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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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CONTRIBUTOR
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|
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
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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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