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.

| \ | \ _ | |) | | | | |) | '_/ \ / / ` | '| | /| || | /| | | () | (| (| | |
|| _, || || \/ __,|| |/ 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 "", line 1, in File "/home/k0171/k017113/deepmd-kit/envs/pyprocar/lib/python3.8/site-packages/pyprocar/scriptFermi2D.py", line 187, in fermi2D fs.st(sx=symm.sx, sy=symm.sy, sz=symm.sz, noarrow=noarrow, spin=spin) File "/home/k0171/k017113/deepmd-kit/envs/pyprocar/lib/python3.8/site-packages/pyprocar/fermisurface/fermisurface.py", line 143, in st bnew.append(griddata((x, y), band, (xnew, ynew), method="cubic")) File "/home/k0171/k017113/.local/lib/python3.8/site-packages/scipy/interpolate/ndgriddata.py", line 264, in griddata ip = CloughTocher2DInterpolator(points, values, fill_value=fill_value, File "interpnd.pyx", line 908, in scipy.interpolate.interpnd.CloughTocher2DInterpolator.init File "qhull.pyx", line 1839, in scipy.spatial.qhull.Delaunay.init File "qhull.pyx", line 355, in scipy.spatial.qhull._Qhull.init scipy.spatial.qhull.QhullError: QH6154 Qhull precision error: Initial simplex is flat (facet 1 is coplanar with the interior point)

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

romerogroup / pyprocar

fermi2d have problem after rotation #72

add one or more points to make the input full dimensional.