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From: balabi <ba...@qq...> - 2017-11-07 13:27:33
|
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<div>
<div>Dear Togo,</div><div> Thank you so much. I will check that.</div><div><br></div><div>best regards</div>
</div><div class="J-reply" style="background-color:#f2f2f2;color:black;padding-top:6px;padding-bottom:6px;border-radius:3px;-moz-border-radius:3px;-webkit-border-radius:3px;margin-top:45px;margin-bottom:20px;font-family:'微软雅黑';">
<div style="font-size:14px;line-height:1.5;word-break:break-all;margin-left:10px;margin-right:10px">On <span class="mail-date">11/7/2017 17:08</span>，<a class="mail-to" style="text-decoration:none;color:#2a83f2;" href="mailto:atz...@gm...">Atsushi Togo<atz...@gm...></a> wrote： </div>
</div>
<blockquote id="ntes-pcmail-quote" style="margin: 0; padding: 0; font-size: 14px; font-family: '微软雅黑';">
You can read International tables for crystallography volume A.
<br>I have nothing to say more.
<br>
<br>Togo
<br>
<br>On Tue, Nov 7, 2017 at 5:54 PM, balabi <ba...@qq...> wrote:
<br>> Dear Togo,
<br>> Thank you so much for quick reply.
<br>> You got me confused. But according to wiki page
<br>> https://en.wikipedia.org/wiki/List_of_space_groups#List_of_Monoclinic
<br>> The graph clearly shows that monoclinic group has beta≠90. So I thought
<br>> this should imply that if beta=90, then the group can not be monoclinic.
<br>> I really don't know what is wrong with my logic?
<br>>
<br>> best regards
<br>>
<br>> On 11/7/2017 16:39，Atsushi Togo<atz...@gm...> wrote：
<br>>
<br>> Hi,
<br>>
<br>> Do you think if the lattice is orthorhombic, the space group type has
<br>> to be of orthorhombic? I don't think so.
<br>>
<br>> Togo
<br>>
<br>> On Tue, Nov 7, 2017 at 5:29 PM, balabi <ba...@qq...> wrote:
<br>>> Dear developers,
<br>>> I have a WTe2 monolayer structure which has alpha,beta,gamma all
<br>>> equals
<br>>> 90 degree. However, spglib gives space group 6, which is monoclinic. As
<br>>> far
<br>>> as I know, monoclinic has one angle not equal to 90 degree. So how could
<br>>> it
<br>>> be possible?
<br>>>
<br>>> below is script
<br>>>
<br>>> import sys
<br>>> import numpy as np
<br>>> import spglib
<br>>> test_cell=(np.array([[ 6.24900000000000e+00, 0.00000000000000e+00,
<br>>> 0.00000000000000e+00],
<br>>> [ 0.00000000000000e+00, 3.47700000000000e+00,
<br>>> 0.00000000000000e+00],
<br>>> [ 0, 0.00000000000000e+00,
<br>>> 1.91998000000000e+01]]), np.array([[ 0.65606 , 0.5 ,
<br>>> 0.392155],
<br>>> [ 0.15039 , 0. , 0.424309],
<br>>> [ 0.00392 , 0.5 , 0.575625],
<br>>> [ 0.5 , 0. , 0.607845],
<br>>> [ 0.75699 , 0. , 0.494495],
<br>>> [ 0.39741 , 0.5 , 0.505607]]), np.array([52, 52, 52, 52, 74,
<br>>> 74]))
<br>>> spglib.get_symmetry_dataset(test_cell,symprec=0.01)
<br>>>
<br>>> Is it a bug?
<br>>>
<br>>> best regards
<br>>>
<br>>>
<br>>> ------------------------------------------------------------------------------
<br>>> Check out the vibrant tech community on one of the world's most
<br>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
<br>>> _______________________________________________
<br>>> Spglib-users mailing list
<br>>> Spg...@li...
<br>>> https://lists.sourceforge.net/lists/listinfo/spglib-users
<br>>>
<br>>
<br>>
<br>>
<br>> --
<br>> Atsushi Togo
<br>> Elements Strategy Initiative for Structural Materials, Kyoto university
<br>> E-mail: atz...@gm...
<br>>
<br>> ------------------------------------------------------------------------------
<br>> Check out the vibrant tech community on one of the world's most
<br>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
<br>> _______________________________________________
<br>> Spglib-users mailing list
<br>> Spg...@li...
<br>> https://lists.sourceforge.net/lists/listinfo/spglib-users
<br>>
<br>>
<br>> ------------------------------------------------------------------------------
<br>> Check out the vibrant tech community on one of the world's most
<br>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
<br>> _______________________________________________
<br>> Spglib-users mailing list
<br>> Spg...@li...
<br>> https://lists.sourceforge.net/lists/listinfo/spglib-users
<br>>
<br>
<br>
<br>
<br>--
<br>Atsushi Togo
<br>Elements Strategy Initiative for Structural Materials, Kyoto university
<br>E-mail: atz...@gm...
<br></blockquote><style type="text/css">
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|
From: Atsushi T. <atz...@gm...> - 2017-11-07 09:09:03
|
You can read International tables for crystallography volume A. I have nothing to say more. Togo On Tue, Nov 7, 2017 at 5:54 PM, balabi <ba...@qq...> wrote: > Dear Togo, > Thank you so much for quick reply. > You got me confused. But according to wiki page > https://en.wikipedia.org/wiki/List_of_space_groups#List_of_Monoclinic > The graph clearly shows that monoclinic group has beta≠90. So I thought > this should imply that if beta=90, then the group can not be monoclinic. > I really don't know what is wrong with my logic? > > best regards > > On 11/7/2017 16:39，Atsushi Togo<atz...@gm...> wrote： > > Hi, > > Do you think if the lattice is orthorhombic, the space group type has > to be of orthorhombic? I don't think so. > > Togo > > On Tue, Nov 7, 2017 at 5:29 PM, balabi <ba...@qq...> wrote: >> Dear developers, >> I have a WTe2 monolayer structure which has alpha,beta,gamma all >> equals >> 90 degree. However, spglib gives space group 6, which is monoclinic. As >> far >> as I know, monoclinic has one angle not equal to 90 degree. So how could >> it >> be possible? >> >> below is script >> >> import sys >> import numpy as np >> import spglib >> test_cell=(np.array([[ 6.24900000000000e+00, 0.00000000000000e+00, >> 0.00000000000000e+00], >> [ 0.00000000000000e+00, 3.47700000000000e+00, >> 0.00000000000000e+00], >> [ 0, 0.00000000000000e+00, >> 1.91998000000000e+01]]), np.array([[ 0.65606 , 0.5 , >> 0.392155], >> [ 0.15039 , 0. , 0.424309], >> [ 0.00392 , 0.5 , 0.575625], >> [ 0.5 , 0. , 0.607845], >> [ 0.75699 , 0. , 0.494495], >> [ 0.39741 , 0.5 , 0.505607]]), np.array([52, 52, 52, 52, 74, >> 74])) >> spglib.get_symmetry_dataset(test_cell,symprec=0.01) >> >> Is it a bug? >> >> best regards >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Spglib-users mailing list >> Spg...@li... >> https://lists.sourceforge.net/lists/listinfo/spglib-users >> > > > > -- > Atsushi Togo > Elements Strategy Initiative for Structural Materials, Kyoto university > E-mail: atz...@gm... > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
|
From: balabi <ba...@qq...> - 2017-11-07 08:55:16
|
<html>
<head>
<meta http-equiv='Content-Type' content='text/html; charset=UTF-8'>
</head>
<body>
<style>
font{
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}
</style>
<div style = 'font-family:"微软雅黑"; font-size: 14px; color:#000000; line-height:1.7;'>
<div>
<div>Dear Togo,</div><div> Thank you so much for quick reply.</div><div> You got me confused. But according to wiki page <a href="https://en.wikipedia.org/wiki/List_of_space_groups#List_of_Monoclinic" _src="https://en.wikipedia.org/wiki/List_of_space_groups#List_of_Monoclinic" style="line-height: 1.7;">https://en.wikipedia.org/wiki/List_of_space_groups#List_of_Monoclinic</a></div><div> The graph clearly shows that monoclinic group has beta≠90. So I thought this should imply that if beta=90, then the group can not be monoclinic.</div><div> I really don't know what is wrong with my logic?</div><div><br></div><div>best regards</div><div id="ntes-pcmail-signature" style="font-family:'微软雅黑'"><font style="padding: 0; margin:0;"> </font>
</div><br>
</div><div class="J-reply" style="background-color:#f2f2f2;color:black;padding-top:6px;padding-bottom:6px;border-radius:3px;-moz-border-radius:3px;-webkit-border-radius:3px;margin-top:45px;margin-bottom:20px;font-family:'微软雅黑';">
<div style="font-size:14px;line-height:1.5;word-break:break-all;margin-left:10px;margin-right:10px">On <span class="mail-date">11/7/2017 16:39</span>，<a class="mail-to" style="text-decoration:none;color:#2a83f2;" href="mailto:atz...@gm...">Atsushi Togo<atz...@gm...></a> wrote： </div>
</div>
<blockquote id="ntes-pcmail-quote" style="margin: 0; padding: 0; font-size: 14px; font-family: '微软雅黑';">
Hi,
<br>
<br>Do you think if the lattice is orthorhombic, the space group type has
<br>to be of orthorhombic? I don't think so.
<br>
<br>Togo
<br>
<br>On Tue, Nov 7, 2017 at 5:29 PM, balabi <ba...@qq...> wrote:
<br>> Dear developers,
<br>> I have a WTe2 monolayer structure which has alpha,beta,gamma all equals
<br>> 90 degree. However, spglib gives space group 6, which is monoclinic. As far
<br>> as I know, monoclinic has one angle not equal to 90 degree. So how could it
<br>> be possible?
<br>>
<br>> below is script
<br>>
<br>> import sys
<br>> import numpy as np
<br>> import spglib
<br>> test_cell=(np.array([[ 6.24900000000000e+00, 0.00000000000000e+00,
<br>> 0.00000000000000e+00],
<br>> [ 0.00000000000000e+00, 3.47700000000000e+00,
<br>> 0.00000000000000e+00],
<br>> [ 0, 0.00000000000000e+00,
<br>> 1.91998000000000e+01]]), np.array([[ 0.65606 , 0.5 ,
<br>> 0.392155],
<br>> [ 0.15039 , 0. , 0.424309],
<br>> [ 0.00392 , 0.5 , 0.575625],
<br>> [ 0.5 , 0. , 0.607845],
<br>> [ 0.75699 , 0. , 0.494495],
<br>> [ 0.39741 , 0.5 , 0.505607]]), np.array([52, 52, 52, 52, 74,
<br>> 74]))
<br>> spglib.get_symmetry_dataset(test_cell,symprec=0.01)
<br>>
<br>> Is it a bug?
<br>>
<br>> best regards
<br>>
<br>> ------------------------------------------------------------------------------
<br>> Check out the vibrant tech community on one of the world's most
<br>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
<br>> _______________________________________________
<br>> Spglib-users mailing list
<br>> Spg...@li...
<br>> https://lists.sourceforge.net/lists/listinfo/spglib-users
<br>>
<br>
<br>
<br>
<br>--
<br>Atsushi Togo
<br>Elements Strategy Initiative for Structural Materials, Kyoto university
<br>E-mail: atz...@gm...
<br>
<br>------------------------------------------------------------------------------
<br>Check out the vibrant tech community on one of the world's most
<br>engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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From: Atsushi T. <atz...@gm...> - 2017-11-07 08:39:11
|
Hi, Do you think if the lattice is orthorhombic, the space group type has to be of orthorhombic? I don't think so. Togo On Tue, Nov 7, 2017 at 5:29 PM, balabi <ba...@qq...> wrote: > Dear developers, > I have a WTe2 monolayer structure which has alpha,beta,gamma all equals > 90 degree. However, spglib gives space group 6, which is monoclinic. As far > as I know, monoclinic has one angle not equal to 90 degree. So how could it > be possible? > > below is script > > import sys > import numpy as np > import spglib > test_cell=(np.array([[ 6.24900000000000e+00, 0.00000000000000e+00, > 0.00000000000000e+00], > [ 0.00000000000000e+00, 3.47700000000000e+00, > 0.00000000000000e+00], > [ 0, 0.00000000000000e+00, > 1.91998000000000e+01]]), np.array([[ 0.65606 , 0.5 , > 0.392155], > [ 0.15039 , 0. , 0.424309], > [ 0.00392 , 0.5 , 0.575625], > [ 0.5 , 0. , 0.607845], > [ 0.75699 , 0. , 0.494495], > [ 0.39741 , 0.5 , 0.505607]]), np.array([52, 52, 52, 52, 74, > 74])) > spglib.get_symmetry_dataset(test_cell,symprec=0.01) > > Is it a bug? > > best regards > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
|
From: balabi <ba...@qq...> - 2017-11-07 08:29:49
|
<html>
<head>
<meta http-equiv='Content-Type' content='text/html; charset=UTF-8'>
</head>
<body>
<style>
font{
line-height: 1.7;
}
</style>
<div style = 'font-family:"微软雅黑"; font-size: 14px; color:#000000; line-height:1.7;'>
<div>
<div>Dear developers,</div><div> I have a WTe2 monolayer structure which has alpha,beta,gamma all equals 90 degree. However, spglib gives space group 6, which is monoclinic. As far as I know, monoclinic has one angle not equal to 90 degree. So how could it be possible?</div><div><br></div><div> below is script</div><div><div><br></div><div>import sys</div><div><span style="line-height: 1.7;">import numpy as np</span></div><div>import spglib</div></div><div><div>test_cell=(np.array([[ 6.24900000000000e+00, 0.00000000000000e+00,</div><div> 0.00000000000000e+00],</div><div> [ 0.00000000000000e+00, 3.47700000000000e+00,</div><div> 0.00000000000000e+00],</div><div> [ 0, 0.00000000000000e+00,</div><div> 1.91998000000000e+01]]), np.array([[ 0.65606 , 0.5 , 0.392155],</div><div> [ 0.15039 , 0. , 0.424309],</div><div> [ 0.00392 , 0.5 , 0.575625],</div><div> [ 0.5 , 0. , 0.607845],</div><div> [ 0.75699 , 0. , 0.494495],</div><div> [ 0.39741 , 0.5 , 0.505607]]), np.array([52, 52, 52, 52, 74, 74]))</div></div><div id="ntes-pcmail-signature" style="font-family:'微软雅黑'"><font style="padding: 0; margin:0;"> </font>
</div>spglib.get_symmetry_dataset(test_cell,symprec=0.01)
</div><div><br></div><div>Is it a bug?</div><div><br></div><div>best regards</div><style type="text/css">
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From: Atsushi T. <atz...@gm...> - 2017-10-27 09:07:33
|
Dear spglib users, Spglib v1.10.1 is released. No change of features and no change of API were made. But two new files are added, src/determination.c and src/determination.h. I made a code refactoring to make the flow of the code hopefully better understandable. I am preparing a manuscript on spglib for whom might be interested in it. Togo -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
|
From: Atsushi T. <atz...@gm...> - 2017-10-22 04:51:18
|
Dear spglib users,
Spglib v1.10.0 is released.
- 'mapping_to_primitive' and 'std_mapping_to_primitive' in the spglib
dataset are available.
- 'spg_get_hall_number_from_symmetry' function
('get_hall_number_from_symmetry' method for python) is also available
as an experimental feature.
- ASE Atoms class-like input of crystal structure for python wrapper
is deprecated. DeprecationWarning is issued when using it. See the
detail at
https://atztogo.github.io/spglib/python-spglib.html#ase-atoms-like-input-is-deprecated
This feature will be usable for a while until people will be aware
of it. Following the comment by Maja-Olivia Lenz, I wrote some
document on it.
The ChangeLog is found here,
https://github.com/atztogo/spglib/blob/master/ChangeLog
Togo
--
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...
|
|
From: Atsushi T. <atz...@gm...> - 2017-10-11 22:12:32
|
Hi, It seems your setuptools is old. Can you update it? Togo On Thu, Oct 12, 2017 at 2:57 AM, Khemka, Jyotsna <jyo...@in...> wrote: > > > Hi Users, > > > > I am trying to install spglib from https://pypi.python.org/pypi/spglib: > spglib-1.9.10.1.tar.gz (md5) (4ce58ebee60f07114517b71fc4b51812) > > I am getting following error: > > > > [jkhemka@eln6 spglib-1.9.10.1]$ python setup.py install > --prefix=/panfs/users/jkhemka/customer/iisc/physics_dept/spglib/ > > setuptools is used. > > Traceback (most recent call last): > > File "setup.py", line 138, in <module> > > ext_modules=[extension]) > > File "/usr/lib64/python2.7/distutils/core.py", line 112, in setup > > _setup_distribution = dist = klass(attrs) > > File "/usr/lib/python2.7/site-packages/setuptools/dist.py", line 265, in > __init__ > > self.fetch_build_eggs(attrs.pop('setup_requires')) > > File "/usr/lib/python2.7/site-packages/setuptools/dist.py", line 289, in > fetch_build_eggs > > parse_requirements(requires), installer=self.fetch_build_egg > > File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 630, in > resolve > > raise VersionConflict(dist,req) # XXX put more info here > > pkg_resources.VersionConflict: (setuptools 0.9.8 > (/usr/lib/python2.7/site-packages), Requirement.parse('setuptools>=18.0')) > > > > Please could anyone help here. > > > > Thanks, > > > > Kind regards, > > Jyotsna > > > > > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
|
From: Khemka, J. <jyo...@in...> - 2017-10-11 17:58:06
|
Hi Users, I am trying to install spglib from https://pypi.python.org/pypi/spglib: spglib-1.9.10.1.tar.gz<https://pypi.python.org/packages/aa/7e/56617da619e6d8056b2e346cbecb6f0233510a8a5f8cd8b55d408c2e507a/spglib-1.9.10.1.tar.gz#md5=4ce58ebee60f07114517b71fc4b51812> (md5<https://pypi.python.org/pypi?:action=show_md5&digest=4ce58ebee60f07114517b71fc4b51812>) (4ce58ebee60f07114517b71fc4b51812) I am getting following error: [jkhemka@eln6 spglib-1.9.10.1]$ python setup.py install --prefix=/panfs/users/jkhemka/customer/iisc/physics_dept/spglib/ setuptools is used. Traceback (most recent call last): File "setup.py", line 138, in <module> ext_modules=[extension]) File "/usr/lib64/python2.7/distutils/core.py", line 112, in setup _setup_distribution = dist = klass(attrs) File "/usr/lib/python2.7/site-packages/setuptools/dist.py", line 265, in __init__ self.fetch_build_eggs(attrs.pop('setup_requires')) File "/usr/lib/python2.7/site-packages/setuptools/dist.py", line 289, in fetch_build_eggs parse_requirements(requires), installer=self.fetch_build_egg File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 630, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (setuptools 0.9.8 (/usr/lib/python2.7/site-packages), Requirement.parse('setuptools>=18.0')) Please could anyone help here. Thanks, Kind regards, Jyotsna |
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From: Atsushi T. <atz...@gm...> - 2017-10-11 08:27:14
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Hi Maja, Thanks for your reply! ASE Atoms is not just a container of crystal structure. I feel spglib is more fundamental than ASE Atoms. Like pymatgen, ASE can have spglib its inside and I may expect it from the recent commit of ASE repository, https://gitlab.com/ase/ase/blob/master/ase/spacegroup/spacegroup.py Best regards, Togo On Wed, Oct 11, 2017 at 5:13 PM, Maja-Olivia Lenz <le...@fh...> wrote: > Dear Togo, > > I hope you just mean to stop answering questions concerning that. To > remove the functionality itself would be a step backwards in my opinion. > It should just be made very clear to the users, that just the basic > functionality is supported. > > Regards, > Maja > > On 10/11/2017 10:04 AM, Atsushi Togo wrote: >> Dear spglib-users, >> >> I have a question to spglib-for-python users. >> >> Currently spglib for python supports limited features of ASE >> Atoms-like-class as its input crystal structure for symmetry search. >> But users may think that spglib supports full feature of ASE >> Atoms-like-class, which is confusing. Spglib is getting to be popular >> and popular. I am afraid of problems to happen. So I am considering to >> stop spglib's ASE-Atoms support as soon as possible. >> >> Is it OK for spglib-users? Is there any problem? >> >> Togo >> > > -- > ---------------------------------------------------------------------- > Maja-Olivia Lenz > Fritz-Haber-Institut der Max-Planck-Gesellschaft > Faradayweg 4-6 > D-14195 Berlin > E-Mail: le...@fh... > ---------------------key:1-0.0735-11600-23.05:fhi-------------------- > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
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From: Maja-Olivia L. <le...@fh...> - 2017-10-11 08:13:58
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Dear Togo, I hope you just mean to stop answering questions concerning that. To remove the functionality itself would be a step backwards in my opinion. It should just be made very clear to the users, that just the basic functionality is supported. Regards, Maja On 10/11/2017 10:04 AM, Atsushi Togo wrote: > Dear spglib-users, > > I have a question to spglib-for-python users. > > Currently spglib for python supports limited features of ASE > Atoms-like-class as its input crystal structure for symmetry search. > But users may think that spglib supports full feature of ASE > Atoms-like-class, which is confusing. Spglib is getting to be popular > and popular. I am afraid of problems to happen. So I am considering to > stop spglib's ASE-Atoms support as soon as possible. > > Is it OK for spglib-users? Is there any problem? > > Togo > -- ---------------------------------------------------------------------- Maja-Olivia Lenz Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin E-Mail: le...@fh... ---------------------key:1-0.0735-11600-23.05:fhi-------------------- |
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From: Atsushi T. <atz...@gm...> - 2017-10-11 08:04:22
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Dear spglib-users, I have a question to spglib-for-python users. Currently spglib for python supports limited features of ASE Atoms-like-class as its input crystal structure for symmetry search. But users may think that spglib supports full feature of ASE Atoms-like-class, which is confusing. Spglib is getting to be popular and popular. I am afraid of problems to happen. So I am considering to stop spglib's ASE-Atoms support as soon as possible. Is it OK for spglib-users? Is there any problem? Togo -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
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From: Atsushi T. <atz...@gm...> - 2017-10-11 07:51:13
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Hi,
Spglib doesn't support Atoms object fully.
structure.pbc = (1, 1, 0)
This doesn't work.
Togo
On Wed, Oct 11, 2017 at 3:42 PM, Anders Christian Riis-Jensen
<ac...@fy...> wrote:
> Here is my code:
>
>
> import sys
> import spglib
> import numpy as np
> from numpy import pi, sin, cos, arccos, sqrt, dot
> from ase import Atoms
>
> # Input: Structure
> a = 2.46
> cell = np.array([[a, 0, 0,], [-a/2, a*sin(60*pi/180), 0], [0, 0, 5*a]])
>
> structure = Atoms('C2', cell=cell,
> scaled_positions=np.array([[0, 0, 0],
> [2./3, 1./3, 0]]),
> )
>
> structure.pbc = (1, 1, 0)
>
> cell = structure.get_cell()
>
> #Define rotation matrix:
> rot60 = np.array([[1/2, -sqrt(3)/2, 0], [sqrt(3)/2, 1/2, 0], [0, 0, 1]])
>
> # Get all symmetry operations
> symop = spglib.get_symmetry(structure, symprec=1e-5)
> rotaa = symop['rotations']
> trlaa = symop['translations']
>
> rotxy = []
> trlxy = []
>
> #Transform matrices to cartesian coordinates:
> for j in range(len(rotaa)):
> rot_t = np.dot(np.linalg.inv(cell), np.dot(rotaa[j], cell))
> trl_t = np.dot(np.dot(np.linalg.inv(cell), trlaa[j]), cell)
> rotxy.append(rot_t)
> trlxy.append(trl_t)
>
>
>
>
> Anders
>
> ________________________________
> Fra: Atsushi Togo <atz...@gm...>
> Sendt: 11. oktober 2017 02:14:17
> Til: Anders Christian Riis-Jensen
> Cc: spg...@li...
> Emne: Re: [Spglib-users] get_symmetry basis
>
> Hi,
>
> Could you give your script?
>
> Togo
>
> On Tue, Oct 10, 2017 at 7:18 PM, Anders Christian Riis-Jensen
> <ac...@fy...> wrote:
>> I am using the built-in function get_symmetry from spglib, and I seem to
>> have some issues with this. In this context I have a question.
>> I will here give an example showing my problem:
>>
>> If I define the unit cell for graphene:
>> cell = np.array([[a, 0, 0,], [-a/2, a*sin(60*pi/180), 0], [0, 0, 5*a]])
>> and put the carbon atoms in the (scaled) positions [0,0,0] and [0, 2/3,
>> 1/3]
>> I then run spglib.get_symmetry on the system (with the default tolerance).
>> I
>> get a set of symmetry transformations (I understand each transformation is
>> a
>> combination of a matrix multiplication and a translation). I want to have
>> the symmetry matrices (M) in cartesian coordinates and therefore make the
>> following basis transformation:
>> inverse(cell).M.cell
>> And here I would for example expect to find the standard 60 degrees
>> rotation
>> matrix, however this I dot not get. I therefore realize that the original
>> symmetry matrices might not be written in the lattice basis as I expected.
>>
>> Which basis is used and what is the proper transformation to get to
>> cartesian coordinates?
>>
>> Any answer will be greatly appreciated.
>>
>> Best regards
>> Anders Riis-Jensen
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Spglib-users mailing list
>> Spg...@li...
>> https://lists.sourceforge.net/lists/listinfo/spglib-users
>>
>
>
>
> --
> Atsushi Togo
> Elements Strategy Initiative for Structural Materials, Kyoto university
> E-mail: atz...@gm...
--
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...
|
|
From: Anders C. Riis-J. <ac...@fy...> - 2017-10-11 06:42:42
|
Here is my code:
import sys
import spglib
import numpy as np
from numpy import pi, sin, cos, arccos, sqrt, dot
from ase import Atoms
# Input: Structure
a = 2.46
cell = np.array([[a, 0, 0,], [-a/2, a*sin(60*pi/180), 0], [0, 0, 5*a]])
structure = Atoms('C2', cell=cell,
scaled_positions=np.array([[0, 0, 0],
[2./3, 1./3, 0]]),
)
structure.pbc = (1, 1, 0)
cell = structure.get_cell()
#Define rotation matrix:
rot60 = np.array([[1/2, -sqrt(3)/2, 0], [sqrt(3)/2, 1/2, 0], [0, 0, 1]])
# Get all symmetry operations
symop = spglib.get_symmetry(structure, symprec=1e-5)
rotaa = symop['rotations']
trlaa = symop['translations']
rotxy = []
trlxy = []
#Transform matrices to cartesian coordinates:
for j in range(len(rotaa)):
rot_t = np.dot(np.linalg.inv(cell), np.dot(rotaa[j], cell))
trl_t = np.dot(np.dot(np.linalg.inv(cell), trlaa[j]), cell)
rotxy.append(rot_t)
trlxy.append(trl_t)
Anders
________________________________
Fra: Atsushi Togo <atz...@gm...>
Sendt: 11. oktober 2017 02:14:17
Til: Anders Christian Riis-Jensen
Cc: spg...@li...
Emne: Re: [Spglib-users] get_symmetry basis
Hi,
Could you give your script?
Togo
On Tue, Oct 10, 2017 at 7:18 PM, Anders Christian Riis-Jensen
<ac...@fy...> wrote:
> I am using the built-in function get_symmetry from spglib, and I seem to
> have some issues with this. In this context I have a question.
> I will here give an example showing my problem:
>
> If I define the unit cell for graphene:
> cell = np.array([[a, 0, 0,], [-a/2, a*sin(60*pi/180), 0], [0, 0, 5*a]])
> and put the carbon atoms in the (scaled) positions [0,0,0] and [0, 2/3, 1/3]
> I then run spglib.get_symmetry on the system (with the default tolerance). I
> get a set of symmetry transformations (I understand each transformation is a
> combination of a matrix multiplication and a translation). I want to have
> the symmetry matrices (M) in cartesian coordinates and therefore make the
> following basis transformation:
> inverse(cell).M.cell
> And here I would for example expect to find the standard 60 degrees rotation
> matrix, however this I dot not get. I therefore realize that the original
> symmetry matrices might not be written in the lattice basis as I expected.
>
> Which basis is used and what is the proper transformation to get to
> cartesian coordinates?
>
> Any answer will be greatly appreciated.
>
> Best regards
> Anders Riis-Jensen
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users
>
--
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...
|
|
From: Atsushi T. <atz...@gm...> - 2017-10-11 00:14:24
|
Hi, Could you give your script? Togo On Tue, Oct 10, 2017 at 7:18 PM, Anders Christian Riis-Jensen <ac...@fy...> wrote: > I am using the built-in function get_symmetry from spglib, and I seem to > have some issues with this. In this context I have a question. > I will here give an example showing my problem: > > If I define the unit cell for graphene: > cell = np.array([[a, 0, 0,], [-a/2, a*sin(60*pi/180), 0], [0, 0, 5*a]]) > and put the carbon atoms in the (scaled) positions [0,0,0] and [0, 2/3, 1/3] > I then run spglib.get_symmetry on the system (with the default tolerance). I > get a set of symmetry transformations (I understand each transformation is a > combination of a matrix multiplication and a translation). I want to have > the symmetry matrices (M) in cartesian coordinates and therefore make the > following basis transformation: > inverse(cell).M.cell > And here I would for example expect to find the standard 60 degrees rotation > matrix, however this I dot not get. I therefore realize that the original > symmetry matrices might not be written in the lattice basis as I expected. > > Which basis is used and what is the proper transformation to get to > cartesian coordinates? > > Any answer will be greatly appreciated. > > Best regards > Anders Riis-Jensen > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
|
From: Anders C. Riis-J. <ac...@fy...> - 2017-10-10 13:52:03
|
I am using the built-in function get_symmetry from spglib, and I seem to have some issues with this. In this context I have a question. I will here give an example showing my problem: If I define the unit cell for graphene: cell = np.array([[a, 0, 0,], [-a/2, a*sin(60*pi/180), 0], [0, 0, 5*a]]) and put the carbon atoms in the (scaled) positions [0,0,0] and [0, 2/3, 1/3] I then run spglib.get_symmetry on the system (with the default tolerance). I get a set of symmetry transformations (I understand each transformation is a combination of a matrix multiplication and a translation). I want to have the symmetry matrices (M) in cartesian coordinates and therefore make the following basis transformation: inverse(cell).M.cell And here I would for example expect to find the standard 60 degrees rotation matrix, however this I dot not get. I therefore realize that the original symmetry matrices might not be written in the lattice basis as I expected. Which basis is used and what is the proper transformation to get to cartesian coordinates? Any answer will be greatly appreciated. Best regards Anders Riis-Jensen |
|
From: Atsushi T. <atz...@gm...> - 2017-10-10 00:29:56
|
Dear Goutham, I reply to the spglib mailing list. About the crystallography, I think you are correct. But, - I don't know what is mvc-11541. - I don't know SpacegroupAnalyzer. So if you want to get some answer (not guaranteed though), please your problem down to that spglib can directly apply. Togo On Tue, Oct 10, 2017 at 5:43 AM, Goutham Sreekar A. R. <sre...@gm...> wrote: > Hi Togo, > > The discussion I had at Materials Project discussion group led me to post > this question in spglib mailing lists. May be this link > https://discuss.materialsproject.org/t/discrepancy-in-data-for-mvc-11541/782 > provide you some information as to why I posted this query. > > Regards, > Goutham > > A R Goutham Sreekar > Dept. of Metallurgical and Materials Science, > Indian Institute of Technology Madras, > Chennai, India-600036. > > On Mon, Oct 9, 2017 at 7:45 PM, Goutham Sreekar A. R. > <sre...@gm...> wrote: >> >> Hi Togo, >> >> Thank you for replying. May be I did not articulate well, the point that I >> am trying to make is, according to Crystallography, a Hexagonal crystal >> system can have either "6" or "-6" or "6/m" or "622" or "6mm" or "-62m" or >> "6/mmm" as point symmetries. Only a Orthorhombic Crystal system can have a >> "mmm" point symmetry. Therefore, I feel that the point symmetry for >> mvc-11541 is incorrect or am I missing something? >> >> The above mentioned information can be found in >> http://pd.chem.ucl.ac.uk/pdnn/symm2/group32.htm >> >> >> Regards, >> Goutham >> >> A R Goutham Sreekar >> Dept. of Metallurgical and Materials Science, >> Indian Institute of Technology Madras, >> Chennai, India-600036. >> >> On Sun, Oct 8, 2017 at 6:42 PM, Atsushi Togo <atz...@gm...> wrote: >>> >>> Hi, >>> >>> I don't see what you mean. >>> >>> Togo >>> >>> On Sun, Oct 8, 2017 at 10:05 PM, Goutham Sreekar A. R. >>> <sre...@gm...> wrote: >>> > Hi, >>> > Could you please verify the point group of mvc-11541? As far as I know >>> > a >>> > simple hexagonal crystal structure cannot have “mmm” point group >>> > symmetry. >>> > >>> > A R Goutham Sreekar >>> > Dept. of Metallurgical and Materials Science, >>> > Indian Institute of Technology Madras, >>> > Chennai, India-600036. >>> > >>> > >>> > ------------------------------------------------------------------------------ >>> > Check out the vibrant tech community on one of the world's most >>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> > _______________________________________________ >>> > Spglib-users mailing list >>> > Spg...@li... >>> > https://lists.sourceforge.net/lists/listinfo/spglib-users >>> > >>> >>> >>> >>> -- >>> Atsushi Togo >>> Elements Strategy Initiative for Structural Materials, Kyoto university >>> E-mail: atz...@gm... >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Spglib-users mailing list >>> Spg...@li... >>> https://lists.sourceforge.net/lists/listinfo/spglib-users >> >> > -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
|
From: Atsushi T. <atz...@gm...> - 2017-10-08 13:12:34
|
Hi, I don't see what you mean. Togo On Sun, Oct 8, 2017 at 10:05 PM, Goutham Sreekar A. R. <sre...@gm...> wrote: > Hi, > Could you please verify the point group of mvc-11541? As far as I know a > simple hexagonal crystal structure cannot have “mmm” point group symmetry. > > A R Goutham Sreekar > Dept. of Metallurgical and Materials Science, > Indian Institute of Technology Madras, > Chennai, India-600036. > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
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From: Goutham S. A. R. <sre...@gm...> - 2017-10-08 13:05:23
|
Hi, Could you please verify the point group of mvc-11541? As far as I know a simple hexagonal crystal structure cannot have “mmm” point group symmetry. A R Goutham Sreekar Dept. of Metallurgical and Materials Science, Indian Institute of Technology Madras, Chennai, India-600036. |
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From: Atsushi T. <atz...@gm...> - 2017-09-25 13:54:43
|
Good! Togo On Mon, Sep 25, 2017 at 10:49 PM, Noam Bernstein <noa...@nr...> wrote: > On Sep 25, 2017, at 9:15 AM, Atsushi Togo <atz...@gm...> wrote: > > If the distortion is not that much, then the approach by > Grosse-Kunstleve and Adams should work. If you write a python script, > I think I can comment to it. The C-code is about here, > https://github.com/atztogo/spglib/blob/master/src/site_symmetry.c#L244 > > > > Hmm. I tried something like this initially, and it wasn't working at all, > but I must have had a bug, since I redid it cleanly (so I could show the > code), and the new version's apparently working. Maybe because I was coding > for an audience I was more careful. In any case, while I think it would be > useful to have a version of standardize_cell() that only moved atoms, > without touching the cell vectors, I think my problem is solved for now > (especially if I can recode it without a tight loop in python). It should > probably be redone without so many tight loops in explicit python, but here > it is, in case it’s useful for anyone else: > > #!/usr/bin/env python > > import os, sys > import spglib, ase, ase.io > import numpy as np > > at = ase.io.read(sys.argv[1]) > > dataset = spglib.get_symmetry_dataset(at, symprec=1.0e-5) > sys.stderr.write("precise initial symmetry group number {}, international > (Hermann-Mauguin) {} Hall {} prec > {}\n".format(dataset["number"],dataset["international"],dataset["hall"],1.0e-5)) > dataset = spglib.get_symmetry_dataset(at, symprec=0.1) > sys.stderr.write("loose initial symmetry group number {}, international > (Hermann-Mauguin) {} Hall {} prec > {}\n".format(dataset["number"],dataset["international"],dataset["hall"],0.1)) > > p = at.get_scaled_positions() > cell = at.get_cell() > > new_position = np.zeros(at.get_positions().shape) > for i in range(len(at)): > # zero accumulators for rot and transl > mean_r = np.zeros((3,3)) > mean_t = np.zeros((3)) > n_contrib=0 > position = p[i][:] > # loop over opreations > for (r, t) in zip(dataset['rotations'], dataset['translations']): > # transformed position > pos = np.dot(r, position) + t > # if it's close to periodic image, contribute to accumulators > dp = pos - position > dp_in_cell = dp - np.round(dp) > if np.linalg.norm(dp_in_cell) < 0.1: > mean_r += r > mean_t += t - np.round(dp) > n_contrib += 1 > mean_r /= float(n_contrib) > mean_t /= float(n_contrib) > > new_position[i,:] = np.dot(position, mean_r) + mean_t > > at.set_scaled_positions(new_position) > dataset = spglib.get_symmetry_dataset(at, symprec=1.0e-5) > sys.stderr.write("manual symmetrization got symmetry group number {}, > international (Hermann-Mauguin) {} Hall {} prec > {}\n".format(dataset["number"],dataset["international"],dataset["hall"],1.0e-5)) > ase.io.write(sys.stdout, at, format="extxyz") > > > > thanks again, > Noam -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
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From: Noam B. <noa...@nr...> - 2017-09-25 13:49:26
|
> On Sep 25, 2017, at 9:15 AM, Atsushi Togo <atz...@gm...> wrote: > > If the distortion is not that much, then the approach by > Grosse-Kunstleve and Adams should work. If you write a python script, > I think I can comment to it. The C-code is about here, > https://github.com/atztogo/spglib/blob/master/src/site_symmetry.c#L244 <https://github.com/atztogo/spglib/blob/master/src/site_symmetry.c#L244> Hmm. I tried something like this initially, and it wasn't working at all, but I must have had a bug, since I redid it cleanly (so I could show the code), and the new version's apparently working. Maybe because I was coding for an audience I was more careful. In any case, while I think it would be useful to have a version of standardize_cell() that only moved atoms, without touching the cell vectors, I think my problem is solved for now (especially if I can recode it without a tight loop in python). It should probably be redone without so many tight loops in explicit python, but here it is, in case it’s useful for anyone else: #!/usr/bin/env python import os, sys import spglib, ase, ase.io import numpy as np at = ase.io.read(sys.argv[1]) dataset = spglib.get_symmetry_dataset(at, symprec=1.0e-5) sys.stderr.write("precise initial symmetry group number {}, international (Hermann-Mauguin) {} Hall {} prec {}\n".format(dataset["number"],dataset["international"],dataset["hall"],1.0e-5)) dataset = spglib.get_symmetry_dataset(at, symprec=0.1) sys.stderr.write("loose initial symmetry group number {}, international (Hermann-Mauguin) {} Hall {} prec {}\n".format(dataset["number"],dataset["international"],dataset["hall"],0.1)) p = at.get_scaled_positions() cell = at.get_cell() new_position = np.zeros(at.get_positions().shape) for i in range(len(at)): # zero accumulators for rot and transl mean_r = np.zeros((3,3)) mean_t = np.zeros((3)) n_contrib=0 position = p[i][:] # loop over opreations for (r, t) in zip(dataset['rotations'], dataset['translations']): # transformed position pos = np.dot(r, position) + t # if it's close to periodic image, contribute to accumulators dp = pos - position dp_in_cell = dp - np.round(dp) if np.linalg.norm(dp_in_cell) < 0.1: mean_r += r mean_t += t - np.round(dp) n_contrib += 1 mean_r /= float(n_contrib) mean_t /= float(n_contrib) new_position[i,:] = np.dot(position, mean_r) + mean_t at.set_scaled_positions(new_position) dataset = spglib.get_symmetry_dataset(at, symprec=1.0e-5) sys.stderr.write("manual symmetrization got symmetry group number {}, international (Hermann-Mauguin) {} Hall {} prec {}\n".format(dataset["number"],dataset["international"],dataset["hall"],1.0e-5)) ase.io.write(sys.stdout, at, format="extxyz") thanks again, Noam |
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From: Atsushi T. <atz...@gm...> - 2017-09-25 13:15:14
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If the distortion is not that much, then the approach by Grosse-Kunstleve and Adams should work. If you write a python script, I think I can comment to it. The C-code is about here, https://github.com/atztogo/spglib/blob/master/src/site_symmetry.c#L244 Togo On Mon, Sep 25, 2017 at 10:08 PM, Noam Bernstein <noa...@nr...> wrote: > > On Sep 25, 2017, at 8:54 AM, Atsushi Togo <atz...@gm...> wrote: > > Hi, > > Hi Togo - thanks for the quick response. Since I’m using the python > interface, which I don’t think has direct access to that routine, I’m not > sure, but I don’t think so, at least if I’m reading the documentation > correctly. > > > This for python, > https://atztogo.github.io/spglib/python-spglib.html#standardize-cell > > > thanks. > > > I'm sure that the paper's scheme works for atomic positions, but the > paper doesn't mention about symmetrization of basis vectors if I > remember correctly. > > > I don’t actually care about cell vectors right now, so if I could just get > atomic positions symmetrized I’d be satisfied. > > > Let me put together an example based on the underlying C library, to take > the python interface out of the process, and I’ll post a followup. > > > But symmetrization is uneasy since it means the original input > structure is distorted. So we have to determine how we want to > symmetrize it. This makes me difficult to answer this type of > question. > > > I know what symmetry group I want the final configuration to be (it’s > determined by spglib, in fact, just based on a loose symprec). Basically, I > think what I want is “no_idealize=0”, so move the atoms to symmetry required > positions, but without touching the unit cell vectors at all. Neither > transforming into a primitive cell (what happens when to_primitive=1), nor > transforming into a standard cell (what happens when to_primitive=0). Just > the original lattice vectors. > > Noam > > ____________ > | > | > | > U.S. NAVAL > | > | > _RESEARCH_ > | > LABORATORY > > Noam Bernstein, Ph.D. > Center for Materials Physics and Technology > U.S. Naval Research Laboratory > T +1 202 404 8628 F +1 202 404 7546 > https://www.nrl.navy.mil > -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
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From: Noam B. <noa...@nr...> - 2017-09-25 13:08:22
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> On Sep 25, 2017, at 8:54 AM, Atsushi Togo <atz...@gm...> wrote: > > Hi, > >> Hi Togo - thanks for the quick response. Since I’m using the python >> interface, which I don’t think has direct access to that routine, I’m not >> sure, but I don’t think so, at least if I’m reading the documentation >> correctly. > > This for python, > https://atztogo.github.io/spglib/python-spglib.html#standardize-cell <https://atztogo.github.io/spglib/python-spglib.html#standardize-cell> thanks. > > I'm sure that the paper's scheme works for atomic positions, but the > paper doesn't mention about symmetrization of basis vectors if I > remember correctly. I don’t actually care about cell vectors right now, so if I could just get atomic positions symmetrized I’d be satisfied. > >> Let me put together an example based on the underlying C library, to take >> the python interface out of the process, and I’ll post a followup. > > But symmetrization is uneasy since it means the original input > structure is distorted. So we have to determine how we want to > symmetrize it. This makes me difficult to answer this type of > question. > I know what symmetry group I want the final configuration to be (it’s determined by spglib, in fact, just based on a loose symprec). Basically, I think what I want is “no_idealize=0”, so move the atoms to symmetry required positions, but without touching the unit cell vectors at all. Neither transforming into a primitive cell (what happens when to_primitive=1), nor transforming into a standard cell (what happens when to_primitive=0). Just the original lattice vectors. Noam ____________ || |U.S. NAVAL| |_RESEARCH_| LABORATORY Noam Bernstein, Ph.D. Center for Materials Physics and Technology U.S. Naval Research Laboratory T +1 202 404 8628 F +1 202 404 7546 https://www.nrl.navy.mil <https://www.nrl.navy.mil/> |
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From: Atsushi T. <atz...@gm...> - 2017-09-25 12:54:32
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Hi, > Hi Togo - thanks for the quick response. Since I’m using the python > interface, which I don’t think has direct access to that routine, I’m not > sure, but I don’t think so, at least if I’m reading the documentation > correctly. This for python, https://atztogo.github.io/spglib/python-spglib.html#standardize-cell > From what I can tell, that _will_ transform to the conventional > crystallographic cell (e.g. a diamond structure fcc + 2 atom basis to simple > cubic + 8 atom basis), and that’s exactly what I don’t want. I’ll try to > test it today. > > > Or if you want detailed control, you may use the dataset obtained by > spg_get_dataset with additional some operations by yourself. > https://atztogo.github.io/spglib/api.html#spg-get-dataset-and-spg-get-dataset-with-hall-number > > > So I have tried an approach using the actual symmetry operations, but wasn’t > able to figure out how to use them to symmetrize positions. I tried putting > atoms at the mean of the positions after transformation by each operation, > but that didn’t work. Then I dug into the source, to see how the > symmetrization works, and looked at the Grosse-Kunstleve and Adams paper > that’s referred to. However, that algorithm didn’t make sense to me. As > far as I can tell, for each atom it loops over transformations, then checks > to see if each operation maps an atom to a periodic image of itself to > within some precision. If so, it adds the rotation matrix and translation > vector to a running total, to it can compute mean rotation and mean > translation, which are then used to generate the symmetrize positions. > However, I don’t understand why that’s the right thing to do, and it doesn’t > seem to be working for me. For my 2 atom diamond structure example, If a > particular symmetry operation transforms atom 0 into atom 1, for example, > the transformed atom 0 position is _not_ off by a lattice vector from the > original atom 0 position, so that operation does not figure into the > symmetrization at all. It therefore does nothing. I'm sure that the paper's scheme works for atomic positions, but the paper doesn't mention about symmetrization of basis vectors if I remember correctly. > Let me put together an example based on the underlying C library, to take > the python interface out of the process, and I’ll post a followup. But symmetrization is uneasy since it means the original input structure is distorted. So we have to determine how we want to symmetrize it. This makes me difficult to answer this type of question. Togo > > thanks, > Noam > -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
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From: Noam B. <noa...@nr...> - 2017-09-25 12:40:14
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> On Sep 22, 2017, at 9:08 PM, Atsushi Togo <atz...@gm...> wrote: > > Hi, > > Do you want the following? > > https://atztogo.github.io/spglib/api.html#spg-standardize-cell > with to_primitive=0 and no_idealize=1 Hi Togo - thanks for the quick response. Since I’m using the python interface, which I don’t think has direct access to that routine, I’m not sure, but I don’t think so, at least if I’m reading the documentation correctly. From what I can tell, that _will_ transform to the conventional crystallographic cell (e.g. a diamond structure fcc + 2 atom basis to simple cubic + 8 atom basis), and that’s exactly what I don’t want. I’ll try to test it today. > > Or if you want detailed control, you may use the dataset obtained by > spg_get_dataset with additional some operations by yourself. > https://atztogo.github.io/spglib/api.html#spg-get-dataset-and-spg-get-dataset-with-hall-number <https://atztogo.github.io/spglib/api.html#spg-get-dataset-and-spg-get-dataset-with-hall-number> So I have tried an approach using the actual symmetry operations, but wasn’t able to figure out how to use them to symmetrize positions. I tried putting atoms at the mean of the positions after transformation by each operation, but that didn’t work. Then I dug into the source, to see how the symmetrization works, and looked at the Grosse-Kunstleve and Adams paper that’s referred to. However, that algorithm didn’t make sense to me. As far as I can tell, for each atom it loops over transformations, then checks to see if each operation maps an atom to a periodic image of itself to within some precision. If so, it adds the rotation matrix and translation vector to a running total, to it can compute mean rotation and mean translation, which are then used to generate the symmetrize positions. However, I don’t understand why that’s the right thing to do, and it doesn’t seem to be working for me. For my 2 atom diamond structure example, If a particular symmetry operation transforms atom 0 into atom 1, for example, the transformed atom 0 position is _not_ off by a lattice vector from the original atom 0 position, so that operation does not figure into the symmetrization at all. It therefore does nothing. Let me put together an example based on the underlying C library, to take the python interface out of the process, and I’ll post a followup. thanks, Noam |
