[Spglib-users] spacegroup is not analyzed correctly
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[Spglib-users] spacegroup is not analyzed correctly
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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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