Segmentation fault at line 194 in tests/mulliken.py

[rwexler]

Encountered a seg fault at line 194 in mulliken.py:

python -m pdb mulliken.py 
> /Users/robertwexler/hb/hotbit/lib/python/hotbit/test/mulliken.py(1)<module>()
-> from ase import *
(Pdb) until 194
/Users/robertwexler/hb/hotbit/lib/python/box/misc.py:50: LinAlgWarning: Ill-conditioned matrix (rcond=1.73652e-17): result may not be accurate.
  c=solve(A,b)
/Users/robertwexler/hb/hotbit/lib/python/box/misc.py:50: LinAlgWarning: Ill-conditioned matrix (rcond=3.55489e-25): result may not be accurate.
  c=solve(A,b)
/Users/robertwexler/hb/hotbit/lib/python/box/misc.py:50: LinAlgWarning: Ill-conditioned matrix (rcond=1.03818e-17): result may not be accurate.
  c=solve(A,b)
/Users/robertwexler/hb/hotbit/lib/python/box/misc.py:50: LinAlgWarning: Ill-conditioned matrix (rcond=7.80523e-18): result may not be accurate.
  c=solve(A,b)
/Users/robertwexler/hb/hotbit/lib/python/box/misc.py:50: LinAlgWarning: Ill-conditioned matrix (rcond=2.24815e-26): result may not be accurate.
  c=solve(A,b)
/Users/robertwexler/hb/hotbit/lib/python/box/misc.py:50: LinAlgWarning: Ill-conditioned matrix (rcond=9.19242e-25): result may not be accurate.
  c=solve(A,b)
> /Users/robertwexler/hb/hotbit/lib/python/hotbit/test/mulliken.py(194)<module>()
-> atoms.get_potential_energy()
(Pdb) n
Segmentation fault: 11

Here's the line in the source code:

183 #
184 #   BONDING ANALYSIS
185 #
186 
187 #
188 #   Mayer bond order
189 #
190 if True:
191     atoms = graphene(4,4,1.42)
192     calc = Hotbit(SCC=False,kpts=(8,8,1),txt='-',**default_param)
193     atoms.set_calculator(calc)
194     atoms.get_potential_energy()
195     assert abs(calc.get_mayer_bond_order(1,2)-1.24155188722)<eps
196     assert abs(calc.get_atom_energy(0)-6.95260830265)<eps
197     assert abs(calc.get_atom_and_bond_energy(0)--9.62628777865)<eps
198     assert abs(calc.get_promotion_energy(0)-6.95260830265)<eps
199     assert abs(calc.get_bond_energy(1,2)--12.0027553172)<eps
200 
201     #print 'graphene'
202     #print 'A_C:',calc.get_atom_energy(0)
203     #print 'AB_C:',calc.get_atom_and_bond_energy(0)
204     #print 'prom_C',calc.get_promotion_energy(0)
205     #print 'B_CC:',calc.get_bond_energy(1,2)

Didn't have an issue with the preceding calls to atoms.get_potential_energy() though.

My specs:
Python 3.7.6 | packaged by conda-forge | (default, Mar 23 2020, 22:45:16)
ASE 3.19.1
macOS Catalina, Version 10.15.3

Please let me know if you need any other information. Thanks in advance for your help!

Best,
Rob

[pekkosk]

Hmm... segfaults are awful. Is there something strange related to graphene here? I would first try modifying the structure.