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Bug fix in solute defect parsing
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Lattice parameters are not extracted from NWChem output
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[
"Thanks. That would be much appreciated.\nWe have not implement lattice parameters as we primarily use NWChem for molecular calculations at the moment. But I am sure this feature would be useful for many other users.\n",
"Very well then, I will open my fork of the code and start implementing the lattice parameter extraction there.\n",
"Feature implemented in pull request #205 (merged).\n"
] | 2015-04-02T15:43:22
| 2015-04-07T16:58:11
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2015-04-07T16:58:11Z
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CONTRIBUTOR
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It seems that the lattice parameters are not extracted from the output of NWChem, a feature that would be nice to have. I wonder whether the developers feel positive about this development. I could implement it and present in a form of pull request if there is any possibility of such an improvement to get into the packaged version of pymatgen.
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Bug fix in solute conc input
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2015-04-02T23:16:13Z
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Patch proposed in issue #203 (Lattice parameters are not extracted from NWChem output)
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[] | 2015-04-07T14:10:43
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2015-04-07T16:36:27Z
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CONTRIBUTOR
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This pull request implements parsing the lattice parameters from NWChem's output, if present. If lattice parameters are found in the output, an instance of `Structure` is created instead of `Molecule` and pushed in a separate list.
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| 67,221,336
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MDU6SXNzdWU2NzIyMTMzNg==
| 206
|
InsecurePlatformWarning for MPRester method
|
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[
"As far as I know, this is not an issue yet. Not sure about future. \n"
] | 2015-04-08T21:12:42
| 2015-04-14T00:36:16
|
2015-04-14T00:36:16Z
|
MEMBER
|
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Reproduction (using Python 2.7.8, pymatgen 3.0.13):
```
from pymatgen import MPRester
from os import environ
mpr = MPRester(environ['MAPI_KEY'])
my_bs = mpr.get_bandstructure_by_material_id('mp-754937')
```
Output:
/Users/dwinston/.virtualenvs/mp/lib/python2.7/site-packages/requests/packages/urllib3/util/ssl_.py:79: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
InsecurePlatformWarning
From the link above:
> Certain Python platforms (specifically, versions of Python earlier than 2.7.9) have restrictions in their ssl module that limit the configuration that urllib3 can apply. In particular, this can cause HTTPS requests that would succeed on more featureful platforms to fail, and can cause certain security features to be unavailable.
>
> If you encounter this warning, it is strongly recommended you upgrade to a newer Python version, or that you use pyOpenSSL as described in the OpenSSL / PyOpenSSL section.
Does this mean that users with Python < 2.7.9 (released 2014-12-10) will fail at making REST queries? The MP web site is running Python 2.7.8.
|
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MDU6SXNzdWU2Nzk2MTM4OQ==
| 207
|
Scripts require Python2, but use Python3 when pymatgen is installed for 3.x
|
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[
"Thanks for letting me know. I have just pushed a fix for potcar_setup. Is that the only one? I know that pmg works in Py3.\n\nShyue Ping\n\nOn April 12, 2015 at 2:21:35 PM, Michael Lamparski (notifications@github.com) wrote:\n\nVarious scripts in the scripts directory (such as potcar_setup) do not support Python 3. However, if pymatgen is installed from source as a Python 3 module via the following command:\n\npython3 setup.py install\n\nThen the scripts installed to /usr/local/bin will begin with #!/path/to/python3, causing them to fail when they encounter any old 2.x features:\n\n$ potcar_setup\n Traceback (most recent call last):\n File \"/usr/local/bin/potcar_setup\", line 5, in <module>\n pkg_resources.run_script('pymatgen==3.0.13', 'potcar_setup')\n File \"/usr/lib/python3/dist-packages/pkg_resources.py\", line 528, in run_script\n self.require(requires)[0].run_script(script_name, ns)\n File \"/usr/lib/python3/dist-packages/pkg_resources.py\", line 1394, in run_script\n execfile(script_filename, namespace, namespace)\n File \"/usr/lib/python3/dist-packages/pkg_resources.py\", line 55, in execfile\n exec(compile(open(fn).read(), fn, 'exec'), globs, locs)\n File \"/usr/local/lib/python3.4/dist-packages/pymatgen-3.0.13-py3.4-linux-x86_64.egg/EGG-INFO/scripts/potcar_setup\", line 16, in <module>\n pspdir = raw_input(\"Please enter full path where the POT_GGA_PAW_PBE, \"\nNameError: name 'raw_input' is not defined\n\n—\nReply to this email directly or view it on GitHub.\n",
"I'm not sure I have the necessary kind of input files to test all of them, but `diff_incar.py` and `feff_input_generation.py` break right off the bat, and `gaussian_analyzer` produces \"TypeError: the JSON object must be str, not 'bytes'\".\n\nFunny, when I run pmg with Python3, I get this:\n\n```\n$ pmg\nTraceback (most recent call last):\n File \"/usr/local/bin/pmg\", line 5, in <module>\n pkg_resources.run_script('pymatgen==3.0.13', 'pmg')\n File \"/usr/lib/python3/dist-packages/pkg_resources.py\", line 528, in run_script\n self.require(requires)[0].run_script(script_name, ns)\n File \"/usr/lib/python3/dist-packages/pkg_resources.py\", line 1394, in run_script\nexecfile(script_filename, namespace, namespace)\n File \"/usr/lib/python3/dist-packages/pkg_resources.py\", line 55, in execfile\n exec(compile(open(fn).read(), fn, 'exec'), globs, locs)\n File \"/usr/local/lib/python3.4/dist-packages/pymatgen-3.0.13-py3.4-linux-x86_64.egg/EGG-INFO/scripts/pmg\", line 514, in <module>\n main()\n File \"/usr/local/lib/python3.4/dist-packages/pymatgen-3.0.13-py3.4-linux-x86_64.egg/EGG-INFO/scripts/pmg\", line 510, in main\n args.func(args)\nAttributeError: 'Namespace' object has no attribute 'func'\n```\n\nThis appears to be related to a post-3.0 change: http://bugs.python.org/issue16308pyton\nEdit: My python version is 3.4.0\nEdit 2: It looks like this error only occurs if no arguments are given.\n",
"Ok, I just pushed a fix to test two problems. One of them is a unicode handling issue. the other is a change in the behavior of argparse when no sub parsers are specified. I have implemented workaround for that.\n\nShyue Ping\n\nOn April 12, 2015 at 2:52:48 PM, Michael Lamparski (notifications@github.com) wrote:\n\nI'm not sure I have the necessary kind of input files to test all of them, but diff_incar.py and feff_input_generation.py break right off the bat, and gaussian_analyzer produces \"TypeError: the JSON object must be str, not 'bytes'\".\n\nFunny, when I run pmg with Python3, I get this:\n\n$ pmg\nTraceback (most recent call last):\n File \"/usr/local/bin/pmg\", line 5, in <module>\n pkg_resources.run_script('pymatgen==3.0.13', 'pmg')\n File \"/usr/lib/python3/dist-packages/pkg_resources.py\", line 528, in run_script\n self.require(requires)[0].run_script(script_name, ns)\n File \"/usr/lib/python3/dist-packages/pkg_resources.py\", line 1394, in run_script\nexecfile(script_filename, namespace, namespace)\n File \"/usr/lib/python3/dist-packages/pkg_resources.py\", line 55, in execfile\n exec(compile(open(fn).read(), fn, 'exec'), globs, locs)\n File \"/usr/local/lib/python3.4/dist-packages/pymatgen-3.0.13-py3.4-linux-x86_64.egg/EGG-INFO/scripts/pmg\", line 514, in <module>\n main()\n File \"/usr/local/lib/python3.4/dist-packages/pymatgen-3.0.13-py3.4-linux-x86_64.egg/EGG-INFO/scripts/pmg\", line 510, in main\n args.func(args)\nAttributeError: 'Namespace' object has no attribute 'func'\n\nThis appears to be related to a post-3.0 change: http://bugs.python.org/issue16308pyton\n\n—\nReply to this email directly or view it on GitHub.\n"
] | 2015-04-12T21:21:34
| 2015-04-14T00:36:04
|
2015-04-14T00:36:04Z
|
CONTRIBUTOR
|
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Various scripts in the `scripts` directory (such as `potcar_setup`) do not support Python 3. However, if pymatgen is installed from source as a Python 3 module via the following command:
```
python3 setup.py install
```
Then the scripts installed to `/usr/local/bin` will begin with `#!/path/to/python3`, causing them to fail when they encounter any old 2.x features:
```
$ potcar_setup
Traceback (most recent call last):
File "/usr/local/bin/potcar_setup", line 5, in <module>
pkg_resources.run_script('pymatgen==3.0.13', 'potcar_setup')
File "/usr/lib/python3/dist-packages/pkg_resources.py", line 528, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python3/dist-packages/pkg_resources.py", line 1394, in run_script
execfile(script_filename, namespace, namespace)
File "/usr/lib/python3/dist-packages/pkg_resources.py", line 55, in execfile
exec(compile(open(fn).read(), fn, 'exec'), globs, locs)
File "/usr/local/lib/python3.4/dist-packages/pymatgen-3.0.13-py3.4-linux-x86_64.egg/EGG-INFO/scripts/potcar_setup", line 16, in <module>
pspdir = raw_input("Please enter full path where the POT_GGA_PAW_PBE, "
NameError: name 'raw_input' is not defined
$ python2 `which potcar_setup`
Please enter full path where the POT_GGA_PAW_PBE, etc. subdirs are present. If y
ou obtained the PSPs directly from VASP, this should typically be the directory
that you untar the files to :
```
|
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MDExOlB1bGxSZXF1ZXN0MzMxNjk4MDQ=
| 208
|
Fix VaspInput.write_input (TypeError)
|
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[
"Thanks.\n"
] | 2015-04-13T14:42:08
| 2015-04-13T15:05:17
|
2015-04-13T14:51:26Z
|
CONTRIBUTOR
|
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It was producing TypeError when used due to it passing in Incar/Potcar/etc instances to the file.write method.
Also, none of the tests called this method, so I added one.
|
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MDU6SXNzdWU2ODIyMzE4MA==
| 209
|
Bug in the updated dos code
|
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[] | 2015-04-13T23:59:46
| 2015-04-14T00:35:40
|
2015-04-14T00:35:40Z
|
CONTRIBUTOR
|
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Hello Shyue,
I am noticing this error when running the updated code on the same xml file:
Traceback (most recent call last):
File "./my_dos_plotter.py", line 53, in <module>
dp.add_dos_dict(cdos.get_site_spd_dos(cdos.structure.sites[0]))
File "/home/mbkumar/venv1/pymatgen/pymatgen/electronic_structure/dos.py", line 332, in get_site_spd_dos
orb_type = orb.orbital_type
AttributeError: 'str' object has no attribute 'orbital_type'
|
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https://github.com/materialsproject/pymatgen/issues/210
| 74,407,337
|
MDU6SXNzdWU3NDQwNzMzNw==
| 210
|
electronic_structure.plotter.DosPlotter raises ValueError for some MP materials
|
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[] | null |
[
"This is really a data problem. I am not sure what is happening. But the energies has 581 elements and the densities has 601 elements. That cannot be the case.\n\nAlso, this seems to be non-spin-polarized, which is strange since we always do spin-polarized calculations. I suspect that the vasp run resulted in a bad DOS (e.g., one of the ****\\* values type), which is non-fatal in parsing, but is fatal when trying to plot it.\n\nThe DOS object itself does not perform a check on the length of the arrays. \n\nIn conclusion, someone needs to trace back the original data source. It is not a pymatgen problem. Closing this issue.\n"
] | 2015-05-08T15:48:31
| 2015-07-30T21:55:07
|
2015-07-30T21:55:07Z
|
MEMBER
|
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I'm getting a ValueError pertaining to numpy array shapes when trying to get the DOS plots for a couple of materials. Out of 500 sample materials, I found only two that fail to plot, so the problem may be upstream, e.g. the db data is misformatted. However, `MPRester.get_dos_by_material_id` succeeds in instantiating a `pymatgen.electronic_structure.dos.CompleteDos`, which should always be plottable.
Reproduction:
``` python
from pymatgen import MPRester
from pymatgen.electronic_structure.plotter import DosPlotter
culprits = ['mp-560581', 'mp-3318']
m = MPRester()
dos = m.get_dos_by_material_id('mp-3318')
dp = DosPlotter()
dp.add_dos_dict(dos.get_element_dos())
dp.get_plot() # ValueError: x and y must have same first dimension
```
Trace:
```
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-40-65680dbbf86a> in <module>()
7 dp = DosPlotter()
8 dp.add_dos_dict(dos.get_element_dos())
----> 9 dp.get_plot() # ValueError: x and y must have same first dimension
/Users/dwinston/.virtualenvs/mp/lib/python2.7/site-packages/pymatgen/electronic_structure/plotter.pyc in get_plot(self, xlim, ylim)
172 else:
173 ppl.plot(x, y, color=colors[i % ncolors],
--> 174 label=str(key),linewidth=3)
175 if not self.zero_at_efermi:
176 ylim = plt.ylim()
/Users/dwinston/.virtualenvs/mp/lib/python2.7/site-packages/prettyplotlib/colors.pyc in wrapper(*args, **kwargs)
33 def wrapper(*args, **kwargs):
34 with mpl.rc_context(rc=rcParams):
---> 35 return func(*args, **kwargs)
36 return wrapper
37
/Users/dwinston/.virtualenvs/mp/lib/python2.7/site-packages/prettyplotlib/_plot.pyc in plot(*args, **kwargs)
10 show_ticks = kwargs.pop('show_ticks', False)
11
---> 12 lines = ax.plot(*args, **kwargs)
13 remove_chartjunk(ax, ['top', 'right'], show_ticks=show_ticks)
14 return lines
/Users/dwinston/.virtualenvs/mp/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-macosx-10.10-x86_64.egg/matplotlib/axes/_axes.pyc in plot(self, *args, **kwargs)
1371 lines = []
1372
-> 1373 for line in self._get_lines(*args, **kwargs):
1374 self.add_line(line)
1375 lines.append(line)
/Users/dwinston/.virtualenvs/mp/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-macosx-10.10-x86_64.egg/matplotlib/axes/_base.pyc in _grab_next_args(self, *args, **kwargs)
302 return
303 if len(remaining) <= 3:
--> 304 for seg in self._plot_args(remaining, kwargs):
305 yield seg
306 return
/Users/dwinston/.virtualenvs/mp/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-macosx-10.10-x86_64.egg/matplotlib/axes/_base.pyc in _plot_args(self, tup, kwargs)
280 x = np.arange(y.shape[0], dtype=float)
281
--> 282 x, y = self._xy_from_xy(x, y)
283
284 if self.command == 'plot':
/Users/dwinston/.virtualenvs/mp/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-macosx-10.10-x86_64.egg/matplotlib/axes/_base.pyc in _xy_from_xy(self, x, y)
221 y = np.atleast_1d(y)
222 if x.shape[0] != y.shape[0]:
--> 223 raise ValueError("x and y must have same first dimension")
224 if x.ndim > 2 or y.ndim > 2:
225 raise ValueError("x and y can be no greater than 2-D")
ValueError: x and y must have same first dimension
```
|
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| 76,729,551
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MDExOlB1bGxSZXF1ZXN0MzU1MTM3MDg=
| 211
|
Additional zeo++ functionality upon user request
|
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[] | 2015-05-15T13:40:38
| 2015-05-15T16:25:38
|
2015-05-15T16:25:38Z
|
CONTRIBUTOR
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| 79,203,765
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| 212
|
Cleaned up ...
|
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[] | 2015-05-21T23:32:56
| 2015-05-21T23:38:14
|
2015-05-21T23:38:14Z
|
CONTRIBUTOR
|
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|
...getting oxidation-state decorated structure for interstitial finder
|
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MDU6SXNzdWU5Mjc1ODc2MQ==
| 213
|
semvar?
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[
"Generally, pymatgen follows pretty closely to semvar, though backwards incompatible changes do occur at what is so-called the minor version.\n\nThe evolution of pymatgen is too rapid to use standard semvar. Many “patches” in fact are new functionality development. The time between minor versions tend to be fairly long. E.g., it is almost a year between 3.0.0 and 3.1.0. Lots of time was given with deprecation messages on the removal of SymmetryFinder.\n\nIf we use standard semvar, the version number of pymatgen will be something like 99.1.0. \n\nShyue Ping\n\nOn July 3, 2015 at 07:40:33, Donny Winston (notifications@github.com) wrote:\n\nWhat is this project's policy for version tagging? May I suggest using that of http://semver.org/?\nThere were some deprecations introduced in v3.0.5 that are now incompatible changes as of v3.1. For example, the MP web code has a line\n\nfrom pymatgen.symmetry.finder import SymmetryFinder\n\nfor the crystal toolkit app that is now broken. This is not a bad thing -- I'll change the line -- it's just that I figured \"pymatgen v4.0.0rc1\" would be the time to expect lots of dangling deprecated code to require replacement.\n\n—\nReply to this email directly or view it on GitHub.\n"
] | 2015-07-02T23:40:29
| 2015-07-03T00:31:54
|
2015-07-03T00:31:54Z
|
MEMBER
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What is this project's policy for version tagging? May I suggest using that of http://semver.org/?
There were some [deprecations](https://github.com/materialsproject/pymatgen/blob/master/CHANGES.rst#v305) introduced in v3.0.5 that are now incompatible changes as of v3.1. For example, the MP web code has a line
```
from pymatgen.symmetry.finder import SymmetryFinder
```
for the crystal toolkit app that is now broken. This is not a bad thing -- I'll change the line -- it's just that I figured "pymatgen v4.0.0rc1" would be the time to expect lots of dangling deprecated code to require replacement.
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MDU6SXNzdWU5NTMwNzc5Mw==
| 214
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SpacegroupAnalyzer crashes with `alpha` not calculated
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[
"Below the affected code. It seems that `alpha` needs to be set to 90.\n\n```\n if new_matrix is None:\n #this if is to treat the case\n #where alpha==90 (but we still have a monoclinic sg\n new_matrix = [[a, 0, 0],\n [0, b, 0],\n [0, c * cos(alpha), c * sin(alpha)]]\n```\n",
"Pls contact @hautierg to fix this problem, as well as ensure that unittests are written to ensure that this bug does not occur again. I don't want to fix this as I am not sure what's the right procedure.\n",
"Already fixed. Closing/\n"
] | 2015-07-15T22:56:16
| 2015-07-30T21:48:02
|
2015-07-30T21:48:02Z
|
MEMBER
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In pymatgen 3.0.14, the `get_conventional_standard_structure` function crashes in line 618 with the error message: `local variable 'alpha' referenced before assignment`. For the special case with a monoclinic lattice type, a space group starting with 'C', and angle `landang[1][0] = 90`, the variable `alpha` is never calculated and constructing `new_matrix` hence fails.
@shyuep: This issue is important for the `mgcloud` project, since it causes two of the test jobs to crash (BaTiO3, LiCoO2) and we're not sure how this issue would scale when running many calculations. FYI, @computron and @kristinpersson
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MDU6SXNzdWU5NzUxODk4Mw==
| 215
|
parsing of LORBIT and NELM by io.vaspio.Vasprun
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[
"I just pushed a fix to the NELM issue. But I cannot do anything about LORBIT. If the vasprun.xml does not report the right value, I can only leave it be. \n"
] | 2015-07-27T17:57:46
| 2015-07-28T04:18:26
|
2015-07-27T20:41:56Z
|
NONE
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vasprun.xml does not seem to read a numeric LORBIT correctly. When it is set in INCAR as an integer, it will be seen as a boolean tag and assigned False. The same could happen to other tags. Instead, OUTCAR has the right value, straight from INCAR.
NELM appears once in OUTCAR, but twice in vasprun.xml, one in 'electronic convergence', another in 'response functions'. The latter one has the default value 1, replacing the default value 60 of the former and causes vasprun.parameters to get the wrong value. Thus vasprun.converged_electronic always returns False.
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| 216
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Anonymous formula is chemistry dependent
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[
"My preference is if the anonymous formula is not built off the \"pretty formula\" but rather the reduced formula. ie. I would want Li2O2 to have anonymous formula for AB.\n",
"I am fine with this. Can someone fix this?\n"
] | 2015-07-30T17:54:15
| 2015-07-31T15:00:10
|
2015-07-31T15:00:10Z
|
CONTRIBUTOR
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The anonymous formula currently uses the list of special formulas to determine the reduced formula. For example, Li2O2 has anonymous formula A2B2 instead of AB. Is this desired functionality (and does anyone depend on it)?
As it is now, chemical substitutions applied to a structure can (sometimes) change its anonymous formula, which I think is quite counterintuitive.
|
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Allowing CIF data_* header to be prefixed with spaces and tabulations.
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[
"Thanks for the contribution. I will merge it.\n"
] | 2015-07-31T08:34:05
| 2015-07-31T14:00:28
|
2015-07-31T14:00:28Z
|
CONTRIBUTOR
|
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Current parser for CIF format files forbids CIF data_\* header to be prefixed with space, what is completely normal, according to IUCr's CIF syntax specification (http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax).
MWE (test.cif):
```
data_test_1
data_test_2
```
MWE (python script):
``` python
from pymatgen.io.cifio import CifParser
c = CifParser("test.cif")
c.as_dict()
```
should produce:
``` python
OrderedDict([(u'test_1', {}), (u'test_2', {})])
```
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MDU6SXNzdWU5ODYyMzQ3Mg==
| 218
|
pymatgen.io.vaspio.Incar() object copy method returns plain dict, rather than another object
|
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[
"You don't actually need to do .copy(). Just Incar(incar_old) will do.\n\nIn general, I don't want to override copy(). Incar inherits dict, which is why it returns a dict. For most purposes, an Incar is like a dict.\n"
] | 2015-08-02T17:23:05
| 2015-08-02T20:09:05
|
2015-08-02T20:09:05Z
|
NONE
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Don't know if it's intended to be. Of course, pymatgen.io.vaspio.Incar(incar_old.copy()) still works.
|
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MDU6SXNzdWU5ODY2Mjc4MQ==
| 219
|
Read WAVEDER(F) from Vasp LOPTICS runs?
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[
"Dear Miguel,\n\nI think this would be a nice addition. I have no idea how to read the WAVEDER without delving deep into the VASP source code to find out how it is generated (something I avoid). I think providing the facility to read the WAVEDERF is fine, as long as you document in the code that this is only useful if people use a specific version of compiled vasp.\n",
"Dear Shyue,\n\nthanks for the quick reply and your interest. Before submitting a pull request, maybe you can have a look at migueldiascosta/pymatgen@31f49648359acf9c041a5a53357e4b5e7415de67 and comment? \n\nEven being so simple, there were already a few choices to be made. For instante, on the type of data, I chose a numpy array for performance and multidimensional slicing.\n\nI also left out the band indexes, energies and occupations as these are already available, as well as the kpoint coordinates, but one could also make a case for having this class more self-contained.\n\nFor testing, you can download a (large) WAVEDERF file here: https://db.tt/FfAOm163\n\nAlso, do let me know of any guidelines I may have missed.\n",
"Hi Miguel,\n\nThe class looks great. Using numpy arrays is always a good idea. \n\nThe only minor thing I would change is to use \"with zopen() as f:\" instead of f = zopen.... That guarantees that the file handler is closed (something that you did not do) and prevents a memory leak. \n\nAfter you make that minor change, can you submit the pull request pls? Thanks.\n\nRegards,\nShyue Ping\n",
"Oh, you should also add a Author: Miguel Dias Costa in the doc. I always want to make sure that the authors are recognized for their contributions.\n",
"hello, could I get helps about transition dipole from you? I now can calculate dipole moment matrix, also the strength of dipole moment accurately, but I can not figure out the direction of dipole moment. Since in the WaVEDERF output, the dx, dy,dz seems are in cart coordinates but not to be the coordinates of used by kpoints. For instance, I calculate ZnO along gamma_A(0,0,0.5), but dipole moment has no value along dz direction, I am quite puzzle about the cart coordinates used by dipole moment. ",
" I am wirting to ask helps from you for VASP calculation about optic transition dipole matrix \r\n(output by Linear_optic.F).\r\n\r\n I now can calculate dipole moment matrix, also the strength of dipole moment accurately, but \r\nI can not figure out the direction of dipole moment. Since in the WAVEDERF output, the dx, dy,dz \r\nseems are in cart coordinates but not to be the coordinates of used by kpoints (kx, ky ,kz). \r\n \r\n The dipole moment is defined as, <Psi_Val | r_i | Psi_Con> = <Psi_Val | d/dk_i | Psi_Con> but \r\nI can not figure out the \"i,j,k\", the CDUM(1),CDUM(2),CDUM(3) directions in linear_optic.F files.\r\nCDUM(1:3)=CDER_BETWEEN_STATES(NB1,NB2,NK,ISP,1:3) \r\n\r\n My quesition is, the direction or axis for CDUM(1), CDUM(2) and CDUM(3) ; is it along kx, ky \r\nand kz, respectively? \r\n\r\n For instance, I calculate Hexagonal w-ZnO along gamma_A (0,0,0.5) in rec kpoints coordinates, \r\nbut dipole moment has zero value along dz direction, but a strong Zn-O bond are along \r\ngamma_A direction seems leads to strong dipole along kz. \r\n\r\n I would be very appreciated if I could I could get hleps from you. \r\n\r\nBest,\r\nTianjiao Shao ",
"Hi,\r\nCan anyone share an example of WAVEDERF file with me? I want to see what exactly it writes i.e. in which format. I am still struggling to compile the VASP to generate the WAVEDERF file. \r\n\r\nBest,\r\nDebmalya Ray",
"@debmalyakan see if this helps: https://gist.github.com/migueldiascosta/aeae055c024bf26f595b3ed4dcbce341",
"@shaojim sorry for the (very) late reply, but I'm not sure if I can help you. In your example, do you mean all dipoles along z direction are zero? In general the dipole at a specific k point between a specific pair of bands depends on the orbital character of those bands at that point, and in many cases may well be zero due to selection rules...",
"Dear Debmalya Ray, \n\n\nPlease find in attach I calculate the wavederf. \n\n\nBest, \nTianjiao Shao \n\n\n\n\n\n\nAt 2018-02-22 02:45:34, \"debmalyakan\" <notifications@github.com> wrote:\n\n\nHi,\nCan anyone share an example of WAVEDERF file with me? I want to see what exactly it writes i.e. in which format. I am still struggling to compile the VASP to generate the WAVEDERF file.\n\nBest,\nDebmalya Ray\n\n—\nYou are receiving this because you commented.\nReply to this email directly, view it on GitHub, or mute the thread.",
"One need to modify the linear_optic.f in vasp program, to uncomment and let them output to wavederf document, the wavedef is like this \r\n 1 60 8\r\n 1 1 (1.8741009E-10,2.5399544E-12)\r\n 1 2 (0.4166370,0.1413575)\r\n 1 3 (0.1636533,8.6130545E-02)\r\n 1 4 (0.1836701,5.7265228E-03)\r\n 1 5 (6.5361980E-11,1.2927599E-09)\r\n 1 6 (1.9887898E-09,1.2232620E-09)\r\n 1 7 (1.1974201E-02,6.9308490E-02)",
"[modified_script_optic.zip](https://github.com/materialsproject/pymatgen/files/1855271/modified_script_optic.zip)\r\n",
"@migueldiascosta Dear Migueldiascosta, Thank you very much for replying me. I also think dipole defined as <Psi_m |r| Psi_n> are used to describe the transition, when dipole equal to zero which indicates the forbidden for transition, and now I can get wavederf in vasp. But I want to ask a favor of you, is the vasp output the dipole in units of atomic units ? the vasp codes are written in atomic units ? I am appreciated for getting your helps ",
"@debmalyakan Dear Debmalya Ray please find my attached files and I appologize to reply later \r\n[modified_script_optic.zip](https://github.com/materialsproject/pymatgen/files/1855307/modified_script_optic.zip)\r\n",
"Hi Can you please let me know how to calculate transition probability ( if there is a script available ?) i have wavederf file with me ...Thanks",
"I use semi-conductor bloch equation to compute probability, please find in PRL 113, 073901 (2014)",
"Hi, i am a newbie. I would like to calculate square of dipole transition matrix ie transition probability from vbm to cbm. i have wavederf file but i dont know how should i proceed. Any help would be great (like any script or code) Thanks.",
"@priyashrv Pls post this at https://pymatgen.discourse.group .",
"> Hello all,\r\n> \r\n> we've recently been uncommenting a line (CALL WRT_CDER_BETWEEN_STATES_FORMATTED..) in vasp linear_optics.F which writes WAVEDERF, a formatted version of WAVEDER, to get the optical transition matrix elements, and we were thinking this could be a nice addition to vasp_output.py, since coupled with other band structure features of pymatgen it can allow interesting analyses and/or visualizations.\r\n> \r\n> However, since the default output is unformatted, do you have a recommendation for how to read it from python or do you just avoid these files altogether? If the latter, we can easily read from WAVEDERF but that will only be present if people uncomment that line and recompile vasp...\r\n> \r\n> Cheers,\r\n> Miguel\r\n\r\nDear Miguel\r\n I want to plot optical transition probability from WAVEDER file,But I don't know how to run \"linear_optics.F\" This program, thank you very much for your help.\r\n\r\n\r\nHaysun",
"@Haysun the routines in `linear_optics.F` are run when you run VASP with `LOPTICS`. \r\n\r\nSo, if you simply uncomment the `! CALL WRT_CDER_BETWEEN_STATES_FORMATTED(` line in `linear_optics.F` and recompile VASP, the WAVEDERF file will be created alongside the WAVEDER file when VASP is run with `LOPTICS`\r\n\r\n(I haven't tested this with VASP 6, or used this at all in years, but the commented line is still there)",
"@migueldiascosta ,Thank you very much for your reply, I will use the method you said to get WAVEDERF, but I have a doubt that how do we get the transition matrix through WAVEDERF? \r\nThanks for your help and good luck.",
"@Haysun see if this helps, https://gist.github.com/migueldiascosta/aeae055c024bf26f595b3ed4dcbce341, and you can also have a look at the vasp code itself"
] | 2015-08-03T03:11:45
| 2020-06-05T07:52:15
|
2015-08-04T00:59:07Z
|
CONTRIBUTOR
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Hello all,
we've recently been uncommenting a line (CALL WRT_CDER_BETWEEN_STATES_FORMATTED..) in vasp linear_optics.F which writes WAVEDERF, a formatted version of WAVEDER, to get the optical transition matrix elements, and we were thinking this could be a nice addition to vasp_output.py, since coupled with other band structure features of pymatgen it can allow interesting analyses and/or visualizations.
However, since the default output is unformatted, do you have a recommendation for how to read it from python or do you just avoid these files altogether? If the latter, we can easily read from WAVEDERF but that will only be present if people uncomment that line and recompile vasp...
Cheers,
Miguel
|
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Add class for parsing WAVEDERF file
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[
"Thanks!\n"
] | 2015-08-04T00:53:20
| 2015-08-04T01:45:51
|
2015-08-04T00:58:48Z
|
CONTRIBUTOR
|
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Implements materialsproject/pymatgen#219, after adding Shyue's corrections and rebasing.
|
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| 99,130,526
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MDExOlB1bGxSZXF1ZXN0NDE2NDU2MTc=
| 221
|
Multiple dielectricfunction elements in vasprun.xml
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[] | null |
[
"Thanks for the contribution. I made a minor modification to maintain Py3k compatibility.\n"
] | 2015-08-05T05:57:57
| 2015-08-05T15:11:19
|
2015-08-05T13:33:03Z
|
CONTRIBUTOR
|
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When [using the GW routines for the determination of frequency dependent dielectric matrix](http://cms.mpi.univie.ac.at/vasp/vasp/Using_GW_routines_determination_frequency_dependent_dielectric_matrix.html), there are multiple dielectricfuction elements in vasprun.xml, distinguished by element comments, and the Vasprun class is keeping the last one, which is actually the 'screened Coulomb potential'.
This tries to add support for these additional dielectricfunction elements without breaking the default behaviour by
1. if there is no comment (there is only one dielectricfunction element), keeping the previous behaviour
2. if an element with comment "INVERSE MACROSCOPIC DIELECTRIC TENSOR (including local field effects in RPA (Hartree))" exists, storing it in the default dielectric attribute and
3. storing any others (e.g., comments "HEAD OF MICROSCOPIC DIELECTRIC TENSOR (INDEPENDENT PARTICLE)", "1 + v P, with REDUCIBLE POLARIZABILTY P=P_0 (1 -(v+f) P_0)^-1", "screened Coulomb potential") in an other_dielectric dictionary using the comment as key.
For your consideration.
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| 99,295,381
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MDU6SXNzdWU5OTI5NTM4MQ==
| 222
|
pymatgen.Structure.from_str() does not really implement arg "primitive", except for cif
|
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[] | 2015-08-05T20:47:59
| 2015-08-05T21:05:49
|
2015-08-05T21:05:49Z
|
NONE
|
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And it makes the primitive cell claim in the docstring of `pymatgen.Structure.from_file()` unexpected.
`pymatgen.Structure.from_str` looks like this:
``` python
@classmethod
def from_str(cls, input_string, fmt, primitive=False, sort=False):
...
if fmt == "cif":
parser = CifParser.from_string(input_string)
s = parser.get_structures(primitive=primitive)[0]
elif fmt == "poscar":
s = Poscar.from_string(input_string, False).structure
elif fmt == "cssr":
cssr = Cssr.from_string(input_string)
s = cssr.structure
elif fmt == "json":
d = json.loads(input_string)
s = cls.from_dict(d)
elif fmt == "yaml":
d = yaml.load(input_string)
s = cls.from_dict(d)
else:
raise ValueError("Unrecognized format!")
```
The docstring of `pymatgen.Structure.from_file` is:
``` python
"""
Args:
filename (str): The filename to read from.
primitive (bool): Whether to convert to a primitive cell
Only available for cifs, POSCAR, CSSR, JSON, YAML
Defaults to True.
"""
```
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MDU6SXNzdWU5OTMxMDE2Mg==
| 223
|
ase name clash
|
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[
"I am not sure how there can be a name conflict. The ase package is properly namespaced in pymatgen. You just do \n\n```\nfrom pymatgen.io.ase import AseAtomsAdaptor\n```\n\nThis works perfectly fine to me.\n",
"Hi shyuep,\nYes, that works fine, but when i do the following(structure is a Structure object):\n\n> > > AseAtomsAdaptor().get_atoms(structure)\n\ni get\n\nTraceback (most recent call last):\n File \"<stdin>\", line 1, in <module>\n File \"/home/matk/Software/mpint2/lib/python2.7/site-packages/pymatgen-3.1.5-py2.7-linux-x86_64.egg/pymatgen/io/ase.py\", line 48, in get_atoms\n return Atoms(symbols=symbols, positions=positions, pbc=True, cell=cell)\nNameError: global name 'Atoms' is not defined\n",
"Just pushed a fix.\n"
] | 2015-08-05T22:11:15
| 2015-08-06T01:57:45
|
2015-08-05T22:45:09Z
|
CONTRIBUTOR
|
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Hi,
I just installed pymatgen version 3.1.5 and i was trying to use the aseadaptor from io/ase.py module. It seems like the module name clashes with the ase package and the statement 'from ase import Atoms' doesnt run evenafter installing ase. I was using version 3.1.0 before and didnt have any trouble using the adaptors.
-Kiran
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MDU6SXNzdWU5OTU3NDA2MA==
| 224
|
pmg.io.vasp.Kpoints.from_string() problem at picking up the IBZKPT style input
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[
"Thanks. I have fixed it the explicit kpoint parsing.\nThe get_kpoints doesn't really matter since numpy arrays are effectively lists for the most part. Is there a specific use case you find a problem with the numpy arrays?\n",
"No, not at all. It (kpoints.kpts) just didn't print out uniformly if there are lists and arrays. That's all. But the generated kpoints file is good.\n\nSo I kept trying to work the hybrid band gap calculation out, and noticed a few things.\n1. In `pmg.io.vasp.Vasprun.get_band_structure`, there seems to be some work under progress, with a TODO list \"make a decision on the convention with 2*pi or not.\" I assume it's related with VASP's cartesian k-points 2 pi/a notation. `Structure.to('POSCAR')` writes a file with a = 1, so the only factor is the 2 pi. But that doesn't make the reciprocal lattice 2 pi times more. Of course, if used for plotting, it doesn't really matter, because the scale is relative. But is there a reason behind this?\n \n ``` python\n lattice_new = Lattice(self.lattice_rec.matrix * 2 * math.pi)\n ```\n \n And it doesn't consider cartesian input.\n \n ``` python\n return BandStructureSymmLine(kpoints, eigenvals, lattice_new,\n efermi, labels_dict,\n structure=self.final_structure,\n projections=p_eigenvals)\n else:\n return BandStructure(kpoints, eigenvals, lattice_new, efermi,\n structure=self.final_structure,\n projections=p_eigenvals)\n ```\n \n While the instantiation syntax of BandStructure/BandStructureSymmLine is\n \n ``` python\n def __init__(self, kpoints, eigenvals, lattice, efermi, labels_dict,\n coords_are_cartesian=False, structure=None,\n ```\n \n If cartesian k-points are considered at all, since this method belongs to the vasp io, the actual kpts need to be multiplied by 2 pi.\n2. The reason I was caught up with it, is that `pmg.symmetry.bandstructure.HighSymmKpath.get_kpoints` currently returns only cartesian coordinates. (and it's not in the format of VASP, but that's good, because `pmg.symmetry.bandstructure.HighSymmKpath` should be QM code agnostic.)\n3. `pmg.electronic_structure.plotter.BSPlotter.get_plot` has line `rc('text', usetex=True)`, which implicitly depends on a Latex installation, and changes the matplotlib environment, but the current label setup doesn't quite need the external Latex support. Can it fall back to matplotlib's Tex if there is no Latex installed?\n",
"For this, I will direct your question to @hautierg, who was the one who implemented the Bandstructure algorithms and plotting. For (3), I would say yes, we should make sure that Latex installation is not a pre-req. Geoffroy, can you make the changes?\n",
"Hi Terence,\n\nThanks for your comments and for pointing this out. There are two conventions for reciprocal space vectors: the physics one with a 2pi factor and the crystallography one (without). Pymatgen uses the physics one. This 2pi factor was not necessary (as already taken care by pymatgen.lattice), I have removed it.\nAs for running HSE band structures with pymatgen, no need to read the IBZKPT. You could generate the k-point file directly using MPBSHSEVaspInputSet(). I have just fixed a problem in there that was related to your question of HighSymmKPath returning cartesian kpoints.\nLet me know if you have any other questions.\nI will look at the tex problem now.\n",
"I see. Wish there is a tutorial using the input sets. It looks like a junction between pymatgen and fireworks. Pymatgen provides the inputs, while fireworks defines the workflow.\n\nI don't want to intrude, but sometimes I just needed a small implementation, and use a few core objects and functions from pymatgen, rather than the sets, at least before they are more accessible. That's why I wish I could call\n`pmg.symmetry.bandstructure.HighSymmKpath.get_kpoints(kpoints_division, return_cartesian=False)` and get the fractional kpts.\n\nFractional kpts is more flexible, isn't it?\n",
"I agree that the user should be able to use cartesian or fractional at the HighSymmKpath level. I have modified the code to do so.\n",
"There were a lot of items mixed into this issue and I think the LaTeX part got left behind. On my current system I have to set `rc('text', usetex=True)` to be `rc('text', usetex=False)` to get it to work (the plot renders fine). Not sure why I get the error in the first place since I have LaTeX installed. I can probably get it working on my system by fiddling around but it would be better for pymatgen overall if the original suggestion to not require tex installation.\n",
"I pushed a fix to this by adding a try catch on the rc. In general, I would strongly recommend against using rc to set anything. That really should be left to the user to set it since it is a global matplotlib setting.\n"
] | 2015-08-07T03:59:06
| 2016-04-20T04:55:04
|
2015-08-11T17:19:54Z
|
NONE
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This is what pmg.io.vasp.Kpoints has in 3.1.5.
``` python
#Assume explicit KPOINTS if all else fails.
style = Kpoints.supported_modes.Cartesian if style == "ck" \
else Kpoints.supported_modes.Reciprocal
kpts = []
kpts_weights = []
labels = []
tet_number = 0
tet_weight = 0
tet_connections = None
for i in range(3, 3 + num_kpts):
toks = lines[i].split()
kpts.append([[float(j) for j in toks[0:3]]])
```
Should the `if style == "ck"` be changed to `in "ck"`? And `kpts.append([[float(j) for j in toks[0:3]]])` changed to `kpts.append([float(j) for j in toks[0:3]])`? The list level is one more than being correct.
Also, `pmg.symmetry.bandstructure.HighSymmKpath().get_kpoints()` returns the kpoints as a list of bunch of numpy arrays. It feels unnecessary and inconsistent for the use of numpy array here on explicit kpoints, after it's been calculated and generated, of course.
P.S. I was intending to manually construct a new kpoints file from the DFT IBZKPT and the line kpoints for the hybrid run.
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MDExOlB1bGxSZXF1ZXN0NDIwNDkzNDY=
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Charged defects
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[] | 2015-08-10T18:17:02
| 2015-08-10T18:17:40
|
2015-08-10T18:17:40Z
|
CONTRIBUTOR
|
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New branch to contribute code related to charged defects.
Initial code commits include place holder for Freysoldt correction, defect analyzer.
|
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| 100,188,765
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MDExOlB1bGxSZXF1ZXN0NDIwNzY2MjU=
| 226
|
create draft of sxdefectalign calling script
|
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[] | 2015-08-10T23:09:03
| 2015-08-11T05:15:53
|
2015-08-11T05:15:53Z
|
CONTRIBUTOR
|
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This is first working version of sxdefectalign calling script. I had to comment out the @requires command to get it to work for me...? Also note that this script can just be run once if you don't care about potential alignment screening...(just call .get_singlecorrection)
|
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|
sxdefect capabilities increased
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[] | 2015-08-11T21:19:02
| 2015-08-11T22:12:49
|
2015-08-11T22:12:49Z
|
CONTRIBUTOR
|
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Added easier compatibility for sxdefect wrapper, added the unit test for sxdefectwrapper as well as included two new LOCPOTs for unit testing. There are two LOCPOTs that are 3MB each, while the original LOCPOT for the Locpot class unit test is only 0.5MB...
Could change the original Locpot unit test so that it runs the test on one of my LOCPOTs that are being used for the sxdefectalignwrapper unit test
|
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abinitio needs to be refactored
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[] | 2015-08-12T14:22:44
| 2015-10-01T21:10:23
|
2015-10-01T21:10:23Z
|
MEMBER
|
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abinitio needs to be refactored to simply abinit to be consistent with the rest of the IO modules.
@gmatteo can you take care of this? I don't want to break anything in abipy because of what I do. But let me know if you prefer me to do it? For me, it's just a quick rename in an IDE.
|
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MDU6SXNzdWUxMDA4NDg3MDA=
| 229
|
SpacegroupAnalyzer init failing
|
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[
"You have an old spglib? Try doing python setup.py develop again first. \n\nShyue Ping\n\nOn August 13, 2015 at 12:25:59, Bharat Medasani (notifications@github.com) wrote:\n\nHello Shyue,\n\nI am getting the following error when trying to use SpacegroupAnalyzer.\n\nTraceback (most recent call last):\nFile \"BaBrF_vacancy_scaling.py\", line 9, in\nvac = Vacancy(uc, {}, {})\nFile \"/Users/mbkumar/Research/Defects/pymatgen/pymatgen/analysis/defects/point_defects.py\", line 284, in init\nsymm_finder = SpacegroupAnalyzer(self.structure)\nFile \"/Users/mbkumar/Research/Defects/pymatgen/pymatgen/symmetry/analyzer.py\", line 125, in __init_\ndataset['hall'] = dataset['hall'].strip()\nAttributeError: 'list' object has no attribute 'strip'\n\n—\nReply to this email directly or view it on GitHub.\n",
"Thanks.\n"
] | 2015-08-13T19:25:59
| 2015-08-13T19:42:13
|
2015-08-13T19:42:13Z
|
CONTRIBUTOR
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Hello Shyue,
I am getting the following error when trying to use SpacegroupAnalyzer.
Traceback (most recent call last):
File "BaBrF_vacancy_scaling.py", line 9, in <module>
vac = Vacancy(uc, {}, {})
File "/Users/mbkumar/Research/Defects/pymatgen/pymatgen/analysis/defects/point_defects.py", line 284, in **init**
symm_finder = SpacegroupAnalyzer(self._structure)
File "/Users/mbkumar/Research/Defects/pymatgen/pymatgen/symmetry/analyzer.py", line 125, in __init__
dataset['hall'] = dataset['hall'].strip()
AttributeError: 'list' object has no attribute 'strip'
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MDU6SXNzdWUxMDE5MzgyNzI=
| 230
|
Lattice.find_all_mappings change handedness
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[
"Yeah, this is desired. If you want to to map a non-centrosymmetric\nstructure to its mirror image, you need the rotoinversions. Unless I'm\nmissing something....\n\nOn Wed, Aug 19, 2015 at 12:25 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> The Lattice.find_all_mappings can return aligned lattices that change the\n> handedness of the coordinate system. E.g., try\n> \n> [[ 4.71115317 -0.32497418 -2.99516511]\n> [ -3.51444478 5.01683676 -0.34400454]\n> [ 0.1531054 -0.85080479 18.69400637]]\n> \n> mapping with itself.\n> \n> Is this really the desired behavior?\n> \n> @wmdrichards https://github.com/wmdrichards @sdacek\n> https://github.com/sdacek - pls check\n> \n> —\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/230.\n",
"Ok. But the consequence is that the reduction algorithms can swap handedness of lattices. I don't think that's the right behavior. \n",
"I don't really understand why the reduction algorithms need to use the find_mapping at all, but if its really an issue then find_mapping (rather than find_all_mappings) could be changed to always return proper rotations. \n\nThis wont cause any backwards incompatibility since lattices all have an inversion center, and if a mapping exists there must also be one without inversion.\n",
"It is not needed for LLL,but niggli reduction only determines the reduced lattice parameters, not the actual lattice matrix.\n",
"pmg.analysis.structure_matcher.StructureMatcher has get_supercell_matrix(), and get_transformation(), sometimes return transformations that will change the handedness.\n\nTry:\n\n``` python\nst = m.get_structure_by_material_id('mp-542189')\nspga = mg.symmetry.analyzer.SpacegroupAnalyzer(st, 0.01)\nst_Cc = spga.get_conventional_standard_structure()\nstm = mg.analysis.structure_matcher.StructureMatcher(primitive_cell=False, attempt_supercell=True)\nstm.get_transformation(st_Cc, st_Cc) # returns matrix with diagnals [1, -1, 1]\n\n# stm.get_transformation(st, st) is good\n```\n\nIs this the intended behavior?\n\nAccording to the docs, StructureMatcher uses niggli reduction scheme too.\n",
"I wouldn't worry too much about this. The handedness has no impact in normal crystals, except that the convention is right-handed. VASP will fail if you give it a left-handed crystal, but the VASP output sets already automatically correct for handedness.\n"
] | 2015-08-19T16:25:11
| 2015-09-02T16:52:41
|
2015-09-02T16:52:41Z
|
MEMBER
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The Lattice.find_all_mappings can return aligned lattices that change the handedness of the coordinate system. E.g., try
[[ 4.71115317 -0.32497418 -2.99516511]
[ -3.51444478 5.01683676 -0.34400454]
[ 0.1531054 -0.85080479 18.69400637]]
mapping with itself.
Is this really the desired behavior?
@wmdrichards @sdacek - pls check
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Added charged_defects_maker.py and tests/test_charged_defects_maker.py
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[] | 2015-08-20T22:17:19
| 2015-08-20T22:18:32
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2015-08-20T22:18:32Z
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CONTRIBUTOR
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agl_thermal
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[
"Hi Comac,\n\nCan you pls move agl_thermal to under analysis. And have a more informative name than \"agl_\" (I have no idea what agl stands for). You also should not be commiting the distribute packages. \n"
] | 2015-08-22T01:29:04
| 2016-09-25T20:09:53
|
2016-09-25T20:09:53Z
|
NONE
|
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Request for code review only. Further modifications may be required to enable operation with MPWorks framework.
|
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| 233
|
Bug fixes
|
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[] | 2015-08-22T17:34:14
| 2015-08-23T01:40:51
|
2015-08-23T01:40:51Z
|
CONTRIBUTOR
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This unit test works when I run it on Hopper.
|
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MDExOlB1bGxSZXF1ZXN0NDMyMDAxNTg=
| 234
|
Charged defects
|
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[] | 2015-08-24T17:32:32
| 2015-08-24T17:32:51
|
2015-08-24T17:32:51Z
|
CONTRIBUTOR
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Unit tests for charge_defects_analyzer
|
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MDExOlB1bGxSZXF1ZXN0NDMyNDE3MTk=
| 235
|
Introduced MPChargedDefectsVaspInputSet and edited ChargedDefectsStru…
|
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[
"Hello Nils,\n\nThanks for the code additions. IMO the VaspSet code needs slight changes to conform with the existing code. Please take a look at MITNEBVaspInputSet implementation for reference. Basically we are subclassing from MPVaspInputSet, all the settings and modifying them slightly. So the **init** function should call the DictVaspInputSet superclass as \nsuper(MPChargedDefectsVaspInputSet, self).**init**(\n \"MP Charged Defects\",\n loadfn(os.path.join(MODULE_DIR, \"MPVaspInputSet.yaml\")),\n user_incar_settings=defaults, ediff_per_atom=False, **kwargs)\n\nI will wait for your fixes. \n\nThanks,\n",
"Hi Bharat,\n\nwill consider your directions shortly. Have a couple of other things \non my plate until next week. But will get back to you then.\n\nCheers,\n\nNils\n\nPS: Hope your start at PNNL has been smooth?\n\nQuoting Bharat Medasani notifications@github.com:\n\n> Hello Nils,\n> \n> Thanks for the code additions. IMO the VaspSet code needs slight \n> changes to conform with the existing code. Please take a look at \n> MITNEBVaspInputSet implementation for reference. Basically we are \n> subclassing from MPVaspInputSet, all the settings and modifying them \n> slightly. So the **init** function should call the DictVaspInputSet \n> superclass as\n> super(MPChargedDefectsVaspInputSet, self).**init**(\n> \"MP Charged Defects\",\n> loadfn(os.path.join(MODULE_DIR, \"MPVaspInputSet.yaml\")),\n> user_incar_settings=defaults, ediff_per_atom=False, **kwargs)\n> \n> I will wait for your fixes.\n> \n> Thanks,\n> \n> ---\n> \n> Reply to this email directly or view it on GitHub:\n> https://github.com/materialsproject/pymatgen/pull/235#issuecomment-139282383\n"
] | 2015-08-25T01:47:48
| 2016-09-25T20:09:43
|
2016-09-25T20:09:43Z
|
CONTRIBUTOR
|
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…ctures and their unit tests
|
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MDU6SXNzdWUxMDM1MDMyNDg=
| 236
|
command not found (python script treated as bash script)
|
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[
"Thanks for reporting this. I just pushed out a version taht fixes this.\n"
] | 2015-08-27T13:03:00
| 2015-08-27T15:32:38
|
2015-08-27T15:13:26Z
|
NONE
|
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|
I install pymatgen through pip on Ubuntu 14.04. When I run `pmg`, the following error info is outputed:
```
from: can't read /var/mail/__future__
/usr/local/bin/pmg: line 10: $'\nA master convenience script with many tools for vasp and structure analysis.\n': command not found
/usr/local/bin/pmg: line 12: __author__: command not found
/usr/local/bin/pmg: line 13: __copyright__: command not found
/usr/local/bin/pmg: line 14: __version__: command not found
```
`#!/usr/bin/env python` should be put in the first line. Otherwise it'll be treated as shell script.
|
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| 103,895,917
|
MDU6SXNzdWUxMDM4OTU5MTc=
| 237
|
Overlapping of labels when generating XRD pattern
|
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[] | null |
[
"Thanks for reporting this. But this is merely a problem that it is difficult to programmatically determine the optimal positions to place the labels. If you wish, you can turn off labels in the XRD plot, and then do the labels manually. I am also open to suggestions about how to allocate label positions.\n",
"I am closing this issue for now. Please feel free to re-open if the above has not solved your problem.\n"
] | 2015-08-30T02:45:05
| 2015-09-02T16:52:03
|
2015-09-02T16:52:03Z
|
NONE
|
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Hi Developers,
I'm trying to use `pymatgen`'s `XRDCalculator` to calculate XRD pattern,
``` python
from pymatgen.io.vaspio import Poscar
p=Poscar.from_file('POSCAR')
from pymatgen import Lattice, Structure
from pymatgen.analysis.diffraction.xrd import XRDCalculator
from IPython.display import Image, display
c = XRDCalculator()
c.show_xrd_plot(p.structure)
```
But the labels are overlapping (see the first picture, the second one is generated by [Mercury](http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/Pages/Mercury.aspx) for comparison).
And the `POSCAR` file is:
```
EA703 4.479 6.253 4.483 89.98 88.52 89.99 Sym.group: 140
1.0000
4.434782 -0.333569 -0.535297
0.604649 6.109109 1.190892
0.574509 -0.904071 4.352654
Ca Si O
4 4 12
Direct
0.420441 0.172183 0.487161
0.919817 0.672187 0.986671
0.920353 0.172163 0.987238
0.419788 0.672152 0.486645
0.920094 0.922161 0.486902
0.420073 0.422169 0.986922
0.920092 0.422161 0.486960
0.420120 0.922172 0.986910
0.169153 0.884713 0.235905
0.169748 0.459624 0.236617
0.669827 0.422907 0.237193
0.171091 0.922894 0.735926
0.383425 0.172178 0.025121
0.170364 0.421446 0.736663
0.456774 0.672145 0.948672
0.671102 0.959633 0.737915
0.956984 0.172181 0.448904
0.883232 0.672166 0.525021
0.670406 0.384719 0.737275
0.669141 0.921438 0.237865
```
Btw, I've also tried the examples from [Calculating XRD patterns](http://pymatgen.org/_static/Calculating%20XRD%20patterns.html). They are totally fine. No such problem.
|
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| 103,983,274
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MDU6SXNzdWUxMDM5ODMyNzQ=
| 238
|
pmg.analysis.structure_matcher.StructureMatcher() primitive_cell setting uses pmg.Structure.find_primitive_structure() without specifying tolerance.
|
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[] | null |
[
"@wmdrichards or @sdacek , can you please look into this? Thanks.\n",
"Do you have a specific case where this is an issue? Choosing default tolerances is kind of tricky, and this tolerance works as desired in almost all instances that I am aware of. You can always avoid calling Structure.find_primitive_structure() by passing primitive_cell=False to the StructureMatcher and making the primitive cells manually.\n\nThe tolerance of Structure.find_primitive_structure() is usually much tighter than stol, since stol is scaled by (vol/natoms)**1/3, but the primitive cell tolerance is in angstroms. I guess for artificially low volume structures or when stol is very small this isn't necessarily the case.\n",
"Oh. I did not notice that the default tolerance of Structure.get_primitive_structure() refers to Angstrom. 0.25 Å is a reasonable amount.\n\nI guess what I was trying to reach is that since stol controls the atomic position test, it should also be the precision for the primitive cell finding, with the consideration of the scale and proper unit. That way, when the user wants to specify a large/default stol, primitive_cell=True will truly honor the criterion. I don't know if this leads to any side effect, but seems more coherent.\n\nAre the default values ltol and stol aggressive or OK? I don't have enough experience how far relaxations can go but the cell still can be treated the same structure.\n\nWhat's the unit of the symprec of Dr. Togo's spglib? I can't seem to find a source. Is it Angstrom too?\n",
"The default values are pretty well-tested over the entire ICSD. It should work in most instances. Of course, it all depends on the energy landscape and how likely you are to get stuck in local minima. In general, the tighter the tolerances, the more structures you get and the greater the computational cost, but at the advantage of being less likely to miss out potentially unique structures.\n\nspglib is in Angstroms. \n",
"@wmdrichards Maybe you can set primitve tol to == min(stol, 0.25)?\n",
"I will close this issue for now, since it is not an particular problem. \n"
] | 2015-08-31T04:39:51
| 2015-09-18T22:47:18
|
2015-09-18T22:47:18Z
|
NONE
|
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I had a glimpse of the source code, and realized it uses Structure.find_primitive_structure() with the default precision rather than the args ltol or stol, which is quite large (0.25), and will bend a lot of less symmetric structures to a primitive cell.
|
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| 104,189,739
|
MDU6SXNzdWUxMDQxODk3Mzk=
| 239
|
In some cases pmg.symmetry.analyzer.SpacegroupAnalyzer.get_conventional_standard_structure() returns structure not matching the spacegroup it detects.
|
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[] | null |
[
"The `get_*_standard_structure` method first uses `spglib` to get a refined structure. That modifies the atoms such that they are in the expected symmetry positions. \r\n\r\nBut that really should only preserve or increase symmetry. It is odd that it actually decreases symmetry.\r\n\r\n@hautierg Can you investigate if there is a problem with the `get_conventional_standard`?\r\n",
"Looks like this was fixed sometime in the last 7 years. :)\r\n\r\n```py\r\nfrom pymatgen.ext.matproj import MPRester\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\n\r\nmpr = MPRester()\r\nst = mpr.get_structure_by_material_id(\"mp-542189\")\r\nspga = SpacegroupAnalyzer(st, 0.1)\r\nprint(spga.get_space_group_symbol()) # Cc\r\n\r\nst1 = spga.get_conventional_standard_structure()\r\nspga1 = SpacegroupAnalyzer(st1, 0.1)\r\nprint(spga1.get_space_group_symbol()) # C2/c\r\n```"
] | 2015-09-01T05:26:43
| 2022-10-22T20:20:58
|
2022-10-22T20:20:58Z
|
NONE
|
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``` python
st = m.get_structure_by_material_id('mp-542189')
spga = mg.symmetry.analyzer.SpacegroupAnalyzer(st, 0.1)
print(spga.get_spacegroup()) # C2/c
st1 = spga.get_conventional_standard_structure()
spga1 = mg.symmetry.analyzer.SpacegroupAnalyzer(st1, 0.1) # this symprec doesn't help
print(spga1.get_spacegroup()) # P1
```
The curious thing is when either of the two symprec 0.1 above is changed to 0.15, both report C2/c. I can understand why changing the second 0.1 to 0.15 works, because it lowers the tolerance.
After setting the first 0.1 to 0.15, the returned structure has a few sites different from the structured from the 0.1 setting. This difference is very ordered, every five sites within Mo and S.
|
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| 104,381,019
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MDU6SXNzdWUxMDQzODEwMTk=
| 240
|
selective_dynamics not deserialized in poscar deserialization
|
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[] | null |
[
"If we look at the VASP example, the selective dynamics are indicated as T/F, not 1 or 0. The unittests for the T/F case show that it works perfectly fine. \n\nTo do 1/0 is easy, but is this really needed?\n",
"not really, i used numpy arrays to automatically set the flags for slab relaxations as it would give me finer control over relaxtion settings..\nconverting the nump array to list solves the issue..\nthanks\n",
"I see. OK, I have pushed a simple fix to the serialization routine (by down converting the numpy array to a list first). Let me know if it solves your problem?\n",
"it works as long as numpy array is not used to set the flags in the poscar object. Now the list value for ''selective dynamics'' key in the above example is passed directly to the numpy array. I think the **setattr** in the poscar already does that. i think it should be run through the monty decoder process_d, the same way you do it for deserializing vaspinputset in the vaspjob\ni fixed by changing my code to use numpy arrays to do the required manupulations and then converting that to a list before creating the poscar object which is then serialized.\n",
"Ok thanks. I think there might be minor issues. The conversion to list is not proper. Using list(value) for numpy arrays is bad. So instead of that, I do a np.array(value).tolist(). That forces a proper conversion to a list in the input so that it is always consistent.\n",
"yes, i agree, thats the fix that i did in my code.\n"
] | 2015-09-02T00:29:23
| 2015-09-03T14:15:57
|
2015-09-03T14:10:50Z
|
CONTRIBUTOR
|
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in Poscar.from_dict, the selective dynamics is not properly deserialized and consequently the **setattr** raises exception because it expects a numpy array
example serialized selective dynamics:
"selective_dynamics": [
{
"dtype": "float64",
"data": [
1.0,
1.0,
1.0
],
"@class": "array",
"@module": "numpy"
},
{
"dtype": "float64",
"data": [
1.0,
1.0,
1.0
],
"@class": "array",
"@module": "numpy"
},
{
"dtype": "float64",
"data": [
0.0,
0.0,
0.0
],
"@class": "array",
"@module": "numpy"
},
{
"dtype": "float64",
"data": [
1.0,
1.0,
1.0
],
"@class": "array",
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pmg.io.cif.CifWriter with symprec option
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[
"Note quite sure what is happening, but I suspect the problem is that the original structure from MP is a primitive structure.\n"
] | 2015-09-03T16:42:53
| 2015-10-02T19:39:35
|
2015-10-02T19:39:35Z
|
NONE
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I tried to use the symprec optional arg, but the returned cif files show up funky (clustered) in VESTA, and when reparsed by pymatgen, the total number of atoms is a bit more.
try:
``` python
st = m.get_structure_by_material_id('mp-542189')
mg.io.cif.CifWriter(st, 0.01).write_file('Cc.cif')
mg.io.cif.CifWriter(st, 0.1).write_file('C2_m.cif')
mg.Structure.from_file('Cc.cif',primitive=False)
mg.Structure.from_file('C2_m.cif',primitive=False)
```
Both volumes are 449.5, but number of atoms are different, for example.
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MDExOlB1bGxSZXF1ZXN0NDQ1NDk0ODU=
| 242
|
fixed python3 compatibility, fixed tabs/spaces
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[
"Hello Alex,\n\nDanny forwarded your email. Thank you for adding your modifications and you are always welcome to contribute code and bug fixes.\n\nBlind removal of 6th line in LOCPOT file within pymatgen is a bad idea. The LOCPOT object created by pymatgen ignores the 6th line. If we are using those LOCPOTs (written to a file by pymatgen), then removing 6th line will introduce a bug. So please change the code such that LOCPOT modification is optional.\n",
"Hi, actually I'm not modifying the LOCPOT but creating a copy called LOCPOT.sxd in the same directory and submit this to sxdefectalign. The only thing I was wondering was if this should be a) deleted afterwards and/or b) done in a scratch directory.\n",
"Hello Alex,\n\nI understand that. What I mean is the input LOCPOT file may have the 6th\nline deleted already. (This happens automatically when pymatgen reads and\nwrites a LOCPOT file). So, please make the copying of LOCPOT to LOCPOT.sxd\noptional.\n\nIn case of copying to LOCPOT.sxd, do it in scratch directory. That way you\ndon't have to delete it explicitly.\n\nOn Mon, Sep 14, 2015 at 6:33 AM, sonium notifications@github.com wrote:\n\n> Hi, actually I'm not modifying the LOCPOT but creating a copy called\n> LOCPOT.sxd in the same directory and submit this to sxdefectalign. The only\n> thing I was wondering was if this should be a) deleted afterwards and/or b)\n> done in a scratch directory.\n> \n> —\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/242#issuecomment-140077029\n> .\n\n## \n\nBharat\nPostdoc\nLawrence Berkeley Lab\n510-984-8628\n"
] | 2015-09-09T13:30:07
| 2016-09-25T20:09:44
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2016-09-25T20:09:44Z
|
NONE
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MDU6SXNzdWUxMDY2NDkxMDA=
| 243
|
MPRester.get_entries returns empty data dict.
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[
"This is normal. But I added functionality to allow you to get specific data. Pull the latest changes and you should be ale to do what you want.\n"
] | 2015-09-15T21:16:14
| 2015-09-17T16:52:02
|
2015-09-17T16:51:31Z
|
CONTRIBUTOR
|
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mpr = MPRester(api_key=API_KEY, endpoint="https://www.materialsproject.org/rest/v2")
entry = mpr.get_entries("mp-10",inc_structure="final")[0]
print entry.data
Output gives me an empty data dictionary. Is it normal?
MPRester.get_data work for me though.
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MDU6SXNzdWUxMDcwMDMxODk=
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pymatgen.io.cif unable to parse empty multiline strings from CIF loops
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[] | 2015-09-17T14:54:13
| 2015-09-17T17:37:23
|
2015-09-17T17:37:23Z
|
CONTRIBUTOR
|
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Minimal working example (syntactically valid CIF):
```
data_mwe
loop_
_tag
;
;
```
Error & trace:
``` python
In [6]: CifFile.from_file("mwe.cif")
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-6-149e94c9034e> in <module>()
----> 1 CifFile.from_file("mwe.cif")
/home/merkys/src/pymatgen/pymatgen/io/cif.py in from_file(cls, filename)
251 def from_file(cls, filename):
252 with zopen(filename, "rt") as f:
--> 253 return cls.from_string(f.read())
254
255
/home/merkys/src/pymatgen/pymatgen/io/cif.py in from_string(cls, string)
244 for x in re.split("^\s*data_", "x\n"+string,
245 flags=re.MULTILINE | re.DOTALL)[1:]:
--> 246 c = CifBlock.from_string("data_"+x)
247 d[c.header] = c
248 return cls(d, string)
/home/merkys/src/pymatgen/pymatgen/io/cif.py in from_string(cls, string)
199 while q:
200 s = q[0]
--> 201 if s[0].startswith("loop_") or not s[0].startswith("_"):
202 break
203 columns.append("".join(q.popleft()))
IndexError: string index out of range
```
|
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|
NwOutput : support parsing hessian matrices.
|
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[
"THanks for the nice contribution!\n"
] | 2015-09-21T05:44:04
| 2015-09-21T05:49:36
|
2015-09-21T05:49:27Z
|
CONTRIBUTOR
|
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- Support parsing hessian & projected hessian matrices from nwchem outputs.
- Support parsing raw frequencies.
- Unit tests are added and tested.
|
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MDU6SXNzdWUxMDc3NzkxNTg=
| 246
|
scipy.constants
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[
"Sorry, I have just found constants in the core. Can I add several constants (h and c) ?\nGermain\n",
"Sure go ahead. Using scipy is fine too since we already incldue scipy as a dependency,\n"
] | 2015-09-22T18:59:22
| 2015-09-22T19:55:09
|
2015-09-22T19:55:09Z
|
CONTRIBUTOR
|
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Hello,
Is it possible to use `scipy.constants` module in the implementation of methods or new dependencies are not recommended ?
Are standard physical constants accessible somewhere in pymatgen ?
Thanks
|
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Gauss
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[
"Thanks for the contributions!\n"
] | 2015-09-22T20:25:07
| 2015-09-22T20:27:41
|
2015-09-22T20:27:33Z
|
CONTRIBUTOR
|
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- fix compatibility issues between gaussian03/gaussian09
- new methods to read potential energy surface computed with gaussian
- new methods to read electronic transitions computed with TD-DFT
|
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New version of pymatgen.io.abinit. Requires Abinit v7.11.11 and new monty
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[] | 2015-10-01T21:08:50
| 2015-10-01T21:11:29
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2015-10-01T21:11:28Z
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| 109,413,286
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MDExOlB1bGxSZXF1ZXN0NDY1OTQ2MDM=
| 249
|
Disable unit test for flow.pickle_dumps
|
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[] | 2015-10-02T01:02:32
| 2015-10-02T02:17:29
|
2015-10-02T02:17:29Z
|
CONTRIBUTOR
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MDU6SXNzdWUxMDk1NDc2NTc=
| 250
|
Lattice.get_all_distance_and_image does not return ALL nearest neighbors
|
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[
"I'm not entirely sure what get_all_distance_and_image is supposed to return -- as far as I can tell, its a method that you created from part of the code from get_distance_and_image. I don't think it should be its own function because the sites that it returns are entirely dependent on the lattice representation, and I'm not really sure what you'd ever want those sites for. (get distance and image is useful because it always returns the single closest image)\n",
"This issue seems to no longer be present, and since the example is in Python 2 also can be closed :-)"
] | 2015-10-02T18:35:33
| 2020-07-11T02:47:54
|
2020-07-11T02:47:54Z
|
MEMBER
|
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This is actually a strange bug. I am not sure if there are any major implicaitons. Maybe it does not guarantee the validity of get_all_distances.
Try the following code::
```
from pymatgen.util.testing import PymatgenTest
cscl = PymatgenTest.get_structure("CsCl")
gen = SlabGenerator(cscl, (1, 1, 1), 10, 10)
o = gen.oriented_unit_cell
f1 = o[0].frac_coords
f2 = o[1].frac_coords
lattice = o.lattice
print len([image for dist, image in lattice.get_all_distance_and_image(
f1, f2) if dist < 4])
import itertools
for image in itertools.product(range(-2, 3), range(-2, 3), range(-2, 3)):
dist, image = lattice.get_distance_and_image(f1, f2, image)
if dist < 4:
print image
```
In essence, only 6 Cl atoms were found at dist < 4 from Cs. This is because some of the nearest neighbors lie outside the range of -1 <= image <= 1.
But the get_sites_in_sphere of structure class works properly because it does not depend on this mehtod. I am just not sure if there are other methods that rely on this.
@wmdrichards Can you take a look and review?
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MDU6SXNzdWUxMTAzNTY4NTU=
| 251
|
How can I shorten time of make band structure?
|
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[
"Hi\nI got the same issues with large numbers of Kpoints or huge vasprun.xml files (several hundred of Mo). I guess there are too many xml tags/attribute in the file. In that cases I used Poscar class instead. I am working on it because, for the moment, that class does not return an electronic_strucure.Band object. Moreover there is a bug because in the case of spin polarized calculations, because only beta bands are returned.\n\nI will push a commit about that quickly. I wrote the code but I need time to check the band structure object and compare two objects extracted from Vasprun or Procar class.\n",
"I have added a BSVasprun class. Use it if you are only parsing a vasprun.xml for bandstructures. It is at least 2-3x faster. \n\nI am closing this issue.\n"
] | 2015-10-08T01:58:36
| 2015-10-30T22:43:36
|
2015-10-30T22:43:36Z
|
NONE
|
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--- CODE ---
run = Vasprun(pwd+"/Band-DOS/vasprun.xml",parse_projected_eigen = True)
bands = run.get_band_structure(pwd+"/Band-DOS/KPOINTS",efermi = dosrun.efermi,line_mode = True)
plotter = BSPlotterProjected(bands)
graph = plotter.get_elt_projected_plots_color()
--- CODE end ---
when I use small vasprun.xml (500KB~1MB) , It takes few seconds.
But If size of vasprun.xml file is big (about 20MB ?), it takes so long time.. 3~4 minutes
How can I shorten time?? Can pymatgen use python multiprocessing or Parallel Python ??
Thanks
|
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MDExOlB1bGxSZXF1ZXN0NDcyNTI4ODk=
| 252
|
Converter between AiiDA StructureData object and pymatgen Molecule/Structure objects
|
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[
"Thanks!\n"
] | 2015-10-09T09:50:32
| 2015-10-09T13:27:55
|
2015-10-09T13:27:48Z
|
CONTRIBUTOR
|
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I present a converter between AiiDA StructureData and pymatgen Molecule/Structure objects. Since testing requires a sophisticated environment, it is done at AiiDA side.
Please check whether the method names comply with the pymatgen's style.
|
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Support parsing gradients (forces) from nwchem output files.
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[] | 2015-10-12T11:01:28
| 2015-10-12T13:24:41
|
2015-10-12T13:24:41Z
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CONTRIBUTOR
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- Support parsing gradients (forces) from nwchem output files.
- Unittests are added and tested.
|
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MDExOlB1bGxSZXF1ZXN0NDc2MDY3NjQ=
| 254
|
Xdatcar class did not read last configuration
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[] | 2015-10-14T00:48:11
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2015-10-14T03:25:41Z
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CONTRIBUTOR
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Changed Xdatcar class and unit test so that last configuration in XDATCAR is also read. The expected number of configurations read from the test files was incorrect (3); each XDATCAR test file contains 4 configurations
|
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IO/abinit queueadapter made MSONable + new priority scheme for the automatic definition of mpi processes
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[] | 2015-10-14T15:13:58
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2015-10-14T15:43:52Z
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|
Problem with multiple preambles in XDATCAR
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[
"thanks\n"
] | 2015-10-16T01:16:15
| 2015-10-16T01:41:36
|
2015-10-16T01:41:30Z
|
CONTRIBUTOR
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I've extended the constructor of Xdatcar to enable successful treatment of multiple consecutive preambles in XDATCAR. That case seems rare, but I've just encountered it.
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MDU6SXNzdWUxMTI0MTUxNDc=
| 257
|
Bandstructure __init__ variable type error
|
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[
"Thanks for reporting this.\n"
] | 2015-10-20T17:03:24
| 2015-10-20T18:45:17
|
2015-10-20T18:45:00Z
|
NONE
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In line 704 and 705 of pymatgen/electronic_structure/bandstructure.py, the lines:
704 "name": (self._kpoints[b[0]].label + "-" +
705 self._kpoints[b[-1]].label)})
throw a variable compatibility error:
TypeError: unsupported operand type(s) for +: 'NoneType' and 'unicode'
I believe the obvious fix is to update the 'NoneType' variables to strings:
704 "name": (str(self._kpoints[b[0]].label) + "-" +
705 str(self._kpoints[b[-1]].label))})
This fixes the error. However, I am not sure if something deeper needs to be changes so that these variables are 'unicode' and note 'NoneType' from the beginning.
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|
MSONable queueadapter in io/abinit + mrgddb of abinit run with --nostrict option
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[] | 2015-10-22T14:13:08
| 2015-10-22T14:22:18
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2015-10-22T14:22:18Z
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Enhance: GaussianOutput
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[
"I will fix my codes and then give a new pull request.\n"
] | 2015-10-30T11:23:29
| 2015-10-30T11:52:19
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2015-10-30T11:52:19Z
|
CONTRIBUTOR
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The class `GaussianOutput` now supports parsing:
- Cartesian forces
- Frequencies
- Normal modes
Also add some unit tests.
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Enhance: GaussianOutput
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[
"thanks!\n",
"I have added you to the list of authors for the gaussian module in recognition for your efforts.\n"
] | 2015-10-30T12:12:36
| 2015-10-30T22:45:41
|
2015-10-30T13:38:38Z
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CONTRIBUTOR
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The class `GaussianOutput` now supports parsing:
- Frequencies
- Normal modes
- Cartesian forces
Python 3 compatible.
Unit tests are added.
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Lattice.find_all_mappings test fails with latest numpy.
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[
"The new numpy version has a very bad bug with non contiguous data in np.inner calls:\nhttps://github.com/numpy/numpy/issues/6532\n",
"@shyuep Could you try with the 1.10.2rc1 release?\n",
"numpy 1.10.2rc1 seems to have fixed it\n",
"Yes, I confirm that too. Thanks !\n"
] | 2015-10-30T23:13:12
| 2015-11-14T15:31:33
|
2015-11-14T15:31:33Z
|
MEMBER
|
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Pls investigate. Error message below:
AssertionError:
Arrays are not almost equal to 5 decimals
(mismatch 100.0%)
x: array([[ 0.54756, -0.03654, -0.14159],
[ 0.06854, -0.38895, -0.89413],
[-1.78544, -0.24974, -0.0563 ]])
y: array([[ 0.2, -0.4, -1.4],
[ 0. , -0.4, -1. ],
[-0.6, -0.9, -0.2]])
only seems to be a problem with latest numpy.
|
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Add keyword ``gen_basis`` to `GaussianInput``
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[] | 2015-11-01T14:12:44
| 2015-11-01T15:17:49
|
2015-11-01T15:17:49Z
|
CONTRIBUTOR
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- User-specified basis sets can be used to do Gaussian calculations.
- Tests are added.
- Python3 compatible.
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Master memory overhead possible in PBS chunks + added tests
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[] | 2015-11-05T14:23:12
| 2015-11-05T15:34:30
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2015-11-05T15:34:30Z
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| 264
|
Deformed structure set
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[
"Thanks. This looks great in terms of coding, but can you move the entire elasticity branch under the analysis package. The pymagen.X level if reserved for high-level abstraction. Specific property analyses are parked under pymatgen.analysis.\n",
"BTW, you do not need to withdraw the pull request. You simplt need to commit and add on the commits to this pull request. Let me know when it is ready.\n",
"Okay, I think it's ready now.\n"
] | 2015-11-06T22:50:32
| 2015-11-07T03:26:37
|
2015-11-07T03:26:37Z
|
CONTRIBUTOR
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Added the `elasticity` package, which includes modules
- tensors.py - `SQTensor` base class for 2-D tensors and relevant matrix operations
- stress.py - `Stress` class for various operations related to stress
- strain.py - `Deformation`, `Strain`, and `DeformedStructureSet` classes for operations related to structural deformation and strain
- elastic.py - `ElasticTensor` class for operations related to the elastic tensor
Also added unit tests for each module.
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Cannot understand Vasprun parser error in reading a vasprun.xml file - please advise
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[
"We use the python ElementTree XML parser for vasprun. While I think there is a way to change the error handling, it is generally not a good idea to ignore errors in XML. There is no way to ensure that the parsing gives reasonable results. \n\nI would say that if you know that there is a misprint, you can preprocess the XML file itself to fix those misprint and try parsing again.\n\nBut you should really check your VASP compilation. Such errors are usually the result of a bad compile, which is not good in a first principles code.\n"
] | 2015-11-08T23:28:31
| 2015-11-09T00:35:37
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2015-11-09T00:35:37Z
|
NONE
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I get the error:
ParseError: mismatched tag: line 773, column 4
when using the Vasprun parser in pymatgen.io.vasp.outputs on a perfectly written out and converged vasprun.xml .. Any reason for this ?
The OUTCAR file yields a perfectly converged energy.
The line flagged in the vasprun.xml is one of the closing lines of an ionic step appears to have a misprinted angle bracket. The issue seems to be a random occurrence at random points in a high throughput run through different structures .. Can the parser somehow ignore the misprint mismatch in the vasprun.xml and recover the still useful information, for example the calculation is converged ?
|
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| 266
|
A question about BSplotter()
|
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[
"Hi,\n\nGithub issues is for reporting bugs and feature requests. For such questions, please keep it in the pymatgen Google groups.\n",
"It is a common convention/practice in insulators and semiconductors to set the zero of energy at the VBM.\n\nGeoffroy\n\n> On 10 Nov 2015, at 15:37, 91bsjun notifications@github.com wrote:\n> \n> Hi, I have a new question.\n> \n> I want to know one of the operation in the bs_plot_data()\n> \n> (In the class of BSplotter() )\n> \n> why do this operation when non metalic band structure ?\n> \n> zero_energy = self._bs.get_vbm()['energy']\n> \n> --- script ---\n> \n> ```\n> if self._bs.is_metal():\n> zero_energy = self._bs.efermi\n> else:\n> zero_energy = self._bs.get_vbm()['energy']\n> ```\n> \n> I want to know why adjust zero_energy to vbm.\n> \n> —\n> Reply to this email directly or view it on GitHub https://github.com/materialsproject/pymatgen/issues/266.\n"
] | 2015-11-10T14:37:18
| 2015-11-10T14:52:16
|
2015-11-10T14:48:25Z
|
NONE
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Hi, I have a new question.
I want to know one of the operation in the bs_plot_data()
(In the class of BSplotter() )
why do this operation when non metalic band structure ?
> > > zero_energy = self._bs.get_vbm()['energy']
--- script ---
```
if self._bs.is_metal():
zero_energy = self._bs.efermi
else:
zero_energy = self._bs.get_vbm()['energy']
```
---
I want to know why adjust zero_energy to vbm.
|
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| 116,468,243
|
MDU6SXNzdWUxMTY0NjgyNDM=
| 267
|
use SlabGenerator.get_slab to generate a surface has a bug for ZnO(010)
|
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[
"Although I use get_sorted_structure() and get the right POSCAR format, I still want to know the reason. \n",
"Hi,\n\nPls post your technical questions to the pymatgen Google groups. Github issues are for reporting bugs and problems.\n\nAs for your specific problem, the structures returned by get_slab() is not sorted. The format for the POSCAR is not wrong at all. In fact, that POSCAR can run perfectly if you do the POTCAR right.\n\nBut if you want to make sure the POSCAR is sorted properly, do\n\nAl55.get_sorted_structure().to(….)\n\nShyue Ping\n\nOn November 11, 2015 at 6:45:33 PM, wangnumber14 (notifications@github.com) wrote:\n\nhello, I use SlabGenerator.get_slab to generate ZnO(010) surface, while I got more atoms and wrong POSCAR format。 why?\nMy code is following:\n\nZnO=Structure.from_file(\"ZnO.cif\",primitive=False)\nAl55=SlabGenerator(ZnO,[0,1,0],5.3,5.0,lll_reduce=False,center_slab=False).get_slab()\nIStructure.to(Al55,\"poscar\",filename=\"POSCAR\")\n\nTwo layers I get, the POSCAR is:\n\nZn4 O4\n1.0\n-3.249300 0.000000 -0.000000\n0.000000 0.000000 -5.205400\n6.498600 -11.255905 -0.000000\nZn O Zn O\n2 2 2 2\ndirect\n0.666670 0.000000 0.083333 Zn\n0.333330 0.500000 0.166667 Zn\n0.666670 0.617400 0.083333 O\n0.333330 0.117400 0.166667 O\n0.666670 0.000000 0.333333 Zn\n0.333330 0.500000 0.416667 Zn\n0.666670 0.617400 0.333333 O\n0.333330 0.117400 0.416667 O\n\nThe format is wrong for POSCAR, why ?\n\nIn additions, I want to know the two arguments: \"min_slab_size\", \"min_vacuum_size\", min_vacuum_size means the vacuum I wanted to use between layers?or sums of the vacuum sizes in all the layers, I think the latter is right. While the min_slab_size, I really do not understand your mean? Can you tell me ? Thanks a lot!\n\n—\nReply to this email directly or view it on GitHub.\n",
"The reason why you need to use get_sorted_structure is because by default, the slab orders the atoms in terms of increasing c coordinate. This is useful when you want to know what are the atoms near the surface in order to do further manipulations, e.g., adding an adsorbate atom. \n\nThe Poscar class does not assume whether your structure is sorted or not. This is because there are sometimes very good reasons to not sort the structure, eg. when you want to treat certain atoms differently even though they are the same structure.\n\nIf you want to avoid this, one way is to use one of the sets in pymatgen.io.vasp.sets to generate the entire set of input files.\n",
"Thanks a lot. I want to known two arguments: \"min_slab_size\", \"min_vacuum_size\", min_vacuum_size means the vacuum I wanted to use between layers?or sums of the vacuum sizes in all the layers, I think the latter is right. While the min_slab_size, I really do not understand your mean? Can you tell me ? Thanks a lot! (I can not attach the pymatgen Google groups), And another question is slab generation can not support that the surface go through one specified atom. I am not sure.\n",
"As the doc says, it is simply the normal distance for the Slab and the vacuum respectively. The actual # of layers will be determined based on what you specify. To take a simple example, if you have a 3A cubic cell and you are generating a (100) slab. You set min_slab_size and min_vac_size to 4A. The code will determine that you need at least 2 layers to generate the structure. You will end up with a slab taht is 6A thick with a vacuum of 6A. Both slab and vacuum are defined in term of multiples of the oriented unit cell. \n\nSlabGenerator can generate all slabs with all distinct terminations via the get_all_slabs() method. One of them should have the atom you want at the surface.\n",
"Thanks a lot, I do not know if I understand your mean. Your mean is that min_slab_size determines the layers(I thinks so), one question is one crystal has different lattice parameters, for example, a=2A, b=3A, c=4A, I want to generate (001) slab, I set min_slab_size=6A, the layers is at least 2 or 3? The layers is determined by the smallest values? I think it should be 2 layers, while use the crystal POSCAR as flows:\nLi1\n1.0\n2.000000 0.000000 0.000000\n0.000000 4.000000 0.000000\n0.000000 0.000000 2.000000\nLi\n1\ndirect\n0.500000 0.500000 0.500000 Li\nI get the c from follows:\nLi=Structure.from_file(\"POSCAR\")\nA5=SlabGenerator(Li,[0,1,1],7.0,2.0,lll_reduce=False,center_slab=False).get_slab()\na,b,c=A5.oriented_unit_cell.lattice.matrix\nI get c=[ 0. 0. -2.] and nlayers=9,\nwhile the slab POSCAR is:\nLi4\n1.0\n-2.000000 0.000000 0.000000\n0.000000 4.000000 -2.000000\n0.000000 0.000000 -12.000000\nLi\n4\ndirect\n0.500000 0.500000 0.000000 Li\n0.500000 0.500000 0.166667 Li\n0.500000 0.500000 0.333333 Li\n0.500000 0.500000 0.500000 Li\n\nObviously, there are 4 layers, and why the c is not (0,0,-18)?\n Thanks a lot for your reply!\n",
"It is based on normal distance. In your case, the c vector is not perpendicular to a and b. If you take the surface normal, you see why. Alternatively, set the max_normal_search.\n"
] | 2015-11-12T02:45:31
| 2015-11-12T06:52:36
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2015-11-12T03:26:25Z
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NONE
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hello, I use SlabGenerator.get_slab to generate ZnO(010) surface, while I got more atoms and wrong POSCAR format。 why?
My code is following:
ZnO=Structure.from_file("ZnO.cif",primitive=False)
Al55=SlabGenerator(ZnO,[0,1,0],5.3,5.0,lll_reduce=False,center_slab=False).get_slab()
IStructure.to(Al55,"poscar",filename="POSCAR")
Two layers I get, the POSCAR is:
Zn4 O4
1.0
-3.249300 0.000000 -0.000000
0.000000 0.000000 -5.205400
6.498600 -11.255905 -0.000000
Zn O Zn O
2 2 2 2
direct
0.666670 0.000000 0.083333 Zn
0.333330 0.500000 0.166667 Zn
0.666670 0.617400 0.083333 O
0.333330 0.117400 0.166667 O
0.666670 0.000000 0.333333 Zn
0.333330 0.500000 0.416667 Zn
0.666670 0.617400 0.333333 O
0.333330 0.117400 0.416667 O
The format is wrong for POSCAR, why ?
In additions, I want to know the two arguments: "min_slab_size", "min_vacuum_size", min_vacuum_size means the vacuum I wanted to use between layers?or sums of the vacuum sizes in all the layers, I think the latter is right. While the min_slab_size, I really do not understand your mean? Can you tell me ? Thanks a lot!
|
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added explicit polar decomposition method to allow for more flexible …
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[
"Hmm... not quite sure why we need to implement an explicity polar decompositno method?\n",
"We were having an issue with the scipy dependency, since the polar method was implemented in sciyp/0.14.0 and some folks seem to be using older versions. Since it was the only scipy dependency in analysis.elasticity, I made it explicit to remove the scipy dependency but keep the method, but an alternative would be to just remove the method, since scipy.linalg.polar can be used with the object anyway.\n",
"0.14.0 is ancient. I think the folks should upgrade. pymatgen's requirements.txt already stipulates scipy 0.16.0. So there really isn;t a reason for < 0.14.0.\n",
"Ah, I thought scipy was optional. Probably just leave it, then.\n"
] | 2015-11-14T01:03:46
| 2015-11-14T05:48:29
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2015-11-14T05:48:29Z
|
CONTRIBUTOR
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…scipy compatibility
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MDU6SXNzdWUxMTY5MjI3ODE=
| 269
|
SlabGenerator.get_slab can not make sure the specific atom on the surface?
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[
"You can create the Slab first and then replace one of the surface atoms. The surface atoms is always the lowest or higher c fractional coordinate.\n",
"Thanks for your advice, I want to dope first and then create the slab, Pymatgen now can not satify this? \nThanks for your reply.\n",
"Not quite sure what you are trying to achieve. But like I said in my previous replies, the get_all_slabs should return all distinct terminations, which should include one with Cu on the surface. If you want to use the get_slab method, the shift should work with some value and testing.\n",
"My demand is that creating a slab from a doping structure, and the specific slab(e.g., 001) contains the specific doping atoms. \nMy demand can be achieved by this method: first create a slab, and then dope some atoms on the surface;\nwhile if I want to dope some atoms in the structure first, and then create a slab from the doping structure, and make sure the doped atoms exposed on the specific surface of the slab. (I mean that this demand can not be achieved) \n",
"Try with get_all_slabs. If that can't be done, dope the surface.\n",
"Thanks a lot ! I will think about other methods !\n"
] | 2015-11-14T12:40:46
| 2015-11-17T00:48:16
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2015-11-14T15:51:40Z
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NONE
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I want to use slabgenerator.get_slab to get (111)Fe.cif (2x2x2supercell) with one Cu dopant, and make sure that the Cu atom lies on the surface, or the atom sites the mesh origin(i.e., (0,0,0) site), how should I do? Whether Pymatgen.surface module supply this function?
I try use shift to adjust the surface, but the result is not what I expected. Thanks for your help!
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Fiesta io
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[] | 2015-11-18T12:22:44
| 2015-11-18T12:23:25
|
2015-11-18T12:23:25Z
|
NONE
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- add io for Fiesta code (http://perso.neel.cnrs.fr/xavier.blase/fiesta/index.html): GW and BSE calculations with gaussian basis set.
- add time to io.nwchem.NwOutput
Nicolas Dardenne
UCL Belgium
|
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| 117,777,206
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MDExOlB1bGxSZXF1ZXN0NTExOTk5NDk=
| 271
|
io.fiesta + mod to io.nwchem
|
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[] | 2015-11-19T09:46:32
| 2015-11-24T07:53:27
|
2015-11-24T07:53:27Z
|
NONE
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Input and Output for Fiesta code
Mod to nwchem
|
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MDU6SXNzdWUxMTc4Njc2MDI=
| 272
|
pymatgen.core.periodic_table: block property
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[
"Your change appears to assign Lu and Lr to the \"f\"-block (rather than \nthe \"d\"-block). But perhaps that was intentional?\n- Randy\n\nOn 11/19/2015 10:33 AM, Shyue Ping Ong wrote:\n\n> Closed #272 https://github.com/materialsproject/pymatgen/issues/272 \n> via 91acf19 \n> https://github.com/materialsproject/pymatgen/commit/91acf192283f704c95169ea9930d1a0e1adc5758.\n> \n> —\n> Reply to this email directly or view it on GitHub \n> https://github.com/materialsproject/pymatgen/issues/272#event-469512362.\n",
"Just pushed a fix.\n"
] | 2015-11-19T17:44:39
| 2015-11-19T19:54:59
|
2015-11-19T18:33:30Z
|
NONE
|
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Not being a materials scientist, perhaps I am simply naive, but I find some of the current block assignments to be surprising. The relevant code is:
> ```
> @property
> def block(self):
> """
> Return the block character "s,p,d,f"
> """
> block = ""
> if self.group in [1, 2]:
> block = "s"
> elif self.group in range(13, 19):
> block = "p"
> elif self.is_actinoid or self.is_lanthanoid:
> block = "f"
> elif self.group in range(3, 13):
> block = "d"
> else:
> print("unable to determine block")
> return block
> ```
Which results in lanthanides with periodic number 67-70 and actinides with periodic number 99-102 being assigned to "p"-block, whereas I expected them to be assigned to "f"-block. Perhaps the two lines of "p"-block code were placed above the "f"-block code to prevent Lu and Lr from being assigned to "f"-block (and the full consequences were not immediately obvious)? Or perhaps my notion of "f"-block is simply inaccurate.
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MDU6SXNzdWUxMTc4Njc3ODk=
| 273
|
pymatgen.analysis.structure_analyzer: get_voronoi_polyhedra()
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[] | 2015-11-19T17:45:35
| 2015-11-19T19:57:30
|
2015-11-19T19:57:30Z
|
NONE
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Looking at the first few lines of the get_voronoi_polyhedra code:
> def get_voronoi_polyhedra(self, n):
> ...
> localtarget = self._target
> center = self._structure[n]
> neighbors = self._structure.get_sites_in_sphere(
> center.coords, VoronoiCoordFinder.default_cutoff)
Unless you are intentionally preventing the users from adjusting the
default_cutoff, it seems like the last line should be:
> ```
> neighbors = self._structure.get_sites_in_sphere(
> center.coords, self.default_cutoff)
> ```
Or am I missing something?
|
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| 117,944,350
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MDU6SXNzdWUxMTc5NDQzNTA=
| 274
|
Fix is_supergroup() and is_subgroup() methods of SymmetryGroup class in pymatgen.symmetry.groups
|
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[] | null |
[
"Tess, I just pushed a quick fix that uses data obtained form the bilbao crystallographic server. Pls test it and see if it works. I haven't tried to really implement a true super-sub group matching. I merely saved the tree of relationships and used that for the super and sub group test.\n",
"Hi Shyue Ping, Thanks for adding the fix -- grabbing data from Bilbao was also my first thought as well -- if only they had an API! I'll test what you've added.\n",
"Yeah, they don't have an API. But I cheated and basically used a combination of requests url downloading and postprocessing with BeautifulSoup to grab the data. It wasn't that much effort. \n\nThe point group data is missing, but there are only 32 of them. So that;s a smaller problem.\n",
"I've created similar scripts using mechanize and BeautifulSoup. For example, I often need to compare whether two structures are actually distortions of one another. To do this, I created functions that grab data from Bilbao's STRUCTURE RELATIONS app (http://www.cryst.ehu.es/cryst/rel.html) so that I can determine whether it's possible to transform the higher symmetry structure into it's lower symmetry setting. \n"
] | 2015-11-20T01:10:19
| 2015-11-20T18:35:36
|
2015-11-20T15:33:07Z
|
CONTRIBUTOR
|
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See pymatgen google group discussion: https://groups.google.com/forum/#!topic/pymatgen/iP1tb5OkO7Q
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| 118,008,511
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MDU6SXNzdWUxMTgwMDg1MTE=
| 275
|
Help me using VASP input sets.
|
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[
"AbstractVaspINputSet is an abstract base class. You need to use one of the concrete implementations. E.g., MPVaspInputSet().get_all_vasp_input(s1).\n\nThis is not a bug.\n"
] | 2015-11-20T10:13:27
| 2015-11-20T13:55:00
|
2015-11-20T13:55:00Z
|
NONE
|
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from pymatgen.core import *
from pymatgen.io.vasp.sets import *
s1 = IStructure.from_file("tst.cif")
AbstractVaspInputSet.get_all_vasp_input(s1)
Here is the error.
File "<stdin>", line 1, in <module>
TypeError: unbound method get_all_vasp_input() must be called with AbstractVaspInputSet instance as first argument (got IStructure instance instead)
|
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| 118,339,629
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| 276
|
io fiesta and modified io nwchem
|
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[] | 2015-11-23T08:51:37
| 2015-11-23T14:48:03
|
2015-11-23T14:48:03Z
|
NONE
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- io.fiesta for code Fiesta (GW and BSE with gaussian basis set)
- modified nwchem with basis set option and time info
|
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| 118,875,413
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MDU6SXNzdWUxMTg4NzU0MTM=
| 277
|
Spglib issue with pymatgen 3.2.7
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[
"What command did you use to upgrade? \n",
"I used: \n\npip install pymatgen --upgrade --no-deps\n\nI also tried uninstalling, upgrading pyspglib, and the reinstalling with pip.\n\nSince I posted I have installed 3.2.7 successfully on other systems, but I am still encountering the same issue on the original computer.\n",
"Hmm... as far as I know, there are no changes to spglib in 3.2.6 -> 3.2.7. It may be that there was a compilation error during the upgrade on the original computer. What OS is the original computer?\n",
"CentOS 5.4\n\nBut your advice made me think of something that I probably should have checked earlier. Reinstalling with the --no-cache-dir option to pip fixed our issue. Thanks for your time.\n",
"I just encountered the same `ImportError` message myself when using pymatgen 3.4.0, even though `import spglib` was working just fine. This was because the Python package `pyspglib` was renamed to `spglib` for version 1.9 of spglib. To fix, I manually downloaded the last 1.8.x release of spglib and manually installed the Python package from there, and it works fine. Not sure if it's worth adding another try/except statement to analyzer.py with `import spglib._spglib as spg` for those people who are using newer versions of spglib?\n",
"Sure, we can add that. BUt generally, it's better to just use the spglib that ships with pymatgen. The reason is that we cannot guarantee compatibility with API except to the shipped version.\n"
] | 2015-11-25T16:37:25
| 2016-04-07T22:49:46
|
2015-11-25T20:18:31Z
|
NONE
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I upgraded to 3.2.7 and can no longer import pymatgen, and have the following error:
File "<stdin>", line 1, in <module>
File ".../lib/python2.7/site-packages/pymatgen/**init**.py", line 17, in <module>
from .io.smart import read_structure, write_structure, read_mol, write_mol
File "...0/lib/python2.7/site-packages/pymatgen/io/smart.py", line 28, in <module>
from pymatgen.io.cif import CifParser, CifWriter
File "...2.3.0/lib/python2.7/site-packages/pymatgen/io/cif.py", line 43, in <module>
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
File ".../python2.7/site-packages/pymatgen/symmetry/analyzer.py", line 54, in <module>
raise ImportError(msg)
ImportError: Spglib required. Please either run python setup.py install for pymatgen, or install pyspglib from spglib.
but spglib and pyspglib are both installed. Thankfully when reverting to 3.2.6 there is no longer any issue
|
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|
S Correction
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[
"This is not the correct implementation. You are changing anything that has a S. That is not correct. What happens with sulfates?\n\nThe correct way of dealing with sulfide is not mdify the sulfide itself, but to add it to the compound energies. That way, anything that has reduced_formula = \"S\" will be modified to the right sulfur energy.\n",
"Make energy correction on sulfur rather than sulfide. \n"
] | 2015-12-02T23:39:03
| 2015-12-03T03:14:47
|
2015-12-03T03:14:47Z
|
CONTRIBUTOR
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add S correction and unit test.
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ADF
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[
"Thanks!\n"
] | 2015-12-03T10:10:59
| 2015-12-03T14:44:35
|
2015-12-03T14:19:40Z
|
CONTRIBUTOR
|
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- Support creating ADF input files.
- Basic support for parsing ADF output files.
- Python 2/3 compatible.
- Unit tests are added.
|
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MDU6SXNzdWUxMjAzMTUwOTM=
| 280
|
Issue with get_point_group() in SpacegroupAnalyzer
|
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[
"Try modifying the symprec. The default is pretty high. \n\nShyue Ping\n\nOn Thu, Dec 3, 2015 at 5:57 PM -0800, \"gcheon\" notifications@github.com wrote:\n\nHello,\n\nI'm trying to analyze a structure with no screw axes(I intentionally modified the structure to break that symmetry- the screw axis was the z axis, so I copied the unit cell in a random position along the z axis. Structure on the bottom), but get_point_group() keeps saying that it has a screw axis(point group 32) no matter what I do. Could you explain how exactly get_point_group() works? Also, I ran get_symmetry_operations() to see what was happening, and I got:\n\n[Rot:\n\n[[ 1. 0. 0.]\n\n [ 0. 1. 0.]\n\n [ 0. 0. 1.]]\n\ntau\n\n[ 0. 0. 0.], Rot:\n\n[[ 0. -1. 0.]\n\n [ 1. -1. 0.]\n\n [ 0. 0. 1.]]\n\ntau\n\n[ 0. 0. 0.], Rot:\n\n[[-1. 1. 0.]\n\n [-1. 0. 0.]\n\n [ 0. 0. 1.]]\n\ntau\n\n[ 0. 0. 0.], Rot:\n\n[[ 0. -1. 0.]\n\n [-1. 0. 0.]\n\n [ 0. 0. -1.]]\n\ntau\n\n[ 0. 0. 0.36890909], Rot:\n\n[[-1. 1. 0.]\n\n [ 0. 1. 0.]\n\n [ 0. 0. -1.]]\n\ntau\n\n[ 0. 0. 0.36890909], Rot:\n\n[[ 1. 0. 0.]\n\n [ 1. -1. 0.]\n\n [ 0. 0. -1.]]\n\ntau\n\n[ 0. 0. 0.36890909]]\n\nand the value of tau does not look like 1/3 or 2/3, which also seems strange. \n\nThanks for your help!\n\nGowoon Cheon\n\nStructure Summary\n\nLattice\n\n```\nabc : 6.2220912549552922 6.2220912549552922 55.459783010650753\n```\n\n angles : 90.0 90.0 119.99999999999999\n\n volume : 1859.4373503805373\n\n```\n A : 3.1110456274776461 -5.3884890914562815 0.0\n\n B : 3.1110456274776461 5.3884890914562815 0.0\n\n C : 0.0 0.0 55.459783010650753\n```\n\nPeriodicSite: Sc (0.0000, 0.0000, 30.2508) [0.0000, 0.0000, 0.5455]\n\nPeriodicSite: Ag (3.1110, -1.7962, 30.2508) [0.6667, 0.3333, 0.5455]\n\nPeriodicSite: P (3.1110, 1.7962, 29.1383) [0.3333, 0.6667, 0.5254]\n\nPeriodicSite: P (3.1110, 1.7962, 31.3633) [0.3333, 0.6667, 0.5655]\n\nPeriodicSite: S (3.9499, 3.5671, 31.9314) [0.3038, 0.9658, 0.5758]\n\nPeriodicSite: S (4.2252, 0.1842, 31.9314) [0.6620, 0.6962, 0.5758]\n\nPeriodicSite: S (1.1579, 1.6372, 31.9314) [0.0342, 0.3380, 0.5758]\n\nPeriodicSite: S (5.0641, 1.6372, 28.5702) [0.6620, 0.9658, 0.5152]\n\nPeriodicSite: S (2.2721, 3.5671, 28.5702) [0.0342, 0.6962, 0.5152]\n\nPeriodicSite: S (1.9968, 0.1842, 28.5702) [0.3038, 0.3380, 0.5152]\n\nPeriodicSite: Sc (0.0000, 0.0000, 45.6686) [0.0000, 0.0000, 0.8235]\n\nPeriodicSite: Ag (3.1110, -1.7962, 45.6686) [0.6667, 0.3333, 0.8235]\n\nPeriodicSite: P (3.1110, 1.7962, 44.5561) [0.3333, 0.6667, 0.8034]\n\nPeriodicSite: P (3.1110, 1.7962, 46.7811) [0.3333, 0.6667, 0.8435]\n\nPeriodicSite: S (3.9499, 3.5671, 47.3492) [0.3038, 0.9658, 0.8538]\n\nPeriodicSite: S (4.2252, 0.1842, 47.3492) [0.6620, 0.6962, 0.8538]\n\nPeriodicSite: S (1.1579, 1.6372, 47.3492) [0.0342, 0.3380, 0.8538]\n\nPeriodicSite: S (5.0641, 1.6372, 43.9880) [0.6620, 0.9658, 0.7932]\n\nPeriodicSite: S (2.2721, 3.5671, 43.9880) [0.0342, 0.6962, 0.7932]\n\nPeriodicSite: S (1.9968, 0.1842, 43.9880) [0.3038, 0.3380, 0.7932]\n\n—\nReply to this email directly or view it on GitHub.\n",
"Closing this issue. Pls reopen if issue persists.\n"
] | 2015-12-04T01:57:42
| 2015-12-06T17:19:50
|
2015-12-06T17:19:49Z
|
CONTRIBUTOR
|
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Hello,
I'm trying to analyze a structure with no screw axes(I intentionally modified the structure to break that symmetry- the screw axis was the z axis, so I copied the unit cell in a random position along the z axis. Structure on the bottom), but get_point_group() keeps saying that it has a screw axis(point group 32) no matter what I do. Could you explain how exactly get_point_group() works? Also, I ran get_symmetry_operations() to see what was happening, and I got:
[Rot:
[[ 1. 0. 0.]
[ 0. 1. 0.]
[ 0. 0. 1.]]
tau
[ 0. 0. 0.], Rot:
[[ 0. -1. 0.]
[ 1. -1. 0.]
[ 0. 0. 1.]]
tau
[ 0. 0. 0.], Rot:
[[-1. 1. 0.]
[-1. 0. 0.]
[ 0. 0. 1.]]
tau
[ 0. 0. 0.], Rot:
[[ 0. -1. 0.]
[-1. 0. 0.]
[ 0. 0. -1.]]
tau
[ 0. 0. 0.36890909], Rot:
[[-1. 1. 0.]
[ 0. 1. 0.]
[ 0. 0. -1.]]
tau
[ 0. 0. 0.36890909], Rot:
[[ 1. 0. 0.]
[ 1. -1. 0.]
[ 0. 0. -1.]]
tau
[ 0. 0. 0.36890909]]
and the value of tau does not look like 1/3 or 2/3, which also seems strange.
Thanks for your help!
Gowoon Cheon
Structure Summary
Lattice
abc : 6.2220912549552922 6.2220912549552922 55.459783010650753
angles : 90.0 90.0 119.99999999999999
volume : 1859.4373503805373
A : 3.1110456274776461 -5.3884890914562815 0.0
B : 3.1110456274776461 5.3884890914562815 0.0
C : 0.0 0.0 55.459783010650753
PeriodicSite: Sc (0.0000, 0.0000, 30.2508) [0.0000, 0.0000, 0.5455]
PeriodicSite: Ag (3.1110, -1.7962, 30.2508) [0.6667, 0.3333, 0.5455]
PeriodicSite: P (3.1110, 1.7962, 29.1383) [0.3333, 0.6667, 0.5254]
PeriodicSite: P (3.1110, 1.7962, 31.3633) [0.3333, 0.6667, 0.5655]
PeriodicSite: S (3.9499, 3.5671, 31.9314) [0.3038, 0.9658, 0.5758]
PeriodicSite: S (4.2252, 0.1842, 31.9314) [0.6620, 0.6962, 0.5758]
PeriodicSite: S (1.1579, 1.6372, 31.9314) [0.0342, 0.3380, 0.5758]
PeriodicSite: S (5.0641, 1.6372, 28.5702) [0.6620, 0.9658, 0.5152]
PeriodicSite: S (2.2721, 3.5671, 28.5702) [0.0342, 0.6962, 0.5152]
PeriodicSite: S (1.9968, 0.1842, 28.5702) [0.3038, 0.3380, 0.5152]
PeriodicSite: Sc (0.0000, 0.0000, 45.6686) [0.0000, 0.0000, 0.8235]
PeriodicSite: Ag (3.1110, -1.7962, 45.6686) [0.6667, 0.3333, 0.8235]
PeriodicSite: P (3.1110, 1.7962, 44.5561) [0.3333, 0.6667, 0.8034]
PeriodicSite: P (3.1110, 1.7962, 46.7811) [0.3333, 0.6667, 0.8435]
PeriodicSite: S (3.9499, 3.5671, 47.3492) [0.3038, 0.9658, 0.8538]
PeriodicSite: S (4.2252, 0.1842, 47.3492) [0.6620, 0.6962, 0.8538]
PeriodicSite: S (1.1579, 1.6372, 47.3492) [0.0342, 0.3380, 0.8538]
PeriodicSite: S (5.0641, 1.6372, 43.9880) [0.6620, 0.9658, 0.7932]
PeriodicSite: S (2.2721, 3.5671, 43.9880) [0.0342, 0.6962, 0.7932]
PeriodicSite: S (1.9968, 0.1842, 43.9880) [0.3038, 0.3380, 0.7932]
|
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MDU6SXNzdWUxMjA2MjQ4ODI=
| 281
|
Any chance using scipy's hull implementation instead of pyhull
|
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[
"We cannot abandon pyhull completely for two undocumented reasons. Pymatgen is used in the Materials Project to generate phase diagrams. To make sure we can do it in a reasonably fast fashion, we use multiprocessing. The problem we had was that scipy's implementation of the convex hull does not work in multiprocessing and leads to crashes or worse, bad data. That was several versions of scipy ago. So I don't know if that holds true today. Second, some functions of pymatgen still rely on pyhull and has no fall back on\n\nThe best I can do is to make it an optional dependency. That would enable you to install pymatgen, with perhaps a slight loss in functionality.\n",
"That would be great!\n",
"Try the latest beta: https://github.com/materialsproject/pymatgen/releases/tag/v3.2.8b and let me know if it works.\n",
"I am closing this issue and adding two other issues specific to the dependency of electronic structure and Pourbaix packages on pyhull. Otherwise, pymatgen should install without needing pyhull with the latest 3.2.8 release.\n"
] | 2015-12-06T10:41:26
| 2015-12-06T17:19:16
|
2015-12-06T17:19:16Z
|
NONE
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Hi all,
the main problem I have with using pymatgen is that is uninstallable right now under a windows in 64 bit (32 bit seems to work though). The reason for this is the installation of pyhull. Is there any chance that pyhull could just be replaced by the scipy implementation?
As a side note, even the maintainer of pyhull states that the scipy implementation is actually 50% faster:
(from the pyhull Readme.md - https://github.com/materialsvirtuallab/pyhull)
"At the time of development of pyhull, the scipy.spatial package was the only other package that supports the computation of higher dimensional convex hulls. However, the version of scipy at that time (scipy 0.11.0) only supported the computation of Delaunay triangulation and the convex hull was computed from the Delaunay triangulation, which is slower and less reliable than directly computing the convex hull. As of version 0.12.0, scipy now supports the direct computation of convex hulls and is in fact ~50% faster than pyhull for larger hulls. I will still make pyhull available for the simple reason that the scipy package is fairly large and not everyone wants to install such a large package for computing hulls."
As scipy is anyway a requirement for pymatgen, it would make sense to reduce the dependencies.
Clemens
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MDU6SXNzdWUxMjA2NDY0MTM=
| 282
|
Make electronic structure classes independent of Pyhull
|
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[
"Looks like this was fixed in [v2017.12.8](https://github.com/materialsproject/pymatgen/releases/tag/v2017.12.8)."
] | 2015-12-06T17:17:00
| 2023-05-29T18:24:20
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2023-05-29T18:24:20Z
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MEMBER
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Pyhull is still used in the BSPlotter. Can these be switched over to scipy's implementation? It does not seem too difficult for the electronic structure classes. The plan is to move to a Pyhull-free pymatgen for easier support on more platforms.
|
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MDU6SXNzdWUxMjA2NDY0ODM=
| 283
|
Make Pourbaix free of Pyhull
|
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[] | 2015-12-06T17:18:05
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2017-12-06T23:21:25Z
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Pyhull is still used in the Pourbaix. Can these be switched over to scipy's implementation? This seems a bit more work since the halfspace and other functions used by Pourbaix does not seem to have an equivalent in scipy.
The plan is to move to a Pyhull-free pymatgen for easier support on more platforms.
|
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MDU6SXNzdWUxMjExNjcyNzY=
| 284
|
ValueError: total size of new array must be unchanged when use analyzer module
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[
"This is almost certainly a tolerance issue. You have one lattice vector that is 68A!\nTry playing around with the tolerances.\n\nShyue Ping\n\nOn December 8, 2015 at 10:03:28 PM, wangnumber14 (notifications@github.com) wrote:\n\nwhen I use\nsym=SpacegroupAnalyzer(IStructure.from_file(\"POSCAR\",False, False))\nprim = sym.get_primitive_standard_structure(international_monoclinic=False)\n\nIt has errors. It's the first time to see this error.\n\nI got the messages in follows:\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\nprim = sym.get_primitive_standard_structure(international_monoclinic=False)\nFile \"/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/symmetry/analyzer.py\", line 439, in get_primitive_standard_structure\ninternational_monoclinic=international_monoclinic)\nFile \"/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/symmetry/analyzer.py\", line 507, in get_conventional_standard_structure\nstruct = self.get_refined_structure()\nFile \"/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/symmetry/analyzer.py\", line 364, in get_refined_structure\nreturn s.get_sorted_structure()\nFile \"/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/core/structure.py\", line 868, in get_sorted_structure\nreturn self.class.from_sites(sites)\nFile \"/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/core/structure.py\", line 442, in from_sites\nto_unit_cell=to_unit_cell)\nFile \"/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/core/structure.py\", line 2126, in init\nsite_properties=site_properties)\nFile \"/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/core/structure.py\", line 385, in init\nself.lattice = Lattice(lattice)\nFile \"/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/core/lattice.py\", line 59, in __init_\nm = np.array(matrix, dtype=np.float64).reshape((3, 3))\nValueError: total size of new array must be unchanged\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\nThe POSCAR I use is：\nCd10 I20\n1.0\n-2.120000 -3.671948 -0.000000\n2.120000 -3.671948 -0.000000\n-0.000000 -2.447965 68.340000\nCd I\n10 20\ndirect\n0.125137 0.125003 0.624890 Cd2+\n0.258467 0.258333 0.224900 Cd2+\n0.325137 0.325003 0.024890 Cd2+\n0.758397 0.758363 0.724910 Cd2+\n0.624997 0.625063 0.124910 Cd2+\n0.691737 0.691703 0.924890 Cd2+\n0.191797 0.191663 0.424910 Cd2+\n0.058467 0.058333 0.824900 Cd2+\n0.825067 0.825033 0.524900 Cd2+\n0.891737 0.891703 0.324890 Cd2+\n0.349997 0.350063 0.949910 I-\n0.483337 0.483403 0.549890 I-\n0.800067 0.800033 0.599900 I-\n0.966737 0.966703 0.099890 I-\n0.516667 0.516733 0.449900 I-\n0.233467 0.233333 0.299900 I-\n0.100137 0.100003 0.699890 I-\n0.549997 0.550063 0.349910 I-\n0.000067 0.000033 0.999900 I-\n0.033467 0.033333 0.899900 I-\n0.649997 0.650063 0.049910 I-\n0.866737 0.866703 0.399890 I-\n0.383337 0.383403 0.849890 I-\n0.583337 0.583403 0.249890 I-\n0.733397 0.733363 0.799910 I-\n0.166797 0.166663 0.499910 I-\n0.416667 0.416733 0.749900 I-\n0.283467 0.283333 0.149900 I-\n0.449997 0.450063 0.649910 I-\n0.933397 0.933363 0.199910 I-\n\nwhat should I do to solve this problem?\nThanks a lot !\n\n—\nReply to this email directly or view it on GitHub.\n",
"Thanks a lot ! What is the max tolerance? \n",
"There is no max. It depends on what you think the error is.\n",
"I am not clear what your mean, I try to reduce the lattice vector value(from 68 to 49), It works。\nFrom your answer, the reason may be not the size of lattice vector value, but the errors. \nI cannot find the solutions just now!\n",
"The problem is with the value of the tol in the find_primitive method or the symprec. You'd have to test those parameters.\n",
"Thanks for your reply, I reduce the tolerance, the space group can be analyzed, however, the wrong results is obtained. The structure information shown above, the space group is R3MH, while use \nsym=SpacegroupAnalyzer(IStructure.from_file(\"POSCAR\",False, False), symprec=1e-5) can analyze the structure, but get the spacegroup is P1, while, I use default value symprec=0.001, the errors above are also presented.\n"
] | 2015-12-09T06:03:26
| 2015-12-15T03:15:22
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2015-12-15T02:12:39Z
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when I use
sym=SpacegroupAnalyzer(IStructure.from_file("POSCAR",False, False))
prim = sym.get_primitive_standard_structure(international_monoclinic=False)
It has errors. It's the first time to see this error.
I got the messages in follows:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
prim = sym.get_primitive_standard_structure(international_monoclinic=False)
File "/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/symmetry/analyzer.py", line 439, in get_primitive_standard_structure
international_monoclinic=international_monoclinic)
File "/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/symmetry/analyzer.py", line 507, in get_conventional_standard_structure
struct = self.get_refined_structure()
File "/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/symmetry/analyzer.py", line 364, in get_refined_structure
return s.get_sorted_structure()
File "/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/core/structure.py", line 868, in get_sorted_structure
return self.**class**.from_sites(sites)
File "/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/core/structure.py", line 442, in from_sites
to_unit_cell=to_unit_cell)
File "/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/core/structure.py", line 2126, in **init**
site_properties=site_properties)
File "/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/core/structure.py", line 385, in **init**
self._lattice = Lattice(lattice)
File "/home/matcloud/install/python2.7/lib/python2.7/site-packages/pymatgen-3.2.8-py2.7-linux-x86_64.egg/pymatgen/core/lattice.py", line 59, in __init__
m = np.array(matrix, dtype=np.float64).reshape((3, 3))
ValueError: total size of new array must be unchanged
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The POSCAR I use is：
Cd10 I20
1.0
-2.120000 -3.671948 -0.000000
2.120000 -3.671948 -0.000000
-0.000000 -2.447965 68.340000
Cd I
10 20
direct
0.125137 0.125003 0.624890 Cd2+
0.258467 0.258333 0.224900 Cd2+
0.325137 0.325003 0.024890 Cd2+
0.758397 0.758363 0.724910 Cd2+
0.624997 0.625063 0.124910 Cd2+
0.691737 0.691703 0.924890 Cd2+
0.191797 0.191663 0.424910 Cd2+
0.058467 0.058333 0.824900 Cd2+
0.825067 0.825033 0.524900 Cd2+
0.891737 0.891703 0.324890 Cd2+
0.349997 0.350063 0.949910 I-
0.483337 0.483403 0.549890 I-
0.800067 0.800033 0.599900 I-
0.966737 0.966703 0.099890 I-
0.516667 0.516733 0.449900 I-
0.233467 0.233333 0.299900 I-
0.100137 0.100003 0.699890 I-
0.549997 0.550063 0.349910 I-
0.000067 0.000033 0.999900 I-
0.033467 0.033333 0.899900 I-
0.649997 0.650063 0.049910 I-
0.866737 0.866703 0.399890 I-
0.383337 0.383403 0.849890 I-
0.583337 0.583403 0.249890 I-
0.733397 0.733363 0.799910 I-
0.166797 0.166663 0.499910 I-
0.416667 0.416733 0.749900 I-
0.283467 0.283333 0.149900 I-
0.449997 0.450063 0.649910 I-
0.933397 0.933363 0.199910 I-
what should I do to solve this problem?
Thanks a lot !
|
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| 121,392,020
|
MDExOlB1bGxSZXF1ZXN0NTMyMTA2MzE=
| 285
|
small fix on physical_constant removal
|
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[] | 2015-12-10T03:12:38
| 2015-12-10T03:13:06
|
2015-12-10T03:13:06Z
|
CONTRIBUTOR
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remove the phyc in get_arrhenius_plot
|
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| 122,167,647
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MDU6SXNzdWUxMjIxNjc2NDc=
| 286
|
pymatgen units and math.sqrt
|
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[
"I don't think this is actually doable. With *\\* 0.5, the behavior is specified by the **pow** magic function, which we can specify a behavior for the units. I have no idea what the math.sqrt function internally does to compute the sqrt. The same goes for math.pow and the functions.\n",
"If you read the official docs for math.pow, it is explicitly stated that args and return values are converted to float for pow. Sqrt is probably the same. So I don't think there is a way beyond using *\\* for everything with units. \n"
] | 2015-12-15T00:58:07
| 2015-12-15T03:21:34
|
2015-12-15T02:10:37Z
|
MEMBER
|
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I am playing with the pymatgen units class, which on the whole I find to be really nice.
I am having a problem with applying math.sqrt() on FloatWithUnit and am wondering why it is not supported.
i.e., this does not work:
```
from pymatgen.core.units import FloatWithUnit
import math
x = FloatWithUnit(9, "m^2 s^-2")
math.sqrt(x).unit
```
with the error
```
Traceback (most recent call last):
File "/Users/ajain/PycharmProjects/scratch_work/scratch/scratch2.py", line 6, in <module>
math.sqrt(x).unit
AttributeError: 'float' object has no attribute 'unit'
```
but this is fine:
```
from pymatgen.core.units import FloatWithUnit
x = FloatWithUnit(9, "m^2 s^-2")
(x**0.5).unit
```
|
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|
add as_base_units for FloatWithUnit and ArrayWithUnit. This is helps …
|
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[
"Note - there is a second commit that helps the unitized decorator function as expected when returning unit objects.\n"
] | 2015-12-15T01:32:52
| 2015-12-15T02:07:52
|
2015-12-15T02:07:52Z
|
MEMBER
|
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This adds an `as_base_units` functionality to FloatWithUnit and ArrayWithUnit. When I have these two objects, I often want to quickly convert them to base units and would find this function a handy shortcut.
|
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MDExOlB1bGxSZXF1ZXN0NTM2NTEzMzc=
| 288
|
add unit tests for @unitize mods
|
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[] | 2015-12-15T02:13:33
| 2015-12-15T02:52:16
|
2015-12-15T02:14:37Z
|
MEMBER
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MDU6SXNzdWUxMjIyNTg5NTQ=
| 289
|
Compilation on Windows with MSVC 2008.
|
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[
"Hi, unfortunately we cannot support all the different compilers. I have discussed with the spglib author and we think it's best if you use standard gcc to compile this.\n"
] | 2015-12-15T12:09:27
| 2016-01-18T19:17:41
|
2016-01-18T19:17:41Z
|
NONE
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[patches.zip](https://github.com/materialsproject/pymatgen/files/62412/patches.zip)
Hi,
I had some issues building pymatgen-3.2.8.tar.gz on windows using Python 2.7.2 and MSVC 2008.
1. The spglib C files do not have topmost variable declarations. Trick used to was to rename all .c files to .cpp files:
find -name '*.c' | xargs -i mv {} {}pp
in the /dependencies/spglib-1.7.4 directory.
1. The spglib file refinements.cpp need sqrt(3) changed to sqrt(3.0) to work with MSVC 2008.
2. setup.py must be patched to use .cpp instead of .c (diff attached).
3. The SOURCES.txt contains src file entries that are not in the src tree (diff attached).
4. Updating to newer version works fine on Ubuntu 14.04. But on Windows it fails:
python -measy_install -U pymatgen
Searching for pymatgen
Reading https://pypi.python.org/simple/pymatgen/
Best match: pymatgen 3.2.9
Downloading https://pypi.python.org/packages/source/p/pymatgen/pymatgen-3.2.9.tar.gz#md5=9373a9943a956c4a4d910b90b42bc5e7
Processing pymatgen-3.2.9.tar.gz
Writing c:\cygwin64\tmp\easy_install-vnhubw\pymatgen-3.2.9\setup.cfg
Running pymatgen-3.2.9\setup.py -q bdist_egg --dist-dir c:\cygwin64\tmp\easy_install-vnhubw\pymatgen-3.2.9\egg-dist-tmp-kfqswp
error: c:\cygwin64\tmp\easy_install-vnhubw\pymatgen-3.2.9\pymatgen.egg-info\SOURCES.txt: The process cannot access the file because it is being used by another process
|
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MDU6SXNzdWUxMjM1MTE4Mjk=
| 290
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zeo++ in pymatgen
|
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[
"Hello Kamal,\n\nThe svn access was modified slightly. Try the links to download Zeo++ and\nVoro++\n\nhttps://code.lbl.gov/scm/?group_id=97\n\nhttps://code.lbl.gov/scm/?group_id=108\n\nIn the Zeo++ trunk folder, cython folder is present.\\\nKeep in mind, there is a naming clash with zeo++ in pymatgen at present. I\nwill push a fix soon.\n\nBharat\n\nOn Tue, Dec 22, 2015 at 8:21 AM, kamal-ch notifications@github.com wrote:\n\n> Hi\n> I would like to use interstitial package in pymatgen\n> I installed cython, voro++ and zeo++ on a linux machine separately, but I\n> don't see any cython_wrapper code as mentioned in the following link , and\n> perhaps thats why I can't import zeo in python\n> \n> https://08315912851165136057googlegroupscom/attach/e8c3e6f353747/ZeoPython_Linux_instructionstxt?part=02&view=1&vt=ANaJVrF_4PpYvza7CM9okdbJNI_321GLYGzgY02QsM7r4t25LgTmtX9LYBB5-xDavHUgwj-7eEB8_fIQUjHDn_9DUet9f2Fv2_YVIDe3IDujOtu0nebsmQc\n> \n> I didn't use svn because it didn't give me permission to download Could\n> anyone help me in this?\n> \n> Best Regards\n> Kamal\n> \n> —\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/290.\n",
"Just for the sake of having all of Bharat's helpful tips in one place, to install Zeo++/Voro++ and use them in Pymatgen:\n\nDownload and install Voro++\n\n```\n$ cd ~\n$ mkdir Voro++; mkdir Voro++/voro\n$ cd Voro++/voro\n$ svn checkout --username anonsvn https://code.lbl.gov/svn/voro/trunk # password is 'anonsvn'\n$ cd trunk\n```\n\nAdd -fPIC to the CFLAGS variable in config.mk, and then\n\n```\n$ make\n```\n\n---\n\nDownload and install Zeo++\n\n```\n$ cd ~\n$ mkdir Zeo++; mkdir Zeo++/zeo\n$ cd Zeo++/zeo\n$ svn checkout --username anonsvn https://code.lbl.gov/svn/zeo/trunk # password is 'anonsvn'\n$ cd trunk\n$ make dylib\n```\n\n---\n\nCreate python bindings with Cython\n\n```\n$ pip install cython\n$ cd cython_wrapper\n$ python setup_alt.py develop\n```\n\n---\n\nTest that the installation worked, and use it in Pymatgen\n\n```\n$ ipython # or whatever you would like to use\n```\n\n``` python\nIn [1]: from pymatgen.analysis.defects.point_defects import Interstitial, ValenceIonicRadiusEvaluator\n\nIn [2]: from pymatgen.core.structure import Structure\n\nIn [3]: structure = Structure.from_file('/path/to/file')\n\nIn [4]: evaluator = ValenceIonicRadiusEvaluator(structure)\n\nIn [5]: interstitial = Interstitial(structure, radii=evaluator.radii, valences=evaluator.valences)\n\nIn [6]: print interstitial._defect_sites\n```\n",
"Thanks. I just added this to the official pymatgen installation page:\n\nhttp://pymatgen.org/installation.html#zeo\n\nShyue Ping\n\nFrom: ashtonmv notifications@github.com\nReply: materialsproject/pymatgen reply@reply.github.com\nDate: February 19, 2016 at 7:13:06 AM\nTo: materialsproject/pymatgen pymatgen@noreply.github.com\nSubject: Re: [pymatgen] zeo++ in pymatgen (#290) \n\nJust for the sake of having all of Bharat's helpful tips in one place, to install Zeo++/Voro++ and use them in Pymatgen:\n\nDownload and install Voro++\n\n$ cd ~\n$ mkdir Voro++; mkdir Voro++/voro\n$ cd Voro++/voro\n$ svn checkout --username anonsvn https://code.lbl.gov/svn/voro/trunk # password is 'anonsvn'\n$ cd trunk\n\nAdd -fPIC to the CFLAGS variable in config.mk, and then\n\n$ make\n\nDownload and install Zeo++\n\n$ cd ~\n$ mkdir Zeo++; mkdir Zeo++/zeo\n$ cd Zeo++/zeo\n$ svn checkout --username anonsvn https://code.lbl.gov/svn/zeo/trunk # password is 'anonsvn'\n$ cd trunk\n$ make dylib\n\nCreate python bindings with Cython\n\n$ pip install cython\n$ cd cython_wrapper\n$ python setup_alt.py develop\n\nTest that the installation worked, and use it in Pymatgen\n\n$ ipython # or whatever you would like to use\n\nIn [1]: from pymatgen.analysis.defects.point_defects import Interstitial\n\nIn [2]: from pymatgen.core.structure import Structure\n\nIn [3]: structure = Structure.from_file('/path/to/file')\n\nIn [4]: radii, valences = {}, {}\n\nIn [5]: for element in structure.composition.elements:\n ...: radii[element.symbol] = element.atomic_radius\n ...: valence = element.group # Just a first guess..\n ...: if element.group > 12:\n ...: valence -= 10\n ...: valences[element.symbol] = valence\n\nIn [6]: interstitial = Interstitial(structure, radii=radii, valences=valences)\n\nIn [7]: interstitial._defect_sites\n—\nReply to this email directly or view it on GitHub.\n"
] | 2015-12-22T16:21:00
| 2016-02-19T18:28:12
|
2016-02-19T18:28:12Z
|
NONE
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Hi
I would like to use interstitial package in pymatgen.
I installed cython, voro++ and zeo++ on a linux machine separately, but I don't see any cython_wrapper code as mentioned in the following link , and perhaps thats why I can't import zeo in python
https://08315912851165136057.googlegroups.com/attach/e8c3e6f353747/ZeoPython_Linux_instructions.txt?part=0.2&view=1&vt=ANaJVrF_4PpYvza7CM9okdbJNI_321GLYGzgY02QsM7r4t25LgTmtX9LYBB5-xDavHUgwj-7eEB8_fIQUjHDn_9DUet9f2Fv2_YVIDe3IDujOtu0nebsmQc
I didn't use svn because it didn't give me permission to download. Could anyone help linking my installed zeo++ with pymatgen?
Best Regards
Kamal
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|
Bug fix for zeroing negative values in tensors
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[] | 2015-12-22T22:05:37
| 2015-12-22T22:18:51
|
2015-12-22T22:18:51Z
|
CONTRIBUTOR
|
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Fix to analysis/elasticity/tensors.py and related test to ensure negative values aren't zeroed in the elastic tensor fitting procedure.
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Upstrm
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[
"Trying to cherrypick a particular commit, but not happening.\n"
] | 2015-12-25T18:40:03
| 2015-12-25T18:50:29
|
2015-12-25T18:50:19Z
|
CONTRIBUTOR
|
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Renaming zeo.py in pymatgen/io/zeo.pyy to pymatgen/io/zeopp.py to resolve naming conflict.
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MDExOlB1bGxSZXF1ZXN0NTQ1OTIxNjc=
| 293
|
Fix for naming clash with zeo++ cython code
|
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[] | 2015-12-25T18:58:04
| 2015-12-25T19:42:20
|
2015-12-25T19:42:20Z
|
CONTRIBUTOR
|
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Renaming zeo.py in pymatgen/io/zeo.pyy to pymatgen/io/zeopp.py to resolve naming conflict.
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MDU6SXNzdWUxMjQ1NzM5OTU=
| 294
|
Breaking tests in test_outputs for bandstructure
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[
"Fixed.\n"
] | 2016-01-02T04:00:06
| 2016-01-05T00:35:46
|
2016-01-05T00:35:46Z
|
MEMBER
|
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I enforced the Enum type for Spin and Orbital. That's the only thing I did. But test_outputs.py in pymatgen.io.vasp now has problems with vbm in bandstructures. I suspect because it is a bad conversion due to enforcement of Enum.
@hautierg Can you pls investigate since I don't know the BS code that well? Thanks.
|
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| 124,865,215
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MDExOlB1bGxSZXF1ZXN0NTUwMzg1MTE=
| 295
|
fixed issue with elastic tensor fitting and corresponding nosetests
|
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[] | 2016-01-04T23:50:13
| 2016-01-04T23:53:54
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2016-01-04T23:53:54Z
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CONTRIBUTOR
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MDU6SXNzdWUxMjU0NTUwMDM=
| 296
|
Cannot use makesupercell on a slab in pmg 3.3.1
|
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[] | null |
[
"For constructing supercells, it might be better to convert the Slab to a Structure first, e.g., Strcture.from_sites(slab)\n\nShyue Ping\n\nOn January 7, 2016 at 10:18:07 AM, rtrottie (notifications@github.com) wrote:\n\nCalling make_supercell (or using the pythonic \\* (#,#,#) ) on a slab produces the following error:\n\nFile \"/anaconda2/lib/python27/site-packages/pymatgen/core/structurepy\", line 667, in mul\nreturn self__class__from_sites(new_sites)\nFile \"/anaconda2/lib/python27/site-packages/pymatgen/core/structurepy\", line 439, in from_sites\nto_unit_cell=to_unit_cell)\nTypeError: init() takes at least 8 arguments (7 given)\n\nthis was not an issue in 328 and I would guess it stems from slab class requiring miller indices in addition to the structure parameters\n\n—\nReply to this email directly or view it on GitHub.\n"
] | 2016-01-07T18:18:06
| 2016-01-08T16:08:54
|
2016-01-08T16:08:54Z
|
NONE
|
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Calling make_supercell (or using the pythonic \* (#,#,#) ) on a slab produces the following error:
File "/anaconda2/lib/python2.7/site-packages/pymatgen/core/structure.py", line 667, in **mul**
return self.**class**.from_sites(new_sites)
File "/anaconda2/lib/python2.7/site-packages/pymatgen/core/structure.py", line 439, in from_sites
to_unit_cell=to_unit_cell)
TypeError: **init**() takes at least 8 arguments (7 given)
this was not an issue in 3.2.8 and I would guess it stems from slab class requiring miller indices in addition to the structure parameters
|
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| 297
|
fix for abinit
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Support "elasticity" property bundle in MPRester
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Added an order parameter class for analysis of local structural features
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[
"Thanks for the excellent contribution. However, I would like to suggest a few changes.\n\ni. the in_bound method seems to be more easily dealt with as max(lower, min(upper, value)). In fact, a variant is used in pymatgen.utils.num_utils.abs_cap.\n\nii. While the prototype structure is useful, the implementation is not the most efficient. The standard fcc, bcc and hcp structures can already be generated using Structure.from_spacegroup(\"Fm-3m\", ...) for example. While I recognize the value of these convenience methods, I think it would be best to add them as a classmethod in Structure, e.g., Structure.fcc(a, species). Then a user only needs to specify the desired lattice parameters and species to get an fcc structure.\n",
"Thanks, Prof. Ong. I'll implement your suggestions ASAP.\n",
"Prof. Ong, can the order parameter class now be merged with pymatgen? Or, are there any other changes that you suggest? The checks have passed successfully now that I have addressed problems in the unit tests related to numerical precision. \n",
"Hi Niels, have the changes been implemented?\n",
"Yes. I have however removed the prototype structure class.\n"
] | 2016-01-14T01:03:48
| 2016-02-05T15:56:44
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2016-02-05T15:56:43Z
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CONTRIBUTOR
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… plus required unit tests.
My thoughts were to put the entire class actually into the structure_analyzer.py, if this is wanted from other people, too.
prototype_structures.py is mainly a helper class to easily set up prototypic structures for the order parameter unit tests. But they could be generally also valuable to have.
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Having trouble setting selective dynamics after Poscar creation
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[] | 2016-01-15T22:31:35
| 2016-01-15T22:53:19
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2016-01-15T22:53:19Z
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CONTRIBUTOR
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I used to be able to set selective_dynamics directly.
Now it seems that I must create a new Poscar with the structure and include selective_dynamics at that point, rather than being able to set it after the fact.
Also, only a numpy array .tolist() seems to work, and not giving just an array.
[poscar_selective_dynamics.docx](https://github.com/materialsproject/pymatgen/files/92613/poscar_selective_dynamics.docx)
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