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https://api.github.com/repos/materialsproject/pymatgen/issues/401
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MDExOlB1bGxSZXF1ZXN0NzI0NDMwOTE=
| 401
|
fix rotational symmetry operations check in pointgroupanalyzer
|
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[] | 2016-06-03T01:43:02
| 2016-06-03T02:12:22
|
2016-06-03T02:12:22Z
|
CONTRIBUTOR
|
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## Summary
- addresses issue #400
- split the the conditional statements
|
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https://github.com/materialsproject/pymatgen/issues/402
| 158,337,973
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MDU6SXNzdWUxNTgzMzc5NzM=
| 402
|
Cannot import MPGGAVaspInputSet
|
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[] | 2016-06-03T10:29:05
| 2016-06-03T12:26:47
|
2016-06-03T12:26:47Z
|
CONTRIBUTOR
|
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## System
- Pymatgen version: master
- Python version:2.7.11
- OS version: Red Hat Enterprise Linux Server release 6.3
## Summary
FireWorks, MPWorks can't import MPGGAVaspInputSet
## Example code
many FireWorks commend, such as `qlaunch` `lpad get_fws`
## Error message
error message of `lpad get_fws -i 9686`
```
kl_me2 environment
/lustre/home/umjzhh-1/kl_me2/codes/pymatgen/pymatgen/io/vasp/sets_deprecated.py:460: DeprecationWarning: __init__ is deprecated
All vasp input sets have been replaced by equivalents pymatgen.io.sets. Will be removed in pmg 4.0.
return DictVaspInputSet(name, loadfn(filename), **kwargs)
/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py:335: UserWarning: None in mpworks.firetasks.elastic_tasks cannot be loaded because of cannot import name MPGGAVaspInputSet. Skipping..
% (m_object, mod_name, str(ex)))
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/firetasks/elastic_tasks.py", line 24, in <module>
from mpworks.workflows import snl_to_wf
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/workflows/snl_to_wf.py", line 15, in <module>
from pymatgen.io.vasp.sets import MPVaspInputSet, MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py:335: UserWarning: None in mpworks.examples.wf_ex cannot be loaded because of cannot import name MPGGAVaspInputSet. Skipping..
% (m_object, mod_name, str(ex)))
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/examples/wf_ex.py", line 12, in <module>
from pymatgen.io.vasp.sets import MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/firetasks/elastic_tasks.py", line 24, in <module>
from mpworks.workflows import snl_to_wf
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/workflows/snl_to_wf.py", line 15, in <module>
from pymatgen.io.vasp.sets import MPVaspInputSet, MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/examples/wf_ex.py", line 12, in <module>
from pymatgen.io.vasp.sets import MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
{
"name": "Ba1_Te2_Zn1--VASP_db_insertion",
"fw_id": 9686,
"created_on": "2016-05-16T11:57:28.974998",
"state": "WAITING",
"updated_on": "2016-05-16T11:57:28.975000"
}
```
error message of `qlaunch -r rapidfire --nlaunches infinite -m 6 --sleep 30 -b 10000`
``` sh
kl_me2 environment
/lustre/home/umjzhh-1/kl_me2/codes/pymatgen/pymatgen/io/vasp/sets_deprecated.py:460: DeprecationWarning: __init__ is deprecated
All vasp input sets have been replaced by equivalents pymatgen.io.sets. Will be removed in pmg 4.0.
return DictVaspInputSet(name, loadfn(filename), **kwargs)
/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py:335: UserWarning: None in mpworks.firetasks.elastic_tasks cannot be loaded because of cannot import name MPGGAVaspInputSet. Skipping..
% (m_object, mod_name, str(ex)))
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/firetasks/elastic_tasks.py", line 24, in <module>
from mpworks.workflows import snl_to_wf
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/workflows/snl_to_wf.py", line 15, in <module>
from pymatgen.io.vasp.sets import MPVaspInputSet, MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py:335: UserWarning: None in mpworks.examples.wf_ex cannot be loaded because of cannot import name MPGGAVaspInputSet. Skipping..
% (m_object, mod_name, str(ex)))
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/examples/wf_ex.py", line 12, in <module>
from pymatgen.io.vasp.sets import MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
2016-06-03 18:11:39,839 INFO getting queue adapter
2016-06-03 18:11:39,840 INFO Found previous block, using /lustre/home/umjzhh-1/launcher/layered_material/ycute2/substitution_02ndRun/block_2016-05-14-16-47-10-805399
2016-06-03 18:11:39,910 INFO The number of jobs currently in the queue is: 5
2016-06-03 18:11:39,911 INFO 5 jobs in queue. Maximum allowed by user: 6
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/firetasks/elastic_tasks.py", line 24, in <module>
from mpworks.workflows import snl_to_wf
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/workflows/snl_to_wf.py", line 15, in <module>
from pymatgen.io.vasp.sets import MPVaspInputSet, MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/examples/wf_ex.py", line 12, in <module>
from pymatgen.io.vasp.sets import MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/firetasks/elastic_tasks.py", line 24, in <module>
from mpworks.workflows import snl_to_wf
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/workflows/snl_to_wf.py", line 15, in <module>
from pymatgen.io.vasp.sets import MPVaspInputSet, MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/examples/wf_ex.py", line 12, in <module>
from pymatgen.io.vasp.sets import MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
2016-06-03 18:11:40,038 DEBUG Querying for duplicates, fw_id: 4334
2016-06-03 18:11:40,040 DEBUG FW with id: 4334 is unique!
2016-06-03 18:11:40,040 INFO Launching a rocket!
2016-06-03 18:11:40,096 DEBUG Querying for duplicates, fw_id: 4334
2016-06-03 18:11:40,098 DEBUG FW with id: 4334 is unique!
2016-06-03 18:11:40,121 DEBUG Querying for duplicates, fw_id: 4334
2016-06-03 18:11:40,122 DEBUG FW with id: 4334 is unique!
2016-06-03 18:11:40,142 DEBUG Reserved FW with id: 4334
2016-06-03 18:11:40,143 INFO reserved FW with fw_id: 4334
2016-06-03 18:11:40,145 INFO Created new dir /lustre/home/umjzhh-1/launcher/layered_material/ycute2/substitution_02ndRun/block_2016-05-14-16-47-10-805399/launcher_2016-06-03-10-11-40-143401
2016-06-03 18:11:40,148 INFO moving to launch_dir /lustre/home/umjzhh-1/launcher/layered_material/ycute2/substitution_02ndRun/block_2016-05-14-16-47-10-805399/launcher_2016-06-03-10-11-40-143401
2016-06-03 18:11:40,187 INFO submitting queue script
2016-06-03 18:11:40,218 INFO Job submission was successful and job_id is 36594
```
error message in `*.error` of firework
``` sh
/lustre/home/umjzhh-1/kl_me2/codes/pymatgen/pymatgen/io/vasp/sets_deprecated.py:460: DeprecationWarning: __init__ is deprecated
All vasp input sets have been replaced by equivalents pymatgen.io.sets. Will be removed in pmg 4.0.
return DictVaspInputSet(name, loadfn(filename), **kwargs)
/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py:335: UserWarning: None in mpworks.firetasks.elastic_tasks cannot be loaded because of cannot import name MPGGAVaspInputSet. Skipping..
% (m_object, mod_name, str(ex)))
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/firetasks/elastic_tasks.py", line 24, in <module>
from mpworks.workflows import snl_to_wf
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/workflows/snl_to_wf.py", line 15, in <module>
from pymatgen.io.vasp.sets import MPVaspInputSet, MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py:335: UserWarning: None in mpworks.examples.wf_ex cannot be loaded because of cannot import name MPGGAVaspInputSet. Skipping..
% (m_object, mod_name, str(ex)))
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/examples/wf_ex.py", line 12, in <module>
from pymatgen.io.vasp.sets import MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/firetasks/elastic_tasks.py", line 24, in <module>
from mpworks.workflows import snl_to_wf
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/workflows/snl_to_wf.py", line 15, in <module>
from pymatgen.io.vasp.sets import MPVaspInputSet, MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
Traceback (most recent call last):
File "/lustre/home/umjzhh-1/kl_me2/codes/fireworks/fireworks/utilities/fw_serializers.py", line 327, in load_object
m_module = importlib.import_module(mod_name)
File "/lustre/home/umjzhh-1/kl_me2/virtenv_kl_me2/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/lustre/home/umjzhh-1/kl_me2/codes/MPWorks/mpworks/examples/wf_ex.py", line 12, in <module>
from pymatgen.io.vasp.sets import MPGGAVaspInputSet
ImportError: cannot import name MPGGAVaspInputSet
```
## Suggested solution (if any)
I have tried to `import MPGGAVaspInputSet` from `pymatgen/io/vasp/sets_deprecated.py` to `pymatgen/io/vasp/sets.py`, but didn't work.
|
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| 158,418,812
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MDExOlB1bGxSZXF1ZXN0NzI1NDM5MjU=
| 403
|
Minor bug fix for DictSet
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[] | 2016-06-03T17:46:54
| 2016-06-03T18:12:58
|
2016-06-03T18:12:58Z
|
CONTRIBUTOR
|
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fix INCAR EDIFF analyzing bug to allow EDIFFG to be passed to final INCAR setting
|
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| 158,472,840
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MDU6SXNzdWUxNTg0NzI4NDA=
| 404
|
deprecated sets - EDIFF_PER_ATOM
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[] | null |
[
"(this also pertains to a few others like MITVaspInputSet, MPHSEVaspInputSet)\n",
"The new input sets are called MPRelaxSet.yaml. And it retains EDIFF_PER_ATOM of the old MPVaspInputSet..\n",
"The old MPVaspInputSet.yaml is only used by the old deprecated sets.\n",
"I know ... that's also what my message says. In order to maintain the behavior of the old deprecated sets, it should be EDIFF_PER_ATOM for those. I am trying to make sure that people who are using deprecated sets (not me) don't have different behavior in their runs.\n",
"It will not have that problem. The logic in the old deprecated sets is different. EDIFF is interpreted as per atom by default and you have to supply ediff_per_atom=False to cause it to be interpreted as absolute. In fact, the old input sets don't even support EDIFF_PER_ATOM. \n\nThe new input sets (which uses a different set of YAML) interprets EDIFF_PER_ATOM and EDIFF differently.\n",
"Ok got it\n"
] | 2016-06-03T23:28:21
| 2016-06-04T00:35:16
|
2016-06-03T23:35:34Z
|
MEMBER
|
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I think that MPVaspInputSet.yaml should use EDIFF_PER_ATOM (not EDIFF) to maintain the old behavior of deprecated sets. Just confirming this is true rather than pushing the change directly.
I don't think this affects any of the new input sets either way...
|
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|
change attribute name to support automatic serialization
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[] | 2016-06-05T06:27:46
| 2016-06-05T14:27:36
|
2016-06-05T14:27:36Z
|
CONTRIBUTOR
|
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change attribute name to support automatic serialization
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| 158,797,727
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MDU6SXNzdWUxNTg3OTc3Mjc=
| 406
|
Likely an issue in Structure.as_dict() for abivars format
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[] | null |
[
"Hi,\n\nAbinit supports different set of variables for the specification of the crystal structure.\nThat section is supposed to handle the case in which the dictionary specifies the lattice in terms of \nangles and vector lengths.\nThere's obviously an issue when `geomode == \"angdeg\"`. I will fix it.\nThanks for reporting the problem.\n\nBest,\nMatteo\n",
"Has this been fixed?\n",
"@gmatteo Has this been fixed? Can we close this issue?",
"Yes, fixed in #720"
] | 2016-06-06T23:24:59
| 2017-07-12T16:01:03
|
2017-07-12T16:01:03Z
|
MEMBER
|
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Line 1322 of structure.py reads:
```
elif geomode == "angdeg":
d.update(dict(
acell=3 * [1.0],
angdeg=angdeg))
```
But in the last line, it looks like angdeg is never defined (at least, it is underlined in red in my IDE). So if this code were to be run, it would likely choke.
This won't affect things unless the abivars format is specified for the dict and the geomode is "angdeg" (I have no idea what these mean)
|
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MDU6SXNzdWUxNTkwMzQ0NjA=
| 407
|
don't set ISYM=0 for NCSFVaspInputSet (?)
|
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[
"I have no objection, but I will leave the rest to comment. My suspicion is that you set ISYM to 0 to avoid symmetrization of the charge density. Does it really matter? This is a one step run. I doubt the cost is very much different.\n",
"Ok I am going to leave it as is for now. In some (static scf) HSE runs I have been finding that ISYM=0 is leading to very different (lower energy) configurations than ISYM=1. To be on the safe side I will leave it as ISYM=0.\n",
"in hse as well as beyond dft calculations (gw etc that involve the calculation of the susceptibility \\chi) degenerate or near degenerate eigen values are 'cleaned up'(set to same value) for ISYM>0\n"
] | 2016-06-07T21:57:31
| 2016-06-08T18:04:03
|
2016-06-08T17:35:57Z
|
MEMBER
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The NCSFVaspInputSet by default forces ISYM = 0.
I am thinking to change this so that ISYM is left alone, i.e., if the scf run was done with ISYM=1, to leave that setting the same for the nscf run. It is trivial to implement but I want to make sure this procedure is correct, hence the ticket.
Any objections / comments / suggestions?
|
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Ieee
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[] | 2016-06-09T21:52:11
| 2016-06-09T22:37:16
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2016-06-09T22:37:16Z
|
CONTRIBUTOR
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## Summary
Adds a method to TensorBase that allows conversion to the IEEE standard, and a small fix to TensorBase.transform
- IEEE conversion based on rules from 1987 standard
- TensorBase.transform now returns the class of the instance
## TODO (if any)
IEEE conversion should be generalized to allow conversion based on primitive or other cells. In principle, this is possible if one can generate a conventional lattice/structure (using something like get_refined_cell) with the same coordinate axes as an input structure.
*get_ieee_tensor supports conversion from conventional cell settings only.
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added conversion data for tensor unit test
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[] | 2016-06-09T23:00:18
| 2019-02-07T01:29:03
|
2016-06-09T23:01:32Z
|
CONTRIBUTOR
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## Summary
Adds test data.
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| 410
|
update lammps package
|
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[] | 2016-06-12T00:09:33
| 2016-06-12T01:39:55
|
2016-06-12T01:39:55Z
|
CONTRIBUTOR
|
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## Summary
- set topology directly from the molecule
- set forcefield from file
- add/update unittests
- minor cleanup
|
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py3k fix in lammps
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[] | 2016-06-13T16:07:24
| 2016-06-13T16:08:31
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2016-06-13T16:08:30Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0NzM3ODEzMjA=
| 412
|
updates to lammps topology and forcefield
|
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[] | 2016-06-14T17:33:05
| 2016-06-14T18:17:22
|
2016-06-14T18:17:22Z
|
CONTRIBUTOR
|
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## Summary
- read pair and improper dihedral forcefield coefficients
- set site charges in topology
- more unittests
- cleanup and minor refactoring
|
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| 413
|
internal pmg4 compat: use scipy.constants
|
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[] | 2016-06-14T20:37:09
| 2016-06-14T20:39:35
|
2016-06-14T20:39:35Z
|
MEMBER
|
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## Summary
If the `core.physical_constants` module will be removed in pmg 4.0 as the module warns, this change or similar is necessary. Currently, a deprecation warning is given with as little as `from pymatgen import __version__`.
- `pymatgen.core.physical_constants` --> `scipy.constants`
- define `HARTREE_TO_ELECTRON_VOLT` locally
- Other constants (`h`, `c`, and `e`) used in file are already members of `scipy.constants`
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MDU6SXNzdWUxNjAyODI0MDE=
| 414
|
Zeo++ - pymatgen extension not python3 compatible
|
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[] | null |
[
"I am experiencing this same issue. I have also posted to the pymatgen google group. Any updates here?",
"I am the developer of the Zeo++ python extension. I wrote it with python\n2.7 in mind. I stopped working on Zeo++ more than a year ago.\nDue to the many requests, I will make this a high priority.\n\nBharat\n\nOn Tue, Dec 6, 2016 at 10:09 AM, thiassaith <notifications@github.com>\nwrote:\n\n> I am experiencing this same issue. I have also posted to the pymatgen\n> google group. Any updates here?\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/414#issuecomment-265225857>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AD2qkMW5FBgea2GOUX_XKO-uYSh_dfYSks5rFaTqgaJpZM4I1wRk>\n> .\n>\n\n\n\n-- \n\nBharat Medasani\nPostdoctoral Associate,\nPacific Northwest National Lab\nRichland, WA 99354\nUSA\n",
"@shyuep This has been fixed on Zeo++ side. You can close this.",
"Good! I will have to test it out today"
] | 2016-06-14T20:58:44
| 2017-02-24T14:15:11
|
2017-02-24T14:12:57Z
|
NONE
|
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## System
- Pymatgen version: "master"
- Python version: 3.5
- OS version: Linux - Ubuntu 16
## Summary
The Zeo++ extension io/zeopp.py has some python2 -> 3 problems regarding str vs. bytes. I did some simple fixes to the calls by applying `encode('utf-8')` to all the string input arguments to cython. However the program still crashes my python session
Is the Zeo++ extension known to be unstable?
## Example code
``` python
# Get structure from somewhere (Y2Ti2O7) in my case
from pymatgen.transformations.defect_transformations import InterstitialTransformation
t1 = InterstitialTransformation('He', (1, 1, 1))
t1.apply_transformation(structure, 20)
```
## Error message
_python session crashes_
|
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MDU6SXNzdWUxNjAzMDEyMTI=
| 415
|
MaterialsProjectCompatibility.get_explanation_dict broken?
|
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[
"Thanks!\n"
] | 2016-06-14T22:41:53
| 2016-06-14T23:08:33
|
2016-06-14T22:49:18Z
|
MEMBER
|
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## System
- Pymatgen version: "master" vs. 3.6.1
- Python version: 2.7.10
- OS version: OSX 10.11
## Summary
- New `pymatgen.io.vasp.sets` class `MPRelaxSet` has no `name` attribute, so breaks `get_explanation_dict` for `MaterialsProjectCompatibility` instance.
- Not sure if this is a bug or a pmg4 change. If the latter, no deprecation warning appears in pymatgen 3.6.1, so this will come as a surprise to downstream users.
## Example code
``` python
from pymatgen.entries.compatibility import MaterialsProjectCompatibility
from pymatgen import MPRester
_compat = MaterialsProjectCompatibility()
mpr = MPRester()
entries = mpr.get_entries({'original_task_id': 'mp-2340'})
entry = _compat.process_entries(entries)[0]
energy_explained = _compat.get_explanation_dict(entry)
```
## Error message
```
AttributeError Traceback (most recent call last)
<ipython-input-8-6e21a5a3d506> in <module>()
----> 1 energy_explained = _compat.get_explanation_dict(entry)
/Users/dwinston/Dropbox/materialsproject/pymatgen/pymatgen/entries/compatibility.pyc in get_explanation_dict(self, entry)
468 corr_dict = self.get_corrections_dict(entry)
469 for c in self.corrections:
--> 470 cd = {"name": str(c)}
471 cd["description"] = c.__doc__.split("Args")[0].strip()
472 cd["value"] = corr_dict.get(str(c), 0)
/Users/dwinston/Dropbox/materialsproject/pymatgen/pymatgen/entries/compatibility.pyc in __str__(self)
160
161 def __str__(self):
--> 162 return "{} Potcar Correction".format(self.input_set.name)
163
164
AttributeError: type object 'MPRelaxSet' has no attribute 'name'
```
## Suggested solution (if any)
- See "Summary" above. I don't know if this issue represents a bug or a missing deprecation warning. Change committed as b84e1fee2c6b6645f2cd60c2fb38613e6d2ba33a, so @shyuep please clarify.
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MDExOlB1bGxSZXF1ZXN0NzM4NjI1MjI=
| 416
|
Gaussian eigenvalues and eigenvectors
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[] | null |
[
"Can you make sure you pull the latest pymatgen master and resolve all conflict first? There are merge conflicts according to Github. Thanks,\n",
"That is True, I did not work on the last pymatgen version.\nI did a new pull request with no merge conflict\nGermain\n\nLe mer. 15 juin 2016 à 14:30, Shyue Ping Ong notifications@github.com a\nécrit :\n\n> Can you make sure you pull the latest pymatgen master and resolve all\n> conflict first? There are merge conflicts according to Github. Thanks,\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/416#issuecomment-226172734,\n> or mute the thread\n> https://github.com/notifications/unsubscribe/AFKoOicPS7E9XhxxbqpHeY6YgsNipHz9ks5qL_BYgaJpZM4I2ECC\n> .\n> \n> ## \n> \n> Germain Salvato Vallverdu\n> 06 88 59 08 87\n> http://gvallver.perso.univ-pau.fr *(page perso) *\n> https://github.com/gVallverdu *(GitHub) *\n",
"I am not sure I realy need to do a new pull request. The branch appears ok now.\nTell me if you want a new one.\n"
] | 2016-06-15T07:16:12
| 2016-06-16T22:47:06
|
2016-06-16T22:47:06Z
|
CONTRIBUTOR
|
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I added attributes to the GaussianOutput class containing eigenvalues and eigenvectors.
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MDExOlB1bGxSZXF1ZXN0NzQzMzIyMzc=
| 417
|
io.lammps updates
|
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[] | 2016-06-18T09:02:38
| 2016-06-18T13:38:36
|
2016-06-18T13:38:36Z
|
CONTRIBUTOR
|
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## Summary
- major bug fixes in setting lammps data from molecular forcefield and topology
- update unittests: replace simple testscase with more complex ones
- refactoring/cleanup/doc updates
|
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MDExOlB1bGxSZXF1ZXN0NzQ0ODc2Mzk=
| 418
|
add utility module in io.lammps
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[] | 2016-06-20T18:13:03
| 2016-06-20T18:33:12
|
2016-06-20T18:33:12Z
|
CONTRIBUTOR
|
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|
## Summary
- disable reading pair coeffs for i!=j atom pairs in forcefield
- generate polymer chains via random walk
- wrapper for [packmol](https://github.com/leandromartinez98/packmol) software
- unittests
|
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|
Ieee universal
|
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[] | 2016-06-20T19:56:54
| 2016-06-20T20:20:33
|
2016-06-20T20:20:33Z
|
CONTRIBUTOR
|
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|
## Summary
Support for "universal" conversion of tensors to IEEE standard format.
- TensorBase.convert_to_ieee can convert tensors without restrictions to the input structure (previously, only conventional was supported). Thanks to Atsushi Togo for assistance via the spglib mailing list.
- Applies to ElasticTensor and PiezoTensor classes
## TODO
Adding more robust unit testing for certain structures.
|
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MDU6SXNzdWUxNjEyOTQ2MjE=
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|
get_band_gap fails if LDAUJ is not specified
|
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[] | 2016-06-20T21:04:44
| 2016-06-20T22:17:07
|
2016-06-20T22:17:07Z
|
NONE
|
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## System
- Pymatgen version: 3.7.0
- Python version: 2.7
- OS version: CentOS
## Summary
When LDAUJ is not specified, the band gap cann not be determined
## Example code
``` python
v = Vasprun('vasprun.xml')
bs = v.get_band_structure()
print bs.get_band_gap() #<-- crash
```
## Error message
```
Traceback (most recent call last):
File "/home/apps/anaconda/2.5.0/lib/python2.7/pdb.py", line 1314, in main
pdb._runscript(mainpyfile)
File "/home/apps/anaconda/2.5.0/lib/python2.7/pdb.py", line 1233, in _runscript
self.run(statement)
File "/home/apps/anaconda/2.5.0/lib/python2.7/bdb.py", line 400, in run
exec cmd in globals, locals
File "<string>", line 1, in <module>
File "/home/rytr1806/bin/VTST-Tools/band-gap.py", line 3, in <module>
from pymatgen.io.vasp.outputs import *
File "/home/apps/anaconda/modules-2.7/pymatgen/io/vasp/outputs.py", line 697, in get_band_structure
dict_eigen = self.as_dict()['output']['eigenvalues']
File "/home/apps/anaconda/modules-2.7/pymatgen/io/vasp/outputs.py", line 843, in as_dict
d["is_hubbard"] = self.is_hubbard
File "/home/apps/anaconda/modules-2.7/pymatgen/io/vasp/outputs.py", line 604, in is_hubbard
if len(self.hubbards) == 0:
File "/home/apps/anaconda/modules-2.7/pymatgen/io/vasp/outputs.py", line 578, in hubbards
return {symbols[i]: us[i] - js[i] for i in range(len(symbols))}
File "/home/apps/anaconda/modules-2.7/pymatgen/io/vasp/outputs.py", line 578, in <dictcomp>
return {symbols[i]: us[i] - js[i] for i in range(len(symbols))}
IndexError: list index out of range
```
output from pdb:
```
573 if not self.incar.get("LDAU", False):
574 return {}
575 us = self.incar.get("LDAUU", self.parameters.get("LDAUU"))
576 js = self.incar.get("LDAUJ", self.parameters.get("LDAUJ"))
577 if len(us) == len(symbols):
578 -> return {symbols[i]: us[i] - js[i] for i in range(len(symbols))}
579 elif sum(us) == 0 and sum(js) == 0:
580 return {}
581 else:
582 raise VaspParserError("Length of U value parameters and atomic "
583 "symbols are mismatched")
```
## Suggested solution (if any)
If LDAUJ is not specified, VASP assumes a value of 0 for all atoms. It would be convenient for pymatgen to do the same. perhaps a line like the following could be added after 577:
``` python
if len(js) != len(us) and len(js) == 1:
js = [0] * len(us)
```
|
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| 161,737,585
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MDU6SXNzdWUxNjE3Mzc1ODU=
| 421
|
spacegroupanalyzer returns spacegroup number as long() type
|
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[
"Python `long` values are not cast to String values in MongoDB. They are stored as [NumberLong](https://docs.mongodb.com/manual/core/shell-types/#numberlong)s in MongoDB, i.e. 64-bit integers.\n\nI tried to reproduce your issue, but I could not. I tried MongoDB 3.2 and 2.6, and I'm using pymongo 3.2 and pymatgen 3.7.1, although I don't think this has ever been an issue with MongoDB/pymongo. Please provide a reproduction, with pymatgen/pymongo/MongoDB versions.\n",
"Thanks for looking into this -\n\nI think the problem is actually in the fact that I am using jsanitize() before db insertion:\n\n```\np = Poscar.from_file(\"POSCAR\")\nsym_finder = SpacegroupAnalyzer(p.structure, symprec=0.1)\nx = sym_finder.get_spacegroup_number()\n\nprint type(x), type(jsanitize(x, allow_bson=True))\n```\n\nprints:\n\n`<type 'long'> <type 'str'>`\n\nThe three ways forward are:\n1. Do nothing\n2. Return int in spacegroupanalyzer (this is what the method signature says) instead of long\n3. Update jsanitize() so that it handles long, especially with allow_bson=True\n",
"I recommend both 2 and 3. I've submitted a [PR](https://github.com/materialsvirtuallab/monty/pull/29) for 3 in the monty repo. I think jsanitize() should pass through long unconditionally, as `json.dumps` supports serializing `long`s.\n\nAnd yes, I can think of no reason to store an integer value ranging from 1 to 230 in a `long`.\n"
] | 2016-06-22T17:12:50
| 2016-06-26T21:29:24
|
2016-06-26T21:29:24Z
|
MEMBER
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Spacegroup analyzer returns spacegroup number as "_long_" type, e.g.:
```
sga = SpacegroupAnalyzer(structure)
print(type(sga.get_spacegroup_number()))
```
This is not a problem when working purely in Python, but inserting _long_ types into MongoDB causes them to be cast to String - so that spacegroup numbers are strings in MongoDB.
Either you can leave things be, or you can simply cast to _int_ before returning the spacegroup num - in which case you are introducing a backward incompatibility for anyone who uses both the old and new code to put spacegroup nums into MongoDB. Up to you ...
|
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MDExOlB1bGxSZXF1ZXN0NzQ4NDE0Mjk=
| 422
|
Cast spacegroup_number to int
|
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[] | 2016-06-22T19:21:37
| 2016-06-26T21:29:24
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2016-06-26T21:29:24Z
|
MEMBER
|
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## Summary
_spacegroup_data["number"] is `long`. Can safely cast to `int` and match method signature.
Closes #421
|
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MDExOlB1bGxSZXF1ZXN0NzUxNDQwMjY=
| 423
|
Added Xr class to I/O module
|
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[] | 2016-06-24T17:05:40
| 2016-06-24T19:52:27
|
2016-06-24T19:52:27Z
|
CONTRIBUTOR
|
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|
## Summary
<Short few sentences, and summary of the major changes in bullet
points>
- Feature 1
- Feature 2
- Fix 1
- Fix 2
## Additional dependencies introduced (if any)
<List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. If you are putting anything here, you should
provide a justification why that dependency is needed. Especially
frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.>
## TODO (if any)
<If this is a work-in-progress, write something about what else needs
to be done>
- Feature 1 supports a, but not b.
The class is useful for reading another standard GULP relaxation-output file format. It includes a flag to specifically deal with core-shell models.
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MDExOlB1bGxSZXF1ZXN0NzUxOTk2NTQ=
| 424
|
Classify sulfur compounds
|
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[] | 2016-06-25T08:32:47
| 2016-06-26T21:29:13
|
2016-06-26T21:29:13Z
|
CONTRIBUTOR
|
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|
## Summary
Method for sulfide type determination based on crystal structure by checking the oxidation states from coordinated atoms of S. Output str listed below:
- "None" if it is an element, or it does not contain S, or S is coordinated by anions.
- "polysulfide" if any S is found to be bonded by S.
- "sulfide" for the rest.
## Additional dependencies introduced (if any)
None
## TODO (if any)
Fix AnionCorrection.
- Apply sulfide correction from the new structure based strategy (might require to label docs in MP DB)
- Combine oxide and sulfide correction (this kind of structures do exist)
|
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| 162,366,077
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MDExOlB1bGxSZXF1ZXN0NzUyNTE2NjI=
| 425
|
fix anion correction when S and O are both anions
|
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[] | 2016-06-27T03:03:14
| 2016-06-27T10:45:05
|
2016-06-27T10:45:05Z
|
CONTRIBUTOR
|
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## Summary
Fix anion correction when S and O are both anions. No corrections on polysulfides for now, which means they are destabilized.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
|
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MDExOlB1bGxSZXF1ZXN0NzUzMjk5MTA=
| 426
|
io.lammps updates
|
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[] | 2016-06-27T15:20:38
| 2016-06-27T19:52:27
|
2016-06-27T19:52:27Z
|
CONTRIBUTOR
|
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## Summary
- add LammpsRunner wrapper
- py3k bug fix
- other minor bug fixes and cleanup
|
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MDU6SXNzdWUxNjI2NDcwMzg=
| 427
|
Illegal filename on windows
|
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[] | 2016-06-28T09:56:37
| 2016-06-28T11:16:10
|
2016-06-28T11:16:10Z
|
NONE
|
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## System
- Pymatgen version: 3.7.1
- Python version: 2.7
- OS version: Windows 10
## Summary
- The directory pymatgen-3.7.1\pymatgen\analysis\chemenv\coordination_environments\coordination_geometries_files contains filenames with the '?' character. This is not valid on windows. Trying install on windows produces:
copying pymatgen\analysis\chemenv\coordination_environments\coordination_geometries_files\allcg.txt -> build\lib.win-amd64-2.7\pymatgen\analysis\chemenv\coordination_environments\coordination_geometries_files
error: can't copy 'pymatgen\analysis\chemenv\coordination_environments\coordination_geometries_files\AC?12.json': doesn't exist or not a regular file
make: **\* [makeincludes/packages/pymatgen.mk:63: /home/cliff/git/qw/external-libs/src/pymatgen-3.7.1/make-stamp] Error 1
Installing version does not have this problem 3.2.8.
|
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MDExOlB1bGxSZXF1ZXN0NzU1NTM5ODA=
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|
Misc NMR code updates
|
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[] | null |
[] | 2016-06-28T21:30:10
| 2016-06-28T21:32:50
|
2016-06-28T21:32:50Z
|
CONTRIBUTOR
|
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|
## Summary
Misc NMR code updates
<Short few sentences, and summary of the major changes in bullet
points>
- Parsing both "core only" and "valence and core" NMR chemical shift values
- Fix parsing of NMR vapsrun.xml SC step energy, which actually consists of several ionic steps but shown as single one.
- Organiza NMR test files to one folder
## Additional dependencies introduced (if any)
|
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Add support for Abinit8
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[] | null |
[] | 2016-06-29T12:59:42
| 2016-06-29T20:46:50
|
2016-06-29T20:46:50Z
|
CONTRIBUTOR
|
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## Summary
- Add support for Abinit8, drop support for Abinit7
- Remove from_abivars and to_abivars methods
- Add enumerator for libxc XC functionals and XcFunc object
- Move dojo_report object to pseudo_dojo
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Added Calculated properties to elastic tensor
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2016-09-25T20:09:54Z
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NONE
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Added Young's modulus
Added Christoffel tensor and acoustic wave velocities
Added Born elastic stability criterion
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fixed bug in TensorBase.convert_to_ieee with certain tetragonal systems
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2016-06-30T01:16:48Z
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CONTRIBUTOR
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allows for proper sorting of tetragonal system lattice vectors where lengths are precisely equal.
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Added Rotate_Tensor method to TensorBase class which rotates a tensor…
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[
"There are failing tests. See https://circleci.com/gh/materialsproject/pymatgen/4958?utm_campaign=build-failed&utm_medium=email&utm_source=notification . Pls fix and resubmit.\n"
] | 2016-06-30T07:25:04
| 2016-06-30T08:12:09
|
2016-06-30T07:50:46Z
|
CONTRIBUTOR
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Added a Rotate_Tensor method to the TensorBase class which rotates a tensor from a given initial structure's basis to the final structure's basis, useful for comparing tensors from the primitive unit cell to the conventional cell or whatever final reference from we look at. Associated unit tests also added.
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|
Rotate_Tensor Method
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[
"Is this working? It looks like there are still bugs in both the test and the new method. Also, should it really be called \"rotate_tensor\"? We have a \"rotate\" method already which takes a rotation matrix and transforms the tensor based on that. I think the new method should have a more descriptive name.\n\nNote that the IEEE standard structure and the conventional standard structure aren't always the same, so testing this using that conversion data might not work.\n",
"I can change the name, that seems like a good idea. Could you be more specific on what the errors are? I tested the method and tests locally and they seem to pass. I used the IEEE structure because that was the only system which had tensors in two different reference frames and associated structures. I don't think it matters whether they are necessarily the conventional structure. \n",
"rotationprim isn't defined on line 131 of tensors.py.\n\nsee https://github.com/dongsenfo/pymatgen/blob/master/pymatgen/analysis/elasticity/tensors.py\n\nMaybe your latest local commit isn't pushed?\n",
"Ah yes sorry I didn't push my last commit, I'll resubmit it. \n",
"Is this still active or can this be closed?\n",
"It can be closed, thanks.\n\nBest,\nHandong Ling\n\nOn Mon, Aug 8, 2016 at 10:35 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> Is this still active or can this be closed?\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/433#issuecomment-238458083,\n> or mute the thread\n> https://github.com/notifications/unsubscribe-auth/AGz8KHfMNyxmfYrKIPgMxA8PNHY0x-yGks5qeBGOgaJpZM4JCafX\n> .\n"
] | 2016-06-30T17:51:06
| 2016-09-25T20:09:56
|
2016-09-25T20:09:55Z
|
CONTRIBUTOR
|
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Pushed correct rotate_tensor method and tests which rotates a tensor from an initial structure's basis to a final structure's basis
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Fix to TensorBase.convert_to_ieee
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[] | null |
[] | 2016-07-05T20:02:41
| 2016-07-20T22:06:46
|
2016-07-20T22:06:46Z
|
CONTRIBUTOR
|
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## Summary
Fixed a few bugs in get_ieee_tensor that caused problems in structures with lattice vectors that are close. Thanks to @dmrdjenovich for feedback and a pretty extensive test dataset.
- Removes atol/ltol from TensorBase.convert_to_ieee, they shouldn't be necessary.
- Fixes some bugs in comparison procedures for lattice vectors related to sorting
- Adds unittest data for previously problematic materials.
|
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| 164,483,579
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MDU6SXNzdWUxNjQ0ODM1Nzk=
| 435
|
unittest2 should be a required library in setup.py
|
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[] | null |
[] | 2016-07-08T08:35:22
| 2016-07-08T20:29:21
|
2016-07-08T20:29:21Z
|
MEMBER
|
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This line of pymatgen requires unittest2:
pymatgen/util/testing.py:15
Since this could be considered a "core" test, unittest2 should be a required installation library for pymatgen.
Currently I get CircleCI failures for a derived library (MatMiner) that reuses PymatgenTest to get some structures for testing. The CircleCI failures indicate that unittest2 is not installed, even though pymatgen is a dependency of MatMiner.
|
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| 164,609,632
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MDU6SXNzdWUxNjQ2MDk2MzI=
| 436
|
k-point file generated by MPStaticSet
|
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[] | null |
[] | 2016-07-08T20:25:35
| 2016-07-09T07:25:00
|
2016-07-09T07:25:00Z
|
CONTRIBUTOR
|
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## System
- Pymatgen version: 4.0.0
- Python version: 2.7.9
- OS version: Linux
## Summary
- Changing the "reciprocal_density" argument of MPStaticSet doesn't seem to have an effect on the generated k-point grid
## Example code
``` python
from pymatgen.io.vasp.sets import MPStaticSet
from pymatgen.util.testing import PymatgenTest
structure = PymatgenTest.get_structure("Si")
set_1 = MPStaticSet(structure)
set_2 = MPStaticSet(structure, reciprocal_density = 20000)
set_1.write_input("set_1")
set_2.write_input("set_2")
```
## Error message
No error message, but the generated KPOINTS files are the same, i. e. both
```
pymatgen generated KPOINTS with grid density = 619 / atom
0
Monkhorst
8 8 8
```
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MDExOlB1bGxSZXF1ZXN0NzY4NDQyNjU=
| 437
|
Fixed absolute path installation issue
|
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[] | 2016-07-09T10:47:59
| 2016-07-09T12:56:12
|
2016-07-09T12:56:11Z
|
CONTRIBUTOR
|
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## Summary
Removed os.path.abspath because this was preventing installation from the extracted tar.gz source when running setup.py install under Windows OS (not sure if it manifests on Linux). The setup() function should only need relative paths.
## Note
Please test this under Mac OS X / Linux to confirm the changes do not impact installation on these systems.
Thanks and kind regards,
Liam Deacon
|
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| 438
|
Different tolerance values for same site detection are used while reading CIF files
|
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[] | null |
[
"Many thanks, @shyuep!\n"
] | 2016-07-13T11:59:01
| 2016-07-13T13:13:40
|
2016-07-13T12:36:07Z
|
CONTRIBUTOR
|
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Different tolerance values for same site detection are used here:
- https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/cif.py#L469, modifiable, 1e-5 by default
- https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/cif.py#L308, hard-coded, 1e-3
I suggest using the same variable `self._site_tolerance`, or make the second, hard-coded value, modifiable in `CifParser.__init__()`.
|
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| 165,616,980
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MDExOlB1bGxSZXF1ZXN0Nzc0OTUwMjQ=
| 439
|
io.lammps updates
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[] | null |
[] | 2016-07-14T17:36:54
| 2016-07-14T20:06:49
|
2016-07-14T20:06:49Z
|
CONTRIBUTOR
|
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## Summary
minor bug fixes and refactoring in the lammps subpackage
|
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| 166,166,294
|
MDExOlB1bGxSZXF1ZXN0Nzc4NTk0NDM=
| 440
|
incorporate capabilities in CifParser to handle various errors faced while parsing CIFs from the Springer materials/Pauling file DBs
|
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[] | 2016-07-18T18:55:27
| 2016-07-18T19:03:33
|
2016-07-18T19:03:33Z
|
CONTRIBUTOR
|
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## Summary
While parsing 225k CIF files from the Springer materials/Pauling file DBs using CifParser, numerous errors were faced, which were earlier fixed at my end, but now I have tried to introduce those capabilities directly in CifParser.
Here's a summary of changes made. They passed all the tests in test_cif.py (including the new ones added in this request) so hopefully that shouldn't throw any errors. Also, I am of course open to discussing if some of these changes should be implemented in a different/better way.
- Feature: the following line in a CIF file,
T1(o) '0.75Si + 0.25Al' .4i .1 0.0098(1) 0.1747(1) 0.2113(1) 1 ? '?'
made the file unparsable due to unrecognizable label and symbol. The fix recognizes this as a disordered site with occupancies parsed from the symbol string "0.75Si + 0.25Al".
- Feature: the following line in a CIF file,
Nb,Zr '0.8Nb + 0.2Zr' .2a .m-3m 0 0 0 1 ? '?'
event though didn't throw an error while parsing, was previously recognized as an ordered site containing Nb with occupancy=1. The fix recognizes this as a disordered site with occupancies parsed from the symbol string "0.8Nb + 0.2Zr".
- Feature: parse the structures from CIFs that contain incomplete powder diffraction data by skipping over that data block (previously threw an error).
- Feature: print user warnings for CIFs that contain molecular species OH, OH2.
- Add unit tests and example CIF files.
|
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| 166,189,923
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MDU6SXNzdWUxNjYxODk5MjM=
| 441
|
Error when parsing structure from gulp output with pymatgen.command_line.gulp_caller.GulpIO.get_relaxed_structure(gout)
|
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[] | null |
[
"Is this the new behavior of GULP or is the output specific to your input file?",
"It's specific to this input file. I have since run GULP on different systems/input files, and the outputs did contain the string:\r\n\r\n\"Final fractional coordinates of atoms\"",
"Seems like this issue has been defunct for 7 years. Closing...."
] | 2016-07-18T20:48:39
| 2023-08-08T21:17:33
|
2023-08-08T21:17:33Z
|
NONE
|
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<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
- Pymatgen version: 3.7.1
- Python version: 2.7.8
- OS version: Linux Fedora, release 21
- GULP version: 4.4
## Summary
The pymatgen.command_line.gulp_caller.GulpIO.get_relaxed_structure(gout) method is not parsing the structure from gulp output, even though the gulp calculation ran properly and the gulp output contains the relaxed structure.
## Here is an example script that will cause the error, along with the provided gulp input file (example.gin). It is assumed that the example.gin file is located in the current working directory, and that gulp is installed and can be called with the command "gulp", which needs to be in the path.
```
import os
from pymatgen.command_line.gulp_caller import GulpCaller, GulpIO
# make GulpCaller and GulpIO objects
gulp_caller = GulpCaller()
gulp_io = GulpIO()
# get the working directory
current_dir = os.getcwd()
# get the gulp input from the file and put it in a string
gin_file = open(current_dir + '/example.gin', 'r')
gulp_input = gin_file.read()
# run gulp via GulpCaller.run() and store the output as a string
gulp_output = gulp_caller.run(gulp_input)
# print gulp output to a file for reference
gout_file = open(current_dir + '/example.gout', 'w')
gout_file.write(gulp_output)
# parse the relaxed structure from the gulp output using GulpIO.get_relaxed_structure
relaxed_structure = gulp_io.get_relaxed_structure(gulp_output) # this line causes the error
```
## Error message
```
Traceback (most recent call last):
File "gulp_io_error.py", line 23, in <module>
relaxed_structure = gulp_io.get_relaxed_structure(gulp_output) # this line causes the error
File "/n/srv/brevard/venv/lib/python2.7/site-packages/pymatgen/command_line/gulp_caller.py", line 468, in get_relaxed_structure
raise IOError("No structure found")
IOError: No structure found
```
## Suggested solution
I noticed that the GulpIO.get_relaxed_structure(gout) method searches for the following string when trying to parse the positions of the atoms from the gulp output:
"Final fractional coordinates of atoms"
However, this string is not contained in the gulp output (written to example.gout by the script above). Instead, it looks like the atomic positions are given after this string:
"Final asymmetric unit coordinates"
I think modifying the GulpIO.get_relaxed_structure(gout) method to search for this string will solve the problem.
## The gulp input file (example.gin) has been pasted below.
```
opti conp conj
switch_minimiser bfgs gnorm 0.02
cell
3.14234315719 3.14993532397 3.68431921347 94.7366201574 104.887692682 74.1046376087
frac
Au core 0.431215374033 0.708509636366 0.676326109399
Au core 0.994879647339 0.196971981584 0.135903401186
space
2
lennard 12 6
Au core Au core 214180.2000 625.482 40.000 0 0
```
|
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| 166,440,187
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MDExOlB1bGxSZXF1ZXN0NzgwNTI0Nzg=
| 442
|
Update to REST Api for the substrate analyzer
|
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[] | null |
[
"You need to provide a proper description. I do not merge unless there is one.\n",
"@shyamd `orient` should default to `None` (avoid mutable values like `[]`), and if so, elide the \"orient\" field in the query string.\n\nAlso, let's thicken up the docstring. Include that `n=0` means \"no limit\" (perhaps this should be the default for an MPRester call?). Mention the sort order (increasing elastic energy if available, MCIA if not).\n\nFinally, FYI I put up a public [endpoint](https://materialsproject.org/rest/v2/materials/all_substrate_ids) requiring no login/api_key to access the list of blessed substrate mp-ids currently used by the builder.\n"
] | 2016-07-19T21:28:55
| 2016-07-20T16:21:16
|
2016-07-20T16:21:16Z
|
NONE
|
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- Added in get_substrates to the REST API to pull pre-calculated substrate matches from the materials project database based on substrate orientation, matching area, and elastic energy
|
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MDExOlB1bGxSZXF1ZXN0NzgxMDM5ODY=
| 443
|
Fixed missing LDAU params in input sets derived with from_prev_calc methods
|
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[] | 2016-07-20T08:03:23
| 2016-07-20T13:12:16
|
2016-07-20T13:12:16Z
|
CONTRIBUTOR
|
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## Summary
get_structure_from_prev_run used to pop LDAU parameters in incar of the passed vasprun object in place. This resulted in missing LDAUU, LDAUJ and LDAUL parameters (all become empty lists) for all input sets created (e.g. MPStaticSet) with from_prev_calc methods.
|
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MDExOlB1bGxSZXF1ZXN0Nzg1NjA5OTM=
| 444
|
Change the implementation of Structure.interpolate_lattices.
|
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[
"@sdacek can you fix this?\nThis implementation breaks when the input lattice is a rotation. See commit 2f60449\n"
] | 2016-07-23T02:41:34
| 2016-07-25T22:36:55
|
2016-07-23T04:25:41Z
|
CONTRIBUTOR
|
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## Summary
Change the implementation of interpolate_lattices. Previously, the
parameters for the lattice (a, b, c, alpha, beta, gamma) were all
linearly interpolated to the parameters of the second structure.
However, this can lead to various issues, including
that the interpolated volumes are not guarenteed monotonic. This is
resolved via interpolating the lattice matrices directly.
|
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| 167,497,684
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MDU6SXNzdWUxNjc0OTc2ODQ=
| 445
|
Key Error when parsing projected band structure for spin-orbit coupling VASP runs
|
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[] | null |
[
"Can you post an example SOC file?\n",
"Hi Shyue Ping, \n\n[Here are example vasprun.xml and KPOINTS files for a SOC band structure run. (The vasprun.xml is bigger than github allows for posts)](https://www.dropbox.com/sh/esiw6o6rao3w2c4/AAA0ezVqpkEMpCGAp6horVGVa?dl=0)\n\nI made a temporary fix of the key error today that is sufficient for making BSPlotterProjected plots which effectively treats SOC runs as non spin-polarized (only looking at the projected charge density not the three component spin density). \n\nIt's currently part of the color_band branch of my forked repository which also has some additional plot options for BSPlotterProjected (get_color_grouped and get_color_sites). See the last diff for pymatgen/io/vasp/outputs.py on [this page](https://github.com/blondegeek/pymatgen/commit/92433c059df5ae522633319ff744b70640f2ffed). \n\nIf this fix seems good enough for now, I can clean up my color_band branch and make a pull request or I can make a pull request with just the changes that fix the key error.\n\nLet me know what you think is best.\n\nThanks!\nTess\n",
"ok. Though I think this is a reasonable fix, I would actual prefer proper parsing of SOC bandstructures. I just implemented a change. Pls see if it works,\n",
"This fixes the key error. Thanks!\n"
] | 2016-07-26T00:47:17
| 2016-08-03T03:39:15
|
2016-08-03T03:39:15Z
|
CONTRIBUTOR
|
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A Key Error is returned when BSVasprun(parse_projected_eigen=True).get_band_structure() is used to read spin-orbit coupling VASP runs.
## Example code
``` python
# while this works:
vasp_run = BSVasprun('vasprun.xml')
bs = vasp_run.get_band_structure(line_mode=True)
# this throws a key error:
vasp_run = BSVasprun('vasprun.xml',parse_projected_eigen=True)
bs = vasp_run.get_band_structure(line_mode=True)
```
## Error message
```
Traceback (most recent call last):
File "plot_band.py", line 6, in <module>
bs = vasp_run.get_band_structure(line_mode=True)
File "/usr/local/lib/python2.7/site-packages/pymatgen/io/vasp/outputs.py", line 702, in get_band_structure
dict_eigen = self.as_dict()['output']['eigenvalues']
File "/usr/local/lib/python2.7/site-packages/pymatgen/io/vasp/outputs.py", line 1280, in as_dict
beigen = peigen[kpoint_index][str(spin)][band_index]
KeyError: '-1'
```
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|
Major changes and improvements in chemenv
|
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[
"The tests seems to be failing?\n",
"Hi Shyue,\n\nI think its a compatibility problem with python 3. I'm running with python\n2.7, I'll test with python on my machine and make the necessary changes.\n\nDavid\n\nOn Wed, Jul 27, 2016 at 3:01 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> The tests seems to be failing?\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/446#issuecomment-235577594,\n> or mute the thread\n> https://github.com/notifications/unsubscribe-auth/ADdRUHBhyFOyrtMDVmeDNKr_DunFvcBbks5qZ1avgaJpZM4JWFn-\n> .\n",
"Ok. I suggest you look into using pyenv. It's highly useful for having multiple python versions on the same machine. In any case, my group has moved to a \"default\" Py3k system. So everyone uses Py3k unless it is on a cluster where there is no Py3k. So far, no ill effects.\n",
"Hi,\n\nI am using virtualenv. I think I just fixed the bugs and I committed my\nchanges.\n\nDavid\n\nOn Wed, Jul 27, 2016 at 4:48 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> Ok. I suggest you look into using pyenv. It's highly useful for having\n> multiple python versions on the same machine. In any case, my group has\n> moved to a \"default\" Py3k system. So everyone uses Py3k unless it is on a\n> cluster where there is no Py3k. So far, no ill effects.\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/446#issuecomment-235609038,\n> or mute the thread\n> https://github.com/notifications/unsubscribe-auth/ADdRUFg0Ghvso7bea1r-hUYS7GDsVFUNks5qZ2_DgaJpZM4JWFn-\n> .\n"
] | 2016-07-27T11:19:30
| 2016-07-27T15:36:30
|
2016-07-27T15:36:30Z
|
CONTRIBUTOR
|
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## Summary
- New strategy to identify coordination environments
- More convenient way to store and retrieve neighbors (NeighborsSets in StructureEnvironments and LightStructureEnvironments
- Tests are now much faster
- Added new tests for the new strategy and for the LightStructureEnvironments
- Fixed miscellaneous bugs
## Additional dependencies introduced (if any)
None
## TODO (if any)
- Add the connectivity analysis
|
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MDU6SXNzdWUxNjg1MzMyNzM=
| 447
|
Error with parsing of core state eigenenergies
|
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[
"Thanks. Can you submit a pull request?\n"
] | 2016-07-31T19:15:27
| 2016-08-12T04:14:49
|
2016-08-12T04:14:49Z
|
MEMBER
|
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## System
- Pymatgen version: 4.2.0
- Python version: 3.5.2
- OS version: OS X 10.11.6
## Summary
Parsing of core state eigenenergies fails, I suspect because it assumes that the number of lines equals the number of atoms: it's not handling entries for atoms which use multiple lines correctly (for example, because there are lots of orbitals).
I have a fix below, which works for me. I haven't submitted this as a pull request because it's a bit hacky and I haven't had a chance to test it on other OUTCARs yet.
Maybe also worth updating the output to use the Orbital Enum type used elsewhere in pymatgen, and to return the actual Species from the structure instead of just a number too?
## Example code
``` python
import pymatgen as mg
outcar = mg.io.vasp.outputs.Outcar('OUTCAR')
outcar.read_core_state_eigen()
```
## Error message
```
pymatgen/io/vasp/outputs.py in read_core_state_eigen(self)
2069 data = line.split()[1:]
2070 for i in range(0, len(data), 2):
-> 2071 cl[iat][data[i]].append(float(data[i + 1]))
2072 return cl
2073
ValueError: could not convert string to float: '4s'
```
## Suggested solution (if any)
Since we don't know how many lines to parse without knowing what species are present, using the number of elements on a given line to see whether it's an entry for a new ion, or whether the line is a continuation of the previous line. This is a bit hacky, but works for me.
``` python
def read_core_state_eigen(self):
"""
Read the core state eigenenergies at each ionic step.
Returns:
A list of dict over the atom such as [{"AO":[core state eig]}].
The core state eigenenergie list for each AO is over all ionic
step.
Example:
The core state eigenenergie of the 2s AO of the 6th atom of the
structure at the last ionic step is [5]["2s"][-1]
"""
with zopen(self.filename, "rt") as foutcar:
line = foutcar.readline()
while line != "":
line = foutcar.readline()
if "NIONS =" in line:
natom = int(line.split("NIONS =")[1])
cl = [defaultdict(list) for i in range(natom)]
if "the core state eigen" in line:
iat = -1
while line != "":
line = foutcar.readline()
# don't know number of lines to parse without knowing
# specific species, so stop parsing when we reach
# "E-fermi" instead
if "E-fermi" in line:
break
data = line.split()
# data will contain odd number of elements if it is
# the start of a new entry, or even number of elements
# if it continues the previous entry
if len(data) % 2 == 1:
iat += 1 # started parsing a new ion
data = data[1:] # remove element with ion number
for i in range(0, len(data), 2):
cl[iat][data[i]].append(float(data[i + 1]))
return cl
```
## Files (if any)
Relevant part of OUTCAR here:
```
the core state eigenenergies are
1- 1s -26553.6923 2s -3928.6671 2p -3517.4901 3s -723.8627 3p -588.5749
3d -378.6566 4s -93.2431 4p -54.2730
2- 1s -484.2608
E-fermi : 4.1283 XC(G=0): -7.2922 alpha+bet : -9.6200
```
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| 169,630,532
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MDExOlB1bGxSZXF1ZXN0ODAyNjAxMzg=
| 448
|
Fix PDEntry.from_dict to accommodate no-name dicts
|
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[] | 2016-08-05T15:16:55
| 2016-08-05T15:17:25
|
2016-08-05T15:17:25Z
|
MEMBER
|
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## Summary
Fix PDEntry.from_dict to accommodate no-name entry dicts. Add a test for this.
I encountered this issue when using `monty.json.MontyEncoder` to `json.dumps` Pourbaix entries. I could ensure this dumps 'name's for each entry, but `PDEntry.from_dict` should also just accommodate no-name entries as `PDEntry.__init__` specifies.
|
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MDU6SXNzdWUxNjk5NTU4ODY=
| 449
|
Significant mismatch between the bandgap values computed by bandstructure class and Dos class
|
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[] | null |
[
"Don't think this is a bug? Band gap determination is ultimately a exercise in tolerances. The DOS and BS classes use different methods of determining the gap. In general, I would argue the DOS gives a much better band gap than the BS estimate.\n",
"the default tolerance for dos is 0.001. also the indirect gap reported on materialsproject is 0.6\n",
"Yes, but that's MP's problem. In general, the gap obtained from a much finer mesh in a DOS run is better than using the bandstructure. \n\nMP should in fact be using gaps from the uniform runs, not the BS runs.\n",
"I agree this is a tolerance issue.\n\nHowever, the gaps are in general better from the BS along symmetry lines. This is because most of CBM and VBMs are along these lines…\nOur uniform meshes are not that dense. So I would not recommend switching to using them for the gap.\n\nIdeally, a method using by default BS along symmetry lines and checking if the uniform mesh is consistent would be the best.\n\nBest,\n\nGeoffroy\n\n> On 08 Aug 2016, at 17:54, Shyue Ping Ong notifications@github.com wrote:\n> \n> Yes, but that's MP's problem. In general, the gap obtained from a much finer mesh in a DOS run is better than using the bandstructure.\n> \n> MP should in fact be using gaps from the uniform runs, not the BS runs.\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub https://github.com/materialsproject/pymatgen/issues/449#issuecomment-238281729, or mute the thread https://github.com/notifications/unsubscribe-auth/AA3l94yTTjIs82b7tU8KSQdvCVOONTuvks5qd1EdgaJpZM4JfLnQ.\n",
"What I mean by \"this is a tolerance issue\" is this is not a bug.\nJust different k-point sampling give different gaps.\n\nGeoffroy\n\n> On 08 Aug 2016, at 17:57, Geoffroy Hautier geoffroy.hautier@uclouvain.be wrote:\n> \n> I agree this is a tolerance issue.\n> \n> However, the gaps are in general better from the BS along symmetry lines. This is because most of CBM and VBMs are along these lines…\n> Our uniform meshes are not that dense. So I would not recommend switching to using them for the gap.\n> \n> Ideally, a method using by default BS along symmetry lines and checking if the uniform mesh is consistent would be the best.\n> \n> Best,\n> \n> Geoffroy\n> \n> > On 08 Aug 2016, at 17:54, Shyue Ping Ong <notifications@github.com <mailto:notifications@github.com>> wrote:\n> > \n> > Yes, but that's MP's problem. In general, the gap obtained from a much finer mesh in a DOS run is better than using the bandstructure.\n> > \n> > MP should in fact be using gaps from the uniform runs, not the BS runs.\n> > \n> > —\n> > You are receiving this because you are subscribed to this thread.\n> > Reply to this email directly, view it on GitHub https://github.com/materialsproject/pymatgen/issues/449#issuecomment-238281729, or mute the thread https://github.com/notifications/unsubscribe-auth/AA3l94yTTjIs82b7tU8KSQdvCVOONTuvks5qd1EdgaJpZM4JfLnQ.\n",
"i understand that between calculations with different kpoint meshes there will be differences, but for the given calculation shouldnt there be one to one match between the indirect gap obtained from bandstructure along symmtery lines and the dos ?\n"
] | 2016-08-08T15:46:23
| 2017-06-03T14:32:24
|
2017-06-03T14:32:24Z
|
CONTRIBUTOR
|
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## System
- Pymatgen version: master branch
- Python version: 3.5
- OS version: ubuntu 16.04
## Summary
- difference in gap of about 0.27 for Silicon(NEDOS=601 in INCAR)
- the value reported by Bandstructure object matches the value reported on the materialsproject(mp-149)
## Example code
``` python
from pymatgen.io.vasp.outputs import Vasprun
vrun = Vasprun("vasprun.xml.gz")
bs = vrun.get_band_structure()
print("FROM BS\nvbm:{}, cbm:{}, fermi:{}, gap:{}".format(bs.get_vbm()["energy"],
bs.get_cbm()["energy"],
bs.efermi,
bs.get_band_gap()["energy"]))
dos = vrun.complete_dos
print("FROM DOS\nvbm:{}, cbm:{}, fermi:{}, gap:{}".format(dos.get_cbm_vbm()[1],
dos.get_cbm_vbm()[0],
dos.efermi,
dos.get_gap()))
```
## Output
```
FROM BS
vbm:5.614, cbm:6.2243, fermi:5.63746936, gap:0.6103000000000005
FROM DOS
vbm:5.2918, cbm:6.1767, fermi:5.63746936, gap:0.8849
```
## Files (if any)
[vasprun.xml.gz](https://drive.google.com/file/d/0B3SvuOHwFoR7dXVUMTNpdzh5eUk/view?usp=sharing)
|
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MDExOlB1bGxSZXF1ZXN0ODA4NzE4NTY=
| 450
|
using *POSCAR* in to and from_file functions to add more flexibility
|
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[] | 2016-08-10T21:35:22
| 2016-08-11T02:54:22
|
2016-08-11T02:54:21Z
|
CONTRIBUTOR
|
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This is a suggestion. I was using the format material_name_POSCAR for several of my materials and I needed to read them via Structure.from_file but I couldn't. With _POSCAR_ file naming is more flexible than just POSCAR\* which was previously.
|
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| 170,733,133
|
MDExOlB1bGxSZXF1ZXN0ODEwMjEyMjM=
| 451
|
Fixes parsing of core state eigenenergies #447 and adds additional test
|
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[] | null |
[] | 2016-08-11T20:02:49
| 2016-08-12T04:14:49
|
2016-08-12T04:14:49Z
|
MEMBER
|
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Added a fix for the core state eigenenergies parsing, and also an additional test and an associated OUTCAR (GaAs from mp-2534 with ICORELEVEL=1) since none of the existing OUTCARs in test_files have core state eigenenergies with d-levels.
Fixes #447
|
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| 171,453,018
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MDU6SXNzdWUxNzE0NTMwMTg=
| 452
|
vasprun.get_band_structure(line_mode=True) causes occasional mislabeling high symmetry k-point as 'None'.
|
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[] | null |
[] | 2016-08-16T16:01:18
| 2016-09-04T04:32:09
|
2016-09-04T04:32:09Z
|
NONE
|
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## System
- Pymatgen version: 3.6.1
- Python version: 3.5.1
- OS version: OS X El Capitan
## Summary
- vasprun.get_band_structure(line_mode=True) constructs labels_dict with 'None' as a key, resulting in occasional mislabeling if 'None's value is a high symmetry k-point.
## Example code
``` python
# line 745 in pymatgen/io/vasp/outputs.py
for i in range(len(kpts.kpts)):
if kpts.labels[i] is not None:
labels_dict[kpts.labels[i]] = \
kpts.kpts[i]
```
## Error message
Some labels in the final band structure plot show 'None'.
## Suggested solution (if any)
``` python
for i in range(start_bs_index, len(kpts.kpts)):
```
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MDExOlB1bGxSZXF1ZXN0ODE4NDMyMjE=
| 453
|
update TranslateSiteTransformations
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[] | 2016-08-18T16:06:58
| 2016-08-18T17:13:37
|
2016-08-18T17:13:37Z
|
CONTRIBUTOR
|
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## Summary
- add capability to translate each site separately: example:- displacing sites along normal modes
- add and update corresponding unittests
|
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MDU6SXNzdWUxNzQ0MDM1OTc=
| 454
|
Spacegroup 165 should have hexagonal lattice system?
|
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[] | null |
[
"Space Group 165 should not be hexagonal, it is indeed trigonal\n(rhombohedral). http://img.chem.ucl.ac.uk/sgp/large/sgp.htm\n\nBest,\nWenhao Sun\n\nOn Wed, Aug 31, 2016 at 4:33 PM, Tess notifications@github.com wrote:\n\n> Hello,\n> \n> I believe spacegroup 165 should have a hexagonal rather than a\n> rhombohedral lattice system.\n> \n> For example, see ICSD Collection Code 3 -- a crystal structure with this\n> spacegroup. Using the lattice information for this structure:\n> \n> lattice = Lattice.from_lengths_and_angles((7.1849999999999996, 7.1850000000000005, 7.351),\n> (90.0, 90.0, 119.99999999999999))\n> sg = SpaceGroup.from_int_number(165)\n> sg.is_compatible(lattice)>> False\n> \n> This returns False because SpaceGroup.from_int_number(165).symbol does\n> not have an 'H' appending it's spacegroup symbol which is needed for\n> is_compatible to verify a hexagonal lattice --thus it's assumed that it\n> must have rhombohedral lattice system (all lengths equal in lattice).\n> \n> To temporarily fix this issue locally, I have added a degenerate copy of\n> lines 2455-2461 with the symbol P-3c1H in symm_data.yaml\n> https://github.com/materialsproject/pymatgen/blob/master/pymatgen/symmetry/symm_data.yaml#L2455.\n> This allows me to reproduce a cif that matches the ICSD. However, I'm a bit\n> fuzzy on my crystallography, so I'm uncertain whether generally the \"enc\"\n> (symmetry encoding) given in the YAML file for these spacegroup is specific\n> to a rhombohedral lattice system or already appropriate for a hexagonal\n> lattice system.\n> \n> I suspect there may be several trigonal spacegroups that this issue\n> applies to. What would be the best fix? Rewriting the is_compatible method\n> for the SpaceGroup class or adding spacegroup information to the YAML that\n> includes the 'H' designation?\n> \n> Thanks!\n> Tess\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/454, or mute the\n> thread\n> https://github.com/notifications/unsubscribe-auth/ABvGo3lFmgs-QisBNtt5LO81PY6goeLcks5qlg9bgaJpZM4JyK94\n> .\n\n## \n\nCeder Research Group http://web.mit.edu/ceder/ | Massachusetts Institute\nof Technology\nDepartment of Materials Science and Engineering\n77 Massachusetts Ave | Room 13-5065 | Cambridge, MA, 02139\n",
"Trigonal crystal system, but hexagonal lattice system. [See the table here.](https://en.wikipedia.org/wiki/Crystal_system)\n",
"Ah, I see, my fault. Hopefully someone else can assist you with this.\n\nOn Wed, Aug 31, 2016 at 4:41 PM, Tess notifications@github.com wrote:\n\n> Trigonal crystal system, but hexagonal lattice system. See the table here.\n> https://en.wikipedia.org/wiki/Crystal_system\n> \n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/454#issuecomment-243935323,\n> or mute the thread\n> https://github.com/notifications/unsubscribe-auth/ABvGo6e71-uxszYiX78nOCfVZseFq0Hnks5qlhFBgaJpZM4JyK94\n> .\n\n## \n\nCeder Research Group http://web.mit.edu/ceder/ | Massachusetts Institute\nof Technology\nDepartment of Materials Science and Engineering\n77 Massachusetts Ave | Room 13-5065 | Cambridge, MA, 02139\n",
"No worries! Thanks for your time!\n",
"The enc is for a trigonal setting, not a hexagonal setting. The symmetry encoding cannot be transferred to a hexagonal setting directly. I guess the best way is to add another set of enc for the hexagonal system, but this is not trivial.\n",
"I just fixed this. The only thing that needs to be done is to add the hexagonal trigonal lattices as a special case."
] | 2016-08-31T23:33:45
| 2017-06-03T14:29:07
|
2017-06-03T14:28:35Z
|
CONTRIBUTOR
|
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Hello,
I believe spacegroup 165 should have a hexagonal rather than a rhombohedral lattice system.
For example, see ICSD Collection Code 3 -- a crystal structure with this spacegroup. Using the lattice information for this structure:
``` python
lattice = Lattice.from_lengths_and_angles((7.1849999999999996, 7.1850000000000005, 7.351),
(90.0, 90.0, 119.99999999999999))
sg = SpaceGroup.from_int_number(165)
sg.is_compatible(lattice)
>> False
```
This returns False because SpaceGroup.from_int_number(165).symbol does not have an 'H' appending it's spacegroup symbol which is needed for is_compatible to verify a hexagonal lattice --thus it's assumed that it must have rhombohedral lattice system (all lengths equal in lattice).
To temporarily fix this issue locally, I have added a degenerate copy of lines 2455-2461 with the symbol P-3c1H in [symm_data.yaml](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/symmetry/symm_data.yaml#L2455). This allows me to reproduce a cif that matches the ICSD. However, I'm a bit fuzzy on my crystallography, so I'm uncertain whether generally the "enc" (symmetry encoding) given in the YAML file for these spacegroup is specific to a rhombohedral lattice system or already appropriate for a hexagonal lattice system.
I suspect there may be several trigonal spacegroups that this issue applies to. What would be the best fix? Rewriting the is_compatible method for the SpaceGroup class or adding spacegroup information to the YAML that includes the 'H' designation?
Thanks!
Tess
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MDU6SXNzdWUxNzQ4MzI1MjY=
| 455
|
Different gaps from Vasprun.eigenvalue_band_properties and Bandstructure.get_band_gap()
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[
"Note - i don't think the vbm is listed in the above output, but it was above the Fermi level (I think something on the order of 1.85?)\n",
"Assigned to @hautierg \n",
"The two methods define differently what is the band gap.\nThe eigenvalue_band_properties looks at occupations. Here there are partial occupations of your upper bands. Therefore this depends on the smearing you use.\nThe Bandstructure.get_band_gap() looks at bands above and below fermi level. Here there are bands crossing the fermi level. So the method considers it as a metal and gives you a zero band gap.\nI would stress though that if you want to have an accurate band gap determination you should not rely on a relaxation run (it looks like this is a relaxation run) but instead use a dense k-point grid (with a non-self-consistent run if you want) on a static run. This k-point grid can be uniform or on specific paths. The k-point meshes for relaxation is usually way too coarse to give an accurate estimate of the band gap.\n",
"Ok\n\nI agree that in my experience, get_band_structure().get_band_gap() works better. I used that method when coding MatMethods parsers, etc.\n\nMy issue is that this is not really documented anywhere. To give an example, someone external was recently trying to code a FireTask that checked the band gap, and if it was less than a threshold value, to defuse the rest of the workflow. That person had no idea what was the difference between eigenvalue_band_properties and get_band_gap and used the former one (anyway, that is one directly part of Vasprun). This caused erroneous results as many of their jobs ended up not being defused even though they were metallic systems due to the problems in eigenvalue_band_properties that you describe. It is very difficult for an outside user to know how to use these methods properly.\n",
"Btw the \"agree that get_band_gap is more reliable\" comes from an email that @hautierg wrote me but isn't reflected in this chain\n"
] | 2016-09-02T19:32:25
| 2016-09-26T04:33:44
|
2016-09-25T16:01:55Z
|
CONTRIBUTOR
|
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Hello,
I get very different band gaps from Vasprun.eigenvalue_band_properties and Bandstructure.get_band_gap(). The former gives a gap of 1.3011 while the other 0. This seems to be because the maximum valence band is above the fermi level but still has some electron occupation.
```
vrun = Vasprun('vasprun.xml')
(gap, cbm, vbm, is_direct) = vrun.eigenvalue_band_properties
gap
>>1.3011
bs = vrun.get_band_structure()
bs.get_band_gap()
>>{u'direct': False, u'energy': 0.0, u'transition': None}
vrun.efermi
>>1.71998034
```
I've attached a zipped copy of the vasprun.xml.
[vasprun.zip](https://github.com/materialsproject/pymatgen/files/452773/vasprun.zip)
Thanks!
Tess
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MDU6SXNzdWUxNzQ5MjgwNDA=
| 456
|
Structure.get_distance() -- ValueError: ndarray is not C-contiguous
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[
"I ran this exact code nd I did not have any error. I suspect you have a problem with your numpy setup because that sounds like a compile error. Maybe your python version and numpy compile version is not compatible.\n",
"Hi Shyue Ping,\n\nThanks for your time. I am getting this error when switching between different branches of my forked pymatgen repo for a editable pip installation: master which is up to date with materialsproject's repo and polarization_temp which is 447 commits behind. My master branch is having the \"ValueError: ndarray is not C-contiguous\" error when running get_distance() but my polarization_temp branch is not. \n\nThe problem may be that the since the C libraries pymatgen uses are not recompiled when I'm switching branches, I'm using old, incompatible libraries for the master branch. What is the easiest way to recompile these libraries after switching branches?\n\nThanks,\nTess\n",
"You can recompile by typing python setup.py develop. But unless you believe\nthe new code is going to override your changes, you should pull the layers\nchanges. That will usually make sure you get the bug fixes. Alternatively,\nyou can set up different envs.\n\nOn Sun, Sep 4, 2016, 12:46 Tess notifications@github.com wrote:\n\n> Hi Shyue Ping,\n> \n> Thanks for your time. I am getting this error when switching between\n> different branches of my forked pymatgen repo for a editable pip\n> installation: master which is up to date with materialsproject's repo and\n> polarization_temp which is 447 commits behind. My master branch is having\n> the \"ValueError: ndarray is not C-contiguous\" error when running\n> get_distance() but my polarization_temp branch is not.\n> \n> The problem may be that the since the C libraries pymatgen uses are not\n> recompiled when I'm switching branches, I'm using old, incompatible\n> libraries for the master branch. What is the easiest way to recompile these\n> libraries after switching branches?\n> \n> Thanks,\n> Tess\n> \n> —\n> You are receiving this because you modified the open/close state.\n> \n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/456#issuecomment-244624623,\n> or mute the thread\n> https://github.com/notifications/unsubscribe-auth/AAjOU5d1kXVt-JAxHDKvJzuAQ6m1Vdtnks5qmyAwgaJpZM4J0cUa\n> .\n",
"Thanks again for your help. I'm not sure I understand what you mean by \"pull the layers\nchanges\" -- could you please explain this further?\n",
"Recompiling fixed the error. I'm surprised I haven't run into problem sooner! Thanks again!\n",
"Sorry, I mean latest. Autocorrect\n\nOn Sun, Sep 4, 2016, 12:58 Tess notifications@github.com wrote:\n\n> Recompiling fixed the error. I'm surprised I haven't run into problem\n> sooner! Thanks again!\n> \n> —\n> You are receiving this because you modified the open/close state.\n> \n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/456#issuecomment-244625188,\n> or mute the thread\n> https://github.com/notifications/unsubscribe-auth/AAjOU_9pgSiMJ4RrSiYtdYOOCYOEg01-ks5qmyLLgaJpZM4J0cUa\n> .\n"
] | 2016-09-04T02:39:19
| 2016-09-04T20:11:09
|
2016-09-04T04:19:24Z
|
CONTRIBUTOR
|
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Hello,
I get a "ValueError: ndarray is not C-contiguous" when running the following script:
```
from pymatgen.matproj.rest import MPRester
a = MPRester()
Si = a.query({'material_id':'mp-149'},['structure']).pop()['structure']
Si.get_distance(0,1)
```
Thanks!
Tess
|
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Added remove_duplicates method to Structure.
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[
"Thanks Tess. Can you implement a few unit tests? Also, the clustering code should use scipy hierarchical clustering using the distance matrix. See the point group analyzer for an example of how it is done.\n",
"I would suggest that it use the same tolerance and clustering code as Structure.merge_sites()\n",
"Hi Shyue Ping and Will, \nI've added two tests for remove_sites, rewritten remove_sites to use scipy hierarchical clustering, and changed the default tolerance for remove sites to be 0.01 AA in my most recent commit on my master branch.\nThanks!\nTess\n",
"@blondegeek @wmdrichards I have merged, but devided the two methods are better as 1. I have retained merge_sites, but added a mode parameter. mode=\"sum\" is the default behavior for merge-sites where the occupancies are summed. mode=\"delete\" is same as remove_duplicates, in which only one site is retained.\n",
"Sounds good! Thanks!\n"
] | 2016-09-04T20:19:47
| 2016-09-06T03:02:04
|
2016-09-06T02:07:38Z
|
CONTRIBUTOR
|
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The Structure.remove_duplicates method can be used for deleting PeriodicSites that are within a tolerance of each other and have identical species_and_occu property. This is useful for deleting degenerate atoms that are generated when creating a Structure.from_spacegroup where the desired structure is to be in a lower spacegroup setting than it would otherwise be refined to be. One such situation that this could be used for is building the endpoints of an interpolation of a phase transition.
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ImportError: cannot import name optimization
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[
"Did you run python setup.py install or develop and there were no errors? This seems like you did not install pymatgen correctly.\n",
"Oh, sorry. I didn't. It's working now. Thank you, Prof Ong!\n"
] | 2016-09-06T22:01:52
| 2016-09-08T21:12:48
|
2016-09-08T21:12:48Z
|
NONE
|
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<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
- Pymatgen version: <Write "branch_name" if it is development version.>
- Python version: 2.7.9
- OS version: <If you are writing Windows here, you are on your own.>
## Summary
- <Short 1-2 bullet points stating the problem.>
## Example code
``` python
from pymatgen import Structure
```
## Error message
```
ImportError Traceback (most recent call last)
<ipython-input-2-665dff898462> in <module>()
----> 1 from pymatgen import Structure
/Users/Jianli/Documents/pymatgen/pymatgen/__init__.py in <module>()
35 # failures when loading shared libraries.
36 import spglib
---> 37 from . import optimization, util
38 del(spglib, optimization, util)
39
ImportError: cannot import name optimization
```
## Suggested solution (if any)
- <If you have a suggestion on how to solve the issue, you may write it
here.>
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
```
|
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| 175,414,011
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MDExOlB1bGxSZXF1ZXN0ODQyMzc1Njg=
| 459
|
PathFinder module pull request
|
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[
"The tests are failing. Pls fix the tests before I merge.\n",
"Dear Prof. Ong\n\nCan you please have a try commit 6df01df, commit 4086da3 was trying to use git-lfs tracker for the big CHGCAR file and as I found out I didn't have access to do that to a public forked repo.\n\nOnce you think it passed the test, please consider use git-lfs to track the large CHGCAR file or just delete it...\n\nThank you.\n"
] | 2016-09-07T05:10:34
| 2016-09-11T01:51:16
|
2016-09-11T01:51:16Z
|
CONTRIBUTOR
|
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## Summary
Added PathFinder module under pymatgen.analysis, added unit test cases for PathFinder module as well.
## TODO
In order to write unit test codes for PathFinder module, I had to include a CHGCAR file under test_files/path_finder, this file is very large (around 80MB), thus system suggests using git-lfs. However, I don't have the right to create large file pointer for a public forked repo. Thus we need to deal with this large file. Or otherwise people donwloading pymatgen codes are downloading 80MB nearly unnecessary content.
Please consider either deleting this large file or using git-lfs.
|
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| 175,863,945
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MDU6SXNzdWUxNzU4NjM5NDU=
| 460
|
BSPlotterProjected Isssue
|
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[
"I just pushed a fix, and also released v4.2.5 which should fix this problem. THis was due to some refactoring of the bandstructure classes.\n",
"Thank you so much. Is working back again!\n"
] | 2016-09-08T21:03:23
| 2016-09-08T21:24:30
|
2016-09-08T21:06:31Z
|
NONE
|
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Until Tuesday Night the code bellow was working perfectly fine:
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter, BSPlotterProjected
from pymatgen.electronic_structure.core import Spin, OrbitalType
emin = -2.0
emax = 2.0
v = Vasprun("./vasprun.xml", parse_projected_eigen=True)
bs = v.get_band_structure(line_mode=True)
plotter = BSPlotterProjected(bs)
plotter.get_elt_projected_plots(zero_to_fermi=True, ylim=[emin,emax]).savefig(filename="test.png", img_format="png")
However, I upgraded to the latest version of pymatgen and now I'm getting the gollowing error:
Traceback (most recent call last):
File "bands_test.py", line 12, in <module>
plotter = BSPlotterProjected(bs)
File "/home/guzmand/codes_mat/Miniconda/miniconda3/lib/python3.5/site-packages/pymatgen/electronic_structure/plotter.py", line 694, in **init**
if len(bs._projections) == 0:
AttributeError: 'BandStructureSymmLine' object has no attribute '_projections'
Where line 12 corresponds to:
plotter = BSPlotterProjected(bs)
Any help would be very much appreciated.
Regards,
David
|
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| 176,143,104
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MDU6SXNzdWUxNzYxNDMxMDQ=
| 461
|
Custom k-point density for MPRelaxSet
|
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[] | null |
[
"There is a reciprocal density arg already?\n",
"Does this work for MPRelaxSet? I'm getting an error:\n\n```\n>>> from pymatgen.io.vasp.sets import MPRelaxSet\n>>> from pymatgen.util.testing import PymatgenTest\n>>> struct = PymatgenTest.get_structure(\"Si\")\n>>> mpr = MPRelaxSet(struct, reciprocal_density=1000)\nTraceback (most recent call last):\n File \"<stdin>\", line 1, in <module>\n File \"/global/u1/m/montoyjh/envs/jhm_test_edison/codes/pymatgen/pymatgen/io/vasp/sets.py\", line 414, in __init__\n structure, MPRelaxSet.CONFIG, **kwargs)\nTypeError: __init__() got an unexpected keyword argument 'reciprocal_density'\n```\n"
] | 2016-09-10T00:38:10
| 2016-09-10T02:47:56
|
2016-09-10T02:47:56Z
|
CONTRIBUTOR
|
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For some of the MP workflows, the initial optimization step needs a higher k-point density than what's standard in the MPRelaxSet. I can customize the input set by modifying the config_dict, but then when it's serialized via as_dict, my changes are lost. I'm thinking it might be worthwhile to add a parameter to customize k-points in the MPRelax set, but am not sure if it'd more appropriate as something like "reciprocal_density" as in MPStaticSet or something more general in DictSet.
|
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A question about the criterion on generating high symmetry K ponits
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[
"@hautierg Can you look into this? This seems a rather huge bug?\n",
"@hautierg Any updates?",
"Closing, non-bug (thanks @munrojm for taking a sanity check!)"
] | 2016-09-10T15:14:38
| 2020-07-13T04:35:08
|
2020-07-13T04:35:07Z
|
CONTRIBUTOR
|
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## System
- Pymatgen version: 4.2.5
- Python version: 2.7.11
## Summary
It seems that in generating the high symmetry K points for bandstructure calculations for the definite lattice system, the developer forgot to transfer the parameters of the sine function from degree to radian, thus may leading an error in generating the right high symmetry K points for monoclinic lattice system.
## Error message
pymatgen/symmetry/bandstructure.py:127:sin(alpha) may not be compatible with cos(alpha pi / 180) as thought
```
<Error message>
```
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| 176,184,898
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MDU6SXNzdWUxNzYxODQ4OTg=
| 463
|
Likely an issue in SpacegroupAnalyzer.get_spacegroup()
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[
"Thanks for fix.\n\nBut it still puzzles me.\n\nSince there's a `get_point_group()` method which claims to return a `Pointgroup` object( actually it returns a `String`, another issue) and a `get_point_group_operations()` method which returns a `PointgroupOperations` object, it's kind of weird that there's only a `get_spacegroup()` method which returns a `SpacegroupOperations` object. What if someone needs a `Spacegroup()` object?\n\nBy the way, the `PointgroupAnalyzer.get_point_group()` method turns out to return a `PointgroupOperations` object rather than a `Pointgroup` object as the doc reads.\n",
"The spacegroup object is constructed from the int number. It is mean for generating structures from scratch in a particular group.\n\nThe SpacegroupOperations is generated from the detected symmetry operations for the crystal itself. \n\nThe two are not the same thing. \n\nI agree there is some inconsistency in the naming of the methods. I will refactor the method names.\n",
"I see. Thanks for your time.\n"
] | 2016-09-10T15:21:13
| 2016-09-11T14:15:37
|
2016-09-10T17:49:04Z
|
NONE
|
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Hello,
Line 102 in analyzer.py reads
``` python
"""
Get the Spacegroup for the Structure.
Returns:
Spacgroup object.
"""
```
however, the SpacegroupAnalyzer.get_spacegroup() method actually returns a SpacegroupOperations object as Line 109 reads
``` python
return SpacegroupOperations(self.get_spacegroup_symbol(),
self.get_spacegroup_number(),
self.get_symmetry_operations())
```
|
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| 464
|
Dev elastic
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[
"There seems to be failing tests. Pls fix before I merge.\n",
"Should pass the tests now, forgot to update the unit tests when I renamed one of the methods.\n"
] | 2016-09-10T20:37:19
| 2016-09-11T01:50:22
|
2016-09-11T01:50:22Z
|
CONTRIBUTOR
|
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## Major update to elasticity analysis package
Major update to the elasticity analysis package, including a significant refactoring of voigt-notation tensors and addition of properties to elastic tensor class. Thanks to @saurabh02 for the initial import of the thermal properties and to Ian Winter for sharing his method of deformation gradient determination.
- Voigt-notation conversion is now abstracted to the TensorBase class, with _vscale attributes of subclasses allowing for scaling of individual elements of the voigt representation.
- Strain objects will construct a deformation gradient via diagonalization of the strain matrix, and no longer require a deformation matrix for many of the associated methods.
- Various thermal properties estimated from the elastic tensor (conductivity, debye temperature, transverse and longitudinal sound velocities) are now included as methods to the ElasticTensor object, with appropriate unit tests derived from former workflow results.
## TODO (if any)
- Many of the new elastic tensor properties depend on structural parameters (density, etc.). For right now, these methods take a structure object as an argument, but it may be better to allow users to "attach" structures to the tensors in order to allow for simpler syntax. I'm not yet sure how best to implement this.
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major refactor of feff io
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[] | 2016-09-10T23:48:46
| 2016-09-11T00:21:40
|
2016-09-11T00:21:40Z
|
CONTRIBUTOR
|
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## Summary
- split the classes into inputs and outputs
- complete overahul of sets module to enable custom xanes and exafs runs
- update/cleanup the unittests
|
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updates
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[] | 2016-09-11T21:29:58
| 2016-09-11T21:31:46
|
2016-09-11T21:31:46Z
|
CONTRIBUTOR
|
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## Summary
- feff io: major cleanup in feff.io.inputs. make cluster radius a controllable parameter. some other minor cleanups
- fix the sign issue in the phonon example notebook.
|
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| 467
|
Added effective total strain to substrate analyzer
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Added effective total strain calculated by the von Mises equivalent strain criterion. This is useful for correlating to interfacial defects such as in microelectronics.
- Added von Misses strain to strain class
- Added output of effective total strain to substrate analyzer output
|
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feff io updates
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2016-09-12T19:28:33Z
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CONTRIBUTOR
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## Summary
- critical bug fixes
- refactor and cleanup outputs.
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| 469
|
Miscellaneous small bug fixes in chemenv + self.structures in NEBAnalysis
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[
"Can you also as the same time change the use of Pyhull's Voronoi class to the scipy.spatial Voronoi class in chemenv? I would like to start systematically remove use of pyhull. Note that scipy's implementation is faster.\n"
] | 2016-09-15T10:05:36
| 2016-09-21T12:03:23
|
2016-09-21T12:03:23Z
|
CONTRIBUTOR
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## Summary
- Switch from pyhull.VoronoiTess to scipy.spatial.Voronoi
- Fixed small bugs in chemenv
- Added classmethod to MultiWeightsChemenvStrategy in order to ease it's use
- Added self.structures in NEBAnalysis
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MDU6SXNzdWUxNzcxNDQ3MzQ=
| 470
|
KeyError in point_defects.py
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[
"@mbkumar Can you look into this pls?\n",
"The problem seems to be in SpacegroupAnalyzer. Within **init** method there is a loop which checks for magnetic moment of each site of voronoi polyhedral. \n\n```\n for site in structure:\n if hasattr(site, 'magmom'):\n magmoms.append(site.magmom)\n elif site.is_ordered and hasattr(site.specie, 'spin'):\n magmoms.append(site.specie.spin)\n else:\n magmoms.append(0)\n```\n\nThese sites have no magmom attribute, hence the elif branch is executed. Here the function hasattr(site.specie,'spin') is called.\nsite.specie belongs to the class DummySpecie so that **getattr** is called. \n\n```\n def __getattr__(self, a):\n # overriding getattr doens't play nice with pickle, so we\n # can't use self._properties\n p = object.__getattribute__(self, '_properties')\n if a in p:\n return p[a] \n try:\n return getattr(self._el, a)\n except:\n raise AttributeError(a)\n\n```\n\nobject.**getattribute** returns empty list, so try: is executed and calls the getattr again.\nThis process is repeated infinitely.\n",
"@shyuep \r\nShyue,\r\nApologies for not checking the forum categorized emails for the last few months. Just checking out all the pymatgen related emails.\r\n\r\n@vladimirovpv , could you post the CIF file as an attachment. When I try to cut and paste your cif file, I am getting error. Or send it to mbkumar at gmail\r\n\r\n",
"Dear Bharat,\n\nI do not know how to attach the file at github so I send it directly to you. Sorry for some delay with answer.\n\n\nWith k?ind regards,\nPavel\n\nDr. P. Vladimirov\nLeader of the Atomic Modeling and Validation Group\n___________________________________________________________________________________\nKarlsruhe Institute of Technology (KIT)\nInstitute for Applied Materials - Applied Materials Physics\n\nHermann-von-Helmholtz-Platz 1\nIAM-AWP/MW, Bld. 681, Room 245\n76344 Eggenstein-Leopoldshafen\nGermany\n\nPhone: +49 (0) 721 / 6082-4243\nFax: +49 (0) 721 / 6082-4567\nE-mail: Pavel.Vladimirov@kit.edu\n\nKIT - University of the State of Baden-Wuerttemberg and National Laboratory of the Helmholtz Association\n\n________________________________\nFrom: Bharat Medasani <notifications@github.com>\nSent: 08 December 2016 19:10\nTo: materialsproject/pymatgen\nCc: Vladimirov, Pavel (IAM); Mention\nSubject: Re: [materialsproject/pymatgen] KeyError in point_defects.py (#470)\n\n\n@shyuep<https://github.com/shyuep>\nShyue,\nApologies for not checking the forum categorized emails for the last few months. Just checking out all the pymatgen related emails.\n\n@vladimirovpv<https://github.com/vladimirovpv> , could you post the CIF file as an attachment. When I try to cut and paste your cif file, I am getting error. Or send it to mbkumar at gmail\n\n-\nYou are receiving this because you were mentioned.\nReply to this email directly, view it on GitHub<https://github.com/materialsproject/pymatgen/issues/470#issuecomment-265811278>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AVLusHrM8WDIT08Q93wgppIiJTHpnBFeks5rGEf9gaJpZM4J9urL>.\n",
"I've finally figured out how to attach the file. Hope it is in a good shape.\r\n\r\n\r\n[TiBe12_616454.cif.txt](https://github.com/materialsproject/pymatgen/files/648978/TiBe12_616454.cif.txt)",
"OK, I will look into this over the weekend.\n\nOn Tue, Dec 13, 2016 at 4:57 AM, vladimirovpv <notifications@github.com>\nwrote:\n\n> I've finally figured out how to attach the file. Hope it is in a good\n> shape.\n>\n> TiBe12_616454.cif.txt\n> <https://github.com/materialsproject/pymatgen/files/648978/TiBe12_616454.cif.txt>\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/470#issuecomment-266731783>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AD2qkJTkPigxToy_xpzXUaQzw5bZpZwSks5rHpY6gaJpZM4J9urL>\n> .\n>\n\n\n\n-- \n\nBharat Medasani\nPostdoctoral Associate,\nPacific Northwest National Lab\nRichland, WA 99354\nUSA\n",
"@mbkumar Have you had a chance to look at the problem?",
"@vladimirovpv This was fixed. Please test with the updated pymatgen and let\nme know if you are still seeing it.\n\nOn Wed, Dec 21, 2016 at 11:42 PM, vladimirovpv <notifications@github.com>\nwrote:\n\n> @mbkumar <https://github.com/mbkumar> Have you had a chance to look at\n> the problem?\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/470#issuecomment-268738638>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AD2qkIcTSj0lARkKK3cCwuUOggnstA4fks5rKin7gaJpZM4J9urL>\n> .\n>\n\n\n\n-- \n\nBharat Medasani\nPostdoctoral Associate,\nPacific Northwest National Lab\nRichland, WA 99354\nUSA\n",
"@shyuep, I guess you can close this."
] | 2016-09-15T10:46:07
| 2017-06-07T13:07:22
|
2017-06-07T13:07:22Z
|
NONE
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## System
- Pymatgen version: pymatgen (4.3.0)
- Python version: Python 2.7.6
- OS version: Ubuntu 14.04.4 LTS
## Summary
- I am trying to find possible non-equivalent interstitial positions in TiBe12 (intermetallic of ThMn12-type) structure using pymatgen.analysis.defects.point_defects. In fact I do need neither radii of atoms nor their valance states, as I am looking for geometrical places being equally far from atoms in the lattice (i.e., Voronoi vertices).
- Reading cif file names my species as Ti0+ and Be0+, therefore using the example posted at [http://pymatgen.org/installation.html#zeo] results in error message from zeo which cannot find radius for Ti0+.
<Example output>
Ti
Be
True temp_zeo1.rad
Reading input file: temp_zeo1.cssr
Unable to find radius for Ti0+ in table. Please provide it
in a reference file or check you input file.
Exiting ...
So I've changed element.symbol to element in my code.
- Using accuracy='Normal' results in segmentation fault, so I use explicit setting of accuracy="High"
' The code below finishes with error
## Example code
`import pymatgen as mg
from pymatgen.analysis.defects.point_defects import Interstitial
structure = mg.Structure.from_file("TiBe12_616454.cif")
radii, valences = {}, {}
for element in structure.composition.elements:
print element
radii[element] = element.atomic_radius
valence = element.group
if element.group > 12:
valence -= 10
valences[element] = valence
interstitial = Interstitial(structure, radii=radii, valences=valences, site_type='voronoi_vertex', symmetry_flag=True, oxi_state=False, accuracy='High')
`
## Error message
Ti0+
Be0+
True temp_zeo1.rad
Reading input file: temp_zeo1.cssr
Radii analysis: the smallest atom r = 1.05 while the largest atoms r = 1.4.
Box dimensions:
va=(4.190000 0 0)
vb=(0.000000 7.350000 0)
vc=(0.000000 0.000000 7.350000)
Total particles = 26
Internal grid size = (2 2 2)
Using voro++ with radii for particles.
Performing Voronoi decomposition.
Volume check:
Total domain volume = 226.354275
Total Voronoi volume = 226.354275
Voronoi decomposition finished. Rerouting Voronoi network information.
Finished rerouting information.
Box dimensions:
va=(4.190000 0 0)
vb=(0.000000 7.350000 0)
vc=(0.000000 0.000000 7.350000)
Total particles = 86
Internal grid size = (2 3 3)
Using voro++ with radii for particles.
Performing Voronoi decomposition.
Volume check:
Total domain volume = 226.354275
Total Voronoi volume = 226.354275
Voronoi decomposition finished. Rerouting Voronoi network information.
Finished rerouting information.
144 417
size of reduced vornet 340
340
size of reduced vornet 289
289
Finding channels and pockets in Dijkstra network of 289 node(s). 289 are expected to compose pores.
Analyzed and assigned 289 nodes.
Identified 0 channels and 289 pockets.
289 nodes assigned to pores.
Traceback (most recent call last):
File "int.py", line 17, in <module>
interstitial = Interstitial(s2, radii=radii, valences=valences, site_type='voronoi_vertex', symmetry_flag=True, oxi_state=False, accuracy='High')
File "/usr/local/lib/python2.7/dist-packages/pymatgen/analysis/defects/point_defects.py", line 643, in **init**
coord_no, coord_sites, chrg = self._get_coord_no_sites_chrg(site)
File "/usr/local/lib/python2.7/dist-packages/pymatgen/analysis/defects/point_defects.py", line 677, in _get_coord_no_sites_chrg
coord_chrg += weight \* self._valence_dict[site.species_string]
KeyError: u'Be0+'
## Suggested solution (if any)
- no solution available
## Files (contents of CIF file: TiBe12_616454.cif)
data_616454-ICSD
_database_code_ICSD 616454
_audit_creation_date 2009-08-01
_chemical_name_systematic 'Beryllium titanium (12/1)'
_chemical_formula_structural 'Be12 Ti'
_chemical_formula_sum 'Be12 Ti1'
_chemical_name_structure_type Mn12Th
_exptl_crystal_density_diffrn 2.29
_publ_section_title 'The beryllides of Ti, V, Cr, Zr, Nb, Mo, Hf and Ta'
loop_
_citation_id
_citation_journal_full
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary 'Acta Crystallographica (1,1948-23,1967)' 1961 14 63 65 ACCRA9
loop_
_publ_author_name
'Zalkin, A.'
'Sands, E.'
'Bedford, R.G.'
'Krikorian, O.H.'
_cell_length_a 7.35
_cell_length_b 7.35
_cell_length_c 4.19
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 90.
_cell_volume 226.35
_cell_formula_units_Z 2
_symmetry_space_group_name_H-M 'I 4/m m m'
_symmetry_Int_Tables_number 139
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'y, x, -z'
2 '-y, -x, -z'
3 '-y, x, -z'
4 'y, -x, -z'
5 '-x, y, -z'
6 'x, -y, -z'
7 'x, y, -z'
8 '-x, -y, -z'
9 '-y, -x, z'
10 'y, x, z'
11 'y, -x, z'
12 '-y, x, z'
13 'x, -y, z'
14 '-x, y, z'
15 '-x, -y, z'
16 'x, y, z'
17 'y+1/2, x+1/2, -z+1/2'
18 '-y+1/2, -x+1/2, -z+1/2'
19 '-y+1/2, x+1/2, -z+1/2'
20 'y+1/2, -x+1/2, -z+1/2'
21 '-x+1/2, y+1/2, -z+1/2'
22 'x+1/2, -y+1/2, -z+1/2'
23 'x+1/2, y+1/2, -z+1/2'
24 '-x+1/2, -y+1/2, -z+1/2'
25 '-y+1/2, -x+1/2, z+1/2'
26 'y+1/2, x+1/2, z+1/2'
27 'y+1/2, -x+1/2, z+1/2'
28 '-y+1/2, x+1/2, z+1/2'
29 'x+1/2, -y+1/2, z+1/2'
30 '-x+1/2, y+1/2, z+1/2'
31 '-x+1/2, -y+1/2, z+1/2'
32 'x+1/2, y+1/2, z+1/2'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Be 0
Ti 0
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
_atom_site_attached_hydrogens
Be1 Be 8 f 0.25 0.25 0.25 . 1. 0
Be2 Be 8 i 0.35 0 0 . 1. 0
Be3 Be 8 j 0.28 0.5 0 . 1. 0
Ti1 Ti 2 a 0 0 0 . 1. 0
# End of TTdata_616454-ICSD
|
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https://github.com/materialsproject/pymatgen/pull/471
| 177,435,358
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MDExOlB1bGxSZXF1ZXN0ODU1ODAwNjQ=
| 471
|
updates
|
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[
"Sure I can revert Eos.py. I used the unittests as the reference for refactoring. In future please make sure that the unittests actually test the important API so that these sort of issues won't happen. Also I noticed that the original Eos.py module looks almost exactly the same as the one in ase python package(just the class names are changed). https://wiki.fysik.dtu.dk/ase/_modules/ase/eos.html#EquationOfState\nDid you copy the module from there? If so I think that must be mentioned in the module .. any comments on this bhfl @shyuep\n",
"Yes, I agree with @matk86 . While I agree with the general principle that API changes should be minimized, especially for core classes, refactoring should be expected. The benchmarking of what the API actually is should be the unittests that actually test against the expected API. Once that is done properly, the person implementing the new scheme can try to do a proper deprecation.\n\n@matk86 I saw that you reverted the EOS changes. I suggest you put the new EOS back in as maybe eos_2.py. That way, @gmatteo can integrate your changes properly and add unittests.\n",
"Yes, I took the equations from ase and the the deltafactor_polyfit from the deltafactor package. \nWe use eos.py to compare ground state calculations done with different codes and different\npython frameworks hence it's important to have a similar implementation to reduce numerical noise. \nEOS_fit is a wrapper around the different equations and provides extra tools for post-processing.\n",
"doesn't copying without mentioning the source violate ase's license agreement?\n",
"There was a comment in `deltafactor_polyfit`\n\n```\nTaken from deltafactor/eosfit.py\n```\n\nthat, actually, you removed in your version.\nI will mention in the docstring that the version of eos.py is inspired to a similar implementation provided by ase.\n",
"ase wasn't mentioned anywhere\n"
] | 2016-09-16T14:10:56
| 2016-09-20T22:55:04
|
2016-09-16T14:18:30Z
|
CONTRIBUTOR
|
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## Summary
- feff io: add api to parse the atomic luster as molecule, some cleanup
- refactor and cleanup analysis.eos.py
|
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| 177,441,321
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MDExOlB1bGxSZXF1ZXN0ODU1ODQyNDk=
| 472
|
update phonon example notebook
|
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[] | 2016-09-16T14:36:39
| 2016-09-16T15:35:54
|
2016-09-16T15:35:53Z
|
CONTRIBUTOR
|
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## Summary
- add phonon dos to the example notebook and rename it
|
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MDExOlB1bGxSZXF1ZXN0ODU2NTI2ODk=
| 473
|
bug fix in eos.py
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[] | 2016-09-16T23:13:31
| 2016-09-17T03:09:09
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2016-09-17T03:09:09Z
|
CONTRIBUTOR
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| 177,724,658
|
MDU6SXNzdWUxNzc3MjQ2NTg=
| 474
|
Incorrect Structure from CIF if _symmetry_equiv_pos_as_xyz values are not a list
|
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[] | null |
[
"Thanks for reporting this. I have pushed a fix.\n",
"Thanks, @shyuep!\n"
] | 2016-09-19T08:04:57
| 2016-09-20T06:48:39
|
2016-09-19T12:51:46Z
|
CONTRIBUTOR
|
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## System
- Pymatgen version: 4.3.1
- Python version: 2.7.3
- OS version: Ubuntu 12.04
## Summary
- value of CIF tag `_symmetry_equiv_pos_as_xyz` may be single and unlooped (basically for P1 space group, when it's `x,y,z`);
- CIF construction `_symmetry_equiv_pos_as_xyz x,y,z` results in incorrect list of symmetry operators thus leading to incorrect structure;
- bug manifests in flattened structures and overlapping atoms.
## Example code
``` python
from pymatgen import Structure
Structure.from_file("mwe-PASS.cif")
Structure.from_file("mwe-FAIL.cif")
```
## Files
Both files are adapted from [COD entry 2002297](http://www.crystallography.net/cod/2002297.cif). Both files are valid CIFs and should generate the same structure.
- mwe-PASS.cif:
```
data_2002297
loop_
_symmetry_equiv_pos_as_xyz x,y,z
_cell_angle_alpha 90.(0)
_cell_angle_beta 118.99
_cell_angle_gamma 90.(0)
_cell_length_a 5.387
_cell_length_b 8.575
_cell_length_c 5.22
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Pb1 0.0599 0.25 0.0302
Pb2 0.947 0.7501 0.974
Ga1 0.3488 0.0535 0.7127
Ga2 0.6585 0.9486 0.368
Ga3 0.6576 0.5523 0.3674
Ga4 0.3478 0.4476 0.7118
O1 0.3684 0.0607 0.3715
O2 0.3668 0.4426 0.3667
O3 0.0042 0.9985 0.6753
O4 0.001 0.5028 0.6724
O5 0.6349 0.8408 0.0012
O6 0.6399 0.5608 0.0042
O7 0.6242 0.7523 0.4883
O8 0.3868 0.2494 0.8706
```
- mwe-FAIL.cif:
```
data_2002297
_symmetry_equiv_pos_as_xyz x,y,z
_cell_angle_alpha 90.(0)
_cell_angle_beta 118.99
_cell_angle_gamma 90.(0)
_cell_length_a 5.387
_cell_length_b 8.575
_cell_length_c 5.22
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Pb1 0.0599 0.25 0.0302
Pb2 0.947 0.7501 0.974
Ga1 0.3488 0.0535 0.7127
Ga2 0.6585 0.9486 0.368
Ga3 0.6576 0.5523 0.3674
Ga4 0.3478 0.4476 0.7118
O1 0.3684 0.0607 0.3715
O2 0.3668 0.4426 0.3667
O3 0.0042 0.9985 0.6753
O4 0.001 0.5028 0.6724
O5 0.6349 0.8408 0.0012
O6 0.6399 0.5608 0.0042
O7 0.6242 0.7523 0.4883
O8 0.3868 0.2494 0.8706
```
|
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| 177,912,223
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MDExOlB1bGxSZXF1ZXN0ODU4NzkyNDk=
| 475
|
DO NOT MERGE: Request for review of Eqn of State Thermal
|
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[] | null |
[
"at-mentioning to track discussion: @tschaume @montoyjh @kristinpersson \n",
"The hegemon does not need to be involved in this discussion right?\n",
"It is impossible to code review something that has 758 changed files. Pls copy your repo, refork the code, and then make only the changes that are on top of the existing pymatgen. \n",
"Duplicate of #481\n"
] | 2016-09-19T22:12:34
| 2016-09-21T17:37:11
|
2016-09-21T17:37:11Z
|
NONE
|
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Pull request for review of equation of state thermal properties code for Materials Project.
FAO: Patrick Huck, Donny Winston, Joey Montoya, Kristin Persson
Code is in pymatgen/analysis/eqn_of_state_thermal
Branch eos_thermal_pmg4 is implemented in pytmatgen 4
Fits E(V) data to equations of state and Debye-Grueneisen model to obtain thermal properties.
|
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MDU6SXNzdWUxNzc5MTk0Njc=
| 476
|
Problem parsing vasprun.xml affecting many jobs
|
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[] | null |
[
"Note: the files in the above Dropbox link are all you need to reproduce the error. But, if you want to look at the entire run, it is available here:\n\nhttps://www.dropbox.com/sh/a0j604ek0pacjml/AABVyg7xL3HAvpN8j5TLWf8Va?dl=0\n",
"Fixed, but if you have a file that is much smaller that can be used for testing, it would be great. This file is so large that parsing is monstrously slow.\n",
"I couldn't find one that was smaller that had the exact same error, but the following file has a similar error in the older pymatgen that is now fixed\n\nhttps://www.dropbox.com/sh/8g89dxlwfufpazx/AADBFp6PrTbn8Q41Qs1elpApa?dl=0\n"
] | 2016-09-19T22:54:54
| 2016-09-20T20:55:12
|
2016-09-20T02:31:10Z
|
MEMBER
|
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## System
- Pymatgen version: master
- Python version: 2.7
- OS version: both Mac + Linux
## Summary
- Type the example code below
- You will get an error in parsing the vasprun.xml file
- This error seems to affect many high-throughput jobs
## Example code
``` python
from pymatgen.io.vasp.outputs import Vasprun
vr = Vasprun("vasprun.xml.gz", parse_eigen=True, parse_projected_eigen=True)
bs = vr.get_band_structure(line_mode=False)
```
## Error message
```
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/io/vasp/outputs.py", line 729, in get_band_structure
for j in range(len(kpoints))]
KeyError: u'-1'
```
## Suggested solution (if any)
- None, I haven't looked into the issue in detail
## Files (if any)
https://www.dropbox.com/sh/6equ9s91ljg3xgj/AACgTOg_h5p3t2wpHDjHSEw0a?dl=0
|
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|
Small update for abinit
|
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[] | 2016-09-20T13:16:18
| 2016-09-20T13:45:49
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2016-09-20T13:45:49Z
|
CONTRIBUTOR
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| 478
|
revert eos.py
|
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[] | 2016-09-20T22:11:09
| 2016-09-20T22:18:37
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2016-09-20T22:18:37Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0ODYwNjg0NDI=
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|
add eos_2.py
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[] | 2016-09-20T22:31:54
| 2016-09-20T23:08:48
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2016-09-20T23:08:48Z
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CONTRIBUTOR
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|
Use Element attributes to specify element sets for MPRester.parse_criteria
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[
"@shyuep recent PRs are failing checks due to a missing MAPI_KEY env var. Perhaps this is related to the introduction of .pmgrc.yaml?\n",
"Looks good Donny. \n\nCan we add not in:\n\n``` python\nif '$nin' in val:\n elt_list = [e for e in elt_list\n if getattr(e, field) not in val['$nin']]\n```\n",
"Not failing on master branch....\n"
] | 2016-09-21T00:14:59
| 2016-09-25T20:09:56
|
2016-09-25T20:09:56Z
|
MEMBER
|
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Please do not merge. This PR, though a working implementation, is for discussion/review. Please comment (esp. @shyamd).
## Summary
Allow filtering on `pymatgen.core.periodic_table.Element` attributes, using a subset of MongoDB filter syntax, in order to specify element sets as part of `MPRester.query` calls. Enables criteria strings such as
``` python
'{"group":1}-O'
'{"group":1}-{"group":2}-*'
'{"X":{"$lt":1,"$gt":0.9}}'
'{"$or":[{"is_alkali":true},{"is_alkaline":true}]}-{"group":{"$in":[13,14,15,16]}}'
# etc.
```
Uses `json.loads`, so use `true`/`false` (not `True`/`False`) and `null` (not `None`).
## TODO
- Only a limited subset of MongoDB operators (`$in`, `$or`, `$lt`, `$gt`) currently supported.
- Determine if this is in fact a valuable addition, and if so, weigh this design/approach against alternatives.
|
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|
DO NOT MERGE: Request for review of Eqn of State Thermal
|
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[] | 2016-09-21T00:27:44
| 2016-09-25T20:09:57
|
2016-09-25T20:09:57Z
|
NONE
|
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Pull request for review of equation of state thermal properties code for Materials Project.
FAO: Patrick Huck, Donny Winston, Joey Montoya, Kristin Persson
Code is in pymatgen/analysis/eqn_of_state_thermal
Branch eos_thermal_pmg4 is implemented in pytmatgen 4
Fits E(V) data to equations of state and Debye-Grueneisen model to obtain thermal properties.
|
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Wrong structure from spacegroup I4/mmm
|
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[] | null |
[
"Your input is wrong. The [\"Be\", \"Ti\"] should be [\"Be\", \"Ti\", \"Ti\", \"Ti\"] I think.\n",
"Thank you! Now it works.\nThe correct input should be other way round: [\"Be\",\"Be\",\"Be\",\"Ti\"].\n"
] | 2016-09-21T07:31:50
| 2016-09-21T12:28:14
|
2016-09-21T12:17:23Z
|
NONE
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## System
- Pymatgen version: pymatgen (4.3.0)
- Python version: Python 2.7.6
- OS version: Ubuntu 14.04.4 LTS
## Summary
- The following code should generate structure of Be12Ti. For both spacegroup "I4/mmm" or its number "139" (as in example below) the code generate POSCAR file with 8 Ti and 8 Be atoms, which is obviously wrong as the ratio of Be/Ti should be 12.
- The input data for the structure are based on ICSD 616454.
## Example code
``` python
import pymatgen as mg
from pymatgen.analysis.defects.point_defects import Interstitial
lat = mg.Lattice.tetragonal(7.35,4.19)
structure = mg.Structure.from_spacegroup("139",lat,["Be","Ti"],
[[0.25, 0.25, 0.25],
[0.35, 0.0, 0.0 ],
[0.28, 0.50, 0.0 ],
[0.0, 0.0, 0.0 ]])
structure.to(filename="POSCAR")
```
## Error message
```
no error message, but wrong output to POSCAR
```
## Suggested solution (if any)
- Too many symmetry operations were applied to Ti atoms, while for Be some were missing.
## Files (output POSCAR)
```
Ti8 Be8
1.0
7.350000 0.000000 0.000000
0.000000 7.350000 0.000000
0.000000 0.000000 4.190000
Be Ti
8 8
direct
0.250000 0.250000 0.250000 Be
0.750000 0.750000 0.750000 Be
0.750000 0.750000 0.250000 Be
0.750000 0.250000 0.250000 Be
0.750000 0.250000 0.750000 Be
0.250000 0.250000 0.750000 Be
0.250000 0.750000 0.750000 Be
0.250000 0.750000 0.250000 Be
0.350000 0.000000 0.000000 Ti
0.650000 0.000000 0.000000 Ti
0.850000 0.500000 0.500000 Ti
0.000000 0.350000 0.000000 Ti
0.150000 0.500000 0.500000 Ti
0.000000 0.650000 0.000000 Ti
0.500000 0.850000 0.500000 Ti
0.500000 0.150000 0.500000 Ti
```
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MDU6SXNzdWUxNzg1MzAwMDA=
| 483
|
Incorrect structure generated from "CIF" file for some systems
|
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[
"I think it’s your symprec, your probably forcing a higher or lower symmetry in writing the gif.\n\nbest,\nMichiel\n\n> On 22 Sep 2016, at 08:10, Guoqiang Lan notifications@github.com wrote:\n> \n> this is a feature request, please simply state the requested feature.>\n> \n> System\n> \n> Pymatgen version: 4.3.2\n> Python version: 2.7\n> OS version: Linux\n> Summary\n> \n> Some structures (e. g. Fe2O3, mp-19306) generated from \"CIF\" files are incorrect\n> Example code\n> \n> from pymatgen.io.cif import CifWriter\n> material_id = \"mp-19306\"\n> structure = mpr.get_structure_by_material_id(material_id, final=True)\n> print structure.composition.reduced_formula\n> cif = CifWriter(structure, symprec=0.1)\n> cif.write_file(material_id+\".cif\")\n> structure2 = Structure.from_file(material_id+\".cif\")\n> print structure2.composition.reduced_formula\n> output\n> \n> Fe3O4\n> Fe5O4\n> Description of problem\n> \n> Firstly, I generated a \"CIF\" file from the computed structure from the materials project database. Then I regenerate a pymatgen structure object from this \"CIF\" file, but the structure was not correct anymore. I can make sure that the crystal information in \"CIF\" file is correct. There should be some bugs in \"Structure.from_file\" function when dealing with \"CIF\" file?\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub https://github.com/materialsproject/pymatgen/issues/483, or mute the thread https://github.com/notifications/unsubscribe-auth/AF0i-D0otxL3Gn3phxk218o9u40XE5TVks5qshvIgaJpZM4KDjnO.\n",
"@wmdrichards Can you look into this pls?\n",
"I agree with Michiel - the SpacegroupAnalyzer returns a nonsense structure\nwith symprec=0.1 (look at the written out cif).\nMaybe we should warn users trying too large values for symprec? Though I\nhaven't figured out its exact implementation, so I don't know what would be\nconsidered large enough to have this problem. Or we could do a composition\ncheck on SpacegroupAnalyzer.get_refined_structure()\n\nOn Thu, Sep 22, 2016 at 6:56 AM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> @wmdrichards https://github.com/wmdrichards Can you look into this pls?\n> \n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/483#issuecomment-248869682,\n> or mute the thread\n> https://github.com/notifications/unsubscribe-auth/ABDqPXI8V8ZM0rOGwfpj6ax4OMKeA-00ks5qsl7KgaJpZM4KDjnO\n> .\n",
"@wmdrichards \nHi, it is nothing to do with the symprec. I try to input this \"CIF\" file to \"Vesta\" to generate a new POSCAR. This POSCAR is correct with correct atomic ratio, Fe:O=3:4. But the \"Structure.from_file\" function didn't output a structure correctly.\nBy the way, the purpose I used a large symprec (0.1) is to get the symmetry of Fe3O4 back. The spacegrop of the computed structure of Fe3O4 in the material project database is \"R-3m\", but it should be with \"Fd-3m\" spacegroup. Only by using large symprec can I get the \"Fd-3m\" symmetry back.\nRegards \nGuoqiang\n",
"It was a symprec issue in the cif generation. Closed with bc4096e\n"
] | 2016-09-22T06:10:13
| 2016-09-25T22:30:03
|
2016-09-25T22:30:02Z
|
NONE
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<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
- Pymatgen version: 4.3.2
- Python version: 2.7
- OS version: Linux
## Summary
1. Some structures (e. g. Fe2O3, mp-19306) generated from "CIF" files are incorrect
## Example code
``` python
from pymatgen.io.cif import CifWriter
material_id = "mp-19306"
structure = mpr.get_structure_by_material_id(material_id, final=True)
print structure.composition.reduced_formula
cif = CifWriter(structure, symprec=0.1)
cif.write_file(material_id+".cif")
structure2 = Structure.from_file(material_id+".cif")
print structure2.composition.reduced_formula
```
## output
```
Fe3O4
Fe5O4
```
## Description of problem
Firstly, I generated a "CIF" file from the computed structure from the materials project database. Then I regenerate a pymatgen structure object from this "CIF" file, but the structure was not correct anymore. I can make sure that the crystal information in "CIF" file is correct. There should be some bugs in "Structure.from_file" function when dealing with "CIF" file?
|
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| 178,548,103
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MDExOlB1bGxSZXF1ZXN0ODYyOTQ4MDQ=
| 484
|
ce_symbol in chemenv and fix of piecewise polynomial in nebanalysis for scipy > 0.18
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[] | 2016-09-22T08:15:22
| 2016-09-22T10:55:31
|
2016-09-22T10:55:31Z
|
CONTRIBUTOR
|
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|
## Summary
- Added property ce_symbol in CoordinationGeometry (same as mp_symbol) in chemenv
- Fixed NEBAnalysis's piecewise polynomial construction for scipy versions > 0.18.
|
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| 178,883,815
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MDExOlB1bGxSZXF1ZXN0ODY1MTY3OTI=
| 485
|
Chemenv improvent + NEBAnalysis improvements
|
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[
"Hi Shyue,\n\nI made the changes that you suggested and reopened a pull request but the\ncircleCI failed for some tests. The thing is I checked which tests failed\nand I never touched these files or anything related to that. The tests that\nare failing are related to the MPRester so maybe the MaterialsProject was\nnot accessible at the time of the circleCI's build/tests and I can't find a\nway to ask for a \"rebuild\".\n\nDavid\n\nOn Sun, Sep 25, 2016 at 10:10 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> Closed #485 https://github.com/materialsproject/pymatgen/pull/485.\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/485#event-801594176,\n> or mute the thread\n> https://github.com/notifications/unsubscribe-auth/ADdRUJR1HzcpC7eEJRINK_PTEd888nYmks5qttUcgaJpZM4KFAS4\n> .\n"
] | 2016-09-23T13:54:23
| 2016-09-29T08:32:39
|
2016-09-25T20:09:59Z
|
CONTRIBUTOR
|
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|
## Summary
- Removed old and commented code from chemenv.
- Made NEBAnalysis MSONable.
- Made NEBAnalysis's **init** method independent from vasp (NEB structures and energies could come from any other code).
- Created from_outcars method for NEBAnalysis (to replace old **init**).
- Created test for NEBAnalysis.
|
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| 179,342,570
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MDExOlB1bGxSZXF1ZXN0ODY4MjI5NDM=
| 486
|
minor io.feff update
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[] | 2016-09-26T21:31:50
| 2016-09-26T21:41:14
|
2016-09-26T21:41:14Z
|
CONTRIBUTOR
|
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- add cluster attribute to Atoms and refactor input file generation
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Chemenv improvents + NEBAnalysis improvements
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[] | 2016-09-27T10:21:15
| 2016-09-29T13:16:40
|
2016-09-29T13:16:40Z
|
CONTRIBUTOR
|
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## Summary
- Added method compute_coordination_environments in LocalGeometryFinder (now, a one-line command gets the environment of a given structure for a given "strategy").
- Removed old and commented code from chemenv.
- Made NEBAnalysis MSONable (as_dict() method has to be implemented because structures is a list of Structure objects in **init** and then the default as_dict() in MSONable does not allow for BSON format).
- Made NEBAnalysis's **init** method independent from vasp (NEB structures and energies could come from any other code).
- Created from_outcars method for NEBAnalysis (to replace old **init**).
- Created test for NEBAnalysis.
- Possibility to force the qnodes parameter for some queue in abinit/io/qadapters. This can be used for example when a queue allows a shared mode (for which when you ask e.g. 10 processors, these processors can be split onto up to 10 nodes) but you want to get your cpus on the same node (as much as possible, depending on the hardware).
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MDU6SXNzdWUxNzk3NDIzODg=
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|
Incorrect Structure from CIF after defaulting to P1
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[
"While this can certainly be done, I do not think it is something that is useful. The problem with taking the symmetry operations from the spacegroups is that many spacegroups have different settings. Without explicit statement of the operations, it is impossible to be sure what setting the atomic positions are given in. \n",
"I agree that such approach would not produce correct results in 100% cases. We at the Crystallography Open Database have tabulated the list of the most prominent space groups (https://github.com/sauliusg/cod-tools/blob/master/src/lib/perl5/COD/Spacegroups/Lookup/COD.pm, could be reused) and it produces correct results as long as all extra settings are provided.\n\nAnyway, producing correct symmetry operators for guessed P1 space group would be enough to fix the bug for now.\n",
"Actually, the CIF parser code already attempts to determine the space group from the H-M symbol. However, the symbol in this case is P121/n1, which is not the standard setting. The spacegroup class in pymatgen only contains the main standard settings, e.g., P21/c.\n",
"I can certainly copy the COD.pm file and use it as a backup. IS there an issue with using the CoD.pm file?\n",
"I see. I haven't noticed that this case is in non-standard setting. Only issue with COD.pm is licensing, since it's a part of cod-tools package (https://github.com/sauliusg/cod-tools), which is licensed under GNU GPL v2.\n",
"If it is GPL v2, then I should be able to use it. I will of course indicate it is obtained from COD.\n",
"OK, I have fixed this.\n",
"Great, thanks!\n"
] | 2016-09-28T11:01:49
| 2016-09-30T06:58:02
|
2016-09-29T18:21:44Z
|
CONTRIBUTOR
|
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<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
- Pymatgen version: 4.3.2
- Python version: 2.7.3
- OS version: Ubuntu 12.04
## Summary
- if CIF file does not contain the list of symmetry operators (`_symmetry_equiv_pos_as_xyz` data item), P1 space group is selected by default;
- however, this results in incorrect list of symmetry operators thus leading to incorrect structure;
- bug manifests in "linear" structures (y and z coordinates of all atoms are set to `0.000000`).
## Example code
``` python
from pymatgen import Structure
Structure.from_file("2002023.cif")
Structure.from_file("2105667.cif")
```
## Error message
```
/usr/local/lib/python2.7/dist-packages/pymatgen/io/cif.py:422: UserWarning: No _symmetry_equiv_pos_as_xyz type key found. Defaulting to P1.
warnings.warn("No _symmetry_equiv_pos_as_xyz type key found. "
```
## Suggested solution
- I suggest taking lists of symmetry operators according to the values of `_symmetry_space_group_name_Hall`, `_symmetry_space_group_name_H-M` and like tags. It should fix this issue as well as incorrect assumption of space groups.
## Files (if any)
- http://www.crystallography.net/cod/2002023.cif@186821
- http://www.crystallography.net/cod/2105667.cif@186821
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io.feff updates
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[] | 2016-09-28T19:04:33
| 2016-09-28T19:33:15
|
2016-09-28T19:33:15Z
|
CONTRIBUTOR
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- bug fix and minor refactoring in Atoms
- add more unittests
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DO NOT MERGE: Request for review of Eqn of State Thermal
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[
"I have just briefly skimmed this and I have a few questions.\n\n1) Why did you implement a class for an isotropic strain on your structure? Your class does one thing, which is running the `apply_strain()` method and you that transformation in one place. Why didn't you just use the `apply_strain()` method in the first place?\n\n2) Your `ModifiedVolumeStructureSet` class only has `init()` as a method. That is a strong sign that you should just be writing a function that returns a list of modified structures. I can see how you might want to use the `strainfactors` property later, but you don't use it now and you could easily calculate it by comparing the volume of the strained structure to the volume of the relaxed structure. \n\nI would also suggest that whether or not you make this a function that you change the step size parameter to the maximum strain, for example 10% strain. The reason for this is that no matter if a user wants to create 5 structures or (for some reason) 100, they will always get a realistic volume deformations. Here your code would apply a 50% strain if a user passed in `nstructs=100` and did not change the step size. I would suggest using NumPy's linspace to go from `-strain` to `strain` with `nstructs`, where `strain` is again something reasonable like 10%. Also, 28 structures seems like a strange default, but that is a nit-pick. \n\nAs I was writing this, I went and looked at your MPWorks commits. I would highly suggest taking a look at the [MatMethods project on GitHub](https://github.com/hackingmaterials/matmethods), which has preset workflows already built for thermal properties calculations with both the Debye model and using phonons with the phonopy project. It uses FireWorks, pymatgen, and custodian, and if you are running MPWorks, MatMethods should be as close to a drop-in replacement that is out there. \n",
"Hi Brandon,\n\nJust FYI on your final point, MatMethods is the future of MP production workflows, but MPWorks is likely going to be used for a little while longer, mostly because of changes in DB infrastructure that we're in the process of implementing in order to get MatMethods production ready.\n",
"@montoyjh, you're right, I should have mentioned that. I wasn't sure if @ctoher knew about MatMethods and I wanted to help him and others who come across this to know that there are other solutions out there so they don't spend too much time re-implement code that already exists. As you know, MatMethods lets you choose from several EOS, which is not implemented here. That being said, those analysis functions might be more in the scope of pymatgen than MatMethods. \n",
"PR #592 implements the numerical eos.Thermal properties can be evaluated using atomate package. So this PR can be closed.",
"Agreed. Thanks!"
] | 2016-09-28T23:42:05
| 2017-02-23T20:59:19
|
2017-02-23T20:58:58Z
|
NONE
|
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Pull request for review of equation of state thermal properties code for Materials Project. Updated to re-clone pymatgen source and update fork after changes to pymatgen repo.
FAO: Patrick Huck, Donny Winston, Joey Montoya, Kristin Persson
Code is in pymatgen/analysis/eqn_of_state_thermal
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| 180,419,734
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MDU6SXNzdWUxODA0MTk3MzQ=
| 491
|
BandStructureSymmLine.as_dict fails for NoneType vbm energy
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[
"Thanks!\n"
] | 2016-09-30T23:05:34
| 2016-09-30T23:37:51
|
2016-09-30T23:12:10Z
|
MEMBER
|
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A [recent commit](https://github.com/materialsproject/pymatgen/commit/3f1d4a06ef40439bd95ef8af837cac08222e0d24) breaks serialization of objects that have no (`None`) vbm["energy"], e.g. zero-gap materials, by trying to call `tolist` on `None`.
## System
- Pymatgen version: 4.4.0
- Python version: 2.7.*
- OS version: OSX
## Example code
``` python
from pymatgen import MPRester
m = MPRester()
m.get_bandstructure_by_material_id('mp-81') # Au
```
## Error message
```
MPRestError: 'NoneType' object has no attribute
'tolist'. Content: {"valid_response": false, "version":
{"pymatgen": "4.4.0", "db": "2.0.0", "rest": "2.0"}, "traceback": "Traceback (most
recent call last):\n File
\"/var/www/python/matgen/materials_django/rest/rest.py\", line
91, in wrapped\n d = func(*args, **kwargs)\n File
\"/var/www/python/matgen/materials_django/materials/rest.py\",
line 52, in get_vasp_property\n prop: s.as_dict()})\n File
\"/var/www/python/matgen/lib/python2.7/site-packages/pymatgen/electronic_structure/bandstructure.py\",
line 781, in as_dict\n d[\"vbm\"] = {\"energy\":
vbm[\"energy\"].tolist(),\nAttributeError: 'NoneType' object has
no attribute
'tolist'\n", "created_at": "2016-09-30T15:51:21.079279", "error": "'NoneType'
object has no attribute 'tolist'"}
```
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| 180,660,530
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MDExOlB1bGxSZXF1ZXN0ODc3MzAzODM=
| 492
|
feff io updates
|
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[] | 2016-10-03T14:50:44
| 2016-10-03T15:55:14
|
2016-10-03T15:55:14Z
|
CONTRIBUTOR
|
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- support for EELS io
- EELS(near edge and extended spectrum) input sets
- added and updated unittests
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| 180,937,336
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MDExOlB1bGxSZXF1ZXN0ODc5MjU3NjI=
| 493
|
Added a MultiStructuresVis to visualize series of structures (used to visualize from e.g. NEB or MD simulations)
|
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[
"I do not understand the mymul method for structure. How is that different from structure \\* [2, 2, 2]?\n",
"Hi Shyue,\n\nIt just allows to disable the fallback to the unit cell. I wasnt sure\nwhether I could add an optional parameter to the __mul__method but I\nthought not as it is a \"built-in\" method.\n\nDavid\n\nOn Wed, Oct 5, 2016 at 2:30 AM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> I do not understand the mymul method for structure. How is that different\n> from structure \\* [2, 2, 2]?\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/493#issuecomment-251551975,\n> or mute the thread\n> https://github.com/notifications/unsubscribe-auth/ADdRUOtIiABFfs9pjywYeiEuo12TyEVNks5qwu-pgaJpZM4KN3cm\n> .\n",
"If that is the preference, simply remove the to_unit_cell in **mul**. I am not a fan of having methods that do exactly the same thing with one different sub behavior. Structure already has way too methods as it is.\n",
"Hi Shyue,\n\nI remove the to_unit_cell in **mul** and removed mymul.\n\nDavid\n\nOn Wed, Oct 5, 2016 at 5:40 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> If that is the preference, simply remove the to_unit_cell in _mul_. I am\n> not a fan of having methods that do exactly the same thing with one\n> different sub behavior. Structure already has way too methods as it is.\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/493#issuecomment-251712662,\n> or mute the thread\n> https://github.com/notifications/unsubscribe-auth/ADdRUI3ldUQMrGT4iStuCDQMZt1oAdyfks5qw8T-gaJpZM4KN3cm\n> .\n"
] | 2016-10-04T16:09:25
| 2016-10-06T15:35:18
|
2016-10-06T15:35:18Z
|
CONTRIBUTOR
|
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## Summary
Added a MultiStructuresVis to visualize series of structures (used to visualize from e.g. NEB or MD simulations)
- Visualization of multiple structures with vtk (using "n" and "p" keys to go from one structure to another)
- Possibility to have an "animated" movie of the structures (using the "m" key).
- Possibility to tag (e.g. in red) specific sites in the structures in order to "follow" them in the MultiStructuresVis
- Small refactoring of the **mul** method in Structure (sites were automatically falled back to the unit cell while I needed them not to be falled back for the visualization ... the **mul** method behavior is not changed)
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|
Added rotate_sites method for Molecule and option to offset center for get_boxed_structure
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[
"Thanks. I cannot merge this request as you are adding back 5 files. I think the only thing that was changed in structure.py? Pls make a copy, refork, and clone, and move structure,py over. Also, for all new functionality, pls implement unittests.\n"
] | 2016-10-04T20:36:12
| 2016-10-05T02:58:41
|
2016-10-05T02:58:41Z
|
CONTRIBUTOR
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These methods are useful for defining a specific orientation (rotation and translation) of a Molecule in a boxed structure.
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added rotate_sites and modified get_boxed_structure. tests included.
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fatal: refusing to merge unrelated histories
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[
"Recently, we hit the limit for Github repo sizes on pymatgen because of all the large test files. I had to do a history cleanup. Please make a copy of your existing pyamtgen repo, refork pymatgen, reclone pymatgen, and copy your new changes (I am guessing only files in the pymatgen package directory) over to the new repo. Do a recommit.\n"
] | 2016-10-05T14:49:26
| 2016-10-05T15:34:03
|
2016-10-05T15:34:03Z
|
CONTRIBUTOR
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We are trying to merge merge pymatgen/master
in our branches but git refuses to merge with the following error:
- branch master -> FETCH_HEAD
fatal: refusing to merge unrelated histories
If I look at the history, I see that the commits before Sep 25, 2016 now
have two different ids e.g.
```
Merge branch 'master' of github.com:materialsproject/pymatgen …
Former-commit-id: 948c455b573851b2e89ed83a784c8b0fa788bc99 [formerly 5842306]
Former-commit-id: b149932fa3eecf656d194b87bc4111b73e45c4b0
```
See:
https://github.com/materialsproject/pymatgen/commit/3895853c7f2b4c5a6c89e9c785ea8644d7d841ef
It seems that something changed in the history and git refuses to merge because of that.
github now says that my branch is: 11434 commits ahead, 11509 commits behind materialsproject:master and similar messages are found in the forks of many other developers.
Any idea on what's happening and what could have caused this?
Best,
Matteo
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io.feff updates
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[] | 2016-10-07T17:04:15
| 2016-10-07T17:45:59
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2016-10-07T17:45:59Z
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CONTRIBUTOR
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- support for running feff in reciprocal space mode
- added unittests
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Developed new functionalities for Xdatcar class in pymatgen.io.vasp module
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[
"I'm not sure as to why the checks have failed. I modified only one class that doesn't seem to be imported elsewhere (except for two test cases (i) pymatgen/io/vasp/tests/test_outputs.py and (ii) pymatgen/analysis/tests/test_structure_analyzer.py). I also have not changed the default behavior.\n\n**Update-1:** I think the error appears to be due to lack of API-KEY. But I'm not sure how to pass my API-KEY to the testing environment\n",
"Thanks. Don't worry about the API key. That is a matter for the maintainer, i.e., me. \n",
"Thanks Shyue. That helps.\n"
] | 2016-10-08T04:20:00
| 2016-10-08T18:31:44
|
2016-10-08T18:20:33Z
|
NONE
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## Summary
<Incorporated options to select structures, concatenate new structures with existing one and write the Xdatcar class into a file>
- Added functionality to provide the starting and ending ionic step, to enable removal of structures in NVT AIMD before equilibration.
- Created a function concatenate new structures from a file into existing Xdatcar. Helps in concatenating multiple Xdatcars obtained through restart into a single Xdatcar class.
- Created a function to write the structures in Xdatcar class into a file.
## Additional dependencies introduced (if any)
The default behavior of Xdatcar was not modified only additional optional parameters were introduced in the `__init__` function. So it must not affect any other testcase or code where Xdatcar class is used
<None>
## TODO (if any)
1. Concatenate function needs validation to ensure that the new file contains the same lattice and atoms as that of the Xdatcar class.
2. The class needs to be made MSONable to be able to export the class as a dict to store in json format.
[XdatcarTest.zip](https://github.com/materialsproject/pymatgen/files/517428/XdatcarTest.zip)
crystal lattice and atoms as that of the Xdatcar class >
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| 182,056,705
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MDExOlB1bGxSZXF1ZXN0ODg2OTE2OTA=
| 499
|
feff updates
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[] | 2016-10-10T16:21:02
| 2016-10-10T16:52:27
|
2016-10-10T16:52:27Z
|
CONTRIBUTOR
|
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- support for size dependent feff runs(real v reciprocal)
- add unittest
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MDU6SXNzdWUxODI3MTI5MDI=
| 500
|
orbital key missing in bandstructure vbm and cbm 'projections'
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[
"This is not a bug. In v4.4.0, the format of the projections and eigenvalues objects are changed to a ndarray. THis is much more memory and computationally efficient. All serializations has to work with the new formats.\n",
"but bs.as_dict() fails with \"IndexError: arrays used as indices must be of integer (or boolean) type\"\n",
"Nevermind, no error now..my mistake\n"
] | 2016-10-13T07:14:37
| 2016-10-13T15:11:15
|
2016-10-13T15:03:58Z
|
CONTRIBUTOR
|
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vrun = Vasprun(vasprun.xml.gz, parse_eigen=True, parse_projected_eigen=True)
bs = vrun.get_band_structure(line_mode=True)
before version 4.4.0 bs.get_vbm()['projections'] returned:
{Spin.up: 1: {Orbital.py: 1: array([ 0.1277, 0.1277]),
Orbital.dxy: 4: array([ 0., 0.]),
Orbital.dyz: 5: array([ 0., 0.]),
Orbital.px: 3: array([ 0.0001, 0.0001]),
Orbital.dxz: 7: array([ 0., 0.]),
Orbital.dz2: 6: array([ 0., 0.]),
Orbital.pz: 2: array([ 0.086, 0.086]),
Orbital.s: 0: array([ 0., 0.]),
Orbital.dx2: 8: array([ 0., 0.])}}
Now it returns:
{Spin.up: 1: array([[ 0.00000000e+00, 0.00000000e+00],
[ 1.27700000e-01, 1.27700000e-01],
[ 8.60000000e-02, 8.60000000e-02],
[ 1.00000000e-04, 1.00000000e-04],
[ 0.00000000e+00, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00]])}
This messes up the bandstructure serialization..
vasprun.xml file attached
[vasprun.xml.gz](https://github.com/materialsproject/pymatgen/files/526513/vasprun.xml.gz)
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