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updates
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[] | 2016-10-14T04:33:04
| 2016-10-14T04:48:07
|
2016-10-14T04:48:07Z
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CONTRIBUTOR
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- feff: the absorbing atom can be specified by either its symbol or the site index. added test
- Bandstructure serialization fix: make the vbm and cbm projections consistent with the latest refactoring. The stray old style serialization in the Bandstructure class causes trouble if the projections are read in and the line mode is set to false in the get_bandstructure call(this is why i was getting the error( issue #500))
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|
Small bug fixes in MultiStructureVis and qadapters + Small fix of of CONTCAR reading
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[] | 2016-10-20T09:37:08
| 2016-10-20T13:36:14
|
2016-10-20T13:36:14Z
|
CONTRIBUTOR
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## Summary
1 Ability to read CONTCAR files with more than 20 groups of atoms (in which case, the atoms and number of atoms are spread over more than just one line each)
2 Added test for the previous case.
3 Small fix in MultiStructureVis
4 Small fix in io.abinit.qadapters
## TODO (if any)
- Feature 1 is not compatible with vasp 4.
|
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|
A question about the symmetry operations
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[
"spglib's symmetry operations are those that apply to that specific crystal. For example, if you have a supercell or a different setting, the actual symmetry operations are different from those in a standard conventional setting.\n\nThe pymatgen.symmetry.groups operations are those that apply the standard conventional setting, with all atoms in their ideal symmetry positions.\n"
] | 2016-10-23T13:46:41
| 2016-10-23T20:56:02
|
2016-10-23T20:56:02Z
|
CONTRIBUTOR
|
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<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
- Pymatgen version: <Write "branch_name" if it is development version.>
- Python version: <Only 2.7.* and 3.* supported.>
- OS version: <If you are writing Windows here, you are on your own.>
## Summary
What's the difference between the symmetry operations generated by the spglib and the symmetry operations generated in the _generate_full_symmetry_ops in pymatgen.symmetry.groups using the concept in <<Structure of Materials>>? I have tried several systems, and the spglib.get_symmetry_operations give different operations from that generated by the _generate_full_symmetry. However, both group of operations are closed.
## Example code
``` python
<Example code generating error>
```
## Error message
```
<Error message>
```
## Suggested solution (if any)
- <If you have a suggestion on how to solve the issue, you may write it
here.>
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
```
|
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MDU6SXNzdWUxODUyNDE2Njk=
| 504
|
Help retrieving names of all elements
|
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[
"Element is now an enum. If you want all the elements with Z 1-50, you simply do\n\n``` python\nfrom pymatgen import Element\nsymbols = [Element.from_Z(z).symbol for z in range(1, 51)]\n```\n\nI should point out that the code is from citrine's website. Pls contact them if you have problem with their code.\n",
"@shyuep, thanks! Worked nicely. Yes, the code is from citrine's site. But I was using it for a different purpose.\n"
] | 2016-10-25T21:41:27
| 2016-10-27T00:25:11
|
2016-10-25T22:32:15Z
|
NONE
|
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Hi,
I am a new user of pymatgen and I am using version 4.4.9. I need some help.
1. I would like to create a list of all elements. I found some example code that does the job using this:
``` python
from pymatgen import MPRester, periodic_table
import itertools
allBinaries = itertools.combinations(periodic_table.all_symbols(), 2)
```
This code is supposed to create a list of all possible binaries. Unfortunately it does not work. It seems the all_symbols() function is not available anymore.
I would like to create a list of all elements, then retrieve their corresponding atomic numbers. Any help regarding this?
1. For a given range of atomic numbers, say 1-50 I would like to create a list of corresponding elements. How can I do this?
|
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MDU6SXNzdWUxODU5NzYwNjg=
| 505
|
Some input sets override user_incar_settings
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[] | 2016-10-28T17:19:55
| 2016-10-28T22:06:40
|
2016-10-28T22:06:40Z
|
CONTRIBUTOR
|
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## System
- Pymatgen version: 4.3
- Python version: 2.7
## Summary
- The MVLSlabSet overrides user_incar_settings. Upon inspection, it seems as if MVLSlabSet.incar sets several of the parameters specific to that set after calling super, which is where the user_incar_settings are added. My quick fix added `incar.update(self.user_incar_settings)` to MVLSlabSet.incar before the return statement, but it seems like there might be a more elegant general method.
## Example code
``` python
from pymatgen.io.vasp.sets import MVLSlabSet
from pymatgen.util.testing import PymatgenTest
si = PymatgenTest.get_structure('Si')
vis = MVLSlabSet(si, user_incar_settings={"AMIX":0.1})
vis.write_input('.')
# Upon inspection of incar, AMIX is 2
```
|
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| 186,877,665
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MDU6SXNzdWUxODY4Nzc2NjU=
| 506
|
importing pymatgen takes a long time
|
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[
"I sped up the import a bit by disabling the spglib loading. But ultimately, the profiling tells me that the major factor is the creation of the Element enum type. That is however required for proper functioning. There is a way to speed up by ~50% if I disable unit checking, but that may break stuff. I will need to work this out a bit more.\n\nThat said, I am very surprised if it takes 3-10 seconds for import. By my count, it takes 1s or less.\n",
"Thanks for looking into this:\n\n> > That said, I am very surprised if it takes 3-10 seconds for import. By my count, it takes 1s or less.\n\nIf you want to reproduce, you can try on tscc\n- ssh to tscc\n - load the matmethods environment on our project account (\"use_matmethods_env\")\n - start a python shell\n - type \"from pymatgen import Composition\"\n - count cursor blinks as a crude approximation or write code to do a more formal test\n",
"I found a way to speed up. I tried the TSCC load. It now takes ~1.1 secs. I think that's about as fast as I can make it without major surgery. Still not as fast as we would like, but not too bad.\n",
"Ok thanks, I confirmed it is much faster on my local machine\n"
] | 2016-11-02T18:06:11
| 2016-11-03T15:57:39
|
2016-11-02T21:30:55Z
|
MEMBER
|
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## System
* Pymatgen version: master
* Python version: 2.7.x
* OS version: Mac / Linux
## Summary
* Importing pymatgen objects takes a long time
* e.g., "from pymatgen import Composition" takes about 3 seconds on my machine; on NERSC it is like 10 seconds. These times vary depending on whether you run the test multiple times in a row which will affect what files are in RAM, etc., but they are always fairly long compared to other libraries like numpy which are instantaneous
* This causes a problem if I am hacking on an analysis script with pymatgen. Rather than getting instant results, I have a major (to me) delay every time I run my code. I am currently trying to avoid importing pymatgen for as long as possible to get speed
## Example code
```python
from pymatgen import Composition
```
## Error message
<slow>
## Suggested solution (if any)
don't know
|
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| 187,802,174
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MDU6SXNzdWUxODc4MDIxNzQ=
| 507
|
Help retrieving lattice parameter from Materials Project data
|
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[] | null |
[
"This approach is far too complicated. You just need to do:\n\n``` python\nfrom pymatgen import MPRester\nm = MPRester()\nfor s in m.get_structures(\"LiBeH3\"):\n print(s.lattice.abc)\n print(s.lattice.angles)\n```\n\nFor future reference, pls submit questions to the google groups. Github Issues are meant for actual bug reports or feature requests.\n",
"Thanks!\n\nI was not aware of the google group. I looked for something like that, but could not find.\n",
"It is at https://groups.google.com/forum/?fromgroups#!forum/pymatgen\n"
] | 2016-11-07T19:19:17
| 2016-11-07T19:39:27
|
2016-11-07T19:33:34Z
|
NONE
|
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Hi,
I am using pymatgen (v4.5.0) to retrieve material data from materials project and extract the lattice parameters. When a material data is retrieved from Materials Project, it seems the lattice parameter data is buried into the cif data. It seems there are several options to write cif data, but not so much to retrieve lattice parameters. I tried to convert the cif data into a structure. But now I cannot find a way to extract the lattice parameters. I need the a, b, c, alpha, beta and gamma. The code I wrote so far looks like this:
```
from pymatgen import Element, MPRester
from pymatgen.io.cif import CifParser
API_KEY = '<api_key>'
with MPRester(API_KEY) as m:
data = m.get_data("LiBeH3")
for mat in data:
cif_str=str(mat['cif'])
tempcif='temp.cif'
with open(tempcif, 'w', newline='') as cif:
cif.write(cif_str)
parser = CifParser(tempcif)
structure = parser.get_structures()[0]
print(structure)
```
Is there a way to extract lattice parameters or I am missing something?
|
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MDU6SXNzdWUxODc4NDg0NzM=
| 508
|
Adding magCIF support
|
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[
"All this sounds good. I await your pull request!\n",
"Just to update on this, I've got a `MagCifWriter` and `MagCifParser` in testing, and also a `MagSymmOp` and I'm working on a magnetic version of `SpaceGroup` too (have constructed a JSON file from a magnetic space groups data file which we have permission to use) – this will hopefully enable an equivalent `Structure.from_magnetic_spacegroup()` method. When this is all further along in development I'll submit a PR for code review.\r\n\r\nHowever, there have been a few issues that might need clarifying:\r\n\r\n* As I can see, there are currently three representations in use for magnetic moments/spin in pymatgen. There's the list of scalar magmoms, there's the vector (list of lists) magmoms used by `MPSOCSet`, and there's the individual spin attribute on a Specie.\r\n\r\n At present, from a magCIF file we get a Structure with a list-of-lists magmom representation. Then, if it passes a collinear test, I convert this to a scalar magmom representation. But then `Structure.get_primitive_structure()` doesn't respect the magmom tags unless I've also added the spin attribute too (which, as I understand it, is only intended for 'idealised' spins).\r\n\r\n This all seems internally consistent, but it's also leading to a lot of code that's changing from one representation to another.\r\n\r\n* All real magnetically ordered materials have vector magnetic moments. Magnetic symmetry is only properly defined with *vector* moments. So if we one day we ever add a `MagneticSymmetryAnalyzer`, we will need the vector magmom representation.\r\n\r\n* `Structure.get_space_group_info()` returns the crystallographic symmetry if you give it a Structure with magmoms, but gives something else if you give it a Structure with spins. In the latter case, this is really useful, because it gives us a symmetry group we can use to classify collinear magnetically ordered Structures. However, this symmetry group isn't technically the magnetic symmetry, nor is it really the crystallographic symmetry, and it isn't the exchange symmetry either (which I think is a symmetry group that considers *only* the relative directions of the magnetic moments). I'm not sure if we should clarify this.\r\n\r\nNone of these issues are causing problems, but I'm wondering if anyone has any thoughts? I think having multiple representations of essentially the same quantity could end up causing confusion down the road, especially if more magnetic code is added.",
"As a high-level framework, I suggest we (i) add support for vector magmoms since that is the most general formulation, (ii) define scalar spins as special cases of vector magmoms, e.g., spin z == z * [1, 0, 0]. I suggest we can add a separate Magmom class under electronic_structure.core.\r\n\r\nYes, spacegroup info right now does not really support magnetic spacegroup. We should indeed clarify that. ",
"A separate `Magmom` class in `electronic_structure.core` definitely seems like a good way to go...\r\n\r\nNew problem: at the moment, disordered magnetic structures cannot exist, because (vector) magnetic moments are a site property and not a species property.\r\n\r\nAs a proposal, how about, the Specie spin property could be an instance of this new `Magmom` class, instead of just a float? Would that work? Or perhaps an alternative approach?",
"Okay, I'm implementing a basic `electronic_structure.core.Magmom` class that includes support for vector or scalar magmoms, and includes an internal spin axis variable (by default [0,0,1]) to correspond with VASP's 'SAXIS' tag.\r\n\r\nThis class could then be adopted as the `magmom` site property or even as the Specie `spin` property (in the case of disordered magnetic structures, which are defined by the magCIF spec).\r\n\r\nI added a `__float__` method to it so that existing code in e.g. `vasp.io.sets` could be trivially modified so that, for example:\r\n\r\n```\r\nif hasattr(site, 'magmom'):\r\n mag.append(site.magmom)\r\n```\r\n\r\ncould become\r\n\r\n```\r\nif hasattr(site, 'magmom'):\r\n mag.append(float(site.magmom))\r\n```\r\n\r\nThat way, if people continue to use old-style magmoms, pymatgen would still work as expected, but if the extra functionality is required for SOC/magnetism calculations, the new-style `Magmom` class can be used, and magCIF files can be parsed using this class by default.\r\n\r\nHow does this sound? Can submit a PR for code review if this sounds like a good approach."
] | 2016-11-07T22:30:38
| 2017-05-24T13:36:23
|
2017-05-24T13:36:23Z
|
MEMBER
|
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## Summary
magCIF is a relatively new standard (2014) for storing structures of magnetic materials. Adding magCIF functionality to pymatgen would be useful to (a) be able to incorporate existing magCIF structures into a Materials Project workflow and (b) to allow easier visualisation of magnetically ordered structures.
I've created this issue just to check to see if anybody had already started working on this, and also to ask for general feedback on the functionality.
## Suggested solution
I was going to:
(1) Add read support, to go from the magCIF file to a Structure object + its associated MAGMOM tag, provided that the magCIF file has ` _atom_site_moment_` information included. This should hopefully be straight-forward given that pymatgen already supports CIF.
(2) Add partial write support, to visualise Structure objects with their magnetic moments. This would write a magCIF file without any magnetic symmetry information (i.e. with primitive magnetic symmetry), but including `_atom_site_moment_` information. JMol, VESTA, etc. already support magCIF, so this could be useful for visualisation.
(3) Add full write support. To do this, we'd have to add detection of magnetic symmetry groups to pymatgen, which seems like a much larger problem for a future date... (I know spglib has partial support for collinear magnetic symmetry, but adding support for detection of any arbitrary (non-collinear) magnetic ordering seems like it's going to be a bigger task, though worth doing?).
Any feedback is welcome!
All the best,
Matthew
(p.s. To introduce myself briefly: I'll be joining Prof Persson's group at LBNL in February, and will be working on magnetic materials. As such, if there's any magnetic functionality that would be useful to add to pymatgen, please get in touch! MKHorton@lbl.gov)
|
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| 188,333,767
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MDExOlB1bGxSZXF1ZXN0OTMwMjUxNDk=
| 509
|
feff updates
|
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[] | 2016-11-09T19:37:44
| 2016-11-09T19:49:02
|
2016-11-09T19:49:02Z
|
CONTRIBUTOR
|
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* remove kwargs in inputsets: keep it simple
* fix parsing of the absorbing atom from the reciprocal space calculation outputs
|
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| 188,713,540
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MDU6SXNzdWUxODg3MTM1NDA=
| 510
|
Failed to read cifs files download from ICSD-Desktop
|
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[] | null |
[
"I fixed for all the ICSD files. I cannot fix the abinit version because the abinit version has serious problems. First, the symmetry positions is not properly preceded with a _. Second, the atomic positions reported are already replicated for symmetrically equivalent sites but the symm ops is not P1. This results in each site having a site occupancy of 4, which is ridiculous. The ABINIT people @gmatteo should fix their CIF format.\n",
"I am also encountering this issue with cifs from the CSD. Can you please elaborate on how to fix it?",
"Pls post an example CIF that cannot be parsed.",
"Here is an example file. I'm trying to parse it using pymatgen and I get the following error:\r\n\r\nThe line that calls the parser:\r\n 74 # Read the coordinates from the cif file using pymatgen\r\n 75 f1=CifParser(cif_file_name)\r\n 76 struct=f1.get_structures()[0]\r\n\r\nThe error:\r\n\r\nTraceback (most recent call last):\r\n File \"../../SRC/myscript.py\", line 76, in <module>\r\n struct=f1.get_structures()[0]\r\n File \"/home/nsb4513/.local/lib/python3.4/site-packages/pymatgen/io/cif.py\", line 708, in get_structures\r\n raise ValueError(\"Invalid cif file with no structures!\")\r\nValueError: Invalid cif file with no structures!\r\n\r\n\r\n[ABACUF.MOF_subset.zip](https://github.com/materialsproject/pymatgen/files/743539/ABACUF.MOF_subset.zip)\r\n",
"There is a warning that tells you that the CIF file has occupancies greater than 1. In your file, tehre are overlapping atoms. For example, Ba1 and Ba1* are the same fractional coordinates. I am not sure of the format of the CSD files. Are you supposed to ignore the labels with a *?",
"In any case, you can also get around the problem by setting a high occupancy tolerance. E.g.,\r\n\r\n```python\r\nfrom pymatgen.io.cif import CifParser\r\ns = CifParser(\"ABACUF.MOF_subset.cif\", occupancy_tolerance=100).get_structures()[0]\r\nprint(s)\r\n```\r\n\r\nThe occupancy tolerance allows the occupancy to take a value from 1 to the tolerance value, but will rescale every occupancy to 1.",
"I am unsure about the asterisk issue, but I will look into. Meanwhile the tolerance work-around appears to be working. Thanks for your help."
] | 2016-11-11T08:58:03
| 2017-02-01T02:43:57
|
2016-11-11T16:37:36Z
|
CONTRIBUTOR
|
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## System
* Pymatgen version: 4.5.0
* Python version: 3.5.2
* OS version: macOS Sierra
## Summary
* Sometimes, Pymatgen failed to read cif files directly downloaded from ICSD-Desktop. The format of these cif files is slightly different from the standard one.
* Pymatgen also failed to deal with cif files written by Abinit (prtcif=1). This cif file might not have the exact standard ICSD format.
## Example code
```python
from pymatgen import Structure
s = Structure.from_file('MyBaseFileNameCollCode59959.cif')
print(s)
```
## Error message
```
/Users/wzb/.pyenv/versions/3.5.2/Python.framework/Versions/3.5/lib/python3.5/site-packages/pymatgen-4.5.0-py3.5-macosx-10.11-x86_64.egg/pymatgen/io/cif.py:703: UserWarning: could not convert string to float: '.'
warnings.warn(str(exc))
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-74-b53b5635bdc2> in <module>()
1 from pymatgen import Structure
2
----> 3 s = Structure.from_file('MyBaseFileNameCollCode59959.cif')
/Users/wzb/.pyenv/versions/3.5.2/Python.framework/Versions/3.5/lib/python3.5/site-packages/pymatgen-4.5.0-py3.5-macosx-10.11-x86_64.egg/pymatgen/core/structure.py in from_file(cls, filename, primitive, sort, merge_tol)
1450 return cls.from_str(contents, fmt="cif",
1451 primitive=primitive, sort=sort,
-> 1452 merge_tol=merge_tol)
1453 elif fnmatch(fname, "*POSCAR*") or fnmatch(fname, "*CONTCAR*"):
1454 s = cls.from_str(contents, fmt="poscar",
/Users/wzb/.pyenv/versions/3.5.2/Python.framework/Versions/3.5/lib/python3.5/site-packages/pymatgen-4.5.0-py3.5-macosx-10.11-x86_64.egg/pymatgen/core/structure.py in from_str(cls, input_string, fmt, primitive, sort, merge_tol)
1390 if fmt == "cif":
1391 parser = CifParser.from_string(input_string)
-> 1392 s = parser.get_structures(primitive=primitive)[0]
1393 elif fmt == "poscar":
1394 s = Poscar.from_string(input_string, False).structure
/Users/wzb/.pyenv/versions/3.5.2/Python.framework/Versions/3.5/lib/python3.5/site-packages/pymatgen-4.5.0-py3.5-macosx-10.11-x86_64.egg/pymatgen/io/cif.py in get_structures(self, primitive)
703 warnings.warn(str(exc))
704 if len(structures) == 0:
--> 705 raise ValueError("Invalid cif file with no structures!")
706 return structures
707
ValueError: Invalid cif file with no structures!
```
## Suggested solution (if any)
* <If you have a suggestion on how to solve the issue, you may write it
here.>
## Files (if any)
[cifs.zip](https://github.com/materialsproject/pymatgen/files/585348/cifs.zip)
```
two example cif files from ICSD-Desktop and one from Abinit calc.(prtcif = 1)
```
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| 189,048,077
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MDExOlB1bGxSZXF1ZXN0OTM1MjEwNjI=
| 511
|
improve readability of get_elt_projected_plots with colors.
|
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[] | 2016-11-14T07:46:45
| 2016-11-14T15:11:49
|
2016-11-14T15:11:49Z
|
CONTRIBUTOR
|
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## Summary
Adding colors to get_elt_projected_plots to make these plots more readable specially in compounds with more than 3 elements where other colored plots are not available.
## TODO
Coming up with better color combination later.
|
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MDU6SXNzdWUxODkwOTc4OTY=
| 512
|
Bandstructure class can't get bands properly after encoding with MontyEncoder
|
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[] | null |
[] | 2016-11-14T12:14:36
| 2016-11-15T17:43:01
|
2016-11-15T17:43:01Z
|
CONTRIBUTOR
|
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## System
* Pymatgen version: <4.5.0 pip>
* Python version: <2.7.12>
* OS version: <OSX 10.11.6>
## Summary
* Bandstructure.bands should be numpy.array consisting of float lists.
* but after `json.dumps(bs.as_dict(), cls=MontyEncoder)`, Bandstructure.bands turn to array consisting of dicts, and it's not able to convert back by `from_dict()`.
* This is part of the current workflow of MPWorks before Boltztrap calculation.
## Example code
```python
# !/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import json
from monty.os.path import zpath
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.core.structure import Structure
from pymatgen.electronic_structure.bandstructure import BandStructure
from pymatgen import MontyEncoder
# but i really do not find where MontyEncoder inherited in pymatgen
# get bs from vasprun
vasp_dir = "<the folder you run vasp like Uniform type>"
line_mode = False
vasprun_loc = zpath(os.path.join(vasp_dir, 'vasprun.xml'))
kpoints_loc = zpath(os.path.join(vasp_dir, 'KPOINTS'))
poscar_loc = zpath(os.path.join(vasp_dir, 'POSCAR'))
vasprun = Vasprun(vasprun_loc)
bs = vasprun.get_band_structure(
kpoints_filename=kpoints_loc, line_mode=line_mode)
# directly as_dict then from_dict
bs_dict = bs.as_dict()
bs_bak = BandStructure.from_dict(bs_dict)
# print(bs_bak.bands)
print(bs_bak.bands.values()[0][0][0])
# as_dict then encoder with MontyEnoder, finally from_dict
bs_json = json.dumps(bs.as_dict(), cls=MontyEncoder)
bs_json_dict = json.loads(bs_json)
bs_json_dict['structure'] = Structure.from_file(poscar_loc).as_dict()
bs_json_bak = BandStructure.from_dict(bs_json_dict)
# print(bs_json_bak.bands)
print(bs_json_bak.bands.values()[0][0][0])
```
## Error message
```
-7.868 #right output
Traceback (most recent call last):
File "<script path>", line 36, in <module>
print(bs_json_bak.bands.values()[0][0][0])
IndexError: too many indices for array
```
|
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| 189,456,442
|
MDExOlB1bGxSZXF1ZXN0OTM4MTE4ODI=
| 513
|
fix from_dict() after bs dict() with MontyEncoder
|
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[] | 2016-11-15T17:32:13
| 2016-11-15T17:43:01
|
2016-11-15T17:43:01Z
|
CONTRIBUTOR
|
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|
## Summary
fix #512
|
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https://github.com/materialsproject/pymatgen/issues/514
| 189,535,030
|
MDU6SXNzdWUxODk1MzUwMzA=
| 514
|
git push error on LFP_CHGCAR.gz
|
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[] | null |
[
"You just reforked? If not, pls delete your fork (making sure you still have your own local copy). Then refork, reclone, add whatever changes you need and push.\n\nI had to rebase the git branches because the total repo size is close to the Github limit. Unfortunately, that means the git history is no longer consistent with local copies.\n",
"Ok, I do a new clone and copy my changes. Now it works fine. \nThe pull request should come soon :)\nThanks\n"
] | 2016-11-15T23:14:51
| 2016-11-15T23:44:47
|
2016-11-15T23:44:47Z
|
CONTRIBUTOR
|
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|
Hello
I download and update a fresh version of pymatgen (last commit 15 november). I just forked the repository. But if I tried to push commits on my own repository I got the following error :
```
open /Users/gvallver/git/pymatgen/test_files/path_finder/LFP_CHGCAR: no such file or directory
error: failed to push some refs to 'https://github.com/gVallverdu/pymatgen.git'
```
Actually, the CHGCAR file is zipped both on the remote and my local system.
Thanks
system : OS X 10.11
git version 2.7.4 (Apple Git-66)
|
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| 190,281,556
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MDExOlB1bGxSZXF1ZXN0OTQzMzQzNjY=
| 515
|
Frequency and hessian matrix from gaussian output files
|
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[] | 2016-11-18T10:10:18
| 2016-11-18T11:49:13
|
2016-11-18T11:49:13Z
|
CONTRIBUTOR
|
{
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|
## Summary
* read in hessian matrix : need #P in route line
* read IR intensity, force constant and reduce mass
* compatibility break on frequency attributes of GaussianOutput object. Frequency is still a list for each frequency calculations and for each mode. But for each mode it contains a dictionary such as :
```py
{'IR_intensity': 97.3057,
'f_constant': 1.7649,
'frequency': 1662.8033,
'mode': [0.0, 0.07, 0.0, -0.42, -0.56, 0.0, 0.42, -0.56, 0.0],
'r_mass': 1.0834,
'symmetry': "A'"},
```
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| 191,035,145
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MDExOlB1bGxSZXF1ZXN0OTQ4MzM5NDE=
| 516
|
Optionnal possibility to specify that the saddle_point in the NEB sho…
|
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[] | null |
[
"I will merge but I will make some edits.",
"I pushed my changes. Can I request that we avoid introducing too much cruft and code that duplicates. When you have the exact same call to CubicSpline, that is a problem.\r\n\r\nAlso, when can we remove the old scipy spline? Pymatgen already pins the latest scipy as a requirement. Do we need that?\r\n\r\n",
"also, pls implement a unit test for the spline_options code. Right now, I have no way of knowning whether my changes broke anything.",
"Hi Shyue,\n\nOk, I'll implement a unit test tomorrow (already late tonight).\n\nOn the other hand, I will re-add the \"setup_spline\" method if you don't\nmind, because we dont store the spline itself in the as_dict(), and we\nmight want to use a given spline_options in some cases and another one in\nsome others. In this way, reading back the NEBAnalysis using from_dict()\nyou can setup the spline option you want.\n\nDavid\n\nOn Tue, Nov 22, 2016 at 7:48 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> also, pls implement a unit test for the spline_options code. Right now, I\n> have no way of knowning whether my changes broke anything.\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/516#issuecomment-262329235,\n> or mute the thread\n> https://github.com/notifications/unsubscribe-auth/ADdRUDOJacEOIonMw6hh31d2sXUkOOFyks5rAzj7gaJpZM4K5jpB\n> .\n"
] | 2016-11-22T15:18:23
| 2016-11-22T19:31:54
|
2016-11-22T18:35:06Z
|
CONTRIBUTOR
|
{
"total": 0,
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|
## Summary
* Possibility to setup the spline in the NEB analysis so that the slope is zero for the saddle point (works only for new versions of scipy).
|
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| 191,261,702
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MDExOlB1bGxSZXF1ZXN0OTQ5OTY1NDY=
| 517
|
Added test for spline_option "saddle_point" "zero_slope".
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[] | 2016-11-23T12:46:38
| 2016-11-23T16:33:29
|
2016-11-23T16:33:29Z
|
CONTRIBUTOR
|
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## Summary
* Added setup_spline method to NEBAnalysis.
* Added test for zero_slope at the saddle point option for splines in NEBAnalysis
|
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MDU6SXNzdWUxOTEzODI5NzY=
| 518
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CIF written after finding symmetry is in P1 space group
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[
"Yes, you need to supply a symprec. If you want to try to get a standard setting, you can try using SpacegroupAnalyzer's get_conventional_standard_cell to get a conventional structure before writing it out with CifWriter. That still does not guarantee that a standard setting is always written though, but it should work in many instances."
] | 2016-11-23T21:24:46
| 2016-11-23T22:02:02
|
2016-11-23T22:02:02Z
|
CONTRIBUTOR
|
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## System
* Pymatgen version: 4.5.2
* Python version: 2.7.12
* OS version: RHEL 6.8
## Summary
I want to use pymatgen to read in a POSCAR and output a cif with the symmetry information included a la FINDSYM.
However, when I write the cif file using the CifWriter, the spacegroup is still P1 and the symmetry equivalent position list is not included.
## Example code
'''
from pymatgen.io.vasp import Poscar
from pymatgen.io.cif import CifWriter
from pymatgen.symmetry import analyzer
from pymatgen.io.cif import CifParser
p = Poscar.from_file('POSCAR')
sga = analyzer.SpacegroupAnalyzer(p.structure)
new_struct = sga.get_conventional_standard_structure()
z = CifWriter(new_struct)
z.write_file('new_struct.cif')
'''
## Suggested solution (if any)
If I supply a symprec argument to the CifWriter, a cif with the correct symmetry is written out, but not always in the standard setting. Is there a way to output a symmetrized cif in the standard setting?
## Files (if any)
I have provided my POSCAR, pymatgen's written cif, and the output from aflow's implementation of findsym
```
[BaTiO3_hexagonal_findsym.cif.txt](https://github.com/materialsproject/pymatgen/files/610038/BaTiO3_hexagonal_findsym.cif.txt)
[POSCAR.txt](https://github.com/materialsproject/pymatgen/files/610039/POSCAR.txt)
[new_struct.cif.txt](https://github.com/materialsproject/pymatgen/files/610040/new_struct.cif.txt)
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MDU6SXNzdWUxOTE2MDg5Nzc=
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|
Missing dependency pybtex
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[
"This is deliberate. Pybtex is only used in one place. There is no need to add it as a required dependency. Also, it uses a primiive 2to3 method of maintaining Py27 and Py3k compatibility, which makes it difficult of pymatgen to create condo packages using it."
] | 2016-11-25T01:18:51
| 2016-11-25T02:41:49
|
2016-11-25T02:41:49Z
|
CONTRIBUTOR
|
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<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: <pip>
* Python version: <2.7.12.2>
* OS version: <Linux.>
## Summary
should add pybtex to requirement
|
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MDU6SXNzdWUxOTE5MzExMjA=
| 520
|
A tiny problem in ewald.py file
|
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[
"EwaldSummation requires oxidation state decorated structures. That means they have Specie, which has oxi_state."
] | 2016-11-28T06:45:45
| 2016-11-28T08:02:46
|
2016-11-28T08:02:46Z
|
CONTRIBUTOR
|
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## System
* Pymatgen version: 4.5.2
* Python version: 2.7.11
## Summary
It seems there is a tiny problem in the **compute_average_oxidation_state** function in **ewald.py** file in the directory analysis/ewald.py for two reasons.
(1) There is no attribute **oxi_state** but **oxidation_states** in the Element class.
(2) The **oxidation_states** attribute returns a tuple which can not be summed up.
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MDExOlB1bGxSZXF1ZXN0OTU2MzM0NzU=
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Alternative interstitial finder
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[] | 2016-11-29T06:26:44
| 2016-11-29T11:14:49
|
2016-11-29T11:14:49Z
|
CONTRIBUTOR
|
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## Summary
An alternative interstitial finder was add, which works on the basis of a systematic structure-motif search in the unit cell by spanning a grid and using local order parameters for motif recognition. The interstitial finder is used in the Python Charged Defect Toolkit (PyCDT).
## TODO (if any)
Additional structure motifs can be added if there are well-defined criteria that are efficiently computable.
|
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| 192,331,501
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MDU6SXNzdWUxOTIzMzE1MDE=
| 522
|
Structure.make_supercell() hangs
|
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[
"This is not a bug. make_supercell actually modifies the structure in place. For the non-working codes, you are effectively iteratively building larger and larger supercells within the same structure. That is why it never completes. The last example you wrote actually recreates the structure before making a supercell, which is why it works. If you want to use the first two examples, you need to do \r\n\r\n```\r\nnew_structure = wurzite_structure.copy()\r\n```\r\n\r\nJust simply doing the assigning only creates a reference to the original structure. Please consult Python's documentation about passing by reference.",
"thank you for the reminder on pass by reference (or call-by-object more precisely). I haven't dealt with this specific case of passing objects by reference in awhile. "
] | 2016-11-29T16:32:35
| 2016-11-30T17:55:18
|
2016-11-30T17:32:01Z
|
NONE
|
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## System
* Pymatgen version: 4.5.2
* Python version: 3.5.2
* OS version: OS X 10.10.5
## Summary
* structure.make_supercell() seems to hang after a certain number of iterative updates
* copying a structure also runs into the same problem
## Example code
This will not complete:
```python
wurzite_structure = Structure.from_file("project/tmp/Cd_2_Te_2_Se_0/POSCAR")
for encut in range(100, 700, 100):
for supercell_size in range(1, 4, 1):
wurzite_structure.make_supercell([supercell_size, supercell_size, supercell_size])
```
This will not complete:
```python
wurzite_structure = Structure.from_file("project/tmp/Cd_2_Te_2_Se_0/POSCAR")
for encut in range(100, 700, 100):
for supercell_size in range(1, 4, 1):
new_structure = wurzite_structure
new_structure.make_supercell([supercell_size, supercell_size, supercell_size])
```
This will:
```python
for encut in range(100, 700, 100):
for supercell_size in range(1, 4, 1):
wurzite_structure = Structure.from_file("project/tmp/Cd_2_Te_2_Se_0/POSCAR")
wurzite_structure.make_supercell([supercell_size, supercell_size, supercell_size])
```
## Suggested solution (if any)
* This may be part of the larger structure copying problem for which an issue is already open.
## Files (if any)
This file was downloaded from the materials explorer
```
CdTe wurtzite
1.0
4.684303 0.000000 0.000000
-2.342151 4.056725 0.000000
0.000000 0.000000 7.673695
Cd Te
2 2
direct
0.333333 0.666667 0.000092 Cd
0.666667 0.333333 0.500092 Cd
0.333333 0.666667 0.374908 Te
0.666667 0.333333 0.874908 Te
```
|
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| 193,918,849
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MDExOlB1bGxSZXF1ZXN0OTY4MzEwMDY=
| 523
|
adding parse_intrans method to BoltztrapAnalyzer to obtain scissor value, etc
|
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[] | null |
[
"Can we have a unittest for the new functionality pls?",
"THanks"
] | 2016-12-06T23:45:57
| 2016-12-07T17:26:27
|
2016-12-07T17:26:21Z
|
CONTRIBUTOR
|
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## Summary
a few things are added to BoltztrapAnalyzer:
intrans as an input: it is a dictionary of inputs with which the boltztrap had been run before; it can be obtained via parse_intrans method from boltztrap.intrans file if BoltztrapAnalyzer is called via "from_files" method.
Justification:
when I call BoltztrapAnalyzer on a bunch of files that belong to a boltztrap run, I want to know if the run was on a normal band structure that was untouched or it was on a scissored band structure. In this way, we can also differentiate later in the database between the data from these two types of results.
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MDU6SXNzdWUxOTQxNzUwNTE=
| 524
|
Structure object doesn't play well with pandas due to complex issue
|
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[
"I pushed a fix. Honestly, pprint doesn't look good with a structure in a dataframe. ",
"Thanks! I'll usually have separate columns for composition and spacegroup\nthat are more helpful from a visual standpoint anyway. The main thing is\nthat at least I can throw a Structure into a DataFrame and not have it\nhijack the rest of the fields\n\nOn Wed, Dec 7, 2016 at 2:42 PM, Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> I pushed a fix. Honestly, pprint doesn't look good with a structure in a\n> dataframe.\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/524#issuecomment-265597059>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AA8Ohwp_JojLHuHIhB65hKyAzHFjgM8Xks5rFzZKgaJpZM4LHIZ3>\n> .\n>\n\n\n\n-- \nBest,\nAnubhav\n"
] | 2016-12-07T21:28:22
| 2016-12-07T23:38:05
|
2016-12-07T22:41:31Z
|
MEMBER
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## System
* Pymatgen version: master
* Python version: 2.7
## Summary
* I want to put Structure objects in a pandas Dataframe
* This works so long as I don't try to print the Dataframe or call a method like df.head(). This chokes if you put a Structure object in the DataFrame
* The reason for this is complex; pandas has its own pprint method that tries to detect the object type and print things accordingly (rather than just call str() on the object). Because PeriodicSite objects in pymatgen are sequence-like but not really sequences, the pandas print code chokes. More details below.
## Example code
```python
from pymatgen import Structure, Lattice
import pandas as pd
s = Structure(Lattice.cubic(5), ["Si"], [[0,0,0]])
data = [[s]]
df = pd.DataFrame(data, columns=["structure"])
print(df)
```
## Error message
```
Traceback (most recent call last):
File "/Users/ajain/PycharmProjects/scratch_work/scratch/scratch.py", line 8, in <module>
print(df)
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/core/base.py", line 51, in __str__
return self.__bytes__()
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/core/base.py", line 63, in __bytes__
return self.__unicode__().encode(encoding, 'replace')
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/core/frame.py", line 577, in __unicode__
line_width=width, show_dimensions=show_dimensions)
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/core/frame.py", line 1554, in to_string
formatter.to_string()
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/format.py", line 567, in to_string
strcols = self._to_str_columns()
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/format.py", line 494, in _to_str_columns
fmt_values = self._format_col(i)
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/format.py", line 675, in _format_col
space=self.col_space, decimal=self.decimal)
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/format.py", line 1934, in format_array
return fmt_obj.get_result()
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/format.py", line 1953, in get_result
fmt_values = self._format_strings()
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/format.py", line 1998, in _format_strings
fmt_values.append(' %s' % _format(v))
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/format.py", line 1980, in _format
return '%s' % formatter(x)
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/format.py", line 1967, in <lambda>
(lambda x: pprint_thing(x, escape_chars=('\t', '\r', '\n'))))
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/printing.py", line 220, in pprint_thing
max_seq_items=max_seq_items)
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/printing.py", line 117, in _pprint_seq
next(s), _nest_lvl + 1, max_seq_items=max_seq_items, **kwds))
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/printing.py", line 220, in pprint_thing
max_seq_items=max_seq_items)
File "/Users/ajain/miniconda3/envs/py2/lib/python2.7/site-packages/pandas/formats/printing.py", line 117, in _pprint_seq
next(s), _nest_lvl + 1, max_seq_items=max_seq_items, **kwds))
File "/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/core/sites.py", line 195, in __getitem__
return self._species[el]
File "/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/core/composition.py", line 145, in __getitem__
type(item), ex))
TypeError: Invalid key 0, <type 'int'> for Composition
ValueError exception:
No element with this atomic number 0
```
## Suggested solution (if any)
* The problem here is the pprint_thing() method used by pandas to format objects.
* For example, calling pprint_thing() directly from pandas on a Structure gives the same error as the one from the more complicated code above. e.g.:
```
from pandas.formats.printing import pprint_thing
from pymatgen import Structure, Lattice
s = Structure(Lattice.cubic(5), ["Si"], [[0,0,0]])
pprint_thing(s)
```
The above is a more direct way to test the code than creating the dataframe, etc.
* What is happening is that first, pandas is detecting Structure to be a sequence-like object. This is fine, since Structure is indeed a sequence of PeriodicSite, and all is fine so far.
* But then, pandas checks for nested sequences. It thinks PeriodicSite is *also* a sequence because it has a length (number of species) and you can call iter() on it. So it tries to iterate over PeriodicSite like a sequence, but this chokes.
* An even more direct way to create the error is to simply try to treat the site like a sequence and try to get the first item, e.g.:
```
from pymatgen import Structure, Lattice
s = Structure(Lattice.cubic(5), ["Si"], [[0,0,0]])
site = s[0]
print(site[0]) # fails
```
* So either Site/PeriodicSite should be written in a way that it doesn't appear like a sequence to pandas (e.g., it no longer has a length, or calling iter() on the Site raises an Error), or something like site[0] should be valid syntax to get the first species
|
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| 194,188,609
|
MDExOlB1bGxSZXF1ZXN0OTcwMTk2NDY=
| 525
|
Minor fix/cleanup to elastic tensor fitting
|
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[] | null |
[] | 2016-12-07T22:20:59
| 2016-12-07T22:30:17
|
2016-12-07T22:30:17Z
|
CONTRIBUTOR
|
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|
## Summary
Minor fix/cleanup to elastic tensor fitting.
|
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| 194,457,064
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MDU6SXNzdWUxOTQ0NTcwNjQ=
| 526
|
get_elt_projected_plots_color fails for metals
|
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[] | null |
[] | 2016-12-08T22:04:56
| 2016-12-09T17:27:10
|
2016-12-09T17:27:10Z
|
NONE
|
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|
## System
* Pymatgen version: 4.5.3
* Python version: 2.7
* OS version: Mac OS 10.11.4
## Summary
get_elt_projected_plots_color() assumes that a material has both CBm and VBM, and crashes if it doesn't.
## Example code
```python
vasprun = Vasprun('vasprun.xml', parse_projected_eigen=True)
bs = vasprun.get_band_structure('KPOINTS', line_mode=True)
bspp = BSPlotterProjected(bs)
plot = bspp.get_elt_projected_plots_color()
```
## Error message
For any metallic material,
```python
> 961 plt.ylim(data['vbm'][0][1] - 4.0, data['cbm'][0][1] + 2.0)
IndexError: list index out of range
```
## Suggested solution
* The creation of ylim on line 961 of electronic_structure.plotter needs to be wrapped in a similar "if not a metal" statement as it is elsewhere in the module:
```python
961 if self._bs.is_metal():
962 if zero_to_efermi:
963 plt.ylim(e_min, e_max)
964 else:
965 plt.ylim(self._bs.efermi + e_min, self._bs.efermi
966 + e_max)
967 else:
968 plt.ylim(data['vbm'][0][1] - 4.0, data['cbm'][0][1] + 2.0)
```
or something similar should do the trick. Thank you guys for an awesome package.
|
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| 194,701,608
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MDExOlB1bGxSZXF1ZXN0OTczODM2MTg=
| 527
|
High-symmetry k-points are added to IBZKPT from static
|
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[] | null |
[] | 2016-12-09T21:31:07
| 2016-12-09T22:43:33
|
2016-12-09T22:43:33Z
|
CONTRIBUTOR
|
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|
## Summary
In the previous implementation only high-symmetry points are included in the KPOINTS file which result in a wrong band structure (I tested this on ZnS). So now, the from_prev_calc method either only adds the VBM and CBM k-points (mode=="Uniform") or add the entire high-symmetry k-points (mode =="Line")
|
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| 194,729,817
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MDExOlB1bGxSZXF1ZXN0OTc0MDM4MzU=
| 528
|
test passed locally. The number of k-points are supposed to be 203 now
|
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[] | null |
[] | 2016-12-10T00:32:07
| 2016-12-10T00:40:04
|
2016-12-10T00:40:04Z
|
CONTRIBUTOR
|
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|
## Summary
sorry I didn't update the tests before. It was failing because now we are adding more k-points in the Line-mode
|
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MDExOlB1bGxSZXF1ZXN0OTc1NzIzOTA=
| 529
|
read the resume block of gaussian output file
|
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[] | 2016-12-12T15:24:05
| 2016-12-12T16:24:50
|
2016-12-12T16:24:50Z
|
CONTRIBUTOR
|
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## Summary
Read all resumes blocks in a gaussian output file and return them as a list of strings.
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| 195,150,421
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MDExOlB1bGxSZXF1ZXN0OTc2ODAyODc=
| 530
|
adding the option "gap" to mode in MPHSEBSSet.from_prev_calc
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[] | 2016-12-13T03:24:53
| 2016-12-13T03:29:28
|
2016-12-13T03:29:28Z
|
CONTRIBUTOR
|
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## Summary
adding the option "gap" to the argument mode in MPHSEBSSet to distinguish between "uniform" and "gap" modes when ran from previous calculations. Also a test was added for the "gap" mode. Sometimes we want just to run the uniform k-points and don't need the CBM and VBM but the previous implementation didn't allow that.
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| 531
|
Bug fixes for Interstitial creation with no valence dictionary
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[] | 2016-12-14T17:30:11
| 2016-12-14T17:46:32
|
2016-12-14T17:46:32Z
|
CONTRIBUTOR
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## Summary
<When interstitial is created with no valences dictionary, ignore charge assignment>
* When interstitial is created with no valences dictionary, ignore charge assignment
## Additional dependencies introduced (if any)
## TODO (if any)
<Merge the Zeo++ python 3 changes and debug spglib errors>
|
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| 532
|
add BSDOS plotter
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[
"I changed the fontsizes slightly and made them tunable, now it (by default) looks like this:\r\n\r\n\r\n",
"@computron, requests:\r\n\r\n1. as a user I'd prefer to set emin and emax directly rather than setting cb_energy_range; sometimes I want to compare plots of 2-4 materials (e.g. doped or substituted) at a fixed emin, emax range. If I am dealing with one plot, I can always calculate the band gap myself and plot again with emin, emax that make the plot look better.\r\n\r\n2. It would be nice to have dos_xmax as an argument with a default of None, sometimes, I just want to focus on the band edges. Or for supercells, automatic dos_xmax is too large.",
"1. The auto emax is nicer if you just want to auto-plot things without having to manually figure out different parameters for different materials. i.e., to get a nice looking plot without the user needing to input any parameters at all into BSDOSPlotter. For your use case, you can just subtract the band gap from the value you put in cb_energy_range if you really want the same energy axis for multiple plots.\r\n\r\n2. Why not just set your energy limits to focus on the band edges in that case instead of having a DOS plot that overruns its x-axis for certain energies? the latter will be ugly IMO. I would just set vb_energy_range to 1 eV and cb_energy_range to 1 eV, for example. Note the DOS x-limit is auto scaled for the energy range you put in, so even if there is a high DOS outside the energy range, it won't affect your scaling for your target energy range and you should have a nice looking plot",
"Actually for #1 I realized that you want to retain the same BSDOSPlotter object for all these w/o redoing the settings. OK I will add an option to turn off the gap addition",
"thank you!",
"Re xlim, I would say that we shouldn't pollute the code with too many options. Just return a pyplot object and the user can then set xlim or ylim or whatever else themselves."
] | 2016-12-14T19:13:29
| 2016-12-15T00:56:06
|
2016-12-15T00:55:20Z
|
MEMBER
|
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## Summary
A new band structure plotter that puts band structure and DOS on the same plot, aligned.
* Band structures include spin polarization
* Element projections on band structures supported
* Element and orbital projections on DOS supported
* Code is relatively straightforward to use, understand and modify as needed
## Additional dependencies introduced (if any)
None
## TODO (if any)
Things that could be done:
- support element projections for band structures with 4 or more elements (only 3 of those elements would actually be projected, the remaining elements ignored)
- support element+orbital projections for band structures
## Example images
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Question about LAECHG in MPStaticSet
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[
"Yes. For MP, the charges are analyzed to get an estimate of the oxidation state.",
"@albalu were you saying that these files are no longer needed for Bader charge analysis in the newest VASP / bader code? Please explain further...",
"@computron, I read the website more carefully again and it turns out it's still needed and I was wrong. The way it was presented at the top mislead me to believe that the files are not needed anymore (bader chargefile) see [here](http://theory.cm.utexas.edu/henkelman/code/bader/). I tried both ways (with and without AECCAR0-2) for NiP2 and the charges were almost exactly the same. However, I haven't done this for so many materials so I can't be sure. \r\n\r\nAll in all, it might be worth to actually do this test but based on the documentation these files are needed. \r\n\r\nFor MatMethods, I can make a pull request to run Static w/ LAECHG=False by default.",
">> For MatMethods, I can make a pull request to run Static w/ LAECHG=False by default.\r\n\r\nNote - let's discuss this further offline or in the MatMethods thread (i.e. not here), but we probably want to make this a config option for MatMethods with default=True."
] | 2016-12-15T00:59:57
| 2016-12-15T17:08:53
|
2016-12-15T01:03:11Z
|
CONTRIBUTOR
|
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I was wondering why LAECHG is set to True in MPStaticSet ? Is the only goal to generate AECCAR0-2 files for bader charge analysis? If yes, keeping it as False makes a big difference as these files (AECCAR0-2) are relatively large and shouldn't be printed by default if they are not generally needed.
|
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| 196,192,167
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MDExOlB1bGxSZXF1ZXN0OTg0MzA4ODg=
| 534
|
opt section added allowing for torsion constraints
|
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[] | 2016-12-17T03:02:37
| 2016-12-17T03:03:52
|
2016-12-17T03:03:52Z
|
CONTRIBUTOR
|
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## Summary
I've added the opt section to the qchem input file, which allows for constraining bond lengths, torsion angles, etc.
* Opt CONSTRAINT section added to qchem input files
* Opt section parser added
* unittest added
* unittest switch from unittest2 to unittest
## TODO (if any)
* only CONSTRAINT added to opt section as this point. Others opt options such as FIXED would need to added
|
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|
Fixed energy density
|
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[] | 2016-12-20T22:33:18
| 2016-12-20T22:54:26
|
2016-12-20T22:54:26Z
|
NONE
|
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Energy density conversion factor was off by a decimal place
Fixed the conversion factor to be easier to read
Updated the test and double checked it with another calculation
|
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| 197,068,442
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MDExOlB1bGxSZXF1ZXN0OTkwMzA0NTU=
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|
Old bandstructure
|
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[] | 2016-12-22T00:43:41
| 2016-12-22T00:46:31
|
2016-12-22T00:46:31Z
|
MEMBER
|
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## Summary
For some reason, I could not get the projections to work for band structures stored in the old format. i.e., BandStructureSymmLine.from_old_dict() worked but did not do the projections correctly (calling get_projection_on_elements() resulted in failure).
This fixes that.
* BandStructureSymmLine.from_old_dict() ensures properly creating Spin objects and numpy arrays for the projection key
* documentation fixes on the correct format of the projection key
* better auto-detection of when from_old_dict() is needed in the normal from_dict() method
* unit test
## Additional dependencies introduced (if any)
none
## TODO (if any)
none
|
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| 197,274,679
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MDExOlB1bGxSZXF1ZXN0OTkxNzU4ODk=
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|
bug fix in point_defects: incorrect usage of get attribute
|
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[] | 2016-12-22T21:55:31
| 2016-12-28T14:13:10
|
2016-12-28T14:13:10Z
|
CONTRIBUTOR
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MDU6SXNzdWUxOTc3NDU3ODU=
| 538
|
pathlib.Path.expanduser is available only for python3.5
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[] | 2016-12-27T19:14:59
| 2016-12-28T05:22:38
|
2016-12-28T05:22:38Z
|
CONTRIBUTOR
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* used in pymatgen.__init__.py for loading pmgrc
* it doesnt work for the other versons of python3(like 3.4 on tscc)
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| 197,836,713
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MDExOlB1bGxSZXF1ZXN0OTk1MzcxMDg=
| 539
|
Improvements in chemenv
|
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[
"Pls fix the failing tests first. Thanks."
] | 2016-12-28T11:11:57
| 2016-12-28T15:49:34
|
2016-12-28T15:49:34Z
|
CONTRIBUTOR
|
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## Summary
Improvements in chemenv : neighbors sets, tests, plotting.
* Image cell for neighbors in LightStructureEnvironments as an array of three integers (i.e. the neighbor is then the site with the index given translated by this array in fractional coordinates).
* Updated test structure_environments files.
* Added test for StructureEnvironments.NeighborsSet.
* Added plotting of environments figures.
|
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| 540
|
lattice_type is not complete
|
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[
"Our approach for high symmetry k-point follows what is proposed by Setyawan et al.: Setyawan, W.; Curtarolo, S. Comput. Mater. Sci. 2010, 49 (2), 299–312. There the face centered A and B representations are not considered. This is only a representation and those are not recommended by the crystallographic community as far as I know. I would suggest that you \"standardize\" the cell of your material to bring it back to a standard crystallographic representation and use that cell for your band structure (using get_primitive_standard_structure).\r\n\r\nI will try to change the code to throw a more explicit warning or exception when the setting is A or B...\r\n\r\n\r\n"
] | 2017-01-04T07:02:00
| 2017-06-03T14:13:08
|
2017-06-03T14:13:08Z
|
NONE
|
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<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: <4.5.7.>
* Python version: <Only 2.7.* and 3.* supported.>
## Summary
* In the source code, pymatgen.symmetry.bandstructure.py, it gives all the HighSymmKpath,
while when I use this code, I find one mistake.
When "A" or "B" in the apg_symbol, the kpath is not supplied.
Can this type of lattice type be supplied?
## Example code
```python
<Example code generating error>
```
## Error message
```
<Error message>
```
## Suggested solution (if any)
* <If you have a suggestion on how to solve the issue, you may write it
here.>
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
```
|
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MDExOlB1bGxSZXF1ZXN0MTAwNDY5NDk4
| 541
|
small update of boltztrap.py
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[] | null |
[
"Thanks. Can you implement a few unittests to make sure it all works as expected? ",
"Thanks\r\n"
] | 2017-01-06T14:50:30
| 2017-01-06T16:40:50
|
2017-01-06T16:40:46Z
|
CONTRIBUTOR
|
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|
## Summary
- bands check works for metals
- update the write_proj function to use properly the Orbital enum and new projections format
- added the k_el option to the get_thermal_conductivity function
(k_el = True is the default output k_0 -PF*T, as before. If False k_0 is returned)
- fixed a bug in the FERMI mode
- included a check of ERROR msg in the boltztrap output inside the convergence loop of BoltztrapRunner
- fix kpt_line option for bands mode. Now it works for both a list of fractional coords as arrays or a list of Kpoint objects.
- fix case lpfac > max_lpfac in case of convergence=False (fermi,bands,dos cases)
|
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| 542
|
Speed up Ewald summation
|
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[] | 2017-01-09T20:38:24
| 2017-01-09T20:38:45
|
2017-01-09T20:38:45Z
|
CONTRIBUTOR
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## Summary
Speeds up Ewald summation by doing more in-place math
|
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MDU6SXNzdWUyMDAzMjk1NTM=
| 543
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get_reconstructed_band_structure method outdated
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[
"@shyuep Unfortunately, this fix doesn't work as `BandStructure.bands` are `numpy` arrays.\r\n\r\nAs such, the line `eigenvals[Spin.up][i].append(e)` errors with:\r\n`AttributeError: 'numpy.ndarray' object has no attribute 'append'`\r\n\r\nThis is also the case I think for `BandStructure.projections`.\r\n\r\nI'm not sure of the cleanest way to get around this.",
"I think @hautierg, the original author of that method, should fix this and also include unittests for the method so that future refactorings will ensure it works."
] | 2017-01-12T10:24:49
| 2018-01-15T13:42:22
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2018-01-15T13:42:22Z
|
MEMBER
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## System
* Pymatgen version: master/stable
* Python version: 2.7
## Summary
* The get `get_reconstructed_band_structure` method in `pymatgen/electronic_structure/bandstructure.py` contains references to `bs._bands` and `bs._kpoints`. These are obselete as the `BandStructure` class now uses the `bs.bands` and `bs.kpoints` attributes.
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Pymatgen won't work if installed with intel compilers
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[
"Can you provide an actual env that this occurs? What is the compilation method?",
"Also, where does it happen? \r\n\r\n1) in the compilation of pymatgen C source code (e.g. coords_utils_cython.c), in this case, it can be solved by configuring the compiler option; \r\n\r\n2) in the installation of dependent packages (e.g. numpy/scipy), it is a much harder situation to address. ",
"It happens on Matgen when you don't unload the intel module (module unload\nintel)\n\nerror points to util/coord_utils_cython\n\nOn Thu, Jan 12, 2017 at 1:49 PM, Xiaohui Qu <notifications@github.com>\nwrote:\n\n> Also, where does happen? 1) in the compilation of pymatgen C source code\n> (e.g. coords_utils_cython.c), in this case, it can be solved by configuring\n> the compiler option. 2) in the installation of dependent packages (e.g.\n> numpy/scipy), it is a much harder situation to address.\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/544#issuecomment-272294579>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AK_v4UX1dNDJB9Guxn3kZFMJ0Cae1Idbks5rRp_dgaJpZM4LiNhi>\n> .\n>\n\n\n\n-- \nApplied Science & Technology PhD Program\nUniversity of California, Berkeley\n\nb.wood@berkeley.edu\n715-505-8447\nHearst Mining Building RM 150\n",
"Can we add the following statements to \"setup.cfg\"?\r\n\r\n```\r\n[build_ext] \r\ncompiler=gcc\r\n```\r\n\r\nAny idea what is the adverse effect of doing this?\r\n",
"Well, in general, I would impose compiler restrictions only if it is proven that only certain compilers work. BAsed on my understanding, Cython does not have a requirement of gcc. ",
"Here is the build output and then invocation to cause the error on matgen. \r\nOnly loaded modules are python/2.7.3 and intel/13.0.1\r\n\r\n~~~~\r\n(temp)-bash-3.2$ python setup.py develop\r\nrunning develop\r\nrunning egg_info\r\nwriting requirements to pymatgen.egg-info/requires.txt\r\nwriting pymatgen.egg-info/PKG-INFO\r\nwriting top-level names to pymatgen.egg-info/top_level.txt\r\nwriting dependency_links to pymatgen.egg-info/dependency_links.txt\r\nwriting entry points to pymatgen.egg-info/entry_points.txt\r\nreading manifest file 'pymatgen.egg-info/SOURCES.txt'\r\nreading manifest template 'MANIFEST.in'\r\nwriting manifest file 'pymatgen.egg-info/SOURCES.txt'\r\nrunning build_ext\r\nbuilding 'pymatgen.optimization.linear_assignment' extension\r\nicc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/common/usg/python/2.7.3/include/python2.7 -I/usr/common/usg/python/numpy/1.9.2/lib/python/numpy/core/include -c pymatgen/optimization/linear_assignment.c -o build/temp.linux-x86_64-2.7/pymatgen/optimization/linear_assignment.o\r\nicc: command line warning #10006: ignoring unknown option '-fwrapv'\r\n/usr/common/usg/python/numpy/1.9.2/lib/python/numpy/core/include/numpy/npy_1_7_deprecated_api.h(15): warning #1224: #warning directive: \"Using deprecated NumPy API, disable it by \" \"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION\"\r\n #warning \"Using deprecated NumPy API, disable it by \" \\\r\n ^\r\n\r\npymatgen/optimization/linear_assignment.c(24302): warning #592: variable \"x\" is used before its value is set\r\n return PyInt_AsSsize_t(x);\r\n ^\r\n\r\ngcc -pthread -shared build/temp.linux-x86_64-2.7/pymatgen/optimization/linear_assignment.o -L/usr/common/usg/python/2.7.3/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/pymatgen/optimization/linear_assignment.so\r\nbuilding 'pymatgen.util.coord_utils_cython' extension\r\nicc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/common/usg/python/2.7.3/include/python2.7 -I/usr/common/usg/python/numpy/1.9.2/lib/python/numpy/core/include -c pymatgen/util/coord_utils_cython.c -o build/temp.linux-x86_64-2.7/pymatgen/util/coord_utils_cython.o\r\nicc: command line warning #10006: ignoring unknown option '-fwrapv'\r\n/usr/common/usg/python/numpy/1.9.2/lib/python/numpy/core/include/numpy/npy_1_7_deprecated_api.h(15): warning #1224: #warning directive: \"Using deprecated NumPy API, disable it by \" \"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION\"\r\n #warning \"Using deprecated NumPy API, disable it by \" \\\r\n ^\r\n\r\npymatgen/util/coord_utils_cython.c(26080): warning #592: variable \"x\" is used before its value is set\r\n return PyInt_AsSsize_t(x);\r\n ^\r\n\r\ngcc -pthread -shared build/temp.linux-x86_64-2.7/pymatgen/util/coord_utils_cython.o -L/usr/common/usg/python/2.7.3/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/pymatgen/util/coord_utils_cython.so\r\ncopying build/lib.linux-x86_64-2.7/pymatgen/optimization/linear_assignment.so -> pymatgen/optimization\r\ncopying build/lib.linux-x86_64-2.7/pymatgen/util/coord_utils_cython.so -> pymatgen/util\r\nCreating /global/u1/s/shyamd/temp/lib/python2.7/site-packages/pymatgen.egg-link (link to .)\r\npymatgen 4.5.7 is already the active version in easy-install.pth\r\nInstalling feff_plot_dos script to /global/u1/s/shyamd/temp/bin\r\nInstalling get_environment script to /global/u1/s/shyamd/temp/bin\r\nInstalling gaussian_analyzer script to /global/u1/s/shyamd/temp/bin\r\nInstalling feff_plot_cross_section script to /global/u1/s/shyamd/temp/bin\r\nInstalling pydii script to /global/u1/s/shyamd/temp/bin\r\nInstalling feff_input_generation script to /global/u1/s/shyamd/temp/bin\r\nInstalling pmg script to /global/u1/s/shyamd/temp/bin\r\n\r\nInstalled /global/u1/s/shyamd/temp/codes/pymatgen\r\nProcessing dependencies for pymatgen==4.5.7\r\nSearching for pathlib2==2.2.0\r\nBest match: pathlib2 2.2.0\r\nAdding pathlib2 2.2.0 to easy-install.pth file\r\n\r\nUsing /global/u1/s/shyamd/temp/lib/python2.7/site-packages\r\nSearching for enum34==1.1.6\r\nBest match: enum34 1.1.6\r\nAdding enum34 1.1.6 to easy-install.pth file\r\n\r\nUsing /global/u1/s/shyamd/temp/lib/python2.7/site-packages\r\nSearching for palettable==2.1.1\r\nBest match: palettable 2.1.1\r\nAdding palettable 2.1.1 to easy-install.pth file\r\n\r\nUsing /global/u1/s/shyamd/temp/lib/python2.7/site-packages\r\nSearching for matplotlib==1.2.1\r\nBest match: matplotlib 1.2.1\r\nAdding matplotlib 1.2.1 to easy-install.pth file\r\n\r\nUsing /global/common/matgen/usg/python/matplotlib/1.2.1/lib/python\r\nSearching for spglib==1.9.9.18\r\nBest match: spglib 1.9.9.18\r\nAdding spglib 1.9.9.18 to easy-install.pth file\r\n\r\nUsing /global/u1/s/shyamd/temp/lib/python2.7/site-packages\r\nSearching for tabulate==0.7.7\r\nBest match: tabulate 0.7.7\r\nAdding tabulate 0.7.7 to easy-install.pth file\r\nInstalling tabulate script to /global/u1/s/shyamd/temp/bin\r\n\r\nUsing /global/u1/s/shyamd/temp/lib/python2.7/site-packages\r\nSearching for PyDispatcher==2.0.5\r\nBest match: PyDispatcher 2.0.5\r\nAdding PyDispatcher 2.0.5 to easy-install.pth file\r\n\r\nUsing /global/u1/s/shyamd/temp/lib/python2.7/site-packages\r\nSearching for scipy==0.14.0\r\nBest match: scipy 0.14.0\r\nAdding scipy 0.14.0 to easy-install.pth file\r\n\r\nUsing /global/common/matgen/usg/python/scipy/0.14.0/lib/python\r\nSearching for monty==0.9.6\r\nBest match: monty 0.9.6\r\nAdding monty 0.9.6 to easy-install.pth file\r\n\r\nUsing /global/u1/s/shyamd/temp/lib/python2.7/site-packages\r\nSearching for PyYAML==3.12\r\nBest match: PyYAML 3.12\r\nAdding PyYAML 3.12 to easy-install.pth file\r\n\r\nUsing /global/u1/s/shyamd/temp/lib/python2.7/site-packages\r\nSearching for requests==2.4.3\r\nBest match: requests 2.4.3\r\nAdding requests 2.4.3 to easy-install.pth file\r\n\r\nUsing /global/common/matgen/usg/python/python-libs/2.7.3/lib/python2.7/site-packages\r\nSearching for six==1.10.0\r\nBest match: six 1.10.0\r\nAdding six 1.10.0 to easy-install.pth file\r\n\r\nUsing /global/common/matgen/usg/python/2.7.3/lib/python2.7/site-packages\r\nSearching for numpy==1.9.2\r\nBest match: numpy 1.9.2\r\nAdding numpy 1.9.2 to easy-install.pth file\r\n\r\nUsing /global/common/matgen/usg/python/numpy/1.9.2/lib/python\r\nSearching for scandir==1.4\r\nBest match: scandir 1.4\r\nAdding scandir 1.4 to easy-install.pth file\r\n\r\nUsing /global/u1/s/shyamd/temp/lib/python2.7/site-packages\r\nFinished processing dependencies for pymatgen==4.5.7\r\n(temp)-bash-3.2$ python\r\nPython 2.7.3 (default, Aug 29 2012, 00:35:34)\r\n[GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> import pymatgen\r\npymatgen/__init__.py:34: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a \"PMG_\". E.g., \"PMG_VASP_PSP_DIR\" instead of \"VASP_PSP_DIR\".\r\n warnings.warn('With effect from pmg 5.0, all pymatgen settings are'\r\nTraceback (most recent call last):\r\n File \"<stdin>\", line 1, in <module>\r\n File \"pymatgen/__init__.py\", line 53, in <module>\r\n from pymatgen.core import *\r\n File \"pymatgen/core/__init__.py\", line 9, in <module>\r\n from .structure import Structure, IStructure, Molecule, IMolecule\r\n File \"pymatgen/core/structure.py\", line 30, in <module>\r\n from pymatgen.core.lattice import Lattice\r\n File \"pymatgen/core/lattice.py\", line 18, in <module>\r\n from pymatgen.util.coord_utils import pbc_shortest_vectors\r\n File \"pymatgen/util/coord_utils.py\", line 11, in <module>\r\n from . import coord_utils_cython as cuc\r\nImportError: pymatgen/util/coord_utils_cython.so: undefined symbol: _intel_fast_memcpy\r\n~~~~",
"I will let @wmdrichards advise if there is a way around this.",
"Yeah the intel compilers can be a bit tricky. It looks like running this build command works:\r\n\r\nCC=icc LINKCC=icc LDSHARED=\"icc -shared\" python setup.py develop\r\n\r\nrunning it without LDSHARED gives the error you report.\r\n",
"I receive the same `_intel_fast_memcpy` error when using `pip` to install Pymatgen if the version is >= 2018.1.19. Versions that are <= 2017.12.30 do not give me this error. I have unloaded all Intel compilers and am left with only gcc compilers loaded on the given machine, but the error remains for newer versions of Pymatgen. I'm using a supercomputer that is notoriously difficult to install things on sometimes, so it may not be worth debugging this issue further, but I just wanted to share this workaround in case others are in the same situation."
] | 2017-01-12T20:43:53
| 2018-06-07T15:40:08
|
2017-01-19T16:10:59Z
|
NONE
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I'm not sure how this should be fixed but it's kind of a recurring problem that can be easily forgotten.
Currently, pymatgen will throw "undefined symbol: _intel_fast_memcpy" errors when trying to use it if compiled using intel compilers. This seems like a silly problem that should be fixed either by throwing an error on compile or fixing pymatgen itself to work with intel compilers.
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MDExOlB1bGxSZXF1ZXN0MTAxNTg2MzUw
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fix user_incar_settings bug in MPNonSCFSet and MPSOCSet
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[
"fix it."
] | 2017-01-15T06:11:16
| 2017-01-15T14:47:27
|
2017-01-15T14:47:27Z
|
CONTRIBUTOR
|
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## Summary
* Fix user_incar_settings update issue in MPNonSCFSet and MPSOCSet and add corresponding unittest
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MDU6SXNzdWUyMDExODU2NDY=
| 546
|
CIF test failing with Python 3.6
|
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[
"Thanks. I implemented the fix as suggested."
] | 2017-01-17T06:19:57
| 2017-01-19T06:41:24
|
2017-01-19T06:41:13Z
|
MEMBER
|
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## System
* Pymatgen version: 4.5.7
* Python version: 3.6.0
* OS version: macOS 10.12.2
## Summary
* `test_specie_cifwriter` fails in `test_cif.py`
* output of CifWriter() is basically correct, but ordering of species has changed, and thus atom labels change too
Output is:
```
_atom_site_occupancy
X3- X1 1 0.500000 0.500000 0.500000 1
Si3+ Si2 1 0.750000 0.500000 0.750000 0.5
X3- X3 1 0.750000 0.500000 0.750000 0.5
Si4+ Si4 1 0.000000 0.000000 0.000000 1
```
when test expects:
```
_atom_site_occupancy
X3- X1 1 0.500000 0.500000 0.500000 1
X3- X2 1 0.750000 0.500000 0.750000 0.5
Si3+ Si3 1 0.750000 0.500000 0.750000 0.5
Si4+ Si4 1 0.000000 0.000000 0.000000 1
```
## Error message
```
======================================================================
FAIL: test_specie_cifwriter (pymatgen.io.tests.test_cif.CifIOTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/work/Development/git/pymatgen/pymatgen/io/tests/test_cif.py", line 800, in test_specie_cifwriter
self.assertEqual(l1.strip(), l2.strip())
AssertionError: 'Si3+ Si2 1 0.750000 0.500000 0.750000 0.5' != 'X3- X2 1 0.750000 0.500000 0.750000 0.5'
- Si3+ Si2 1 0.750000 0.500000 0.750000 0.5
? ^^ ^^^^^
+ X3- X2 1 0.750000 0.500000 0.750000 0.5
? ^ ^^^^
----------------------------------------------------------------------
```
## Suggested solution
Was previously using Python 3.5.2 without problems, where this test passes. Suspect this is due to dictionaries now being ordered in Python 3.6 (see: http://stackoverflow.com/questions/39980323/dictionaries-are-ordered-in-cpython-3-6)
Test will pass if the following is changed:
` for sp, occu in site.species_and_occu.items():` (cif.py, line 808)
to
` for sp, occu in sorted(site.species_and_occu.items()):`
However, I'm not sure this is the best solution. Maybe it would be better to either change `Composition` either to output a consistent ordering of species (so that it's the same between Python versions), or just change the unit test?
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| 201,681,162
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MDExOlB1bGxSZXF1ZXN0MTAyMTQxMzA1
| 547
|
Minor elastic fix
|
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[
"Tests are failing. Pls fix."
] | 2017-01-18T20:17:23
| 2017-01-18T20:31:48
|
2017-01-18T20:19:56Z
|
CONTRIBUTOR
|
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## Changes to elasticity module
Minor reorganization and bug fixes.
* elasticity classes/functions can now be imported from the top-level module, i. e. `from pymatgen.analysis.elasticity import ElasticTensor`.
* Minor bug fix concerning improper rotations with the option to exclude for TensorBase
* Added a test to deformation/strain conversion function
|
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minor fix related to rounding errors in eigenvalue rotation
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[] | 2017-01-18T21:24:12
| 2019-04-04T02:40:39
|
2017-01-18T21:28:15Z
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CONTRIBUTOR
|
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## Summary
Fixes failing test for deformation gradient generation in substrate analyzer.
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Adsorption new
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[] | null |
[
"Tests are failing because of use of pyhull. Pls try to use scipy.spatial where possible."
] | 2017-01-21T00:08:55
| 2017-01-23T18:01:41
|
2017-01-23T18:01:41Z
|
CONTRIBUTOR
|
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## Summary
This PR introduces an adsorption site finder analysis tool in analysis/adsorption.py. Using it, one can enumerate symmetrically distinct adsorption sites on a slab and generate structures with molecular adsorbates at those sites.
* AdsorptionSiteFinder class, which has an find_adsorption_sites method for finding symmetrically distinct adsorption sites
* A few new transformation classes (SlabTransformation and AddSitePropertyTransformation), which facilitate workflows for adsorption energies.
* Unit tests for AdsorbateSiteFinder
* A fix to structure.py that was preventing derivative structures from inheriting site properties
* A minor edit to VoronoiCoordFinder that allows for the analysis to work on slab geometries, where the coordination analysis results in vertices at infinity
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MDExOlB1bGxSZXF1ZXN0MTAyODMzODgy
| 550
|
update cbm module to make 0eV cbm discoverable
|
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[
"Pls add a unittest. and resubmit"
] | 2017-01-24T01:02:53
| 2017-01-24T01:33:37
|
2017-01-24T01:32:48Z
|
CONTRIBUTOR
|
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previously, if the conduction band minimum is equal to Fermi level, the code excludes it and return a neighbor data point.
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MDExOlB1bGxSZXF1ZXN0MTAyODM2OTAz
| 551
|
Revert "update cbm module to make 0eV cbm discoverable"
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[
"Pls add a unit test before I merge."
] | 2017-01-24T01:33:02
| 2018-03-25T13:28:33
|
2017-01-24T01:33:29Z
|
MEMBER
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Reverts materialsproject/pymatgen#550
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| 202,923,850
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MDExOlB1bGxSZXF1ZXN0MTAyOTkxNzkw
| 552
|
visualize pymatgen structures in jupyter notebook
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[
"@aykol is there any way to convert `Structure` to a pdb file (or string)?\r\n\r\nWe ([nglview](https://github.com/arose/nglview)) would like to support it too? cheers.\r\n\r\n(or even better, PR to `nglview` is welcome: https://github.com/arose/nglview/blob/master/nglview/adaptor.py)",
"@hainm thank you, it will be nice if nglview can support pymatgen ``Structure``. It can be written to a string using the ``to`` method in \"cif\", \"poscar\", \"cssr\" or as \"json\". \r\n\r\nIf these are not helpful, I'll be happy to look into it in 1-2 weeks and write an adaptor.",
"@aykol `nglview` can read `cif` from rcsb but for some reasons, it (nglview) can not read from `pymatgen`. \r\n\r\n> If these are not helpful, I'll be happy to look into it in 1-2 weeks and write an adaptor.\r\n\r\nyes please.",
"@hainm I looked into some of the options. Writing an adaptor doesn't seem straightforward because other than \"cif\", there seems to be no common format supported by nglview (pdb, gro, cif, mol2, sdf) and pymatgen.Structure. I can verify that \"cif\" option does not work for some reason.\r\n\r\nOne option is to create support for pymatgen.Molecule, for which pymatgen provides \"xyz\", \"gjf\" and \"g03\" output formats natively. In this case \"pdb\" is supported through the optional OpenBabel dependency. And support for pymatgen.Structure could be further provided via creating an intermediate Molecule object for visualization purposes as in e.g.:\r\n\r\n`` _pmg_molecule = pymatgen.Molecule.from_sites(pmg_structure.sites)``\r\n``structure_string = _pmg_molecule.to(fmt='pdb')``\r\n\r\nHowever, I personally don't think this option is efficient because of OpenBabel dependency. Are there any plans on nglview side to support \"xyz\", \"gjf\" or \"g03\"?",
" > I can verify that \"cif\" option does not work for some reason. \r\n\r\nmay be the key is here 'to make cif works'? ",
"I agree. Note that pmg's CIF parsing is reasonably robust. If nglview does not work, the likelihood is that ngl's parsing is not robust.",
"ping @arose ",
"There are different cif dictonaries, ngl does support the macromolecular dictionary (e.g. atom_site cetegory) and the one for chemical components (e.g. chem_comp_atom category). Can you give me an example cif file outputted by pymatgen? Thanks.\r\n\r\nWhat format would retain the most information from pymatgen? I guess xyz would contain the least. Never hear of gjf and g03. I am happy to look into writing parsers if there is specific benefit.",
"@arose here is a sample cif file generated by pymatgen.\r\n[mp-1143.cif.zip](https://github.com/materialsproject/pymatgen/files/891503/mp-1143.cif.zip)\r\n\r\n",
"thanks @aykol, that is a crystallographic cif file using the core dictionary (http://www.iucr.org/resources/cif/dictionaries/cif_core). Need to think about how I want to support fractional coordinates. Maybe for starters just calculate cartesian ones during parsing."
] | 2017-01-24T19:57:27
| 2017-04-03T22:03:27
|
2017-01-24T19:58:51Z
|
CONTRIBUTOR
|
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## Summary
* A handy function for quick visualization of pymatgen structures in jupyter notebook.
## Additional dependencies introduced (if any)
Optional dependency on an external package called chemview (https://github.com/gabrielelanaro/chemview). Will raise a proper import error upon use if chemview is not installed.
|
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modified BSE ouptut : modified reg pattern
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[] | 2017-01-25T10:52:21
| 2017-01-25T14:28:50
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2017-01-25T14:28:50Z
|
NONE
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## Summary
modified BSE ouptut from the Fiesta code so modified reg pattern for BSEoutput
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| 203,255,331
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MDExOlB1bGxSZXF1ZXN0MTAzMjI3OTY5
| 554
|
Phonon band structure and dos objects
|
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[
"Thanks."
] | 2017-01-25T23:39:00
| 2017-01-26T00:18:09
|
2017-01-26T00:18:00Z
|
CONTRIBUTOR
|
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## Summary
This PR introduces phonon related objects for archiving and plotting. The objects have been modeled on those contained in the electronic_structure module. No common class hierarchy has been introduced since the attributes of the electronic objects heavily rely on dictionaries containing Spin and Orbitals, that have no meaning for phonons.
PhononBandStructure accepts eigendisplacements (not eigenvectors) as optional argument.
* PhononBandStructure and PhononDos objects
* PhononBSPlotter PhononDosPlotter for plotting
* Parsers for phonopy output
* Tests
Feedbacks from other users interested in phonons about the objects and in particular about the choice of adding the eigendisplacements to the band structure are welcome. Thanks
|
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MDU6SXNzdWUyMDQ2NTM0NTY=
| 555
|
Pre-link script warnings with conda install
|
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[
"This can be ignored for now.",
"I have this pre-link issue with mpi4py. Then, the program I ran shows... ImportError: Please install mpi4py. I use Anaconda, and \"conda list\" shows that mpi4py is already installed. Do you know how to fix this?"
] | 2017-02-01T17:41:08
| 2017-10-31T21:08:42
|
2017-02-01T23:24:00Z
|
NONE
|
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## System
* Pymatgen version: 4.6.0
* Python version: 2.7.13 (Anaconda Distribution)
* OS version: Linux
## Summary
* Conda advises on installation that matsci dependencies are using dangerous pre-link scripts.
* Package matsci::palettable-2.1.1-py_0 uses a pre-link script
* Package matsci::pydispatcher-2.0.5-py_0 uses a pre-link script
* Package matsci::tabulate-0.7.7-py_0 uses a pre-link script
## Example code
```wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh -b -p $(pwd)/env
export PATH=$(pwd)/env/bin:$PATH
conda update --all --yes
conda install --channel matsci pymatgen
```
## Error message
For example:
```
env/lib/python2.7/site-packages/conda/core/link.py:446: UserWarning: Package matsci::palettable-2.1.1-py_0 uses a pre-link script. Pre-link scripts are potentially dangerous.
This is because pre-link scripts have the ability to change the package contents in the
package cache, and therefore modify the underlying files for already-created conda
environments. Future versions of conda may deprecate and ignore pre-link scripts.```
|
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MDExOlB1bGxSZXF1ZXN0MTA0ODI5ODIw
| 556
|
Update strain.py
|
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[] | 2017-02-06T16:18:10
| 2017-02-06T16:42:01
|
2017-02-06T16:42:01Z
|
CONTRIBUTOR
|
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Replace SpacegroupAnalyzer initialization argument keyword "tol" with "symprec" to match usage in SpacegroupAnalyzer class.
|
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| 205,635,131
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MDU6SXNzdWUyMDU2MzUxMzE=
| 557
|
equation of state modules
|
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[
"Go ahead and replace.",
"This was fixed in #558 and can be closed"
] | 2017-02-06T16:21:48
| 2017-03-31T22:35:30
|
2017-03-31T22:35:30Z
|
CONTRIBUTOR
|
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@shyuep @gmatteo Are we going to replace pymatgen.analysis.eos.py with pymatgen.analysis.eos_2.py anytime soon or its going to be like that forever?
|
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MDExOlB1bGxSZXF1ZXN0MTA0ODM0MzE3
| 558
|
replace eos.py with eos_2.py
|
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[] | 2017-02-06T16:39:52
| 2017-02-06T16:41:52
|
2017-02-06T16:41:52Z
|
CONTRIBUTOR
|
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* same functionality but bit cleaner + added reference to ase from which the classes/functions were adopted by the original author of the module.
|
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| 205,773,837
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MDExOlB1bGxSZXF1ZXN0MTA0OTI5MTE4
| 559
|
Added new order parameters
|
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[] | 2017-02-07T03:14:11
| 2017-02-07T04:59:49
|
2017-02-07T04:59:49Z
|
CONTRIBUTOR
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## Order parameters were added that specifically recognize simple linear and bent coordination as well as coordination with a square and regular triangle (to form a pyramid with the central atom) and a square pyramidal OP (central atoms sits in basal plane).
To do:
- more unit tests (so far, only square pyramidal test added).
|
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MDExOlB1bGxSZXF1ZXN0MTA1MTE4Mjgw
| 560
|
Removed 2 bugs from order paramerter code and finished unit tests.
|
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[] | 2017-02-07T23:35:00
| 2017-02-07T23:38:03
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2017-02-07T23:38:03Z
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| 561
|
Interstitial module can not handle "symmetry_flag=True" case
|
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[
"@mbkumar, can you have a look at this issue?",
"This escaped my attention. I will check this at the earliest.\n\nOn Sep 11, 2017 3:34 PM, \"Nils Zimmermann\" <notifications@github.com> wrote:\n\n> @mbkumar <https://github.com/mbkumar>, can you have a look at this issue?\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/561#issuecomment-328678042>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AD2qkNw8wtv3h_MdPhYb_bB2_vhKLg8Pks5shbVpgaJpZM4L6OUd>\n> .\n>\n",
"Seems like this issue has been defunct for 7 years. Closing...."
] | 2017-02-08T00:26:04
| 2023-08-08T21:17:56
|
2023-08-08T21:17:55Z
|
NONE
|
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<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: 4.6.1
* Python version: 2.7.13
## Summary
* when I use interstitial module, and set
interstitial=Interstitial(structure,valences,radii)
the symmetry_flag is default True,
then there will be some errors:
"TypeError: "NoneType" Object has no attribute '__getitem__'";
while I change the symmetry_flag to False, i.e.:
interstitial=Interstitial(structure,valences,radii,symmetry_flag=False)
the code works,
why?
## Suggested solution (if any)
* <If you have a suggestion on how to solve the issue, you may write it
here.>
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
```
|
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MDU6SXNzdWUyMDY3NTEwNTA=
| 562
|
Unwanted x margins in `get_elt_projected_plots_color`
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[
"@91bsjun Thanks for reporting. For later reference, here's before (top) and after (bottom) adding the suggested snippet:\r\n\r\n\r\n"
] | 2017-02-10T09:47:50
| 2023-05-29T16:03:50
|
2023-05-29T16:03:50Z
|
NONE
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`get_elt_projected_plots_color` is missing
```py
x_max = data['distances'][-1][-1]
plt.xlim(0, x_max)
```
Causes odd margins on the left and right side of the figure.
|
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|
git complaining about missing file
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[
"If you want to make a private repo of pymatgen, you need to clone the current version. Then create the private repo on github and clone that. Move the files from the clone to the private repo, and push it. The error you are seeing is probably due to the rebasing of pymatgen done a few months back. I suggest you clone a fresh version."
] | 2017-02-10T18:44:03
| 2017-02-10T18:55:02
|
2017-02-10T18:55:02Z
|
MEMBER
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I'm trying to make a (temporarily private) development fork of pymatgen on github to share code with colleagues, but get errors related to `git lfs`:
`[531e5b64ee126c2e0fba128fd0317662f36cbf02f651610ba085ba4354b96c6f] Object does not exist on the server: [404] Object does not exist on the server`
I think it's related to this PR: https://github.com/materialsproject/pymatgen/pull/459/files
It looks like the LFP_CHGCAR was committed, but then deleted and replaced with LFP_CHGCAR.gz, and this is causing the error?
Was following the instructions given here https://help.github.com/articles/duplicating-a-repository/ since github doesn't allow private forks of public repos.
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io.feff: generate scattering paths
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2017-02-11T15:52:42Z
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* added class Paths: takes in a list of site indices that describes scattering path legs and generate corresponding custom scattering paths input file for feff.
* add unittests
* fall back to the deafult exhcnage setting for exafs
* some minor cleanups
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Feature request for atom projected band structure
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[
"@hautierg Can you assign someone to implement this pls? I think this is indeed a useful feature to have.",
"Seems like this issue has been defunct for 6 years. Closing...."
] | 2017-02-15T00:30:10
| 2023-08-08T21:18:19
|
2023-08-08T21:18:18Z
|
NONE
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<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
Python version 2.7 tested
## Summary
The documentation for BSPlotterProjected states "Class to plot or get data to facilitate the plot of band structure objects projected along orbitals, elements or sites", however, it is not possible to project a single site onto the band structure which can be useful for plots such as band inversion in topological insulator slabs.
## Suggested solution (if any)
The addition of a new method to class BSPlotterProjected that would enable the generation of a band structure plot onto a list of atoms and Orbitals. Minimally, it would be still useful to have the projection onto a single atom with a specified orbital.
Perhaps an extension to the dictionary-like selection procedure in the get_projected_plots_dots method of BSPlotterProjected would be a simple and general solution.
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Enable NPT-AIMD simulation
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[
"You need to provide unittests that test the NpT functionality. The current pull request does not have that, only the old tests which only tests the NvT ensemble.\r\n\r\nPls run an NpT simulation with a simple small cell like Li2O or something and add the output file for NpT analysis.",
"Okay.",
"NpT output file has been added to test_files."
] | 2017-02-16T00:26:20
| 2017-02-16T20:52:55
|
2017-02-16T20:52:55Z
|
CONTRIBUTOR
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## Summary
Make DiffusionAnalyzer class compatible with NPT-AIMD diffusion analysis.
* Added a new attribute *lattices*. For NVT simulation, the attribute is a one-item list; for NPT simulation, the attribute includes all lattice matrix, which is used in *get_drift_corrected_structures()*.
* Use fractional coordinates instead of Cartesian coordinates.
* Minor change for the unit test
* Throw warning when *get_framework_rms_plot()* is called during NPT analysis.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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| 208,133,047
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MDExOlB1bGxSZXF1ZXN0MTA2NTMzNTI1
| 568
|
Method to load the averaged core potentials from OUTCAR
|
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[
"The tests are failing. Pls look at the Travis log. You used itertools.izip, which I htink in Python 3 is no longer available. Just use zip. Also, pls upgade to Py3 soon. Py27 support is now on its way out."
] | 2017-02-16T14:15:33
| 2017-02-16T14:54:41
|
2017-02-16T14:54:41Z
|
MEMBER
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## Summary
Added a new function to the `Outcar` class to load in the average core potentials of each atom at all ionic steps. A test for this method was also added and is passing.
Some blank spaces at the end of lines were removed by vim python-mode- apologies for cluttering the pull request.
|
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| 569
|
unittest2 incompatible with python 3.5
|
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[
"This is a unittest2 issue. Python 3.5 was still in beta when unittest2 was last released and it seems abandoned. Do you have a reason to use unittest2?\r\n\r\nEdit: I see now that it is in the source. This should probably be changed.",
"unittest2 is used in the pymatgen code. So the solution is to use a python version < 3.5 for unit testing until there is a release of unittest2 compatible with python 3.5?",
"I just pushed a change that removes all unittest2. This should fix these problems. Pull the latest version."
] | 2017-02-16T15:04:53
| 2017-02-16T21:20:23
|
2017-02-16T21:20:23Z
|
CONTRIBUTOR
|
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I am trying to run unittest of the master branch, but unittest2 seems incompatible with python 3.5.2
## System
pymatgen version: master branch
python version: python 3.5.2
conda version: 4.2.12
OS version: linux-64
## Summary
Running any test file returns:
```bash
ImportError: No module named 'unittest2'
```
and when I try to install the module, I get
```bash
UnsatisfiableError: The following specifications were found to be in conflict:
- python 3.5*
- unittest2
```
The page [https://pypi.python.org/pypi/unittest2](https://pypi.python.org/pypi/unittest2) states that the module is a backport for unittest for python <=3.4
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| 208,202,682
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MDExOlB1bGxSZXF1ZXN0MTA2NTgzMzk1
| 570
|
get_average_eff_mass improved and small patch for dos run_type
|
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[
"There are failing tests. Pls check the travis log and fix pls. Thanks.",
"Thank you."
] | 2017-02-16T18:14:47
| 2017-02-17T14:30:36
|
2017-02-17T14:30:27Z
|
CONTRIBUTOR
|
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- get_average_eff_mass upgrade: now it returns values for all the energies,
using doping_level=False like other functions
- small patch for DOS run_type
|
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MDU6SXNzdWUyMDgyMjU3OTQ=
| 571
|
Errors in trying to back-convert old band structures
|
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[
"Try to use the from_old_dict rather than from_dict method to deserialize the old format.",
"Did you actually try this?\r\n\r\n1. There is no from_old_dict() in the BandStructure class (only available for symm line band structures) and the first failure I get is for regular BandStructure\r\n2. Anyway, I had modified BandStructureSymmLine in the past to try to do a better job of automatically using from_old_dict() when needed\r\n\r\nI tried switching the code to \"from_old_dict\" for BandStructureSymmLine and get the same error.\r\n\r\nHere is an even shorter code example which will work with any MMVaspDB in atomate:\r\n\r\n```\r\nmmdb = get_mmdb()\r\nbs = mmdb.get_band_structure(199) # this is fine\r\nx = bs.as_dict() # gives error\r\n```",
"here is a slightly clearer version of that code:\r\n```\r\nfrom mqm.utils import get_mmdb\r\nmmdb = get_mmdb()\r\nbs = mmdb.get_band_structure(199) # this is a uniform band structure : no old dict possible!\r\nprint(type(bs)) # <class 'pymatgen.electronic_structure.bandstructure.BandStructure'>\r\nx = bs.as_dict()\r\n```",
"I did push a fix that implemented from_old_dict for the BandStructure (no SymmLine) object. I tested it and seems to work?",
"I missed the commit, thanks!"
] | 2017-02-16T19:46:55
| 2017-02-18T00:45:15
|
2017-02-18T00:32:38Z
|
MEMBER
|
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Note: only @shyuep can run the code example
## System
* Pymatgen version: master
* Python version: 2.7
* OS version: Mac
## Summary
* I am trying to back-convert old BandStructure and BandStructureSymmLine objects into the new format, and subsequently re-insert them into the database.
* I am successfully able to load the dict format of the old band structure objects into the (new) pymatgen objects
* But, calling as_dict() on those objects results in an error
* The errors seems to be the format of the "projections" key returned by the get_vbm() method. The get_vbm() seems to return an object that is {"Spin": {dict of other stuff...}} - in line with its documentation. However, the as_dict seems to expect {"Spin": [np.array of other stuff]}. Note that from_dict() seems to be consistent with as_dict(), i.e., {"Spin": [np.array of other stuff]}. I believe this is also the case for get_cbm()
## Example code
Running this code requires access to a private repo.
```python
import gridfs
import zlib
import json
from monty.json import MontyEncoder
from mqm.utils import get_mmdb
from pymatgen.electronic_structure.bandstructure import BandStructure, BandStructureSymmLine
if __name__ == "__main__":
mmdb = get_mmdb()
fs = gridfs.GridFS(mmdb.db, 'bandstructure_fs')
# loop through all our old band structures
for e in mmdb.db["bandstructure_fs.files"].find():
# load the old band structure
bs_json = zlib.decompress(fs.get(e["_id"]).read())
bs_dict = json.loads(bs_json)
if bs_dict["@class"] == "BandStructure":
bs = BandStructure.from_dict(bs_dict)
elif bs_dict["@class"] == "BandStructureSymmLine":
bs = BandStructureSymmLine.from_dict(bs_dict)
else:
raise ValueError("Invalid @class: {}".format(bs_dict["@class"]))
# assert: bs contains either a BandStructure or BandStructureSymmLine object
x1 = bs.as_dict()
x2 = json.dumps(bs.as_dict(), cls=MontyEncoder)
```
## Error message
```
Traceback (most recent call last):
File "/Users/ajain/Documents/code_matgen/mqm/mqm/eie/phase2/fix_bandstructure_format.py", line 29, in <module>
print(bs.as_dict())
File "/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/electronic_structure/bandstructure.py", line 503, in as_dict
'projections'].items()}}
File "/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/electronic_structure/bandstructure.py", line 502, in <dictcomp>
'projections': {str(spin): v.tolist() for spin, v in vbm[
AttributeError: 'dict' object has no attribute 'tolist'
```
## Suggested solution (if any)
* Not really...either modify as_dict() or modify get_cbm()/get_vbm() to have consistent formats. Not sure the best way of doing this w/o breaking other stuff(?) or which way is the intended format.
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MDExOlB1bGxSZXF1ZXN0MTA2NjYxNzU0
| 572
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PDAnalyzer.get_critical_compositions()
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[] | 2017-02-17T03:23:30
| 2017-02-17T03:27:02
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2017-02-17T03:25:09Z
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CONTRIBUTOR
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Adds method to get critical compositions in tieline, and line intersections with a simplex
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Class for I/O of exciting input
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[
"Thanks. However, can you make the following changes:\r\ni. This pull request is huge and affects a lot of files. A lot of the changes seem to be changing the permissions of the files. Pls keep your changes to only the specific files taht are modified.\r\nii. The class names should be CamelCase. So it should be ExcitingInput, not excitingInput. \r\n",
"Great thanks."
] | 2017-02-17T10:00:24
| 2017-02-20T14:38:17
|
2017-02-20T14:38:17Z
|
CONTRIBUTOR
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## Summary
New class for the input of structure objects from the exciting input*.xml files, and the output of structures and bandstructure paths to exciting files.
## New Features
* `Structure.from_file` includes exciting files
* separate `excitingInput` object with `write_string` and `write_file` routines
|
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|
New function to plot fermi surfaces using Mayavi tool
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[
"Great. Many thanks."
] | 2017-02-17T17:19:39
| 2017-02-17T17:21:08
|
2017-02-17T17:21:08Z
|
CONTRIBUTOR
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The function plot_fermi_surface of plotter module has been rewritten.
It now uses Mayavi package (mandatory) to calculate and potting the surface.
The dependency from ASE for reading CUBE files has been replaced with a new internal function.
It allows to plot fermi surfaces from cube file produces by both boltztrap (using BoltztrapAnalyzer.fermi_surface_data) or other softwares (reading the file with the read_cube_file function).
It plots different surfaces in different figures or all in one figure.
It returns both the last figure and the module mayavi in order to allow you to plot different data
in the same figure.
Color and transparency of surfaces are tunable.
Labels of kpoints will be shown in the Brillouin zone if a proper dictionary of kpoints coords is provided.
|
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|
Add rgb_legend style to BSDOSPlotter
|
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[
"note - element labels are now all black b/c the green \"K\" label in the ternary example is way too low-contrast to read"
] | 2017-02-17T21:44:46
| 2017-02-17T22:46:21
|
2017-02-17T22:46:20Z
|
MEMBER
|
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## Summary
This PR adds a new style of legend to the BSDOSPlotter, the rgb_legend, which is by default False. If enabled, it can add a colored RGB triangle (ternaries) or RB bar (binaries) to show how the various colors on projected plots map to element ratios.
Note that the alternate (default) style is a more conventional style of legend.
Some examples of the rgb_legend style are shown below
Also, thanks to Jan Pohls for sharing his code from which this was based.
## Additional dependencies introduced (if any)
None
## TODO (if any)
* Unfortunately, as can be seen in the above diagrams, the band structure plots can overlap the legend diagrams in some systems. In the limited time I had to develop this, I was not able to develop a fix. e.g., simply adding a matplotlib rectangle Patch object to try to cover up the band structure and create more of a "legend" style didn't work. The overlap can cause things to look a little funny which is one reason the rgb_legend style is not default for now.
This branch can be safely deleted after merge.
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|
Pass the user defined symprec to spglib.get_ir_reciprocal_mesh
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[] | null |
[] | 2017-02-18T00:46:44
| 2017-02-18T00:59:46
|
2017-02-18T00:59:46Z
|
CONTRIBUTOR
|
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## Summary
In SpacegroupAnalyzer the defined value of symprec is not propagated to spglib when calling the get_ir_reciprocal_mesh function, that instead uses a default of 1e-5. This may lead to unexpected behaviours and inconsistencies between the obtained space group and the list of irreducible kpoints. This pull request fixes this problem passing self._symprec to the function.
Notice that the get_ir_reciprocal_mesh function in spglib does not accept angle_tolerance as an argument.
|
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MDExOlB1bGxSZXF1ZXN0MTA2ODUxNTU0
| 577
|
Third-order elastic constants fitting procedure
|
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[] | null |
[] | 2017-02-18T06:54:54
| 2017-02-18T14:27:01
|
2017-02-18T14:27:01Z
|
CONTRIBUTOR
|
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## Summary
This PR adds a fitting procedure that fits third-order elastic constants based on a central-difference scheme for finding first and second derivatives of the stress-strain relation.
* toec_fit function in elastic.py with unittest
* fixes a minor issue in generating eigenspace rotations related to deformation gradient determination from strain tensors
## Additional dependencies introduced (if any)
Adds conditional dependence on sympy, but not explicitly required. Unit tests are skipped without sympy and toec_fit uses monty.dev.requires to print error message without sympy.
|
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MDExOlB1bGxSZXF1ZXN0MTA2ODUzMDg5
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|
BSDOS color interpolation update
|
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[] | null |
[] | 2017-02-18T07:51:06
| 2017-02-18T14:26:46
|
2017-02-18T14:26:46Z
|
MEMBER
|
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## Summary
This is just a subtle change to the BSDOS coloring (both in the plot as well as in the legend). RGB values are interpolated based on square values. The reasoning is explained in this video:
https://youtu.be/LKnqECcg6Gw
Thanks to Matt Horton for pointing this out.
The squared values indeed lead to more pleasing results as can be seen in the before/after shots below. A blind test of a colleague demonstrated that in the GaP plot in particular, more information was gleaned about the band structure projections using the new coloring. For the KTaO3 example it's clearest to see how the coloring changes in the legend, the actual plot looks similar.
Before:
After:
Before:
After:
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MDExOlB1bGxSZXF1ZXN0MTA2ODcxNTc1
| 579
|
Symprec variable fixed
|
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[] | null |
[] | 2017-02-18T18:25:49
| 2017-02-18T18:32:16
|
2017-02-18T18:32:16Z
|
CONTRIBUTOR
|
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Symprec variable has been fixed:
- the default value now is 1e-3 consistent with other method in pymatgen
- it is also possible to pass a different symprec to BoltztrapRunner when
the list of kpoints has been generated with a different symprec.
This can be useful to cure the "factorization error" of BoltzTraP calculations.
|
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|
Simplex speedups
|
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[] | null |
[] | 2017-02-19T20:05:33
| 2017-02-20T15:49:44
|
2017-02-19T23:11:21Z
|
CONTRIBUTOR
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MDU6SXNzdWUyMDg3NTc5MzY=
| 581
|
Defining the correct usage of HighSymmKpath
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[
"I have no objection to issuing a warning or even raise an error if the structure does not correspond to primitive standard. Can you implement pls? Thanks."
] | 2017-02-19T23:59:22
| 2017-02-21T14:08:47
|
2017-02-21T14:08:47Z
|
CONTRIBUTOR
|
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## Summary
I would like to signal a common misunderstanding that I have seen happen to many different people with the HighSymmKpath object.
HighSymmKpath is basically a hardcoded list of kpoints based on Setyawan-Curtarolo's paper, that uses the input structure just to get its spacegroup. On the other hand, at the first usage most of the people expect that the list of kpoints would be meaningful even if they are passing a structure which is not the standard primitive. On top of that, the symprec default value in HighSymmKpath (1e-2) is larger than the default in SpacegroupAnalyzer (1e-3), so one could have even generated the standard primitive with the analyzer and get the path for a different spacegroup, if the structure is just slightly distorted. An additional source of possible misunderstandings is the fact that in SpaceGroupAnalyzer.get_primitive_standard_structure the default for international_monoclinic is True, while a False value is needed to reproduce the structure from the paper and be used by the HighSymmKpath object (Also, the international_monoclinic option is not documented in SpaceGroupAnalyzer, making the things even more difficult to understand). The problem is quite nasty as of course the produced band structure won't show any relevant problem and only a close inspection of the result can reveal the error.
## Suggested solution (if any)
My first suggestion would be to stress the intended usage of the HighSymmKpath object in the docstring. However, I personally think that it would be better having a warning or even raising an error if the structure does not correspond to the primitive standard obtained using the given symprec and angle_tolerance.
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| 208,870,553
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MDU6SXNzdWUyMDg4NzA1NTM=
| 582
|
plotting fermi surface from vasp calculation
|
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[
"Hi,\r\nyou can run BoltztrapRunner using FERMI mode and selecting the index of the band you want to study.\r\nThen, you can import the output with BoltztrapAnalyzer and plot it with the function plot_fermi_surface.\r\nhere a general example:\r\n\r\nvrun = Vasprun('vasprun.xml.gz')\r\nbs = vrun.get_band_structure()\r\nnelect = vrun.parameters['NELECT']\r\nvbm = int(nelect/2 -1)\r\nBoltztrapRunner(bs=bs,nelec=nelect,lpfac=100,run_type='FERMI',band_nb=vbm,cond_band=False).run(path_dir='vbm/')\r\nan=BoltztrapAnalyzer.from_files(\"vbm/boltztrap/\")\r\nplot_fermi_surface(an.fermi_surface_data,bs.structure,cbm=False,energy_levels=[-0.01])\r\n\r\nIf you already have a CUBE file containing your band in a 3D grid of kpoints, you can read it\r\nusing the read_cube_file function (in boltztrap.py module) and plot it passing thee data you get in output.\r\n\r\nYou are welcome to try this method and report any issue you get.\r\nThank you",
"@fraricci Can you copy this code and put it in an ipython notebook in the examples folder? I think it will be very useful for new users. Thanks.",
"I know this issue is old, but the example given above does not work for me. I ave Bolztrap2 installed, and bolztrap 1.25 in path. after importing the modules needed I get a 'file not found' error for the folder where BoltzrapRunner is supposed to put the outputs. What Am I doung wrong ? Thanks for the help!",
"I just realized that I've never moved this script to a notebook in matgenb, sorry. \r\nI'll that soon together with an equivalent way using boltztrap2.\r\n\r\n@mdforti does the folder you're giving exist?",
"ok I kind of worked out that the folders given to the run_path argument must be there beforehand, they are not created by BoltrztrapRunner. Also, the BoltzTrap executable must be in the path, but it has to be the version 1 of boltztrap. Implementation of Bolztrap2 can not read vasprun from spin polarized vasprun.\r\nAlso, a working example for vasp in the notebooks would be helpfull !\r\nthanks for the reply!"
] | 2017-02-20T12:48:38
| 2020-06-24T16:43:51
|
2017-02-20T14:37:22Z
|
NONE
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Hi,
I would like to ask about whether we could obtain Fermi surface and plot it via pymatgen (or other programs) from VASP calculations? I see the class BoltztrapRunner but not sure if it could achieve this task. Thank you very much.
|
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| 208,976,927
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MDExOlB1bGxSZXF1ZXN0MTA3MDcyODg1
| 583
|
Improvements to BSDOSPlotter legend
|
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[] | 2017-02-20T20:37:30
| 2017-05-05T17:31:31
|
2017-02-20T21:26:03Z
|
MEMBER
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## Summary
Various improvements to fancy BSDOSPlotter legend
* Uses a separate inset axis to plot legend
* This ensures the aspect ratio of legend stays consistent for different band structures
* It also visually separates the legend from the background better
* Now rgb_legend style is by default True
The plots now look like this:
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MDU6SXNzdWUyMDkwMDYyNzY=
| 584
|
error in plotting fermi surface
|
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[
"I have attached a small vasprun.xml (30 MB) that reproduces the error in the dropbox.\r\n\r\nhttps://www.dropbox.com/s/itz8etvh4424nwa/vasprun.xml?dl=0\r\n\r\nWould you like to take a look and see what might go wrong? Thank you very much.",
"If you run VASP using an automatic mesh, this is a typical error due to the disagreement between VASP and spglib (used by pymatgen) finding the symmetry of your structure.\r\nThere are different possible solutions:\r\n1. rerun VASP using an explicit kpoint list generated by pymatgen\r\n2. rerun VASP using a automatic mesh but turning off symmetries (so kpoints spread on the entire BZ)\r\n3. check which symmetry group is found by VASP and play with symprec variable of SpacegroupAnalyzer (in pymatgen) until you find the same group. Then you run BoltztrapRunner with the selected symprec (only possible with the last version of pymatgen).\r\n\r\nI hope this is useful\r\n\r\n\r\n",
"I attempted the 2nd procedure by setting ISYM=0. With KPoints being,\r\n\r\npymatgen generated KPOINTS with grid density = 1000 / atom\r\n0\r\nGamma\r\n6 6 4\r\n\r\nHowever, the same error persists... I attached my vasprun.xml in the dropbox\r\n\r\nhttps://www.dropbox.com/s/gif7q9sbwss3wg7/vasprun.xml?dl=0\r\n\r\nWould you please help to see what might go wrong? Thank you very much.",
"I forgot to add that in this case you have to edit the .struct file writing \"1\" \r\ninstead of the number you have in the 5th line. \r\nIt correnspond to the number of symmetries.\r\nAfter you need to run boltztrap manually.",
"Thank you very much for your prompt response. However, after I change boltztrap.struct (5th line: from 12 to 1) I still got the error:\r\n```\r\n\r\n$ cat boltztrap.struct \r\nLa3 Ir9 R-3m\r\n-5.14256 -8.90718 0.00000\r\n5.14256 -8.90718 0.00000\r\n0.00000 -5.93812 16.81815\r\n1\r\n1 0 0\r\n0 1 0\r\n0 0 1\r\n-1 0 0\r\n0 -1 0\r\n0 0 -1\r\n0 1 0\r\n-1 -1 -1\r\n0 0 1\r\n0 -1 0\r\n1 1 1\r\n0 0 -1\r\n-1 -1 -1\r\n1 0 0\r\n0 0 1\r\n1 1 1\r\n-1 0 0\r\n0 0 -1\r\n0 -1 0\r\n-1 0 0\r\n0 0 -1\r\n0 1 0\r\n1 0 0\r\n0 0 1\r\n1 1 1\r\n0 -1 0\r\n0 0 -1\r\n-1 -1 -1\r\n0 1 0\r\n0 0 1\r\n-1 0 0\r\n1 1 1\r\n0 0 -1\r\n1 0 0\r\n-1 -1 -1\r\n0 0 1\r\n$ x_trans BoltzTraP -so\r\n ================ BoltzTraP vs 1.2.5 =============\r\nNote: The following floating-point exceptions are signalling: IEEE_DENORMAL\r\nSTOP error in factorization\r\n0.088u 0.007s 0:00.06 133.3%\t0+0k 0+1io 0pf+0w\r\n\r\n```\r\n\r\nDo you know what might go wrong? Thank you very much. I have attached my BoltzTrap folder here: https://www.dropbox.com/sh/v6esf6vgcjxq51f/AAClowvGfox7UWXnzJosSEf9a?dl=0 \r\n\r\nThank you very much again.",
"After everything, I tried the 1st method to generate explicit kpoint with your help. Now the boltztrap runner is successful. However, when performing boltztrap analyzer: I get this issue.\r\n\r\n```\r\n$ python plot_fermi_surface.py \r\nlpfac, energy_grid: 10 0.005\r\n ================ BoltzTraP vs 1.2.5 =============\r\n1.521u 0.094s 0:01.56 103.2%\t0+0k 14+39io 121pf+0w\r\n\r\n\r\nTraceback (most recent call last):\r\n File \"plot_fermi_surface.py\", line 18, in <module>\r\n an=BoltztrapAnalyzer.from_files(\"vbm/boltztrap/\")\r\n File \"/Users/me/anaconda2/lib/python2.7/site-packages/pymatgen/electronic_structure/boltztrap.py\", line 1870, in from_files\r\n raise ValueError(\"FERMI mode parsing is currently unavailable!\")\r\nValueError: FERMI mode parsing is currently unavailable!\r\n\r\n```\r\n\r\nIt seems it fermi parsing is unavailable.... do you know what shall i do as next step to plot fermi surface? Thank you very much for your all the way.",
"Which version of pymatgen are you using?\r\nThe fermi mode is available only in the last version.",
"great! thank you very much, I upgraded to 4.6.2 and everything starts to work.... However, there is still some issue:\r\n\r\nrunning the last line:\r\n\r\n`plot_fermi_surface(an.fermi_surface_data,bs.structure,cbm=False,energy_levels=[-0.01])\r\n`\r\nit has the error:\r\n\r\n`BoltztrapError: BoltztrapError : energy level -0.01 not in the range of possible energies: [-13592.0873173, -3.60221607003]\r\n`\r\n\r\nSo I guess I might need to specify the fermi surface level. So I do (I am running in ipython)\r\n\r\n`e_fermi = v_dos.efermi\r\n`\r\n\r\nbut then it is \r\n\r\n```\r\nIn [8]: e_fermi\r\nOut[8]: 9.06922155\r\n\r\n```\r\n\r\nI am really confused in this case... Do you know what should i do? Thank you very much. You are really of great help to me.\r\n\r\nI attached everything in this folder. It's a bit large (990MB) if you want to reproduce the error.\r\n\r\nhttps://www.dropbox.com/sh/vd3twn4zjmm4qhv/AADxBEFHn1delh-UdGy23Baoa?dl=0\r\n\r\n\r\n",
"-3.60221607003 is the max value of the band you're studying.\r\nSo select a value starting from it.\r\nIf you don't specify any energy_level, it will be set to the max/min\r\n value of the band -/+ 0.01 eV.\r\n\r\n",
"Thank you very much for your prompt response. I tried playing around with the code without luck....\r\n\r\nEhm.... does it mean that for my computation, the fermi level is 9.06eV, but the max value of the band we have considered so far is -3.602eV? Since our purpose is to plot the fermi surface at Fermi energy level which is specified to be 9.06922155... My calculation is with spin orbit coupling, not sure if this adds another layer of complexity. \r\n\r\nI checked my PROCAR, we have 114 electrons and our valence band is the number 114 band as shown as below, and it seems 9.06922155 is indeed our fermi level and all necessary bands should have been computed in our calculations...:\r\n\r\n> k-point 257 : 0.31578947 0.00000000 0.18181818 weight = 0.00151095\r\n> \r\n> band 1 # energy -23.09042420 # occ. 1.00000000\r\n> ....\r\n> band 113 # energy 8.91340620 # occ. 0.99999476\r\n> \r\n> ion s py pz px dxy dyz dz2 dxz dx2 f-3 f-2 f-1 f0 f1 f2 f3 tot\r\n> 1 0.000 0.003 0.000 0.001 0.001 0.004 0.000 0.002 0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.015\r\n> ....\r\n> band 114 # energy 8.91342568 # occ. 0.99999475\r\n> \r\n> ion s py pz px dxy dyz dz2 dxz dx2 f-3 f-2 f-1 f0 f1 f2 f3 tot\r\n> 1 0.000 0.003 0.000 0.001 0.001 0.004 0.001 0.002 0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.015\r\n> ....\r\n> band 115 # energy 9.12415065 # occ. 0.06013640\r\n> \r\n> ion s py pz px dxy dyz dz2 dxz dx2 f-3 f-2 f-1 f0 f1 f2 f3 tot\r\n> 1 0.000 0.000 0.000 0.000 0.001 0.002 0.001 0.001 0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.008\r\n> ....\r\n\r\nIn this case, I believe BoltztrapRunner arguments n_band should be n_elect = 114.... Therefore, I run as followed:\r\n\r\n```\r\nfrom pymatgen.io.vasp.outputs import Vasprun\r\nfrom pymatgen.electronic_structure.plotter import BSPlotter, DosPlotter, BSDOSPlotter, BoltztrapPlotter, plot_fermi_surface\r\nfrom pymatgen.electronic_structure.core import Spin, Orbital, OrbitalType\r\nfrom pymatgen.electronic_structure.dos import Dos\r\nfrom pymatgen.electronic_structure.boltztrap import BoltztrapRunner, BoltztrapAnalyzer\r\n\r\nv_dos = Vasprun(\"./explicit_kpt_1/vasprun.xml\")\r\ne_fermi = v_dos.efermi\r\nbs = v_dos.get_band_structure()\r\nnelect = v_dos.parameters['NELECT']\r\nvbm = int(nelect)\r\nprint (\"nelect is \",nelect)\r\nprint (\"vbm is \",vbm)\r\nBoltztrapRunner(bs=bs,nelec=nelect,lpfac=100,run_type='FERMI',band_nb=vbm,cond_band=False,soc=True).run(path_dir='./vbm/')\r\nan=BoltztrapAnalyzer.from_files(\"vbm/boltztrap/\")\r\nplot_fermi_surface(an.fermi_surface_data,bs.structure,cbm=False,energy_levels=[e_fermi])\r\n\r\n```\r\n\r\nbut the output is,\r\n\r\n```\r\n$ python plot_fermi_surface.py \r\n('nelect is ', 114.0)\r\n('vbm is ', 114)\r\nlpfac, energy_grid: 100 0.005\r\n ================ BoltzTraP vs 1.2.5 =============\r\n19.864u 0.569s 0:18.89 108.0%\t0+0k 1+60io 122pf+0w\r\n\r\n\r\nTraceback (most recent call last):\r\n File \"plot_fermi_surface.py\", line 21, in <module>\r\n plot_fermi_surface(an.fermi_surface_data,bs.structure,cbm=False,energy_levels=[e_fermi])\r\n File \"/Users/me/Desktop/software/pymatgen/pymatgen/electronic_structure/plotter.py\", line 1707, in plot_fermi_surface\r\n str(en_min) + \", \" + str(en_max) + \"]\")\r\npymatgen.electronic_structure.boltztrap.BoltztrapError: BoltztrapError : energy level 9.06922155 not in the range of possible energies: [-13592.0873173, 0.483561295849]\r\n\r\n```\r\n\r\nI think we actually considered the correct number 114 band, but for some reason it says the possible energy rang is [-13592.0873173, 0.483561295849] .... do you know what might happen? Thank you very much again.\r\n\r\nAgain, I put everything here so that you could reproduce the error: https://www.dropbox.com/sh/vd3twn4zjmm4qhv/AADxBEFHn1delh-UdGy23Baoa?dl=0",
"Sorry for bothering. I still could not resolve this issue. I will wait for you if you could might have some insight into this problem... Thank you very much.",
"0.483561295849 is the max value of the band considered minus the fermi energy.\r\nplay also changing the band index to under stand if you're getting the right one.",
"I see. In this case, the problem is fully resolved by setting \r\n\r\n`energy_levels=[0]\r\n`\r\nin\r\n\r\n`plot_fermi_surface(an.fermi_surface_data,bs.structure,cbm=False,energy_levels=[0])\r\n`\r\nThank you very much for your help along the way!"
] | 2017-02-20T23:42:51
| 2017-03-09T23:22:19
|
2017-02-21T14:09:04Z
|
NONE
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After performing Spin Orbit Coupling calculation on VASP. I tried to use pymatgen to plot the fermi surface as followed:
```
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter, DosPlotter, BSDOSPlotter, BoltztrapPlotter
from pymatgen.electronic_structure.core import Spin, Orbital, OrbitalType
from pymatgen.electronic_structure.dos import Dos
from pymatgen.electronic_structure.boltztrap import BoltztrapRunner, BoltztrapAnalyzer
v_dos = Vasprun("./DOS/vasprun.xml")
bs = v_dos.get_band_structure()
nelect = v_dos.parameters['NELECT']
vbm = int(nelect/2 -1)
BoltztrapRunner(bs=bs,nelec=nelect,lpfac=100,run_type='FERMI',band_nb=vbm,cond_band=False,soc=True).run(path_dir='./vbm/')
an=BoltztrapAnalyzer.from_files("vbm/boltztrap/")
BoltztrapPlotter.plot_fermi_surface(an.fermi_surface_data,bs.structure,cbm=False,energy_levels=[-0.01])
```
However, I get this error.
```
lpfac, energy_grid: 100 0.005
================ BoltzTraP vs 1.2.5 =============
10.775u 0.208s 0:06.19 177.2% 0+0k 0+0io 90pf+0w
STOP error in factorization
Traceback (most recent call last):
File "plot_fermi_surface.py", line 14, in <module>
BoltztrapRunner(bs=bs,nelec=nelect,lpfac=100,run_type='FERMI',band_nb=vbm,cond_band=False,soc=True).run(path_dir='./vbm/')
File "/Users/me/anaconda2/lib/python2.7/site-packages/pymatgen/electronic_structure/boltztrap.py", line 593, in run
raise BoltztrapError("STOP error in factorization")
pymatgen.electronic_structure.boltztrap.BoltztrapError: BoltztrapError : STOP error in factorization
```
Do you know what should i do to resolve this? Thank you.
|
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MDExOlB1bGxSZXF1ZXN0MTA3MTk0ODE5
| 585
|
Warning for non standard structures in HighSymmKpath
|
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[
"Thanks.",
"My understanding is that if the lattice/structure doesn't match the primitive, then the output of HighSymmKPath will be incorrect.\r\n\r\nIf that's the case I would prefer an error, i.e., bad input should result in an error, not a warning. Under no circumstances should a code knowingly return bad output. A warning might simply be neglected by, say, an automatic workflow running the job.",
"Hi all,\r\n\r\n> the output of HighSymmKPath will be incorrect\r\n\r\nRight but the physical results are still ok, in the sense that they represent a set of KS eigenvalues\r\ndefined on a set of lines and k-points that may not be of high-symmetry.\r\nWhat is incorrect it's the labelling of the k-points and therefore the interpretation of the band dispersion given by the user.\r\n\r\nHighSymmKPath is used in several workflows to obtain a k-path in an automatic way\r\nand the fact that HighSymmKPath may be incorrect is not critical for the correctness of the workflow (ab-initio codes usually need wavefunctions and energies computed on a mesh for further calculations)\r\nIf we raise an exception at this stage, we should then try to figure out how to handle it at the workflow level\r\nWhat do we do?\r\n\r\n- Abort the worflow completely\r\n- Skip the band structure calculation and continue with the other steps of the workflow\r\n- Use a hard-coded path that is just following that Bravais lattice vectors?\r\n\r\nThere are also cases in which HighSymmKPath is just used to plot band energies with matplotlib.\r\nwith minimal user intervention. \r\nIn phonon calculations for example the ab-initio interatomic constants can be interpolated everywhere in q-space and we use HighSymmKPath to get the list \r\nof points at runtime if the q-path is not given explicitly.\r\nAlso in this case, the results are correct but the interpretation may be wrong\r\nSill I would prefer to show the phonon band dispersion to the user instead of a python backtrace.\r\n\r\nA possible solution could be to change the labels of the k-points, e.g. by adding an \"?\"\r\nor an extra string such as \"_wrong_kpath\" so that users and scripts can easily detect \r\nthat the k-point path does not correspond to the one given in Setyawan-Curtarolo's paper.\r\nThen I think we should stress this issue to the users and suggest them to use primitive standard cells whenever possible.\r\n",
"Well, when I call HighSymmKPath, I expect a high symmetry kpath. Saying that is still represents valid kpoints but that are not high symmetry is like saying that it's ok for the math.log() function to not correctly return the logarithm so long as it returns a valid number that can be put into a spreadsheet. \r\n\r\nI am not sure what is the phonon usage of HighSymmKPath. But either the user is intending to force the code to do something strange (in which case, they should set a flag and neither get a warning nor an error since the code is now clearly doing what the user intended), or the user did not tell the code they are trying to do something strange they should get back an error.\r\n\r\nAnyway, that is just my thoughts. The pymatgen BFDL @shyuep gets the final vote on such issues in pymatgen.\r\n\r\n\r\n\r\n",
"(Btw, note that I really prefer \"abort the workflow completely\". Then I see there is an error in the run, fix the workflow and rerun. Much better than the workflow keeps going and 6 months later I realize 10% of my runs were incorrect and need to be rerun again).",
"> (in which case, they should set a flag and neither get a warning nor an error since the code is now clearly doing what the user intended),\r\n\r\nAdding a flag to control the behaviour is a good idea ",
"On my side the main reason to prefer the warning over the error was that there should be a number of cases where, since the list of kpoints is given in fractional coordinates, the output will still be correct, even if the lattice does not exactly match the one produced by get_primitive_standard_structure.\r\nA stupid example: for a simple cubic where the basis is not \r\n[a,0,0]\r\n[0,a,0]\r\n[0,0,a]\r\nbut \r\n[0,0,a]\r\n[a,0,0]\r\n[0,a,0]\r\nthe path and labelling would correspond in the two representation, but the check as it is now would raise an error/warning. It would be rather cumbersome to sort out all the cases where the result is meaningful and where it is not. My main concern in the end was to make people aware of what is the correct usage, so I opted for a warning. \r\n\r\nIf you prefer to control the execution of the check I was thinking of adding the option to skip the check if the given value of atol is <0."
] | 2017-02-21T14:06:18
| 2017-02-21T19:22:58
|
2017-02-21T14:08:30Z
|
CONTRIBUTOR
|
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## Summary
This PR addresses the problem highlighted in issue #581 adding a warning if the lattice of structure does not match the one of the primitive standard.
|
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MDU6SXNzdWUyMDkyMjE0MTY=
| 586
|
generate explicit k-points generation for VASP
|
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[
"This is what the method MPNonSCF does:\r\n\r\n kpoints = Kpoints.automatic_density_by_vol(self.structure,\r\n self.reciprocal_density)\r\n mesh = kpoints.kpts[0]\r\n ir_kpts = SpacegroupAnalyzer(\r\n self.structure,\r\n symprec=self.sym_prec).get_ir_reciprocal_mesh(mesh)\r\n kpts = []\r\n weights = []\r\n for k in ir_kpts:\r\n kpts.append(k[0])\r\n weights.append(int(k[1]))\r\n kpoints = Kpoints(comment=\"Non SCF run on uniform grid\",\r\n style=Kpoints.supported_modes.Reciprocal,\r\n num_kpts=len(ir_kpts),\r\n kpts=kpts, kpts_weights=weights)\r\n\r\n\r\n",
"Thank you very much. Explicit kpoints are generated successfully. This thread is actually targeting #584 for plotting fermi surface. I have posted the latest problem in plotting fermi surface there. Would you like to take a look there? Thank you very much."
] | 2017-02-21T17:46:57
| 2017-02-24T18:20:30
|
2017-02-24T18:20:30Z
|
NONE
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I need to generate explicit k-points (considered symmetry of structure) for the vasp calculations (I also need it for correct Bootstrap fermi-surface calculation). I know that I could generate k-points among high symmetry lines in this way. However, I would need explicit k-points mesh for self consistent calculation (not lines though).
```
import pymatgen as mg
from pymatgen.symmetry.bandstructure import HighSymmKpath
# from pymatgen.io.vaspio.vasp_input import Kpoints
from pymatgen.io.vasp.inputs import Kpoints
from pymatgen import Structure
struct = Structure.from_file("POSCAR")
# First brillouin zone
ibz = HighSymmKpath(struct)
print("ibz type : {0}".format(ibz.name))
# suggested path
print("paths in first brillouin zone :")
for path in ibz.kpath["path"]:
print(path)
kpoints = list()
labels = list()
for path in ibz.kpath["path"]:
for kpts in path:
kpoints.append(ibz.kpath["kpoints"][kpts])
labels.append(kpts)
# print kpoints file
Kpoints(comment = "band diagram for monoclinic cell, unique axes a",
num_kpts = 100,
style = Kpoints.supported_modes.Line_mode,
coord_type = "Reciprocal",
kpts = kpoints,
labels = labels,
).write_file("KPOINTS")
```
However, I have difficulties locating the parts of the code that outputs automatic explicit k-points (for self consistent calculation, not line mode). Would you like to hint me about it? Thank you very much.
|
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| 209,465,693
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MDExOlB1bGxSZXF1ZXN0MTA3NDE1NDE5
| 587
|
Correct error in factorization and update url of bolztrap
|
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[] | 2017-02-22T14:14:22
| 2017-02-22T15:29:24
|
2017-02-22T15:29:24Z
|
CONTRIBUTOR
|
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## Summary
* the url of boltztrap needs update
* the output should be "error in factorization" not "STOP error in factorization" at least in the version 1.2.5
|
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MDExOlB1bGxSZXF1ZXN0MTA3NDQ3MTA2
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|
PDAnalyzer cleanup and missing nosetest
|
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[] | 2017-02-22T16:37:33
| 2017-02-22T18:24:58
|
2017-02-22T18:24:58Z
|
CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MTA3NTA3Nzgz
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|
PDAnalyzer update
|
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[] | 2017-02-22T21:58:26
| 2017-02-23T14:17:51
|
2017-02-22T23:45:58Z
|
CONTRIBUTOR
|
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Better testing with GrandPotentialPhaseDiagrams in PDAnalyzer.get_critical_compositions
|
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MDExOlB1bGxSZXF1ZXN0MTA3NTA5NjQ1
| 590
|
Adsorption new
|
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[] | 2017-02-22T22:08:06
| 2017-02-22T23:45:45
|
2017-02-22T23:45:45Z
|
CONTRIBUTOR
|
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|
## Updates to adsorption module
A few updates to the adsorption module based on issues I've encountered and updates suggested by @richardtran415.
* AdsorbateSiteFinder.find_adsorption_sites can now take "subsurface" in its list of positions arguments. If specified, it will find adsorption sites based on subsurface locations placed into the surface layer. Acknowledgements to @richardtran415 for this.
* AdsorbateSiteFinder.find_adsorption_sites now returns a dictionary according to the site type, i. e. {"ontop":[site1, site2], "bridge":[site1, site2] etc.}
* Fixed a major bug in the method to find the vector corresponding to the miller index, this fixes qhull errors that were occuring due to miller indices in non-orthogonal lattices.
* Unit tests more robust, testing site finding for specific site types
## TODO (if any)
Still could probably use a structure/slab superclass that includes adsorbate information.
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MDExOlB1bGxSZXF1ZXN0MTA3NTQ2MjA5
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|
Bug fixes in Interstitial class and Zeo++ python 3 compatibility
|
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[] | 2017-02-23T03:01:25
| 2017-02-23T03:05:00
|
2017-02-23T03:05:00Z
|
CONTRIBUTOR
|
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## Summary
Long pending modifications with respect to Zeo++ implemented.
* python3 compatibility for Zeo++ python bindings
* SpagegroupAnalyzer.get_symmetrized_structure fails for dense voronoi points. Voronoi points are pruned if close before passing to SpgA
* Zeo++ installation instructions added
## Additional dependencies introduced (if any):
<Zeo++>
|
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MDExOlB1bGxSZXF1ZXN0MTA3NzEwMDQ3
| 592
|
Equation of state updates
|
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[] | 2017-02-23T20:51:14
| 2017-02-23T20:53:40
|
2017-02-23T20:53:40Z
|
CONTRIBUTOR
|
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* add 'numerical eos': the equation of state employed in the quasiharmonic Debye model described in Cormac's paper: 10.1103/PhysRevB.90.174107.
* refactor and cleanup eos.py module
|
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MDExOlB1bGxSZXF1ZXN0MTA3NzEyMDE2
| 593
|
Bug fix in saving dos_plot
|
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[] | 2017-02-23T21:02:23
| 2017-02-23T21:03:21
|
2017-02-23T21:03:21Z
|
CONTRIBUTOR
|
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## Summary
* file argument to saving dos plot is fixed.
|
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MDExOlB1bGxSZXF1ZXN0MTA3ODU4MDQ3
| 594
|
get_projected_plots_dots_patom_pmorb
|
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[] | 2017-02-24T16:10:57
| 2017-02-24T22:09:03
|
2017-02-24T22:09:03Z
|
CONTRIBUTOR
|
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Dear master,
I wrote a new method named "get_projected_plots_dots_patom_pmorb" in plotter.py file. This is an extension of the old method "get_projected_plots_dots" and still in the class "BSPlotterProjected". Here are some features of this method:
- Get projections on specific atoms (e.g. Cu1, O3, Zn4) or on a group of the same-type atoms (e.g. Cu1+ Cu2+ Cu3) in computed structure.
- Get projections on specific individual orbitals (e. g. px, py, pz, dxy, dyz,...) or on sum of these orbitals (e.g. px+py, px+py+pz, s+px+py+pz,...)
- Get projections for selected branches of band-structure in the case you do not want to show all of them.
- Customize the size of the figure and the arrangement of all subfigures (columns and rows).
Best regards,
Anh.
|
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major refactor of eos
|
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[] | 2017-02-24T17:21:27
| 2017-02-24T22:08:54
|
2017-02-24T22:08:54Z
|
CONTRIBUTOR
|
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* got rid off ase crap(only the EOS wrapper class retained for backward compatibility)
* more object oriented implementation: makes it easier for adding more eoses
* added more unittests
|
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| 210,165,629
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MDExOlB1bGxSZXF1ZXN0MTA3OTE0MDg3
| 596
|
fixes to generate_adsorption_structures and tests
|
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[] | null |
[] | 2017-02-24T21:40:26
| 2017-02-24T22:08:37
|
2017-02-24T22:08:37Z
|
CONTRIBUTOR
|
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|
## Summary
Small update to adsorption module, fixes to structure generation for adsorbate structures
* AdsorbateSiteFinder can generate adsorption structures and pass arguments into the site finding function
* Relevant unittests added
|
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MDExOlB1bGxSZXF1ZXN0MTA3OTQ3NDk2
| 597
|
comment out the problematic tests of values obtained from b0 in numerical eos
|
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[] | 2017-02-25T05:20:07
| 2017-02-25T15:07:32
|
2017-02-25T15:07:32Z
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MDExOlB1bGxSZXF1ZXN0MTA4MTYxOTAy
| 598
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Reaction Balancing
|
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[] | 2017-02-27T17:24:02
| 2017-02-27T18:23:25
|
2017-02-27T18:18:40Z
|
CONTRIBUTOR
|
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## Summary
Cleaned up the reaction balancing.
Changed string formatting of reactions to avoid superfluous zeros and decimals. Also made the reaction strings consistent with each other (the formatting of different methods was slightly different).
Redefined and documented how Reactions are balanced by default. This is backwards incompatible, but the previous default was not documented or intuitive.
Fixed some weird balancing issues, for example, balancing
Fe + Na + Li2O + Cl -> FeCl2 + Na2O + Xe + LiCl + Mn
used to return
2 Na + Li2O + 5 FeCl2 -> 5 Fe + 4 Cl2 + Na2O + 2 LiCl
now it returns
Fe + 2 Na + Li2O + 2 Cl2 -> FeCl2 + Na2O + 2 LiCl
which is more reasonable. (Though this is obviously a contrived example.)
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MDExOlB1bGxSZXF1ZXN0MTA4MTk0OTE0
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|
Minor fixes to elastic fitting
|
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[] | 2017-02-27T20:30:59
| 2017-02-27T21:00:27
|
2017-02-27T21:00:27Z
|
CONTRIBUTOR
|
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Recent TOEC PR reverted some changes from previous PR. This adds them back and adds a unittest for the missing functionality.
|
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Refactoring of PDAnalyzer.get_element_profile
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[] | null |
[] | 2017-03-01T03:43:53
| 2017-03-02T14:55:33
|
2017-03-01T20:55:05Z
|
CONTRIBUTOR
|
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|
## Summary
* Refactor PDAnalyzer.get_element_profile to use get_critical_compositions instead of generating new PDs
* More helpful error message in Reaction for underdetermined reactants. I don't think there's a useful result to return in these cases.
* Better unittests for get_element_profile
|
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https://api.github.com/repos/materialsproject/pymatgen/issues/600/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/600",
"html_url": "https://github.com/materialsproject/pymatgen/pull/600",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/600.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/600.patch",
"merged_at": "2017-03-01T20:55:05Z"
}
|
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