romerogroup
fermi2d have problem after rotation
Dear Sir/Madam,
I used pyprocar to plot fermi2d spin texture.
In the beginning, everything works well.
However, after I rotate the structure, some errors came out.
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A Python library for electronic structure pre/post-processing.
Version 5.6.6 created on March 6th, 2022
Please cite: Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.
Developers:
- Francisco Muñoz
- Aldo Romero
- Sobhit Singh
- Uthpala Herath
- Pedram Tavadze
- Eric Bousquet
- Xu He
- Reese Boucher
- Logan Lang
- Freddy Farah
PROCAR repaired. Run with repair=False next time.
file : PROCAR
outcar : OUTCAR
Abinit output : None
atoms : [-1]
orbitals : [-1]
spin comp. : 3
energy : -0.3
fermi energy : None
Rec. basis : None
rot. symmetry : 1
origin (trasl.) : [0, 0, 0]
rotation : [0, 0, 0, 1]
masking thres. : None
save figure : None
st : True
no_arrows : True
Fermi energy found in outcar file = 3.8681
spd shape : (100, 99, 4, 13, 11) [kpoints, bands, spins, atoms+1, orbitals+2]
spd shape : (100, 99, 4, 13, 11) [kpoints, bands, spins, atoms+1, orbitals+2]
spd shape : (100, 99, 4, 13, 11) [kpoints, bands, spins, atoms+1, orbitals+2]
Bands will be shifted by the Fermi energy = 3.8681
Traceback (most recent call last):
File "
While executing: | qhull d Q12 Qz Qt Qc Qbb Options selected for Qhull 2019.1.r 2019/06/21: run-id 305317147 delaunay Q12-allow-wide Qz-infinity-point Qtriangulate Qcoplanar-keep Qbbound-last _pre-merge _zero-centrum Qinterior-keep Pgood _max-width 0.058 Error-roundoff 4e-17 _one-merge 2.8e-16 Visible-distance 8e-17 U-max-coplanar 8e-17 Width-outside 1.6e-16 _wide-facet 4.8e-16 _maxoutside 3.2e-16
The input to qhull appears to be less than 3 dimensional, or a computation has overflowed.
Qhull could not construct a clearly convex simplex from points:
- p50(v4): 0.0032 0.0018 0
- p20(v3): -0.016 -0.009 0.0078
- p90(v2): 0.029 0.016 0.026
- p0(v1): -0.029 -0.016 0.026
The center point is coplanar with a facet, or a vertex is coplanar with a neighboring facet. The maximum round off error for computing distances is 4e-17. The center point, facets and distances to the center point are as follows:
center point -0.003196 -0.001795 0.01502
facet p20 p90 p0 distance= 2.4e-19 facet p50 p90 p0 distance= -6.5e-19 facet p50 p20 p0 distance= -3.7e-18 facet p50 p20 p90 distance= -1.2e-18
These points either have a maximum or minimum x-coordinate, or they maximize the determinant for k coordinates. Trial points are first selected from points that maximize a coordinate.
The min and max coordinates for each dimension are: 0: -0.02876 0.02876 difference= 0.05753 1: -0.01615 0.01615 difference= 0.0323 2: 0 0.02876 difference= 0.02876
If the input should be full dimensional, you have several options that may determine an initial simplex:
- use 'QJ' to joggle the input and make it full dimensional
- use 'QbB' to scale the points to the unit cube
- use 'QR0' to randomly rotate the input for different maximum points
- use 'Qs' to search all points for the initial simplex
- use 'En' to specify a maximum roundoff error less than 4e-17.
- trace execution with 'T3' to see the determinant for each point.
If the input is lower dimensional:
- use 'QJ' to joggle the input and make it full dimensional
- use 'Qbk:0Bk:0' to delete coordinate k from the input. You should pick the coordinate with the least range. The hull will have the correct topology.
- determine the flat containing the points, rotate the points into a coordinate plane, and delete the other coordinates.
- add one or more points to make the input full dimensional.
pyprocar.zip Here is the PROCAR, OUTCAR and POSCAR of the two structures.
The command I used to plot is
pyprocar.fermi2D('PROCAR', outcar='OUTCAR', st=True, energy=0.65, noarrow=True, spin=1, code='vasp')
Every suggestion would be helpful.
Regards
