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From: Atsushi T. <atz...@gm...> - 2017-09-23 01:08:19
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Hi, Do you want the following? https://atztogo.github.io/spglib/api.html#spg-standardize-cell with to_primitive=0 and no_idealize=1 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 Togo On Sat, Sep 23, 2017 at 3:35 AM, Noam Bernstein <noa...@nr...> wrote: > Hi - I’ve been happy using spglib, it’s been a great tool, but I’m now > trying to do something new and can’t figure out whether it’s possible. I’d > like to symmetrize a cell according to a particular spacegroup (which I > found is approximately applicable at a loose symprec). However, > standardize_cell (and its relatives) all modify the cell size, either to > make a primitive cell (much smaller if I have a supercell), or some sort of > conventional cell (bigger, e.g., if my original cell is a primitive diamond > structure). I’d like to fix my positions to exactly follow the symmetry > operations, but without ever changing the overall cell any more than > minimally necessary for symmetry. Is this possible with spglib? > thanks, > 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 > > > ------------------------------------------------------------------------------ > 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: Noam B. <noa...@nr...> - 2017-09-22 19:04:35
|
Hi - I’ve been happy using spglib, it’s been a great tool, but I’m now trying to do something new and can’t figure out whether it’s possible. I’d like to symmetrize a cell according to a particular spacegroup (which I found is approximately applicable at a loose symprec). However, standardize_cell (and its relatives) all modify the cell size, either to make a primitive cell (much smaller if I have a supercell), or some sort of conventional cell (bigger, e.g., if my original cell is a primitive diamond structure). I’d like to fix my positions to exactly follow the symmetry operations, but without ever changing the overall cell any more than minimally necessary for symmetry. Is this possible with spglib? thanks, 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...> - 2017-09-07 17:07:01
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Hi, If pymatgen works, it should work, because pymatgen calls spglib. Togo On Thu, Sep 7, 2017 at 6:36 PM, balabi <ba...@qq...> wrote: > Dear developers, > > I have a cif file (show at the end), and I want to find its spacegroup > symmetry and symmetrized structure. > > If I use spglib.get_symmetry_dataset, it got me spacegroup 156 and all atoms > are inequivalent, like this > > 'choice': '', > 'equivalent_atoms': array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, > 12, 13, 14], dtype=int32), > 'hall': 'P 3 -2"', > 'hall_number': 446, > 'international': 'P3m1', > 'number': 156, > > > However, if I use ISOCIF http://stokes.byu.edu/iso/isocif.php . I can find > the spacegroup is 164 and there 8 inequivalent atoms. > > I also tried pymatgen's pymatgen.symmetry.analyzer.SpacegroupAnalyzer, it > also give 164 spacegroup. > > > So I am wondering whether there is a bug? > > > best regards > > ----------------------------------- > > below is cif file > > > data_global > _cell_length_a 4.138 > _cell_length_b 4.138 > _cell_length_c 48.64 > _cell_angle_alpha 90 > _cell_angle_beta 90 > _cell_angle_gamma 120 > _symmetry_space_group_name_H-M 'P -1' > loop_ > _symmetry_equiv_pos_as_xyz > 'x,y,z' > loop_ > _atom_site_label > _atom_site_fract_x > _atom_site_fract_y > _atom_site_fract_z > Se1 0.333333 0.666667 0.251912 > Bi2 0.666667 0.333333 0.288223 > Se3 -1.00005e-31 -1.00622e-31 0.326888 > Bi4 0.333333 0.666667 0.365554 > Se5 0.666667 0.333333 0.401864 > Se6 -1.56497e-31 -2.21457e-32 0.448184 > Bi7 0.333333 0.666667 0.484495 > Se8 0.666667 0.333333 0.52316 > Bi9 -9.11352e-32 -1.19934e-31 0.561826 > Se11 0.333333 0.666667 0.598136 > Se22 0.666667 0.333333 0.644456 > Bi33 -1.85963e-31 1.8108e-32 0.680766 > Se44 0.333333 0.666667 0.719432 > Bi55 0.666667 0.333333 0.758098 > Se66 -2.32281e-31 -1.91358e-31 0.794408 > > > > ------------------------------------------------------------------------------ > 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: balabi <ba...@qq...> - 2017-09-07 16:36:27
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<div>Dear developers,</div><div><br></div><div>I have a cif file (show at the end), and I want to find its spacegroup symmetry and symmetrized structure.</div><div id="ntes-pcmail-signature" style="font-family:'微软雅黑'"><font style="padding: 0; margin:0;"> </font>
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</div><div>If I use spglib.<span style="line-height: 1.7;">get_symmetry_dataset, it got me spacegroup 156 and all atoms are inequivalent, like this</span></div><div><span style="line-height: 1.7;"><br></span></div><div><pre style="box-sizing: border-box; overflow: auto; line-height: inherit; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; white-space: pre-wrap; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);">'choice': '',
'equivalent_atoms': array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14], dtype=int32),
'hall': 'P 3 -2"',
'hall_number': 446,
'international': 'P3m1',
'number': 156,</pre><pre style="box-sizing: border-box; overflow: auto; line-height: inherit; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; white-space: pre-wrap; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);"><br></pre><pre style="box-sizing: border-box; overflow: auto; line-height: inherit; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; white-space: pre-wrap; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);">However, if I use ISOCIF <a href="http://stokes.byu.edu/iso/isocif.php" _src="http://stokes.byu.edu/iso/isocif.php" style="font-family: 微软雅黑; line-height: 1.7;">http://stokes.byu.edu/iso/isocif.php</a> . I can find the spacegroup is 164 and there 8 inequivalent atoms.</pre><pre style="box-sizing: border-box; overflow: auto; line-height: inherit; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; white-space: pre-wrap; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);">I also tried pymatgen's pymatgen.symmetry.analyzer.SpacegroupAnalyzer, it also give 164 spacegroup.</pre><pre style="box-sizing: border-box; overflow: auto; line-height: inherit; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; white-space: pre-wrap; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);"><br></pre><pre style="box-sizing: border-box; overflow: auto; line-height: inherit; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; white-space: pre-wrap; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);">So I am wondering whether there is a bug?</pre><pre style="box-sizing: border-box; overflow: auto; line-height: inherit; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; white-space: pre-wrap; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);"><br></pre><pre style="box-sizing: border-box; overflow: auto; line-height: inherit; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; white-space: pre-wrap; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);">best regards</pre><pre style="box-sizing: border-box; overflow: auto; line-height: inherit; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; white-space: pre-wrap; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);">-----------------------------------</pre><pre style="box-sizing: border-box; overflow: auto; line-height: inherit; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; white-space: pre-wrap; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);">below is cif file</pre><pre style="box-sizing: border-box; overflow: auto; line-height: inherit; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; white-space: pre-wrap; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);"><br></pre><pre style="box-sizing: border-box; overflow: auto; word-break: break-all; word-wrap: break-word; border: 0px; border-radius: 0px; vertical-align: baseline; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);"><span style="white-space: pre-wrap;">data_global
_cell_length_a 4.138
_cell_length_b 4.138
_cell_length_c 48.64
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 120
_symmetry_space_group_name_H-M 'P -1'
loop_
_symmetry_equiv_pos_as_xyz
'x,y,z'
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Se1 0.333333 0.666667 0.251912
Bi2 0.666667 0.333333 0.288223
Se3 -1.00005e-31 -1.00622e-31 0.326888
Bi4 0.333333 0.666667 0.365554
Se5 0.666667 0.333333 0.401864
Se6 -1.56497e-31 -2.21457e-32 0.448184
Bi7 0.333333 0.666667 0.484495
Se8 0.666667 0.333333 0.52316
Bi9 -9.11352e-32 -1.19934e-31 0.561826
Se11 0.333333 0.666667 0.598136
Se22 0.666667 0.333333 0.644456
Bi33 -1.85963e-31 1.8108e-32 0.680766
Se44 0.333333 0.666667 0.719432
Bi55 0.666667 0.333333 0.758098
Se66 -2.32281e-31 -1.91358e-31 0.794408</span><span style="line-height: inherit; white-space: pre-wrap;">
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From: Atsushi T. <atz...@gm...> - 2017-08-18 03:08:00
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Hi, Maybe it is worth to see and try spacegroup utility in Elk package if you haven't seen it, http://elk.sourceforge.net/ Togo On Thu, Aug 17, 2017 at 11:43 PM, Atsushi Togo <atz...@gm...> wrote: >> Yes but here the lattice is the same in both cell. >> The atom of one cell are a subset of the atoms of the other cell, which >> exclude the possible translation. > > The following is the result of representations for your two cells. I > see there is not internal pure translation for both cells. The > difference of the translation parts comes from the difference of > location of origin shifts. This is all I know. > > {'rotations': array([[[ 1, 0, 0], > [ 0, 1, 0], > [ 0, 0, 1]], > > [[-1, 0, 0], > [ 0, -1, 0], > [ 0, 0, -1]], > > [[ 0, 1, 0], > [ 1, 0, 0], > [ 0, 0, -1]], > > [[ 0, -1, 0], > [-1, 0, 0], > [ 0, 0, 1]]], dtype=int32), 'translations': array([[ 0. , > 0. , 0. ], > [ 0.34, 0.66, 0.72], > [ 0.34, 0.66, 0.22], > [ 1. , 1. , 0.5 ]]), 'equivalent_atoms': array([0, 0], dtype=int32)} > > > {'rotations': array([[[ 1, 0, 0], > [ 0, 1, 0], > [ 0, 0, 1]], > > [[-1, 0, 0], > [ 0, -1, 0], > [ 0, 0, -1]], > > [[ 0, 1, 0], > [ 1, 0, 0], > [ 0, 0, -1]], > > [[ 0, -1, 0], > [-1, 0, 0], > [ 0, 0, 1]]], dtype=int32), 'translations': array([[ > 0.00000000e+00, 0.00000000e+00, 0.00000000e+00], > [ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00], > [ 1.38777878e-17, 0.00000000e+00, 5.00000000e-01], > [ 1.38777878e-17, 0.00000000e+00, 5.00000000e-01]]), > 'equivalent_atoms': array([0, 0, 0, 0], dtype=int32)} > >> This is the full point of what I am trying to understand: >> How can spglib can find the same spacegroup and at the same time different >> symmetry operations for the same lattice? > > Because the coordinates of atoms. Have you studied crystallography > before? If not, please find somebody else who knows it around you and > give the same question. This is not the matter of spglib, but I think > about the basic knowledge on crystallography. > > Togo > > >> This seems to be incompatible to me, but maybe you have a nice explanation >> for it. >> >> Nicolas >> >> >> On 08/17/2017 04:21 PM, Atsushi Togo wrote: >>> >>> What I can guess is >>> 1. lattice translation >>> 2. choice >>> >>> Togo >>> >>> On Thu, Aug 17, 2017 at 11:14 PM, Nicolas Tancogne-Dejean >>> <nic...@mp...> wrote: >>>> >>>> The result of the routine spg_get_symmetry >>>> >>>> Nicolas >>>> >>>> >>>> On 08/17/2017 04:12 PM, Atsushi Togo wrote: >>>> >>>> Can you explain more detail about your definition of the word 'symmetry'? >>>> >>>> Togo >>>> >>>> On Thu, Aug 17, 2017 at 10:56 PM, Nicolas Tancogne-Dejean >>>> <nic...@mp...> wrote: >>>> >>>> Hi, >>>> >>>> But if the spacegroups are the same, why the symmetries returned by >>>> spglib >>>> are different? >>>> Note that I do not use python, but the Fortran interface. >>>> >>>> Nicolas >>>> >>>> >>>> On 08/17/2017 10:52 AM, Atsushi Togo wrote: >>>> >>>> Hi, >>>> >>>> I got 15 for both. I cross-checked using findsym and I got 15 for both. >>>> I'm glad if you give the test in python script from next time as follows. >>>> >>>> import spglib >>>> >>>> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >>>> [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >>>> [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] >>>> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], >>>> [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] >>>> numbers = [1, 1] >>>> cell = (lattice, points, numbers) >>>> print(spglib.get_spacegroup(cell)) >>>> >>>> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >>>> [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >>>> [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] >>>> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], >>>> [ 9.8000000000E-01, 3.2000000000E-01, 3.9000000000E-01], >>>> [ 6.8000000000E-01, 2.0000000000E-02, 8.9000000000E-01], >>>> [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] >>>> numbers = [1, 1, 1, 1] >>>> cell = (lattice, points, numbers) >>>> print(spglib.get_spacegroup(cell)) >>>> >>>> Togo >>>> >>>> On Thu, Aug 17, 2017 at 5:42 PM, Nicolas Tancogne-Dejean >>>> <nic...@mp...> wrote: >>>> >>>> Hi, >>>> >>>> Lattice vectors are stored in rows. >>>> >>>> Nicolas >>>> >>>> >>>> >>>> On 08/17/2017 10:36 AM, Atsushi Togo wrote: >>>> >>>> Lattice vectors are column vectors or row vectors? >>>> >>>> Togo >>>> >>>> On Thu, Aug 17, 2017 at 5:15 PM, Nicolas Tancogne-Dejean >>>> <nic...@mp...> wrote: >>>> >>>> Hi, >>>> >>>> Please find below the definition of two cells, generated by Abinit as >>>> being >>>> spacegroup 9 and 15. >>>> I got from spglib that the spacegroup number in both cases is 15. >>>> >>>> The symmetries returns by spglib are however exactly the same as given >>>> by >>>> Abinit. >>>> >>>> Thanks in advance for your help. >>>> Nicolas >>>> >>>> Cell 1: >>>> >>>> %LatticeParameters >>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >>>> % >>>> %LatticeVectors >>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >>>> % >>>> %ReducedCoordinates >>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >>>> % >>>> >>>> >>>> Cell 2: >>>> >>>> %LatticeParameters >>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >>>> % >>>> %LatticeVectors >>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >>>> % >>>> %ReducedCoordinates >>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >>>> "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01 >>>> "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01 >>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >>>> % >>>> >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 >>>> >>>> >>>> -- >>>> Nicolas Tancogne-Dejean >>>> >>>> Post-doctoral Researcher, >>>> Theory Department, >>>> Max Planck Institute for the Structure and Dynamics of Matter >>>> >>>> Bldg. 99 (CFEL) >>>> Luruper Chaussee 149 >>>> 22761 Hamburg >>>> Phone: + 49 (0) 40 8998-8322 >>>> >>>> >>>> -- >>>> Nicolas Tancogne-Dejean >>>> >>>> Post-doctoral Researcher, >>>> Theory Department, >>>> Max Planck Institute for the Structure and Dynamics of Matter >>>> >>>> Bldg. 99 (CFEL) >>>> Luruper Chaussee 149 >>>> 22761 Hamburg >>>> Phone: + 49 (0) 40 8998-8322 >>>> >>>> >>>> >>>> >>>> -- >>>> Nicolas Tancogne-Dejean >>>> >>>> Post-doctoral Researcher, >>>> Theory Department, >>>> Max Planck Institute for the Structure and Dynamics of Matter >>>> >>>> Bldg. 99 (CFEL) >>>> Luruper Chaussee 149 >>>> 22761 Hamburg >>>> Phone: + 49 (0) 40 8998-8322 >>> >>> >>> >> >> -- >> Nicolas Tancogne-Dejean >> >> Post-doctoral Researcher, >> Theory Department, >> Max Planck Institute for the Structure and Dynamics of Matter >> >> Bldg. 99 (CFEL) >> Luruper Chaussee 149 >> 22761 Hamburg >> Phone: + 49 (0) 40 8998-8322 >> > > > > -- > 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... |
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From: Atsushi T. <atz...@gm...> - 2017-08-17 14:43:17
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> Yes but here the lattice is the same in both cell.
> The atom of one cell are a subset of the atoms of the other cell, which
> exclude the possible translation.
The following is the result of representations for your two cells. I
see there is not internal pure translation for both cells. The
difference of the translation parts comes from the difference of
location of origin shifts. This is all I know.
{'rotations': array([[[ 1, 0, 0],
[ 0, 1, 0],
[ 0, 0, 1]],
[[-1, 0, 0],
[ 0, -1, 0],
[ 0, 0, -1]],
[[ 0, 1, 0],
[ 1, 0, 0],
[ 0, 0, -1]],
[[ 0, -1, 0],
[-1, 0, 0],
[ 0, 0, 1]]], dtype=int32), 'translations': array([[ 0. ,
0. , 0. ],
[ 0.34, 0.66, 0.72],
[ 0.34, 0.66, 0.22],
[ 1. , 1. , 0.5 ]]), 'equivalent_atoms': array([0, 0], dtype=int32)}
{'rotations': array([[[ 1, 0, 0],
[ 0, 1, 0],
[ 0, 0, 1]],
[[-1, 0, 0],
[ 0, -1, 0],
[ 0, 0, -1]],
[[ 0, 1, 0],
[ 1, 0, 0],
[ 0, 0, -1]],
[[ 0, -1, 0],
[-1, 0, 0],
[ 0, 0, 1]]], dtype=int32), 'translations': array([[
0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ 1.38777878e-17, 0.00000000e+00, 5.00000000e-01],
[ 1.38777878e-17, 0.00000000e+00, 5.00000000e-01]]),
'equivalent_atoms': array([0, 0, 0, 0], dtype=int32)}
> This is the full point of what I am trying to understand:
> How can spglib can find the same spacegroup and at the same time different
> symmetry operations for the same lattice?
Because the coordinates of atoms. Have you studied crystallography
before? If not, please find somebody else who knows it around you and
give the same question. This is not the matter of spglib, but I think
about the basic knowledge on crystallography.
Togo
> This seems to be incompatible to me, but maybe you have a nice explanation
> for it.
>
> Nicolas
>
>
> On 08/17/2017 04:21 PM, Atsushi Togo wrote:
>>
>> What I can guess is
>> 1. lattice translation
>> 2. choice
>>
>> Togo
>>
>> On Thu, Aug 17, 2017 at 11:14 PM, Nicolas Tancogne-Dejean
>> <nic...@mp...> wrote:
>>>
>>> The result of the routine spg_get_symmetry
>>>
>>> Nicolas
>>>
>>>
>>> On 08/17/2017 04:12 PM, Atsushi Togo wrote:
>>>
>>> Can you explain more detail about your definition of the word 'symmetry'?
>>>
>>> Togo
>>>
>>> On Thu, Aug 17, 2017 at 10:56 PM, Nicolas Tancogne-Dejean
>>> <nic...@mp...> wrote:
>>>
>>> Hi,
>>>
>>> But if the spacegroups are the same, why the symmetries returned by
>>> spglib
>>> are different?
>>> Note that I do not use python, but the Fortran interface.
>>>
>>> Nicolas
>>>
>>>
>>> On 08/17/2017 10:52 AM, Atsushi Togo wrote:
>>>
>>> Hi,
>>>
>>> I got 15 for both. I cross-checked using findsym and I got 15 for both.
>>> I'm glad if you give the test in python script from next time as follows.
>>>
>>> import spglib
>>>
>>> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
>>> [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
>>> [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]]
>>> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01],
>>> [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]]
>>> numbers = [1, 1]
>>> cell = (lattice, points, numbers)
>>> print(spglib.get_spacegroup(cell))
>>>
>>> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
>>> [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
>>> [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]]
>>> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01],
>>> [ 9.8000000000E-01, 3.2000000000E-01, 3.9000000000E-01],
>>> [ 6.8000000000E-01, 2.0000000000E-02, 8.9000000000E-01],
>>> [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]]
>>> numbers = [1, 1, 1, 1]
>>> cell = (lattice, points, numbers)
>>> print(spglib.get_spacegroup(cell))
>>>
>>> Togo
>>>
>>> On Thu, Aug 17, 2017 at 5:42 PM, Nicolas Tancogne-Dejean
>>> <nic...@mp...> wrote:
>>>
>>> Hi,
>>>
>>> Lattice vectors are stored in rows.
>>>
>>> Nicolas
>>>
>>>
>>>
>>> On 08/17/2017 10:36 AM, Atsushi Togo wrote:
>>>
>>> Lattice vectors are column vectors or row vectors?
>>>
>>> Togo
>>>
>>> On Thu, Aug 17, 2017 at 5:15 PM, Nicolas Tancogne-Dejean
>>> <nic...@mp...> wrote:
>>>
>>> Hi,
>>>
>>> Please find below the definition of two cells, generated by Abinit as
>>> being
>>> spacegroup 9 and 15.
>>> I got from spglib that the spacegroup number in both cases is 15.
>>>
>>> The symmetries returns by spglib are however exactly the same as given
>>> by
>>> Abinit.
>>>
>>> Thanks in advance for your help.
>>> Nicolas
>>>
>>> Cell 1:
>>>
>>> %LatticeParameters
>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00
>>> %
>>> %LatticeVectors
>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00
>>> %
>>> %ReducedCoordinates
>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01
>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01
>>> %
>>>
>>>
>>> Cell 2:
>>>
>>> %LatticeParameters
>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00
>>> %
>>> %LatticeVectors
>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00
>>> %
>>> %ReducedCoordinates
>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01
>>> "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01
>>> "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01
>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01
>>> %
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>>
>>>
>>> --
>>> Nicolas Tancogne-Dejean
>>>
>>> Post-doctoral Researcher,
>>> Theory Department,
>>> Max Planck Institute for the Structure and Dynamics of Matter
>>>
>>> Bldg. 99 (CFEL)
>>> Luruper Chaussee 149
>>> 22761 Hamburg
>>> Phone: + 49 (0) 40 8998-8322
>>>
>>>
>>> --
>>> Nicolas Tancogne-Dejean
>>>
>>> Post-doctoral Researcher,
>>> Theory Department,
>>> Max Planck Institute for the Structure and Dynamics of Matter
>>>
>>> Bldg. 99 (CFEL)
>>> Luruper Chaussee 149
>>> 22761 Hamburg
>>> Phone: + 49 (0) 40 8998-8322
>>>
>>>
>>>
>>>
>>> --
>>> Nicolas Tancogne-Dejean
>>>
>>> Post-doctoral Researcher,
>>> Theory Department,
>>> Max Planck Institute for the Structure and Dynamics of Matter
>>>
>>> Bldg. 99 (CFEL)
>>> Luruper Chaussee 149
>>> 22761 Hamburg
>>> Phone: + 49 (0) 40 8998-8322
>>
>>
>>
>
> --
> Nicolas Tancogne-Dejean
>
> Post-doctoral Researcher,
> Theory Department,
> Max Planck Institute for the Structure and Dynamics of Matter
>
> Bldg. 99 (CFEL)
> Luruper Chaussee 149
> 22761 Hamburg
> Phone: + 49 (0) 40 8998-8322
>
--
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...
|
|
From: Nicolas Tancogne-D. <nic...@mp...> - 2017-08-17 14:26:14
|
Yes but here the lattice is the same in both cell. The atom of one cell are a subset of the atoms of the other cell, which exclude the possible translation. This is the full point of what I am trying to understand: How can spglib can find the same spacegroup and at the same time different symmetry operations for the same lattice? This seems to be incompatible to me, but maybe you have a nice explanation for it. Nicolas On 08/17/2017 04:21 PM, Atsushi Togo wrote: > What I can guess is > 1. lattice translation > 2. choice > > Togo > > On Thu, Aug 17, 2017 at 11:14 PM, Nicolas Tancogne-Dejean > <nic...@mp...> wrote: >> The result of the routine spg_get_symmetry >> >> Nicolas >> >> >> On 08/17/2017 04:12 PM, Atsushi Togo wrote: >> >> Can you explain more detail about your definition of the word 'symmetry'? >> >> Togo >> >> On Thu, Aug 17, 2017 at 10:56 PM, Nicolas Tancogne-Dejean >> <nic...@mp...> wrote: >> >> Hi, >> >> But if the spacegroups are the same, why the symmetries returned by spglib >> are different? >> Note that I do not use python, but the Fortran interface. >> >> Nicolas >> >> >> On 08/17/2017 10:52 AM, Atsushi Togo wrote: >> >> Hi, >> >> I got 15 for both. I cross-checked using findsym and I got 15 for both. >> I'm glad if you give the test in python script from next time as follows. >> >> import spglib >> >> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >> [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >> [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] >> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], >> [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] >> numbers = [1, 1] >> cell = (lattice, points, numbers) >> print(spglib.get_spacegroup(cell)) >> >> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >> [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >> [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] >> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], >> [ 9.8000000000E-01, 3.2000000000E-01, 3.9000000000E-01], >> [ 6.8000000000E-01, 2.0000000000E-02, 8.9000000000E-01], >> [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] >> numbers = [1, 1, 1, 1] >> cell = (lattice, points, numbers) >> print(spglib.get_spacegroup(cell)) >> >> Togo >> >> On Thu, Aug 17, 2017 at 5:42 PM, Nicolas Tancogne-Dejean >> <nic...@mp...> wrote: >> >> Hi, >> >> Lattice vectors are stored in rows. >> >> Nicolas >> >> >> >> On 08/17/2017 10:36 AM, Atsushi Togo wrote: >> >> Lattice vectors are column vectors or row vectors? >> >> Togo >> >> On Thu, Aug 17, 2017 at 5:15 PM, Nicolas Tancogne-Dejean >> <nic...@mp...> wrote: >> >> Hi, >> >> Please find below the definition of two cells, generated by Abinit as >> being >> spacegroup 9 and 15. >> I got from spglib that the spacegroup number in both cases is 15. >> >> The symmetries returns by spglib are however exactly the same as given >> by >> Abinit. >> >> Thanks in advance for your help. >> Nicolas >> >> Cell 1: >> >> %LatticeParameters >> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >> % >> %LatticeVectors >> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >> % >> %ReducedCoordinates >> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >> % >> >> >> Cell 2: >> >> %LatticeParameters >> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >> % >> %LatticeVectors >> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >> % >> %ReducedCoordinates >> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >> "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01 >> "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01 >> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >> % >> >> >> >> >> ------------------------------------------------------------------------------ >> 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 >> >> >> -- >> Nicolas Tancogne-Dejean >> >> Post-doctoral Researcher, >> Theory Department, >> Max Planck Institute for the Structure and Dynamics of Matter >> >> Bldg. 99 (CFEL) >> Luruper Chaussee 149 >> 22761 Hamburg >> Phone: + 49 (0) 40 8998-8322 >> >> >> -- >> Nicolas Tancogne-Dejean >> >> Post-doctoral Researcher, >> Theory Department, >> Max Planck Institute for the Structure and Dynamics of Matter >> >> Bldg. 99 (CFEL) >> Luruper Chaussee 149 >> 22761 Hamburg >> Phone: + 49 (0) 40 8998-8322 >> >> >> >> >> -- >> Nicolas Tancogne-Dejean >> >> Post-doctoral Researcher, >> Theory Department, >> Max Planck Institute for the Structure and Dynamics of Matter >> >> Bldg. 99 (CFEL) >> Luruper Chaussee 149 >> 22761 Hamburg >> Phone: + 49 (0) 40 8998-8322 > > -- Nicolas Tancogne-Dejean Post-doctoral Researcher, Theory Department, Max Planck Institute for the Structure and Dynamics of Matter Bldg. 99 (CFEL) Luruper Chaussee 149 22761 Hamburg Phone: + 49 (0) 40 8998-8322 |
|
From: Atsushi T. <atz...@gm...> - 2017-08-17 14:22:01
|
What I can guess is 1. lattice translation 2. choice Togo On Thu, Aug 17, 2017 at 11:14 PM, Nicolas Tancogne-Dejean <nic...@mp...> wrote: > The result of the routine spg_get_symmetry > > Nicolas > > > On 08/17/2017 04:12 PM, Atsushi Togo wrote: > > Can you explain more detail about your definition of the word 'symmetry'? > > Togo > > On Thu, Aug 17, 2017 at 10:56 PM, Nicolas Tancogne-Dejean > <nic...@mp...> wrote: > > Hi, > > But if the spacegroups are the same, why the symmetries returned by spglib > are different? > Note that I do not use python, but the Fortran interface. > > Nicolas > > > On 08/17/2017 10:52 AM, Atsushi Togo wrote: > > Hi, > > I got 15 for both. I cross-checked using findsym and I got 15 for both. > I'm glad if you give the test in python script from next time as follows. > > import spglib > > lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], > [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], > [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] > points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], > [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] > numbers = [1, 1] > cell = (lattice, points, numbers) > print(spglib.get_spacegroup(cell)) > > lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], > [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], > [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] > points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], > [ 9.8000000000E-01, 3.2000000000E-01, 3.9000000000E-01], > [ 6.8000000000E-01, 2.0000000000E-02, 8.9000000000E-01], > [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] > numbers = [1, 1, 1, 1] > cell = (lattice, points, numbers) > print(spglib.get_spacegroup(cell)) > > Togo > > On Thu, Aug 17, 2017 at 5:42 PM, Nicolas Tancogne-Dejean > <nic...@mp...> wrote: > > Hi, > > Lattice vectors are stored in rows. > > Nicolas > > > > On 08/17/2017 10:36 AM, Atsushi Togo wrote: > > Lattice vectors are column vectors or row vectors? > > Togo > > On Thu, Aug 17, 2017 at 5:15 PM, Nicolas Tancogne-Dejean > <nic...@mp...> wrote: > > Hi, > > Please find below the definition of two cells, generated by Abinit as > being > spacegroup 9 and 15. > I got from spglib that the spacegroup number in both cases is 15. > > The symmetries returns by spglib are however exactly the same as given > by > Abinit. > > Thanks in advance for your help. > Nicolas > > Cell 1: > > %LatticeParameters > 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 > % > %LatticeVectors > 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 > -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 > 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 > % > %ReducedCoordinates > "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 > "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 > % > > > Cell 2: > > %LatticeParameters > 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 > % > %LatticeVectors > 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 > -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 > 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 > % > %ReducedCoordinates > "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 > "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01 > "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01 > "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 > % > > > > > ------------------------------------------------------------------------------ > 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 > > > -- > Nicolas Tancogne-Dejean > > Post-doctoral Researcher, > Theory Department, > Max Planck Institute for the Structure and Dynamics of Matter > > Bldg. 99 (CFEL) > Luruper Chaussee 149 > 22761 Hamburg > Phone: + 49 (0) 40 8998-8322 > > > -- > Nicolas Tancogne-Dejean > > Post-doctoral Researcher, > Theory Department, > Max Planck Institute for the Structure and Dynamics of Matter > > Bldg. 99 (CFEL) > Luruper Chaussee 149 > 22761 Hamburg > Phone: + 49 (0) 40 8998-8322 > > > > > -- > Nicolas Tancogne-Dejean > > Post-doctoral Researcher, > Theory Department, > Max Planck Institute for the Structure and Dynamics of Matter > > Bldg. 99 (CFEL) > Luruper Chaussee 149 > 22761 Hamburg > Phone: + 49 (0) 40 8998-8322 -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
|
From: Nicolas Tancogne-D. <nic...@mp...> - 2017-08-17 14:14:12
|
The result of the routine|**spg_get_symmetry| |Nicolas| ||*|| <https://atztogo.github.io/spglib/api.html#id5>* On 08/17/2017 04:12 PM, Atsushi Togo wrote: > Can you explain more detail about your definition of the word 'symmetry'? > > Togo > > On Thu, Aug 17, 2017 at 10:56 PM, Nicolas Tancogne-Dejean > <nic...@mp...> wrote: >> Hi, >> >> But if the spacegroups are the same, why the symmetries returned by spglib >> are different? >> Note that I do not use python, but the Fortran interface. >> >> Nicolas >> >> >> On 08/17/2017 10:52 AM, Atsushi Togo wrote: >>> Hi, >>> >>> I got 15 for both. I cross-checked using findsym and I got 15 for both. >>> I'm glad if you give the test in python script from next time as follows. >>> >>> import spglib >>> >>> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >>> [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >>> [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] >>> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], >>> [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] >>> numbers = [1, 1] >>> cell = (lattice, points, numbers) >>> print(spglib.get_spacegroup(cell)) >>> >>> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >>> [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >>> [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] >>> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], >>> [ 9.8000000000E-01, 3.2000000000E-01, 3.9000000000E-01], >>> [ 6.8000000000E-01, 2.0000000000E-02, 8.9000000000E-01], >>> [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] >>> numbers = [1, 1, 1, 1] >>> cell = (lattice, points, numbers) >>> print(spglib.get_spacegroup(cell)) >>> >>> Togo >>> >>> On Thu, Aug 17, 2017 at 5:42 PM, Nicolas Tancogne-Dejean >>> <nic...@mp...> wrote: >>>> Hi, >>>> >>>> Lattice vectors are stored in rows. >>>> >>>> Nicolas >>>> >>>> >>>> >>>> On 08/17/2017 10:36 AM, Atsushi Togo wrote: >>>>> Lattice vectors are column vectors or row vectors? >>>>> >>>>> Togo >>>>> >>>>> On Thu, Aug 17, 2017 at 5:15 PM, Nicolas Tancogne-Dejean >>>>> <nic...@mp...> wrote: >>>>>> Hi, >>>>>> >>>>>> Please find below the definition of two cells, generated by Abinit as >>>>>> being >>>>>> spacegroup 9 and 15. >>>>>> I got from spglib that the spacegroup number in both cases is 15. >>>>>> >>>>>> The symmetries returns by spglib are however exactly the same as given >>>>>> by >>>>>> Abinit. >>>>>> >>>>>> Thanks in advance for your help. >>>>>> Nicolas >>>>>> >>>>>> Cell 1: >>>>>> >>>>>> %LatticeParameters >>>>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >>>>>> % >>>>>> %LatticeVectors >>>>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >>>>>> % >>>>>> %ReducedCoordinates >>>>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >>>>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >>>>>> % >>>>>> >>>>>> >>>>>> Cell 2: >>>>>> >>>>>> %LatticeParameters >>>>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >>>>>> % >>>>>> %LatticeVectors >>>>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >>>>>> % >>>>>> %ReducedCoordinates >>>>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >>>>>> "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01 >>>>>> "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01 >>>>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >>>>>> % >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> 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 >>>>> >>>>> >>>> -- >>>> Nicolas Tancogne-Dejean >>>> >>>> Post-doctoral Researcher, >>>> Theory Department, >>>> Max Planck Institute for the Structure and Dynamics of Matter >>>> >>>> Bldg. 99 (CFEL) >>>> Luruper Chaussee 149 >>>> 22761 Hamburg >>>> Phone: + 49 (0) 40 8998-8322 >>>> >>> >> -- >> Nicolas Tancogne-Dejean >> >> Post-doctoral Researcher, >> Theory Department, >> Max Planck Institute for the Structure and Dynamics of Matter >> >> Bldg. 99 (CFEL) >> Luruper Chaussee 149 >> 22761 Hamburg >> Phone: + 49 (0) 40 8998-8322 >> > > -- Nicolas Tancogne-Dejean Post-doctoral Researcher, Theory Department, Max Planck Institute for the Structure and Dynamics of Matter Bldg. 99 (CFEL) Luruper Chaussee 149 22761 Hamburg Phone: + 49 (0) 40 8998-8322 |
|
From: Atsushi T. <atz...@gm...> - 2017-08-17 14:12:32
|
Can you explain more detail about your definition of the word 'symmetry'? Togo On Thu, Aug 17, 2017 at 10:56 PM, Nicolas Tancogne-Dejean <nic...@mp...> wrote: > Hi, > > But if the spacegroups are the same, why the symmetries returned by spglib > are different? > Note that I do not use python, but the Fortran interface. > > Nicolas > > > On 08/17/2017 10:52 AM, Atsushi Togo wrote: >> >> Hi, >> >> I got 15 for both. I cross-checked using findsym and I got 15 for both. >> I'm glad if you give the test in python script from next time as follows. >> >> import spglib >> >> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >> [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >> [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] >> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], >> [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] >> numbers = [1, 1] >> cell = (lattice, points, numbers) >> print(spglib.get_spacegroup(cell)) >> >> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >> [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], >> [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] >> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], >> [ 9.8000000000E-01, 3.2000000000E-01, 3.9000000000E-01], >> [ 6.8000000000E-01, 2.0000000000E-02, 8.9000000000E-01], >> [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] >> numbers = [1, 1, 1, 1] >> cell = (lattice, points, numbers) >> print(spglib.get_spacegroup(cell)) >> >> Togo >> >> On Thu, Aug 17, 2017 at 5:42 PM, Nicolas Tancogne-Dejean >> <nic...@mp...> wrote: >>> >>> Hi, >>> >>> Lattice vectors are stored in rows. >>> >>> Nicolas >>> >>> >>> >>> On 08/17/2017 10:36 AM, Atsushi Togo wrote: >>>> >>>> Lattice vectors are column vectors or row vectors? >>>> >>>> Togo >>>> >>>> On Thu, Aug 17, 2017 at 5:15 PM, Nicolas Tancogne-Dejean >>>> <nic...@mp...> wrote: >>>>> >>>>> Hi, >>>>> >>>>> Please find below the definition of two cells, generated by Abinit as >>>>> being >>>>> spacegroup 9 and 15. >>>>> I got from spglib that the spacegroup number in both cases is 15. >>>>> >>>>> The symmetries returns by spglib are however exactly the same as given >>>>> by >>>>> Abinit. >>>>> >>>>> Thanks in advance for your help. >>>>> Nicolas >>>>> >>>>> Cell 1: >>>>> >>>>> %LatticeParameters >>>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >>>>> % >>>>> %LatticeVectors >>>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >>>>> % >>>>> %ReducedCoordinates >>>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >>>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >>>>> % >>>>> >>>>> >>>>> Cell 2: >>>>> >>>>> %LatticeParameters >>>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >>>>> % >>>>> %LatticeVectors >>>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >>>>> % >>>>> %ReducedCoordinates >>>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >>>>> "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01 >>>>> "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01 >>>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >>>>> % >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> 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 >>>> >>>> >>>> >>> -- >>> Nicolas Tancogne-Dejean >>> >>> Post-doctoral Researcher, >>> Theory Department, >>> Max Planck Institute for the Structure and Dynamics of Matter >>> >>> Bldg. 99 (CFEL) >>> Luruper Chaussee 149 >>> 22761 Hamburg >>> Phone: + 49 (0) 40 8998-8322 >>> >> >> > > -- > Nicolas Tancogne-Dejean > > Post-doctoral Researcher, > Theory Department, > Max Planck Institute for the Structure and Dynamics of Matter > > Bldg. 99 (CFEL) > Luruper Chaussee 149 > 22761 Hamburg > Phone: + 49 (0) 40 8998-8322 > -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
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From: Nicolas Tancogne-D. <nic...@mp...> - 2017-08-17 13:56:37
|
Hi, But if the spacegroups are the same, why the symmetries returned by spglib are different? Note that I do not use python, but the Fortran interface. Nicolas On 08/17/2017 10:52 AM, Atsushi Togo wrote: > Hi, > > I got 15 for both. I cross-checked using findsym and I got 15 for both. > I'm glad if you give the test in python script from next time as follows. > > import spglib > > lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], > [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], > [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] > points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], > [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] > numbers = [1, 1] > cell = (lattice, points, numbers) > print(spglib.get_spacegroup(cell)) > > lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], > [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00], > [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]] > points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01], > [ 9.8000000000E-01, 3.2000000000E-01, 3.9000000000E-01], > [ 6.8000000000E-01, 2.0000000000E-02, 8.9000000000E-01], > [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]] > numbers = [1, 1, 1, 1] > cell = (lattice, points, numbers) > print(spglib.get_spacegroup(cell)) > > Togo > > On Thu, Aug 17, 2017 at 5:42 PM, Nicolas Tancogne-Dejean > <nic...@mp...> wrote: >> Hi, >> >> Lattice vectors are stored in rows. >> >> Nicolas >> >> >> >> On 08/17/2017 10:36 AM, Atsushi Togo wrote: >>> Lattice vectors are column vectors or row vectors? >>> >>> Togo >>> >>> On Thu, Aug 17, 2017 at 5:15 PM, Nicolas Tancogne-Dejean >>> <nic...@mp...> wrote: >>>> Hi, >>>> >>>> Please find below the definition of two cells, generated by Abinit as >>>> being >>>> spacegroup 9 and 15. >>>> I got from spglib that the spacegroup number in both cases is 15. >>>> >>>> The symmetries returns by spglib are however exactly the same as given by >>>> Abinit. >>>> >>>> Thanks in advance for your help. >>>> Nicolas >>>> >>>> Cell 1: >>>> >>>> %LatticeParameters >>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >>>> % >>>> %LatticeVectors >>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >>>> % >>>> %ReducedCoordinates >>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >>>> % >>>> >>>> >>>> Cell 2: >>>> >>>> %LatticeParameters >>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >>>> % >>>> %LatticeVectors >>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >>>> % >>>> %ReducedCoordinates >>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >>>> "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01 >>>> "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01 >>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >>>> % >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 >>> >>> >> -- >> Nicolas Tancogne-Dejean >> >> Post-doctoral Researcher, >> Theory Department, >> Max Planck Institute for the Structure and Dynamics of Matter >> >> Bldg. 99 (CFEL) >> Luruper Chaussee 149 >> 22761 Hamburg >> Phone: + 49 (0) 40 8998-8322 >> > > -- Nicolas Tancogne-Dejean Post-doctoral Researcher, Theory Department, Max Planck Institute for the Structure and Dynamics of Matter Bldg. 99 (CFEL) Luruper Chaussee 149 22761 Hamburg Phone: + 49 (0) 40 8998-8322 |
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From: Nicolas Tancogne-D. <nic...@mp...> - 2017-08-17 09:02:57
|
Hi, Please find below the definition of two cells, generated by Abinit as being spacegroup 9 and 15. I got from spglib that the spacegroup number in both cases is 15. The symmetries returns by spglib are however exactly the same as given by Abinit. Thanks in advance for your help. Nicolas Cell 1: %LatticeParameters 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 % %LatticeVectors 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 % %ReducedCoordinates "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 % Cell 2: %LatticeParameters 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 % %LatticeVectors 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 % %ReducedCoordinates "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01 "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01 "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 % |
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From: Nicolas Tancogne-D. <nic...@mp...> - 2017-08-17 09:02:49
|
Hi, Please find below the definition of two cells, generated by Abinit as being spacegroup 9 and 15. I got from spglib that the spacegroup number in both cases is 15. The symmetries returns by spglib are however exactly the same as given by Abinit. Thanks in advance for your help. Nicolas Cell 1: %LatticeParameters 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 % %LatticeVectors 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 % %ReducedCoordinates "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 % Cell 2: %LatticeParameters 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 % %LatticeVectors 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 % %ReducedCoordinates "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01 "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01 "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 % |
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From: Atsushi T. <atz...@gm...> - 2017-08-17 08:53:04
|
Hi,
I got 15 for both. I cross-checked using findsym and I got 15 for both.
I'm glad if you give the test in python script from next time as follows.
import spglib
lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
[-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
[ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]]
points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01],
[ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]]
numbers = [1, 1]
cell = (lattice, points, numbers)
print(spglib.get_spacegroup(cell))
lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
[-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
[ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]]
points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01],
[ 9.8000000000E-01, 3.2000000000E-01, 3.9000000000E-01],
[ 6.8000000000E-01, 2.0000000000E-02, 8.9000000000E-01],
[ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]]
numbers = [1, 1, 1, 1]
cell = (lattice, points, numbers)
print(spglib.get_spacegroup(cell))
Togo
On Thu, Aug 17, 2017 at 5:42 PM, Nicolas Tancogne-Dejean
<nic...@mp...> wrote:
> Hi,
>
> Lattice vectors are stored in rows.
>
> Nicolas
>
>
>
> On 08/17/2017 10:36 AM, Atsushi Togo wrote:
>>
>> Lattice vectors are column vectors or row vectors?
>>
>> Togo
>>
>> On Thu, Aug 17, 2017 at 5:15 PM, Nicolas Tancogne-Dejean
>> <nic...@mp...> wrote:
>>>
>>> Hi,
>>>
>>> Please find below the definition of two cells, generated by Abinit as
>>> being
>>> spacegroup 9 and 15.
>>> I got from spglib that the spacegroup number in both cases is 15.
>>>
>>> The symmetries returns by spglib are however exactly the same as given by
>>> Abinit.
>>>
>>> Thanks in advance for your help.
>>> Nicolas
>>>
>>> Cell 1:
>>>
>>> %LatticeParameters
>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00
>>> %
>>> %LatticeVectors
>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00
>>> %
>>> %ReducedCoordinates
>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01
>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01
>>> %
>>>
>>>
>>> Cell 2:
>>>
>>> %LatticeParameters
>>> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00
>>> %
>>> %LatticeVectors
>>> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00
>>> %
>>> %ReducedCoordinates
>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01
>>> "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01
>>> "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01
>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01
>>> %
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>
>>
>>
>
> --
> Nicolas Tancogne-Dejean
>
> Post-doctoral Researcher,
> Theory Department,
> Max Planck Institute for the Structure and Dynamics of Matter
>
> Bldg. 99 (CFEL)
> Luruper Chaussee 149
> 22761 Hamburg
> Phone: + 49 (0) 40 8998-8322
>
--
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...
|
|
From: Nicolas Tancogne-D. <nic...@mp...> - 2017-08-17 08:42:53
|
Hi, Lattice vectors are stored in rows. Nicolas On 08/17/2017 10:36 AM, Atsushi Togo wrote: > Lattice vectors are column vectors or row vectors? > > Togo > > On Thu, Aug 17, 2017 at 5:15 PM, Nicolas Tancogne-Dejean > <nic...@mp...> wrote: >> Hi, >> >> Please find below the definition of two cells, generated by Abinit as being >> spacegroup 9 and 15. >> I got from spglib that the spacegroup number in both cases is 15. >> >> The symmetries returns by spglib are however exactly the same as given by >> Abinit. >> >> Thanks in advance for your help. >> Nicolas >> >> Cell 1: >> >> %LatticeParameters >> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >> % >> %LatticeVectors >> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >> % >> %ReducedCoordinates >> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >> % >> >> >> Cell 2: >> >> %LatticeParameters >> 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 >> % >> %LatticeVectors >> 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >> -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 >> 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 >> % >> %ReducedCoordinates >> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 >> "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01 >> "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01 >> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 >> % >> >> >> ------------------------------------------------------------------------------ >> 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 > > -- Nicolas Tancogne-Dejean Post-doctoral Researcher, Theory Department, Max Planck Institute for the Structure and Dynamics of Matter Bldg. 99 (CFEL) Luruper Chaussee 149 22761 Hamburg Phone: + 49 (0) 40 8998-8322 |
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From: Atsushi T. <atz...@gm...> - 2017-08-17 08:37:03
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Lattice vectors are column vectors or row vectors? Togo On Thu, Aug 17, 2017 at 5:15 PM, Nicolas Tancogne-Dejean <nic...@mp...> wrote: > Hi, > > Please find below the definition of two cells, generated by Abinit as being > spacegroup 9 and 15. > I got from spglib that the spacegroup number in both cases is 15. > > The symmetries returns by spglib are however exactly the same as given by > Abinit. > > Thanks in advance for your help. > Nicolas > > Cell 1: > > %LatticeParameters > 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 > % > %LatticeVectors > 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 > -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 > 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 > % > %ReducedCoordinates > "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 > "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 > % > > > Cell 2: > > %LatticeParameters > 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 > % > %LatticeVectors > 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 > -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 > 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 > % > %ReducedCoordinates > "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 > "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01 > "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01 > "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 > % > > > ------------------------------------------------------------------------------ > 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: Nicolas Tancogne-D. <nic...@mp...> - 2017-08-17 08:33:49
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Hi, Please find below the definition of two cells, generated by Abinit as being spacegroup 9 and 15. I got from spglib that the spacegroup number in both cases is 15. The symmetries returns by spglib are however exactly the same as given by Abinit. Thanks in advance for your help. Nicolas Cell 1: %LatticeParameters 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 % %LatticeVectors 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 % %ReducedCoordinates "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 % Cell 2: %LatticeParameters 1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00 % %LatticeVectors 3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00 1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00 % %ReducedCoordinates "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01 "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01 "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01 "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01 % |
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From: Atsushi T. <atz...@gm...> - 2017-07-07 03:43:58
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Many words are already reserved in crystallography. For example, "basis" means roughly speaking lattice for you. If you want to know the words, you can watch International tables for crystallography A. Then, what are the following words? - exact input cell - exact lattice - origin - copy What is your input and what is your desired output? I can't get it. If you really want me to understand, you can even use mathematical notations than using many abstract words. Togo On Fri, Jul 7, 2017 at 12:12 PM, Vyas Ramasubramani <vya...@gm...> wrote: > Here are the relevant data for the cell that I used (I didn't round it in > case that is helpful for you, sorry for the mess). > > lattice: [[1.0849707126617432, 0.0, 0.0], > [-1.0101166481035762e-05, 1.0850275754928589, 0.0], > [0.00016498863988090304, -4.959173747920431e-05, > 1.0849953889846802]] > > positions: [[ 0.25729885, 0.20069639, -0.44741878], > [-0.22380581, -0.29395782, 0.06201724]] > > numbers: [1,1] > > In case your question is just regarding my question being poorly phrased, > I'll try to clarify. What I referred to as the basis are just the positions. > In general, I could take any particle and apply the space group operations, > and I would get out a structure that has a copy of that particle at each > site dictated by those operations. However, that precise set of output > positions would depend on the position of the initial particle to which I > applied the operations. What I want to do, though, is use the output of > spglib to reproduce the exact input cell I originally fed in. > > As I understand it, spglib applies the transformation matrix and the origin > shift to transform the input cell into some unique frame in which it > determines the space group. My hope was that if I simply placed a particle > at the origin, applied the space group operations, and then subtracted the > origin shift and multiplied by the transformation matrix, I would get back > the exact lattice and positions that I fed into spglib. Should that work? I > have not been able to make it work, but I could very well be doing something > wrong. > > On Wed, Jul 5, 2017 at 3:37 AM, Atsushi Togo <atz...@gm...> wrote: >> >> Hi, >> >> I need a bit more detailed information what you mean to answer. For >> example, what are lattice, basis, centred and exact positions? >> >> Togo >> >> On Wed, Jul 5, 2017 at 3:27 AM, Vyas Ramasubramani >> <vya...@gm...> wrote: >> > Hey everyone, >> > >> > I was wondering if there was any way to extract information about the >> > particular vector corresponding to a structure using spglib. By the >> > particular vector, I mean the (x, y, z) vector to which the space group >> > operations are applied in order to generate the positions. By providing >> > a >> > lattice and a basis to spglib, I can get back the space group, but I am >> > wondering if there is a simple way to also get the vector that would >> > generate the exact positions I provided (perhaps rotated into a >> > different >> > basis or centered at a different origin as per spglib's internal >> > representations). I have been trying to back it out of the standardized >> > cell >> > constructed by spglib without success, so any thoughts would be >> > appreciated. >> > >> > Thanks! >> > Vyas >> > >> > >> > ------------------------------------------------------------------------------ >> > 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... |
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From: Vyas R. <vya...@gm...> - 2017-07-07 03:13:07
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Here are the relevant data for the cell that I used (I didn't round it in
case that is helpful for you, sorry for the mess).
lattice: [[1.0849707126617432, 0.0, 0.0],
[-1.0101166481035762e-05, 1.0850275754928589, 0.0],
[0.00016498863988090304, -4.959173747920431e-05,
1.0849953889846802]]
positions: [[ 0.25729885, 0.20069639, -0.44741878],
[-0.22380581, -0.29395782, 0.06201724]]
numbers: [1,1]
In case your question is just regarding my question being poorly phrased,
I'll try to clarify. What I referred to as the basis are just the
positions. In general, I could take any particle and apply the space group
operations, and I would get out a structure that has a copy of that
particle at each site dictated by those operations. However, that precise
set of output positions would depend on the position of the initial
particle to which I applied the operations. What I want to do, though, is
use the output of spglib to reproduce the exact input cell I originally fed
in.
As I understand it, spglib applies the transformation matrix and the origin
shift to transform the input cell into some unique frame in which it
determines the space group. My hope was that if I simply placed a particle
at the origin, applied the space group operations, and then subtracted the
origin shift and multiplied by the transformation matrix, I would get back
the exact lattice and positions that I fed into spglib. Should that work? I
have not been able to make it work, but I could very well be doing
something wrong.
On Wed, Jul 5, 2017 at 3:37 AM, Atsushi Togo <atz...@gm...> wrote:
> Hi,
>
> I need a bit more detailed information what you mean to answer. For
> example, what are lattice, basis, centred and exact positions?
>
> Togo
>
> On Wed, Jul 5, 2017 at 3:27 AM, Vyas Ramasubramani
> <vya...@gm...> wrote:
> > Hey everyone,
> >
> > I was wondering if there was any way to extract information about the
> > particular vector corresponding to a structure using spglib. By the
> > particular vector, I mean the (x, y, z) vector to which the space group
> > operations are applied in order to generate the positions. By providing a
> > lattice and a basis to spglib, I can get back the space group, but I am
> > wondering if there is a simple way to also get the vector that would
> > generate the exact positions I provided (perhaps rotated into a different
> > basis or centered at a different origin as per spglib's internal
> > representations). I have been trying to back it out of the standardized
> cell
> > constructed by spglib without success, so any thoughts would be
> appreciated.
> >
> > Thanks!
> > Vyas
> >
> > ------------------------------------------------------------
> ------------------
> > 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
>
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From: Atsushi T. <atz...@gm...> - 2017-07-05 07:38:00
|
Hi, I need a bit more detailed information what you mean to answer. For example, what are lattice, basis, centred and exact positions? Togo On Wed, Jul 5, 2017 at 3:27 AM, Vyas Ramasubramani <vya...@gm...> wrote: > Hey everyone, > > I was wondering if there was any way to extract information about the > particular vector corresponding to a structure using spglib. By the > particular vector, I mean the (x, y, z) vector to which the space group > operations are applied in order to generate the positions. By providing a > lattice and a basis to spglib, I can get back the space group, but I am > wondering if there is a simple way to also get the vector that would > generate the exact positions I provided (perhaps rotated into a different > basis or centered at a different origin as per spglib's internal > representations). I have been trying to back it out of the standardized cell > constructed by spglib without success, so any thoughts would be appreciated. > > Thanks! > Vyas > > ------------------------------------------------------------------------------ > 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: Vyas R. <vya...@gm...> - 2017-07-04 18:27:41
|
Hey everyone, I was wondering if there was any way to extract information about the particular vector corresponding to a structure using spglib. By the particular vector, I mean the (x, y, z) vector to which the space group operations are applied in order to generate the positions. By providing a lattice and a basis to spglib, I can get back the space group, but I am wondering if there is a simple way to also get the vector that would generate the exact positions I provided (perhaps rotated into a different basis or centered at a different origin as per spglib's internal representations). I have been trying to back it out of the standardized cell constructed by spglib without success, so any thoughts would be appreciated. Thanks! Vyas |
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From: Albert Bartok-P. <apb...@gm...> - 2017-05-18 09:35:33
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Hi all, I would like to use spg_find_primitive() and I am wondering if there is a simple method in the API to get the mapping between corresponding atoms in the original cell and the generated primitive cell. Thanks in advance. Kind regards, Albert |
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From: Tianshi W. <ts...@ud...> - 2017-05-12 21:24:36
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Dear users, Please evaluate whether the following measure works: 1. I calculate on a mesh 100x100x100 instead of 500x500x500. 2. Filter data to get both reducible and irreducible kpoints with coordinates between (-0.15, 0.15) instead of (-0.03, 0.03). 3. Divide all the kpoints by 5. The Brillouin area goes to (-0.03, 0.03), and density is the same as 500x500x500. Thank you very much for your help! Tianshi From: Tianshi Wang [mailto:ts...@ud...] Sent: Friday, May 12, 2017 5:00 PM To: 'spg...@li...' <spg...@li...> Subject: Large mesh problem Dear spglib users, I am dealing with a very large mesh (500x500x500), but I only care a very small region near gamma, e.g. (-0.03, 0.03) for three coordinates. I am trying to find the reducible points for the small region and the mapping relation between irreducible and reducible points. I tried to use Spglib for the full Brillouin zone, but the code crashed for overwhelming data. Is there a way I can do it? Thank you very much! Tianshi Wang Graduate student in materials science, University of Delaware, US |
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From: Tianshi W. <ts...@ud...> - 2017-05-12 21:00:42
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Dear spglib users, I am dealing with a very large mesh (500x500x500), but I only care a very small region near gamma, e.g. (-0.03, 0.03) for three coordinates. I am trying to find the reducible points for the small region and the mapping relation between irreducible and reducible points. I tried to use Spglib for the full Brillouin zone, but the code crashed for overwhelming data. Is there a way I can do it? Thank you very much! Tianshi Wang Graduate student in materials science, University of Delaware, US |
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From: hüsnü k. <hus...@gm...> - 2017-03-09 08:06:15
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