greschd
commented
3 years ago The reason for this error is that the plot.wcc utility (and the other plot and invariant helpers) work only with surface results, not line results. I guess this could produce a nicer error..
As for inspecting the results of your calculation, since it is a 1D calculation it will have only a single set of WCC, or one sum of WCC. You can access the WCC as
print(result_0.wcc)or the sum of WCC as
print(result_0.pol)I'm not intimately familiar with the GNR paper, but suspect it's a different kind of Z2 invariant to the Kane-Mele one. One possibility is that the sum of WCC is quantized to be either 0 or 0.5, which also produces a Z2 invariant.
ybfu
Hi,
Recently I am using the Z2pack to calculate Z2 invariant for one-dimensional graphene nanoribbons. I chose a literature-reported GNR (7-armchair GNR, Phys. Rev. Lett. 2017, 119, 076401, Z2=1). Before this, I tried the sample calculation for Bi and it is successful. However, when I tried the line calculations for the GNR, there was an error.
Here is the input file:
import os import shutil import subprocess
import matplotlib.pyplot as plt import xml.etree.ElementTree as ET
import z2pack
qedir = "{0}/bin".format(os.getenv('EBROOTQUANTUMESPRESSO')) wandir = "{0}/bin".format(os.getenv('EBROOTWANNIER90'))
mpirun = 'mpirun -np 20 ' pwcmd = mpirun + qedir + '/pw.x ' pw2wancmd = mpirun + qedir + '/pw2wannier90.x ' wancmd = wandir + '/wannier90.x'
z2cmd = ( wancmd + ' 7AGNR -pp;' + pwcmd + '< 7AGNR.nscf.in >& pw.log;' + pw2wancmd + '< 7AGNR.pw2wan.in >& pw2wan.log;' )
if not os.path.exists('./plots'): os.mkdir('./plots') if not os.path.exists('./results'): os.mkdir('./results') if not os.path.exists('./scf'): os.makedirs('./scf') print("Running the scf calculation") shutil.copyfile('input/7AGNR.scf.in', 'scf/7AGNR.scf.in') subprocess.call(pwcmd + ' < 7AGNR.scf.in > scf.out', shell=True, cwd='./scf')
cell = ET.parse('scf/7AGNR.xml').find('output').find('atomic_structure' ).find('cell') unit = cell.get('unit', 'Bohr') lattice = '\n'.join([cell.find(vec).text for vec in ['a1', 'a2', 'a3']])
with open('input/tpl_7AGNR.win', 'r') as f: tpl_7AGNR_win = f.read() with open('input/7AGNR.win', 'w') as f: f.write(tpl_7AGNR_win.format(unit=unit, lattice=lattice))
input_files = [ 'input/' + name for name in ["7AGNR.nscf.in", "7AGNR.pw2wan.in", "7AGNR.win"] ] system = z2pack.fp.System( input_files=input_files, kpt_fct=[z2pack.fp.kpoint.qe, z2pack.fp.kpoint.wannier90_full], kpt_path=["7AGNR.nscf.in", "7AGNR.win"], command=z2cmd, executable='/bin/bash', mmn_path='7AGNR.mmn' )
result_0 = z2pack.line.run( system=system, line=lambda t: [t, 0, 0], save_file='./results/res_0.json', load=True )
fig, ax = plt.subplots(1, 2, sharey=True, figsize=(9, 5)) z2pack.plot.wcc(result_0, axis=ax[0]) plt.savefig('plots/plot.pdf', bbox_inches='tight')
print( 'Z2 topological invariant at kx = 0: {0}'.format( z2pack.invariant.z2(result_0) ) )
+----------------------------------------------------------------------+
INFO: 0 of 1 line convergence criteria fulfilled. INFO: Calculating line for N = 8 INFO: Saving line result to file ./results/res_0.json INFO: 0 of 1 line convergence criteria fulfilled. INFO: Calculating line for N = 10 INFO: Saving line result to file ./results/res_0.json INFO: 0 of 1 line convergence criteria fulfilled. INFO: Calculating line for N = 12 INFO: Saving line result to file ./results/res_0.json INFO: 1 of 1 line convergence criteria fulfilled.
+----------------------------------------------------------------------+ Traceback (most recent call last): File "run.py", line 75, in
z2pack.plot.wcc(result_0, axis=ax[0])
File "</sw/installed/Python/3.7.4-GCCcore-8.3.0/lib/python3.7/site-packages/de corator.py:decorator-gen-30>", line 2, in wcc
File "/home/yfu/.local/lib/python3.7/site-packages/z2pack/plot.py", line 36, i n inner
func(data, axis=axis, **kwargs)
File "/home/yfu/.local/lib/python3.7/site-packages/z2pack/plot.py", line 169, in wcc
_plot_gaps(surface_result, axis=axis, gaps=gaps, gap_settings=gap_settings)
File "/home/yfu/.local/lib/python3.7/site-packages/z2pack/plot.py", line 48, i n _plot_gaps
surface_result.t,
File "/home/yfu/.local/lib/python3.7/site-packages/z2pack/_result.py", line 35 , in getattr
return getattr(self.data, name)
File "/home/yfu/.local/lib/python3.7/site-packages/fsc/locker/_locker.py", lin e 45, in inner
return fct(self, key)
File "/home/yfu/.local/lib/python3.7/site-packages/z2pack/line/_data.py", line 70, in getattr
return super().getattribute(name)
AttributeError: 'OverlapLineData' object has no attribute 't'
It mentioned that an attribute reference or assignment fails. Looks like the 't' is not defined. Another strange thing is that the PosCheck is passed but no other detailed information. There is no error in the scf and nscf calculation tasks. I also checked the internet but didn't find a similar error. That is strange.