[ase-users] Failed ASE Test- ValueError: cannot remove a zero-sized axis from an iterator

[Kim, Grace J]

Hello Everyone,

After fixing my pathways, I still have this error message. Does anyone have an idea on how to fix it? Thank you.

Ag-Cu100.py ... ok
CO2_Au111.py ... ok
COCu111_2.py ... ok
aff.py ... ok
ag.py ... ok
atom.py ... ok
atoms_distance.py ... ok
atoms_get_duplicates.py ... ok
atoms_info_copy.py ... ok
bader.py ... ok
bandgap.py ... ok
bandstructure.py ... ok
basin.py ... ok
build.py ... ok
bulk.py ... ok
c60.py ... ok
center.py ... ok
checkpoint.py ... ok
com.py ... ok
coverage.py ... ok
crystal.py ... ok
db.py ... Running: H
Running: H2O
Running: O2
Running: H2
LBFGS:   0  13:50:26        1.158863       4.4619
LBFGS:   1  13:50:26        1.129374       2.9285
LBFGS:   2  13:50:26        1.072359       0.5614
LBFGS:   3  13:50:26        1.070596       0.0991
LBFGS:   4  13:50:26        1.070541       0.0026
Running: O2
LBFGS:   0  13:50:26        0.922681       3.7034
LBFGS:   1  13:50:26        0.691988       1.9589
LBFGS:   2  13:50:26        0.628304       0.5011
LBFGS:   3  13:50:26        0.624816       0.0669
LBFGS:   4  13:50:26        0.624750       0.0019
Running: Cu
Deleted 1 row
Added 9 key-value pairs (0 pairs updated)
Removed 0 key-value pairs
Added 0 key-value pairs (0 pairs updated)
Removed 3 key-value pairs
Running: H
Running: H2O
Running: O2
Running: H2
LBFGS:   0  13:50:28        1.158863       4.4619
LBFGS:   1  13:50:28        1.129374       2.9285
LBFGS:   2  13:50:28        1.072359       0.5614
LBFGS:   3  13:50:28        1.070596       0.0991
LBFGS:   4  13:50:28        1.070541       0.0026
Running: O2
LBFGS:   0  13:50:29        0.922681       3.7034
LBFGS:   1  13:50:29        0.691988       1.9589
LBFGS:   2  13:50:29        0.628304       0.5011
LBFGS:   3  13:50:29        0.624816       0.0669
LBFGS:   4  13:50:29        0.624750       0.0019
Running: Cu
Deleted 1 row
Added 9 key-value pairs (0 pairs updated)
Removed 0 key-value pairs
Added 0 key-value pairs (0 pairs updated)
Removed 3 key-value pairs
ok
db2.py ... ok
db_web.py ... skipped (no flask module) ok
dependency_gtk.py ... ok
dependency_matplotlib.py ... ok
dihedralconstraint.py ... ok
dimer.py ... ok
dimer_method.py ... ok
distance.py ... ok
distmom.py ... ok
doctests.py ... ok
eam_pot.py ... ok
eam_pot_test.py ... ok
eam_test.py ... ok
emt.py ... ok
emt1.py ... ok
emt2.py ... ok
emt_h3o2m.py ... ok
eos.py ... ok
example.py ... ok
external_force.py ... ok
filter.py ... ok
fire.py ... ok
fix_bond_length_mic.py ... ok
franck_condon.py ... ok
geometry.py ... ok
h2.py ... ok
hcp.py ... ok
hookean.py ... ok
idpp.py ... ok
kpts.py ... ok
langevin.py ... ok
maxwellboltzmann.py ... ok
md.py ... ok
mic.py ... ok
minimahop.py ... ok
mopac.py ... skipped (use --calculators=mopac to enable) ok
n2.py ... ok
neb.py ... ok
neb_tr.py ... ok
neighbor.py ... ok
niggli.py ... ERROR
noncollinear.py ... ok
pourbaix.py ... skipped ok
preconlbfgs.py ... ok
properties.py ... ok
pull.py ... ok
qmmm.py ... ok
quaternions.py ... ok
rattle.py ... ok
repeat_FixAtoms.py ... ok
replay.py ... ok
root_test.py ... ok
rotate.py ... ok
rotate_euler.py ... ok
s22.py ... ok
scaled_positions.py ... ok
scientificpython_bug.py ... skipped (no Scientific module) ok
set_get_angle.py ... ok
set_momenta.py ... ok
singlepointcalc.py ... ok
stm.py ... ok
strain.py ... ok
strain_emt.py ... ok
stress.py ... ok
surface.py ... ok
thermochemistry.py ... ok
things.py ... ok
tip3p.py ... ok
unitcellfilter.py ... ok
unitcellfilter2.py ... ok
units.py ... ok
vacancy.py ... ok
verlet.py ... ok
vib.py ... ok
abinit/abinit_Si.py ... skipped (use --calculators=abinit to enable) ok
abinit/abinit_cmdline.py ... ok
aims/H2O_aims.py ... skipped (use --calculators=aims to enable) ok
aims/aims_cmdline.py ... skipped (use --calculators=aims to enable) ok
calculator/al.py ... ok
calculator/bandgap.py ... ok
calculator/h2.py ... ok
calculator/kd2mp.py ... ok
calculator/traj.py ... ok
castep/castep_interface.py ... skipped (use --calculators=castep to enable) ok
constraints/fixatoms.py ... ok
constraints/fixbonds.py ... ok
constraints/getindices.py ... ok
constraints/setpos.py ... ok
cp2k/cp2k_GeoOpt.py ... skipped ($ASE_CP2K_COMMAND not defined) ok
cp2k/cp2k_H2_LDA.py ... skipped ($ASE_CP2K_COMMAND not defined) ok
cp2k/cp2k_H2_LS.py ... skipped ($ASE_CP2K_COMMAND not defined) ok
cp2k/cp2k_H2_None.py ... skipped ($ASE_CP2K_COMMAND not defined) ok
cp2k/cp2k_H2_PBE.py ... skipped ($ASE_CP2K_COMMAND not defined) ok
cp2k/cp2k_H2_libxc.py ... skipped ($ASE_CP2K_COMMAND not defined) ok
cp2k/cp2k_MD.py ... skipped ($ASE_CP2K_COMMAND not defined) ok
cp2k/cp2k_O2.py ... skipped ($ASE_CP2K_COMMAND not defined) ok
cp2k/cp2k_restart.py ... skipped ($ASE_CP2K_COMMAND not defined) ok
cp2k/cp2k_stress.py ... skipped ($ASE_CP2K_COMMAND not defined) ok
demon/h2o.py ... skipped (use --calculators=demon to enable) ok
dftb/test_simple.py ... skipped (DFTB_COMMAND not defined) ok
dftb/test_tricky.py ... skipped (use --calculators=dftb to enable) ok
elk/Al_rmt.py ... skipped (ELK_SPECIES_PATH not set.) ok
elk/elk_cmdline.py ... skipped (use --calculators=elk to enable) ok
eon/eon_masses.py ... ok
eon/eon_readwrite.py ... ok
exciting/exciting.py ... skipped (no lxml module) ok
fio/abinit.py ... ok
fio/cfg.py ... ok
fio/extxyz.py ... ok
fio/info.py ... ok
fio/magmom.py ... ok
fio/netcdftrajectory.py ... skipped (No NetCDF module available (netCDF4-python, scipy.io.netcdf)) ok
fio/nwchem.py ... skipped (use --calculators=nwchem to enable) ok
fio/oi.py ... ok
fio/oldtraj.py ... ok
fio/res.py ... ok
fio/trajectory.py ... ok
fio/v_sim.py ... ok
fio/vasp_out.py ... ok
fio/xsf_spec.py ... ok
fleur/fleur_cmdline.py ... skipped (use --calculators=fleur to enable) ok
ga/basic_example_create_database.py ... ok
ga/basic_example_main_run.py ... ok
ga/create_database.py ... ok
ga/cutandsplicepairing.py ... ok
ga/database_logic.py ... ok
ga/element_operators.py ... ok
ga/mutations.py ... ok
ga/particle_comparators.py ... ok
ga/particle_operators.py ... ok
ga/standardcomparator.py ... ok
gaussian/gaussian_cmdline.py ... skipped (use --calculators=gaussian to enable) ok
gaussian/h2of.py ... skipped (use --calculators=gaussian to enable) ok
gaussian/water.py ... skipped (use --calculators=gaussian to enable) ok
gpaw/no_spin_and_spin.py ... skipped (no gpaw module) ok
gromacs/test_gromacs.py ... skipped (use --calculators=gromacs to enable) ok
jacapo/jacapo.py ... skipped (no Scientific module) ok
nwchem/nwchem_broken_symmetry.py ... skipped (use --calculators=nwchem to enable) ok
nwchem/nwchem_cmdline.py ... skipped (use --calculators=nwchem to enable) ok
nwchem/nwchem_h3o2m.py ... skipped (use --calculators=nwchem to enable) ok
nwchem/nwchem_spin_symmetry.py ... skipped (use --calculators=nwchem to enable) ok
nwchem/nwchem_strong_levelshift.py ... ok
octopus/big-test.py ... skipped (use --calculators=octopus to enable) ok
octopus/restart-octopus.py ... skipped (use --calculators=octopus to enable) ok
octopus/test-octopus.py ... skipped (use --calculators=octopus to enable) ok
onetep/onetep.py ... skipped (use --calculators=onetep to enable) ok
siesta/siesta.py ... skipped (use --calculators=siesta to enable) ok
turbomole/turbomole_H2.py ... skipped (use --calculators=turbomole to enable) ok
turbomole/turbomole_h3o2m.py ... skipped (use --calculators=turbomole to enable) ok
vasp/vasp_Al_volrelax.py ... skipped (Neither VASP_COMMAND nor VASP_SCRIPT defined) ok
vasp/vasp_co.py ... skipped (Neither VASP_COMMAND nor VASP_SCRIPT defined) ok
vasp/vasp_kpoints.py ... skipped (use --calculators=vasp to enable) ok
vasp/vasp_xc.py ... skipped (use --calculators=vasp to enable) ok
vasp/vasp_xml.py ... skipped (Neither VASP_COMMAND nor VASP_SCRIPT defined) ok
COCu111.py ... ok

======================================================================
ERROR: niggli.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/gjk/Library/Python/2.7/lib/python/site-packages/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/Users/gjk/Library/Python/2.7/lib/python/site-packages/ase/test/niggli.py", line 123, in <module>
    niggli_reduce(conf)
  File "/Users/gjk/Library/Python/2.7/lib/python/site-packages/ase/build/tools.py", line 631, in niggli_reduce
    scpos = np.dot(atoms.get_scaled_positions(), np.linalg.inv(C).T)
  File "/Users/gjk/Library/Python/2.7/lib/python/site-packages/ase/atoms.py", line 1511, in get_scaled_positions
    fractional = np.linalg.solve(self.cell.T, self.positions.T).T
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/linalg/linalg.py", line 380, in solve
    r = gufunc(a, b, signature=signature, extobj=extobj)
ValueError: cannot remove a zero-sized axis from an iterator

----------------------------------------------------------------------
Ran 177 tests in 140.721s

FAILED (errors=1)

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