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MDExOlB1bGxSZXF1ZXN0MTc5NzI4MjY=
| 101
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Parallel Transformation class added
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MDExOlB1bGxSZXF1ZXN0MTc5OTE2MjI=
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apply_transformation input args corrected for defect transformations
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Having trouble with matplotlib and band structures
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[
"Try reinstalling matplotlib?\n\nShyue Ping\n\nOn July 5, 2014 at 6:30:09 PM, Anubhav Jain (notifications@github.com) wrote:\n\nI am trying to plot band structures using the following code:\n\nfrom pymatgen import MPRester\nfrom pymatgen.electronic_structure.plotter import BSPlotter\n\nif **name** == \"**main**\":\n MAPI_KEY = None # You must change this to your Materials API key! (or set MAPI_KEY env variable)\n MP_ID = \"mp-19017\" # You must change this to the mp-id of your compound of interest\n\n```\nmpr = MPRester(MAPI_KEY) # object for connecting to MP Rest interface\n\nmy_bs = mpr.get_bandstructure_by_material_id(MP_ID)\nBSPlotter(my_bs).show()\n```\n\nSomething seems to be wrong with my matplotlib configuration and the code trips over the tight_layout, giving me the following error:\n\ntight_layout : falling back to Agg renderer\nTraceback (most recent call last):\n File \"/Users/ajain/Documents/code_testing/aj_scratch/aj_play/scratch.py\", line 12, in <module>\n BSPlotter(my_bs).show()\n File \"/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/electronic_structure/plotter.py\", line 508, in show\n plt = self.get_plot(zero_to_efermi, ylim, smooth)\n File \"/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/electronic_structure/plotter.py\", line 492, in get_plot\n plt.tight_layout()\n File \"/Library/Python/2.7/site-packages/matplotlib/pyplot.py\", line 1055, in tight_layout\n fig.tight_layout(pad=pad, h_pad=h_pad, w_pad=w_pad)\n File \"/Library/Python/2.7/site-packages/matplotlib/figure.py\", line 1414, in tight_layout\n pad=pad, h_pad=h_pad, w_pad=w_pad)\n File \"/Library/Python/2.7/site-packages/matplotlib/tight_layout.py\", line 117, in auto_adjust_subplotpars\n tight_bbox_raw = union([ax.get_tightbbox(renderer) for ax in subplots])\n File \"/Library/Python/2.7/site-packages/matplotlib/axes.py\", line 8362, in get_tightbbox\n bb_xaxis = self.xaxis.get_tightbbox(renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/axis.py\", line 1008, in get_tightbbox\n ticklabelBoxes, ticklabelBoxes2 = self._get_tick_bboxes(ticks_to_draw, renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/axis.py\", line 993, in _get_tick_bboxes\n extent = tick.label1.get_window_extent(renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/text.py\", line 747, in get_window_extent\n bbox, info = self._get_layout(self._renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/text.py\", line 300, in _get_layout\n ismath=False)\n File \"/Library/Python/2.7/site-packages/matplotlib/backends/backend_agg.py\", line 188, in get_text_width_height_descent\n renderer=self)\n File \"/Library/Python/2.7/site-packages/matplotlib/texmanager.py\", line 608, in get_text_width_height_descent\n page = iter(dvi).next()\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 65, in __iter__\n have_page = self._read()\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 121, in _read\n self._dispatch(byte)\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 209, in _dispatch\n self._fnt_def(k, c, s, d, a, l, n)\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 362, in _fnt_def\n tfm = _tfmfile(n[-l:])\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 872, in _tfmfile\n return _fontfile(texname, Tfm, '.tfm', _tfmcache)\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 862, in _fontfile\n filename = find_tex_file(texname + suffix)\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 843, in find_tex_file\n stderr=subprocess.PIPE)\n File \"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py\", line 679, in __init__\n errread, errwrite)\n File \"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py\", line 1228, in _execute_child\n raise child_exception\nOSError: [Errno 2] No such file or directory\n\nI can turn off tight layout (manually commenting it out), and the main portion of the band structure plot renders fine, but the x-labels and y-labels do not render and I get the following error:\n\nTraceback (most recent call last):\n File \"/Library/Python/2.7/site-packages/matplotlib/artist.py\", line 55, in draw_wrapper\n draw(artist, renderer, _args, *_kwargs)\n File \"/Library/Python/2.7/site-packages/matplotlib/figure.py\", line 898, in draw\n func(_args)\n File \"/Library/Python/2.7/site-packages/matplotlib/artist.py\", line 55, in draw_wrapper\n draw(artist, renderer, *args, *_kwargs)\n File \"/Library/Python/2.7/site-packages/matplotlib/axes.py\", line 1997, in draw\n a.draw(renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/artist.py\", line 55, in draw_wrapper\n draw(artist, renderer, _args, *_kwargs)\n File \"/Library/Python/2.7/site-packages/matplotlib/axis.py\", line 1042, in draw\n ticklabelBoxes, ticklabelBoxes2 = self._get_tick_bboxes(ticks_to_draw, renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/axis.py\", line 993, in _get_tick_bboxes\n extent = tick.label1.get_window_extent(renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/text.py\", line 747, in get_window_extent\n bbox, info = self._get_layout(self._renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/text.py\", line 309, in _get_layout\n ismath=ismath)\n File \"/Library/Python/2.7/site-packages/matplotlib/backends/backend_macosx.py\", line 153, in get_text_width_height_descent\n renderer=self)\n File \"/Library/Python/2.7/site-packages/matplotlib/texmanager.py\", line 608, in get_text_width_height_descent\n page = iter(dvi).next()\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 65, in __iter__\n have_page = self._read()\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 121, in _read\n self._dispatch(byte)\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 209, in _dispatch\n self._fnt_def(k, c, s, d, a, l, n)\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 362, in _fnt_def\n tfm = _tfmfile(n[-l:])\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 872, in _tfmfile\n return _fontfile(texname, Tfm, '.tfm', _tfmcache)\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 862, in _fontfile\n filename = find_tex_file(texname + suffix)\n File \"/Library/Python/2.7/site-packages/matplotlib/dviread.py\", line 843, in find_tex_file\n stderr=subprocess.PIPE)\n File \"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py\", line 679, in __init__\n errread, errwrite)\n File \"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py\", line 1228, in _execute_child\n raise child_exception\nOSError: [Errno 2] No such file or directory\nTraceback (most recent call last):\n File \"/Library/Python/2.7/site-packages/matplotlib/artist.py\", line 55, in draw_wrapper\n draw(artist, renderer, _args, *_kwargs)\n File \"/Library/Python/2.7/site-packages/matplotlib/figure.py\", line 898, in draw\n func(_args)\n File \"/Library/Python/2.7/site-packages/matplotlib/artist.py\", line 55, in draw_wrapper\n draw(artist, renderer, *args, *_kwargs)\n File \"/Library/Python/2.7/site-packages/matplotlib/axes.py\", line 1997, in draw\n a.draw(renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/artist.py\", line 55, in draw_wrapper\n draw(artist, renderer, _args, *_kwargs)\n File \"/Library/Python/2.7/site-packages/matplotlib/axis.py\", line 1042, in draw\n ticklabelBoxes, ticklabelBoxes2 = self._get_tick_bboxes(ticks_to_draw, renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/axis.py\", line 993, in _get_tick_bboxes\n extent = tick.label1.get_window_extent(renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/text.py\", line 747, in get_window_extent\n bbox, info = self._get_layout(self._renderer)\n File \"/Library/Python/2.7/site-packages/matplotlib/text.py\", line 309, in _get_layout\n ismath=ismath)\n File \"/Library/Python/2.7/site-packages/matplotlib/backends/backend_macosx.py\", line 153, in get_text_width_height_descent\n renderer=self)\n File 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stderr=subprocess.PIPE)\n File \"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py\", line 679, in __init__\n errread, errwrite)\n File \"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py\", line 1228, in _execute_child\n raise child_exception\nOSError: [Errno 2] No such file or directory\n\n—\nReply to this email directly or view it on GitHub.\n",
"Ok I didn't get this working (e.g. even after reinstalling matplotlib) but I'm pretty sure this is something in my local matplotlib installation rather than pymatgen. Closing the issue\n",
"Btw I finally solved this - the issue has to do with matplotlib not finding LaTeX. The package installer for Mac LaTeX (MacTeX) installs the latex executables in /usr/texbin, which gets added to the PATH. However PyCharm doesn't see this as part of its path, so it can't find LaTeX and can't plot any chart involving LaTeX. If you set your PyCharm run environment to include /usr/texbin all is well\n"
] | 2014-07-06T01:30:07
| 2014-10-31T23:51:15
|
2014-07-07T04:47:13Z
|
MEMBER
|
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I am trying to plot band structures using the following code:
```
from pymatgen import MPRester
from pymatgen.electronic_structure.plotter import BSPlotter
if __name__ == "__main__":
MAPI_KEY = None # You must change this to your Materials API key! (or set MAPI_KEY env variable)
MP_ID = "mp-19017" # You must change this to the mp-id of your compound of interest
mpr = MPRester(MAPI_KEY) # object for connecting to MP Rest interface
my_bs = mpr.get_bandstructure_by_material_id(MP_ID)
BSPlotter(my_bs).show()
```
Something seems to be wrong with my matplotlib configuration and the code trips over the tight_layout, giving me the following error:
```
tight_layout : falling back to Agg renderer
Traceback (most recent call last):
File "/Users/ajain/Documents/code_testing/aj_scratch/aj_play/scratch.py", line 12, in <module>
BSPlotter(my_bs).show()
File "/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/electronic_structure/plotter.py", line 508, in show
plt = self.get_plot(zero_to_efermi, ylim, smooth)
File "/Users/ajain/Documents/code_matgen/pymatgen_repo/pymatgen/electronic_structure/plotter.py", line 492, in get_plot
plt.tight_layout()
File "/Library/Python/2.7/site-packages/matplotlib/pyplot.py", line 1055, in tight_layout
fig.tight_layout(pad=pad, h_pad=h_pad, w_pad=w_pad)
File "/Library/Python/2.7/site-packages/matplotlib/figure.py", line 1414, in tight_layout
pad=pad, h_pad=h_pad, w_pad=w_pad)
File "/Library/Python/2.7/site-packages/matplotlib/tight_layout.py", line 117, in auto_adjust_subplotpars
tight_bbox_raw = union([ax.get_tightbbox(renderer) for ax in subplots])
File "/Library/Python/2.7/site-packages/matplotlib/axes.py", line 8362, in get_tightbbox
bb_xaxis = self.xaxis.get_tightbbox(renderer)
File "/Library/Python/2.7/site-packages/matplotlib/axis.py", line 1008, in get_tightbbox
ticklabelBoxes, ticklabelBoxes2 = self._get_tick_bboxes(ticks_to_draw, renderer)
File "/Library/Python/2.7/site-packages/matplotlib/axis.py", line 993, in _get_tick_bboxes
extent = tick.label1.get_window_extent(renderer)
File "/Library/Python/2.7/site-packages/matplotlib/text.py", line 747, in get_window_extent
bbox, info = self._get_layout(self._renderer)
File "/Library/Python/2.7/site-packages/matplotlib/text.py", line 300, in _get_layout
ismath=False)
File "/Library/Python/2.7/site-packages/matplotlib/backends/backend_agg.py", line 188, in get_text_width_height_descent
renderer=self)
File "/Library/Python/2.7/site-packages/matplotlib/texmanager.py", line 608, in get_text_width_height_descent
page = iter(dvi).next()
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 65, in __iter__
have_page = self._read()
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 121, in _read
self._dispatch(byte)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 209, in _dispatch
self._fnt_def(k, c, s, d, a, l, n)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 362, in _fnt_def
tfm = _tfmfile(n[-l:])
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 872, in _tfmfile
return _fontfile(texname, Tfm, '.tfm', _tfmcache)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 862, in _fontfile
filename = find_tex_file(texname + suffix)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 843, in find_tex_file
stderr=subprocess.PIPE)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 679, in __init__
errread, errwrite)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1228, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
```
I can turn off tight layout (manually commenting it out), and the main portion of the band structure plot renders fine, but the x-labels and y-labels do not render and I get the following error:
```
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/Library/Python/2.7/site-packages/matplotlib/figure.py", line 898, in draw
func(*args)
File "/Library/Python/2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/Library/Python/2.7/site-packages/matplotlib/axes.py", line 1997, in draw
a.draw(renderer)
File "/Library/Python/2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/Library/Python/2.7/site-packages/matplotlib/axis.py", line 1042, in draw
ticklabelBoxes, ticklabelBoxes2 = self._get_tick_bboxes(ticks_to_draw, renderer)
File "/Library/Python/2.7/site-packages/matplotlib/axis.py", line 993, in _get_tick_bboxes
extent = tick.label1.get_window_extent(renderer)
File "/Library/Python/2.7/site-packages/matplotlib/text.py", line 747, in get_window_extent
bbox, info = self._get_layout(self._renderer)
File "/Library/Python/2.7/site-packages/matplotlib/text.py", line 309, in _get_layout
ismath=ismath)
File "/Library/Python/2.7/site-packages/matplotlib/backends/backend_macosx.py", line 153, in get_text_width_height_descent
renderer=self)
File "/Library/Python/2.7/site-packages/matplotlib/texmanager.py", line 608, in get_text_width_height_descent
page = iter(dvi).next()
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 65, in __iter__
have_page = self._read()
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 121, in _read
self._dispatch(byte)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 209, in _dispatch
self._fnt_def(k, c, s, d, a, l, n)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 362, in _fnt_def
tfm = _tfmfile(n[-l:])
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 872, in _tfmfile
return _fontfile(texname, Tfm, '.tfm', _tfmcache)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 862, in _fontfile
filename = find_tex_file(texname + suffix)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 843, in find_tex_file
stderr=subprocess.PIPE)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 679, in __init__
errread, errwrite)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1228, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/Library/Python/2.7/site-packages/matplotlib/figure.py", line 898, in draw
func(*args)
File "/Library/Python/2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/Library/Python/2.7/site-packages/matplotlib/axes.py", line 1997, in draw
a.draw(renderer)
File "/Library/Python/2.7/site-packages/matplotlib/artist.py", line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/Library/Python/2.7/site-packages/matplotlib/axis.py", line 1042, in draw
ticklabelBoxes, ticklabelBoxes2 = self._get_tick_bboxes(ticks_to_draw, renderer)
File "/Library/Python/2.7/site-packages/matplotlib/axis.py", line 993, in _get_tick_bboxes
extent = tick.label1.get_window_extent(renderer)
File "/Library/Python/2.7/site-packages/matplotlib/text.py", line 747, in get_window_extent
bbox, info = self._get_layout(self._renderer)
File "/Library/Python/2.7/site-packages/matplotlib/text.py", line 309, in _get_layout
ismath=ismath)
File "/Library/Python/2.7/site-packages/matplotlib/backends/backend_macosx.py", line 153, in get_text_width_height_descent
renderer=self)
File "/Library/Python/2.7/site-packages/matplotlib/texmanager.py", line 608, in get_text_width_height_descent
page = iter(dvi).next()
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 65, in __iter__
have_page = self._read()
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 121, in _read
self._dispatch(byte)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 209, in _dispatch
self._fnt_def(k, c, s, d, a, l, n)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 362, in _fnt_def
tfm = _tfmfile(n[-l:])
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 872, in _tfmfile
return _fontfile(texname, Tfm, '.tfm', _tfmcache)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 862, in _fontfile
filename = find_tex_file(texname + suffix)
File "/Library/Python/2.7/site-packages/matplotlib/dviread.py", line 843, in find_tex_file
stderr=subprocess.PIPE)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 679, in __init__
errread, errwrite)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1228, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
```
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https://github.com/materialsproject/pymatgen/pull/104
| 37,361,011
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MDExOlB1bGxSZXF1ZXN0MTgwOTY0NDI=
| 104
|
Dos - CHGCAR - OSZICAR
|
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[] | null |
[] | 2014-07-08T11:27:04
| 2014-07-08T13:31:59
|
2014-07-08T13:31:59Z
|
CONTRIBUTOR
|
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Hello
The following methods were added in Dos class:
\* get_element_spd_dos
\* get_site_spd_dos
Oszicar class was improved to suport non polarized calculations and MD calculations.
Volumetric Data output was not compatible with bader program from u-texas because of the header format of the CHGCAR files.
|
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MDExOlB1bGxSZXF1ZXN0MTgzNDc0ODg=
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|
MPVaspInputSet for LOptics calculations
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[] | 2014-07-14T13:17:07
| 2014-07-17T18:52:26
|
2014-07-17T18:52:26Z
|
CONTRIBUTOR
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MDU6SXNzdWUzNzgwMTU3Nw==
| 106
|
Error installing pymatgen with easyinstall
|
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[
"Can you try installing with pip? Do easy_install pip first.\n\nThe sandbox violation may also be due to dependency installations. The pymatgen,org install instructions also recommends that you install numpy and PyCifRW first manually before installing pymatgen.\n\nShyue Ping\n\nOn July 14, 2014 at 9:18:08 AM, jasterz (notifications@github.com) wrote:\n\nHello, I had this problem while installing pymatgen\n\nerror: Setup script exited with error: SandboxViolation: os.open('/tmp/tmpqlHrBT/hZfPbu', 131266, 384) {}\n\nThe package setup script has attempted to modify files on your system\nthat are not within the EasyInstall build area, and has been aborted.\n\nThis package cannot be safely installed by EasyInstall, and may not\nsupport alternate installation locations even if you run its setup\nscript by hand. Please inform the package's author and the EasyInstall\nmaintainers to find out if a fix or workaround is available.\n\nHow can I resolve this problem?\nThanks and regards.\n\n—\nReply to this email directly or view it on GitHub.\n",
"Hello Shyue Ping, thank you very much for the advice, it worked :) pymatgen installed\n"
] | 2014-07-14T16:18:07
| 2014-07-14T23:38:59
|
2014-07-14T23:38:59Z
|
NONE
|
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|
Hello, I had this problem while installing pymatgen
error: Setup script exited with error: SandboxViolation: os.open('/tmp/tmpqlHrBT/hZfPbu', 131266, 384) {}
The package setup script has attempted to modify files on your system
that are not within the EasyInstall build area, and has been aborted.
This package cannot be safely installed by EasyInstall, and may not
support alternate installation locations even if you run its setup
script by hand. Please inform the package's author and the EasyInstall
maintainers to find out if a fix or workaround is available.
How can I resolve this problem?
Thanks and regards.
|
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Bug fixes in defect transformations
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Non-ionic structures treated by InterstitialTransformation, ValenceIonic...
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2014-07-16T14:57:56Z
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...RadiusEvaluator
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No. of structures returned by defect structures can be controlled
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2014-07-21T22:16:03Z
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Conforming the defect substitution print with ideal substitution
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[] | 2014-07-23T21:35:39
| 2014-07-24T04:34:25
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2014-07-24T04:34:25Z
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to simplify life for materials_django developer
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Vacancy class considers species and no. of struct
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[] | 2014-07-28T19:44:09
| 2014-07-28T19:53:26
|
2014-07-28T19:53:26Z
|
CONTRIBUTOR
|
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Vacancy.make_supercell_with_defects method is updated with options to
specify the site species and the number of super cells to be returned.
Useful when using the class for defect transformations.
|
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MDExOlB1bGxSZXF1ZXN0MTg5OTA1NjI=
| 112
|
Bug fix
|
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[] | 2014-07-28T20:14:56
| 2014-07-28T20:15:19
|
2014-07-28T20:15:19Z
|
CONTRIBUTOR
|
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Vacancy.make_supercell_with_defects method is updated with options to
specify the site species and the number of super cells to be returned.
Useful when using the class for defect transformations.
|
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MDExOlB1bGxSZXF1ZXN0MTg5OTA4NTc=
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|
dilute_solution_model.py added to analysis.defects
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[] | 2014-07-28T20:20:18
| 2014-07-28T20:20:47
|
2014-07-28T20:20:47Z
|
CONTRIBUTOR
|
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Code to plot thermal defect concentration based on "Dilute Solution Model" is added.
The function can be used to compute the defect concentrations for intermetals, and oxides
based on the raw defect energies or flip energies, and the input temperature
|
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|
Modular dilute_solution_model and unit tests
|
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[] | 2014-07-30T19:24:53
| 2014-07-30T19:27:15
|
2014-07-30T19:27:15Z
|
CONTRIBUTOR
|
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The function dilute_solution_model is modularized
and now accepts trial chemical potentials as input and can generate either
the defect concentration plot or defect formation energies only.
In addition unit tests are added for dilute_solution_model
|
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MDExOlB1bGxSZXF1ZXN0MTkxMjc1NDM=
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|
Update surface.py
|
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[] | 2014-07-31T01:02:07
| 2014-07-31T01:03:27
|
2014-07-31T01:03:27Z
|
CONTRIBUTOR
|
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|
Updated version of surface.py. The method in the Slab class has been modified to allow for the enumerating of different termination sites in a slab. A unittest has been added to see if the .cif files generated to represent the slabs with different termination sites has been properly generated. I will email the necessary files in a folder needed to perform the unittests which are to be stored in pymatgen/core.
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| 116
|
Surface
|
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[] | 2014-07-31T01:15:08
| 2014-10-21T00:06:51
|
2014-10-21T00:06:33Z
|
CONTRIBUTOR
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Updated version of surface.py. The method in the Slab class has been modified to allow for the enumerating of different termination sites in a slab. A unittest has been added to see if the .cif files generated to represent the slabs with different termination sites has been properly generated. I will email the necessary files in a folder needed to perform the unittests which are to be stored in pymatgen/core.
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Bug fixes
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[] | 2014-07-31T23:30:45
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2014-07-31T23:33:02Z
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Minor improvements and code formatting
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[] | 2014-08-02T05:57:09
| 2014-08-02T06:02:44
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2014-08-02T06:02:44Z
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|
Minor improvements and code refactoring
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[] | 2014-08-06T23:50:50
| 2014-08-06T23:55:00
|
2014-08-06T23:55:00Z
|
CONTRIBUTOR
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| 39,756,266
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MDU6SXNzdWUzOTc1NjI2Ng==
| 120
|
XYZ file reader doesn't work for scientific notations in coordinates
|
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[] | 2014-08-07T18:52:07
| 2014-08-07T19:07:22
|
2014-08-07T19:07:22Z
|
CONTRIBUTOR
|
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Hi Shyue,
I am troubled by XYZ reader now. For the attached XYZ text, if I use smartio.read_mol to read it. All the exponents in the last column will be removed, which leads to very strange structures.
20
6_methyl_12cyano
C 2.39132145462 -0.700993488928 -7.22293142224e-06
C 1.16730636786 -1.38166622735 -2.77112970359e-06
C -0.0462078447832 -0.703253621312 7.25763973975e-06
C -0.0446745627711 0.715145777585 1.28599208666e-05
C 1.17063702541 1.3856617784 7.03984717718e-06
C 2.3835501347 0.693474260302 -2.75869204339e-06
H 1.14848963649 -2.46975173501 -6.2363287689e-06
H 1.17463663825 2.47337182313 1.10803379569e-05
H 3.31762811486 1.25180237659 -6.13629049593e-06
C -2.34243441853 0.705226646945 3.09963750684e-05
C -2.34471786848 -0.675897822192 2.47523176497e-05
H -3.264017739 -1.25260911129 3.00395200288e-05
N -1.19280872262 1.42229526752 2.46478341936e-05
N -1.20107794012 -1.40090704068 1.26672582223e-05
C 3.69216275092 -1.44795920242 -1.50462841396e-05
H 3.5334671294 -2.53131484452 -1.77090479454e-05
H 4.27277978214 -1.19364282351 0.892474148419
H 4.27277269957 -1.19363719569 -0.892507208765
C -3.56979943858 1.44201645038 4.6841037937e-05
N -4.58834672516 2.00150591825 6.02899938044e-05
Thanks.
Best regards,
Xiaohui
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|
Modified MPBSHSEVaspInputSet to be consistent for the Kpoints with MPHSE...
|
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[] | 2014-08-08T13:39:59
| 2014-08-08T13:58:08
|
2014-08-08T13:58:08Z
|
CONTRIBUTOR
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...VaspInputSet. Changed unit test accordingly.
|
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| 122
|
Surface terminations
|
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[] | 2014-08-08T22:16:06
| 2014-08-08T22:16:31
|
2014-08-08T22:16:31Z
|
CONTRIBUTOR
|
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The updated Slab module from surface.py now supports standardization of terminations when standardize = True (default)
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|
Revert "Surface terminations"
|
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[] | 2014-08-08T22:17:51
| 2014-09-10T21:44:05
|
2014-09-10T21:44:05Z
|
CONTRIBUTOR
|
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Reverts materialsproject/pymatgen#122
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|
Surface terminations
|
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[] | 2014-08-08T22:21:09
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2014-08-09T01:32:44Z
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PyDispatcher dependence
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[
"This is an optional dependency. That's why it is not in the official dependency. We generally try to keep core dependencies low.\n"
] | 2014-08-12T00:34:14
| 2014-08-12T04:04:41
|
2014-08-12T04:04:41Z
|
MEMBER
|
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possibly missing dependency PyDispatcher (not PyDispatch, btw!) fails [abinitio/workflows.py](https://github.com/materialsproject/pymatgen/blob/e47f1c3b32ec367df7a701976898d157718f0d7f/pymatgen/io/abinitio/workflows.py#L14) nosetest.
Add to requirements in installation section of docs?
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MDExOlB1bGxSZXF1ZXN0MTk4NTk5NzI=
| 126
|
Electronic_structure/boltztrap.py - fixed from_dict
|
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[] | 2014-08-15T18:42:22
| 2014-08-18T15:20:09
|
2014-08-18T15:20:09Z
|
NONE
|
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the order in electronic_structure/boltztrap.py BoltztrapAnalyzer.from_dict for the **init** arguments was wrong. Switched 'dos_partial', and 'carrier_conc' to not cause errors in other places.
|
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| 127
|
Bug Fix in feffio.py
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[] | 2014-08-18T05:31:09
| 2014-08-18T13:32:49
|
2014-08-18T13:32:49Z
|
NONE
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Found a single bug that gives bad results, needs to be incorporated into the mpmaster.
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MDExOlB1bGxSZXF1ZXN0MjA1OTM2NTI=
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|
Updated defects codes
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[] | 2014-09-02T06:13:19
| 2014-09-02T14:02:28
|
2014-09-02T14:02:28Z
|
CONTRIBUTOR
|
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1) Added voronoi edgecenters as potential Interstitial sites (point_defects.py)
2) Added solute site preference finder in dilute_solution_model.py
3) Eliminated unused unittest
4) Updated docstrings
|
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MDU6SXNzdWU0MjIzMDM5MA==
| 129
|
Failure to get the coordination number
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[
"I think this is a known issue. The Voronoi coordination does not work for all structures. @hautierg can confirm since he wrote this.\n",
"If it is a known and unfixable issue, perhaps a better error message would\nhelp?\n\nOn Mon, Sep 8, 2014 at 4:05 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> I think this is a known issue. The Voronoi coordination does not work for\n> all structures. @hautierg https://github.com/hautierg can confirm since\n> he wrote this.\n> \n> —\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/129#issuecomment-54900707\n> .\n",
"OK, I debuged it a little bit. When the error is happening, the argument to acos is more than 1.0\nsum(map(np.acos,[-0.32433203513863385, 0.32433203514155151, 1.0000000000000002])).\nThe error is due to numerical precision. There are two solutions to this problem. \n(1)One is to add a check such that if abs(x) for any x shoud be > 1.0, round it 1.0 or -1.0. This will give a small acceptable error\n(2)Use a more robust and accurate solid angle calculation formula based on W. Kahan's methods to compute angles and solid angles. His methods helped me a lot previously w.r.t. acos for needle like angles. The commonly used methods to compute angles result in numerical errors. Normally they don't cause issue, except at the extremes. I am attaching his notes on tetrahedron solid angle.\nhttp://www.cs.berkeley.edu/~wkahan/VtetLang.pdf\n",
"I just pushed a change to fix this. This problem actually exists in a lot of places where acos is used (e.g., in lattice). \n\nI support the implementation of (2), but I don't have the time to do it myself. I would certainly be happy if someone else want to take this on.\n"
] | 2014-09-08T18:55:03
| 2014-09-09T22:03:48
|
2014-09-09T22:02:56Z
|
CONTRIBUTOR
|
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Shyue,
For mpid mp-559848, I am getting the following error when trying to calculate the coordination number for the sites in the structure.
## Code:
import MPRester
from pymatgen.analysis.defects.point_defects import ValenceIonicRadiusEvaluator
mpid = "mp-559848"
struct = MPRester().get_structure_by_material_id(mpid)
vire = ValenceIonicRadiusEvaluator(struct)
## Error:
```
Traceback (most recent call last):
```
File "vor_site_gen_2.py", line 110, in <module>
vire = ValenceIonicRadiusEvaluator(struct)
File "/Users/mbkumar/Research/Defects/pymatgen/pymatgen/analysis/defects/point_defects.py", line 41, in **init**
self._ionic_radii = self._get_ionic_radii()
File "/Users/mbkumar/Research/Defects/pymatgen/pymatgen/analysis/defects/point_defects.py", line 100, in _get_ionic_radii
coord_no = int(round(coord_finder.get_coordination_number(i)))
File "/Users/mbkumar/Research/Defects/pymatgen/pymatgen/analysis/structure_analyzer.py", line 97, in get_coordination_number
return sum(self.get_voronoi_polyhedra(n).values())
File "/Users/mbkumar/Research/Defects/pymatgen/pymatgen/analysis/structure_analyzer.py", line 79, in get_voronoi_polyhedra
results[neighbors[nn[1]]] = solid_angle(center.coords, facets)
File "/Users/mbkumar/Research/Defects/pymatgen/pymatgen/analysis/structure_analyzer.py", line 323, in solid_angle
for i in range(len(n) - 1)])
ValueError: math domain error
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| 42,248,353
|
MDExOlB1bGxSZXF1ZXN0MjA5MjA5Njg=
| 130
|
feffio: defaults for header/pot_string_from_file
|
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[] | 2014-09-08T21:58:32
| 2014-09-08T22:57:41
|
2014-09-08T22:57:41Z
|
MEMBER
|
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set _feff.inp_ as default file names for `header/pot_string_from_file` (backward-compatible).
|
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| 42,653,610
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MDExOlB1bGxSZXF1ZXN0MjExNjgxMzc=
| 131
|
More Py3K fixes in abinitio + new classes for GW calculations (work in progress)
|
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[] | 2014-09-12T17:51:30
| 2014-09-12T19:16:09
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2014-09-12T19:16:09Z
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CONTRIBUTOR
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| 132
|
Python3.2 or PEP414?
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[] | null |
[
"you can use six.u\n\nOn Fri, Sep 12, 2014 at 2:14 PM, gmatteo notifications@github.com wrote:\n\n> unicode literals (i.e. u\"foo\") have been reintegrated in python3.3 (See\n> http://legacy.python.org/dev/peps/pep-0414/) but python3.2 does not\n> support them and the interpreter raises a SyntaxError exception.\n> \n> There are two tests that are failing in my branch due to unicode literals\n> (see https://travis-ci.org/materialsproject/pymatgen/jobs/35144219).\n> \n> How do we handle this issue? Do we avoid unicode literals so that we are\n> compatible with python3.2 or do we assume PEP414 and hence python >= 3.3?\n> \n> —\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/132.\n",
"Yes, but as a general rule, I wouldn't worry about compatibility with Python 3.2. Python < 3.3 has been largely disowned by the Py3 community.\n"
] | 2014-09-12T18:14:51
| 2014-09-12T19:13:48
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2014-09-12T19:13:48Z
|
CONTRIBUTOR
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unicode literals (i.e. u"foo") have been reintegrated in python3.3 (See http://legacy.python.org/dev/peps/pep-0414/) but python3.2 does not support them and the interpreter raises a SyntaxError exception.
There are two tests that are failing in my branch due to unicode literals (see https://travis-ci.org/materialsproject/pymatgen/jobs/35144219).
How do we handle this issue? Do we avoid unicode literals so that we are compatible with python3.2 or do we assume PEP414 and hence python >= 3.3?
|
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|
Dilute solution model returns chem potential and formation enthalpies at all stoichem ratios
|
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[] | 2014-09-17T20:59:11
| 2014-09-17T21:03:48
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2014-09-17T21:03:48Z
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CONTRIBUTOR
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|
Failures in test_dilute_solution_model (sympy 0.7.5)
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[] | 2014-09-18T14:42:30
| 2014-12-09T17:12:18
|
2014-12-09T17:12:18Z
|
CONTRIBUTOR
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Hi all,
I have 3 unit tests failing in my branch in test_dilute_solution_model.
All of them use simpy so I guess it's due to a portability problem in sympy.
I'm using Python 2.7.3, sympy 0.7.5 and numpy 1.8..1
#
## ERROR: test_plot_data_with_chem_pot (pymatgen.analysis.defects.tests.test_dilute_solution_model.DiluteSolutionModelTest)
Traceback (most recent call last):
File "/Users/gmatteo/Coding/git_branches/pymatgen/pymatgen/analysis/defects/tests/test_dilute_solution_model.py", line 66, in test_plot_data_with_chem_pot
trial_chem_pot=self.trial_mu,generate='plot')
File "/Users/gmatteo/Coding/git_branches/monty/monty/dev.py", line 88, in decorated
return _callable(_args, *_kwargs)
File "/Users/gmatteo/Coding/git_branches/pymatgen/pymatgen/analysis/defects/dilute_solution_model.py", line 372, in dilute_solution_model
x = nsolve(vector_func,mu,mu_vals,module="numpy")
File "/Users/gmatteo/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/sympy/solvers/solvers.py", line 2475, in nsolve
x = findroot(f, x0, J=J, **kwargs)
File "/Users/gmatteo/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/sympy/mpmath/calculus/optimization.py", line 975, in findroot
% (norm(f(*xl))**2, tol))
ValueError: Could not find root within given tolerance. (1.43144e-12 > 2.1684e-19)
Try another starting point or tweak arguments.
#
## ERROR: test_plot_data_without_chem_pot (pymatgen.analysis.defects.tests.test_dilute_solution_model.DiluteSolutionModelTest)
Traceback (most recent call last):
File "/Users/gmatteo/Coding/git_branches/pymatgen/pymatgen/analysis/defects/tests/test_dilute_solution_model.py", line 59, in test_plot_data_without_chem_pot
self.struct,self.e0,self.vac,self.asites,self.T,generate='plot')
File "/Users/gmatteo/Coding/git_branches/monty/monty/dev.py", line 88, in decorated
return _callable(_args, *_kwargs)
File "/Users/gmatteo/Coding/git_branches/pymatgen/pymatgen/analysis/defects/dilute_solution_model.py", line 372, in dilute_solution_model
x = nsolve(vector_func,mu,mu_vals,module="numpy")
File "/Users/gmatteo/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/sympy/solvers/solvers.py", line 2475, in nsolve
x = findroot(f, x0, J=J, **kwargs)
File "/Users/gmatteo/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/sympy/mpmath/calculus/optimization.py", line 975, in findroot
% (norm(f(*xl))**2, tol))
ValueError: Could not find root within given tolerance. (1.43144e-12 > 2.1684e-19)
Try another starting point or tweak arguments.
-------------------- >> begin captured stdout << ---------------------
[-7.952002320183595, -6.118608940188247]
--------------------- >> end captured stdout << ----------------------
#
## ERROR: test_plot_data_without_chem_pot (pymatgen.analysis.defects.tests.test_dilute_solution_model.SoluteSiteFinderTest)
Traceback (most recent call last):
File "/Users/gmatteo/Coding/git_branches/pymatgen/pymatgen/analysis/defects/tests/test_dilute_solution_model.py", line 88, in test_plot_data_without_chem_pot
solute_concen=0.01)
File "/Users/gmatteo/Coding/git_branches/monty/monty/dev.py", line 88, in decorated
return _callable(_args, *_kwargs)
File "/Users/gmatteo/Coding/git_branches/pymatgen/pymatgen/analysis/defects/dilute_solution_model.py", line 916, in solute_site_preference_finder
mu_vals = compute_mus()
File "/Users/gmatteo/Coding/git_branches/pymatgen/pymatgen/analysis/defects/dilute_solution_model.py", line 897, in compute_mus
m0 = mu_red[mu[0]].subs([(mu[1],m1),(mu[2],m2)])
TypeError: list indices must be integers, not Symbol
-------------------- >> begin captured stdout << ---------------------
(u'mult', [1, 1])
(u'c0', array([[1, 0, 0],
[0, 1, 0],
[0, 0, 0]]))
(u'site_specie', [u'Al', u'Ni', u'Fe'])
(u'site_mu_map', [0, 1, 2])
(u'specie_site_index_map', [(0, 1), (1, 2), (2, 3)])
[[[-1 1]
[-1 0]
[-1 0]]
[[ 0 -1]
[ 1 -1]
[ 0 -1]]
[[ 0 0]
[ 0 0]
[ 1 1]]]
(u'Ni', u'Al')
(u'Al', u'Al')
(1, 1)
(u'se', -2.08)
(u'Al', u'Ni')
(u'Al', u'Ni')
(1, 2)
(u'Ni', u'Ni')
(2, 2)
(u'se', -1.674)
(u'dE', array([[ 6.56 , 3.98 ],
[-0.41 , 7.101],
[-2.08 , -1.674]]))
1
-mu0
(1, -1, 6.5599999999999996)
-mu0 + mu1
(1, -1, -0.40999999999999998)
-mu0 + mu2
(1, -1, -2.0800000000000001)
0
mu0 - mu1
(1, 1, 3.98)
-mu1
(1, 0, 7.101)
-mu1 + mu2
(1, 0, -1.6739999999999999)
0
-mu0
(1, 0, 6.5599999999999996)
-mu0 + mu1
(1, 1, -0.40999999999999998)
-mu0 + mu2
(1, 0, -2.0800000000000001)
1
mu0 - mu1
(1, -1, 3.98)
-mu1
(1, -1, 7.101)
-mu1 + mu2
(1, -1, -1.6739999999999999)
0
-mu0
(1, 0, 6.5599999999999996)
-mu0 + mu1
(1, 0, -0.40999999999999998)
-mu0 + mu2
(1, 1, -2.0800000000000001)
0
mu0 - mu1
(1, 0, 3.98)
-mu1
(1, 0, 7.101)
-mu1 + mu2
(1, 1, -1.6739999999999999)
--------c---------
Matrix([[-8.69064072818453e-34_exp(-11.6045192825566_mu0) - 116.495530311892_exp(-11.6045192825566_mu0 + 11.6045192825566_mu1) - 30390627980.6672_exp(-11.6045192825566_mu0 + 11.6045192825566_mu2) + 1, 8.74340942767173e-21_exp(11.6045192825566_mu0 - 11.6045192825566_mu1)]])
Matrix([[116.495530311892_exp(-11.6045192825566_mu0 + 11.6045192825566_mu1), -1.63129132051346e-36_exp(-11.6045192825566_mu1) - 8.74340942767173e-21_exp(11.6045192825566_mu0 - 11.6045192825566_mu1) - 273268470.678974_exp(-11.6045192825566_mu1 + 11.6045192825566_mu2) + 1]])
Matrix([[30390627980.6672_exp(-11.6045192825566_mu0 + 11.6045192825566_mu2), 273268470.678974_exp(-11.6045192825566_mu1 + 11.6045192825566_mu2)]])
--------c---------
-------c_ratio-------------
(-8.69064072818453e-34_exp(-11.6045192825566_mu0) - 116.495530311892_exp(-11.6045192825566_mu0 + 11.6045192825566_mu1) - 30390627980.6672_exp(-11.6045192825566_mu0 + 11.6045192825566_mu2) + 8.74340942767173e-21_exp(11.6045192825566_mu0 - 11.6045192825566_mu1) + 1)/(-8.69064072818453e-34_exp(-11.6045192825566_mu0) - 1.63129132051346e-36_exp(-11.6045192825566_mu1) + 2)
(-1.63129132051346e-36_exp(-11.6045192825566_mu1) + 116.495530311892_exp(-11.6045192825566_mu0 + 11.6045192825566_mu1) - 8.74340942767173e-21_exp(11.6045192825566_mu0 - 11.6045192825566_mu1) - 273268470.678974_exp(-11.6045192825566_mu1 + 11.6045192825566_mu2) + 1)/(-8.69064072818453e-34_exp(-11.6045192825566_mu0) - 1.63129132051346e-36_exp(-11.6045192825566_mu1) + 2)
(30390627980.6672_exp(-11.6045192825566_mu0 + 11.6045192825566_mu2) + 273268470.678974_exp(-11.6045192825566_mu1 + 11.6045192825566_mu2))/(-8.69064072818453e-34_exp(-11.6045192825566_mu0) - 1.63129132051346e-36_exp(-11.6045192825566_mu1) + 2)
(u'mu_red', [])
(u'y_vect', [0.0, 0.0, 0.01])
[-(-8.69064072818453e-34_exp(-11.6045192825566_mu0) - 116.495530311892_exp(-11.6045192825566_mu0 + 11.6045192825566_mu1) - 30390627980.6672_exp(-11.6045192825566_mu0 + 11.6045192825566_mu2) + 8.74340942767173e-21_exp(11.6045192825566_mu0 - 11.6045192825566_mu1) + 1)/(-8.69064072818453e-34_exp(-11.6045192825566_mu0) - 1.63129132051346e-36_exp(-11.6045192825566_mu1) + 2), -(-1.63129132051346e-36_exp(-11.6045192825566_mu1) + 116.495530311892_exp(-11.6045192825566_mu0 + 11.6045192825566_mu1) - 8.74340942767173e-21_exp(11.6045192825566_mu0 - 11.6045192825566_mu1) - 273268470.678974_exp(-11.6045192825566_mu1 + 11.6045192825566_mu2) + 1)/(-8.69064072818453e-34_exp(-11.6045192825566_mu0) - 1.63129132051346e-36_exp(-11.6045192825566_mu1) + 2), -mu0 - mu1 - 7.48901399237441e-35_exp(-11.6045192825566_mu0) - 1.40573795500994e-37_exp(-11.6045192825566_mu1) - 10.0388070781185_exp(-11.6045192825566_mu0 + 11.6045192825566_mu1) - 7.53448653475411e-22_exp(11.6045192825566_mu0 - 11.6045192825566_mu1) - 10.65875]
--------------------- >> end captured stdout << ----------------------
---
Ran 787 tests in 232.675s
FAILED (SKIP=128, errors=3)
|
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| 43,147,584
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MDExOlB1bGxSZXF1ZXN0MjE0NDIzODU=
| 135
|
This version requires the developmental version of monty
|
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[] | 2014-09-18T15:42:53
| 2014-09-18T15:57:55
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2014-09-18T15:57:55Z
|
CONTRIBUTOR
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| 43,215,556
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MDExOlB1bGxSZXF1ZXN0MjE0ODM3NzE=
| 136
|
Modification of gaussianio
|
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[] | null |
[
"Thanks for the changes. They are extremely useful.\n"
] | 2014-09-19T08:22:22
| 2014-09-19T15:25:32
|
2014-09-19T13:17:30Z
|
NONE
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Hello,
I'm Nicolas Dardenne, Phd student at the UCL NAPS working with Geffroy Hautier as mentionned in a mail yesterday.
At the request of Matteo Giantomassi, I submit modifications of gaussianio directly to you. The changes were made in order to use gaussianio with fireworks for HTP and some minors changes to add some options needed in my project.
Best regards,
Nicolas Dardenne
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|
py3k compatibility bug fixes and minor updates
|
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[] | null |
[] | 2014-09-23T20:37:16
| 2014-09-23T21:09:51
|
2014-09-23T21:09:51Z
|
CONTRIBUTOR
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|
Minor changes
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[] | 2014-09-25T14:37:02
| 2014-09-25T14:48:18
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2014-09-25T14:48:18Z
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CONTRIBUTOR
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|
Use OrderedDict instead of dict in test_qadapters.py because the hash al...
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[] | 2014-09-30T20:23:13
| 2014-09-30T20:24:34
|
2014-09-30T20:24:34Z
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CONTRIBUTOR
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...gorithm has been changed in py3k
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abinitio MoabAdapter
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[] | 2014-10-01T16:35:54
| 2014-10-01T16:38:43
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2014-10-01T16:38:43Z
|
NONE
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Basic MOAB adapter based on LLNL LC resources
https://computing.llnl.gov/tutorials/moab
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Battanalyzer
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[] | 2014-10-01T17:29:09
| 2014-10-01T17:34:44
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2014-10-01T17:34:44Z
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MEMBER
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Unit tests for GW code
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[] | 2014-10-03T13:44:21
| 2014-10-03T14:36:31
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2014-10-03T14:36:31Z
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CONTRIBUTOR
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From monty.pprint import pprint_table
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[] | 2014-10-03T16:39:35
| 2014-10-03T16:45:10
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2014-10-03T16:45:10Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MjIyMjY3Njg=
| 144
|
Add module for Pickle serialization used in abinitio
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2014-10-03T20:19:21Z
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MDExOlB1bGxSZXF1ZXN0MjIyMzM5MDI=
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|
Bug in outputting formation energy and chem potential solved
|
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[] | 2014-10-03T22:27:36
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2014-10-03T23:03:59Z
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CONTRIBUTOR
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MDExOlB1bGxSZXF1ZXN0MjIyMzYyMjc=
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|
Add cost model
|
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[] | 2014-10-03T23:35:31
| 2014-10-03T23:41:39
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2014-10-03T23:40:31Z
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MDExOlB1bGxSZXF1ZXN0MjIyNDEyNjg=
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matproj.snl: set pybtex strict mode False (>=0.18)
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[] | 2014-10-04T08:03:42
| 2014-10-14T02:52:28
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2014-10-04T15:10:44Z
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With the latest version of pybtex (0.18) the [strict mode has been made default](http://pybtex.sourceforge.net/history.html). This means that all former warnings will now cause error exceptions to be raised since the pybtex version has been fixed in pymatgen (see a69eaaeb93191c47aee3d240f41bded0624ac2f7). Hence, the conversion from database dicts to pymatgen objects via `MPStructureNL.from_dict(snl_dict)`, for instance, now won't result in a usable `Structure` object anymore. This pull request adds a call to `pybtex.errors.set_strict_mode(False)` in `matproj.snl.is_valid_bibtex()` to keep treating pybtex _typos_ as warnings in the future (backward-compatibilty)
|
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| 45,148,403
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MDU6SXNzdWU0NTE0ODQwMw==
| 148
|
issue with _parse_dos method in Vasprun for only total DOS
|
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[
"Thanks for reporting this. It has been fixed and I have added a new unittest.\n"
] | 2014-10-07T19:09:30
| 2014-10-07T19:34:26
|
2014-10-07T19:33:33Z
|
NONE
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I noticed that the _parse_dos method in the Vasprun class (which is in the pymatgen.io.vaspio.vasp_output module) only works if projected (or partial) DOS are written during the VASP calculation. If only the total DOS is calculated and written by VASP, the _parse_dos method throws an exception while trying to parse the partial DOS from the vasprun.xml file because the vasprun.xml file doesn't contain any partial DOS values.
|
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| 149
|
Bug fixes and initial commit surface energy error correction
|
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[] | 2014-10-09T16:18:31
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2014-10-19T20:34:21Z
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|
update compatibility for XDATCAR files with vasp 5.XX versions
|
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[] | 2014-10-10T07:56:32
| 2014-10-10T13:41:16
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2014-10-10T13:41:16Z
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CONTRIBUTOR
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|
bug fix reading core state eigen in OUTCAR
|
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[] | 2014-10-13T09:47:11
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2014-10-13T21:08:22Z
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Kpoint by volume
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Fix WorkflowResults class defined twice
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2014-10-19T17:50:34Z
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Bug fix in output generation
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2014-10-23T16:39:53Z
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latex labels in bandstructure.labels_dict.keys() cannot start with $ (problem with MongoDB)
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2014-10-23T20:55:02Z
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MDU6SXNzdWU0Njc3ODQ4Mw==
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|
Primitive cell transformation affects StructureMatcher
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[
"Looks like expected behavior. s2 is just out of tolerance so no primitive cell is found. If you want to match s2 to s1, you can take the primitive cells and use attempt_supercell=True\n"
] | 2014-10-24T20:09:50
| 2014-12-09T17:11:59
|
2014-12-09T17:11:59Z
|
MEMBER
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Here's an example - note that git won't let me upload the JSON files, so you can obtain those here:
https://groups.google.com/forum/#!topic/pymatgen/HvqV79HQPHE
```
from pymatgen import Structure
from pymatgen.analysis.structure_matcher import StructureMatcher
s1 = Structure.from_file("s1.json")
s2 = Structure.from_file("s2.json")
sm = StructureMatcher(primitive_cell=True)
print sm.fit(s1, s2)
sm = StructureMatcher(primitive_cell=False)
print sm.fit(s1, s2)
```
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Minor change in output for concentrations
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[] | 2014-10-24T23:40:53
| 2014-10-24T23:40:58
|
2014-10-24T23:40:58Z
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CONTRIBUTOR
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Concentration output order in conformation with energy output.
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Use monty.json.jsanitize instead of clean_json in plotter.py
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[] | 2014-10-26T18:38:32
| 2014-10-26T21:01:57
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2014-10-26T21:01:57Z
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Contributions from UCL
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[] | 2014-10-29T18:09:07
| 2014-10-29T18:37:36
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2014-10-29T18:37:36Z
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CONTRIBUTOR
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Fix py3k portability issues
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[] | 2014-10-29T20:15:41
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2014-10-29T20:21:14Z
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print_function
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add atomicfile to install_requires
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Scipy is an extra requirement --> ignore ImportError
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2014-11-06T14:32:52Z
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Updates to defects module
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[] | 2014-11-06T18:47:45
| 2014-11-06T18:48:02
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2014-11-06T18:48:02Z
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DiluteSolutionModel bug fix in dC matrix and outputs printing.
Added all option to interstitials.
high accuracy interstitial doesn't return face centers and edge centers.
Update to Zeo++ required.
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Bug fix in vacancy concentration calculation in dilute_solution_model
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[] | 2014-11-06T20:49:34
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2014-11-06T20:49:40Z
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Bug fix in output label for antisite concentrations
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| 2014-11-06T23:32:38
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2014-11-06T23:32:38Z
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Include parsing of the ionic part of the static dielectric constant
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[] | 2014-11-07T01:35:38
| 2014-11-07T01:36:19
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2014-11-07T01:36:19Z
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CONTRIBUTOR
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Changed files vasp_ouput.py and test_vasp_ouput.py to include parsing of the ionic part of the dielectric constant. Also added in pymatgen/test_files/ the file vasprun.xml.dfpt.ionic that includes the ionic part of the dielectic constant for testing purposes
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MDU6SXNzdWU0ODA0NDgxOA==
| 168
|
get_primitive_standard_structure returns structure that doesn't match the original sturcutre
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[
"This is a P1 structure. I am not sure why that would happen, given that it is practically a pass-through for P1 for get_primitive_standard. This should be debugged by @hautierg who implemented that method.\n",
"@hautierg Can you give an update on this? This bug is outstanding and severely affects the MP workflows. So this is rather critical to fix.\n",
"What could be the range of affected cases of this symmetry related issue? Apart from eye-spotting, it's difficult to figure out what's different before and after a structure transformation. So trusting the algorithm is particularly crucial...\n",
"This went out of my radar screen. Sorry about that. I looked back at it.\nI believe the issue comes from get_reduced_structure(\"LLL\") that is called by get_primitive_standard_structure.\n\nIf I do:\n\n```\nmpr=MPRester()\nstruct=mpr.get_structure_by_material_id(\"mp-684713\", True)\nstruct_refined=struct.get_reduced_structure(\"LLL\")\nprint SpacegroupAnalyzer(struct).get_spacegroup()\nprint StructureMatcher(primitive_cell=True, attempt_supercell=True, allow_subset=True).fit(struct, struct_refined)\n```\n\nI am getting:\n\nP1 (1) spacegroup\nFalse\n\n@shyuep , who coded the \"LLL\" reduction in get_reduced_structure?\n\nNote: this bug will only affect triclinic cells.\n",
"I just pushed a fix. The problem is not with any of the algos itself. It is with the fact that the LLL did not defensively copy the structure lattice, leading to modifications of the mutable np.array. That result in an error in structure matching.\n"
] | 2014-11-07T03:45:14
| 2015-08-19T14:38:29
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2015-08-19T14:38:29Z
|
CONTRIBUTOR
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We recently found some static runs give very different energy_per_atom results from the original relaxation results. It seems the get_primitive_standard_structure used for the static runs gives a different structure from the input structure.
Here's one example:
mpr=MPRester()
struct=mpr.get_structure_by_material_id("mp-684713", True)
standard_primitive_struct=SpacegroupAnalyzer(struct,
symprec=0.1).get_primitive_standard_structure(False)
print StructureMatcher(primitive_cell=True, attempt_supercell=True, allow_subset=True).fit(struct, standard_primitive_struct)
for s in [struct, standard_primitive_struct]:
print sorted([VoronoiCoordFinder(s).get_coordination_number(i) for i in range(len(s))], reverse=True)[:5]
The output is:
False
[5.468264142764663, 5.3980422434779465, 5.378317469545274, 5.3781566512430174, 5.197298392607815]
[6.094305973098741, 5.6656446821230135, 5.66564468210721, 5.469559081595328, 5.428248126158461]
So the StructureMatcher thinks the standard primitive structure doesn't match the original structure. And the coordination numbers given by the VoronoiCoordFinder are also very different between the two structures.
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Defect concentration level transition is centered for plotting
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2014-11-07T22:16:43Z
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| 170
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Fixed the method micro_pyawk
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[] | 2014-11-13T07:23:17
| 2014-11-13T15:24:18
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2014-11-13T15:24:18Z
|
CONTRIBUTOR
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Fixed the method micro_pyawk in pymatgen/util/io_utils.py to allow parsing of results from OUTCAR.
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Fixed function micro_pyawk in pymatgen/util/io_utils.py to allow parsing of .gz files
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[] | 2014-11-16T06:01:32
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2014-11-16T17:49:33Z
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CONTRIBUTOR
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| 49,110,466
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MDU6SXNzdWU0OTExMDQ2Ng==
| 172
|
Bug in F2 energy correction
|
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[] | 2014-11-17T16:16:39
| 2014-11-17T17:59:24
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2014-11-17T17:59:24Z
|
CONTRIBUTOR
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In MIT and MP correction schemes, the F2 compound energy is supposed to be set by the correction scheme to get the gas phase energy correct. Currently, this correction isn't applied because F2 isn't in Composition.special_formulas. Either adding F2 to the special formulas, or setting the compound energy of F instead of F2 fixes this, though both of those approaches rely on the composition returning exactly the reduced formula that the correction scheme expects. A better approach could be to compare fractional compositions instead of reduced compositions in the compatibility scheme.
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MDExOlB1bGxSZXF1ZXN0MjQ1ODE4NDc=
| 173
|
Fixed lepsilon parsing in class Outcar
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[
"Before I merge this, can you provide unittests for the new functionality pls? Thanks.\n",
"Ok, I will provide those and will re-submit. Thank you.\n"
] | 2014-11-18T01:17:28
| 2014-11-18T06:31:48
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2014-11-18T06:31:48Z
|
CONTRIBUTOR
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Fixed the following in class Outcar in pymatgen/io/vaspio/vasp_output.py:
1 - Added parsing of ionic part of lepsilon in Outcar.
2 - Changed parsing of piezoelectric tensor units from e.Angstrom to C/m^2.
3 - Fixed results' data structure from numpy array to list.
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Fixed lepsilon parsing from OUTCAR
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[] | 2014-11-18T07:43:00
| 2014-11-18T07:58:44
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2014-11-18T07:58:44Z
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CONTRIBUTOR
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Fixed the following in class Outcar in pymatgen/io/vaspio/vasp_output.py:
1 - Added parsing of ionic part of lepsilon in Outcar.
2 - Changed parsing of piezoelectric tensor units from e.Angstrom to C/m^2.
3 - Fixed results' data structure from numpy array to list.
Added tests in Class OutcarTest in pymatgen/io/vaspio/tests/test_vasp_output.py
Added 2 test files "OUTCAR.lepsilon" and "OUTCAR.lepsilon.gz" in test_files
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|
Returns bulk supercell in worst case for substitution defect transformation
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[] | 2014-11-20T23:55:53
| 2014-11-20T23:56:01
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2014-11-20T23:56:01Z
|
CONTRIBUTOR
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if the specie being substituted is not in structure for substitution defect transformation, bulk cell is returned.
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|
Included parsing of the static dielectric constant without local field effects
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[] | 2014-11-22T00:28:28
| 2014-11-23T02:24:08
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2014-11-23T02:24:08Z
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CONTRIBUTOR
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Changed files:
vasp_output.py in pymategen/io/vaspio/
test_vasp_output.py in pymategen/io/vaspio/tests
|
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| 49,788,825
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MDExOlB1bGxSZXF1ZXN0MjQ4ODgyMTE=
| 177
|
Class methods in core.structure should propagate input __class__
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2014-11-23T02:23:42Z
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Code cleanup in abinitio
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2014-11-30T15:14:20Z
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MDU6SXNzdWU1MTQ1NDQ0NQ==
| 179
|
OrderDisorderedStructureTransformation does not work for oxidation state = 0
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[
"Not sure what the use case is. Ordering doesn't really make sense in this\ncase since they all have the same electrostatic energy -- might as well\njust do an enumeration.\nI agree that its a weird error though - I'll take a look\n\nOn Tue, Dec 9, 2014 at 12:14 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> E.g., when trying to order alloys, this does not work.\n> \n> from pymatgen import Structure, Latticefrom pymatgen.transformations.standard_transformations import OrderDisorderedStructureTransformation\n> \n> specie = {\"Cu0+\": 0.5, \"Au0+\": 0.5}\n> cuau = Structure.from_spacegroup(\"Fm-3m\", Lattice.cubic(3.677), [specie], [[0, 0, 0]])\n> trans = OrderDisorderedStructureTransformation()\n> ss = trans.apply_transformation(cuau, return_ranked_list=100)\n> \n> @wmdrichards https://github.com/wmdrichards - pls debug?\n> \n> —\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/179.\n",
"Note - I think it would be nice if there was an option to skip the ordering portion (don't do Ewald energies, just return all solutions in an unranked way). The oxidation states would only be required if the Ewald stuff was on. Then such alloys can be ordered more quickly.\n",
"The use case is that enumerate transformation is rather buggy and there are weird cases that it fails and I have to fall back on order disordered trans followed by a structure matching. Moreover, OrderDisordered can order much larger structures than enumerate.\n",
"I also second the option to not do the ewald minimizer. There is a huge current bug in the ewald sum anyway, and I don't trust the energies. It also slows down enumerate quite a fair bit if all I want is to get all possible enumerations (with duplicates) in order disorder.\n",
"@wmdrichards Status of this?\n",
"Is there any plan to address this in the near-term? "
] | 2014-12-09T17:14:09
| 2018-05-28T15:38:48
|
2018-05-28T15:38:48Z
|
MEMBER
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E.g., when trying to order alloys, this does not work.
``` python
from pymatgen import Structure, Lattice
from pymatgen.transformations.standard_transformations import OrderDisorderedStructureTransformation
specie = {"Cu0+": 0.5, "Au0+": 0.5}
cuau = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.677), [specie], [[0, 0, 0]])
trans = OrderDisorderedStructureTransformation()
ss = trans.apply_transformation(cuau, return_ranked_list=100)
```
@wmdrichards - pls debug?
|
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MDU6SXNzdWU1MTc5NTI0Mg==
| 180
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Bug: using cif files from the zeolite database
|
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[
"Thanks for reporting this. We have actually fixed this issue in the bleeding edge repo code.\n\nWe will release a new version shortly.\n",
"Hey, thanks for your quick reply and fix.\n\nHowever, I can only confirm that 'pmg view JST.cif' looks good.\n\n'pmg view ABW.cif' looks like having oblique angles but it is orthorhomic.\n`$ cat ABW.cif` gives\n\n```\n#**************************************************************************\n#\n# CIF taken from the IZA-SC Database of Zeolite Structures\n# Ch. Baerlocher and L.B. McCusker\n# Database of Zeolite Structures: http://www.iza-structure.org/databases/ \n#\n# The atom coordinates and the cell parameters were optimized with DLS76\n# assuming a pure SiO2 composition.\n#\n#**************************************************************************\n\n_cell_length_a 9.8730(0)\n_cell_length_b 5.2540(0)\n_cell_length_c 8.7700(0)\n_cell_angle_alpha 90.0000(0)\n_cell_angle_beta 90.0000(0)\n_cell_angle_gamma 90.0000(0)\n\n_symmetry_space_group_name_H-M 'I m m a'\n_symmetry_Int_Tables_number 74\n_symmetry_cell_setting orthorhombic\n\nloop_\n_symmetry_equiv_pos_as_xyz\n'+x,+y,+z'\n'1/2+x,1/2+y,1/2+z'\n'-x,+y,+z'\n'1/2-x,1/2+y,1/2+z'\n'+x,1/2-y,+z'\n'1/2+x,-y,1/2+z'\n'-x,1/2-y,+z'\n'1/2-x,-y,1/2+z'\n'-x,-y,-z'\n'1/2-x,1/2-y,1/2-z'\n'+x,-y,-z'\n'1/2+x,1/2-y,1/2-z'\n'-x,1/2+y,-z'\n'1/2-x,+y,1/2-z'\n'+x,1/2+y,-z'\n'1/2+x,+y,1/2-z'\n\nloop_\n_atom_site_label\n_atom_site_type_symbol\n_atom_site_fract_x\n_atom_site_fract_y\n_atom_site_fract_z\n O1 O 0.5000 0.2500 0.3523\n O2 O 0.3100 0.0000 0.5000\n O3 O 0.2500 0.2500 0.2500\n T1 Si 0.3428 0.2500 0.4007\n```\n\n'pmg convert ABW.cif ABW.cssr' and `$ cat ABW.cssr`\n\n```\n5.2540 7.1062 7.1062\n76.20 68.30 68.30 SPGR = 1 P 1 OPT = 1\n12 0\n0 Si4 O8\n1 Si 0.5928 0.0579 0.2565\n2 Si 0.9072 0.7435 0.9421\n3 Si 0.4072 0.9421 0.7435\n4 Si 0.0928 0.2565 0.0579\n5 O 0.7500 0.8523 0.1477\n6 O 0.2500 0.1477 0.8523\n7 O 0.3100 0.1900 0.1900\n8 O 0.6900 0.8100 0.8100\n9 O 0.8100 0.1900 0.1900\n10 O 0.1900 0.8100 0.8100\n11 O 0.5000 0.0000 0.5000\n12 O 1.0000 0.5000 0.0000\n```\n\nShouldn't be the angles 90 in degrees in cssr output?\n",
"No. pymatgen automatically seeks out the most primitive cell. ABW is a body-centered cell. The cssr output is the primitive cell. For calculations, this is typically what you want (minimize # of atoms in unit cell).\n\nIf you use pymatgen directly, you can \"turn off\" this primtiive cell switching.\n\n``` python\nfrom pymatgen import Structure\ns = Structure.from_file(\"ABW.cif\", primitive=False)\ns.to(filename=\"ABW.cssr\")\n```\n",
"In any case, I just added a conventional_cif option in the pmg script. If you use\n\n```\npmg convert -i conventional_cif ABW.cif ABW.cssr\n```\n\nin the bleeding edge dev repository, you can get the conventional cell instead of primitive.\n",
"I was suspecting that you consider the primitive unit cell instead of the conventional one.\n\nI am actually interested in using pymatgen directly. So the option `primitive=False` is what I was looking for. But in order to compare pymatgen output to other tools it is helpful to generate data in the conventional unit cell. (for instance to openbabel)\n\nCan you point me to your bug fix commit which you are referring to in https://github.com/materialsproject/pymatgen/releases/tag/v3.0.9\n\nyour help is really appreciated.\n",
"If you are referring to the Cif parsing bug fix, it is not so much a single bug fix but rather a series of fixes by Will Richards. Technically, there isn't a bug in Cif parising per se, but rather than CIF is a very loose format and a lot of CIF files out there are non-standard or well-formed. These fixes merely improves the robustness in terms of parsing these CIFs.\n",
"From looking at the cifs, I think the fix was in the symmetry operations.\nPrevious versions didn't parse operations that started with the translation\nvector (e.g. '1/2+x' rather than 'x+1/2') correctly.\n\nWill\n\nOn Fri, Dec 12, 2014 at 11:56 AM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> If you are referring to the Cif parsing bug fix, it is not so much a\n> single bug fix but rather a series of fixes by Will Richards. Technically,\n> there isn't a bug in Cif parising per se, but rather than CIF is a very\n> loose format and a lot of CIF files out there are non-standard or\n> well-formed. These fixes merely improves the robustness in terms of parsing\n> these CIFs.\n> \n> —\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/180#issuecomment-66800493\n> .\n",
"I see. Thank you.\n"
] | 2014-12-12T11:14:30
| 2014-12-15T10:26:36
|
2014-12-12T13:39:44Z
|
NONE
|
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Consider following example cif files:
http://izasc.ethz.ch/fmi/xsl/IZA-SC/cif/ABW.cif
http://izasc.ethz.ch/fmi/xsl/IZA-SC/cif/ACO.cif
http://izasc.ethz.ch/fmi/xsl/IZA-SC/cif/JST.cif
Using 'pmg convert ABW.cif ABW-<version>.cssr' with pymatgen version = 2.10.6, 3.0.6 and 3.0.8:
2.10.6 & 3.0.6 certainly broken (wrong unit cell angles in cssr)
3.0.8 at first site looks ok.
However, as far as I can also judge by using 'pmg view cif-file' with all versions and comparing them to the visualization of http://izasc.ethz.ch/fmi/xsl/IZA-SC/ftc_fw.xsl?-db=Atlas_main&-lay=fw&-max=25&STC=ABW&-find, I dare to say none of them works correctly.
Also determining all bonds fails.
|
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| 51,847,753
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MDU6SXNzdWU1MTg0Nzc1Mw==
| 181
|
reading kpoints from vasprun.xml
|
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[] | 2014-12-12T20:11:05
| 2014-12-12T20:14:06
|
2014-12-12T20:14:06Z
|
CONTRIBUTOR
|
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Hi,
In _parse_kpoints, in io/vaspio/vasp_output, the execution of the following line
k.style = e.attrib["param"] if "params" in e.attrib else "Reciprocal"
always return "Reciprocal" as the style beacuse "params" is not in e.attrib.
Changing "params" to "param" will fix the issue.
regards
Kiran Mathew
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| 52,577,694
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MDExOlB1bGxSZXF1ZXN0MjY0MjEyODY=
| 182
|
Speedup and bug fixes to dilute solution model
|
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[] | 2014-12-20T21:51:06
| 2014-12-20T21:51:22
|
2014-12-20T21:51:22Z
|
CONTRIBUTOR
|
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The update speeds up the dilute solution model mu calculation by improved trial guess for mu.
Also lot of bug fixes w.r.t. the dE and omega definitions and output generation.
|
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MDU6SXNzdWU1MzQ0NTU4NA==
| 183
|
potcar symbol mapping not working
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[
"As far as I can tell, this works perfectly fine. Can you give an example of where it fails?\n",
"when 'sym_potcar_map' is provided, the method 'set_symbols' of class Potcar appends potcar singles objects with its data variable set to 'sym_potcar_map[el]'.\nWhen 'sym_potcar_map' is not given, it actually goes to the potcar files folder and reads the corresponding potcar file into the 'data' variable\n",
"If you provide sym_potcar_map, then you need to provide the actual data in the sym_potcar_map. Otherwse, you shouldn't set it. This is so taht people can arbitarily set the raw data for the POTCAR. It is not meant for general usage.\n",
"ok. thank you\n"
] | 2015-01-05T20:45:05
| 2015-01-05T22:52:47
|
2015-01-05T21:42:29Z
|
CONTRIBUTOR
|
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when symbol mapping dictionary is provided, the data attribute of Potcarsingle class does not have the raw potcar data.
|
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|
SpaceGroup.get_orbit avoids duplicated positions
|
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[] | 2015-01-14T20:58:22
| 2015-01-20T19:43:29
|
2015-01-20T19:43:29Z
|
CONTRIBUTOR
|
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A fractional position such as [0.99999999, 0, 0] might not be recognized as equivalent to [0., 0., 0.].
Solved it with np.round(a, decimals=10).
|
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| 57,849,367
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MDExOlB1bGxSZXF1ZXN0MjkzOTk1Nzc=
| 185
|
get_el_sp should return Element.from_Z if obj is a string that can be co...
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[] | 2015-02-16T20:44:11
| 2015-02-16T20:49:46
|
2015-02-16T20:49:46Z
|
CONTRIBUTOR
|
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...nverted into int e.g. '3.0'
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MDU6SXNzdWU1Nzg4NjM4Ng==
| 186
|
Structure.get_neighbors returning reference site as neighbor (only for image sites)
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[
"This is not a bug I think. Based on your output in line 39, I think you manually created the \"other_site\"? That site is As, not As3-. Pymatgen distinguishes between As3- and As as different species. That will make it such that the last site with As3- is a neighbor within a radius of 2.5 from the site you entered. \n"
] | 2015-02-17T05:53:16
| 2015-02-17T17:59:47
|
2015-02-17T17:59:47Z
|
NONE
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Hello this is a rather small bug and it hasnt been problematic to deal with, but I figured it should be known for future releases. In structure.get_neighbors( site, rmax, index), when a site is passed in which does not belong to the unit cell and is an image, it will return the neighbors as well as the site itself.
For example, in GaAs (tetrahedral coordination):
In [38]: struct
Out[38]:
Structure Summary
Lattice
abc : 3.9977696087943837 3.9977696087943837 3.9977696087943837
angles : 59.999999999999993 60.000000000000007 60.000000000000007
volume : 45.179174211538246
A : -1.7309464020848477e-16 2.8268499999999999 2.8268499999999999
B : 2.8268499999999999 0.0 2.8268499999999999
C : 2.8268499999999999 2.8268499999999999 3.4618928041696953e-16
PeriodicSite: Ga3+ (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
PeriodicSite: As3- (1.4134, 1.4134, 1.4134) [0.2500, 0.2500, 0.2500]
In [39]: other_site
Out[39]: PeriodicSite: As (1.4134, -1.4134, -1.4134) [-0.7500, 0.2500, 0.2500]
In [40]: struct.get_neighbors(other_site,2.5,True)
Out[40]:
[(PeriodicSite: Ga3+ (0.0000, -2.8268, -2.8268) [-1.0000, 0.0000, 0.0000],
2.4481239126880401,
0),
(PeriodicSite: Ga3+ (2.8268, 0.0000, -2.8268) [-1.0000, 0.0000, 1.0000],
2.448123912688041,
0),
(PeriodicSite: Ga3+ (2.8268, -2.8268, 0.0000) [-1.0000, 1.0000, 0.0000],
2.4481239126880396,
0),
(PeriodicSite: Ga3+ (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000],
2.4481239126880401,
0),
(PeriodicSite: As3- (1.4134, -1.4134, -1.4134) [-0.7500, 0.2500, 0.2500],
2.2204460492503131e-16,
1)]
So the last site returned in that list should not be there. The fact that the distance is ~0 agrees.
Thanks
|
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MDU6SXNzdWU1Nzk1NTU4NQ==
| 187
|
How to use jimage to compute distances ?
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[] | null |
[
"The jimage is not returned in get_neighbors. The index returned just simply tells you that the first NN site is O with a distance of 2.098 and corresponds to site # 8 in the structure. The distance already accounts for PBC, so you don't need to take that into account anymore.\n\nIf you really want to know what image, you do site.distance_and_image(other_site). E.g., your other site would be the O atom in this case. What is returned is then the closest distance as well as the image vector taht you need to add to the other_site's fractional coordinates to get the closest atom. \n\nBTW, for clarifications and questions, pls post them on the pymatgen Google Groups page. The Github issues is meant for bug reports and feature requests only. Thanks.\n",
"Thank you and sorry for the bad place of the question.\nGermain\n\n2015-02-17 18:42 GMT+01:00 Shyue Ping Ong notifications@github.com:\n\n> The jimage is not returned in get_neighbors. The index returned just\n> simply tells you that the first NN site is O with a distance of 2.098 and\n> corresponds to site # 8 in the structure. The distance already accounts for\n> PBC, so you don't need to take that into account anymore.\n> \n> If you really want to know what image, you do\n> site.distance_and_image(other_site). E.g., your other site would be the O\n> atom in this case. What is returned is then the closest distance as well as\n> the image vector taht you need to add to the other_site's fractional\n> coordinates to get the closest atom.\n> \n> BTW, for clarifications and questions, pls post them on the pymatgen\n> Google Groups page. The Github issues is meant for bug reports and feature\n> requests only. Thanks.\n> \n> —\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/187#issuecomment-74713392\n> .\n\n## \n\n_Germain Salvato Vallverdu_\n_PagePerso : http://gvallver.perso.univ-pau.fr\nhttp://gvallver.perso.univ-pau.fr_\n_Tel : 06 88 59 08 87_\n"
] | 2015-02-17T17:35:49
| 2015-02-18T12:54:18
|
2015-02-17T17:42:07Z
|
CONTRIBUTOR
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Hello,
I would like to understand the image index which is returned by get_neighbors methods doing
```
s.get_neighbors(site, 3., include_index=True)
```
For example, I got
```
[(PeriodicSite: O (-3.0702, 1.4045, 3.7466) [0.3650, 0.1350, 0.7720],
2.0976135752472325,
8),
(PeriodicSite: O (-5.7897, 2.8090, 3.7466) [0.8650, 0.1350, 0.7720],
2.3069461858444189,
9),
(PeriodicSite: O (-3.0702, 4.2135, 3.7466) [0.8650, 0.6350, 0.7720],
2.0976135752472329,
10),
(PeriodicSite: O (-2.0058, 2.8090, 1.1065) [0.6350, 0.3650, 0.2280],
2.3069461858444189,
12),
(PeriodicSite: O (-4.7253, 4.2135, 1.1065) [1.1350, 0.3650, 0.2280],
2.097613575247232,
13),
(PeriodicSite: O (-4.7253, 1.4045, 1.1065) [0.6350, -0.1350, 0.2280],
2.0976135752472325,
15)]
```
How can I use these last numbers (8, 9, 10, 12, 13, 15) ? For example, item 1 is inside the cell
```
PeriodicSite: O (-3.0702, 1.4045, 3.7466) [0.3650, 0.1350, 0.7720]
```
Why the image_index is 8 ?
Acutally, what I would like to do exactly is to compute distances between all this O neighbors. But I need to know the periodic image of the atom which is in the list.
Thanks
|
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MDExOlB1bGxSZXF1ZXN0Mjk2NDU5MzU=
| 188
|
Version for the school in Pilsen
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[] | 2015-02-19T20:29:58
| 2015-02-21T03:33:14
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2015-02-21T03:33:14Z
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CONTRIBUTOR
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| 189
|
Py3k compatibility
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| 2015-02-21T14:04:31
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2015-02-21T14:04:31Z
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CONTRIBUTOR
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| 190
|
Fix SpinMode.as_dict
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2015-02-21T14:56:48Z
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|
comment out the stable_py3 merge in the circle.yml file
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| 2015-02-21T23:42:15
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2015-02-21T23:42:15Z
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CONTRIBUTOR
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MDU6SXNzdWU1OTkyMzE3MA==
| 192
|
how I get the spacegroup symbol from a cif file
|
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[
"Can you pls supply the actual if file so that we can better advise on what might be the problem? \n\nShyue Ping\n\nOn March 5, 2015 at 01:03:01, wangnumber14 (notifications@github.com) wrote:\n\nI parse some cif files use the method \"CifParser\",\nwhile all the spacegroup names started with \"I\" are all parsed into \"P\", why?\n\nfor example, the icsd_044367.cif Li has the spacegroup_name \"Im-3m\", I use\n\nSpacegroupAnalyzer(IStructure.from_file(icsd_044367.cif).get_spacegroup_symbol()\n\nI get the result: Pm-3m\n\nHow can I get the \"Im-3m\" ?\n\nthank you !\n\n—\nReply to this email directly or view it on GitHub.\n",
"Thanks, for example, the following cif file:\n#####################################\n#------------------------------------------------------------------------------\n#$Date: 2014-07-11 14:35:18 +0000 (Fri, 11 Jul 2014) $\n#$Revision: 120071 $\n#$URL: file:///home/coder/svn-repositories/cod/cif/1/00/11/1001196.cif $\n#------------------------------------------------------------------------------\n#\n\n# This file is available in the Crystallography Open Database (COD),\n\n# http://www.crystallography.net/\n\n#\n\n# All data on this site have been placed in the public domain by the\n\n# contributors.\n\n#\ndata_1001196\n_chemical_name_systematic 'Trizirconium germanium oxide'\n_chemical_formula_structural 'Zr3 Ge O8'\n_chemical_formula_sum 'Ge O8 Zr3'\n_publ_section_title\n;\nNeutron Diffraction Determination of the Structure of an Ordered\nScheelite - Type: Zr~3~ Ge O~8~\n;\nloop_\n_publ_author_name\n 'Ennaciri, A'\n 'Michel, D'\n 'Perez y Jorba, M'\n 'Pannetier, J'\n_journal_name_full 'Materials Research Bulletin'\n_journal_coden_ASTM MRBUAC\n_journal_volume 19\n_journal_year 1984\n_journal_page_first 793\n_journal_page_last 799\n_cell_length_a 5.005(1)\n_cell_length_b 5.005(1)\n_cell_length_c 10.452(2)\n_cell_angle_alpha 90\n_cell_angle_beta 90\n_cell_angle_gamma 90\n_cell_volume 261.8\n_cell_formula_units_Z 2\n_symmetry_space_group_name_H-M 'I -4 2 m'\n_symmetry_Int_Tables_number 121\n_symmetry_cell_setting tetragonal\nloop_\n_symmetry_equiv_pos_as_xyz\n 'x,y,z'\n '-x,-y,z'\n '-x,y,-z'\n 'x,-y,-z'\n '-y,x,-z'\n 'y,-x,-z'\n 'y,x,z'\n '-y,-x,z'\n '1/2+x,1/2+y,1/2+z'\n '1/2-x,1/2-y,1/2+z'\n '1/2-x,1/2+y,1/2-z'\n '1/2+x,1/2-y,1/2-z'\n '1/2-y,1/2+x,1/2-z'\n '1/2+y,1/2-x,1/2-z'\n '1/2+y,1/2+x,1/2+z'\n '1/2-y,1/2-x,1/2+z'\nloop_\n_atom_type_symbol\n_atom_type_oxidation_number\n Zr4+ 4.000\n Ge4+ 4.000\n O2- -2.000\nloop_\n_atom_site_label\n_atom_site_type_symbol\n_atom_site_symmetry_multiplicity\n_atom_site_Wyckoff_symbol\n_atom_site_fract_x\n_atom_site_fract_y\n_atom_site_fract_z\n_atom_site_occupancy\n_atom_site_attached_hydrogens\n_atom_site_calc_flag\n Zr1 Zr4+ 2 b 0. 0. 0.5 1. 0 d\n Zr2 Zr4+ 4 d 0. 0.5 0.25 1. 0 d\n Ge1 Ge4+ 2 a 0. 0. 0. 1. 0 d\n O1 O2- 8 i 0.2004(5) 0.2004(5) 0.3410(6) 1. 0 d\n O2 O2- 8 i 0.2170(5) 0.2170(5) 0.0904(6) 1. 0 d\n_refine_ls_R_factor_all 0.027\n_cod_database_code 1001196\n_journal_paper_doi 10.1016/0025-5408(84)90037-0\n##############################################################\n\nI use the code to get spacegroup information:\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n s=IStructure.from_file(name.cif)\n syms=SpacegroupAnalyzer(s)\n spg_symbol=syms.get_spacegroup_symbol()\n %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n\nand then I get the result is : \" P-42m\" not the real spacegroup \"I -4 2 m\".\n",
"s = Structure.from_file(\"1001196.cif\")\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\na = SpacegroupAnalyzer(s)\nprint a.get_spacegroup_symbol()\nI can’t reproduce the error. The following gives me the right space group\n\nShyue Ping\n\nOn March 6, 2015 at 00:50:39, wangnumber14 (notifications@github.com) wrote:\n\nThanks, for example, the following cif file:\n#####################################\n#------------------------------------------------------------------------------\n#$Date: 2014-07-11 14:35:18 +0000 (Fri, 11 Jul 2014) $\n#$Revision: 120071 $\n#$URL: file:///home/coder/svn-repositories/cod/cif/1/00/11/1001196.cif $\n#------------------------------------------------------------------------------\n#\n\nThis file is available in the Crystallography Open Database (COD),\n\nhttp://www.crystallography.net/\n\n#\n\nAll data on this site have been placed in the public domain by the\n\ncontributors.\n\n#\ndata_1001196\nchemical_name_systematic 'Trizirconium germanium oxide'\n_chemical_formula_structural 'Zr3 Ge O8'\n_chemical_formula_sum 'Ge O8 Zr3'\n_publ_section_title\n;\nNeutron Diffraction Determination of the Structure of an Ordered\nScheelite - Type: Zr~3~ Ge O~8~\n;\nloop\npubl_author_name\n'Ennaciri, A'\n'Michel, D'\n'Perez y Jorba, M'\n'Pannetier, J'\n_journal_name_full 'Materials Research Bulletin'\n_journal_coden_ASTM MRBUAC\n_journal_volume 19\n_journal_year 1984\n_journal_page_first 793\n_journal_page_last 799\n_cell_length_a 5.005(1)\n_cell_length_b 5.005(1)\n_cell_length_c 10.452(2)\n_cell_angle_alpha 90\n_cell_angle_beta 90\n_cell_angle_gamma 90\n_cell_volume 261.8\n_cell_formula_units_Z 2\n_symmetry_space_group_name_H-M 'I -4 2 m'\n_symmetry_Int_Tables_number 121\n_symmetry_cell_setting tetragonal\nloop\nsymmetry_equiv_pos_as_xyz\n'x,y,z'\n'-x,-y,z'\n'-x,y,-z'\n'x,-y,-z'\n'-y,x,-z'\n'y,-x,-z'\n'y,x,z'\n'-y,-x,z'\n'1/2+x,1/2+y,1/2+z'\n'1/2-x,1/2-y,1/2+z'\n'1/2-x,1/2+y,1/2-z'\n'1/2+x,1/2-y,1/2-z'\n'1/2-y,1/2+x,1/2-z'\n'1/2+y,1/2-x,1/2-z'\n'1/2+y,1/2+x,1/2+z'\n'1/2-y,1/2-x,1/2+z'\nloop\natom_type_symbol\n_atom_type_oxidation_number\nZr4+ 4.000\nGe4+ 4.000\nO2- -2.000\nloop\n_atom_site_label\n_atom_site_type_symbol\n_atom_site_symmetry_multiplicity\n_atom_site_Wyckoff_symbol\n_atom_site_fract_x\n_atom_site_fract_y\n_atom_site_fract_z\n_atom_site_occupancy\n_atom_site_attached_hydrogens\n_atom_site_calc_flag\nZr1 Zr4+ 2 b 0. 0. 0.5 1. 0 d\nZr2 Zr4+ 4 d 0. 0.5 0.25 1. 0 d\nGe1 Ge4+ 2 a 0. 0. 0. 1. 0 d\nO1 O2- 8 i 0.2004(5) 0.2004(5) 0.3410(6) 1. 0 d\nO2 O2- 8 i 0.2170(5) 0.2170(5) 0.0904(6) 1. 0 d\n_refine_ls_R_factor_all 0.027\n_cod_database_code 1001196\n_journal_paper_doi 10.1016/0025-5408(84)90037-0\n##############################################################\n\nI use the code to get spacegroup information:\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\ns=IStructure.from_file(name.cif)\nsyms=SpacegroupAnalyzer(s)\nspg_symbol=syms.get_spacegroup_symbol()\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n\nand then I get the result is : \" P-42m\" not the real spacegroup \"I -4 2 m\".\n\n—\nReply to this email directly or view it on GitHub.\n",
"Sorry, I can not see your result, can you resend me again?\n\nI still get the error. \n\n%%%%%%%%%%%%%%%%%%%%\ns1=IStructure.from_file(\"1001196.cif\")\n print SpacegroupAnalyzer(s1).get_spacegroup_symbol()\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\nthe result:\n%%%%%%%%%%%%%%%%%%%%\n[wangzg@localhost parsecif]$ python2.7 Cif2CmlPoscar.py\nP-42m\n%%%%%%%%%%%%%%%%%%%%%%%%%%\nnot the real result is I-42m\n\nthanks\n",
"I get the real result of I-42m. I am not sure why you are getting the P-42m. Do you have the latest pymatgen and spglib installed?Are you on Windows or a Linux / Mac system?\n",
"Out of curiosity: Dr. Ong, what happens when you use IStructure?\n\nOn Thu, Mar 19, 2015 at 8:42 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> I get the real result of I-42m. I am not sure why you are getting the\n> P-42m. Do you have the latest pymatgen and spglib installed?Are you on\n> Windows or a Linux / Mac system?\n> \n> —\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/192#issuecomment-83828110\n> .\n",
"I have installed the latest version (3.0.11) on Linux system yesterday, but I still reproduced this error.\n\nI think the error results from symmetry operations, the \"_symmetry_equiv_pos_as_xyz\" . I use castep to parser cif file and save it as new file in the cif format, and then I use pymatgen to parser it, I get the correct result. I have checked the symmetry operations, there are no differences except that the orders.\n\nI install the new pymatgen version,the spglib should install at same time. right?\n",
"IStructure and Structure are just immutable nad mutable versions. The symmetry detection does not rely on changing the structure. So either one is fine. \n\nI downloaded the cif directly from the website and it parses completely fine. Which is why I am confused why there is a problem. The cif text pasted above has missing _ in front of \"symmetry_equiv_pos_as_xyz\", which could be the reason. That underscore cannot be missing, or the code will not parse correctly. I have never seen a CIF without that _ though. \n",
"I don not think the _missing is the reason, I have send one attachment to your email, including the python shell and cif file, you can test it again.\n\nbelow is the results:\n%%%%%%%%%%%%%%%%\n[wang@localhost 1]$ python2.7 test.py \nPm-3m\nPm-3m (221) spacegroup\n%%%%%%%%%%%%%%%%%%\n\nThank you very much.\n",
"I tried it again. It really does not make a difference. The original cif file that you supplied was determined correctly. The following is an output from my testing. test.cif contains the CIF you supplied in this chain. I also tested with a Fe Im-3m structure that I downloaded from ICSD (Icsd id 53802). The spacegroup analyzer still gives Im-3m as it should, not Pm-3m. I also tried this on two different OSes, a Linux OS and a Mac OS. As expected, using IStructure or Structure makes no difference to the results. \n\nCan you email me the CIF file that you are testing with directly to shyuep@gmail.com? If you use Github, the file does not come through.\n\n``` python\nIn [3]: s = IStructure.from_file(\"test.cif\")\nIn [4]: print s\nStructure Summary (Zr3 Ge1 O8)\nReduced Formula: Zr3GeO8\nabc : 5.005000 5.005000 6.311584\nangles: 113.359134 113.359134 90.000000\nSites (12)\n1 Zr4+ 0.500000 0.500000 0.000000\n2 Zr4+ 0.250000 0.750000 0.500000\n3 Zr4+ 0.750000 0.250000 0.500000\n4 Ge4+ 0.000000 0.000000 0.000000\n5 O2- 0.541400 0.541400 0.682000\n6 O2- 0.140600 0.140600 0.682000\n7 O2- 0.458600 0.859400 0.318000\n8 O2- 0.859400 0.458600 0.318000\n9 O2- 0.307400 0.307400 0.180800\n10 O2- 0.873400 0.873400 0.180800\n11 O2- 0.692600 0.126600 0.819200\n12 O2- 0.126600 0.692600 0.819200\nIn [6]: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer\n\nIn [7]: a = SpacegroupAnalyzer(s, 0.1)\n\nIn [8]: print a.get_spacegroup_symbol()\nI-42m\n```\n",
"Also, can you make sure of your pymatgen version by typing \n\n```\nimport pymatgen\nprint pymatgen.__version__\n```\n\nIt would also be helpful to know your numpy versions. I have never encountered issues there before, but just in case. Also, when you directly print the structure, do you get the same structure as what I show above? If so, then something is wrong with the symmetry determination nad not with the parsing of the file itself.\n",
"I have print my pymatgen version:\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\nPython 2.7.7 (default, Jun 12 2014, 08:23:58) \n[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\n\n> > > import pymatgen\n> > > print pymatgen.**version**\n> > > 3.0.11\n> > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n\nand I loaded the Fe cif file (data_53802), I still reproduced the error.\n\nI have send the attachments in the email shyuep@gmail.com, please check your email.\n\nThanks\n",
"Thanks for the files. I determined that the problem with your cif is that it has the x y z operations as \"x+0.5, y+0.5, z+0.5\".\n\nThese were parsed incorrectly as the cif files we encountered always were in the form:\n\"x+1/2, y+1/2, z+1/2\".\n\nI just pushed a patch to the dev version of pymatgen that fixes that.\n",
"Pls let me know if there are any other cifs that are not parsing correctly.\n",
"I also think the \".5\" form is the main reason, if I can download the latest version to fix the problem? Or need I correct the pymatgen code?\n",
"I have updated the pymatgen version and checked the files, I got the correct results, Thanks a lot. \n\nI have ever tested that changing the \".5\" form to \"1/2\" and got the correct results, but I don not think that you will make this mistake, so I still ask you the real reason, sorry to waste your long time to this question, and thanks a lot for your patience. \n"
] | 2015-03-05T09:02:54
| 2015-03-23T00:53:26
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2015-03-20T13:53:32Z
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NONE
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I parse some cif files use the method "CifParser",
while all the spacegroup names started with "I" are all parsed into "P", why?
for example, the icsd_044367.cif Li has the spacegroup_name "Im-3m", I use
SpacegroupAnalyzer(IStructure.from_file(icsd_044367.cif).get_spacegroup_symbol()
I get the result: Pm-3m
How can I get the "Im-3m" ?
thank you !
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https://github.com/materialsproject/pymatgen/pull/193
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MDExOlB1bGxSZXF1ZXN0MzEwOTE3NTk=
| 193
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MPRester: add get_materials_id_references()
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[] | 2015-03-13T00:44:17
| 2015-03-13T02:02:54
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2015-03-13T02:02:54Z
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MEMBER
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This pull request adds the convenience function `get_materials_id_references(<mp-id>)` and the according test in MPRester to make use of the new MP REST API [endpoint](https://github.com/materialsproject/materials_django/compare/89710d0bf172319455baa47419d7658010523465~1...master) `materials/mp-123/refs`. For the purpose of [pre](https://github.com/materialsproject/pymatgen/compare/master...tschaume:master#diff-6821d60ec5218f73aefdd5318abfbc7eR102)-release [testing](https://gist.github.com/tschaume/fa8d0fc7ed29fe972d2c) (dev or local), MPRester can now be initialized with the more general `endpoint` instead of `host`. Please advise if you can think of a better solution for the latter.
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MPRester: add find_structure()
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This pull request adds the convenience function `find_structure()` and according unit test to MPRester making use of the respective MP REST API [endpoint](https://github.com/materialsproject/materials_django/compare/materialsproject:00ec866...materialsproject:c368a32) ([Usage](https://gist.github.com/tschaume/fa8d0fc7ed29fe972d2c)).
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| 195
|
borg.hive valid paths extension and DYNMAT I/O object
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[] | 2015-03-22T20:48:42
| 2015-06-30T02:43:00
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2015-04-07T16:36:55Z
|
MEMBER
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This pull request extends the valid paths in `apps.borg.hive` to also accept directories without a `vasprun.xml`. VASP output in directories with either a POSCAR or a POSCAR and an OSZICAR is now assimilated by the `VaspToComputedEntryDrone`, too. The update in the valid paths requires more extensive checks regarding the availability of specific VASP output files. The checks have been implemented such that all the available data is still assimilated into the `ComputedEntry`. All tests for `io.vaspio.vasp_output` still succeed but I suggest that @computron and @shyuep take a closer look for any test cases I should implement now since not only the `vasprun.xml` is parsed anymore. The updated `VaspToComputedEntryDrone` is used in the abstract class [`AbstractVaspDirCollParser`](https://github.com/materialsproject/MPContribs/blob/master/mpcontribs/io/vaspdir.py) to support user contributions via MPContribs through a collection of associated VASP directories.
Also included in this pull request is a first version of an I/O object to read and write DYNMAT files along with the corresponding unittest and test file. It includes a `get_phonon_frequencies` method which still needs vetting by the experts/collaborators and subsequent unit testing. See materialsproject/MPContribsUsers#4 for reference.
As a minor additional update, the unit tests for the MPRester functions `get_materials_id_references` and `find_structure` now test against the production MP site since the according endpoints have been released.
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| 196
|
Fix for dilute solute model and script to call dilute solute model from commandline
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[] | 2015-03-23T20:17:59
| 2015-03-23T21:26:12
|
2015-03-23T21:26:12Z
|
CONTRIBUTOR
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Hello Shyue,
I fixed the python 3 version bug in dilute solution model. In addition, I added a new command to compute defect concentrations. Since there are many steps in the computation, I created the command "pydii".
Thanks,
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|
Changed "module" and "class" in BandStructure to "@module" and "@class".
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[] | 2015-03-26T14:20:31
| 2015-03-26T15:44:36
|
2015-03-26T15:44:36Z
|
CONTRIBUTOR
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|
Bug fixes in pydii script
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[] | 2015-03-26T20:40:04
| 2015-03-26T20:47:56
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2015-03-26T20:47:56Z
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CONTRIBUTOR
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Citation added and bug fix
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"organizations_url": "https://api.github.com/users/mbkumar/orgs",
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"events_url": "https://api.github.com/users/mbkumar/events{/privacy}",
"received_events_url": "https://api.github.com/users/mbkumar/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
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"node_id": "",
"avatar_url": "",
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}
|
[] | null |
[] | 2015-03-28T22:04:58
| 2015-03-28T22:27:05
|
2015-03-28T22:27:05Z
|
CONTRIBUTOR
|
{
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"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
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"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
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"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
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{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/199/reactions",
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https://api.github.com/repos/materialsproject/pymatgen/issues/199/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/199",
"html_url": "https://github.com/materialsproject/pymatgen/pull/199",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/199.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/199.patch",
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|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/200
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/200/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/200/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/200/events
|
https://github.com/materialsproject/pymatgen/pull/200
| 65,266,807
|
MDExOlB1bGxSZXF1ZXN0MzIyNTA4MDg=
| 200
|
More bug fixes in pydii script
|
{
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"subscriptions_url": "https://api.github.com/users/mbkumar/subscriptions",
"organizations_url": "https://api.github.com/users/mbkumar/orgs",
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"received_events_url": "https://api.github.com/users/mbkumar/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
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"node_id": "",
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}
|
[] | null |
[] | 2015-03-30T17:58:13
| 2015-03-30T18:24:20
|
2015-03-30T18:24:20Z
|
CONTRIBUTOR
|
{
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"percent_completed": 0
}
|
{
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"node_id": "MDQ6VXNlcjU3NzEwNw==",
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"html_url": "https://github.com/shyuep",
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"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
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https://api.github.com/repos/materialsproject/pymatgen/issues/200/timeline
| null | true
| false
|
{
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"merged_at": "2015-03-30T18:24:20Z"
}
|
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