Hi all,
I am trying to calculate an electronic band structure and I have encountered the NoneType error. I have read the previous topics on this error on this forum. However, my lattice is monoclinic and the fix described in a previous topic is for an orthorhombic lattice. I was wondering if there was a similar fix for a monoclinic lattice. Here is the trace I get while running abiopen.py 8atomes_bande_nso_GSR.nc --expose -sns=paper:
/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/pymatgen/symmetry/kpath.py:178: UserWarning: The input structure does not match the expected standard primitive! The path can be incorrect. Use at your own risk.
warn(
Traceback (most recent call last):
File "/home/laurent/env/abipy/abipy/bin/abiopen.py", line 387, in <module>
sys.exit(main())
File "/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/monty/functools.py", line 405, in wrapper
sys.exit(main())
File "/home/laurent/env/abipy/abipy/bin/abiopen.py", line 248, in main
abifile = abilab.abiopen(options.filepath)
File "/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/abipy/abilab.py", line 304, in abiopen
return cls.from_file(filepath)
File "/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/abipy/electrons/gsr.py", line 54, in from_file
return cls(filepath)
File "/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/abipy/electrons/gsr.py", line 61, in __init__
self._ebands = r.read_ebands()
File "/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/abipy/electrons/ebands.py", line 4088, in read_ebands
kpoints=self.read_kpoints(),
File "/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/abipy/core/kpoints.py", line 1731, in read_kpoints
kpoint.set_name(structure.findname_in_hsym_stars(kpoint))
File "/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/abipy/core/structure.py", line 1277, in findname_in_hsym_stars
for star in self.hsym_stars:
File "/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/monty/functools.py", line 238, in __get__
value = self.__func(inst)
File "/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/abipy/core/structure.py", line 1244, in hsym_stars
return [kpoint.compute_star(self.abi_spacegroup.fm_symmops) for kpoint in self.hsym_kpoints]
File "/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/monty/functools.py", line 238, in __get__
value = self.__func(inst)
File "/home/laurent/env/abipy/abipy/lib/python3.9/site-packages/abipy/core/structure.py", line 1196, in hsym_kpoints
name2frac_coords = self.hsym_kpath.kpath["kpoints"]
TypeError: 'NoneType' object is not subscriptable
Here is the abinit input file for this structure:
#Lattice structure
natom 18
ntypat 2
typat
1 1 1
1 1 1
1 1 2
2 2 2
2 2 2
2 2 2
znucl 1 6
acell 1.0 1.0 1.0
rprim
4.7810070953 0.0000000000 0.0000000000
-2.3905039020 20.6925001670 0.0000000000
0.0000000000 0.0000000000 37.7945224925
#Atomic positions
xred
0.003496888905 0.006680219294 0.423648762388
0.802206591636 0.609412514628 0.440566658623
0.728514852652 0.461777838700 0.570316020799
0.602596094569 0.204887682300 0.429684193353
0.528890119464 0.057255771013 0.559433388316
0.327628574819 0.659985317890 0.576351112179
0.200992673316 0.406226456631 0.434897378559
0.130109346398 0.260440599544 0.565102894076
0.001222751299 -0.001216026743 0.478944028455
0.936500865592 0.863460952152 0.496203019713
0.798188553909 0.603118946409 0.495787062139
0.730941598930 0.466747953274 0.514964352817
0.600165564128 0.199917934567 0.485035803835
0.532922946714 0.063546948613 0.504212925844
0.394622071373 0.803204491687 0.503796321702
0.329892273811 0.667881792651 0.521055896738
0.198829732388 0.401478935827 0.490237466485
0.132276166694 0.265187004965 0.509762713981
#Definition of the planewave basis set
ecut 45
#Definition of the SCF procedure
nstep 50
#Pseudo potentials
pseudos "/home/laurentm/projects/rrg-cotemich-ac/laurentm/pseudos/H.psp8,/home/laurentm/projects/rrg-cotemich-ac/laurentm/pseudos/C.psp8"
#Band structure calculation
getden_filepath "/home/laurentm/projects/rrg-cotemich-ac/laurentm/8atomes_kpoints_ns/8atomes_kpoints_nso_TIM16_DEN.nc"
tolwfr 1e-20
iscf -2
enunit 1
ndivsm 10
kptopt -4
kptbounds
+0.00000 +0.00000 +0.00000 # $\Gamma$
+0.50663 -0.25000 +0.00000 # X
+0.49337 +0.25000 +0.00000 # X_1
+0.00000 +0.50000 +0.00000 # Y
+0.00000 +0.00000 +0.00000 # $\Gamma$
I have tried to run calculation in another input file but I got the same result while trying to produce the band structure with AbiPy. I’ve also tried to update pymatgen and it didn’t solve the problem.