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periodic_table.json not found
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[
"Thanks for letting us know. I have fixed the issue and pushed out the latest release (1.2.4) which should not have this problem, and with some new bug fixes.\n"
] | 2012-02-26T12:10:46
| 2012-02-26T14:52:41
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2012-02-26T14:52:41Z
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After installing the package the "periodic_table.json" file is moved to [base]/data whereas the periodic_table.py file in [base]/pymatgen/core expects it to be in [base]/pymatgen/core
Therefore the _load__pt_data function fails with a "IOError: [Errno 2] No such file or directory:"
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OrderDisorderTransformation breaks with unintuitive error when number of sites insufficient to perform ordering
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[
"Error fixed. Occupancy fractions that result in ambiguous numbers to remove (>.1 from an integer) now raise an error\n"
] | 2012-04-20T14:57:49
| 2012-04-20T18:36:36
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2012-04-20T18:36:36Z
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MEMBER
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The OrderDisorderTransformation fails with an non-intuitive error when the actual cell is too small to perform ordering. E.g., if you use a primitive cell of a NMC material, the cell only contains one atom with a 0.33 Ni, 0.33 Co, 0.33 Mn occu. This has not enough atoms to perform ordering.
The transformation should check that the cell does not contain enough atoms and present an error message to request for a SupercellTransformation to be performed first.
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OrderDisorderTransformation should support different algos, like PartialRemoveSpecie.
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"ODST now supports BEST_FIRST algo. Working on a better one\n"
] | 2012-04-20T15:00:52
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2019-08-26T21:38:29Z
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Title is self-explanatory. Some ordering problems are too large to be done in brute force. Needs a ALGO.
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Order Disorder transformation return_ranked_list does not work.
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[
"There's a num_structures argument that used to be in **init** I've moved it to apply_transformation. As a default it is set to one and so only one structure is calculated. If you want more structures you need to increase that number\n",
"Ok.\n"
] | 2012-04-20T15:25:17
| 2014-06-23T17:11:42
|
2012-04-20T17:27:22Z
|
MEMBER
|
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OrderDisorderedStructureTransformation should support more than 1 structure being returned.
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MDU6SXNzdWU4NDQyNTM1
| 5
|
Bug in Lattice.get_most_compact_basis
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[
"Geoffroy, any update on this? \n"
] | 2012-11-17T16:56:37
| 2014-09-18T13:43:51
|
2014-09-18T13:43:51Z
|
MEMBER
|
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It appears that get_most_compact_basis has a anychange local variable that is effectively unused. Right before the final part of the "while" loop, it sets anychange=True followed by if anychange: break.
Also, unittests are needed to know what is the expected output of this method.
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| 8,447,126
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MDU6SXNzdWU4NDQ3MTI2
| 6
|
use_external_qhull from PDAnalyzer
|
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[] | 2012-11-18T03:01:06
| 2012-11-18T03:40:27
|
2012-11-18T03:40:27Z
|
NONE
|
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When generating a "profile" through the pdanalyzer it internally generates GrandPotentialPhaseDiagram that uses the default "use_external_qhull" which is True. There is no way of setting the use_external_qhull.
On systems without a functional scipy.spatial.Delaunay this will always fail.
Maybe use_external_qhull could be accessible through a kwarg on get_element_profile
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MDU6SXNzdWU4NDQ3Mzc0
| 7
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Trivial fitting in StructureFitter does not work.
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[
"This has been superseded by the new StructureMatcher.\n"
] | 2012-11-18T03:49:08
| 2013-01-13T22:36:52
|
2013-01-13T22:36:52Z
|
MEMBER
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I am not sure whether to classify this as a bug. But it is a very odd thing.
Try the following code
logging.basicConfig(level=logging.DEBUG)
# Use the POSCAR.LiFePO4 from the test_files.
p = Poscar.from_file("test_files/POSCAR.LiFePO4", check_for_POTCAR=False)
s = p.structure
from pymatgen.analysis.structure_fitter import StructureFitter
fitter = StructureFitter(s, s)
print fitter.fit_found
This code should be fitting two identical structures (trivial case). Symmetry is turned off. In this case, simple_fit should result in an immediate fit.
Instead, it takes a full 5 secs to fit. And I get the following which shows that somehow, the initial identity fitting procedure has failed to produce a match. Eyeballing the debug output tells me that the sites seem to be in the exact same position, but the closest distance is somehow computed to be 1.3 A. Note that if I turn on symmetry, this problem disappears and the fit is done within 0.5secs. It does indicate that something is wrong in the test_rotations which is causing a problem.
DEBUG:pymatgen.analysis.structure_fitter:Trying candidate rotation :
Rot:
[[ 1.00000000e+00 0.00000000e+00 1.35525272e-20]
[ -1.69406589e-21 1.00000000e+00 0.00000000e+00]
[ 0.00000000e+00 -4.37102915e-21 1.00000000e+00]]
tau
[ 0. 0. 0.]
DEBUG:pymatgen.analysis.structure_fitter:[ 0. 0. 0.] Li fits on [ 0. 0. 0.] Li
DEBUG:pymatgen.analysis.structure_fitter:[ 1.04101920e+01 3.03176700e+00 -6.86500000e-04] Li fits on [ 1.04101920e+01 3.03176700e+00 -6.86500000e-04] Li
DEBUG:pymatgen.analysis.structure_fitter:[ 5.20528000e+00 -9.35000000e-05 -2.37789150e+00] Li fits on [ 5.20528000e+00 -9.35000000e-05 -2.37789150e+00] Li
DEBUG:pymatgen.analysis.structure_fitter:[ 5.205318 3.0315435 -2.377689 ] Li fits on [ 5.205318 3.0315435 -2.377689 ] Li
DEBUG:pymatgen.analysis.structure_fitter:[ 2.27690836 4.54731145 -2.49612443] Fe fits on [ 2.27690836 4.54731145 -2.49612443] Fe
DEBUG:pymatgen.analysis.structure_fitter:[ 2.92874895 1.5159624 -0.11830796] Fe fits on [ 2.92874895 1.5159624 -0.11830796] Fe
DEBUG:pymatgen.analysis.structure_fitter:[ 7.48188705 4.5471246 -4.63707004] Fe fits on [ 7.48188705 4.5471246 -4.63707004] Fe
DEBUG:pymatgen.analysis.structure_fitter:[ 8.13372764 1.51577555 -2.25925357] Fe fits on [ 8.13372764 1.51577555 -2.25925357] Fe
DEBUG:pymatgen.analysis.structure_fitter:[ 0.98624255 1.51607687 -2.7664278 ] P fits on [ 0.98624255 1.51607687 -2.7664278 ] P
DEBUG:pymatgen.analysis.structure_fitter:[ 4.21854487 4.54796731 -0.38900679] P fits on [ 4.21854487 4.54796731 -0.38900679] P
DEBUG:pymatgen.analysis.structure_fitter:[ 6.19209113 1.51511969 -4.36637121] P fits on [ 6.19209113 1.51511969 -4.36637121] P
DEBUG:pymatgen.analysis.structure_fitter:[ 9.42439345 4.54701013 -1.9889502 ] P fits on [ 9.42439345 4.54701013 -1.9889502 ] P
DEBUG:pymatgen.analysis.structure_fitter:[ 0.45134146 4.54744114 -1.39103578] O fits on [ 0.45134146 4.54744114 -1.39103578] O
DEBUG:pymatgen.analysis.structure_fitter:[ 1.00649435 1.51570063 -1.22899166] O fits on [ 1.00649435 1.51570063 -1.22899166] O
DEBUG:pymatgen.analysis.structure_fitter:[ 1.72451712 0.2800334 -3.39894578] O fits on [ 1.72451712 0.2800334 -3.39894578] O
DEBUG:pymatgen.analysis.structure_fitter:[ 1.72442314 2.75091459 -3.39848116] O fits on [ 1.72442314 2.75091459 -3.39848116] O
DEBUG:pymatgen.analysis.structure_fitter:[ 3.481076 3.31200243 -1.02125134] O fits on [ 3.481076 3.31200243 -1.02125134] O
DEBUG:pymatgen.analysis.structure_fitter:[ 3.48114862 5.78239853 -1.02120044] O fits on [ 3.48114862 5.78239853 -1.02120044] O
DEBUG:pymatgen.analysis.structure_fitter:[ 4.1993318 4.54721898 -3.60672277] O fits on [ 4.1993318 4.54721898 -3.60672277] O
DEBUG:pymatgen.analysis.structure_fitter:[ 4.75374206 1.51577817 -3.76931419] O fits on [ 4.75374206 1.51577817 -3.76931419] O
DEBUG:pymatgen.analysis.structure_fitter:[ 5.65689394 4.54730883 -0.98606381] O fits on [ 5.65689394 4.54730883 -0.98606381] O
DEBUG:pymatgen.analysis.structure_fitter:[ 6.2113042 1.51586802 -1.14865523] O fits on [ 6.2113042 1.51586802 -1.14865523] O
DEBUG:pymatgen.analysis.structure_fitter:[ 6.92948738 0.28068847 -3.73417756] O fits on [ 6.92948738 0.28068847 -3.73417756] O
DEBUG:pymatgen.analysis.structure_fitter:[ 6.92956 2.75108457 -3.73412666] O fits on [ 6.92956 2.75108457 -3.73412666] O
DEBUG:pymatgen.analysis.structure_fitter:[ 8.68621286 3.31217241 -1.35689684] O fits on [ 8.68621286 3.31217241 -1.35689684] O
DEBUG:pymatgen.analysis.structure_fitter:[ 8.68611888 5.7830536 -1.35643222] O fits on [ 8.68611888 5.7830536 -1.35643222] O
DEBUG:pymatgen.analysis.structure_fitter:[ 9.40414165 4.54738637 -3.52638634] O fits on [ 9.40414165 4.54738637 -3.52638634] O
DEBUG:pymatgen.analysis.structure_fitter:[ 9.95929454 1.51564586 -3.36434222] O fits on [ 9.95929454 1.51564586 -3.36434222] O
DEBUG:pymatgen.analysis.structure_fitter:Closest dist too large! Closest dist = 1.31858818396
DEBUG:pymatgen.analysis.structure_fitter:Closest dist too large! Closest dist = 0.75949840042
DEBUG:pymatgen.analysis.structure_fitter:No candidates found.
|
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| 8,515,696
|
MDU6SXNzdWU4NTE1Njk2
| 8
|
pymatgen/electronic_structure/bandstructure.py conditional logic bug
|
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[] | 2012-11-20T18:48:11
| 2012-11-20T19:39:12
|
2012-11-20T19:39:12Z
|
NONE
|
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Line 191 of pymatgen/electronic_structure/bandstructure.py in installation tree has a conditional line
```
if len(projections) != 0 and self._structure is None:
```
that will fail (crash) when projections is NoneType. This line is preceded by the line 187
```
self._projections = projections if projections else {}
```
perhaps the conditional len(projections) should be len(self._projections) ?
I have built this from pymatgen-2.2.6 tar/gz source package
|
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| 8,799,274
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MDU6SXNzdWU4Nzk5Mjc0
| 9
|
reverse_readlines does not work properly for gzipped and bzipped files
|
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[] | 2012-11-29T06:53:57
| 2012-11-29T18:56:54
|
2012-11-29T18:56:54Z
|
MEMBER
|
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Gzipped files fail with ValueError("Seek from end not supported"), and bzipped file reading is extremely slow.
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| 8,839,267
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MDU6SXNzdWU4ODM5MjY3
| 10
|
CHGCAR leads to incorrect results for non-cubic cell.
|
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[] | 2012-11-30T02:09:29
| 2012-11-30T02:11:44
|
2012-11-30T02:11:44Z
|
MEMBER
|
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|
The charge integration does not give the correct results for CHGCAR files, particularly when the CHGCAR is for a non-cubic structure.
|
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| 8,934,331
|
MDU6SXNzdWU4OTM0MzMx
| 11
|
StructurePrediction code should not assume existence of tests or unittests.
|
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[] | 2012-12-03T02:03:32
| 2012-12-03T02:32:32
|
2012-12-03T02:32:32Z
|
MEMBER
|
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The substitutor predictor has code that is meant to do unittests. Furthermore, it assumes that the test_data directory is present.
This assumption is not valid. Esp when releasing packages, the tests directories are all excluded from the final package. The code base should stand on its own without the tests directory. The tests directory should purely be used for unittesting only. Also, there shouldn't be code in substitutor_predictor.py purely for the sake of helping unittesting.
|
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MDU6SXNzdWU5MTgwMTI0
| 12
|
Issue with supercells in new StructureMatcher
|
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[] | 2012-12-11T13:58:36
| 2013-01-13T22:36:33
|
2013-01-13T22:36:33Z
|
MEMBER
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Go to "test_files" and do
../scripts/matgenie.py compare Li2O.cif POSCAR.Li2O
Both are Li2O. Second one is a big-ish supercell. The code fails with a TypeError after a while, given below:
Traceback (most recent call last):
File "../scripts/matgenie.py", line 423, in <module>
args.func(args)
File "../scripts/matgenie.py", line 282, in compare_structures
for i, grp in enumerate(m.group_structures(structures)):
File "/Users/shyuepingong/Documents/Aptana Studio 3 Workspace/pymatgen/pymatgen/analysis/structure_matcher.py", line 271, in group_structures
if s2_ind == -1 and self.fit(s_list[i], s_list[j]):
File "/Users/shyuepingong/Documents/Aptana Studio 3 Workspace/pymatgen/pymatgen/analysis/structure_matcher.py", line 202, in fit
if s2_cart[ind] != []:
TypeError: list indices must be integers, not NoneType
This is likely the issue of finding the primitive cell of the supercell.
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| 12,729,219
|
MDU6SXNzdWUxMjcyOTIxOQ==
| 13
|
Procar will not read in?
|
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[] | 2013-04-02T22:34:54
| 2013-04-02T22:45:22
|
2013-04-02T22:45:22Z
|
CONTRIBUTOR
|
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pymatgen version is 2.6.3 (pip install pymatgen --upgrade, at 17:30 2013-04-02)
> > > import pymatgen
> > > myprocar=pymatgen.io.vaspio.vasp_output.Procar('PROCAR')
> > > Traceback (most recent call last):
> > > File "<stdin>", line 1, in <module>
> > > File "/share/apps/virtualenv/mastenv/lib/python2.7/site-packages/pymatgen/io/vaspio/vasp_output.py", line 1795, in **init**
> > > self._read_file(filename)
> > > File "/share/apps/virtualenv/mastenv/lib/python2.7/site-packages/pymatgen/io/vaspio/vasp_output.py", line 1805, in _read_file
> > > self.name = lines[0]
> > > TypeError: 'generator' object has no attribute '__getitem__'
(mastenv)$ head PROCAR
PROCAR new format
# of k-points: 32 # of bands: 234 # of ions: 39
k-point 1 : 0.12500000 0.12500000 0.12500000 weight = 0.03125000
band 1 # energy -44.06734077 # occ. 1.00000000
ion s p d f tot
1 0.000 0.000 0.000 0.000 0.000
2 0.000 0.000 0.000 0.000 0.000
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MDU6SXNzdWUxMjcyOTQyOQ==
| 14
|
Selective dynamics in Poscar does not work?
|
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[] | null |
[
"I'm not sure why the indentations didn't display properly above...please let me know if there are problems...\n",
"The reason why this problem occured is because a numpy array was supplied as a selective dynamics when it is expecting a list. I have changed the code to support both. Thanks for reporting this.\n"
] | 2013-04-02T22:41:43
| 2013-04-02T23:05:12
|
2013-04-02T22:58:05Z
|
CONTRIBUTOR
|
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(mastenv)$ python test_selectivedynamics.py
Traceback (most recent call last):
File "test_selectivedynamics.py", line 9, in <module>
mypos.selective_dynamics=mysd
File "/share/apps/virtualenv/mastenv/lib/python2.7/site-packages/pymatgen/io/vaspio/vasp_input.py", line 141, in **setattr**
if value:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
> > > > > > > > > > > > > > > test_selectivedynamics.py>>>>>>>>>>>>>>
> > > > > > > > > > > > > > > import pymatgen
> > > > > > > > > > > > > > > import numpy as np
> > > > > > > > > > > > > > > mypos=pymatgen.io.vaspio.Poscar.from_file("CONTCAR")
> > > > > > > > > > > > > > > mypos.write_file("write_once_POSCAR")
> > > > > > > > > > > > > > > mysd=np.zeros([sum(mypos.natoms),3],bool)
> > > > > > > > > > > > > > > mysd[3][1]=True
> > > > > > > > > > > > > > > mysd[3][0]=True
> > > > > > > > > > > > > > > mysd[3][2]=True
> > > > > > > > > > > > > > > mypos.selective_dynamics=mysd
> > > > > > > > > > > > > > > mypos.write_file("write_sd_POSCAR")
These two changes fixed the problem on my local install. Changes in two spots....
> > > > CHANGE 1>>>>>>>>>>>>>>>
> > > > def **setattr**(self, name, value):
> > > > if name in ("selective_dynamics", "velocities"):
> > > > #2013-03-19 enclosing within a "try" statement:
> > > > try:
> > > > if value:
> > > > dim = np.array(value).shape
> > > > if dim[1] != 3 or dim[0] != len(self.structure):
> > > > raise ValueError(name + " array must be same length as" +
> > > > " the structure.")
> > > > except (ValueError):
> > > >
> > > > > CHANGE 2>>>>>>>>>>
> > > > > for (i, site) in enumerate(self.structure):
> > > > > coords = site.frac_coords if direct else site.coords
> > > > > line = " ".join([format_str.format(c) for c in coords])
> > > > > if not (self.selective_dynamics == None): #2013-03-19 "not none"
> > > > > sd = ["T" if j else "F" for j in self.selective_dynamics[i]]
> > > > > line += " %s %s %s" % (sd[0], sd[1], sd[2])
> > > > > line += " " + site.species_string
> > > > > lines.append(line)
|
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| 13,374,297
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MDU6SXNzdWUxMzM3NDI5Nw==
| 15
|
remove_species() behavior
|
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[
"It is a conscious design decision to not treat an Element and a Specie with zero oxidation state the same. A zero oxidation state means that someone has consciously assigned a oxidation state, which then allows the computation of things like Ewald summations. An Element means that no one has specified an oxidation state yet and hence, if you try to get the ewald symmation, it will throw an error. Treating Elements the same way as Specie with zero oxidation state may result in confusing behavior like EWaldSummation returning 0 without errors.\n"
] | 2013-04-18T21:36:18
| 2013-04-19T18:18:24
|
2013-04-19T18:18:24Z
|
CONTRIBUTOR
|
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It seems these two methods don't do the same thing:
(rs1 is a StructureEditor)
rs1.remove_species([Element('Li')])
rs1.remove_species([Specie('Li', 0)])
Why is this the case? It makes it difficult to use remove_species()
|
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| 13,424,763
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MDU6SXNzdWUxMzQyNDc2Mw==
| 16
|
common oxidation states of Vanadium
|
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[
"Btw, for battery purposes I can get around this by using:\n\nmin(e for e in el.oxidation_states if e>1)\n\nwhere el is an Element. But maybe V should be changed anyway?\n",
"I am not sure how to solve this problem very robustly. Different people have different definitions of what constitute a \"common\" oxidation state. This list is from wikipedia. For instance, Fe4+ is a pretty rare oxidation state, but something that battery researchers generally consider (e.g., in oxides).\n\nFor application-specific uses such as batteries, I would suggest we separately define allowable oxidation states by element. E.g., for battery, I would suggest compiling allowable oxidation states for battery purposes. \n",
"(ok)\n"
] | 2013-04-19T23:00:15
| 2013-04-19T23:08:29
|
2013-04-19T23:08:29Z
|
MEMBER
|
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It looks like only +5 is listed as a common oxidation state of Vanadium:
el = Element('V')
print el.common_oxidation_states
> > (5,)
Should +2, +3, and +4 also be on the list?
Note that some of the BatteryAnalyzer code in a different Materials Project repo needs to know how far you can reduce a metal. Currently it was using min(a.common_oxidation_states), but this fails spectacularly for V as it doesn't realize you can go down to 3+ and even 2+. It also fails a bit more silently for Cr, Ti, and Mo. Note that you can't use the min_oxidation_state property of an Element, that usually goes all the way negative
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MDU6SXNzdWUxMzQ2MDM2MA==
| 17
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get_*_structure methods in SymmetryFinder don't retain site_properties
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[] | 2013-04-22T01:44:26
| 2015-09-18T22:48:09
|
2015-09-18T22:48:09Z
|
CONTRIBUTOR
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Given a MAGMOM decorated Structure (set as site_properties), these methods in pymatgen return structures without MAGMOM settings. Is the underlying Spglib able to give a site mapping between the input and output structures?
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|
Pull request for abinitio
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"Thanks Matteo. I just merged the pull request. There is one minor failure in my unittests though. This was the error:\n\n# \n\n## ERROR: test_read_Si2 (pymatgen.io.abinitio.tests.test_netcdf.GSR_Reader_TestCase)\n\nTraceback (most recent call last):\n File \"/Users/shyuepingong/Documents/Aptana Studio 3 Workspace/pymatgen/pymatgen/io/abinitio/tests/test_netcdf.py\", line 60, in test_read_Si2\n data.print_tree()\n File \"/Users/shyuepingong/Documents/Aptana Studio 3 Workspace/pymatgen/pymatgen/io/abinitio/netcdf.py\", line 90, in print_tree\n for children in self.walk_tree():\n File \"/Users/shyuepingong/Documents/Aptana Studio 3 Workspace/pymatgen/pymatgen/io/abinitio/netcdf.py\", line 83, in walk_tree\n values = top.groups.values()\nAttributeError: 'netcdf_file' object has no attribute 'groups'\n-------------------- >> begin captured stdout << ---------------------\n['chemical_symbols', 'occupations', 'residm', 'reduced_symmetry_translations', 'exchange_functional', 'cartesian_forces', 'tphysel', 'entropy', 'deltae', 'pseudopotential_types', 'diffor', 'etotal', 'fermi_energy', 'space_group', 'cartesian_stress_tensor', 'reduced_atom_positions', 'kpoint_weights', 'valence_charges', 'primitive_vectors', 'res2', 'smearing_width', 'smearing_scheme', 'atom_species_names', 'kpoint_grid_vectors', 'number_of_states', 'occopt', 'atom_species', 'reduced_coordinates_of_kpoints', 'istwfk', 'monkhorst_pack_folding', 'correlation_functional', 'kpoint_grid_shift', 'fermie', 'atomic_numbers', 'symafm', 'eigenvalues', 'number_of_electrons', 'reduced_symmetry_matrices']\n\n--------------------- >> end captured stdout << ----------------------\n"
] | 2013-04-29T14:25:27
| 2014-07-04T02:48:18
|
2013-04-29T16:48:15Z
|
CONTRIBUTOR
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I will send an email to you and Geoffroy with more info on what I've doing so far in the abinitio sub-package
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| 13,771,047
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MDExOlB1bGxSZXF1ZXN0NTQyOTY3NQ==
| 19
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solved problem with test_netcdf
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"Thanks Matteo. I have made a minor mod. I think the skip test should be NC_VERSION != 4.\nYou can now merge the master branch of the main branch to your fork to keep it up to date.\n\nThanks for the great work on the abinit support!\n",
"Right, I made a mistake!\nThank you.\n\nOn Mon, Apr 29, 2013 at 7:30 PM, Shyue Ping Ong notifications@github.comwrote:\n\n> Thanks Matteo. I have made a minor mod. I think the skip test should be\n> NC_VERSION != 4.\n> You can now merge the master branch of the main branch to your fork to\n> keep it up to date.\n> \n> Thanks for the great work on the abinit support!\n> \n> —\n> Reply to this email directly or view it on GitHubhttps://github.com/materialsproject/pymatgen/pull/19#issuecomment-17181289\n> .\n\n## \n\nNel 1969, con la potenza di calcolo di due Commodore 64, l'uomo è riuscito\na sbarcare sulla luna. Oggi, per far girare decentemente Windows Vista,\nserve 1GB di RAM... qualcosa deve essere andato storto\n"
] | 2013-04-29T17:22:31
| 2014-07-04T02:48:17
|
2013-04-29T17:28:27Z
|
CONTRIBUTOR
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Hi Shyue,
the problem with the netcdf test is hopefully solved in this revision. I was trying to support both scipy.io.netcdf as well as netcdf4 although the two APIs are not 100% compatible. netcdf4 is more flexible that the interface provided by scipy that only supports netcdf3. Now the test is skipped if netcdf4 is not available. Future versions of abinitio will require netcdf4
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MDExOlB1bGxSZXF1ZXN0NTQ3MDcwNA==
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fix conflict with ape.py (removed in my branch)
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MDU6SXNzdWUxMzg1NDg2Nw==
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having trouble generating POTCAR with sym_potcar_map set
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[
"The sym_potcar_map is meant to be used with a raw potcar string. It is not a mapping of symbol to symbol. \n\nRegards,\nShyue Ping\n\nOn Wednesday, May 1, 2013 at 12:29 PM, cmgtam wrote:\n\n> Code version is apparently 2.7.0b, pulled today at 11:17.\n> Below I have compared sym_potcar_map=None with sym_potcar_map set.\n> \n> > > > mypotcar = pymatgen.io.vaspio.Potcar(symbols=['Si','C','O'], functional=\"PBE\", sym_potcar_map=None)\n> > > > mypotcar[0].enmax\n> > > > 245.345\n> > > > mypotcar = pymatgen.io.vaspio.Potcar(symbols=['Si','C','O'], functional=\"PBE\", sym_potcar_map={\"Si\":\"Si\",\"C\":\"C\",\"O\":\"O_s\"})\n> > > > mypotcar[0].enmax\n> > > > Traceback (most recent call last):\n> > > > File \"\", line 1, in \n> > > > File \"/share/apps/virtualenv/mastenv/lib/python2.7/site-packages/pymatgen-2.7.0b-py2.7-linux-x86_64.egg/pymatgen/io/vaspio/vasp_input.py\", line 1170, in getattr\n> > > > raise AttributeError(a)\n> > > > AttributeError: enmax\n> > > > mypotcar[0].data\n> > > > 'Si' \n> > > > Thanks,\n> > > > Tam \n> \n> —\n> Reply to this email directly or view it on GitHub (https://github.com/materialsproject/pymatgen/issues/21).\n",
"Incidentally, the second version can simply be written as Potcar([\"Si\", \"C\", \"O_s\"]). There is no need to use the sym_potcar_map at all. \nI noticed that the doc on the constructor for Potcar is outdated, which may have led to the confusion. I have corrected the doc.\n\nRegards,\nShyue Ping\n\nOn Wednesday, May 1, 2013 at 12:54 PM, Shyue Ping Ong wrote:\n\n> The sym_potcar_map is meant to be used with a raw potcar string. It is not a mapping of symbol to symbol. \n> \n> Regards,\n> Shyue Ping\n> \n> On Wednesday, May 1, 2013 at 12:29 PM, cmgtam wrote:\n> \n> > Code version is apparently 2.7.0b, pulled today at 11:17.\n> > Below I have compared sym_potcar_map=None with sym_potcar_map set.\n> > \n> > > > > mypotcar = pymatgen.io.vaspio.Potcar(symbols=['Si','C','O'], functional=\"PBE\", sym_potcar_map=None)\n> > > > > mypotcar[0].enmax\n> > > > > 245.345\n> > > > > mypotcar = pymatgen.io.vaspio.Potcar(symbols=['Si','C','O'], functional=\"PBE\", sym_potcar_map={\"Si\":\"Si\",\"C\":\"C\",\"O\":\"O_s\"})\n> > > > > mypotcar[0].enmax\n> > > > > Traceback (most recent call last):\n> > > > > File \"\", line 1, in \n> > > > > File \"/share/apps/virtualenv/mastenv/lib/python2.7/site-packages/pymatgen-2.7.0b-py2.7-linux-x86_64.egg/pymatgen/io/vaspio/vasp_input.py\", line 1170, in getattr\n> > > > > raise AttributeError(a)\n> > > > > AttributeError: enmax\n> > > > > mypotcar[0].data\n> > > > > 'Si' \n> > > > > Thanks,\n> > > > > Tam \n> > \n> > —\n> > Reply to this email directly or view it on GitHub (https://github.com/materialsproject/pymatgen/issues/21).\n",
"Awesome, thanks - that was what I was looking for. It might be worth noting in the docstring that \"O_s\" or \"Mg_pv\" etc. can be used like you said above. Closing issue.\n"
] | 2013-05-01T16:29:20
| 2013-05-01T17:13:38
|
2013-05-01T17:13:38Z
|
CONTRIBUTOR
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Code version is apparently 2.7.0b, pulled today at 11:17.
Below I have compared sym_potcar_map=None with sym_potcar_map set.
> > > mypotcar = pymatgen.io.vaspio.Potcar(symbols=['Si','C','O'], functional="PBE", sym_potcar_map=None)
> > > mypotcar[0].enmax
> > > 245.345
> > > mypotcar = pymatgen.io.vaspio.Potcar(symbols=['Si','C','O'], functional="PBE", sym_potcar_map={"Si":"Si","C":"C","O":"O_s"})
> > > mypotcar[0].enmax
> > > Traceback (most recent call last):
> > > File "<stdin>", line 1, in <module>
> > > File "/share/apps/virtualenv/mastenv/lib/python2.7/site-packages/pymatgen-2.7.0b-py2.7-linux-x86_64.egg/pymatgen/io/vaspio/vasp_input.py", line 1170, in **getattr**
> > > raise AttributeError(a)
> > > AttributeError: enmax
> > > mypotcar[0].data
> > > 'Si'
Thanks,
Tam
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| 13,964,095
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MDExOlB1bGxSZXF1ZXN0NTUzMTE5Mw==
| 22
|
minor change in smart_element_or_specie
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[] | 2013-05-04T13:11:05
| 2014-07-04T02:48:14
|
2013-05-04T13:29:12Z
|
CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0NTYwMTgwMQ==
| 23
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Add ntypat property to SiteCollection (raises AttributeError if not self.is_ordered)
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| 2014-07-04T02:48:13
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2013-05-08T17:57:10Z
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Bug in pymatgen.core.lattice.py?
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[
"Hi there,\n\nI can't reproduce the error. You cannot just specify voronoi_data as site properties because there are only some properties allowed. But otherwise, I can't reproduce the error. Can you give me the exact forms of the variables voronoi_lattice, s and c? For example, the following works just fine:\n\nStructure(Lattice.cubic(3), [\"Fe\"], [[0,0,0]], coords_are_cartesian=True)\n",
"May be what I am doing is wrong. In that case, let me know where I am wrong.\nI am attaching the python script and the input data files.\n\nThanks,\nBharat\n\nOn 5/16/13 4:29 PM, Shyue Ping Ong wrote:\n\n> Hi there,\n> \n> I can't reproduce the error. You cannot just specify voronoi_data as \n> site properties because there are only some properties allowed. But \n> otherwise, I can't reproduce the error. Can you give me the exact \n> forms of the variables voronoi_lattice, s and c? For example, the \n> following works just fine:\n> \n> Structure(Lattice.cubic(3), [\"Fe\"], [[0,0,0]], coords_are_cartesian=True)\n> \n> —\n> Reply to this email directly or view it on GitHub \n> https://github.com/materialsproject/pymatgen/issues/24#issuecomment-18035676.\n> \n> 4.2120 4.2120 4.2120\n> 90.00 90.00 90.00 SPGR = 1 P 1 OPT = 1\n> 8 0\n> 0 Mg4 O4\n> 1 Mg 0.0000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00 \n> 2 Mg 0.5000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00 \n> 3 Mg 0.5000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00 \n> 4 Mg 0.0000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00 \n> 5 O 0.5000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00 \n> 6 O 0.0000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00 \n> 7 O 0.0000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00 \n> 8 O 0.5000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00 \n",
"Hi Bharat, \n\nI don't see an input file. Maybe you can email them directly to me at shyuep@gmail.com? \n\nRegards,\nShyue Ping\n\nOn Thursday, May 16, 2013 at 7:45 PM, mbkumar wrote:\n\n> May be what I am doing is wrong. In that case, let me know where I am wrong.\n> I am attaching the python script and the input data files.\n> \n> Thanks,\n> Bharat\n> \n> On 5/16/13 4:29 PM, Shyue Ping Ong wrote:\n> \n> > Hi there,\n> > \n> > I can't reproduce the error. You cannot just specify voronoi_data as \n> > site properties because there are only some properties allowed. But \n> > otherwise, I can't reproduce the error. Can you give me the exact \n> > forms of the variables voronoi_lattice, s and c? For example, the \n> > following works just fine:\n> > \n> > Structure(Lattice.cubic(3), [\"Fe\"], [[0,0,0]], coords_are_cartesian=True)\n> > \n> > —\n> > Reply to this email directly or view it on GitHub \n> > https://github.com/materialsproject/pymatgen/issues/24#issuecomment-18035676.\n> \n> 4.2120 4.2120 4.2120\n> 90.00 90.00 90.00 SPGR = 1 P 1 OPT = 1\n> 8 0\n> 0 Mg4 O4\n> 1 Mg 0.0000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00 \n> 2 Mg 0.5000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00 \n> 3 Mg 0.5000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00 \n> 4 Mg 0.0000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00 \n> 5 O 0.5000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00 \n> 6 O 0.0000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00 \n> 7 O 0.0000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00 \n> 8 O 0.5000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00 \n> \n> —\n> Reply to this email directly or view it on GitHub (https://github.com/materialsproject/pymatgen/issues/24#issuecomment-18036221).\n",
"I'll send them tomorrow morning.\n\nBharat\n\nOn Thu, 16 May 2013 18:56:18 -0500, Shyue Ping Ong \nnotifications@github.com wrote:\n\n> Hi Bharat,\n> \n> I don't see an input file. Maybe you can email them directly to me at \n> shyuep@gmail.com?\n> \n> Regards,\n> Shyue Ping\n> \n> On Thursday, May 16, 2013 at 7:45 PM, mbkumar wrote:\n> \n> > May be what I am doing is wrong. In that case, let me know where I am \n> > wrong.\n> > I am attaching the python script and the input data files.\n> > \n> > Thanks,\n> > Bharat\n> > \n> > On 5/16/13 4:29 PM, Shyue Ping Ong wrote:\n> > \n> > > Hi there,\n> > > \n> > > I can't reproduce the error. You cannot just specify voronoi_data as\n> > > site properties because there are only some properties allowed. But\n> > > otherwise, I can't reproduce the error. Can you give me the exact\n> > > forms of the variables voronoi_lattice, s and c? For example, the\n> > > following works just fine:\n> > > \n> > > Structure(Lattice.cubic(3), [\"Fe\"], [[0,0,0]], \n> > > coords_are_cartesian=True)\n> > > \n> > > —\n> > > Reply to this email directly or view it on GitHub\n> > > \n> > > https://github.com/materialsproject/pymatgen/issues/24#issuecomment-18035676.\n> > \n> > 4.2120 4.2120 4.2120\n> > 90.00 90.00 90.00 SPGR = 1 P 1 OPT = 1\n> > 8 0\n> > 0 Mg4 O4\n> > 1 Mg 0.0000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00\n> > 2 Mg 0.5000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00\n> > 3 Mg 0.5000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00\n> > 4 Mg 0.0000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00\n> > 5 O 0.5000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00\n> > 6 O 0.0000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00\n> > 7 O 0.0000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00\n> > 8 O 0.5000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00\n> > \n> > —\n> > Reply to this email directly or view it on GitHub \n> > (https://github.com/materialsproject/pymatgen/issues/24#issuecomment-18036221).\n> \n> ---\n> \n> Reply to this email directly or view it on GitHub:\n> https://github.com/materialsproject/pymatgen/issues/24#issuecomment-18036563\n"
] | 2013-05-16T21:22:40
| 2013-05-17T19:59:43
|
2013-05-17T19:59:43Z
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CONTRIBUTOR
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When trying to initialize Structure in core/structure.py, I am getting an error message.
Input to initializer:
1) lattice of type "pymatgen.core.lattice.Lattice"
2) species of type "List of strings"
3) coords of type "List of numpy arrays of size 3"
4) coords_are_cartesian=True
5) site_properties=dict{"property_name":List of numbers}
Error Message:
File "voronoi_node_symmetry.py", line 34, in <module>
voronoi_struct = Structure(voronoi_lattice, s, c, coords_are_cartesian=True, site_properties={"voronoi_data":p})
File "/Library/Python/2.7/site-packages/pymatgen/core/structure.py", line 297, in **init**
properties=prop))
File "/Library/Python/2.7/site-packages/pymatgen/core/sites.py", line 312, in **init**
self._fcoords = self._lattice.get_fractional_coords(coords)
File "/Library/Python/2.7/site-packages/pymatgen/core/lattice.py", line 104, in get_fractional_coords
return dot(cart_coords, self.inv_matrix)
ValueError: data type must provide an itemsize
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SandboxViolation while installing pyhull-1.3.8
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"Hi Matteo, \n\nThis is a known issue. Can you install pyhull using \"pip install pyhull --upgrade\"? Thanks. \n\nShyue Ping\n\nOn Tuesday, May 21, 2013 at 11:49 AM, gmatteo wrote:\n\n> Hi,\n> I've just merged mpmaster in my private branch. I ran the unit tests \n> and many tests were failing in phasediagram due to the fact that now we \n> require pyhull >=1.3.8.\n> I tried to install the new version of pyhull via setup.py but the installation fails\n> with the following error \n> sudo python setup.py install\n> ... \n> Processing dependencies for pymatgen==2.7.2b\n> Searching for pyhull>=1.3.8\n> Reading http://pypi.python.org/simple/pyhull/\n> Reading https://github.com/shyuep/pyhull\n> Best match: pyhull 1.3.8\n> Downloading http://pypi.python.org/packages/source/p/pyhull/pyhull-1.3.8.tar.gz#md5=f8175f0ecb4b85fb26123481019d9f7c\n> Processing pyhull-1.3.8.tar.gz\n> Writing /tmp/easy_install-LIekCW/pyhull-1.3.8/setup.cfg\n> Running pyhull-1.3.8/setup.py -q bdist_egg --dist-dir /tmp/easy_install-LIekCW/pyhull-1.3.8/egg-dist-tmp-nsVEGi\n> warning: no files found matching '_.c'\n> no previously-included directories found matching '_*/tests'\n> error: Setup script exited with error: SandboxViolation: os.open('/tmp/tmpZfTvDd/jrTBn3', 2818, 384) {} \n> The package setup script has attempted to modify files on your system\n> that are not within the EasyInstall build area, and has been aborted. \n> This package cannot be safely installed by EasyInstall, and may not\n> support alternate installation locations even if you run its setup\n> script by hand. Please inform the package's author and the EasyInstall\n> maintainers to find out if a fix or workaround is available. \n> \n> —\n> Reply to this email directly or view it on GitHub (https://github.com/materialsproject/pymatgen/issues/25).\n",
"Hi Shyue, \n\nThe installation completed successfully with pip. \nMany thanks,\nMatteo\n"
] | 2013-05-21T15:49:27
| 2014-01-15T18:09:10
|
2014-01-15T18:09:10Z
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CONTRIBUTOR
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Hi,
I've just merged mpmaster in my private branch. I ran the unit tests
and many tests were failing in phasediagram due to the fact that now we
require pyhull >=1.3.8.
I tried to install the new version of pyhull via setup.py but the installation fails
with the following error
sudo python setup.py install
...
Processing dependencies for pymatgen==2.7.2b
Searching for pyhull>=1.3.8
Reading http://pypi.python.org/simple/pyhull/
Reading https://github.com/shyuep/pyhull
Best match: pyhull 1.3.8
Downloading http://pypi.python.org/packages/source/p/pyhull/pyhull-1.3.8.tar.gz#md5=f8175f0ecb4b85fb26123481019d9f7c
Processing pyhull-1.3.8.tar.gz
Writing /tmp/easy_install-LIekCW/pyhull-1.3.8/setup.cfg
Running pyhull-1.3.8/setup.py -q bdist_egg --dist-dir /tmp/easy_install-LIekCW/pyhull-1.3.8/egg-dist-tmp-nsVEGi
warning: no files found matching '_.c'
no previously-included directories found matching '_*/tests'
error: Setup script exited with error: SandboxViolation: os.open('/tmp/tmpZfTvDd/jrTBn3', 2818, 384) {}
The package setup script has attempted to modify files on your system
that are not within the EasyInstall build area, and has been aborted.
This package cannot be safely installed by EasyInstall, and may not
support alternate installation locations even if you run its setup
script by hand. Please inform the package's author and the EasyInstall
maintainers to find out if a fix or workaround is available.
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New tools I will need for further developments
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Minor changes
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RMSD Molecule Matcher
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[] | 2013-06-09T09:42:53
| 2014-07-04T02:48:05
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2013-06-09T15:15:06Z
|
CONTRIBUTOR
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Match molecules with arbitrary atom order and check whether two molecules are
equal by RMSD
|
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Methane Bug Fixed
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[] | 2013-06-10T01:42:35
| 2014-07-04T02:48:04
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2013-06-10T02:09:19Z
|
CONTRIBUTOR
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The index error for methane is fixed.
MoleculeMatcher is fine for complex molecule, I will add these molecules to the unittest.
Meanwhile, I am thinking a better solution for simple molecules.
|
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| 30
|
Isomorphism Molecule Matcher
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[] | 2013-06-10T12:27:46
| 2014-06-14T19:37:54
|
2013-06-10T12:34:15Z
|
CONTRIBUTOR
|
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1) Add a new IsomorphismMolAtomMapper that calculates the RMSD of all the possible graph isomorphsim mapping and match the atoms using the one with smallest RMSD. The isomorphisms is enumerated by OpenBabel library.
2) Add 21 molecule for unittest
3) Add unit test for the group_molecules(), to_dict() and from_dict() function
|
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MDExOlB1bGxSZXF1ZXN0NjMxMjk4Mg==
| 31
|
changes made to "substitute" function
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[] | 2013-06-13T21:57:14
| 2014-07-04T02:48:02
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2013-06-14T01:03:23Z
|
CONTRIBUTOR
|
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I've modified the "substitute" function in /pymatgen/core/structure.py to add functional group from either user-defined molecule object, or from database functional_groups.json.
Additional files functional_groups.py and functional_groups.json were also added under /pymatgen/core directory.
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MDExOlB1bGxSZXF1ZXN0NjQzOTMxNQ==
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Move code from pymatgen.io.abinitio to pseudo_dojo package (will become client of the pymatgen library)
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[] | 2013-06-20T09:41:00
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2013-06-20T10:13:14Z
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CONTRIBUTOR
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| 15,922,430
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MDExOlB1bGxSZXF1ZXN0NjUwMjI4NA==
| 33
|
Change of return ValueError to raise ValueError in substitutor
|
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[] | 2013-06-24T12:39:39
| 2014-07-04T02:48:00
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2013-06-24T12:42:45Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0NjYxMzc2NQ==
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|
Ordering of the entries in the phase diagrams with 3 entries
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[] | 2013-06-28T11:07:35
| 2014-07-04T02:47:58
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2013-06-28T11:13:52Z
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CONTRIBUTOR
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Added the possibility to order the phase diagram plot (I want this atom at the top corner, that one on the left corner and the last one on the right corner).
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MDExOlB1bGxSZXF1ZXN0Njk5NjY1OQ==
| 35
|
Minor changes in pymatgen.io.abinitio
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2013-07-17T21:00:19Z
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MDExOlB1bGxSZXF1ZXN0NzAxMjg5NQ==
| 36
|
Doc of vtk visualizer + compatibility for vtk v.5
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2013-07-18T14:13:39Z
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Bug Fix for test_molecule_matcher
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[] | 2013-07-18T17:57:15
| 2014-07-04T02:47:54
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2013-07-18T18:03:40Z
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CONTRIBUTOR
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Fixed the error "TypeError: test_fit_with_mapper() takes exactly 2 arguments (1 given)"
The is raised because the function is supposed to be a helper function, however it is also called directly by the unittest class. Just renamed the function to a name not starting with "test", the direct calling form unittest is avoided, and the error is fixed.
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MDExOlB1bGxSZXF1ZXN0NzAzMDk1OQ==
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OpenBabel Installation Instruction Update
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[] | 2013-07-19T00:27:27
| 2014-07-04T02:47:53
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2013-07-19T01:00:39Z
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CONTRIBUTOR
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Solved the OBAlign missing problem.
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Compatibility for vtk v.5 and colormap for the entries in the phase diagram
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[] | 2013-07-24T13:47:48
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2013-07-24T13:49:46Z
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Addition of pymatgen.io.zeoio
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"Hello Shyue, \n\nI updated the tests and fixed the issues related to testing. Can you please check it again.\n\nThanks,\nBharat\n",
"Hi Bharat, you need to issue a new pull request. \n\nRegards,\nShyue Ping\n\nOn Tuesday, August 6, 2013 at 4:12 PM, Bharat Medasani wrote:\n\n> Hello Shyue, \n> I updated the tests and fixed the issues related to testing. Can you please check it again.\n> Thanks,\n> Bharat \n> \n> —\n> Reply to this email directly or view it on GitHub (https://github.com/materialsproject/pymatgen/pull/40#issuecomment-22218912).\n",
"Shyue,\n\nNew pull request is failing with a message like \"A pull request already exists.\" \n\nBharat\n",
"hi Bharat, you need to commit the changes, push the changes to your repo, then resubmit a pull request. \n\nRegards,\nShyue Ping\n\nOn Tuesday, August 6, 2013 at 4:29 PM, Bharat Medasani wrote:\n\n> Shyue,\n> New pull request is failing with a message like \"A pull request already exists.\" \n> Bharat\n> \n> —\n> Reply to this email directly or view it on GitHub (https://github.com/materialsproject/pymatgen/pull/40#issuecomment-22219708).\n"
] | 2013-08-02T17:36:53
| 2014-07-04T02:47:50
|
2013-08-07T19:53:35Z
|
CONTRIBUTOR
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zeoio module adds classes and functions for interface with Zeo++ cython wrapper.
It has dependency on Zeo++.
Zeo++ code can be obtained using "svn checkout https://codeforge.lbl.gov/anonscm/zeo"
The cython wrapper is in trunk/cython_wrapper.
Thanks,
Bharat
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Interface to Zeo++ and GULP, and addition of defects subpackage in analysis
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[] | 2013-08-07T19:56:59
| 2014-07-02T09:32:27
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2013-08-07T20:37:08Z
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CONTRIBUTOR
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Shyue,
I addressed the issues related to previous pull request.
a) The tests are working.
b) Defects package is moved inside analysis.
I updated comments and tests for io.zeoio, command_line.gulp_caller and analysis.defects.point_defects
modules. defects.point_defects is still a work in progress. Some duplicate functionality is present. Unit tests are missing for some classes. Those classes are not used at present and may be deleted or reworked based on future use.
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Minor modifications in abinitio and (backward compatible) change in HighSymmKpath.get_kpath_plot
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| 2014-06-18T09:15:25
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2013-08-24T12:42:17Z
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added more functional groups
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[] | 2013-09-01T21:30:25
| 2014-07-04T02:47:44
|
2013-09-02T01:57:52Z
|
CONTRIBUTOR
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See the comments in units.py for a discussion about the main differences between the protocol implemented in Unit and ArrayWithUnit.
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| 18,869,962
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MDExOlB1bGxSZXF1ZXN0ODAyMzg2MQ==
| 45
|
Remove units_deprecated
|
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[] | 2013-09-02T15:23:12
| 2014-07-04T02:47:43
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2013-09-02T15:26:29Z
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MDU6SXNzdWUxOTEwOTM1NQ==
| 46
|
Some MPRester queries return "local variable 'doc' referenced before assignment"
|
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[
"Thanks for letting us know. We will fix the error message. But yes, this means the DOS is not available for that ID/. \n\nRegards,\nShyue Ping\n\nOn Friday, September 6, 2013 at 7:47 AM, cmgtam wrote:\n\n> Okay:\n> \n> > > > a.get_dos_by_material_id(\"mp-24972\")\n> \n> Strange error - does this mean there is no dos for that material ID?:\n> \n> > > > a.get_dos_by_material_id(\"mp-510408\")\n> > > > Traceback (most recent call last):\n> > > > File \"\", line 1, in \n> > > > File \"/home/tam/.local/lib/python2.7/site-packages/pymatgen/matproj/rest.py\", line 254, in get_dos_by_material_id\n> > > > data = self.get_data(material_id, prop=\"dos\")\n> > > > File \"/home/tam/.local/lib/python2.7/site-packages/pymatgen/matproj/rest.py\", line 146, in get_data\n> > > > raise MPRestError(str(ex))\n> > > > pymatgen.matproj.rest.MPRestError: local variable 'doc' referenced before assignment \n> \n> —\n> Reply to this email directly or view it on GitHub (https://github.com/materialsproject/pymatgen/issues/46).\n",
"This will be fixed in the next update to the Materials Project website.\n"
] | 2013-09-06T14:47:54
| 2013-09-06T17:08:37
|
2013-09-06T17:08:37Z
|
CONTRIBUTOR
|
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Okay:
> > > a.get_dos_by_material_id("mp-24972")
> > > <pymatgen.electronic_structure.dos.CompleteDos object at 0x15b74710>
Strange error - does this mean there is no dos for that material ID?:
> > > a.get_dos_by_material_id("mp-510408")
> > > Traceback (most recent call last):
> > > File "<stdin>", line 1, in <module>
> > > File "/home/tam/.local/lib/python2.7/site-packages/pymatgen/matproj/rest.py", line 254, in get_dos_by_material_id
> > > data = self.get_data(material_id, prop="dos")
> > > File "/home/tam/.local/lib/python2.7/site-packages/pymatgen/matproj/rest.py", line 146, in get_data
> > > raise MPRestError(str(ex))
> > > pymatgen.matproj.rest.MPRestError: local variable 'doc' referenced before assignment
|
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MDExOlB1bGxSZXF1ZXN0ODE4MDgwMQ==
| 47
|
Better treatment of spurious data in HighSymmKpath
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[] | 2013-09-09T15:12:28
| 2014-07-04T02:47:42
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2013-09-09T15:35:51Z
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CONTRIBUTOR
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|
Bug fix in the _spglib.c file shipped with pymatgen (see Yannick's mail)
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[] | 2013-09-10T15:32:50
| 2014-07-04T02:47:40
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2013-09-10T15:58:34Z
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MDU6SXNzdWUxOTQyMjI1MQ==
| 49
|
ionic radii labeled as pm when they are Angstroms?
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[] | 2013-09-12T23:47:59
| 2013-09-13T03:52:04
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2013-09-13T03:52:04Z
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CONTRIBUTOR
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myval
pymatgen.analysis.defects.point_defects.ValenceIonicRadiusEvaluator instance at 0x7841560
myval.radii
{'Mn': 0.785 pm, 'O': 1.26 pm, 'La': 1.172 pm}
I like working with Angstroms better anyway, but it was a little confusing.
VERSION
2.8.0
DATE
Sep 6 2013
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MDExOlB1bGxSZXF1ZXN0ODM1NTg0MA==
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Options for visualizer + options for phase diagrams + MSONabled PhaseDiagram + attributes for PDEntries
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[
"Thanks David, for the changes. However, this is an issue with some of the changes to the PD Plotter. The current PDPlotter supports 2, 3, and 4 component PDs. Does the ordering parameter work for all three types?\n"
] | 2013-09-16T15:49:57
| 2014-07-04T02:47:39
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2013-09-16T17:17:43Z
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Add support for pickle to FloatWithUnit and ArrayWithUnit (unit tests included)
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2013-09-17T15:40:34Z
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Hi Shyue, I've added support for pickle to FloatWithUnit and ArrayWithUnit. The new version works but there are some cases that are not taken into account. I'm still working on it. Bye
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Make unit test more flexible
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Add Support for Multiple Fields theory_directives
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"Pls send a nwchem input file that is supposed to be parsed properly. Nidhi, I am assigning this issue to you together with the parsing of COSMO files. Pls fix it and report back.\n"
] | 2013-09-21T00:33:39
| 2015-12-06T17:26:36
|
2015-12-06T17:26:36Z
|
CONTRIBUTOR
|
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Hi Shyue,
Currently, space is not allowed in the value of theory_directives. Because, NwInput use "theory_directives[theory][toks[0]] = toks[-1]" to parse the theory_directives in the NwInput.from_string().
For example, Lei uses "vectors input atomic". After NwInput.from_string() it will become "vectors atomic".
Luckily, "vector atomic" is also a correct grammar in NWChem, but if it is not what robust code should do.
Furthermore, it will completely fail for more complicated guess options.
This bug will break the NWChem custodian code.
Best regards,
Xiaohui
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new developments in abinito (big patch)
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[] | 2013-10-14T13:57:33
| 2014-07-04T02:47:34
|
2013-10-14T14:27:41Z
|
CONTRIBUTOR
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Hi Shyue,
I've been refactoring a lot of code in abinitio and I've added new features. Sorry for pushing such a big patch.
In the forthcoming pull requests, I will try to commit localized changes in order to facilitate the work of the project leader. Note that now abinitio requires two external packages: pyYAML and pydispatcher (https://pypi.python.org/pypi/PyDispatcher/2.0.1). The latter is a very handy and lightweight package I use for implementing the observer pattern via signals. I haven't added this package to the list of official dependencies of pymatgen but maybe it's worth considering its inclusion.
All the best,
Matteo
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unit tests
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[] | 2013-10-15T19:31:09
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2013-10-15T19:35:35Z
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Better integration with Abinit (YAML format available in my Abinit developmental version)
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[] | 2013-10-17T22:02:45
| 2014-07-04T02:47:27
|
2013-10-17T22:29:45Z
|
CONTRIBUTOR
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Hi Shyue,
I'm gradually moving to pymatgen the new workflows for Phonon calculations with Abinit.
Many of these new features will require Abinit 7.6 that is presently under development.
Note that now abinitio uses the configuration directory $HOME/.abinit/abipy to store important
configuration parameters. The unit tests in abinitio will create this directory the first time we run the test suite.
Sorry for this side effect, but I really need these configuration files to simplify the interface with the end-user.
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"Hi Matteo, \n\nMay I know how is the behavior of iround different from the behavior of python’s round? I think python’s round already gives the behavior you want. \n\nShyue Ping\n\nOn Monday, October 28, 2013 at 0:31, gmatteo wrote:\n\n> You can merge this Pull Request by running\n> git pull https://github.com/gmatteo/pymatgen master\n> Or view, comment on, or merge it at:\n> https://github.com/materialsproject/pymatgen/pull/57\n> Commit Summary\n> Preliminary support for automatic restart.\n> Restart for HaydockBseTask.\n> Add auto_restart flag to AbinitFlow and new node status S_LOCKED\n> Merge remote-tracking branch 'mpmaster/master'\n> Chage g0w0_flow so that we can pass multiple inputs for SIGMA.\n> Add possibilty to select the autoparal configurations with a Mongodb-like syntax\n> Ignore ImportError in boltztrap.py while importing matplotlib (it's not a mandatory requirements of pymatgen)\n> Merge remote-tracking branch 'mpmaster/master'\n> Make EventsParser more robust (sanitize text fields, catch errors ...)\n> Test whether abinitio objects can be encoded/decoded with pickle.\n> Fix bug in the setter methods uses for the TaskManager.\n> Force scheduler shutdown if len(errors) > NUM\n> Make PseudoParser more robust (don't stop if file format is wrong but the error is not critical!)\n> Fix unit tests for Workflows\n> Merge remote-tracking branch 'mpmaster/master'\n> Cleanup abinitio docstrings\n> Typo in latex equation.\n> \n> File Changes\n> M pymatgen/core/design_patterns.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-0) (16) \n> M pymatgen/electronic_structure/boltztrap.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-1) (6) \n> M pymatgen/io/abinitio/abiinspect.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-2) (40) \n> M pymatgen/io/abinitio/abiobjects.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-3) (50) \n> M pymatgen/io/abinitio/calculations.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-4) (12) \n> M pymatgen/io/abinitio/events.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-5) (183) \n> M pymatgen/io/abinitio/flows.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-6) (286) \n> M pymatgen/io/abinitio/launcher.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-7) (146) \n> M pymatgen/io/abinitio/netcdf.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-8) (9) \n> M pymatgen/io/abinitio/pseudos.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-9) (141) \n> M pymatgen/io/abinitio/strategies.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-10) (83) \n> M pymatgen/io/abinitio/tasks.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-11) (436) \n> M pymatgen/io/abinitio/tests/test_abiobjects.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-12) (52) \n> M pymatgen/io/abinitio/tests/test_pseudos.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-13) (10) \n> M pymatgen/io/abinitio/tests/test_tasks.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-14) (4) \n> A pymatgen/io/abinitio/tests/test_utils.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-15) (39) \n> M pymatgen/io/abinitio/tests/test_workflow.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-16) (15) \n> M pymatgen/io/abinitio/utils.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-17) (219) \n> M pymatgen/io/abinitio/workflows.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-18) (143) \n> M pymatgen/io/abinitio/wrappers.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-19) (25) \n> M pymatgen/util/num_utils.py (https://github.com/materialsproject/pymatgen/pull/57/files#diff-20) (14) \n> \n> Patch Links:\n> https://github.com/materialsproject/pymatgen/pull/57.patch\n> https://github.com/materialsproject/pymatgen/pull/57.diff\n",
"Hi Shyue, \n\nthe main difference is that iround returns an int whereas round returns a float:\n\nIn [7]: round(1.4), iround(1.4)\nOut[7]: (1.0, 1)\n\nI use iround when I want an int to select a slice of an an array or when I have to perform some computation with integers.\n",
"I see. But isn’t the code simply int(round(x))? I am wondering why the need for the -0.5 etc. logic. \n\nShyue Ping\n\nOn Monday, October 28, 2013 at 0:54, gmatteo wrote:\n\n> Hi Shyue, \n> the main difference is that iround returns an int whereas round returns a float:\n> In [7]: round(1.4), iround(1.4)\n> Out[7]: (1.0, 1) \n> I use iround when I want an int to select a slice of an an array or when I have to perform some computation with integers.\n> \n> —\n> Reply to this email directly or view it on GitHub (https://github.com/materialsproject/pymatgen/pull/57#issuecomment-27172992).\n",
"Ok, I've removed iround in my last revision. \n"
] | 2013-10-27T16:31:51
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Support for PAW setups in XML format
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[] | 2013-11-25T17:48:53
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2013-11-25T18:35:27Z
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MDExOlB1bGxSZXF1ZXN0MTA1NDA2NDk=
| 62
|
Fix for GulpCaller unit test #3
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[] | 2013-12-05T03:01:50
| 2014-07-04T02:47:15
|
2013-12-05T03:07:46Z
|
CONTRIBUTOR
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Hello Shyue,
I am including the fix for failing test #3.
|
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MDExOlB1bGxSZXF1ZXN0MTA2NTIyNTI=
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Minor changes in abinitio
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[] | 2013-12-09T17:09:00
| 2014-06-18T14:58:56
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2013-12-09T20:44:32Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MTA3NzcyNjA=
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GulpCaller updated
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[] | 2013-12-12T18:29:46
| 2014-07-04T02:47:11
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2013-12-12T18:30:55Z
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CONTRIBUTOR
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BuckinghamPotLewis & BuckinghamPotBush merged into BuckinghamPotential
Camel case for Tersoff_pot class.
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Pull the new pmg
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[] | 2013-12-27T22:03:54
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2013-12-27T22:36:50Z
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NONE
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Issue with symmetryfinder
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[] | 2014-01-15T01:18:19
| 2014-01-15T22:40:15
|
2014-01-15T22:40:15Z
|
CONTRIBUTOR
|
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When trying to get the unit cell from symmetry.finder.SymmetryFinder for the structure with mpid "mp-25145", I am getting error.
Code:
struct = mp.get_structure_by_material_id("mp-25145")
uc = SymmetryFinder(struct).get_conventional_standard_structure()
## Error:
ValueError Traceback (most recent call last)
<ipython-input-11-fb42d30a7204> in <module>()
7 continue
8
----> 9 uc = SymmetryFinder(struct).get_conventional_standard_structure()
/home/mbkumar/lbnl/pymatgen/pymatgen/symmetry/finder.pyc in get_conventional_standard_structure(self)
683 for c in range(len(sorted_dic)):
684 transf[c][sorted_dic[c]['orig_index']] = 1
--> 685 latt = Lattice(new_matrix)
686
687 elif latt_type == "triclinic":
/home/mbkumar/lbnl/pymatgen/pymatgen/core/lattice.pyc in **init**(self, matrix)
52 lattice vectors [10,0,0], [20,10,0] and [0,0,30].
53 """
---> 54 m = np.array(matrix, dtype=np.float64).reshape((3, 3))
55 lengths = np.sqrt(np.sum(m *\* 2, axis=1))
56 angles = np.zeros(3)
ValueError: total size of new array must be unchanged
|
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| 25,778,002
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MDExOlB1bGxSZXF1ZXN0MTE2MDM3OTM=
| 67
|
Minor bug fixes in defects code
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[] | 2014-01-17T00:14:52
| 2014-07-04T02:47:09
|
2014-01-17T00:26:59Z
|
CONTRIBUTOR
|
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Replaced site.species_string with site.specie.symbol .
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| 26,130,656
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MDExOlB1bGxSZXF1ZXN0MTE3ODA0MDc=
| 68
|
Version of abinitio compatible with Abinit 7.6.1
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[] | 2014-01-22T22:57:16
| 2014-07-04T02:47:07
|
2014-01-22T23:54:27Z
|
CONTRIBUTOR
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| 27,074,157
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MDExOlB1bGxSZXF1ZXN0MTIyODExOTk=
| 69
|
Takes care of multiple oxidation states for an element in a structure. Also coordination number is used as input to ionic radius calculation
|
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[] | 2014-02-06T19:00:36
| 2014-07-04T02:47:06
|
2014-02-06T23:14:32Z
|
CONTRIBUTOR
|
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When generating the voronoi nodes, a single ionic radii was used for each species in the structure.
Now, when multiple oxidation states of a single species are present in the structure, different ionic radii for different oxidation states are used.
Also, coordination number is used as input to compute the ionic radius. The file ionic_radii.json contains Shannon's ionic radii database for most of the elements. Data is missing for lanthanide, actinides and for 7th row elements.
Bharat
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Deprecated test removed and More ionic radii added
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[] | 2014-02-07T01:21:47
| 2014-07-04T02:47:05
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2014-02-07T02:09:11Z
|
CONTRIBUTOR
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GULP "wrong-keyword" test removed because the checks for GULP keyword line are no more performed.
Missing ionic radii for lanthanides and actinides and other elements added.
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Replaced MPRest structure with local structure
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2014-02-07T04:59:14Z
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Nearest oxidation station is used in determining ionic radii
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2014-02-11T21:39:25Z
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CONTRIBUTOR
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In case the oxidation state for a particular element is not present in the database, nearest oxidation state is used
in determining the ionic radii.
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JSON question
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[
"Hi there,\n\nI apologize but there was a small bug in the previous release which broke the tasks API. We have just fixed it and released a bug fix. It should work now. \n\nIn any case, if your goal is only to get the relaxed geometry, you just need to query for the structure of a material, which by default is the relaxed structure. There is no need to look for the specific task. The task provides specific calculation details.\n\nAlso, if you are computing phonons, you might want to use the MP relaxed structure, and perhaps run yet another relaxation with tighter convergence criteria before calculating phonons. Phonons tend to be a bit more sensitive to convergence issues.\n",
"@shyuep thanks for the reply.\n\nIndeed, now the link: https://www.materialsproject.org/rest/v1/tasks/mp-602261?API_KEY=MYAPIKEY works :+1: \n\nHowever it doesn't print incar/kpoints/potcar\n\nIf I try https://www.materialsproject.org/rest/v1/tasks/mp-602261/incar?API_KEY=MYAPIKEY I get:\n\n```\n{\"valid_response\": false, \"error\": \"invalid literal for int() with base 10: 'mp-602261'\"}\n```\n\nCIF data in the REST reply is the same as from **Final structure : 10 Sites** on the web (https://materialsproject.org/tasks/mp-602261), that's good, I can use it to generate POSCAR.\n\nthanks for the fast replies and help,\nAlexandr.\n"
] | 2014-02-16T19:28:45
| 2014-03-12T22:47:44
|
2014-03-12T22:47:44Z
|
CONTRIBUTOR
|
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Hi,
I'm trying to get `tasks` JSON reply.
First I go to https://www.materialsproject.org/rest/v1/materials/Fe2O3/vasp?API_KEY=MYAPIKEY
There I get (added newlines for clarity)
``` json
{"created_at": "2014-02-16T09:34:09.995518", "valid_response": true, "version": {"pymatgen": "2.9.1", "db": "2014.02.13", "rest": "1.0"},
"response": [{"energy": -67.16532048, "unit_cell_formula": {"Fe": 4.0, "O": 6.0},
"hubbards": {"Fe": 5.3, "O": 0.0},
"task_ids": ["mp-602261", "mp-714977", "mp-24972"]...
```
Then I try to go to: https://www.materialsproject.org/rest/v1/tasks/mp-714977?API_KEY=MYAPIKEY
I get "Page Not Found".
My ultimate goal is to get VASP incar/poscar/kpoints/potcar to run phonon calculation on top of the relaxed geometry of a material.
Any help will be appreciated,
thanks,
Alexandr.
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Modified the BVAnalyzer in order to be able to assign valences for unord...
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[
"David,\n\nI merged most of these changes. But I think add_oxidation state by site fraction needs to be fixed. The oxidation states seem to be assigned in order of the Composition dict. But the dict has no pre-defined order. That can lead to extremely unpredictablee behavior. For example, you may specify [2, 3] for a site that contains {Mn:0.5, Co:0.5}. Some dats, the Co may return as the first element and other days, Mn may be returned as the first element. Your valence assignment will then switch between Mn2+/Co3+ and Co2+/Mn3+.\n\nShyue Ping\n\nOn February 19, 2014 at 5:01:51 AM, davidwaroquiers (notifications@github.com) wrote:\n\n...ered structures (experimental)\n\nYou can merge this Pull Request by running\n\n git pull https://github.com/davidwaroquiers/pymatgen master\nOr view, comment on, or merge it at:\n\n https://github.com/materialsproject/pymatgen/pull/74\n\nCommit Summary\n\nModified the BVAnalyzer in order to be able to assign valences for unordered structures (experimental)\nFile Changes\n\nM pymatgen/analysis/bond_valence.py (336)\nM pymatgen/core/structure.py (27)\nPatch Links:\n\nhttps://github.com/materialsproject/pymatgen/pull/74.patch\nhttps://github.com/materialsproject/pymatgen/pull/74.diff\n—\nReply to this email directly or view it on GitHub.\n",
"Ok,\n\nThx a lot, I'll fix that.\n\nDavid\n\nOn Thu, Feb 20, 2014 at 4:11 PM, Shyue Ping Ong notifications@github.comwrote:\n\n> David,\n> \n> I merged most of these changes. But I think add_oxidation state by site\n> fraction needs to be fixed. The oxidation states seem to be assigned in\n> order of the Composition dict. But the dict has no pre-defined order. That\n> can lead to extremely unpredictablee behavior. For example, you may specify\n> [2, 3] for a site that contains {Mn:0.5, Co:0.5}. Some dats, the Co may\n> return as the first element and other days, Mn may be returned as the first\n> element. Your valence assignment will then switch between Mn2+/Co3+ and\n> Co2+/Mn3+.\n> \n> Shyue Ping\n> \n> On February 19, 2014 at 5:01:51 AM, davidwaroquiers (\n> notifications@github.com) wrote:\n> \n> ...ered structures (experimental)\n> \n> You can merge this Pull Request by running\n> \n> git pull https://github.com/davidwaroquiers/pymatgen master\n> Or view, comment on, or merge it at:\n> \n> https://github.com/materialsproject/pymatgen/pull/74\n> \n> Commit Summary\n> \n> Modified the BVAnalyzer in order to be able to assign valences for\n> unordered structures (experimental)\n> File Changes\n> \n> M pymatgen/analysis/bond_valence.py (336)\n> M pymatgen/core/structure.py (27)\n> Patch Links:\n> \n> https://github.com/materialsproject/pymatgen/pull/74.patch\n> \n> ## https://github.com/materialsproject/pymatgen/pull/74.diff\n> \n> Reply to this email directly or view it on GitHub.\n> \n> ## \n> \n> Reply to this email directly or view it on GitHubhttps://github.com/materialsproject/pymatgen/pull/74#issuecomment-35630800\n> .\n"
] | 2014-02-19T13:01:50
| 2014-06-27T11:40:14
|
2014-02-20T16:42:57Z
|
CONTRIBUTOR
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...ered structures (experimental)
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| 75
|
Voronoi face centers are also included in the interstitial sites
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[] | 2014-02-23T00:33:06
| 2014-07-04T02:46:54
|
2014-02-23T05:12:39Z
|
CONTRIBUTOR
|
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Interstitial site class returns either voronoi nodes or voronoi face centers as the defect sites.
Latest Zeo++ required.
|
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BVAnalyzer for unordered structures taking into account arbitrary order of the composition of a site
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[] | 2014-02-28T16:05:51
| 2014-07-04T02:46:53
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2014-02-28T16:26:50Z
|
CONTRIBUTOR
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Modified BVAnalyzer for unordered structures in order to take into account possible errors due to the arbitrary ordering of the composition of a given site.
The route finally taken was to add a method to Composition (not change Composition) that returns an ordered list of tuples (element/species, occupation). The elements on the site are ordered in increasing Z and then for same Z, in increasing fractional occupation.
Added the add_oxidation_states_by_site_fraction in Structure
Also added the possibility to exclude a given specie to be used in the BVAnalyzer (for example, if we do not want O- at all)
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Zeo++ high accuracy option enabled
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[
"Hi Bharat,\n\nThanks for the additions. Can you modify your code to use monty.tempfile.ScratchDir for the portions that uses temp dirs and files. That is a much cleaner way of doing this. The usage is simply:\n\n``` python\nwith ScratchDir(...):\n do something\n```\n",
"Sure.\n\nOn Thu, Mar 13, 2014 at 4:02 PM, Shyue Ping Ong notifications@github.comwrote:\n\n> Hi Bharat,\n> \n> Thanks for the additions. Can you modify your code to use\n> monty.tempfile.ScratchDir for the portions that uses temp dirs and files.\n> That is a much cleaner way of doing this. The usage is simply:\n> \n> with ScratchDir(...):\n> do something\n> \n> ## \n> \n> Reply to this email directly or view it on GitHubhttps://github.com/materialsproject/pymatgen/pull/77#issuecomment-37597724\n> .\n\n## \n\nBharat\nPostdoc\nLawrence Berkeley Lab\n510-984-8628\n",
"Hello Shyue,\n\nI have one question.\nWith tempfile module, I don't have to specify where to create the temporary\ndirectory.\nBut with monty.tempfile.ScratchDir, I need to specify the path to scratch\ndirectory.\nWhat is the best way to specify the rootpath argument to ScrathDir that is\nos or system agnostic?\n\nThanks,\nBharat\n\nOn Thu, Mar 13, 2014 at 4:09 PM, M Bharat Kumar mbkumar@gmail.com wrote:\n\n> Sure.\n> \n> On Thu, Mar 13, 2014 at 4:02 PM, Shyue Ping Ong notifications@github.comwrote:\n> \n> > Hi Bharat,\n> > \n> > Thanks for the additions. Can you modify your code to use\n> > monty.tempfile.ScratchDir for the portions that uses temp dirs and files.\n> > That is a much cleaner way of doing this. The usage is simply:\n> > \n> > with ScratchDir(...):\n> > do something\n> > \n> > ## \n> > \n> > Reply to this email directly or view it on GitHubhttps://github.com/materialsproject/pymatgen/pull/77#issuecomment-37597724\n> > .\n> \n> ## \n> \n> Bharat\n> Postdoc\n> Lawrence Berkeley Lab\n> 510-984-8628\n\n## \n\nBharat\nPostdoc\nLawrence Berkeley Lab\n510-984-8628\n",
"U can just use current dir. I.e. \".\". The tempdor created is deleted at the\nend anyway\n On Mar 13, 2014 4:22 PM, \"Bharat Medasani\" notifications@github.com\nwrote:\n\n> Hello Shyue,\n> \n> I have one question.\n> With tempfile module, I don't have to specify where to create the temporary\n> directory.\n> But with monty.tempfile.ScratchDir, I need to specify the path to scratch\n> directory.\n> What is the best way to specify the rootpath argument to ScrathDir that is\n> os or system agnostic?\n> \n> Thanks,\n> Bharat\n> \n> On Thu, Mar 13, 2014 at 4:09 PM, M Bharat Kumar mbkumar@gmail.com wrote:\n> \n> > Sure.\n> > \n> > On Thu, Mar 13, 2014 at 4:02 PM, Shyue Ping Ong <\n> > notifications@github.com>wrote:\n> > \n> > > Hi Bharat,\n> > > \n> > > Thanks for the additions. Can you modify your code to use\n> > > monty.tempfile.ScratchDir for the portions that uses temp dirs and\n> > > files.\n> > > That is a much cleaner way of doing this. The usage is simply:\n> > > \n> > > with ScratchDir(...):\n> > > do something\n> > > \n> > > ## \n> > > \n> > > Reply to this email directly or view it on GitHub<\n> > > https://github.com/materialsproject/pymatgen/pull/77#issuecomment-37597724\n> > > \n> > > .\n> > \n> > ## \n> > \n> > Bharat\n> > Postdoc\n> > Lawrence Berkeley Lab\n> > 510-984-8628\n> \n> ## \n> \n> Bharat\n> Postdoc\n> Lawrence Berkeley Lab\n> 510-984-8628\n> \n> ## \n> \n> Reply to this email directly or view it on GitHubhttps://github.com/materialsproject/pymatgen/pull/77#issuecomment-37599352\n> .\n",
"Done.\n\nOn Thu, Mar 13, 2014 at 4:49 PM, Shyue Ping Ong notifications@github.comwrote:\n\n> U can just use current dir. I.e. \".\". The tempdor created is deleted at the\n> end anyway\n> On Mar 13, 2014 4:22 PM, \"Bharat Medasani\" notifications@github.com\n> wrote:\n> \n> > Hello Shyue,\n> > \n> > I have one question.\n> > With tempfile module, I don't have to specify where to create the\n> > temporary\n> > directory.\n> > But with monty.tempfile.ScratchDir, I need to specify the path to scratch\n> > directory.\n> > What is the best way to specify the rootpath argument to ScrathDir that\n> > is\n> > os or system agnostic?\n> > \n> > Thanks,\n> > Bharat\n> > \n> > On Thu, Mar 13, 2014 at 4:09 PM, M Bharat Kumar mbkumar@gmail.com\n> > wrote:\n> > \n> > > Sure.\n> > > \n> > > On Thu, Mar 13, 2014 at 4:02 PM, Shyue Ping Ong <\n> > > notifications@github.com>wrote:\n> > > \n> > > > Hi Bharat,\n> > > > \n> > > > Thanks for the additions. Can you modify your code to use\n> > > > monty.tempfile.ScratchDir for the portions that uses temp dirs and\n> > > > files.\n> > > > That is a much cleaner way of doing this. The usage is simply:\n> > > > \n> > > > with ScratchDir(...):\n> > > > do something\n> > > > \n> > > > ## \n> > > > \n> > > > Reply to this email directly or view it on GitHub<\n> > \n> > https://github.com/materialsproject/pymatgen/pull/77#issuecomment-37597724\n> > \n> > > > .\n> > > \n> > > ## \n> > > \n> > > Bharat\n> > > Postdoc\n> > > Lawrence Berkeley Lab\n> > > 510-984-8628\n> > \n> > ## \n> > \n> > Bharat\n> > Postdoc\n> > Lawrence Berkeley Lab\n> > 510-984-8628\n> > \n> > ## \n> > \n> > Reply to this email directly or view it on GitHub<\n> > https://github.com/materialsproject/pymatgen/pull/77#issuecomment-37599352\n> > \n> > .\n> \n> ## \n> \n> Reply to this email directly or view it on GitHubhttps://github.com/materialsproject/pymatgen/pull/77#issuecomment-37601287\n> .\n\n## \n\nBharat\nPostdoc\nLawrence Berkeley Lab\n510-984-8628\n",
"Thanks!\n"
] | 2014-03-13T22:56:08
| 2014-07-02T02:21:06
|
2014-03-14T00:31:27Z
|
CONTRIBUTOR
|
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The interstitial class can use the high accuracy option of Zeo++
by using an additional keyword accuracy="High" when initializing.
|
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MDU6SXNzdWUyOTYwNzk3NA==
| 78
|
EnumerateStructureTransformation misses some enumerations
|
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[] | null |
[] | 2014-03-17T23:18:42
| 2014-03-18T20:02:12
|
2014-03-18T20:02:12Z
|
CONTRIBUTOR
|
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When lattice periodicity of ordered sites doesn't match the periodicity of disordered sites (but when they have the same spacegroup), the wrong periodicity is used by spglib, missing some valid enumerations.
Example structure that should have 2 distinct orderings:
```
#\#CIF1.1
##########################################################################
# Crystallographic Information Format file
# Produced by PyCifRW module
#
# This is a CIF file. CIF has been adopted by the International
# Union of Crystallography as the standard for data archiving and
# transmission.
#
# For information on this file format, follow the CIF links at
# http://www.iucr.org
##########################################################################
data_He(Li3H)3
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 5.0
_cell_length_b 5.0
_cell_length_c 5.0
_cell_angle_alpha 90.0
_cell_angle_beta 90.0
_cell_angle_gamma 90.0
_chemical_name_systematic 'Generated by pymatgen'
_symmetry_Int_Tables_number 1
_chemical_formula_structural He(Li3H)3
_chemical_formula_sum 'He1 Li9 H3'
_cell_volume 125.0
_cell_formula_units_Z 1
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_attached_hydrogens
_atom_site_B_iso_or_equiv
_atom_site_occupancy
Li Li1 1 0.250000 0.250000 0.250000 0 . 1.0
Li Li2 1 0.250000 0.750000 0.750000 0 . 1.0
Li Li3 1 0.750000 0.250000 0.750000 0 . 1.0
Li Li4 1 0.750000 0.750000 0.250000 0 . 1.0
Li Li5 1 0.750000 0.750000 0.750000 0 . 1.0
Li Li6 1 0.750000 0.250000 0.250000 0 . 1.0
Li Li7 1 0.250000 0.750000 0.250000 0 . 1.0
Li Li8 1 0.250000 0.250000 0.750000 0 . 1.0
Li Li9 1 0.500000 0.500000 0.500000 0 . 1.0
H H10 1 0.000000 0.000000 0.000000 0 . 0.75
He He11 1 0.000000 0.000000 0.000000 0 . 0.25
H H12 1 0.000000 0.500000 0.500000 0 . 0.75
He He13 1 0.000000 0.500000 0.500000 0 . 0.25
H H14 1 0.500000 0.000000 0.500000 0 . 0.75
He He15 1 0.500000 0.000000 0.500000 0 . 0.25
H H16 1 0.500000 0.500000 0.000000 0 . 0.75
He He17 1 0.500000 0.500000 0.000000 0 . 0.25
```
|
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| 30,707,705
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MDU6SXNzdWUzMDcwNzcwNQ==
| 79
|
VASP KPOINTS file with Line_mode
|
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[
"Hi Germain,\n\nThanks for reporting the issue. I have applied your fix and contributions.\n\nAs for the line-mode, I know that VASP uses Line-mode. But because of the way the Enum design pattern works, I can't use \"-\" in the class. In any case, VASP does not actually look for \"Line-mode\". They only look at the first letter of that line.\n\nRegarding having pymatgen dev and stable versions on the same machine, one possibility is to use virtualenv. Another way is to simply fork the repo to your own Github repo and you can always work off your own fork of pymatgen. When you have some contributions that you would like to share with the community, you can submit a pull request and I can add them.\n",
"hi, i am new to vasp, and ran into this article \nhttp://gvallver.perso.univ-pau.fr/?p=587\nit is very helpful for me, and i applied to a ge-bulk system as an example to learn band structure (L-G-X)\nthere is an error when i get to the point of get_band_structure, \nand i narrowed down the error in pymatgen/electronic_structure/bandstructure.py\nclass BandStructureSymmLine(BandStructure, MSONable):\n......\nself._branches.append({\"start_index\": b[0], \"end_index\": b[-1],\n \"name\": (self._kpoints[b[0]].label + \"-\" +\n self._kpoints[b[-1]].label)})\n.....\n\nand, here for my system, i have tried to None+\"-\"\n(a NoneType and a string)\n----error msg--------------------------\npymatgen/electronic_structure/bandstructure.py\", line 741, in **init**\n \"name\": (self._kpoints[b[0]].label + \"-\" +\n\n## TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'\n\nso, i changed to \nself._branches.append({\"start_index\": b[0], \"end_index\": b[-1],\n \"name\": (str(self._kpoints[b[0]].label) + \"-\" +\n str(self._kpoints[b[-1]].label))})\nand it worked. \n is this a bug?\n",
"Hi,\n\nThanks for your report. Could you send me your vasp files? Send them to me to geoffroy.hautier@uclouvain.be . We'll take it from there.\n",
"I have looked into the files you sent.\nYour KPOINTS file does not have label for each kpoint. this is mandatory for a band structure along symmetry lines.\n\nIt is:\nK-points L-G-X\n25\nLine-mode\nreciprocal\n0.5 0.5 0.5\n0 0 0\n\n0 0 0\n0.5 0.5 0\n\nWhile it should be:\n\nK-points L-G-X\n25\nLine-mode\nreciprocal\n0.5 0.5 0.5 L\n0 0 0 G\n\n0 0 0 G\n0.5 0.5 0 X\n\nI have applied a patch so a clearer exception is now raised when this happens.\n\nGeoffroy\n"
] | 2014-04-02T17:24:55
| 2018-01-11T14:43:54
|
2014-04-30T17:45:34Z
|
CONTRIBUTOR
|
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Hi !
I am new in pymatgen and I try to use it to produce KPOINTS file for band structure calculations with VASP. I use HighSymmKpath and Kpoints classes to produces the kpoints file.
Here is the source code
``` python
import pymatgen as mg
from pymatgen.symmetry.bandstructure import HighSymmKpath
from pymatgen.io.vaspio.vasp_input import Kpoints
struct = mg.read_structure("POSCAR.vasp")
# 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")
```
And this is the KPOINTS file produced
```
band diagram for monoclinic cell, unique axes a
100
Line_mode
0.0 0.0 0.0 ! \Gamma
0.0 0.0 0.5 ! Y
0.0 0.491941 0.525184 ! H
0.0 0.5 0.5 ! C
0.5 0.5 0.5 ! E
0.5 0.508059 0.474816 ! M_1
0.5 0.5 0.0 ! A
0.0 0.5 0.0 ! X
0.0 0.508059 0.474816 ! H_1
0.5 0.491941 0.525184 ! M
0.5 0.0 0.5 ! D
0.5 0.0 0.0 ! Z
0.0 0.0 0.5 ! Y
0.5 0.0 0.5 ! D
```
After the line `Line_mode` in the KPOINTS file, the `coord_type` should be written.
Looking at
http://pymatgen.org/_modules/pymatgen/io/vaspio/vasp_input.html#Kpoints
in the `__str__` method there is these lines
``` python
style = self.style.lower()[0]
if style == "Line-mode":
lines.append(self.coord_type)
```
but line_mode is not written with an underscore as in the supported mode enum and I think this is the bug (or maybe the mistake for only one character ...)
``` python
supported_modes = Enum(("Gamma", "Monkhorst", "Automatic", "Line_mode",
"Cartesian", "Reciprocal"))
```
The following is maybe a request more than a bug. Using VASP, in Line_mode the KPOINTS file should be
```
band diagram for monoclinic cell, unique axes a
100
Line_mode
Reciprocal
0.0 0.0 0.0 ! \Gamma
0.0 0.0 0.5 ! Y
0.0 0.0 0.5 ! Y
0.0 0.491941 0.525184 ! H
0.0 0.491941 0.525184 ! H
0.0 0.5 0.5 ! C
0.0 0.5 0.5 ! C
0.5 0.5 0.5 ! E
0.5 0.5 0.5 ! E
0.5 0.508059 0.474816 ! M_1
0.5 0.508059 0.474816 ! M_1
0.5 0.5 0.0 ! A
0.5 0.5 0.0 ! A
0.0 0.5 0.0 ! X
0.0 0.5 0.0 ! X
0.0 0.508059 0.474816 ! H_1
0.5 0.491941 0.525184 ! M
0.5 0.0 0.5 ! D
0.5 0.0 0.5 ! D
0.5 0.0 0.0 ! Z
0.0 0.0 0.5 ! Y
0.5 0.0 0.5 ! D
```
I have ever talk about the line with "Reciprocal". Then each line of the reciprocal space is defined by 2 k-points separated by a blank line. Is there a way to obtain this directly from pymatgen without postprocessing the KPOITNS file ?
A solution migth be to give the kpath attribute of the HighSymmKpath to a Kpoints class constructor or directely the HighSymmKpath object. But the `__str__` method must be also slithly modified.
I cloned the git repository and did the few changes.
Here is a patch file created with `git diff > patch.txt`
www.pastebin.com/5n6aniLv
I am sorry but I am a beginner with git. I do not know how to make the development version and the stable version of pymatgen to cohabit in the same PC. Thus I did not test my changes ... If you prefer and explain I can commit and push somewhere ?
Thanks
|
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| 31,122,616
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MDExOlB1bGxSZXF1ZXN0MTQ1MzE0MjI=
| 80
|
Warn the user if CifParser raises KeyError
|
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[] | 2014-04-09T01:08:43
| 2014-07-04T02:46:50
|
2014-04-09T01:10:23Z
|
CONTRIBUTOR
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MDU6SXNzdWUzMTUzMjk3Mg==
| 81
|
test suite has 3 failures
|
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[] | null |
[
"Thanks for reporting this. There is a bug in the ewald module that we are trying to fix now. The tests in the current updated branch should pass for now.\n"
] | 2014-04-15T07:58:53
| 2014-09-18T13:40:20
|
2014-09-18T13:40:20Z
|
CONTRIBUTOR
|
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I get some failure in running the test on the main branch:
======================================================== FAILURES =========================================================
_______________________________________ EwaldElectrostaticModelTest.test_get_energy _______________________________________
self = <pymatgen.analysis.tests.test_energy_models.EwaldElectrostaticModelTest testMethod=test_get_energy>
> ```
> self.assertAlmostEqual(m.get_energy(s), 44.1070954178)
> ```
>
> E AssertionError: 661.64440945223498 != 44.1070954178 within 7 places
pymatgen/analysis/tests/test_energy_models.py:45: AssertionError
______________________________________________ EwaldSummationTest.test_init _______________________________________________
self = <pymatgen.analysis.tests.test_ewald.EwaldSummationTest testMethod=test_init>
> ```
> "Real space energy incorrect!")
> ```
>
> E AssertionError: Real space energy incorrect!
pymatgen/analysis/tests/test_ewald.py:22: AssertionError
self = <pymatgen.transformations.tests.test_standard_transformations.OrderDisorderedStructureTransformationTest testMethod=test_best_first>
> ```
> 'got incorrect energy')
> ```
>
> E AssertionError: got incorrect energy
pymatgen/transformations/tests/test_standard_transformations.py:341: AssertionError
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MDU6SXNzdWUzMTU1MTc4MQ==
| 82
|
get_conventional_standard in pymatgen.symmetry.finder.SymmetryFinder changes symmetry
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[
"@hautierg Can you fix this soon pls? This is really a major issue. There is no guarantee that the band structures are right if the symmetry is not preserved.\n",
"I assume the method is now pymatgen.symmetry.analyzer.SpacegroupAnalyzer? I can't reproduce this. symprec is set to 0.1, and SpacegroupAnalyzer correctly finds C2, and the get_conventional_standard method returns a structure with C2 as well. Why is this issue still here?\n",
"This should not be open anymore. I am closing it.\n"
] | 2014-04-15T13:14:34
| 2015-08-19T08:13:24
|
2015-08-19T08:13:24Z
|
MEMBER
|
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Using https://www.materialsproject.org/materials/mp–715572/, when converting the primitive cell to conventional standard, the space group changes from C2 to P1. Given that this is just a basis transformation, this really should be the case.
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| 83
|
Symmetry flag
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[] | 2014-04-16T05:32:56
| 2014-07-04T02:46:48
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2014-04-16T05:36:36Z
|
CONTRIBUTOR
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Symmetry flag to choose either symmetry distinct sites or all the sites
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Behavior of read_structure is inconsistent
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[
"Fixed.\n"
] | 2014-04-30T14:13:04
| 2014-04-30T17:30:26
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2014-04-30T17:30:26Z
|
CONTRIBUTOR
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As it stands, only .cif files have the primitive cell taken after structure import. It appears as though they also have their sites sorted. To achieve consistency across structure file types, I suggest we add primitive_cell and sort_structure tags to the read_structure method. The CifParser may also need this flag added.
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weird interaction between scikit-learn and pymatgen units
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[
"I didn't get any warning running this.\n\nOn Wed, Apr 30, 2014 at 4:08 PM, Anubhav Jain notifications@github.comwrote:\n\n> try the following, you'll get many DeprecationWarnings\n> \n> from sklearn import linear_model\n> from pymatgen import Composition\n> \n> clf = linear_model.LinearRegression()\n> \n> print Composition(\"LiFePO4\")\n> \n> —\n> Reply to this email directly or view it on GitHubhttps://github.com/materialsproject/pymatgen/issues/85\n> .\n",
"I get this in Python interactive shell. Not sure if it has to do with Python 2.7.2 vs 2.7.3+\n\nPython 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34) \n[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\n\n> > > from sklearn import linear_model \n> > > from pymatgen import Composition\n> > > print Composition(\"LiFePO4\") \n> > > /Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/core/units.py:328: DeprecationWarning: object.**init**() takes no parameters\n> > > super(FloatWithUnit, self).**init**(val)\n> > > /Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/core/units.py:328: DeprecationWarning: object.**init**() takes no parameters\n> > > super(FloatWithUnit, self).**init**(val)\n> > > /Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/core/units.py:328: DeprecationWarning: object.**init**() takes no parameters\n> > > super(FloatWithUnit, self).**init**(val)\n> > > /Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/core/units.py:328: DeprecationWarning: object.**init**() takes no parameters\n> > > super(FloatWithUnit, self).**init**(val)\n> > > /Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/core/units.py:328: DeprecationWarning: object.**init**() takes no parameters\n> > > super(FloatWithUnit, self).**init**(val)\n> > > /Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/core/units.py:328: DeprecationWarning: object.**init**() takes no parameters\n> > > super(FloatWithUnit, self).**init**(val)\n> > > /Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/core/units.py:328: DeprecationWarning: object.**init**() takes no parameters\n> > > super(FloatWithUnit, self).**init**(val)\n> > > /Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/core/units.py:328: DeprecationWarning: object.**init**() takes no parameters\n> > > super(FloatWithUnit, self).**init**(val)\n> > > P1 Fe1 O4 Li1\n"
] | 2014-04-30T23:08:50
| 2014-04-30T23:38:00
|
2014-04-30T23:38:00Z
|
MEMBER
|
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try the following, you'll get many DeprecationWarnings
from sklearn import linear_model
from pymatgen import Composition
clf = linear_model.LinearRegression()
print Composition("LiFePO4")
|
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| 86
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Band gap issue with static run
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[
"Thanks for reporting the issue. Do you have a proposed solution? How about instead of a strict cutoff like 1e-8, we look at the delta in occupation between bands?\n",
"I would try to get rid of the partial occupations. rerun wiht tetrahedra ?\n\n ----- Original Message ----- \n From: Shyue Ping Ong \n To: materialsproject/pymatgen \n Sent: Monday, May 05, 2014 5:48 PM\n Subject: Re: [pymatgen] Band gap issue with static run (#86)\n\n Thanks for reporting the issue. Do you have a proposed solution? How about instead of a strict cutoff like 1e-8, we look at the delta in occupation between bands?\n\n —\n Reply to this email directly or view it on GitHub.\n",
"How about using Ef or number of bands (to be occupied based on nelect). for\nexample, for spin calculation with nelect=10, there will be 10 bands with\nideal occupation of 1 and band 11 shall be empty for semiconductor. energy\ndifference between highest band 10 energy and lowest band 11 energy for all\nkpoints gives Eg.\n\nOn Mon, May 5, 2014 at 11:48 AM, Shyue Ping Ong notifications@github.comwrote:\n\n> Thanks for reporting the issue. Do you have a proposed solution? How about\n> instead of a strict cutoff like 1e-8, we look at the delta in occupation\n> between bands?\n> \n> —\n> Reply to this email directly or view it on GitHubhttps://github.com/materialsproject/pymatgen/issues/86#issuecomment-42202539\n> .\n",
"Sounds like a good strategy. Can you implement this in a separate branch and add a test based on the incorrectly parsed output file that you mentioned? Thanks.\n",
"ok I will test it.\n\nOn Mon, May 5, 2014 at 12:54 PM, Shyue Ping Ong notifications@github.comwrote:\n\n> Sounds like a good strategy. Can you implement this in a separate branch\n> and add a test based on the incorrectly parsed output file that you\n> mentioned? Thanks.\n> \n> —\n> Reply to this email directly or view it on GitHubhttps://github.com/materialsproject/pymatgen/issues/86#issuecomment-42209700\n> .\n",
"realize it is not right approach. Will have problem for metals.\n\nOn Mon, May 5, 2014 at 1:20 PM, Hong Zhu zhuhong1984sh@yahoo.com wrote:\n\n> ok I will test it.\n> \n> On Mon, May 5, 2014 at 12:54 PM, Shyue Ping Ong notifications@github.comwrote:\n> \n> > Sounds like a good strategy. Can you implement this in a separate branch\n> > and add a test based on the incorrectly parsed output file that you\n> > mentioned? Thanks.\n> > \n> > —\n> > Reply to this email directly or view it on GitHubhttps://github.com/materialsproject/pymatgen/issues/86#issuecomment-42209700\n> > .\n",
"Any update on this issue?\n"
] | 2014-05-05T15:46:16
| 2015-12-06T17:26:12
|
2015-12-06T17:26:12Z
|
NONE
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Some band gap output analyzed from static run is not correct.
This may be related to the definition of valence band maximum and conduction band minimum with occupation of "occu > 1e-8" in vasp_output.py
For example. In a static run. band gap occurs between band 96 and 97 for one calculation.
The occupation and energy of these two bands at different KPOINT is
band 97 # energy 5.34588712 # occ. 0.00024002
band 97 # energy 5.67445169 # occ. 0.00000000
band 97 # energy 5.49090544 # occ. 0.00000313
band 97 # energy 5.34589837 # occ. 0.00023995
band 97 # energy 5.67446456 # occ. 0.00000000
band 97 # energy 5.49091742 # occ. 0.00000313
band 96 # energy 4.34996188 # occ. 0.99980782
band 96 # energy 4.00965011 # occ. 1.00000000
band 96 # energy 3.78252682 # occ. 1.00000000
band 96 # energy 4.34993175 # occ. 0.99980798
band 96 # energy 4.00962333 # occ. 1.00000000
band 96 # energy 3.78250168 # occ. 1.00000000
The real band gap shall be 5.3459-4.3499 which is ~ 1eV
The band gap in analysis in database is 5.4909-5.3459 which is 0.145 eV. This is some energy difference in CB rather than a band gap.
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| 87
|
Incorrect Ag K wavelength in xrd.py
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[] | 2014-06-03T02:59:40
| 2014-06-03T03:00:47
|
2014-06-03T03:00:47Z
|
CONTRIBUTOR
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They are tens times larger than correct values.
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| 34,967,771
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MDExOlB1bGxSZXF1ZXN0MTY3MTM4NDk=
| 88
|
Add functionality in Procar class
|
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[] | 2014-06-04T15:09:21
| 2014-07-04T02:46:47
|
2014-06-04T15:11:19Z
|
CONTRIBUTOR
|
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Add convenient properties and method to the Procar class in order to get the number of k-points, the number of bands and to get the projection of bands on elements.
The method `get_projection_on_elements(s)` was written from the same method in the BandStructure class.
The PROCAR file is parsed faster than the vasprun.xml file with the `parse_projected_eigen` option.
Germain
|
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MDU6SXNzdWUzNDk4NTM1NQ==
| 89
|
LDA Potcar.from_file() doesn't work on some LDA potcars
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[
"If I understand correctly, this is an issue with VASP POTCARs. Is there another way to auto-detect which POTCAR it is other than the main line? e.g. by the parameters of La vs La_s? That might be a more robust fix so that pymatgen works across all VASP users, rather than just the ones that have updated their POTCARs\n",
"You could do a lookup table of TITEL -> symbol, but it starts to get really\nugly, e.g the PW91 and LDA La pseudopotentials use the same TITEL, but for\nLa_s they are different.\n\nOn Wed, Jun 4, 2014 at 2:09 PM, Anubhav Jain notifications@github.com\nwrote:\n\n> If I understand correctly, this is an issue with VASP POTCARs. Is there\n> another way to auto-detect which POTCAR it is other than the main line?\n> e.g. by the parameters of La vs La_s? That might be a more robust fix so\n> that pymatgen works across all VASP users, rather than just the ones that\n> have updated their POTCARs\n> \n> —\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/89#issuecomment-45127826\n> .\n",
"Also, the TITEL field of POT_LDA_US Zr doesn't distinguish between the Zr and Zr_pv versions.\n",
"Potentially, you could look at the second line in the POTCAR, plus things like ENMAX etc. But yes, that gets really ugly. Frankly, the format of the file is a disaster. I am still waiting for them to correct the Xe->X fiasco.\n"
] | 2014-06-04T17:56:41
| 2014-06-06T15:29:28
|
2014-06-06T15:29:28Z
|
CONTRIBUTOR
|
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The first line of LDA POTCARs are inconsistent. E.g. for POTCAR.La_s, the line is
La: PAW 5s5p 6s5d4f valence
There is actually no occurance of La_s in the file, making it impossible to retrieve the Potcar.symbol from a generated POTCAR file. The only solution is to manually change the POTCAR files in the VASP_PSP directory to conform to the standard used in POT_GGA_PAW_PBE.
Do we want to explicitly check for this issue when generating potcars? Otherwise, if the issue is missed, VASP will run and pymatgen will read the POTCAR without complaint, but will try to set the species to PAW (which will obviously fail) when doing any further analysis.
|
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| 35,104,200
|
MDU6SXNzdWUzNTEwNDIwMA==
| 90
|
Unable to get xrd for some compounds
|
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[] | 2014-06-05T22:29:50
| 2014-06-05T23:04:11
|
2014-06-05T23:04:11Z
|
CONTRIBUTOR
|
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struct=mpr.get_structure_by_material_id("mp-8654")
print XRDCalculator(symprec=0.1).get_xrd_data(struct)
The error message is:
line 235, in get_xrd_data
coeffs[:, :, 0] \* np.exp(-coeffs[:, :, 1] \* s2), axis=1)
IndexError: too many indices
|
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| 35,120,602
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MDU6SXNzdWUzNTEyMDYwMg==
| 91
|
Options to specify data range in get_xrd_data
|
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[] | 2014-06-06T05:53:08
| 2014-06-06T13:58:22
|
2014-06-06T13:58:22Z
|
CONTRIBUTOR
|
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XRD calculator takes very long time to generate patterns for targets with short wavelength. Adding limits of calculation range will accelerate data production, such as 2-theta range or highest index.
struct=mpr.get_structure_by_material_id("mp-19017")
for target in ["Fe", "Cu", "Cr", "Co", "Mo", "Ag"]:
t=datetime.datetime.now()
d=XRDCalculator(wavelength="".join([target, "Ka"]), symprec=0.1).get_xrd_data(struct)
print datetime.datetime.now()-t
Output:
0:00:00.220564
0:00:00.439401
0:00:00.130629
0:00:00.264712
0:00:08.290305
0:00:25.969561
|
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| 35,148,921
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MDU6SXNzdWUzNTE0ODkyMQ==
| 92
|
pymatgen.analysis.diffraction.xrd XRDCalculator.get_xrd_plot error
|
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[] | 2014-06-06T14:14:08
| 2014-06-06T14:28:37
|
2014-06-06T14:28:37Z
|
NONE
|
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Here is an error
File "/usr/local/lib/python2.7/dist-packages/pymatgen/analysis/diffraction/xrd.py", line 298, in get_xrd_plot
for two_theta, i, hkls in self.get_xrd_data(structure):
ValueError: too many values to unpack
Correction :
for two_theta, i, hkls, d in self.get_xrd_data(structure):
get_xrd_data returns also d_hkl (interplanar spacing) which must be read in the list at line 298
http://pymatgen.org/_modules/pymatgen/analysis/diffraction/xrd.html#XRDCalculator.get_xrd_data
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| 35,541,331
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MDU6SXNzdWUzNTU0MTMzMQ==
| 93
|
the undefined behavior when calling function sprintf(symbol, "%s (%d)", symbol, num_spg) in _spglib.c
|
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[] | 2014-06-12T00:36:18
| 2014-06-12T00:43:25
|
2014-06-12T00:43:25Z
|
NONE
|
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In pymatgen/dependencies/spglib-1.6.0/_spglib.c, the line 191:
sprintf(symbol, "%s (%d)", symbol, num_spg);
this function call will have undefined behavior because the source buff and target buff have an overlap.
That will lead to the wrong results when calling get_spacegroup_symbol() in some systems. For example, for spacegroup "Cmcm (63)", call get_spacegroup_symbol() will give only the number "(63)", not the Symbol "Cmcm", which will lead further error when building HighSymmKpath.
The author of spglib have fixed this problem in its newest version on github.
Please also fix it in pymatgen, thank you very much.
|
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MDExOlB1bGxSZXF1ZXN0MTcxMDgxNzg=
| 94
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Corelevel
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[] | 2014-06-13T13:10:18
| 2014-06-13T13:22:10
|
2014-06-13T13:22:10Z
|
CONTRIBUTOR
|
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Add method `read_core_state_eigen()` to class `Outcar` in module `vasp_output.py` in order to read core state eigenenergies which are not available in vasprun.xml (see VASP keywords CL*).
|
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| 36,311,040
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MDU6SXNzdWUzNjMxMTA0MA==
| 95
|
Conversion battery data does not match its phase diagram?
|
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[
"Update - I think I left out a few steps in the diagram above. It looks like the code is skipping the \"three-phase\" regions like 4 & 5. Rather is doing 1->2->3->6->8 in the updated diagram below\n\n",
"The previous comment might be a red herring. There is another \"crossing\" between phase regions between 4&5 (CoO and Li6CoO4), but the code is not showing that, so it is not like it just using two-phase regions. So I don't know what is going on. In any case, regions 4, 5, and 7 are missing in the previous diagram, and 6 & 8 shouldn't really show up as they are just infinitesimal \"crossings\" between phase regions.\n",
"Just to clarify, the two phase regions represent the ONLY possible crossings. So it is not that there are 9 regions. In fact, there should only be 1, 2, 3, 5, 6 and 8. You are missing 6 because the earlier tolerance was too loose. I fixed that. \n"
] | 2014-06-23T17:11:42
| 2014-06-23T18:02:46
|
2014-06-23T18:01:03Z
|
MEMBER
|
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I'd like to generate conversion data starting for CoO2 and lithiating. The phase diagram indicates there should be several steps as per the image below - first to Li0.5CoO2, then LiCoO2, then a mixture of CoO and Li6CoO4, and so on. These are indicated by the numbers in the image.
The problem is that when I run the code to do the conversion electrode, the step with a mixture of CoO and Li6CoO4 (step #4) is not represented properly. Similarly with some of the subsequent steps. Basically CoO seems to "disappear".
Here is the code I am using - the phase diagram prints just like the image I sent, but the output from the summary dict (e.g. the "reactions" key) does not match the image. This is the output I get:
```
['0.500 Li + 1.000 CoO2 -> 0.500 Li(CoO2)2', '0.500 Li + 0.500 Li(CoO2)2 -> 1.000 LiCoO2', '2.000 Li + 1.000 LiCoO2 -> 0.500 Co + 0.500 Li6CoO4', '1.000 Li + 0.500 Li6CoO4 -> 0.500 Co + 2.000 Li2O']
```
and here is the code:
```
from pymatgen import MPRester, Composition
from pymatgen.apps.battery.conversion_battery import ConversionElectrode
from pymatgen.phasediagram.pdmaker import PhaseDiagram
from pymatgen.phasediagram.plotter import PDPlotter
mpr = MPRester()
chemsys = "-".join(["Co","O","Li"])
entries = mpr.get_entries(chemsys, inc_structure=True)
pd = PhaseDiagram(entries)
# plot the Phase Diagram (optional)
plotter = PDPlotter(pd, show_unstable=False) # you can also try show_unstable=True
plotter.show()
# get conversion data
a = ConversionElectrode.from_composition_and_pd(Composition("CoO2"), pd, working_ion_symbol="Li")
print a.get_summary_dict()["reactions"]
```
|
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|
Get_primitive_standard_structure changes atom positions
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[
"Actually, this is not an issue with spglib. It is not really an issue at all. What happened is that pairs of coordinates are being negated. E.g., you have 0.750000 0.810832 0.020666 -> 0.750000 -0.810832 -0.020666 -> 0.750000 0.189168 0.979334 (to unit cell). This is because the get_primitive_standard_structure standarization algorithm is not deterministic in how it flips the coordinates. It is effectively the same structure after 2-fold rotation (monoclinic), which has no effect. You actually get an equivalent site down the list (though the coordinates are not exact for tolerance reasons).\n\nI am not sure if we want to spend the time to try to standardize this since in a crystallographic sense, there is no difference. It is more of a restriction of VASP that you need the sites to be in the same order, in which case I suggest you read the previous structure. Also, if you need the CHGCAR anyway, why don't you generate the structure from the CHGCAR? The Chgcar always has a POSCAR object that corresponds to the final structure, which ensures it is always compatible.\n",
"Thanks for taking a look at this! In fact, I did not report the issue as a\nbug, but tagged it as a \"feature request\". I agree there's no need to\nstandardize the output structure from this method.\n\nOn Tue, Jun 24, 2014 at 5:33 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> Closed #96 https://github.com/materialsproject/pymatgen/issues/96.\n> \n> —\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/96#event-134819459.\n"
] | 2014-06-24T19:03:15
| 2014-06-25T01:37:39
|
2014-06-25T00:33:38Z
|
CONTRIBUTOR
|
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Repeatedly calling symmetryfinder().get_primitive_standard_structure gives the same structure, but for some structures, the atom positions change. For example, calling Y2S3 would reflect the structure along the x-y axis.
from pymatgen.matproj.rest import MPRester
from pymatgen.symmetry.finder import SymmetryFinder
from pymatgen.io.vaspio import Poscar
mpr = MPRester(api_key="", host="www.materialsproject.org")
structure=mpr.get_structure_by_material_id("mp-541289")
s1= structure
s2=SymmetryFinder(s1, symprec=0.01).get_primitive_standard_structure(False)
s3=SymmetryFinder(s2, symprec=0.01).get_primitive_standard_structure(False)
print Poscar(s1)
print Poscar(s2)
print Poscar(s3)
Output:Y12 S18
1.0
4.044194 0.000000 0.000000
0.000000 10.117887 -1.537590
0.000000 -0.005597 17.671811
Y S
12 18
direct
0.250000 0.189168 0.020666 Y
0.750000 0.810832 0.979334 Y
0.250000 0.124510 0.430144 Y
0.750000 0.875490 0.569856 Y
0.250000 0.829185 0.781067 Y
0.750000 0.170815 0.218933 Y
0.250000 0.187265 0.720466 Y
0.750000 0.812735 0.279534 Y
0.250000 0.486438 0.398811 Y
0.750000 0.513562 0.601189 Y
0.250000 0.549553 0.115085 Y
0.750000 0.450447 0.884915 Y
0.250000 0.051400 0.575160 S
0.750000 0.948600 0.424840 S
0.250000 0.268217 0.873161 S
0.750000 0.731783 0.126839 S
0.250000 0.615017 0.966618 S
0.750000 0.384983 0.033382 S
0.250000 0.638270 0.281569 S
0.750000 0.361730 0.718431 S
0.250000 0.007476 0.268105 S
0.750000 0.992524 0.731895 S
0.250000 0.710472 0.630232 S
0.750000 0.289528 0.369768 S
0.250000 0.950664 0.924267 S
0.750000 0.049336 0.075733 S
0.250000 0.320461 0.183433 S
0.750000 0.679539 0.816567 S
0.250000 0.367714 0.531931 S
0.750000 0.632286 0.468069 S
Y12 S18
1.0
4.044194 0.000000 0.000000
0.000000 10.234052 0.000000
0.000000 2.660591 17.470381
Y S
12 18
direct
0.750000 0.810832 0.020666 Y
0.250000 0.189168 0.979334 Y
0.750000 0.875490 0.430144 Y
0.250000 0.124510 0.569856 Y
0.750000 0.170815 0.781067 Y
0.250000 0.829185 0.218933 Y
0.750000 0.812735 0.720466 Y
0.250000 0.187265 0.279534 Y
0.750000 0.513562 0.398811 Y
0.250000 0.486438 0.601189 Y
0.750000 0.450447 0.115085 Y
0.250000 0.549553 0.884915 Y
0.750000 0.948600 0.575160 S
0.250000 0.051400 0.424840 S
0.750000 0.731783 0.873161 S
0.250000 0.268217 0.126839 S
0.750000 0.384983 0.966618 S
0.250000 0.615017 0.033382 S
0.750000 0.361730 0.281569 S
0.250000 0.638270 0.718431 S
0.750000 0.992524 0.268105 S
0.250000 0.007476 0.731895 S
0.750000 0.289528 0.630232 S
0.250000 0.710472 0.369768 S
0.750000 0.049336 0.924267 S
0.250000 0.950664 0.075733 S
0.750000 0.679539 0.183433 S
0.250000 0.320461 0.816567 S
0.750000 0.632286 0.531931 S
0.250000 0.367714 0.468069 S
Y12 S18
1.0
4.044194 0.000000 0.000000
0.000000 10.234052 0.000000
0.000000 2.660591 17.470381
Y S
12 18
direct
0.750000 0.189168 0.979334 Y
0.250000 0.810832 0.020666 Y
0.750000 0.124510 0.569856 Y
0.250000 0.875490 0.430144 Y
0.750000 0.829185 0.218933 Y
0.250000 0.170815 0.781067 Y
0.750000 0.187265 0.279534 Y
0.250000 0.812735 0.720466 Y
0.750000 0.486438 0.601189 Y
0.250000 0.513562 0.398811 Y
0.750000 0.549553 0.884915 Y
0.250000 0.450447 0.115085 Y
0.750000 0.051400 0.424840 S
0.250000 0.948600 0.575160 S
0.750000 0.268217 0.126839 S
0.250000 0.731783 0.873161 S
0.750000 0.615017 0.033382 S
0.250000 0.384983 0.966618 S
0.750000 0.638270 0.718431 S
0.250000 0.361730 0.281569 S
0.750000 0.007476 0.731895 S
0.250000 0.992524 0.268105 S
0.750000 0.710472 0.369768 S
0.250000 0.289528 0.630232 S
0.750000 0.950664 0.075733 S
0.250000 0.049336 0.924267 S
0.750000 0.320461 0.816567 S
0.250000 0.679539 0.183433 S
0.750000 0.367714 0.468069 S
0.250000 0.632286 0.531931 S
|
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MDU6SXNzdWUzNjk0MjY0OA==
| 97
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Inconsistency in ionic radii evaluation
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[
"Hello Prateek,\n\nThanks for reporting it.\nIn the ValenceIonicRadiusEvaluator, its a compromise between not having any value and assigning the radius of the nearest oxidation state. This worked reasonably well for P4+, but is failing for S- in identifying the closest oxidation state. Could you please post the mpid of the structure, so that I can troubleshoot it?\n\nTo expand further, ValenceIonicRadiusEvaluator uses the coordination number of the ion in question in addition to the ion's oxidation number in assigning a radius. However, it assumes all the ions with a particular oxidation state belonging to the same specie have same coordination number. This works reasonably well in most of the cases.\n\nFor complex structures where this doesn't apply, the ions have to be decorated with the coordination number in addition to the oxidation state. However, I haven't thought much about it.\n\nThanks\nBharat\n",
"Hi Bharat,\n\nI actually used the structure reported in this paper. http://pubs.rsc.org/en/content/articlelanding/2013/EE/c2ee23355j#!divAbstract \n\nThis corresponds to mp-696138, mp-696128, mp-721239, mp-721253 (S replaced by Se), etc.\n\nAll these structures give weird oxidation states, Se4- S- and P4+ oxidation states. It would actually be better, in my opinion, that if ValenceIonicRadiusEvaluator fails to assign the correct radii, then it should raise an error or return none instead of returning an incorrect value. \n\nThanks,\n\nPrateek\n",
"PS. It seems to work fine for the oxides in this paper though.\n",
"Prateek, \nTo my understanding, ionic radius is not strictly calculated by many. For example, Zeo++ defines only radius for each element. Pymatgen goes beyond that and takes into account the oxidation state. ValenceIonicRadiusEvaluator tries to take into account the coordination number as well. \n\nThe bond valence method may not be perfect. Also, some of the newer structures reported, indeed, have oxidation states that are not in the Shannon's paper. So, it doesn't make sense to raise Error. Also, the reason for the existence of ValenceIonicRadiusEvaluator is that some people wanted some approximate value when computing ionic radii of structures in all the cases (Raising Error is not wanted). I guess in your case, you can use the first method listed by you in the OP.\n",
"I understand that the newer structures might not have radii in Shannon's paper and the BV is an approximate method. I really appreciate that ValenceIonicRadiusEvaluator tries to make the calculation of ionic radii more accurate by taking into account the coordination number and I would like to use it in my approach. \n\nHowever, when you say that some people want an approximate value when computing the ionic radius, it contradicts this effort of making the calculation of the ionic radius more accurate. It also does not make sense that an approximate value for S- (that does not exist in the shannon table) corresponds to a value for 6-coordinated S4+. In this case the code should, at least in my opinion, include a warning, or let the user specify a keyword argument to indicate whether to raise exceptions. This can default to \"raise_exceptions = False\" where users do not want to raise exceptions, but it also has the possibility for the user to know that the value returned by the code is probably incorrect.\n\nThe authors of the paper in the link I sent you, use ionic radii for Zeo++, and using the ionic radii returned by ValenceIonicRadiusEvaluator gives me contradictory results, for the same structure in their paper. I'm curious how it was done in the paper. It is not very clear how they assigned the radius. Maybe Prof. Ong can help me with this ( @shyuep ).\n",
"Prateek, \nYou misunderstood me. Returnging S4+ radius for S- is a bug and is not supposed to happen. Thats why I want to troubleshoot it. The idea was to return the radius of closest oxidation state (in this case S2-) if there is no radius for a particular oxidation state. This way many failures due to the imperfect BVAnalyzer can be eliminated\n\nHowever I can add a flag which specifies whether the radii are approximated. If it is Shyue's paper, he might have used the standard ionic radii that are returned by specie.ionic_radius\n",
"Prateek,\n\nI fixed the code. Now S- now has a radius of 1.7 Ang.\nExpect couple of days or more for the fix to show up in the main pymatgen repo.\n\nBharat\n",
"Thanks a lot for taking a look at it!\n"
] | 2014-07-02T00:21:59
| 2014-09-18T13:39:47
|
2014-09-18T13:39:47Z
|
NONE
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Hi,
I have been trying to use pymatgen to automatically charge decorate structures, so that I can evaluate their ionic radius. I have considered two ways.
1. Using AutoOxiStateDecorationTransformation to first charge decorate a structure and then use specie.ionic_radius to evaluate the ionic radius for each unique specie in the structure.
2. Using ValenceIonicRadiusEvaluator.
I understand that both these approaches use the bond valence analyzer to assign the oxidation states, and the resulting charge decorated structure is the same (this also sometimes creates weird oxidation states like S- or P4+ etc).
The resulting radii dictionaries in the two cases look like this,
1 . {'Ge4+': 0.67, 'P4+': None, 'P5+': 0.52, 'S2-': 1.7, 'S-': None, 'Li+': 0.9}
2. {'Ge4+': 0.67, 'P4+': 0.43, 'P5+': 0.31, 'S2-': 1.7, 'S-': 0.51, 'Li+': 0.9}
In the second case, you can see that the ionic radii have been assigned to P4+ and S- these elements are not known have such oxidation states. Also, how does the coordination of the sites affect the radius in both these cases? I assume in the first case, the "most common" radius is assigned, but in the second case I see the radii assigned to S- and P4+ are actually the same as the radii of S4+ in coordination VI (http://abulafia.mt.ic.ac.uk/shannon/radius.php?Element=S) and P5+ in coordination V (http://abulafia.mt.ic.ac.uk/shannon/radius.php?Element=P).
The reason I ask is because I want to use zeo++ to calculate channel sizes of these structures, and I need to assign a radius. If there is a better way to do this please let me know.
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| 37,008,865
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MDExOlB1bGxSZXF1ZXN0MTc5MDI1NTM=
| 98
|
Defect transformation module added
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[] | 2014-07-02T18:13:34
| 2014-07-02T18:25:45
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2014-07-02T18:25:45Z
|
CONTRIBUTOR
|
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I added a new module for defect transformations.
In addition the Interstitial class in analysis/defects/point_defects.py is updated for more usage scenarios.
Update to Zeo++ code is required.
Bug fix in ValenceIonicRadiusEvaluator class
|
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Condition InterstitialTransfromation testing
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[] | 2014-07-02T19:45:51
| 2014-07-02T19:59:39
|
2014-07-02T19:59:39Z
|
CONTRIBUTOR
|
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Test skip if not zeo installed and documentation update
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Interstitial Tests updated
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[] | 2014-07-03T06:02:48
| 2014-07-03T15:47:40
|
2014-07-03T15:47:40Z
|
CONTRIBUTOR
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Fixed couple of unittest failures with zeo installed.
Nose got confused due to the presence of "_test" in function name. Removed "_test" to prevent the confusion.
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