actually the number of electrons. In practice I think it will just be the same as `nbands`.",
"Yes, the wave function is not complex if it’s gamma point only.",
"Any idea what's the unit of numbers in cder_data?",
"Seems to be standard unit J/m, right?",
"So can someone fix this and submit a PR?",
"@knc6, you contributed the WAVEDER class, could you comment on this or would you be willing to submit a fix as appropriate?"
] | 2019-04-18T15:08:43
| 2019-06-18T20:05:10
|
2019-06-18T20:05:10Z
|
NONE
|
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Unable to use the Waveder class in pymatgen.io.vasp.outputs
Error message below:
```
4400 cder_data = cder.reshape((nbands, nelect, nk, ispin, 3))
4401 self.cder_data = cder_data
-> 4402 self.nkpoints = nk
4403 self.ispin = ispin
4404 self.nelect = nelect
AttributeError: can't set attribute
```
I think this because nkpoints is a property and cannot be set.
Change nkpoints to _nkpoints and change the nkpoints method accordingly will probably fix the problem.
|
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MDExOlB1bGxSZXF1ZXN0MjcxODE1NDY4
| 1,443
|
Speed up get_ir_reciprocal_mesh function
|
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[
"Fantastic, thank you!"
] | 2019-04-18T19:53:01
| 2019-04-18T20:42:20
|
2019-04-18T20:42:20Z
|
MEMBER
|
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|
## Summary
Currently the implementation of `SpacegroupAnalyzer. get_ir_reciprocal_mesh` is woefully slow for very large meshes (due to unnecessary repeated calls to `list.count`). This pull request massively speeds up the implementation.
GaAs using a 80x80x80 k-point mesh, the time to calculate the ir mesh went from 120 seconds to less than 1 second.
|
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MDExOlB1bGxSZXF1ZXN0MjcyMTIwNzEw
| 1,444
|
Fast pbx
|
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[] | 2019-04-20T00:49:52
| 2019-04-20T00:50:03
|
2019-04-20T00:50:03Z
|
CONTRIBUTOR
|
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|
## Summary
The fast pourbaix construction algorithm is applied to the get_decomposition_energy method within the pourbaix_diagram.py script.
Within the get_decomposition_energy method:
* Checks for a consistent composition between forced entry and pourbaix diagram
* If composition is consistent, calls the fast pourbaix algorithm to evaluate forced entry stability
* If composition is not the same, issues a warning and calls the original pourbaix algorithm to evaluate forced entry stability
|
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MDExOlB1bGxSZXF1ZXN0MjcyMTg0NzE4
| 1,445
|
Updated run_type method.
|
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[
"Hi @darnoceloc, thanks for your PR. Can you review the failing tests, and also check the diff, it looks like this PR is accidentally removing the `Waveder` class? You might be working from an old branch.",
"Some of the errors are coming from test files according to the **python3 setup.py nosetests** routine.\r\nI've checked my versions of the test_phonopy, phonopy, test_cohp and cohp files with your current versions and see no differences in the lines which are causing the errors.\r\n\r\nI also updated my io.vasp.outputs.py file to include the Waveder class, I'm not sure why this update was not synced in my local/remote verions after I compared my remote fork with the original master and submitted a pull request and merged.\r\n\r\nAlso what exactly do you mean by **check the diff**?\r\n\r\n\r\n",
"On GitHub, you can review the changes proposed by your pull request (that’s\nwhat I meant by “check the diff”), in reference to it there were any\ninadvertent changes you didn’t mean to make, such as removing the Waveder\nclass.\n\nOn Sun, Apr 28, 2019 at 18:13, darnoceloc <notifications@github.com> wrote:\n\n> What exactly do you mean by check the diff?\n>\n> —\n> You are receiving this because you commented.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1445#issuecomment-487431530>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRBYJEYPNVTF7A6YOLTPSZDTTANCNFSM4HHKU3EQ>\n> .\n>\n",
"Why would new errors emerge after I already corrected the previous ones?\r\nIf there are issues with test files, does the user/collaborator have to rectify those as well?\r\nAll the errors I am currently encountering are with test files which I did not create or modify.",
"Closed in favor of @darnoceloc's new PR at #1459 "
] | 2019-04-21T00:11:27
| 2019-05-09T02:28:26
|
2019-05-09T02:28:26Z
|
CONTRIBUTOR
|
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Updated run_type method to account for greater range of functional variations and combinations.
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Add prototypes from part 2 of the AFLOW prototype library
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[] | 2019-04-23T17:48:53
| 2023-08-10T14:59:25
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2023-08-10T14:59:25Z
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MEMBER
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AFLOW released ~300 more prototypes as part 2 of their library of crystallographic prototypes. These should be added to the `AflowPrototypeMatcher`.
https://www.sciencedirect.com/science/article/pii/S0927025618307146
Assigning this to myself.
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Plot fatbands from Lobster and option to force the reading of hybrid-like bandstructure for other functionals
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[
"I had to fix another test (a borg test). Not sure it was the correct thing to do.",
"Thanks for this PR, the new functionality looks very useful.\r\n\r\nIt's not clear to me why the Borg test needed to be changed because of the new functionality you've added? How does the ComputedEntry differ from previously?",
"It changed from 8 to 11. I have included a lot of new test data, e.g. 3 new \"vasprun.xml\" files. ",
"Oh, understood, it's just that there are extra vaspruns in the test dir now. Thank you!",
"Okay, great. I will soon demonstrate the functionality in the jupyter notebook with examples for plottig lobster files with pymatgen. ",
"Can it be merged or should I do something else? Thanks.",
"No, I think this is good to go! Thanks.\n\nOn Fri, Apr 26, 2019 at 01:59, J. George <notifications@github.com> wrote:\n\n> Can it be merged or should I do something else? Thanks.\n>\n> —\n> You are receiving this because you commented.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1447#issuecomment-486983182>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWREE55CDUXG32ZIQ7TDPSK76PANCNFSM4HIEDGUQ>\n> .\n>\n",
"Oh, actually there seems to be a large commented out Kpoint test in this PR?",
"Sorry, my fault. I excluded it for running the test faster and did not include it later. I hope it is okay now. ",
"All ok! Thanks again for such a nicely-documented and tested pull request.",
"There are failing CircleCI tests when this was merged. Basically there is a segfault.... Can you two look into this.",
"@JaGeo have you seen this before? Test log is here https://circleci.com/gh/materialsproject/pymatgen/8474 If not, we may have a larger issue, since this isn't the first time we've seen segfaults in Circle recently where the same tests were passing locally and on Travis.",
"I haven't seen this before but I will have a look at it again.",
"It seems that some of my new tests run differently on different operating systems. They worked fine on one but fail on the other. I will open a new pull request with the adapted tests. I also had some other problems while running the tests locally. I hope this will resolve the issue but I am not sure yet.",
"Thanks @JaGeo!\n\nOn Thu, May 2, 2019 at 03:01, J. George <notifications@github.com> wrote:\n\n> It seems that some of my new tests run differently on different operating\n> systems. They worked fine on one but fail on the other. I will open a new\n> pull request with the adapted tests. I also had some other problems while\n> running the tests locally. I hope this will resolve the issue but I am not\n> sure yet.\n>\n> —\n> You are receiving this because you modified the open/close state.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1447#issuecomment-488617770>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRGVYVOTQ5TXITR6ILDPTK3YHANCNFSM4HIEDGUQ>\n> .\n>\n"
] | 2019-04-24T13:49:09
| 2019-05-02T14:30:52
|
2019-04-28T20:54:59Z
|
MEMBER
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##
I included classes and tests to plot FATBAND files from Lobster. I had to add several classes to do so. I also added tests.
Furthermore, I added an option to the Vasprun class to make it possible to read in self-consistent band structure calculations for every type of functional. I have already needed this several times before.
I am happy to rename options or work on the documentary again if anything is unclear.
|
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”UserWarning:The input structure does not match the expected standard primitive!“
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[
"I really want to know the answer. If my description is not clear, please let me know. Thank you very much",
"@hautierg Can you help with this?",
"The issue with CifWriter, which doesn't write the lattice matrix, but rather the a,b,c lengths and angles: https://github.com/materialsproject/pymatgen/blob/9d8c75e87f9d4bb280adf4de274872a031a591a6/pymatgen/io/cif.py#L1226-L1231",
"@shyamd @hautierg The cartesian representation of a lattice has no meaning in crystallography (or in VASP). This is actually something I stress in my crystallography class. I don't remember ever seeing a CIF with the actual lattice matrix in it.\r\n\r\nIf the bandstructure code needs to check lattices, it should be checking the lattice parameters, not the actual cartesian basis vectors.",
"Correct, but the structure needs to be in the correct convention to work with the K-point generation scheme and the CIF format takes that away. @tlsong, make sure you keep your structure as a pymatgen object, otherwise, you will get this warning. ",
"@shyamd I don't see how the kpoint generation scheme is related to what I just said? The CIF format does not take the convention away.",
"@shyuep , Sorry, I implicitly meant that you're correct. This is not a CIFWriter issue, but rather the OPs use of the CIF format. OP gets the warning because they are writing to CIF and then reading back. This causes the read back structure to not be in the convention that HighSymmKPath needs. OP should keep the structure in pymatgen structure format and they won't see this warning.",
"@shyuep @shyamd \r\nThank you very much!\r\n",
"@shyuep @shyamd \r\n\r\nExport the strucutre in POSCAR format, will give true.\r\n**1.**\r\n`\r\nfrom pymatgen import Structure\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\nimport numpy as np\r\n\r\nstructure = Structure.from_file('Si_mp-149_computed.cif')\r\nspg_analy =SpacegroupAnalyzer(structure)\r\nprimitive_standard_structure=spg_analy.get_primitive_standard_structure(international_monoclinic=False)\r\nprimitive_standard_structure.to(fmt=\"poscar\", filename=\"primitive_standard_structure_POSCAR\")\r\n`\r\n**2.**\r\n\r\n`\r\nfrom pymatgen import Structure\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\nimport numpy as np\r\n\r\nstructure = Structure.from_file('primitive_standard_structure_POSCAR')\r\nspg_analy =SpacegroupAnalyzer(structure)\r\nprimitive_standard_structure=spg_analy.get_primitive_standard_structure(international_monoclinic=False)\r\nprint(np.allclose(structure.lattice.matrix,primitive_standard_structure.lattice.matrix))\r\nprint(structure.lattice.matrix)\r\nprint(primitive_standard_structure.lattice.matrix)\r\n`\r\n**output:**\r\nTrue\r\n[[0. 2.734364 2.734364]\r\n [2.734364 0. 2.734364]\r\n [2.734364 2.734364 0. ]]\r\n[[4.39719268e-16 2.73436400e+00 2.73436400e+00]\r\n [2.73436400e+00 0.00000000e+00 2.73436400e+00]\r\n [2.73436400e+00 2.73436400e+00 3.34863012e-16]]\r\n\r\nThank you very much!",
"Sounds good. I'm closing this now."
] | 2019-04-24T16:20:15
| 2019-05-09T02:14:25
|
2019-05-09T02:14:23Z
|
NONE
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Hello, dear developers
When I do the band calculation，it always gives this：
“UserWarning:
The input structure does not match the expected standard primitive! The path can be incorrect. Use at your own risk.”
So，I check it carefully，use these code：
**1. first step:**
`
from pymatgen import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
import numpy as np
structure = Structure.from_file('Si_mp-149_computed.cif')
spg_analy =SpacegroupAnalyzer(structure)
primitive_standard_structure=spg_analy.get_primitive_standard_structure(international_monoclinic=False)
primitive_standard_structure.to(fmt='cif', filename='Si_mp-149_primitive_standard_structure.cif')
print(np.allclose(structure.lattice.matrix,primitive_standard_structure.lattice.matrix))
print(structure.lattice.matrix)
print(primitive_standard_structure.lattice.matrix)
`
**output:**
False
[[3.34889826 0. 1.93348731]
[1.11629942 3.15737156 1.93348731]
[0. 0. 3.86697462]]
[[4.39719264e-16 2.73436398e+00 2.73436398e+00]
[2.73436398e+00 0.00000000e+00 2.73436398e+00]
[2.73436398e+00 2.73436398e+00 3.34863009e-16]]
**2. second step:**
**use the structure file "Si_mp-149_primitive_standard_structure.cif" from step1.**
`
from pymatgen import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
import numpy as np
structure = Structure.from_file('Si_mp-149_primitive_standard_structure.cif')
spg_analy =SpacegroupAnalyzer(structure)
primitive_standard_structure=spg_analy.get_primitive_standard_structure(international_monoclinic=False)
print(np.allclose(structure.lattice.matrix,primitive_standard_structure.lattice.matrix))
print(structure.lattice.matrix)
print(primitive_standard_structure.lattice.matrix)
`
**output:**
False
[[3.34889826 0. 1.93348731]
[1.11629942 3.15737156 1.93348731]
[0. 0. 3.86697462]]
[[4.39719264e-16 2.73436398e+00 2.73436398e+00]
[2.73436398e+00 0.00000000e+00 2.73436398e+00]
[2.73436398e+00 2.73436398e+00 3.34863009e-16]]
**Why does "np.allclose(structure.lattice.matrix,primitive_standard_structure.lattice.matrix)" give "False" in the step 2 ??**
The structure file download from here:
[Si_mp-149_computed.cif](https://materialsproject.org/materials/mp-149/cif?type=computed&download=true)
The pymatgen version is 2019.3.13
Thank you very much！
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NMR symmetrize tensor update
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[
"I'm was having trouble managing my local branches, hopefully this only changes the one nmr file? ",
"Yes, that’s correct, this only changes the one file",
"Hi @dongsenfo, tests need to be updated to reflect this change since they're currently failing.",
"I've updated the test, hopefully things should work now! ",
"Thanks @dongsenfo !"
] | 2019-04-25T23:25:35
| 2019-05-09T02:35:22
|
2019-05-09T02:34:47Z
|
CONTRIBUTOR
|
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## Summary
Symmetrize the tensor before returning the principal axis system
Uses the symmetrize method from the tensor class
|
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MDU6SXNzdWU0Mzc4MzA5MTk=
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Is it possible to apply biaxial deformation?
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[
"@mkhorton I think so?",
"For future reference, pls post queries on https://pymatgen.discourse.group and use Github Issues for only bug reports.",
"Hi @afonari, it's possible to apply any arbitrary deformation. You can initialize directly from a `Strain` object:\r\n\r\n```\r\nfrom pymatgen.analysis.elasticity.strain import Strain\r\nstrain = Strain(your_biaxial_strain_matrix)\r\ndeformation = strain.get_deformation_matrix()\r\ndeformed_structure = deformation.apply_to_structure(your_structure)\r\n```",
"Thanks for the reply @mkhorton. What I meant, is it possible to incorporate biaxial strain into the computations of the elastic modulus. Do you maybe have a any examples of biaxial strains?\r\n\r\nThanks.",
"Ah, yes, I believe so. You can fit an elastic tensor with any system of independent strains, including biaxial strains:\r\n\r\n```\r\nfrom pymatgen.analysis.elasticity.elastic import ElasticTensor\r\ntensor = ElasticTensor.from_independent_strains(list_of_strains, list_of_stresses)\r\n```\r\n\r\nDoes that answer your query? If not maybe @montoyjh would like to comment",
"Some example would definitely help with this, thanks."
] | 2019-04-26T20:19:55
| 2019-05-23T13:46:15
|
2019-05-23T13:46:15Z
|
CONTRIBUTOR
|
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Is it possible to apply biaxial deformation besides shear and non-shear modes defined in the DeformedStructureSet:
```# Generate deformations
for ind in [(0, 0), (1, 1), (2, 2)]:
for amount in norm_strains:
strain = Strain.from_index_amount(ind, amount)
self.deformations.append(strain.get_deformation_matrix())
for ind in [(0, 1), (0, 2), (1, 2)]:
for amount in shear_strains:
strain = Strain.from_index_amount(ind, amount)
self.deformations.append(strain.get_deformation_matrix())
```
|
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MDExOlB1bGxSZXF1ZXN0Mjc0Njk3OTg2
| 1,451
|
Updated publication info for dimensionality module
|
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[
"@utf Nice implementation!\r\n\r\nThe rank calculation is the bottleneck here. The contents of `seen_comp_vertices` is always full-rank, so we can skip recalculating its rank.\r\n\r\nPost-publication it occurred to me that we do not need to add nodes to the queue which are not added to a component. This change (line 234) also reduces calculation time.",
"Thanks.",
"Thanks for this @pmla. Congrats on the publication. This is a really nice method, so I'm glad to see the performance increase by so much."
] | 2019-04-30T11:46:02
| 2019-05-01T18:38:19
|
2019-04-30T13:15:07Z
|
NONE
|
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## Summary
The paper cited in the "get_dimensionality_larsen" function has been published. I have replaced the arXiv reference with the published one.
I have also made a two small changes to the function, which improves the speed by 2-3x.
|
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MDExOlB1bGxSZXF1ZXN0Mjc0ODgxNzA3
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|
A small bug fix for gulp_caller
|
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[
"Thanks @kmu!",
"Many thanks."
] | 2019-04-30T20:46:44
| 2019-04-30T21:28:17
|
2019-04-30T21:28:17Z
|
CONTRIBUTOR
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## Summary
A bug addressed in #1436 was fixed.
Old code can generate a too long line for cell parameters, which cannot be handled by GULP.
This patch fixes this issue.
A unit test was added to reproduce the bug.
|
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MDU6SXNzdWU0MzkyNjQ3MDU=
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MPNonSCFSet k-point generation incompatible with tetrahedron smearing
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"This was a while ago but I remember that the reason we went for explicit generation of k-points is symmetry. VASP uses a certain way of setting symmetries that is sometimes incompatible with other assignment for instance in spglib and from what I remember not super clear from the source code. That means spglib will tell you a certain k-point mesh in the irreducible brillouin zone and VASP another one. When you want to do things outside VASP (I think Boltztrap treatment was one example this would lead to inconsistencies). The MPNonSCFSet method was never intended to be used with the tetrahedron method and I think it used to not set ISMEAR=-5.\r\n\r\nBut as I said this was a while ago for specific purpose and if we want to switch to something else I am fine with it. However, we should keep this issue of symmetry in mind.\r\n\r\nGeoffroy\r\n\r\n\r\n\r\nOn 01 May 2019, at 20:20, Alex Ganose <notifications@github.com<mailto:notifications@github.com>> wrote:\r\n\r\n\r\nCurrently, MPNonSCFSet with mode=uniform creates an explicit list of k-points using SpacegroupAnalyzer.get_ir_reciprocal_mesh. As this list of k-points does not include tetrahedron information, the generated k-points file is incompatible with setting ISMEAR = -5. A recent update to the MPNonSCFSet set the default smearing parameter to ISMEAR = -5, so all uniform NSCF jobs in atomate are currently failing.\r\n\r\nIs there a reason for generating the list of k-points manually rather than letting VASP automatically generate the k-points based on mesh size (e.g., 3x3x3)? VASP will automatically add the tetrahedron information when ISMEAR = -5, so this issue is avoided.\r\n\r\nI really can't see the benefit of EVER generating the list of k-points manually, except for line-mode band structures but maybe I am missing something?\r\n\r\n—\r\nYou are receiving this because you are subscribed to this thread.\r\nReply to this email directly, view it on GitHub<https://github.com/materialsproject/pymatgen/issues/1453>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AAG6L52TV7MBQVFEY7QGILLPTHNNPANCNFSM4HJVJD2A>.\r\n\r\n",
"I think one of the reason was to avoid problems in using boltztrap1.\r\nUsing a list of kpoints generated by spglib in KPOINTS will be compatible\r\nwith the list of symmetry operations (again from with spglib ) provided as input of boltztrap1.\r\n\r\nIf we let VASP decide the kpoints, then spglib could give different sym ops and you get a\r\nfamous \"error in factorization\".\r\n\r\nI am not sure this is still necessary for running boltztrap 2. I'll check that.",
"IMHO, changing the ISMEAR default was not the best move.\r\nIf the intention was to have input file for DOS calculation, \r\nit could be much better to add a new 'dos' mode to MPNonSCFSet and \r\nkeep 'uniform' and 'line' doing what they have done since ever.\r\nConsider also that custom incar parameter can be passed both in pmg and atomate.",
"I imagine this depends whether NonSCFSet is used more for DOS or for BoltzTraP? I imagine most people using it in uniform mode want to calculate a DOS.",
"you said it, 'imagine'. Since we do not know, I would go safe adding a new feature than break a old.\r\nThat's IMHO ;-)",
"Thanks for the information @hautierg and @fraricci. I can see why those settings were chosen. \r\n\r\nGoing forward, I think the default behavior of `MPNonSCFSet` should be compatible with as many VASP smearing parameters as possible. It is perfectly reasonable that a user would want to use `ISMEAR = -5` for an NSCF calculation, whether it is a uniform or optics calculation (tetrahedron smearing is recommended for optics calculations anyway.)\r\n\r\nTo me, the boltztrap behavior should have its own mode as this is a non-standard VASP workaround. ",
"yes, I agree. The current 'uniform' mode could become 'boltztrap'. And new mode 'dos' and/or 'optics' could be added.",
"@fraricci your suggestion has been implemented by @utf and merged, thanks for the discussion!",
"I think I found an important bug in the current \"uniform\" mode.\r\nISYM = 0 remained from previous behavior now implemented as \"boltztrap\" mode.\r\n\r\nWhen someone sets \"uniform\" mode, he want VASP to produce the k-points according\r\nto a certain mesh and the use of symmetries has to be enabled (ISYM=1) to get those k-points only in the irreducible BZ. Now, with ISYM=0, symmetries are disabled and the kpoints are generated in the whole BZ.\r\n\r\nThis can affect the accuracy of the calculation in \"uniform\" mode. An example is \r\nall the properties from Boltztrap (transport, bands, doses).\r\n\r\nAll the calculation done with pmg versions since May 9 have this bug.\r\n\r\n@utf could you double check this?",
"Also tagging @munrojm here.",
"Hi @fraricci \r\n\r\nThanks for flagging this! As far as I can tell, the changes adding the tetrahedron method to the NonSCF set (added in PRs #1382 and #1458) didn't change any of the symmetry settings, unless I'm missing something.\r\n\r\nI'm not sure how this affects the accuracy of Boltztrap properties as symmetry was always disabled for Boltztrap calculations? For \"uniform\" calculations, the lack of symmetry shouldn't affect the accuracy but means that the computational expense will have been unnecessarily higher.\r\n\r\nI'd be in favor of turning on symmetry for \"uniform\" mode, unless anyone has any reason not to. Do you think we should also enable it for \"boltztrap\" mode?\r\n",
"In \"boltztrap\" mode symmetry has to be disabled because the kpoints are provided by spglib already in the irreducible BZ. So, ISYM=0 is the correct choice for this mode.\r\n\r\nFor \"uniform\" mode symmetry has to be ON: ISYM=1 or removed from the incar.\r\nBecause we want VASP to generate the kpoints in the irr-BZ.\r\n\r\nAbout the accuracy you are right. For a given mesh, the number of irreducible kpoints is the same in both cases ISYM=0,1. Therefore, as you said the only problem is the computational expense: with ISYM=0 more kpoint are calculated even they are not necessary. "
] | 2019-05-01T18:20:06
| 2019-12-10T09:57:38
|
2019-05-09T20:50:47Z
|
MEMBER
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Currently, `MPNonSCFSet` with `mode=uniform` creates an explicit list of k-points using `SpacegroupAnalyzer.get_ir_reciprocal_mesh`. As this list of k-points does not include tetrahedron information, the generated k-points file is incompatible with setting `ISMEAR = -5`. A recent update to the MPNonSCFSet set the default smearing parameter to `ISMEAR = -5`, so **all uniform NSCF jobs in atomate are currently failing.** See hackingmaterials/atomate#283.
Is there a reason for generating the list of k-points manually rather than letting VASP automatically generate the k-points based on a mesh size (e.g., 3x3x3)? VASP will automatically add the tetrahedron information when `ISMEAR = -5`, so this issue is avoided.
I really can't see the benefit of EVER generating the list of k-points manually, except for line-mode band structures but maybe I am missing something?
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MDExOlB1bGxSZXF1ZXN0Mjc1MjA1MjUz
| 1,454
|
Updates to defect modules and FermiDos scissor operator fix
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[
"Thanks @dbroberg \r\n\r\nRegarding the velocities issue, I remember there was some discussion of this previously...can you remember where that was, or who wanted it?",
"It was me reporting the issue and the previous fix I made was overly complicated. This fixes the same issue but in a more simple manner.",
"Ah, fantastic :-) Understood -- will merge once the CI tests pass."
] | 2019-05-02T00:48:39
| 2019-05-03T11:53:46
|
2019-05-03T11:53:46Z
|
CONTRIBUTOR
|
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## Summary
A number of major changes and fixes for point defect modules.
* Update multiplicity approach for Defect class such that Vacancy and Substitution defect types raise early ValueErrors if a defect_site is fed to it which isn't in the bulk structure
* Remove overly complicated approach for accommodating structures with velocities. If this is really desired, a defect structure can be initialized with velocity after generation by the Defect object.
* Incorporate Kumagai correction functionalities from PyCDT, with associated utils requirements
* Make use of logging in DefectCompatibility and DefectPhaseDiagram
* Update default parameters for DefectCompatibility based on recent benchmark work
* Add DefectPhaseDiagrams capabilites for: (a) suggesting larger supercells to be rerun, (b) calculating non_equilibrium fermi levels, (c) calculating dopability limits of formation energy plot.
* Fix DefectPhaseDiagram approach for grouping defects to allow for non-identical defects with the same name to be differentiated.
* Fix DefectPhaseDiagram hull for cases with large negative or positive formation energies
* Add plotting capabilities for DefectPhaseDiagram
* Fix to FermiDos scissor operation. Previously, if the fermi level index was the same as the vbm index, then the scissor operator did not result in desired band gap.
* Updates to unit tests to account for all of above.
* Updates to READMEs and variable names for clarity
No additional dependencies introduced.
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MDExOlB1bGxSZXF1ZXN0Mjc1MzAyMjUz
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Repair failing tests
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[
"Note that it is still segfaulting on CircleCI. Is something particularly memory intensive in these tests?",
"I will look into this again. "
] | 2019-05-02T10:07:06
| 2019-05-02T14:56:34
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2019-05-02T14:15:00Z
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MEMBER
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I have adapted some of my new tests so that the CircleCI tests will hopefully pass.
I also had some problems when running "test_cohp.py" and other files locally because there was no "@version" key in my dicts.
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Smaller test file + different testing of bandgap
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[
"It failed again. Any other idea where this could come from? I don't think it is a memory problem.",
"Yeah, honestly I don't know. It passed when you were running it. But failed when I merged it. I think I have an idea... Let me push a fix.",
"What makes you think this isn’t a memory problem?\n\nOn Thu, May 2, 2019 at 15:17, J. George <notifications@github.com> wrote:\n\n> It failed again. Any other idea where this could come from? I don't think\n> it is a memory problem.\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1456#issuecomment-488852027>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRGLVNCWPYQ7QUOWD4TPTNR57ANCNFSM4HKCXBXA>\n> .\n>\n",
"Ok, force-reinstall of phonopy works in removing the segfault. I think the old phonopy (or rather new phonopy v2+) was still in the system, and we previously encountered segfaults with that. \r\n\r\nHowever, there are still failures with the fatbands test. See https://circleci.com/gh/materialsproject/pymatgen/8485 .",
"I would strongly advise against direct comparison of dicts. It is more useful to compare the contents.",
"I will correct this in one of the next days."
] | 2019-05-02T18:05:36
| 2019-05-02T23:12:24
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2019-05-02T21:49:33Z
|
MEMBER
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I think the test_outputs.py is the one that is failing. Thus, I decreased the file size for my test file and also changed the test a little. I hope this helps. If not, I am out of ideas for the moment.
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| 439,951,858
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MDExOlB1bGxSZXF1ZXN0Mjc1NjM4MTg4
| 1,457
|
Fix for fatband tests
|
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[
"It is finally working. Thanks for your help. And, I will avoid assertDictEqual tests in the future... "
] | 2019-05-03T09:00:32
| 2019-05-03T12:26:37
|
2019-05-03T11:53:13Z
|
MEMBER
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I replaced all AssertDictEqual tests with other tests. I hope this fixes the current test problems.
|
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MDExOlB1bGxSZXF1ZXN0Mjc1ODcxOTIy
| 1,458
|
Add boltztrap mode to MPNonSCFSet
|
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[
"Fyi, the `test_optics` tests are failing with this change.",
"Thanks @utf "
] | 2019-05-03T22:55:14
| 2019-05-04T04:08:51
|
2019-05-04T04:08:51Z
|
MEMBER
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## Summary
As discussed in #1453, currently the MPNonSCFSet k-point generation routines are incompatible with tetrahedron smearing for uniform calculations. Historically, this decision was made to enable compatibility with Boltztrap calculations.
As we are transitioning to using tetrahedron smearing for higher quality density of states, I have updated the MPNonSCFSet "uniform" mode to be compatible with tetrahedron smearing. In addition, I have added a "boltztrap" mode which reproduces the legacy behavior.
I have added tests for the new uniform behavior and for the old boltztrap behavior.
|
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MDExOlB1bGxSZXF1ZXN0Mjc2MzcyNjky
| 1,459
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Updated run_type method clean version.
|
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[
"Hi @darnoceloc , thanks for persevering with this. This still needs tests to be updated before it can be merged.\r\n\r\nAlso, I have a request/comment, I saw:\r\n\r\n```\r\n param[\"run_type\"] = \"GGA+U\" if param[\"is_hubbard\"] else Vasprun.run_type\r\n```\r\n\r\nIs this correct? e.g. `is_hubbard` could be true even if the run is not GGA, seems like run_type should always be `Vasprun.run_type` to me?",
"Yes, I agree.\r\nSubmit another request and wait for the tests to be updated?",
"You should update the tests yourself as part of this pull request.",
"I didn't completely modify that line initially since the 'GGA+U' portion had remained unmodified for quite sometime but there are multiple flaws in that section of code including below.\r\n\r\n **param[\"is_hubbard\"] = (\r\n incar.get(\"LDAU\", False) and sum(param[\"hubbards\"].values()) > 0\r\n ) if incar is not None else False\r\n param[\"run_type\"] = None** \r\n\r\nNot quite sure what the idea/intent is for this commented line?\r\n **# param[\"history\"] = _get_transformation_history(path)**",
"The issue is multiple vasprun.xml files in the test_files directory contain the line below for the GGA setting.\r\nWhy would this be the case and what should be the default setting in such scenarios (I assume PBE)?\r\nOr should the default be LDA if no GGA tag is specified? \r\n**i type=\"string\" name=\"GGA\"--/i**\r\n",
"Is this done?",
"This PR looks good now, but need to trigger tests to re-run since @darnoceloc force-pushed new changes.",
"What else is required of me with respect to this PR?",
"You need to add a test that’s all, otherwise it looks good.\n\nOn Wed, Jun 19, 2019 at 11:43, darnoceloc <notifications@github.com> wrote:\n\n> What else is required of me with respect to this PR?\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1459?email_source=notifications&email_token=AAWWWRFD52EC2IJMQ4DZEGLP3J44PA5CNFSM4HLD52KKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYCZH7A#issuecomment-503682044>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRCOKMUVHDG6HJMVIJDP3J44PANCNFSM4HLD52KA>\n> .\n>\n",
"I was planning to modify this file to add the tests or should I create a new test file just for this PR?\r\n**https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/vasp/tests/test_outputs.py**",
"You can modify the test_outputs.py, but just add that modification to this PR",
"Sorry, but this PR modifies 800+ files. We cannot merge a PR with this many changes. Can you close this PR, and resubmit one with the specific changes that you are actually submitting? It helps if your master branch is already up to date with the official master branch.",
"Pardon my error, I am a bit new to the git vcs protocol/workflow and learning as I go.\r\nBut I have closed this PR and resubmitted a new/clean one as you suggested."
] | 2019-05-06T22:39:03
| 2019-06-20T00:21:26
|
2019-06-19T23:44:28Z
|
CONTRIBUTOR
|
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## Summary
Short few sentences, and summary of the major changes in bullet
points
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. Provide a justification why that dependency is needed.
Especially frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* Feature 1 supports a, but not b.
|
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MDU6SXNzdWU0NDEzOTUzMTc=
| 1,460
|
Use 0 based index for CifWriter
|
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[
"If this isn't mandated by the core CIF spec, I'd be on board with changing it.",
"I tested 0 based CIF file and 1 based CIF file by [checkCIF](http://journals.iucr.org/services/cif/checkcif.html) and got essentially identical results.\r\nBoth files can be opened by CrystalMaker and VESTA without problems.\r\n\r\nAny integer seems to be allowed for `_atom_site_label` according to the example shown in [the specification of CIF](http://scripts.iucr.org/cgi-bin/paper?pii=S010876739101067X).",
"OK, I trust checkCIF on this, in that case you would be very welcome to make this change, thank you!"
] | 2019-05-07T18:53:55
| 2019-05-07T21:44:28
|
2019-05-07T21:44:28Z
|
CONTRIBUTOR
|
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I'm wondering why `CifWriter` employs 1 based index, while `Structure` itself uses 0 based index.
https://github.com/materialsproject/pymatgen/blob/19f56d4d918c3b7fdc445aaca7d56d0d9bc3ddb6/pymatgen/io/cif.py#L1283-L1292
I'm always frustrated when I export a structure to a CIF file, open by VESTA, and try to inspect a specific site.
I would like to fix this if there is no compatibility problem or other issues for it.
|
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MDExOlB1bGxSZXF1ZXN0Mjc2NzY3ODk5
| 1,461
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Use 0 based index for CifWriter
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[
"thanks."
] | 2019-05-07T20:52:51
| 2019-05-07T21:43:22
|
2019-05-07T21:43:15Z
|
CONTRIBUTOR
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## Summary
`CifWriter` now uses 0 based index for the consistency with `Structure`.
You can compare the site index in VESTA and that for pymatgen without confusion.
See #1460.
|
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MDU6SXNzdWU0NDE2MzQ3ODg=
| 1,462
|
How to create input files for abinit by using pymatgen?
|
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[
"Please post questions on https://pymatgen.discourse.group . @gmatteo Can you answer this pls? It would be helpful if you write a simple example notebook at https://matgenb.materialsvirtuallab.org for ABINIT io."
] | 2019-05-08T09:19:58
| 2019-05-10T14:10:22
|
2019-05-10T14:10:22Z
|
NONE
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Dear developers,
I found pymatgen supports the input/output operations for abinit, and tried to use pymatgen to generate the input files. However, little documents or descriptions for abinit can be found in http://pymatgen.org/. I found it easy to create POSCAR from cif file for vasp:
```
>>> structure = mg.Structure.from_file("CsCl.cif")
>>> structure.to(fmt="poscar")
>>> structure.to(filename="POSCAR")
```
So, does pymatgen have the similar method to create input file for abinit?
Regards.
|
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| 1,463
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Inconsistency btw SpacegroupAnalyzer & SpaceGroup
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[] | null |
[
"Welcome @mt-huebsch !\r\n\r\nRegarding your bug, I'm not sure I can re-produce. If you look at the 0.1.mcif file, in the file itself we see the symmetry operations:\r\n\r\n```\r\n1 x,y,z,+1 \r\n2 -x,y+1/2,-z,+1 \r\n3 -x,-y,-z,+1 \r\n4 x,-y+1/2,z,+1 \r\n5 x+1/2,-y+1/2,-z+1/2,-1 \r\n6 -x+1/2,-y,z+1/2,-1 \r\n7 -x+1/2,y+1/2,z+1/2,-1 \r\n8 x+1/2,y,-z+1/2,-1 \r\n```\r\n\r\nOr you can check [here](http://img.chem.ucl.ac.uk/sgp/large/062az1.htm) or Bilbao's GENPOS tool for Pnma.\r\n\r\nThis seems to be consistent with the output of the space group class.\r\n\r\nIf you list `a.get_symmetry_dataset()` (returning the dataset for Pnma from spglib), you'll see similar operations defined for Pnma.\r\n\r\nThe reason SpacegroupAnalyzer is giving different symmetry operations is ultimately because of what `spglib.get_symmetry()` returns, and this is actually taking into account the magnetic moments on your cell. If you remove the magnetic moments using `s.remove_site_property('magmom')` you get the correct answer as expected:\r\n\r\n```\r\nAnalyzer:\r\nPnma 62\r\nx, y, z\r\n-x, -y, -z\r\n-x+1/2, -y, z+1/2\r\nx+1/2, y, -z+1/2\r\nx+1/2, -y+1/2, -z+1/2\r\n-x+1/2, y+1/2, z+1/2\r\n-x, y+1/2, -z\r\nx, -y+1/2, z\r\n```\r\n\r\nNote that spglib does not handle magnetic symmetry gracefully (it does not understand magnetic symmetry, but does try to take into account magnetic moments as scalars, so the information it reports is something more similar to exchange group symmetry I believe, though I don't have good documentation for this). In either case, spglib is correctly concluding that the magnetic moments impose a lower symmetry on the lattice while still reporting the correct crystallographic space group. I agree this is misleading. Hopefully spglib will natively support magnetic symmetry correctly one day.",
"Thank you for the quick and easy explanation @mkhorton!\r\n\r\nIt's a bit misleading that ```SpacegroupAnalyzer``` returns Pnma (No. 62) as an info while returning the reduced symmetry operations. I would expect the info also to correspond to the reduced (exchange group) symmetry then...\r\n\r\nAnyways, I am glad there is a way to work around it easily by using ```SpaceGroup``` (and in general to be able to use this package). \r\n\r\nIt seems elsewhere ```pymatgen``` neatly separates between magnetic space groups and space groups, e.g. by having the two modules ```pymatgen.symmetry.groups``` and ```pymatgen.symmetry.maggroups``` (although they currently have different power). Hence in my view, one might consider to strictly keep the separation by not considering time reversal symmetry within ```pymatgen.symmetry.analyzer``` with ```PointGroupAnalyzer```, ```PointGroupOperations```, ```SpacegroupAnalyzer```, ```SpacegroupOperations``` and maybe adding ```MagSpacegroupAnalyzer```, ```MagSpacegroupOperations``` in the long run.\r\n\r\nOn a side note, I adapted this Transformation to apply a magnetic space group symmetry operation. It seems operate_magmom() is handling magnetic moments as axial vector, hence gracefully enough right?\r\n\r\n```\r\nfrom pymatgen.transformations.transformation_abc import AbstractTransformation\r\nclass ApplyMagSymmOpTransformation(AbstractTransformation):\r\n \"\"\" \r\n Transformation to apply magnetic space group symmetry operation.\r\n \"\"\"\r\n def __init__(self, mag_op, fractional=True, to_unit_cell=True):\r\n \"\"\" \r\n Args:\r\n pymatgen.core.operations.MagSymmOp\r\n \"\"\"\r\n self.mag_op = mag_op\r\n self.fractional= fractional\r\n self.to_unit_cell= to_unit_cell\r\n\r\n def apply_transformation(self, structure):\r\n # init new structure\r\n new_structure = structure.copy()\r\n # apply xyz op\r\n new_structure.apply_operation( self.mag_op, fractional=self.fractional )\r\n # back to unit cell\r\n new_structure.translate_sites( [ i for i, _ in enumerate(new_structure.sites)] , [0,0,0] )\r\n # apply time rev symm\r\n new_magmom_list = []\r\n for site in new_structure.sites:\r\n new_magmom_list.append( self.mag_op.operate_magmom( site.properties[\"magmom\"] ) ) \r\n new_structure.add_site_property( \"magmom\", new_magmom_list )\r\n # return new structure\r\n return new_structure\r\n\r\n @property\r\n def is_one_to_many(self):\r\n return False\r\n\r\n @property\r\n def inverse(self):\r\n raise NotImplementedError()\r\n```\r\n\r\nThank you!",
"> Hence in my view, one might consider to strictly keep the separation by not considering time reversal symmetry [...]\r\n\r\nYes, I agree. I think it would make more sense to remove the magnetic moment information entirely from the normal symmetry classes to reduce confusion.\r\n\r\nThe reason for the separation of the pymatgen classes is mostly historical: the `maggroups` module was only added relatively recently, and uses the dataset kindly provided by Stokes and Campbell, but the format of this data is slightly different to that of the regular crystallographic dataset we use. This is why the modules have slightly different (though similar) APIs.\r\n\r\nLikewise, the reason the magnetic moment information is included in the SpacegroupAnalyzer is simply because spglib offers an interface for it, so pymatgen dutifully supplies the magnetic moments. However given that the output is confusing I think this should be disabled by default.\r\n\r\n> It seems operate_magmom() is handling magnetic moments as axial vector\r\n\r\nYes, that's correct. You may also find `Structure.from_magnetic_spacegroup(...)` useful (note that the pip installation of pymatgen is missing the required magnetic symmetry data file, but this will be present in the next pymatgen release, or can be downloaded manually).",
"Thanks for the advise. I am sure it will come in handy.\r\n\r\nOne more thing, do **I** close the issue (or who)?",
"No problem. In general, you can close an issue if it's resolved, but let's leave it open for now until we make the change that was suggested to make the output of SpacegroupAnalyzer less misleading."
] | 2019-05-09T00:30:02
| 2023-08-10T15:07:09
|
2023-08-10T15:07:09Z
|
NONE
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Hello everyone,
I am a first-timer. Thank you for taking the time.
Best, Marie-Therese
**Describe the bug**
The symmetry operations returned by pymatgen.symmetry.analyzer SpacegroupAnalyzer.get_symmetry_operations() and pymatgen.symmetry.groups SpaceGroup.symmetry_ops do not agree.
**To Reproduce**
See here [bug_report.zip](https://github.com/materialsproject/pymatgen/files/3159722/bug_report.zip) or follow these steps:
0. Setup
```
import urllib.request
server_dir = "http://webbdcrista1.ehu.es/magndata/mcif/"
cif_file = "0.1.mcif"
urllib.request.urlretrieve(server_dir + cif_file, cif_file)
```
or download mcif here:
[http://webbdcrista1.ehu.es/magndata/index.php?index=0.1](url)
1. Init Structure and get_space_group_info
```
import pymatgen
s = pymatgen.Structure.from_file( cif_file, primitive=True)
print( "Structure:")
print( s.get_space_group_info() )
```
2. get_space_group_info and operations using pymatgen.symmetry.analyzer
```
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
a = SpacegroupAnalyzer( s )
print( "\nAnalyzer:" )
print( a.get_space_group_symbol(), a.get_space_group_number() )
for op in a.get_symmetry_operations():
print( op.as_xyz_string() )
```
3. Construct SpaceGroup from space_group_info obtained in (2.)
```
from pymatgen.symmetry.groups import SpaceGroup
g = SpaceGroup.from_int_number( s.get_space_group_info()[1] )
print( "\nSpaceGroup:" )
for op in g.symmetry_ops:
print( op.as_xyz_string() )
```
*Output:*
```
Structure:
('Pnma', 62)
Analyzer:
Pnma 62
x, y, z
-x, -y, -z
-x+1/2, -y, z+1/2
x+1/2, y, -z+1/2
SpaceGroup:
x, y, z
-x+1/2, -y, z+1/2
x+1/2, -y+1/2, -z+1/2
-x, y+1/2, -z
-x, -y, -z
x-1/2, y, -z-1/2
-x-1/2, y-1/2, z-1/2
x, -y-1/2, z
```
One may use [http://www.cryst.ehu.es/cgi-bin/cryst/programs/checkgr.pl?tipog=gesp](url) to determine that step 3 correctly returns Pnma (No. 62) and step 2 returns P21/c (No. 14).
**Expected behavior**
a.get_symmetry_operations() and g.symmetry_ops should return the same spg elements.
**Additional info**
By some shallow digging I found that the Analyzer employs Togo senseis library, while SpaceGroup seems to use a preset json.
*ad step 2* pymatgen.symmetry.analyzer SpacegroupAnalyzer._get_symmetry(self) uses spglib.get_symmetry
*ad step 3* pymatgen.symmetry.groups.SpaceGroup uses SYMM_OPS = loadfn(os.path.join(os.path.dirname(__file__), "symm_ops.json"))
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MDU6SXNzdWU0NDIzNTI3NjI=
| 1,464
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Changing the signature of vaspinputset.from_prev()
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"My view is that there are both use cases. The problem with the suggested Option 2 is that the logic flow is strange. Initialization VaspInputSet requires a Structure, which presumably is being read from a previous calculation in these cases. I would also prefer not to wreak havoc on a lot of people's scripts (including a large fraction of my group). \r\n\r\nI would suggest a Third option that will achieve what you want and is totally backwards compatible.\r\n\r\n```python\r\nclass VaspInputSet:\r\n\r\n def __init__(structure, ...):\r\n remains the same.\r\n\r\n def override_from_prev_calc(path=\".\"):\r\n what you are suggesting in the new from_prev\r\n\r\n @classmethod\r\n def from_prev_calc(*still the same API and parameters*):\r\n uses __init__ and override_from_prev_calc to achieve exact same effect as current from_prev_calc\r\n```\r\n\r\nFor atomate, you should use `__init__` and `override_from_prev_calc`, which will allow you to standardize the code.",
"Two comments:\r\n\r\n* The more direct comment is that I don't see how adding override_from_prev_calc helps. Yes, atomate can use this, but then the user has no way to adjust the settings. For example, MPStaticSet.from_prev_calc() currently has a \"small_gap_multiply\" setting that multiplies k-point meshes for small gap systems. An atomate user might want to adjust this parameter in the workflow. If we just use override_from_prev_calc(), there will be no option to modify small_gap_multiply (unless we move that parameter to the constructor as suggested).\r\n\r\n* The more indirect comment is that the fact that VaspInputSet (VIS) requires a structure is also a problem. Often, we want to be able to set up parameters (a VIS object) for a downstream job, but don't yet know exactly what the structure will be. e.g., when writing a workflow like removing Li in the middle, and you don't know what the structure will actually be for the subsequent steps but still need to define a VIS for those runs. Right now we have just two options when trying to set up a VIS in advance of the actual calculation - (i) put in a dummy structure so that we can create the VIS for now (but we need to remember to update it later on, else it will have the wrong structure in it), or (ii) specify the VIS as a String only and only load the full VIS object when the workflow executes. Ideally, the VIS would operate such that the structure is only passed in at the time of creating the input files. Then I could also easily reuse the same VIS for multiple structures.\r\n\r\n",
"i. Yes, I mean we move those things to the constructor. I am asking that you do not break from_prev_calc.\r\nii. We already had extensive debates about whether structure should be part of VIS. It is true that it will require VIS to be constructed for every structure. But the other side of the story is that often structure modification is part of the input file generation. E.g., standardizing a structure to some basis, or setting up some NEB calculations.",
"For (i) - I see, but then we will have duplicated parameters in the constructor and in from_prev() - is that OK with you?",
"We will not have duplicated parameters. Just move the parameters to constructor, remove them from from_prev, and from_prev will simply pass through using *args and **kwargs. That is already the case for other common parameters such as user_incar_settings. We just need to lump these parameters into that.",
"I am happy to implement what has been discussed in this thread, however, I think it is not as simple as simply moving the keyword arguments of `from_prev_calc` to `__init__`. This is mainly because `from_prev_calc` needs to have access to the defaults of the keyword arguments before they are passed through to the constructor.\r\n\r\nA solution to this is to define the defaults required by `from_prev_calc` as class variables, which would then be used by both `from_prev_calc` and `__init__`. We would also then need to check whether the keyword argument had separately been based to `from_prev_calc`, which would introduce some boilerplate. E.g.\r\n\r\n```python\r\nclass VaspInputSet:\r\n\r\n reciprocal_density = 200\r\n\r\n def __init__(structure, reciprocal_density=reciprocal_density, ...):\r\n # remains the same.\r\n\r\n @classmethod\r\n def from_prev_calc(prev_calc_dir, **kwargs):\r\n reciprocal_density = kwargs.get(\"reciprocal_density\", reciprocal_density)\r\n # do something with reciprocal density.\r\n```\r\n\r\nThe input set would therefore require a class variable and the ` kwargs.get(\"reciprocal_density\", reciprocal_density)` boilerplate for every variable required by `from_prev_calc`.\r\n\r\nIf this is acceptable I will implement.",
"I am confused. If the defaults are the same, if you move them to the constructor, there should be no difference from the defaults being in from_prev? E.g., if the original default reciprocal density is 200, putting that number in the constructor now would still mean that from_prev_calc will use the 200 default.",
"In the example I posted, `from_prev_calc` needs to know what the default is before the inputset is constructed, as it will adjust the default value based on the output of the previous calculation. An example from an existing inputset is:\r\n\r\n```python\r\n def from_prev_calc(cls, prev_calc_dir, reciprocal_density=100,\r\n small_gap_multiply=None, ... ):\r\n\r\n ...\r\n\r\n # multiply the reciprocal density if needed:\r\n if small_gap_multiply:\r\n gap = vasprun.eigenvalue_band_properties[0]\r\n if gap <= small_gap_multiply[0]:\r\n reciprocal_density = reciprocal_density * small_gap_multiply[1]\r\n\r\n return cls(reciprocal_density=reciprocal_density, ...)\r\n```\r\n\r\nE.g., If the user does not pass `reciprocal_density` or `small_gap_multiply` to `from_prev_calc`, we need to access the defaults defined in the constructor.",
"@utf No. The idea is that from_prev_calc will now call the constructor AND the new override_from_prev_calc. Obviously, the second call comes after the constructor and therefore would have access to the constructor defaults. We should not be duplicating code in from_prev_calc and override_from_prev_calc.\r\n",
"I understand what you are suggesting now."
] | 2019-05-09T17:40:43
| 2019-05-16T00:13:00
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2019-05-16T00:13:00Z
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Currently, the from_prev() method in the VaspInputSets is a wild west of parameters - i.e., there is no consistency in the signature of from_prev() between different VaspInputSets.
This ends up causing a lot of downstream complexity in atomate. Although the atomate FireTasks can take in a VaspInputSet object to help users control input settings, they usually also mirror the from_prev() parameters to allow users to also control the behavior of the from_prev() method for the VaspInputSet.
The current situation in atomate is unambigously a mess. There are two potential solutions:
i) Atomate uses a single **kwargs style option for updating from_prev() settings in a VASP input set. Thus, at least it would not be mirroring a dozen parameters.
ii) Pymatgen VASP input sets are modified so that *all* parameters (including parameters currently set independently in the from_prev() method) are in the constructor. The method signature of from_prev() is the same for all VaspInputSets, which will be ```my_vaspinputset.from_prev(directory=".")``` - i.e., the only parameter for from_prev is the directory, every other parameter is set in the constructor.
We (atomate discussion team) think (ii) is the much better solution, since it means that once you create an input set, all the rules/flags/etc on the operation of that inputset are determined and can be serialized, etc. e.g., I can serialize my from_prev() settings and not just my "normal" settings. Furthermore, I think this solution is also much cleaner than having atomate create a kwargs-style parameter specifically for passing into the ``from_prev()`` of a vaspinput set.
Thoughts? Is this practical to change?
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MDExOlB1bGxSZXF1ZXN0Mjc3NTAwODg0
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Fix piezo and piezo sensitivity
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[
"Is this ready to merge?",
"I believe @shyamd was going to merge when ready? ",
"Asking because I saw the WIP label disappeared\n\nOn Fri, Aug 23, 2019 at 11:44, dongsenfo <notifications@github.com> wrote:\n\n> I believe @shyamd <https://github.com/shyamd> was going to merge when\n> ready?\n>\n> —\n> You are receiving this because you commented.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1465?email_source=notifications&email_token=AAWWWRFUD2I2UEJKAXFYXITQGAVXRA5CNFSM4HL46KUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5BAVIQ#issuecomment-524421794>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRBMKLFARA65KZIQGX3QGAVXRANCNFSM4HL46KUA>\n> .\n>\n",
"Looks ready to merge but some small PEP8 violations, can you run it through [Black](https://github.com/psf/black) or similar?",
"Still have a few issues in site_symmetries.py (it's why the CI is failing)"
] | 2019-05-09T18:33:05
| 2019-08-26T18:14:48
|
2019-08-26T18:14:48Z
|
CONTRIBUTOR
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Write tests and update style for piezo and piezo sensitivity
## Summary
Past branch accidently merged so this is an update
Added piezo_sensitivity and site_symmetry packages under analysis. Site_symmetries allow for users to get the point symmetries of atomic sites and symmetry operations relating sites. Piezo sensitivity allows for random generation of piezoelectric components and the calculation of the piezoelectric tensor from components.
## TODO
Need to write tests and cleanup variables and style for all of the methods
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Add override_from_prev_calc to VASP input sets
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[
"With regards to the ‘standardize’ option, is there a good reason to prefer the standard primitive over a reduced cell?",
"The main reason would be for defining the k-point lines along which to compute and plot band structure.",
"That’s fair, but the primitive standard cells aren’t always great, eg I saw a case recently where:\r\n\r\n`get_primitive_structure` gives:\r\n```\r\nLattice\r\n abc : 29.205719340811687 10.269670980642069 14.881236907930036\r\n angles : 153.08849008764724 168.90022329343003 24.67294446652493\r\n volume : 358.69649610521316\r\n```\r\n`get_reduced_structure` (Niggli) gives:\r\n```\r\nLattice\r\n abc : 5.7298161670563585 7.373364113749618 9.910301456455453\r\n angles : 71.19293240753842 73.19688199311382 67.13579991473384\r\n volume : 358.6964961052132\r\n```\r\n`get_primitive_standard_structure` gives:\r\n```\r\nLattice\r\n abc : 7.373364129854753 7.373364129854753 10.269670980642069\r\n angles : 65.99141686564593 114.00858313435408 134.2715992359032\r\n volume : 358.69649610521344\r\n```\r\n\r\nThis is actually not *so* bad, but I think I’d still probably prefer the reduced cell for a relaxation. I’m open to being convinced otherwise however. I can certainly see the consistency for band structure calculations being useful.",
"I agree. That is why standardize should default to False unless there is a good reason for it to be true, e.g BS calculations, which I believe is the only place where this is true. "
] | 2019-05-13T20:49:12
| 2019-05-15T22:49:20
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2019-05-15T22:49:20Z
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## Summary
Based on the discussion in #1464, I have added `override_from_prev_calc` methods to the VASP input sets that already define `from_prev_calc`. In each case, the old `from_prev_calc` method has been rewritten to use `override_from_prev_calc`. This new approach has several advantages, including:
- The `from_prev_calc` and `override_from_prev_calc` parameters are now consistent for every input set.
- There are now no duplicated parameters. Previously, some defaults were defined in both `__init__` and `from_prev_calc`, now they are all defined in `__init__`.
- The implementation in atomate should be significantly cleaner.
Some additional notes:
- Previously, some from_prev functions had a `standardize` keyword that would transform the structure to the standardized primitive cell. It seemed like this would be a very useful option for every input set, regardless of whether it was continuing from a previous calculation. E.g. at the start of your workflow, you might want to standardize your structure before relaxing. I have therefore added the `standardize` keyword argument to the base `DictSet`. By default this is set to False (which also matches the previous default behavior of standardize in the from_prev methods).
- `MPHSEBSSet` has a `mode` keyword that controls the type of calculation (line, uniform or gap). The gap option was only available in the from_prev method, where it was the default. The only difference between the gap and uniform modes is that the VBM and CBM of the previous calculation are explicitly added to the k-point list. I have changed the default value of mode in `__init__` to "Gap" because this gives the best compatibility with the previous behavior (it is reproduced exactly). If the user does not continue from a previous calculation, the behavior will be exactly the same as the "uniform" mode (the previous default for the init method). However, if the user continues from a previous calculation then the default will be to add the VBM and CBM k-points unless otherwise specified (again, the default for from_prev).
- `MVLGWSet` has different default values for they `mode` kwarg in the from_prev and init functions. I think this is due to the standard workflow for GW/BSE calculations. To avoid any issues here, I left the `mode` keyword as an option to the `from_prev_calc` method (so that the default behavior is not affected). As the main use of the `override_from_prev_calc` methods will be in atomate which does not use these input sets, the slightly different behavior of `override_from_prev_calc` (it does not use the same default mode as `from_prev_calc`) should not be an issue. I am open to other suggestions for fixing this, however.
- I fixed up the documentation if I noticed it was off.
One thing to note is, I had to introduce a dummy structure in the from_prev_calc methods, so that I could initialise the input set before calling override_from_prev_calc method. This is a bit ugly, but saves reading the vasprun twice to get the structure.
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MDExOlB1bGxSZXF1ZXN0Mjc4NTA2NzQy
| 1,467
|
Interpolate ximages
|
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[
"Thanks. Instead of this approach, I would suggest that you simply allow nimages to take either an int (in which it will be linearly spaced like the default) or if a sequence of values is provided, it will use those to construct the images. ",
"Okay, I can easily make that change. In that case, \"images\" is probably a better name for the variable, but maybe I should leave it as \"nimages\" to maintain backwards compatibility?",
"Yes it is true that images is probably better but for he sake of backwards\ncompatibility, let’s just use nimages. In any case, using specific values\nis probably a more esoteric use case.\n\nOn Wed, May 15, 2019 at 15:54 Mark Turiansky <notifications@github.com>\nwrote:\n\n> Okay, I can easily make that change. In that case, \"images\" is probably a\n> better name for the variable, but maybe I should leave it as \"nimages\" to\n> maintain backwards compatibility?\n>\n> —\n> You are receiving this because you commented.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1467?email_source=notifications&email_token=AAEM4U2UMKS4BGE6TZUIC33PVSIDTA5CNFSM4HMVDHQKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVQFVBI#issuecomment-492853893>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAEM4U3GBRC4HOLZ6WDQDGTPVSIDTANCNFSM4HMVDHQA>\n> .\n>\n-- \nShyue Ping\n",
"Thanks!"
] | 2019-05-14T03:29:06
| 2019-05-16T04:10:55
|
2019-05-16T00:12:40Z
|
CONTRIBUTOR
|
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## Summary
Added the argument "ximages" to IStructure.interpolate. This allows you to define an arbitrary grid of interpolation points between the two lattices. This is useful for making configuration coordinate diagrams.
"nimages" was left intact to maintain backwards compatibility. "ximages" may not be the best name, feel free to change it to something more descriptive.
## Additional dependencies introduced (if any)
N/A
## TODO (if any)
N/A
|
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MDExOlB1bGxSZXF1ZXN0MjgwNTc4NjQ5
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Add ELFCAR support
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[] | 2019-05-20T23:52:45
| 2019-05-20T23:55:25
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2019-05-20T23:53:25Z
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MEMBER
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And some convenience methods for `Composition`.
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MDExOlB1bGxSZXF1ZXN0MjgwOTk3NzEz
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Fix the rgb_label of 2 elements band structure
|
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[] | 2019-05-22T00:56:57
| 2019-05-22T01:02:20
|
2019-05-22T01:02:20Z
|
CONTRIBUTOR
|
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## Summary
* Fix the rgb_label of 2 elements band structure
After fix:
<img src="https://user-images.githubusercontent.com/18021558/58139835-969e8880-7c0a-11e9-8164-ef6039859383.png" width=150/>
Before fix:
<img src="https://user-images.githubusercontent.com/18021558/58139864-b9c93800-7c0a-11e9-9b08-27f80630a767.png" width=150/>
|
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MDExOlB1bGxSZXF1ZXN0MjgxMDI3Mzcz
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|
Segmented drawing different branches of band structure
|
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[
"Thanks."
] | 2019-05-22T04:17:42
| 2019-05-23T13:44:52
|
2019-05-23T13:44:44Z
|
CONTRIBUTOR
|
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## Summary
Segmented drawing different branches of band structure in BSDOSPlotter. Look nicer between two discontinuous k-path branches
* After fix
<img src="https://user-images.githubusercontent.com/18021558/58146970-64028900-7c26-11e9-899c-2188ed9e5de2.png" width=100/>
* Before fix
<img src="https://user-images.githubusercontent.com/18021558/58146963-5816c700-7c26-11e9-95b3-fce220170968.png" width=100/>
|
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MDExOlB1bGxSZXF1ZXN0MjgxNDExMjUz
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Make FermiDos MSONable
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[
"Thanks @utf! I share your concern about breaking backwards compat, but\ncases like this seem pretty clear it should be tidied up. Will merge this\nfix regardless\n\nOn Wed, May 22, 2019 at 18:21, Alex Ganose <notifications@github.com> wrote:\n\n> Summary\n>\n> Currently, FermiDos objects are not MSONable for two reasons:\n>\n> 1. They have a strange constructor that requires a Dos object rather\n> than energies, densities and a Fermi level like other Dos subclasses.\n> 2. The nelecs variable is not stored, even as a private variable.\n>\n> Ideally I'd correct the constructor but I don't want to break other\n> peoples code. Instead, I've added custom to_dict and from_dict methods and\n> fixed point 2.\n>\n> I've also tied up the class, made it pep8 compatible and added type\n> hinting.\n> ------------------------------\n> You can view, comment on, or merge this pull request online at:\n>\n> https://github.com/materialsproject/pymatgen/pull/1471\n> Commit Summary\n>\n> - Tidy FermiDos\n> - Make FermiDos MSONable\n>\n> File Changes\n>\n> - *M* pymatgen/analysis/defects/thermodynamics.py\n> <https://github.com/materialsproject/pymatgen/pull/1471/files#diff-0>\n> (4)\n> - *M* pymatgen/electronic_structure/dos.py\n> <https://github.com/materialsproject/pymatgen/pull/1471/files#diff-1>\n> (242)\n> - *M* pymatgen/electronic_structure/tests/test_dos.py\n> <https://github.com/materialsproject/pymatgen/pull/1471/files#diff-2>\n> (8)\n>\n> Patch Links:\n>\n> - https://github.com/materialsproject/pymatgen/pull/1471.patch\n> - https://github.com/materialsproject/pymatgen/pull/1471.diff\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1471?email_source=notifications&email_token=AAWWWRCTJOVXVHHJZI6SOK3PWXWPRA5CNFSM4HOZE2L2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GVK4XXA>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRH5KJH3LVUNIP6ZTLDPWXWPRANCNFSM4HOZE2LQ>\n> .\n>\n"
] | 2019-05-23T01:20:54
| 2019-05-24T03:56:38
|
2019-05-24T03:56:38Z
|
MEMBER
|
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## Summary
Currently, FermiDos objects are not MSONable for two reasons:
1. They have a strange constructor that requires a Dos object rather than energies, densities and a Fermi level like other Dos subclasses.
2. The nelecs variable is not stored, even as a private variable.
Ideally I'd correct the constructor but I don't want to break other peoples code. Instead, I've added custom to_dict and from_dict methods and fixed point 2.
I've also tied up the class, made it pep8 compliant and added type hinting.
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MDExOlB1bGxSZXF1ZXN0MjgyMTk5Mjk1
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Fix the color issue of segmented drawing different branches of band s…
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[] | 2019-05-25T02:58:27
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2019-05-25T14:12:33Z
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CONTRIBUTOR
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## Summary
Fix the color issue of segmented drawing different branches of the band structure in BSDOSPlotter.
* After fix
* Before fix
This bug was introduced in PR: https://github.com/materialsproject/pymatgen/pull/1470
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MDExOlB1bGxSZXF1ZXN0MjgzNDUxMjE0
| 1,473
|
Add Interface class and InterfaceBuilder
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[
"Thanks @kylebystrom, are you happy for this to merged now while it’s still in “prototype” stage? It already looks quite substantial, though I can’t tell what the test coverage is like from a quick read.",
"Looking back at it, I think the test coverage is still a bit low, so Shyam and I are going to add a couple more unit tests before we merge this. Sorry for the late reply.",
"I have a more general question of how this is different from the SubstrateBuilder?",
"The substrate analyzer merely finds the matching surface lattices and does some simple analysis on that, ie elastic strain energy. This uses that same algorithm and actually builds an interface structure that can be used in DFT for instance to compute interface energies. ",
"Merge the two. I do not wish for multiple modules doing roughly the same thing with minor differences. In fact, I would completely deprecated substrate analyzer and integrate its functionality into interface.\r\n\r\nA side note that we already ahve existing code in our private code base for this purpose. See http://dx.doi.org/10.1021/acs.chemmater.7b04096 . Please coordinate with @HanmeiTang to integrate everything properly in a coherent manner.",
"They don't do the same thing. `SubstrateAnalyzer` determines matching relationships for the epitaxial constraint using the Zur and McGill algorithm. It's designed to crank through lots of surfaces planes and structure combinations quickly to evaluate which combination is most plausible. `InterfaceBuilder` constructs interface structures for evaluating using DFT **if** you already have the two structures and surface planes in mind. You should use the `SubstrateAnalyzer` to determine which planes are appropriate to investigate and then construct that using the `InterfaceBuilder`. I do agree the `SubstrateAnalyzer` name is a bit misleading since it can be used for more than just substrates. \r\n\r\nThe long-term goals are:\r\n1. Have an `Interface` class in `core`. `GrainBoundary` should inherit from this in the future\r\n2. Keep the `ZSLGenerator` in`analysis`. This is just a geometry finding algorithm and is superior to the Stradi algorithm for coherent crystalline interfaces, but building the interface structure for DFT is more of a pain. Hence why the `InterfaceBuilder` does quite a bit. \r\n3. Work with @HanmeiTang to build a `StradiGenerator` so we can use that in either analysis or interface construction. \r\n4. Convert `SubstrateAnalyzer` into `InterfaceCoherencyAnalyzer` to be clear of what the name does. \r\n\r\nI want something working in pymatgen for now, since I have gotten plenty of emails asking for this functionality. Kyle is finishing up at LBL soon and moving for grad school where he will likely work on other projects, so it's better not to let this hang. I'm also not a fan of single monolith classes. This makes understanding what they do near impossible for any but the most steeled pymatgen veterans. ",
"I agree they technically handle two different aspects, but I still want them merged into one module, not separate modules. I can certainly forsee a class method which says Interface.from_structures(a, b, algo=\"Zur\"). ",
"This is ready to merge. I will add an issue to clean up InterfaceBuilder and assign to myself.",
"Ok thanks @kylebystrom @shyamd, I'd like to merge now since it seems immediately useful and we can take discussion of combining these classes to #1491\r\n\r\n@kylebystrom before I can merge could you make sure all functions and methods have docstrings? Overall this PR seems to be nicely documented but there are a few missing in interface.py",
"@mkhorton I documented the helper functions in interface.py. I also removed several functions that aren't currently in use. Some of that functionality might be integrated in #1491. ",
"Thanks @kylebystrom !"
] | 2019-05-29T22:17:55
| 2019-06-17T23:12:00
|
2019-06-17T23:12:00Z
|
CONTRIBUTOR
|
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## Summary
Adding Interface and InterfaceBuilder classes (prototype stage) along with a few basic unit tests. Initial code written by @shyamd and @sivonxay and debugged/documented by myself.
* Store and edit interfaces in the Interface class
* Create new interfaces with the InterfaceBuilder
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MDU6SXNzdWU0NTAzNzMzNzQ=
| 1,474
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WulffShape Construction Not displaying Plot and Matplotlib Deprecation Warning
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[
"For future reference, pls post such questions at http://pymatgen.discourse.group .\r\nYou can ignore the deprecation message. \r\n\r\nThe issue is related to the fact that you are running in a Jupyter notebook. The figure is indeed generated, as can be seen from the `<Figure size ...>` in your output. For matplotlib to display the figure inline, you need to put `%matplotlib inline` first. Alternatively, run the same code as a command line script. \r\n"
] | 2019-05-30T15:45:35
| 2019-05-30T16:42:17
|
2019-05-30T16:42:16Z
|
NONE
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**Describe the bug**
Dear pymatgen communities,
I am running a Si Wulff Shape Construction based on the excellent tutorial from https://matgenb.materialsvirtuallab.org/2017/04/03/Slab-generation-and-Wulff-shape.html
However, when running the code, no Wulff shape plot was displayed at the end, and a warning message related to Matplotlib deprecation also appeared.
**To Reproduce**
I used the exact same code from the tutorial
https://matgenb.materialsvirtuallab.org/2017/04/03/Slab-generation-and-Wulff-shape.html
**Expected behavior**
No Wulff plot displayed, and warning message appeared as
/anaconda3/lib/python3.7/site-packages/matplotlib/cbook/__init__.py:424: MatplotlibDeprecationWarning:
Passing one of 'on', 'true', 'off', 'false' as a boolean is deprecated; use an actual boolean (True/False) instead.
warn_deprecated("2.2", "Passing one of 'on', 'true', 'off', 'false' as a "
**Screenshots**
<img width="817" alt="Screen Shot 2019-05-30 at 11 28 32" src="https://user-images.githubusercontent.com/37195595/58644397-28735900-82cf-11e9-91db-807c778c06c1.png">
**Desktop (please complete the following information):**
- OS: MacOS 10.14.5
- Python 3.7 running on jupyter notebook
- pymatgen v2019.5.1
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MDExOlB1bGxSZXF1ZXN0MjgzNzYwNzYz
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[WIP] Change NearNeighbors API
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[] | 2019-05-30T18:24:33
| 2021-02-13T17:29:18
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2019-07-29T14:55:54Z
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MEMBER
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## Summary
This will be a breaking change. This Is for #1273. If you rely on NearNeighbors please make note of the changes. This is to improve efficiency of the class.
WIP since lots of tedious test changes still to be done.
|
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[WIP] Add pt 2. of the AFLOW prototypes
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[
"@utf do you want this merged?",
"Noting here for future ref, some mineral names have LaTeX in them so need to be proofed, and some mineral names are archaic (see example \"Lavarevi\\'{c}ite\" which apparently is now known as \"Colusite\").",
"another part of the prototype library has been prepared: https://arxiv.org/abs/2012.05961"
] | 2019-05-30T23:15:21
| 2021-10-06T09:29:11
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2021-10-06T09:29:11Z
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MEMBER
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## Summary
Add part 2 of the AFLOW prototype library to the set of prototypes used by `AFLOWPrototypeMatcher`. See #1446.
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Composition accepts non valid formulas
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[
"This might be surprising, but yes, these are valid. Basically, pymatgen treats any non-element symbol starting with an upper-case as a DummySpecie, unless it violates the rule that the upper case letter itself is an element. For example, Composition(\"Stuff\") would not work because S is an element. \r\n\r\nYou can see this clearly when you look deeper at what your example gives. E.g.,\r\n\r\n```python\r\nIn [11]: c = Composition(\"Madeupstuff\")\r\n\r\nIn [12]: print(dict(c))\r\n{DummySpecie Madeupstuff0+: 1.0}\r\n```\r\n\r\nOf course, we can be more restrictive about DummySpecie names. Just not sure how restrictive we want to be.",
"I figured out that’s what was going on but I wasn’t sure if it was expected behaviour.\r\n\r\nI was originally trying to cast to a composition to check if a string was a valid formula. \r\n\r\nThe current behaviour of composition seems fine, but it might be nice to have an ”is_valid_formula” function if that doesn’t already exist in pymatgen. \r\n",
"Thanks Matt!"
] | 2019-05-31T04:23:21
| 2019-05-31T16:15:09
|
2019-05-31T14:05:02Z
|
MEMBER
|
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Composition objects allow initializing with an input that is clearly not a valid formula.
For example:
```python
from pymatgen import Composition
Composition("Madeupstuff")
Composition("Lonsdalite")
Composition("MyGranddadGoesToMarketEveryTuesday")
```
None of which raise an exception.
Is this behavior expected?
|
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MDExOlB1bGxSZXF1ZXN0MjgzOTkzMjQ0
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Add valid property to Composition and strict option to constructor
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[
"Oops realized I created this branch from my NearNeighbors branch instead of from master as intended, will merge later"
] | 2019-05-31T10:39:34
| 2019-05-31T16:21:22
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2019-05-31T12:53:09Z
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MEMBER
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For #1477
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Add strict option to Composition and valid property
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| 2019-05-31T16:21:56
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2019-05-31T14:04:45Z
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MEMBER
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For #1477
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linear scaling method for get all neighbors in a structure
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[
"Hi @chc273 , this looks great!\r\n\r\nIf the output is identical to `get_all_neighbors` why not combine them? You could rename `get_all_neighbors_cell_list` to `_get_all_neighbors_cell_list` and then add a new `method=\"cell_list\"` keyword argument to `get_all_neighbors`. If someone wants the old algorithm, they could change it to `method=\"traditional\"` instead? If the speed up is that good, it should be the default algorithm :-)\r\n\r\nSeparately, could you comment on cell lists vs e.g. something like a k-d tree? My understanding was that cell lists in particular were really useful in MD, in a situation where you had multiple time steps and minimal changes between each time step such that the cell lists would not need to be updated too often, but that for a single isolated structure the advantage was not as great (though still of course better than the traditional method!)",
"I have a few comments:\r\n\r\ni. It would appear to me that this algo should work for a single site as well. Is there a reason why we do not want to do it for get_nn(site)? Of course the speed up is not likely to be very significant for a single site. I just prefer for things to be designed in a coherent manner.\r\n\r\nii. I agree with @mkhorton that we should make this the default and rename the current method to something like get_all_neighbors_old. I would like to preserve the old algo as a cross-check for now. We actually already made this modification once before.\r\n\r\niii. If we agree on the things above, I would actually change the signature of get_all_neighbors somewhat. Basically, \r\n\r\n```\r\ndef get_all_neighbors(indices=None):\r\n```\r\n\r\nIf indices are specified, we will only get all neighbors for specified indices. This would be useful in instances where you only want to analyze certain local-env. Furthermore, the get_nn(site) becomes a trivial exercise of calling this method with a single index. We will merge all algos. ",
"Hi @mkhorton,\r\n\r\nGood suggestions, I will try to merge them together. \r\n\r\nFor k-d tree vs cell lists, my experience using k-d tree is only for high dimensional (n>3) neighbor search. My understanding is that it divides the space by iteratively subdivide each dimension and it works nicely if one wants to query the neighbors for one point, by transversing each dimension. However, distance information is not native to this method. For our problem here, we want neighbors within certain cutoff for all sites. I guess using the k-d tree, the search speed should be slower than O(N)? I don't know. ",
"@shyuep \r\n\r\nAll those can be done. I will push to the PR later. \r\n\r\n",
"@shyuep @mkhorton \r\n\r\nThe `get_all_neighbors` and `get_neighbors` methods are modified. \r\ni. Both methods are now using the new algorithm. The previous algorithms are changed to `get_all_neighbors_old` and `get_neighbors_old`. The `get_neighbors` method calls `get_all_neighbors` by setting the `sites` argument to the specific site. `Comment by @mkhorton and Comment ii by @shyuep` \r\nii. The `get_all_neighbors` methods include two more input parameters `indices` and `sites`. `indices` can be set to a list of indices, a single index or None, for computing the neighbors for a list of sites, a single site and all sites (if `sites` are not set) respectively. `Comment iii by @shyuep`. The `sites` parameters allows a list of Sites, a single Site and None for computing the neighbors for the list of sites, a single site and being not used respectively.` Comment i by @shyuep `\r\n\r\n",
"I have merged and added some fairly robust set of tests for cross-checking old algo with new algo. CircleCI will warn us if something goes awry. The performance is pretty good, with little difference at small cells, but rapidly becoming much faster beyond 100 atoms.\r\n\r\n\r\n",
"@chc273 There seems to be some issues with the new algo and the Magnetic transformations. See https://circleci.com/gh/materialsproject/pymatgen/8522?utm_campaign=chatroom-integration&utm_medium=referral&utm_source=slack . Can you check?",
"I’ll take a look at this tomorrow also since I probably wrote some of that\ncode.\n\nOn Sun, Jun 2, 2019 at 13:48, Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> @chc273 <https://github.com/chc273> There seems to be some issues with\n> the new algo and the Magnetic transformations. See\n> https://circleci.com/gh/materialsproject/pymatgen/8522?utm_campaign=chatroom-integration&utm_medium=referral&utm_source=slack\n> . Can you check?\n>\n> —\n> You are receiving this because you were mentioned.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1480?email_source=notifications&email_token=AAWWWREOBST5SFAEFLDSABLPYQW2DA5CNFSM4HR55HDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWX5W2I#issuecomment-498064233>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWREJNMREL3WDBQP3OCLPYQW2DANCNFSM4HR55HDA>\n> .\n>\n",
"The error seems to be from using `get_neighbors` with a very small cutoff radius. Essentially there are no neighbors within the radius. The current `get_neighbors` and `get_neighbors_old` return an empty list `[]`, but the class expects a list of length 1. @shyuep \r\n\r\nIf Matt is going to take a look, I will leave this to you then @mkhorton Thanks. \r\n\r\n``` \r\nneighbors = structure.get_neighbors(\r\n site,\r\n 0.05, # arbitrary threshold, needs to be << any bond length\r\n # but >> floating point precision issues\r\n include_index=True\r\n )\r\n if len(neighbors) != 1:\r\n raise Exception(\"This shouldn't happen, found neighbors: {}\"\r\n> .format(neighbors))\r\nE Exception: This shouldn't happen, found neighbors: []\r\n```",
"@chc273 I just pushed a change that removed your \"sites\" option. In general, I do not like duplicate mutually exclusive arguments to a function, especially since the sites and indices can be generated quite eaily. However, it has introduced a strange error when inserting a hydroxyl atom. Cna you pull and check it out? Just need to run test_structure.py. \r\n\r\n@mkhorton I think you should look at the MagTransformation since that is the only area where there is a specific broken test.",
"@shyuep I agree . The inclusion of `sites` was to make `get_neighbors` method to call `get_all_neighbors` without much more efforts.\r\nThe added functionality of `sites` is that it can specify additional Sites that are not in the original structure. This can not be handled using `indices`. \r\n\r\nHere the problem seems to be from calling `self.index(site)` to a site that is not in original cell, but is a periodic image of one site in the cell. ",
"@chc273 In that case, I would suggest we keep the sites option and remove the indices option. Let me fix it now.",
"@chc273 I just pushed a fix for this particular problem. ",
"@mkhorton Can you get a fix in for the MagTransformation soon? I would like to do a release soon. The fact that it is the only place where there is a failing test suggest it is a specific issue to magnetic structures.",
"Will do",
"Looks like there's also a failure in `pymatgen.alchemy.tests.test_filters.SpecieProximityFilterTest.test_filter`",
"Fixed it. That's a regression when I refactored some of the things.",
"Ok, I have a minimal example of this bug now:\r\n\r\n```\r\nfrom pymatgen import Structure\r\nfrom pymatgen.electronic_structure.core import Spin\r\nd = {'@module': 'pymatgen.core.structure', '@class': 'Structure', 'charge': None, 'lattice': {'matrix': [[0.0, 0.0, 5.5333], [5.7461, 0.0, 3.518471486290303e-16], [-4.692662837312786e-16, 7.6637, 4.692662837312786e-16]], 'a': 5.5333, 'b': 5.7461, 'c': 7.6637, 'alpha': 90.0, 'beta': 90.0, 'gamma': 90.0, 'volume': 243.66653780778103}, 'sites': [{'species': [{'element': 'Mn', 'oxidation_state': 0, 'properties': {'spin': Spin.down}, 'occu': 1}], 'abc': [0.0, 0.5, 0.5], 'xyz': [2.8730499999999997, 3.83185, 4.1055671618015446e-16], 'label': 'Mn0+,spin=-1', 'properties': {}}, {'species': [{'element': 'Mn', 'oxidation_state': None, 'occu': 1.0}], 'abc': [1.232595164407831e-32, 0.5, 0.5], 'xyz': [2.8730499999999997, 3.83185, 4.105567161801545e-16], 'label': 'Mn', 'properties': {}}]}\r\nstruct = Structure.from_dict(d)\r\nprint(\"new method\", struct.get_neighbors(struct[0], 0.05))\r\nprint(\"old method\", struct.get_neighbors_old(struct[0], 0.05))\r\n```\r\n\r\n@chc273 could you investigate further? Note that this is a slightly pathological case with sites being co-incident with one another but it's important.",
"@mkhorton Will do. Thanks",
"@chc273 I think you should not do a check that the radius is > 1e-10. Once I remove that, everything works fine. ",
"@shyuep sure. Thanks. A distance threshold of >1e-8 was applied in the last step to filter out the centering site itself. If this is what you saw too. \r\nProbably we need to filter the centering site with same index and image vector (0, 0, 0) criterion. \r\n\r\n",
"It's a little tedious, but I sometimes have structures with exactly co-incident sites as an intermediate step prior to merging two sites together (or discarding one of them). There are some edge cases where this is useful, I think it was useful for the grain boundary generator too to discard duplicate sites, so it'd be good to have this fixed. I'm not sure the best way to filter the centering site.",
"@chc273 Yes, I think that would be the way to do it. Also, pls fix the list of lists problem at the same time.",
"@shyuep @mkhorton I am on it. Will push fixes for both cases. ",
"Thanks @chc273 ! "
] | 2019-05-31T20:51:46
| 2019-06-04T22:52:59
|
2019-06-02T20:03:21Z
|
CONTRIBUTOR
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## Summary
Implemented a linear scaling `get_all_neighbors_cell_list` method for `Structure`. This method gives identical results to `get_all_neighbors` but uses a cell list method that scales linearly with the number of atoms, i.e., O(N). The original `get_all_neighbors` has a O(N^2) scaling.
Reference: https://en.wikipedia.org/wiki/Cell_lists
* get_all_neighbors_cell_list
* linear scaling with system size
* Identical results as `get_all_neighbors`
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MDExOlB1bGxSZXF1ZXN0Mjg0MjEwODg5
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|
Lobsterin class to handle input for Lobster
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[
"If more problems occur, I will fix them in one of the next days.",
"Is there anything else I should do before it can be merged. Thanks. ",
"Thanks."
] | 2019-05-31T22:27:19
| 2019-06-03T13:49:51
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2019-06-03T13:49:48Z
|
MEMBER
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## Summary
I have implemented a new Lobsterin class in pymatgen.io.lobster to handle input for Lobster. This class works very similar to the INCAR class (subclass from dict and MSONable). Furthermore, it can write several input files (e.g. lobsterin, INCAR with lobster specific settings, KPOINTS for fatband calculations in Lobster (ISYM=-1))
I have also included tests. I am also happy to rename methods if suggested. I hope there won't be any problems with the automatic tests this time.
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fix CovalentBondNN.get_bonded_structure
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[] | null |
[
"Thanks.",
"Thanks @Ian496! Fyi we are updating this class for better molecule support throughout, the NearNeighbor classes were originally designed with only ordered crystal structures in mind. This may have some minor API changes when this happens."
] | 2019-06-02T14:08:11
| 2019-06-03T16:27:27
|
2019-06-03T13:48:41Z
|
CONTRIBUTOR
|
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## Summary
In the current master branch, `pymatgen.analysis.local_env.CovalentBondNN` returns AttributeError with the following code:
```
from pymatgen.core import Molecule
from pymatgen.analysis.local_env import CovalentBondNN
H2 = Molecule(['H', 'H'], [[0, 0, 0], [0, 0, 1.0]])
bonds = H2.get_covalent_bonds()
assert(len(bonds) == 1)
cbnn = CovalentBondNN()
mg = cbnn.get_bonded_structure(H2)
# -> AttributeError: 'Structure' object has no attribute 'get_covalent_bonds'
```
I find `CovalentBondNN.get_bonded_structure` calls `pymatgen.analysis.graphs.with_local_env_strategy` with defalut flag, and the latter returns not Molecule object but Structure object.
I fix a corresponding part and add test for `CovalentBondNN.get_bonded_structure`.
|
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| 451,527,829
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MDExOlB1bGxSZXF1ZXN0Mjg0NjAwMjU3
| 1,483
|
Fix small bug in Lobsterin
|
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[] | 2019-06-03T14:50:51
| 2019-06-03T16:07:03
|
2019-06-03T16:07:03Z
|
MEMBER
|
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While writing a sample script for the use of the Lobsterin class, I have found a small bug in the automatic determination of the basis functions for Lobster. I have fixed the bug and included test code to avoid the bug in the future.
Furthermore, I have modified the method to generate KPOINTS a bit and included a test.
|
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| 452,207,567
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MDExOlB1bGxSZXF1ZXN0Mjg1MTQzOTE4
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|
Bug fix for Structure.get_all_neighbors if cutoff radius is too small
|
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[
"Actually this is still not correct. The legnth of the list of lists should be equal to number of sites.",
"Pls resubmit a PR and include a test for this case."
] | 2019-06-04T21:04:37
| 2019-06-04T21:13:23
|
2019-06-04T21:07:46Z
|
CONTRIBUTOR
|
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## Bug fix for Structure.get_all_neighbors
Previously if the cutoff radius is too small and no neighbors are found, the `get_all_neighbors` method will return an empty list `[]`, while it should be a list of empty list `[[]]`.
This PR corrects return types.
|
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| 452,316,212
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MDExOlB1bGxSZXF1ZXN0Mjg1MjI4MzYw
| 1,485
|
Bug fix for get_all_neighbors
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[
"I added one more test for the small distance as well as @mkhorton's Mag structure coincident site test. I also removed the unnecessary checks for empty lists. Those checks are more trouble than it is worth. Without those, the code automatically returns the correct list of empty lists when cutoff is too small."
] | 2019-06-05T05:04:06
| 2019-06-05T13:34:44
|
2019-06-05T13:24:52Z
|
CONTRIBUTOR
|
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## Summary
1. Fixed the return type of `get_all_neighbors` when no neighbors are found. It should return a list of length n, where each item is `[]` and n is the number of atoms
2. Fixed the `magnetism` test problem. It is an issue with coincide sites. The site with DummySpecie coincides with a normal site and now the `get_neighbors` can find the correct neighbors from the Dummy site.
## Possible issue
In the case where two identical sites exist in a structure, the `get_neighbors_old` will not find any neighbors using one of the site (small cutoff). However, if one site has a different specie, then the algorithm will be able to find neighbors. It does not seem to be physical since neighboring relationship is only spatial information and should have nothing to do with the Specie. Now I set `get_neighbors` to have the same behavior as `get_neighbors_old`. If this needs to change, it can be easily fixed.
## Comparisons between `get_all_neighbors_old` and `get_all_neighbors`
The `get_all_neighbors_old` may give different results compared to `get_neighbors_old`, for example, in structures with coincide sites. For comparisons, always compare `get_all_neighbors` and `get_neighbors` to `get_neighbors_old`.
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MDU6SXNzdWU0NTI1MzM1OTQ=
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MagOrderingTransformation Bug with New Enumlib
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[
"@mkhorton I suspect this has to do with the fact that MagOrdering now creates Dummy sites that collide with existing sites. But I can't be sure. In any case, I am unclear why the collision needs to occur. Shouldn't the transformation just replace existing sites with dummy sites rather than adding?",
"It’s because unlike enumeration of disordered structures where you enumerate species, the enumeration has to be of the spin itself (these lattices of dummy atoms containing spin). These are enumerated and then merged with the actual species after enumeration has occurred.\r\n\r\nI can try and explain better if necessary, but basically this was necessary to get a lot of ferrimagnetic cases correct, where the spin down lattice could be from different sites of the same species or from sites from a different species.\r\n\r\nThe get_neighbors function was just a convenient way of merging the “spin lattice” with the “atom lattice.”\r\n\r\nI am sure there are other ways to do this also, but it seemed to work quite well.",
"In any case, I'm also getting this. I think it's some change with how max_cell_size is handled, will investigate.",
"@mkhorton I understand how it works broadly. What I meant is that colliding sites is not an ideal way (though the current get_all_neighbors has been fixed to deal with this). What I would suggest is that you initially do a mapping:\r\n\r\n1. Fe2+ -> Mma: Spin.up: 0.5 and Mmb: Spin.down: 0.5\r\n2. Replace all Fe2+ with the above (not create duplicate sites).\r\n3. Do enumeration.\r\n4. Reverse the mapping Mma -> Fe2+:Spin.up and MMb->Fe2+:Spin.down.\r\n\r\nI think the site merge function is not very robust and subject to tolerances. Species mapping is trivial and will always work.\r\n",
"Ah yes, that sounds much more sensible.",
"In fact, it sounds so sensible I'm not sure why the other method was chosen...will have to re-visit.\r\n\r\nIn terms of the test failure, the enum.x output gives:\r\n\r\n> Original d-set member was not inside the unit cell. It has been remapped.\r\nOriginal: 4.528 2.614 3.453\r\nRemapped: 0.000 -0.000 -0.000\r\n\r\n> d-vector didn't permute in map_dvector_permutation\r\n This usually means that the d-set from the input structure and the d-set\r\n from the struct_enum.out have a different origin or don't live in the same\r\n unit cell. This probably isn't your fault---the code should overcome this.\r\n\r\nSo may just be a bug in the new enum.x, will report to enumlib maintainers to see if they have ideas.",
"https://github.com/msg-byu/enumlib/issues/83",
"Thanks,",
"FYI, Gus Hart replied -- bug known, fix promised within a few weeks, apparently significantly improved enumeration speeds also.",
"Ok. I would suggest in the meantime that you also simplify the MagOrderingTransformation logic.",
"Yes, was going to take a look at that regardless\n\nOn Fri, Jun 7, 2019 at 09:21, Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> Ok. I would suggest in the meantime that you also simplify the\n> MagOrderingTransformation logic.\n>\n> —\n> You are receiving this because you were mentioned.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1486?email_source=notifications&email_token=AAWWWRHTHA2UMJJQWMTGA5LPZKDJ7A5CNFSM4HTZOZ22YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXGJ6DQ#issuecomment-499949326>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRBDG37YLFVLJNTQTBLPZKDJ7ANCNFSM4HTZOZ2Q>\n> .\n>\n",
"Any update?",
"If you're asking about the enumlib bug, I'm keeping an eye on it -- myself and @ncfrey have been testing the latest enumlib version, and it seems like the bug might be fixed but only with certain compilers (it seems to work with @ncfrey via ifort, but not for myself via gfortran). But there still seems to be some weirdness going on so I'm waiting for the official release.",
"No i mean the alternative strategy of enumerating the ordering. I find the current mag transformation way too clunky. The bug with enumlib is a separate issue.",
"Ah yes, ok. There was a reason for the current method which I didn’t recall during previous discussion. So you outlined the following algorithm:\r\n\r\n1. Fe2+ -> Mma: Spin.up: 0.5 and Mmb: Spin.down: 0.5\r\n2. Replace all Fe2+ with the above (not create duplicate sites).\r\n3. Do enumeration.\r\n4. Reverse the mapping Mma -> Fe2+:Spin.up and MMb->Fe2+:Spin.down.\r\n\r\nThis works well for for a single species substitution, and the mapping is easily reversible (in fact, in this case, we could just do Fe2+ -> Fe2+,spin=1/2 and Fe2+,spin=-1/2).\r\n\r\nHowever, the problem comes when you want to do an ordering on multiple subsystems of different species. For example, imagine you have two magnetic species, Fe and Co, and one species compensates the other. Here the mapping combines both species (Fe and Co) under one label to do the enumeration (to ensure that net spin is zero, for example). Then we get the output from enumlib, and because both Fe and Co were given the same label, we can no longer reverse the mapping without reference to the original input structure. This is why the combining of sites takes place.\r\n\r\nSo there was a reason the current system was in place. There were some actual real, scientifically relevant case studies that motivated it, I should see if I can dig them up. Perhaps there is also a simpler implementation still though, so I can have a think about it.",
"Perhaps I do not understand the scenario here. I understand of course you can have two magnetic species. But when can't Fe be assigned Mma and Mmb nad Co be assigned Mmc and Mmd with the appropriate occupancies for the enumeration? For instance, with say a 50-50 split for both species, you simply assign the occupancies of all of them to 0.25. Why wouldn't that give a proper net zero spin?",
"It would give a net zero spin, but would also introduce an additional constraint you may not want, namely in this example that there are equal amounts of up and down spin in each species: it would exclude a possible enumeration where one species has a disproportionate amount of up spin, and the other species a corresponding disproportionate amount of down spin, for a total net spin of zero. The current method doesn't see this constraint. (The physical relevance here is for those cases where one species might itself have multiple co-ordination environments, which leads to complex orderings such as this.)",
"Isn’t this just two sequential enumeration problems? One on spin and one on species? In any case, I am curious how common this is. Most species have different spins and are not drop-in replacements. E.g., Co3+ and Fe3+ have different magmoms. ",
"It can be; it depends on what information you know about the system beforehand. There are more targeted enumerations you can do if you have a good idea about the system, this algorithm was born as a solution to the very general case. Not so common but it happens. And yes, it's true, but we might not know the specific oxidation state ahead of time (or if it's high-spin, low-spin etc.) so the enumeration can be done purely on ordering of up/down spins irrespective of magnitude (since this defines the exchange symmetry of the system)."
] | 2019-06-05T14:27:58
| 2023-08-10T14:59:52
|
2023-08-10T14:59:52Z
|
MEMBER
|
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**Describe the bug**
MagOrderingTransformation seems to work with old enumlib, but fails with new enumlib. CircleCI tests are passing because those are based on the old enumlib.
**To Reproduce**
Steps to reproduce the behavior:
1. Compile enumlib from https://github.com/msg-byu/enumlib.git
2. Make the new enumlib default in the path.
3. Run test_advanced_transformations.
4. MagOrderingTransformation tests will fail with unable to enumerate. Given that other enumeration transformation tests passes, this is unique to the MagOrderingTransformation.
**Desktop (please complete the following information):**
- OS: MacOS
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MDU6SXNzdWU0NTMyNjQxNjY=
| 1,487
|
Inconsistent direct band gap of mp-782693 using `get_band_gap` and `get_direct_band_gap`
|
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[
"This is because the two functions use different methodologies. `get_band_gap` uses the CBM and VBM points, so it doesn't care about the spin. `get_direct_band_gap` is spin-aware and it turns out in this material the CBM and VBM are from different spins, so `get_direct_band_gap` finds \"another\" direct band_gap where the spin doesn't change for the transition. This logic is 7 years old from when @hautierg first wrote it. ",
"I see, thanks @shyamd "
] | 2019-06-06T22:23:42
| 2019-06-07T15:51:13
|
2019-06-07T15:51:13Z
|
CONTRIBUTOR
|
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**`Bandstructure.get_direct_band_gap` reports different value from `get_band_gap` for material with direct band gap**
I queried the band structure of `mp-782693` using `MPRester.get_bandstructure_by_material_id`. This material has a band gap (direct) of 0.685 eV as shown on the site and as computed by `get_band_gap` method. However, if I use `get_direct_band_gap` method on the BandStructure object, the function returns 1.555 eV.
I have checked a few other materials with direct band gap, and such anomaly does not exist. I wonder why such things happened? Is it necessary for `BandStructure.get_direct_band_gap` to firstly check if the material has a direct band gap and if so, just return the value from `get_band_gap`?
**To Reproduce**
```
from pymatgen import MPRester
mpr = MPRester()
bs = mpr.get_bandstructure_by_material_id('mp-782693')
print(bs.get_band_gap())
print(bs.get_direct_band_gap())
```
{'direct': True, 'energy': 0.6847, 'transition': '\\Gamma-\\Gamma'}
1.5554999999999999
**Expected behavior**
Both results should show a gap energy of 0.6847 eV.
**Desktop (please complete the following information):**
- OS: [e.g. iOS]
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| 453,623,868
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MDExOlB1bGxSZXF1ZXN0Mjg2Mjc3MzM2
| 1,488
|
fix Site.coords docstring to say Cartesian instead of fractional
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[] | 2019-06-07T17:43:27
| 2019-06-07T18:20:46
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2019-06-07T18:20:46Z
|
CONTRIBUTOR
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Quick fix, just a docstring typo. Previously the docstring for Site.coords said that the coordinates were fractional, but actually they are cartesian.
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MDU6SXNzdWU0NTQzMDEwMDg=
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Inconsistent number of layers in surface slabs
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[
"@richardtran415 Can you look into this?",
"Looking into it\n\nOn Tue, Jun 11, 2019 at 12:44 PM Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> @richardtran415 <https://github.com/richardtran415> Can you look into\n> this?\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1489?email_source=notifications&email_token=AB5J5VX3CUA3EBKUXOMI3ODPZ76ARA5CNFSM4HWV67AKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXOJE4Y#issuecomment-500994675>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AB5J5VUKWZCB6HPJWF4DVODPZ76ARANCNFSM4HWV67AA>\n> .\n>\n\n\n-- \n\nRichard Tran\nPhone: (415) 425-7660\nEmail: rit001@eng.ucsd.edu\n<https://acs-webmail.ucsd.edu/squirrelmail/src/compose.php?send_to=rit001%40ucsd.edu>\n"
] | 2019-06-10T18:18:38
| 2019-06-22T01:38:03
|
2019-06-22T01:38:03Z
|
NONE
|
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**Is your feature request related to a problem? Please describe.**
I want to generate some (111) surfaces of simple FCC metals (e.g., Ag, Au, Cu, Pd, Pt, Rh, and so on), and I need them to have the same number of layers of atoms. My strategy so far has been this:
```python
from pymatgen import Structure, Lattice
from pymatgen.core.surface import SlabGenerator, Slab
# Optimized lattice constants for materials
lattice_constants = {
"Ag": 4.2222795599999996,
"Au": 4.2188627199999997,
"Cu": 3.6526440600000001,
"Pd": 3.9962848399999999,
"Pt": 4.0050728199999996,
"Rh": 3.8727893799999999,
}
# Specify the structures and facets we will want
bulk_structures = {
element: Structure.from_spacegroup(
"Fm-3m", Lattice.cubic(a=lattice_constant), [element], [[0, 0, 0]]
)
for element, lattice_constant in lattice_constants.items()
}
# Now make the surfaces.
# Form slab from bulk crystals.
bare_surfaces = {}
for element, bulk_structure in bulk_structures.items():
sg = SlabGenerator(
initial_structure=bulk_structure,
miller_index=[1, 1, 1],
min_slab_size=3,
in_unit_planes=True,
min_vacuum_size=8,
max_normal_search=8
)
slab = sg.get_slabs()[0]
slab.make_supercell([3, 3, 1])
bare_surfaces[element] = slab
```
I am using the `in_unit_planes` option to request a certain number of atom layers. I'm also cutting bulk structures that are exactly the same symmetry group, differing only in atom identity and lattice constant.
**However, when I generate the slabs, only Au and Pd have the correct number of layers of atoms. All of the other slabs have twice as many layers.**
The problem appears to occur in this section of `pymatgen.core.surface`:
```python
h = self._proj_height
p = h/self.parent.lattice.d_hkl(self.miller_index)
if self.in_unit_planes:
nlayers_slab = int(math.ceil(self.min_slab_size / p))
nlayers_vac = int(math.ceil(self.min_vac_size / p))
```
Here, the division operation that calculates `p` seems to have enough floating point error to give it different values for different lattice constants. It appears to arise from slightly different values for the projected height (`self._proj_height = abs(np.dot(normal, c))`) and the *hkl* plane distance from the origin (`self.parent.lattice.d_hkl(self.miller_index)`). Logging the value of `p` throughout the generation of the six slabs gives the following:
Element: Ag
Lattice constant: 4.22227956
p value: 2.9999999999999996
Number of atoms in slab: 54
Element: Au
Lattice constant: 4.21886272
p value: 3.0
Number of atoms in slab: 27
Element: Cu
Lattice constant: 3.65264406
p value: 2.9999999999999996
Number of atoms in slab: 54
Element: Pd
Lattice constant: 3.99628484
p value: 3.0
Number of atoms in slab: 27
Element: Pt
Lattice constant: 4.00507282
p value: 2.999999999999999
Number of atoms in slab: 54
Element: Rh
Lattice constant: 3.87278938
p value: 2.9999999999999996
Number of atoms in slab: 54
**Describe the solution you'd like**
I know that the design of `SlabGenerator` is that the user can only specify a minimum number of layers. But it would be really nice to be able to enforce consistency across multiple slab simulations. Can we give the user the option to use rounding to a user-specified tolerance instead of `math.ceil` when using the `in_unit_planes` option?
**Describe alternatives you've considered**
Maybe something like this in `pymatgen.core.surface.SlabGenerator.get_slab`?
```python
def get_slab(self, shift=0, tol=0.1, energy=None, ptol=1e-4):
"""
This method takes in shift value for the c lattice direction and
generates a slab based on the given shift. You should rarely use this
method. Instead, it is used by other generation algorithms to obtain
all slabs.
Arg:
shift (float): A shift value in Angstrom that determines how much a
slab should be shifted.
tol (float): Tolerance to determine primitive cell.
energy (float): An energy to assign to the slab.
ptol (float): Tolerance used in determining how close to match the specified number of slab layers (min_slab_size).
Returns:
(Slab) A Slab object with a particular shifted oriented unit cell.
"""
h = self._proj_height
p = h/self.parent.lattice.d_hkl(self.miller_index)
if self.in_unit_planes:
if ptol:
nlayers_slab = int(round(self.min_slab_size / p), -math.log10(ptol))
nlayers_vac = int(round(self.min_vac_size / p), -math.log10(ptol))
else:
nlayers_slab = int(math.ceil(self.min_slab_size / p))
nlayers_vac = int(math.ceil(self.min_vac_size / p))
else:
nlayers_slab = int(math.ceil(self.min_slab_size / h))
nlayers_vac = int(math.ceil(self.min_vac_size / h))
nlayers = nlayers_slab + nlayers_vac
```
**Additional context**
Thanks!
|
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| 454,372,881
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MDExOlB1bGxSZXF1ZXN0Mjg2ODM3NDE5
| 1,490
|
Added from_vasp_voigt method to piezo.
|
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[] | null |
[] | 2019-06-10T21:05:23
| 2019-06-11T17:16:54
|
2019-06-11T17:16:54Z
|
CONTRIBUTOR
|
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## Summary
Added from_vasp_voigt method to piezo and tests
Vasp reports the piezoelectric tensor not in the proper voigt notation, this method converts the vasp generated tensor into the full 3x3x3 tensor.
|
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MDU6SXNzdWU0NTQ3NTI4MzY=
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|
Clean Up Interface Analysis
|
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[] | 2019-06-11T15:17:58
| 2023-08-13T16:32:53
|
2023-08-13T16:32:53Z
|
NONE
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The interface classes need some clean up.
- `Interface` needs to be moved to core
- `analysis` needs an interfaces sub_module with `ZSLGenerator`, `StradiGenerator` ,`SubstrateAnalyzer`, and `InterfaceBuilder`
- Convert `GrainBoundary` to inherit from `Interface`
|
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MDExOlB1bGxSZXF1ZXN0Mjg3NTQ0ODY1
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|
Fix for issue #1442
|
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[
"Thanks. Can you add unittests to ensure those bugs don't recur in future? ",
"Great catch for the shape of the cder_data!\r\n\r\nBased on the discussion in #1442, it seems like the datatype of the records can be float64 instead of complex64 if the wave function is generated using the gamma point version of VASP. \r\n\r\nPlease can you also add an option in the init method called `gamma_only` which defaults to False and will toggle the datatype correctly.",
"I've added the option proposed by @utf .\r\n\r\nRegarding unit tests, I have never done them before, so I might need a bit to figure out what to test.",
"Added a unit test. \r\nIt would be great if somebody can look over it to see if its useful this way.",
"Great. THanks. I will merge now.\r\n"
] | 2019-06-12T14:50:06
| 2019-06-13T14:18:54
|
2019-06-13T14:18:54Z
|
CONTRIBUTOR
|
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## Summary
This commit tries to fix issue #1442 in the pymatgen.io.vasp.outputs.Waveder class.
* Fix 1
The original issue is raised by the fact that the variables and member functions have the same name.
This has been fixed by prepending a underscore to the variable names.
* Fix 2
Additionally, the datatype of the records read into cder should be of type np.complex64.
This has been changed.
* Fix 3
Furthermore, the order of the reshape call for cder_data needs to be inverted, otherwise the mapping between bands, kpoints and spin won't be correct
* Feature 1
I also introduced a property function for the orbital derivative between states.
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MDU6SXNzdWU0NTU0NzcxMjE=
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FEFF IO mistakenly parses feff.inp files
|
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[] | 2019-06-13T00:06:03
| 2019-06-13T04:19:07
|
2019-06-13T04:19:07Z
|
CONTRIBUTOR
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**Describe the bug**
.io.feff tests to see if a feff.inp file was created by Pymatgen by checking to see if the word 'pymatgen' shows up in the first line. It does this via the find method for a string, which returns the index of the string at which the desired substring first appears.
```
try:
feffpmg = f[0].find("pymatgen")
except IndexError:
feffpmg = False
```
However, the find() method for a string returns the integer -1 if it is not in the string. This is truthy in Python, so it will always think that a feff.inp file was generated by Pymatgen. This causes an issue when it tries to parse the file. This same issue occurs later on in the same file.
**To Reproduce**
Steps to reproduce the behavior:
The following FEFF input file, taken from the materials project website, will cause an error when the method
`Header.from_file('feff.inp')`
is called on this file:
```
KMESH 10 10 10
EXCHANGE 0 0.0 0.0 2
TARGET 1
XANES 3.7 0.04 0.1
CONTROL 1 1 1 1 1 1
FMS 9 0
LDOS -30.0 30.0 0.1
COREHOLE Rpa
EDGE K
RPATH -1
CIF Cu1.cif
RECIPROCAL
SCF 7 0 30 0.2 3
PRINT 1 0 0 0 0 0
S02 0.0
```
**Additional context**
A simple fix would be to add two extra lines after the find method is called, saying
```
if feffpmg==-1:
feffpmg=False
```
When an input file that was not generated by pymatgen is then passed, it eventually will guide takes the user to the string
```
return "Header not generated by pymatgen, cannot return header object"
```
as was intended.
This should probably be a warning, or a raised error, but that is beyond the scope of this issue and I leave that in your hands :) I will submit a pull request fixing this.
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MDExOlB1bGxSZXF1ZXN0Mjg3NzIxNjE0
| 1,494
|
Fixed Issue 1493: bug in feff IO when parsing non-pymatgen generated file
|
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[
"Thanks @stevetorr !"
] | 2019-06-13T00:33:22
| 2019-06-13T04:19:02
|
2019-06-13T04:19:02Z
|
CONTRIBUTOR
|
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## Summary
This pull request fixes a minor bug in the FEFF IO script which is summarized in Issue 1493:
https://github.com/materialsproject/pymatgen/issues/1493
|
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Add Outcar method to parse on-site density matrix and tests
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[
"Thanks @clegaspi for help with the regex on this one, @mhsiron this should be ready for your workflow now if you pull from master",
"Did you mean to change the row pattern for spin down? Shouldn't it be the same as spin up? ",
"Hmm, good catch. Yes, I’ll change that. Thanks!"
] | 2019-06-14T00:38:56
| 2021-02-13T17:29:06
|
2019-06-14T01:38:37Z
|
MEMBER
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Will merge once CI passes.
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Incorrect results from MagneticSpaceGroup
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"Thanks Simon! I’ll take a look at this.\n\nOn Fri, Jun 14, 2019 at 03:10, Simon Ward <notifications@github.com> wrote:\n\n> *Describe the bug*\n> Some magnetic structures are not being described properly by\n> MagneticSpaceGroup. There has probably been a small error when originally\n> parsing https://stokes.byu.edu/iso/magnetic_data.txt\n>\n> *To Reproduce*\n> Steps to reproduce the behavior. E.g the R-3c' spacegroup:\n>\n> from pymatgen.symmetry.maggroups import *\n> msg = MagneticSpaceGroup([167, 107]) # this is the BNS reference to R-3c'\n> r, v = msg.get_orbit([1/8 0 1/4], 1)\n>\n> *Expected behavior*\n> The operators and Wyckoff Positions are given as:\n>\n> BNS: 167.107 R-3c'\n> Operators: (1|0,0,0) (2y|0,0,0) (3xyz-1|0,0,0) (2-xy|0,0,0)\n> (4z-1|0,0,0) (2-yz|0,0,0) (3xyz|0,0,1/2)'\n> (3xy-z-1|0,0,1/2)' (3-xyz|0,0,1/2)' (2-xz|0,0,1/2)'\n> (2xz|0,0,1/2)' (4x|0,0,1/2)'\n> Wyckoff Positions: (2/3,1/3,1/3)+ (1/3,2/3,2/3)+\n> 36f (x,y,z;mx,my,mz) (y,-x-y,z;my,-mx-my,mz) (-x-y,x,z;-mx-my,mx,mz)\n> (x,-x-y,-z+1/2;-mx,mx+my,mz) (y,x,-z+1/2;-my,-mx,mz)\n> (-x-y,y,-z+1/2;mx+my,-my,mz) (-x,-y,-z;mx,my,mz)\n> (-y,x+y,-z;my,-mx-my,mz) (x+y,-x,-z;-mx-my,mx,mz)\n> (-x,x+y,z+1/2;-mx,mx+my,mz) (-y,-x,z+1/2;-my,-mx,mz)\n> (x+y,-y,z+1/2;mx+my,-my,mz)\n> 18e (x,0,1/4;mx+2my,0,mz) (y,0,1/4;-2mx-my,0,mz)\n> (-x-y,0,1/4;mx-my,0,mz) (-x,0,3/4;mx+2my,0,mz)\n> (-y,0,3/4;-2mx-my,0,mz) (x+y,0,3/4;mx-my,0,mz)\n> 18d (1/2,0,0;mx,my,mz) (0,1/2,0;my,-mx-my,mz)\n> (1/2,1/2,0;-mx-my,mx,mz) (1/2,0,1/2;-mx,mx+my,mz)\n> (0,1/2,1/2;-my,-mx,mz) (1/2,1/2,1/2;mx+my,-my,mz)\n> 12c (0,0,z;0,0,mz) (0,0,-z+1/2;0,0,mz) (0,0,-z;0,0,mz)\n> (0,0,z+1/2;0,0,mz)\n> 6b (0,0,0;0,0,mz) (0,0,1/2;0,0,mz)\n> 6a (0,0,1/4;0,0,mz) (0,0,3/4;0,0,mz)\n>\n> From the Bilbao Crystallographic Server (which uses the same data source)\n> we get:\n>\n> 36f (x,y,z | mx,my,mz)\t(-y,x-y,z | -my,mx-my,mz)\n> (-x+y,-x,z | -mx+my,-mx,mz)\t(x-y,-y,-z+1/2 | -mx+my,my,mz)\n> (y,x,-z+1/2 | -my,-mx,mz)\t(-x,-x+y,-z+1/2 | mx,mx-my,mz)\n> (-x,-y,-z | mx,my,mz)\t(y,-x+y,-z | -my,mx-my,mz)\n> (x-y,x,-z | -mx+my,-mx,mz)\t(-x+y,y,z+1/2 | -mx+my,my,mz)\n> (-y,-x,z+1/2 | -my,-mx,mz)\t(x,x-y,z+1/2 | mx,mx-my,mz)\n> 18e (x,0,1/4 | mx,2mx,mz) (0,x,1/4 | -2mx,-mx,mz)\n> (-x,-x,1/4 | mx,-mx,mz) (-x,0,3/4 | mx,2mx,mz)\n> (0,-x,3/4 | -2mx,-mx,mz) (x,x,3/4 | mx,-mx,mz)\n> 18d (1/2,0,0 | mx,my,mz) (0,1/2,0 | -my,mx-my,mz)\n> (1/2,1/2,0 | -mx+my,-mx,mz) | (1/2,0,1/2 | -mx+my,my,mz)\n> (0,1/2,1/2 | -my,-mx,mz) | (1/2,1/2,1/2 | mx,mx-my,mz)\n> 12c (0,0,z | 0,0,mz) (0,0,-z+1/2 | 0,0,mz)\n> (0,0,-z | 0,0,mz) | (0,0,z+1/2 | 0,0,mz)\n> 6b (0,0,0 | 0,0,mz) (0,0,1/2 | 0,0,mz)\n> 6a (0,0,1/4| 0,0,mz) (0,0,3/4 | 0,0,mz)\n>\n> I have also verified this manually against the International Tables for\n> Crystallography https://www.iucr.org/publ/978-0-9553602-2-0\n>\n> This means that the generated positions r and the magnetic vectors v are\n> incorrect. And indeed, they are not compatible with the base non-magnetic\n> spacegroup.\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1496?email_source=notifications&email_token=AAWWWRAEGFS6736DDLHVJ5DP2NVDBA5CNFSM4HYGOIG2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GZQS3BA>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRC4CXQMK66VMZU7Z73P2NVDBANCNFSM4HYGOIGQ>\n> .\n>\n",
"I've looked a bit and it might be the case that the matrices in http://stokes.byu.edu/iso/magnetic_data.txt were read in rows rather than columns. In the above case I think it works if read in this way. \r\nI'll also do a few tests and if this is the case, I'll submit a pull request with a few transpose operations as this should sort it.",
"That would be excellent, thank you!\r\n\r\nI just checked the human-readable tables on ISO-MAG, and this is the one for 167.107 so it looks like there is a difference:\r\n\r\n```\r\nBNS: 167.107 R-3c' OG: 167.5.1338 R-3c'\r\nOperators: (1|0,0,0) (3z|0,0,0) (3z-1|0,0,0) (2x|0,0,1/2)' (2xy|0,0,1/2)'\r\n (2y|0,0,1/2)' (-1|0,0,0) (-3z|0,0,0) (-3z-1|0,0,0) (mx|0,0,1/2)'\r\n (mxy|0,0,1/2)' (my|0,0,1/2)'\r\nWyckoff positions: (0,0,0)+ (2/3,1/3,1/3)+ (1/3,2/3,2/3)+\r\n36f (x,y,z;mx,my,mz) (-y,x-y,z;-my,mx-my,mz) (-x+y,-x,z;-mx+my,-mx,mz)\r\n (x-y,-y,-z+1/2;-mx+my,my,mz) (y,x,-z+1/2;-my,-mx,mz)\r\n (-x,-x+y,-z+1/2;mx,mx-my,mz) (-x,-y,-z;mx,my,mz) (y,-x+y,-z;-my,mx-my,mz)\r\n (x-y,x,-z;-mx+my,-mx,mz) (-x+y,y,z+1/2;-mx+my,my,mz)\r\n (-y,-x,z+1/2;-my,-mx,mz) (x,x-y,z+1/2;mx,mx-my,mz)\r\n18e (x,0,1/4;mx,2mx,mz) (0,x,1/4;-2mx,-mx,mz) (-x,-x,1/4;mx,-mx,mz)\r\n (-x,0,3/4;mx,2mx,mz) (0,-x,3/4;-2mx,-mx,mz) (x,x,3/4;mx,-mx,mz)\r\n18d (1/2,0,0;mx,my,mz) (0,1/2,0;-my,mx-my,mz) (1/2,1/2,0;-mx+my,-mx,mz)\r\n (1/2,0,1/2;-mx+my,my,mz) (0,1/2,1/2;-my,-mx,mz) (1/2,1/2,1/2;mx,mx-my,mz)\r\n12c (0,0,z;0,0,mz) (0,0,-z+1/2;0,0,mz) (0,0,-z;0,0,mz) (0,0,z+1/2;0,0,mz)\r\n6b (0,0,0;0,0,mz) (0,0,1/2;0,0,mz)\r\n6a (0,0,1/4;0,0,mz) (0,0,3/4;0,0,mz)\r\n```",
"Yep, I also cross referenced with VASP and you get the same.\r\nAny thoughts or more rigorous testing? I ask as it seems that the test cases are all of the more 'basic' spacegroups and could be easily extended.",
"I'd definitely be happy for more rigorous testing, I mostly tested some of these manually when I added them. I think I cross-checked against the normal crystallographic groups, but I didn't have a good source to do more than manual testing for the magnetic (b+w) groups. I'm glad you caught this.",
"Created pull request #1502 which fixes the problem. \r\nAs for unit testing, I was thinking that pulling results from the Bilbao Crystallographic Server would work, though that would be comparing tuples instead of string literals. A good starting place is https://subversion.xray.aps.anl.gov/trac/pyGSAS/browser/trunk/kSUBGROUPSMAG.py \r\n\r\n\r\n"
] | 2019-06-14T10:10:54
| 2019-06-20T18:05:15
|
2019-06-20T18:05:15Z
|
NONE
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**Describe the bug**
Some magnetic structures are not being described properly by MagneticSpaceGroup. There has probably been a small error when originally parsing https://stokes.byu.edu/iso/magnetic_data.txt
**To Reproduce**
Steps to reproduce the behavior. E.g the R-3c' spacegroup:
```python
from pymatgen.symmetry.maggroups import *
msg = MagneticSpaceGroup([167, 107]) # this is the BNS reference to R-3c'
r, v = msg.get_orbit([1/8 0 1/4], 1)
```
**Expected behavior**
The operators and Wyckoff Positions are given as:
```
BNS: 167.107 R-3c'
Operators: (1|0,0,0) (2y|0,0,0) (3xyz-1|0,0,0) (2-xy|0,0,0)
(4z-1|0,0,0) (2-yz|0,0,0) (3xyz|0,0,1/2)'
(3xy-z-1|0,0,1/2)' (3-xyz|0,0,1/2)' (2-xz|0,0,1/2)'
(2xz|0,0,1/2)' (4x|0,0,1/2)'
Wyckoff Positions: (2/3,1/3,1/3)+ (1/3,2/3,2/3)+
36f (x,y,z;mx,my,mz) (y,-x-y,z;my,-mx-my,mz) (-x-y,x,z;-mx-my,mx,mz)
(x,-x-y,-z+1/2;-mx,mx+my,mz) (y,x,-z+1/2;-my,-mx,mz)
(-x-y,y,-z+1/2;mx+my,-my,mz) (-x,-y,-z;mx,my,mz)
(-y,x+y,-z;my,-mx-my,mz) (x+y,-x,-z;-mx-my,mx,mz)
(-x,x+y,z+1/2;-mx,mx+my,mz) (-y,-x,z+1/2;-my,-mx,mz)
(x+y,-y,z+1/2;mx+my,-my,mz)
18e (x,0,1/4;mx+2my,0,mz) (y,0,1/4;-2mx-my,0,mz)
(-x-y,0,1/4;mx-my,0,mz) (-x,0,3/4;mx+2my,0,mz)
(-y,0,3/4;-2mx-my,0,mz) (x+y,0,3/4;mx-my,0,mz)
18d (1/2,0,0;mx,my,mz) (0,1/2,0;my,-mx-my,mz)
(1/2,1/2,0;-mx-my,mx,mz) (1/2,0,1/2;-mx,mx+my,mz)
(0,1/2,1/2;-my,-mx,mz) (1/2,1/2,1/2;mx+my,-my,mz)
12c (0,0,z;0,0,mz) (0,0,-z+1/2;0,0,mz) (0,0,-z;0,0,mz)
(0,0,z+1/2;0,0,mz)
6b (0,0,0;0,0,mz) (0,0,1/2;0,0,mz)
6a (0,0,1/4;0,0,mz) (0,0,3/4;0,0,mz)
```
From the Bilbao Crystallographic Server (which uses the same data source) we get:
```
36f (x,y,z | mx,my,mz) (-y,x-y,z | -my,mx-my,mz)
(-x+y,-x,z | -mx+my,-mx,mz) (x-y,-y,-z+1/2 | -mx+my,my,mz)
(y,x,-z+1/2 | -my,-mx,mz) (-x,-x+y,-z+1/2 | mx,mx-my,mz)
(-x,-y,-z | mx,my,mz) (y,-x+y,-z | -my,mx-my,mz)
(x-y,x,-z | -mx+my,-mx,mz) (-x+y,y,z+1/2 | -mx+my,my,mz)
(-y,-x,z+1/2 | -my,-mx,mz) (x,x-y,z+1/2 | mx,mx-my,mz)
18e (x,0,1/4 | mx,2mx,mz) (0,x,1/4 | -2mx,-mx,mz)
(-x,-x,1/4 | mx,-mx,mz) (-x,0,3/4 | mx,2mx,mz)
(0,-x,3/4 | -2mx,-mx,mz) (x,x,3/4 | mx,-mx,mz)
18d (1/2,0,0 | mx,my,mz) (0,1/2,0 | -my,mx-my,mz)
(1/2,1/2,0 | -mx+my,-mx,mz) | (1/2,0,1/2 | -mx+my,my,mz)
(0,1/2,1/2 | -my,-mx,mz) | (1/2,1/2,1/2 | mx,mx-my,mz)
12c (0,0,z | 0,0,mz) (0,0,-z+1/2 | 0,0,mz)
(0,0,-z | 0,0,mz) | (0,0,z+1/2 | 0,0,mz)
6b (0,0,0 | 0,0,mz) (0,0,1/2 | 0,0,mz)
6a (0,0,1/4| 0,0,mz) (0,0,3/4 | 0,0,mz)
```
I have also verified this manually against the International Tables for Crystallography https://www.iucr.org/publ/978-0-9553602-2-0
This means that the generated positions `r` and the magnetic vectors `v` are incorrect. And indeed, they are not compatible with the base non-magnetic spacegroup.
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MDExOlB1bGxSZXF1ZXN0Mjg4NTA5ODUw
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Minor updates to surface.py and get_cohesive_energy
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[
"Thanks @richardtran415, labelling bulk Wyckoff sites seems especially useful.\r\n\r\nDo you have any idea why CircleCI is segfaulting with this PR? As far as I can tell nothing in this PR should cause this.",
"I honestly don't know why that would happen, I'll do some additional nosetests on my laptop and CircleCi to figure out what's going on and make another git push later on.\r\n\r\nThanks ",
"Ok, can you manually trigger the CircleCI test to re-rerun? We've been having some issues with seg faults with Circle previously, I'd want to merge this PR if it passes though. It seems to me this is (again) a CI fault not anything wrong with the PR.",
"Thanks @richardtran415 -- fyi for future ref you can log in to CircleCI and trigger a test re-run yourself (obviously this should be deterministic but with a seg fault who knows). I just didn't have permission to do this on your fork.",
"I might be wrong, but my guess was that pymatgen doesn't use circleci tests by default anymore and instead switched to travis-ci. I know some other PRs that don't have CircleCi checks and pass everything else just fine, but the ones that do have CircleCi don't. Since I previously created my own CircleCi account to specifically check my fork of pymatgen, that might be triggering the test to run whenever I do a PR when it's not suppose to run in the first place. That doesn't explain the segmentation fault, but perhaps there needs to be something updated on CircleCi for it to work? I could just remove my fork from my CircleCi account, then all the tests should pass.",
"Even so I need to see that the Travis tests pass first\n\nOn Tue, Jun 18, 2019 at 10:51 Richard Tran <notifications@github.com> wrote:\n\n> I might be wrong, but my guess was that pymatgen doesn't use circleci\n> tests by default anymore and instead switched to travis-ci. I know some\n> other PRs that don't have CircleCi checks and pass everything else just\n> fine, but the ones that do have CircleCi don't. Since I previously created\n> my own CircleCi account to specifically check my fork of pymatgen, that\n> might be triggering the test to run whenever I do a PR when it's not\n> suppose to run in the first place. That doesn't explain the segmentation\n> fault, but perhaps there needs to be something updated on CircleCi for it\n> to work? I could just remove my fork from my CircleCi account, then all the\n> tests should pass.\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1497?email_source=notifications&email_token=AAEM4U2FWGTARB6JN3IUWLLP3A5RVA5CNFSM4HYNV32KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODX45UUI#issuecomment-502913617>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAEM4UY2EOP7U6EEOQ6F6BLP3A5RVANCNFSM4HYNV32A>\n> .\n>\n-- \nShyue Ping\n",
"@mkhorton I think I see what happened, my pymatgen was not completely up-to-date with the master branch when CircleCi was failing, that was my mistake, sorry.",
"No worries, glad it wasn't anything significant!"
] | 2019-06-14T23:16:34
| 2019-06-18T05:50:56
|
2019-06-18T05:50:56Z
|
CONTRIBUTOR
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## Summary
- Bug fix when using the in_unit_planes parameter in SlabGenerator for getting slabs of a consistent number of atoms. Number of unit planes (p) is always rounded to nearest int to avoid floats such as 2.999999999 or 2.000000001. This should address issue #1489
- Distinguish tol from ftol. These parameters do two different things and should not be the same. tol is used for structure matching and getting a primitive cell. ftol is the parameter for clustering sites as terminations when using fcluster.
- Made default ftol larger. This prevents the generation of any nonsensical slabs when dealing with crystal structures with high symmetry.
- Added site_properties that allow us to identify corresponding bulk Wyckoff and bulk equivalent sites. Useful for doing slab analysis and transformations such as reconstructions.
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| 456,528,072
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MDExOlB1bGxSZXF1ZXN0Mjg4NTUwNTE0
| 1,498
|
Fix pip install
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[
"I have also corrected for another bug in the calculation of nbands... and adapted one test to avoid this in the future."
] | 2019-06-15T11:20:48
| 2019-06-15T17:04:49
|
2019-06-15T17:04:49Z
|
MEMBER
|
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## Summary
After using pip install, "BASIS_PBE_54.yaml" was not found. I have changed the "setup.py" to correct this.
|
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MDExOlB1bGxSZXF1ZXN0Mjg5NjIyODI1
| 1,499
|
Another small update to Lobsterin class
|
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[
"Better bug fixes than bugs!\r\n\r\nQuestion regarding the io, why the write_INCAR function instead of a `LobsterSet` in io.vasp.sets? The latter may be easier for other people to discover",
"I will probably write a LobsterSet in the future. I have to think a bit more about the design at first. I am not sure about the standard settings for the calculations yet. ",
"And, thanks for merging."
] | 2019-06-19T09:45:21
| 2019-06-19T15:59:10
|
2019-06-19T15:39:55Z
|
MEMBER
|
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|
## Summary
Small BugFix in the lobsterin class to also change LWAVE from False to True when writing a new INCAR. I also adapted the tests.
I am sorry for the very frequent bug fixes at the moment. I hope this will be one of the last ones for now.
|
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MDExOlB1bGxSZXF1ZXN0Mjg5OTE1NzMz
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Fix serialization of Interface
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[
"Usually it's better not to have to write custom as_dict/from_dict methods -- what specifically about Interface means they're necessary? (Not a problem if it is necessary)",
"Ok, verdict is that it’s because of Structure’s from_dict. Also making a note that get_sorted_structure and from_sites won’t work on subclasses as present, will need to address this in future. ",
"`test_copy` broke on this",
"Looks like it. Looking into this now",
"Okay, @mkhorton. Issues resolved"
] | 2019-06-19T23:41:47
| 2019-06-21T02:11:23
|
2019-06-21T02:11:23Z
|
CONTRIBUTOR
|
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## Summary
-Override the as_dict() and from_dict() functions from pymatgen.core.structure.Structure for proper serialization
- Cleaned up extraneous imports
- Fixed option to create copy with site properties (Previously documented as such, with no functionality)
- Override get_sorted_structure() from Structure. Not sure if this was the right way to fix the issue; the alternative is to make an Interface.from_sites() function, although one will likely never make an interface from a list of sites.
## TODO (if any)
- Unit tests
|
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