Re: [Spglib-users] problem with spg_get_ir_reciprocal_mesh
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Re: [Spglib-users] problem with spg_get_ir_reciprocal_mesh
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From: Atsushi T. <atz...@gm...> - 2016-12-12 23:26:34
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Hi,
I confirmed your results in spglib. Spglib outputs is wrong.
I implemented supposing mesh doesn't break symmetry. In this case,
algorithm with integers can handle dense mesh, e.g. 100x100x100 mesh is
easily handled.
Anyway spglib results are clearly wrong. To avoid this and to implement an
algorithm to obtain the similar results by CASTEP that is as fast as
current spglib routine together with keeping the user interface, I need
some time to implement it. I show work-around in the last part of the
test-code below, which uses least common multiple.
Togo
----------test-code----------
#!/usr/bin/env python
import spglib
lattice = [[ 2.9306368570142554, 0.0000000000000000, 0.0000000000000000],
[-1.4653184285071277, 2.5380059674413284, 0.0000000000000000],
[ 0.0000000000000000, 0.0000000000000000, 4.6381396667889572]]
numbers = [1, 1]
points = [[0.6666666666666665, 0.3333333333333333, 0.7500000000000000],
[0.3333333333333334, 0.6666666666666667, 0.2500000000000000]]
cell = (lattice, points, numbers)
print("-----------")
mesh = [3, 3, 1]
mapping, grid = spglib.get_ir_reciprocal_mesh(mesh, cell, is_shift=[0, 0,
0])
for m, g in zip(mapping, grid):
print(("%2d " * 4) % (g[0], g[1], g[2], m))
print("-----------")
mesh = [3, 5, 1]
mapping, grid = spglib.get_ir_reciprocal_mesh(mesh, cell, is_shift=[0, 0,
0])
for m, g in zip(mapping, grid):
print(("%2d " * 4) % (g[0], g[1], g[2], m))
print("-----------")
mesh = [15, 15, 1]
mapping, grid = spglib.get_ir_reciprocal_mesh(mesh, cell, is_shift=[0, 0,
0])
import numpy as np
red_grid = np.array([(g, m) for g, m in zip(grid, mapping) if (g % [5, 3,
1] == [0, 0, 0]).all()])
for g, m in red_grid:
print(("%2d " * 4) % (g[0], g[1], g[2], m))
for g, m in red_grid:
print(("%f " * 3 + "%d") % (g[0] / 15.0, g[1] / 15.0, g[2], m))
Togo
On Tue, Dec 13, 2016 at 4:17 AM, Corsetti, Fabiano <
fab...@im...> wrote:
> Corsetti, Fabiano has shared OneDrive for Business files with you. To view
> them, click the links below.
>
> <https://imperiallondon-my.sharepoint.com/personal/fc08_ic_ac_uk/Documents/Email%20attachments/input_data.txt>
> input_data.txt
> <https://imperiallondon-my.sharepoint.com/personal/fc08_ic_ac_uk/Documents/Email%20attachments/input_data.txt>
>
> <https://imperiallondon-my.sharepoint.com/personal/fc08_ic_ac_uk/Documents/Email%20attachments/input_data.txt>
>
>
> <https://imperiallondon-my.sharepoint.com/personal/fc08_ic_ac_uk/Documents/Email%20attachments/test(1).f90>
> test(1).f90
> <https://imperiallondon-my.sharepoint.com/personal/fc08_ic_ac_uk/Documents/Email%20attachments/test(1).f90>
>
> <https://imperiallondon-my.sharepoint.com/personal/fc08_ic_ac_uk/Documents/Email%20attachments/test(1).f90>
>
> Dear all,
>
>
> I am having a problem generating the list of irreducible k-points with
> spglib for certain cases.
>
>
> I have written a minimal example to demonstrate this in the attached code
> (it's in Fortran using the spglib_f08.f90 interface). The system is a
> hexagonal unit cell of graphene with two carbon atoms. If I set
> mesh=(3,3,1) and is_shift=(0,0,0), a call to spg_get_ir_reciprocal_mesh
> gives me the expected output:
>
>
> number of irreducible k-points: 3
>
> map:
>
> 0.0000000 0.0000000 0.0000000 0
> 0.3333333 0.0000000 0.0000000 1
> -0.3333333 0.0000000 0.0000000 1
> 0.0000000 0.3333333 0.0000000 1
> 0.3333333 0.3333333 0.0000000 1
> -0.3333333 0.3333333 0.0000000 5
> 0.0000000 -0.3333333 0.0000000 1
> 0.3333333 -0.3333333 0.0000000 5
> -0.3333333 -0.3333333 0.0000000 1
>
> This agrees entirely with the output given by a CASTEP calculation for the
> same system:
>
> -------------------------------
> k-Points For BZ Sampling
> -------------------------------
> MP grid size for SCF calculation is 3 3 1
> with an offset of 0.000 0.000 0.000
> Number of kpoints used = 3
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++
> + Number Fractional coordinates Weight +
> +-----------------------------------------------------+
> + 1 0.000000 -0.333333 0.000000 0.6666667 +
> + 2 0.000000 0.000000 0.000000 0.1111111 +
> + 3 0.333333 -0.333333 0.000000 0.2222222 +
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> However, changing mesh=(3,5,1) now gives me:
>
> number of irreducible k-points: 3
>
> map:
> 0.0000000 0.0000000 0.0000000 0
> 0.3333333 0.0000000 0.0000000 1
> -0.3333333 0.0000000 0.0000000 1
> 0.0000000 0.2000000 0.0000000 1
> 0.3333333 0.2000000 0.0000000 1
> -0.3333333 0.2000000 0.0000000 5
> 0.0000000 0.4000000 0.0000000 1
> 0.3333333 0.4000000 0.0000000 5
> -0.3333333 0.4000000 0.0000000 5
> 0.0000000 -0.4000000 0.0000000 1
> 0.3333333 -0.4000000 0.0000000 5
> -0.3333333 -0.4000000 0.0000000 5
> 0.0000000 -0.2000000 0.0000000 1
> 0.3333333 -0.2000000 0.0000000 5
> -0.3333333 -0.2000000 0.0000000 1
>
> This does not seem to me to be correct, and indeed CASTEP gives a larger
> irreducible wedge:
>
>
> -------------------------------
> k-Points For BZ Sampling
> -------------------------------
> MP grid size for SCF calculation is 3 5 1
> with an offset of 0.000 0.000 0.000
> Number of kpoints used = 8
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++
> + Number Fractional coordinates Weight +
> +-----------------------------------------------------+
> + 1 -0.333333 -0.200000 0.000000 0.1333333 +
> + 2 -0.333333 0.200000 0.000000 0.1333333 +
> + 3 -0.333333 0.400000 0.000000 0.1333333 +
> + 4 0.000000 -0.400000 0.000000 0.1333333 +
> + 5 0.000000 0.000000 0.000000 0.0666667 +
> + 6 0.000000 0.200000 0.000000 0.1333333 +
> + 7 0.333333 0.000000 0.000000 0.1333333 +
> + 8 0.333333 0.400000 0.000000 0.1333333 +
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> Is somebody able to advise me whether this is indeed a bug in spglib, or
> if I have done something wrong? I should also mention that the list of
> symmetry operations found with spglib agree with CASTEP.
>
>
> Many thanks in advance!
>
>
> Kind regards,
>
>
> Fabiano Corsetti
>
>
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>
--
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...
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