[ase-users] ase-gui related issues
Iyemperumal, Satish Kumar
siyemperumal at wpi.edu
Sun Jul 30 17:08:04 CEST 2017
Hello ASE users,
One of the students in our lab (who is still not approved to join this list yet) was facing some issues post installation of ASE related ase-gui and bond visualization. The details are forwarded.
Could someone give some ideas on this.
Thank you.
Best,
Satish Kumar Iyemperumal
PhD Candidate '18
Department of Chemical Engineering
Worcester Polytechnic Institute
Worcester, MA
________________________________
From: Pham, Thang Duc
Sent: Friday, July 28, 2017 8:40 PM
To: Iyemperumal, Satish Kumar
Subject: V/v: ASE errors
1) Whenever I open ASE, this error pops up (no matter what the input file is):
Traceback (most recent call last):
File "/home/thang/.local/lib/python2.7/site-packages/ase/gui/view.py", line 730, release(self=<ase.gui.gui.GUI instance>, drawing_area=<gtk.DrawingArea object at 0x7f28c21098c0 (GtkDrawingArea at 0x25ad6c0)>, event=<gtk.gdk.Event at 0x7f28c0a93260: GDK_BUTTON_RELEASE x=829.00, y=293.00, button=1>)
if event.time < self.t0 + 200: # 200 ms
d = self.P - self.xy
variables: {'event.time': ('local', 1714293)}
AttributeError: GUI instance has no attribute 't0'
2) When I open an xyz geometry file, I can create the bond (Ctrl + b) normally. However, when I open any POSCAR, this error shows up and I don't see any bonds. The POSCAR file is attached.
Traceback (most recent call last):
File "/home/thang/.local/lib/python2.7/site-packages/ase/gui/view.py", line 346, toggle_show_bonds(self=<ase.gui.gui.GUI instance>, action=<gtk.ToggleAction object at 0x7fd03cb3f690 (GtkToggleAction at 0x24e62b0)>)
def toggle_show_bonds(self, action):
self.set_coordinates()
variables: {'self.set_coordinates': ('local', <bound method GUI.set_coordinates of <ase.gui.gui.GUI instance at 0x7fd03b3d9b90>>)}
File "/home/thang/.local/lib/python2.7/site-packages/ase/gui/view.py", line 58, set_coordinates(self=<ase.gui.gui.GUI instance>, frame=0, focus=None)
self.make_box()
self.bind(frame)
n = self.images.natoms
variables: {'self.bind': ('local', <bound method GUI.bind of <ase.gui.gui.GUI instance at 0x7fd03b3d9b90>>), 'frame': ('local', None)}
File "/home/thang/.local/lib/python2.7/site-packages/ase/gui/view.py", line 215, bind(self=<ase.gui.gui.GUI instance>, frame=0)
i = self.bonds[:n2, 2:].any(1)
self.bonds[n2:, 0] = self.bonds[i, 1]
self.bonds[n2:, 1] = self.bonds[i, 0]
variables: {'i': ('local', array([False, False, False, False, False, True, False, False, False,
False, False, False, False, False, False, False, False, False,
False, False, False, True, False, False, False, False, False,
False, False, False, False, False, True, False, False, False,
False, False, False, False, False, False, False, False, False,
False, False, False, False, False, False, False, False, False,
False, False, False, False, False, False, False, False, False,
False, False, False, True, False, False, True, False, False,
False, False, False, False, False, False, False, False, True,
False, False, True, False, False, False, False, False, False,
False, False, True, False, False, True, False, False, False,
False, False, False, False, False, True, False, False, False,
False, False, False, False, False, False, False, True, False,
False, False, False, False, False, False, False, False, True,
False, False, False, False, False, False, False, False, False,
False, True, True, True, True, False, False, False, False,
False, False, False, False, False, False, False, True, False,
False, False, False, False, False, False, False, False, False,
False, False, False, True, True, True, True, False, False,
False, False, False, True, False, False, False, True, True,
True, False, True, True, True, True, True, True, False,
False, True, False, False, False, True, False, False, True,
True, True, True, False, True, True, True, False, False,
True, False, False, True, False, False, True, True, True,
True, True, True, True, True, True, True, False, True,
True, True], dtype=bool)), 'n2': ('local', 227), 'self.bonds': ('local', array([[ 0, 49, 0,
0, 0],
[ 0, 50, 0,
0, 0],
[ 1, 48, 0,
0, 0],
...,
[4607182418800017408, 4602127357993785218, 4607182418800017408,
4607182418800017408, 4602770729369123861],
[4607182418800017408, 4607182418800017408, 4603138370155031656,
4607182418800017408, 4607182418800017408],
[4603506010940939452, 4607182418800017408, 4607182418800017408,
4603873651726847247, 4607182418800017408]]))}
IndexError: boolean index did not match indexed array along dimension 0; dimension is 282 but corresponding boolean dimension is 227
3) Finally, this is the error when I ran "python -m ase.test":
platform Linux-4.10.0-28-generic-x86_64-with-Ubuntu-16.04-xenial
python-2.7.12 /usr/bin/python
ase-3.11.0 /home/thang/.local/lib/python2.7/site-packages/ase/
numpy-1.13.1 /home/thang/.local/lib/python2.7/site-packages/numpy/
scipy-0.19.1 /home/thang/.local/lib/python2.7/site-packages/scipy/
test-dir /tmp/ase-test-EurVEb
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
basin.py ... ok
build.py ... ok
bulk.py ... ok
center.py ... ok
collection.py ... ok
com.py ... ok
constr_setpos.py ... ok
coverage.py ... ok
crystal.py ... ok
db.py ... Running: H
Running: H2O
Running: O2
Running: H2
LBFGS: 0 10:59:49 1.158864 4.4619
LBFGS: 1 10:59:49 1.129374 2.9285
LBFGS: 2 10:59:49 1.072359 0.5614
LBFGS: 3 10:59:49 1.070596 0.0991
LBFGS: 4 10:59:49 1.070541 0.0026
Running: O2
LBFGS: 0 10:59:49 0.922681 3.7034
LBFGS: 1 10:59:49 0.691988 1.9589
LBFGS: 2 10:59:49 0.628304 0.5011
LBFGS: 3 10:59:49 0.624816 0.0669
LBFGS: 4 10:59:49 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 10:59:52 1.158864 4.4619
LBFGS: 1 10:59:52 1.129374 2.9285
LBFGS: 2 10:59:52 1.072359 0.5614
LBFGS: 3 10:59:52 1.070596 0.0991
LBFGS: 4 10:59:52 1.070541 0.0026
Running: O2
LBFGS: 0 10:59:52 0.922681 3.7034
LBFGS: 1 10:59:52 0.691988 1.9589
LBFGS: 2 10:59:52 0.628304 0.5011
LBFGS: 3 10:59:52 0.624816 0.0669
LBFGS: 4 10:59:52 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
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_test.py ... ok
emt.py ... ok
emt1.py ... ok
emt2.py ... ok
emt_h3o2m.py ... ok
eos.py ... ok
example.py ... ok
filter.py ... ok
fix_bond_length_mic.py ... ok
geometry.py ... ok
h2.py ... ok
hcp.py ... ok
hookean.py ... ok
idpp.py ... ok
maxwellboltzmann.py ... ok
md.py ... ok
mic.py ... ok
minimahop.py ... ok
mopac.py ... skipped ok
n2.py ... ok
neb.py ... ok
neb_tr.py ... ok
neighbor.py ... ok
niggli.py ... ok
noncollinear.py ... ok
pourbaix.py ... skipped ok
properties.py ... ok
pull.py ... ok
qmmm.py ... ok
rattle.py ... ok
repeat_FixAtoms.py ... ok
replay.py ... ok
root_test.py ... ok
rotate.py ... ok
rotate_euler.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
vacancy.py ... ok
verlet.py ... ok
vib.py ... ok
abinit/abinit_Si.py ... skipped ok
abinit/abinit_cmdline.py ... ok
aims/H2O_aims.py ... skipped ok
aims/aims_cmdline.py ... skipped 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 ... ok
dftb/test_simple.py ... skipped ok
dftb/test_tricky.py ... skipped ok
elk/Al_rmt.py ... skipped ok
elk/elk_cmdline.py ... skipped 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/netcdf.py ... /home/thang/.local/lib/python2.7/site-packages/scipy/io/netcdf.py:299: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.)
), category=RuntimeWarning)
ok
fio/netcdftrajectory.py ... skipped ok
fio/nwchem.py ... skipped ok
fio/oi.py ... ERROR
fio/oldtraj.py ... ok
fio/res.py ... ok
fio/trajectory.py ... ok
fio/v_sim.py ... ok
fleur/fleur_cmdline.py ... skipped 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 ok
gaussian/h2of.py ... skipped ok
gaussian/water.py ... skipped ok
gromacs/test_gromacs.py ... skipped ok
jacapo/jacapo.py ... skipped (no Scientific module) ok
nwchem/nwchem_broken_symmetry.py ... ok
nwchem/nwchem_cmdline.py ... skipped ok
nwchem/nwchem_h3o2m.py ... skipped ok
nwchem/nwchem_spin_symmetry.py ... ok
nwchem/nwchem_strong_levelshift.py ... ok
octopus/restart-octopus.py ... skipped ok
octopus/test-octopus.py ... skipped ok
turbomole/turbomole_H2.py ... skipped ok
turbomole/turbomole_h3o2m.py ... skipped ok
vasp/vasp_Al_volrelax.py ... skipped ok
vasp/vasp_co.py ... skipped ok
COCu111.py ... ok
======================================================================
ERROR: fio/oi.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/thang/.local/lib/python2.7/site-packages/ase/test/__init__.py", line 53, in testfile
{'display': self.display})
File "/home/thang/.local/lib/python2.7/site-packages/ase/test/fio/oi.py", line 90, in <module>
write(fname1, atoms, format=format)
File "/home/thang/.local/lib/python2.7/site-packages/ase/io/formats.py", line 252, in write
io.write(fd, images, **kwargs)
File "/home/thang/.local/lib/python2.7/site-packages/ase/io/png.py", line 46, in write_png
PNG(atoms, **parameters).write(filename)
File "/home/thang/.local/lib/python2.7/site-packages/ase/io/eps.py", line 140, in write
self.write_trailer()
File "/home/thang/.local/lib/python2.7/site-packages/ase/io/png.py", line 38, in write_trailer
_png.write_png(x, self.w, self.h, self.filename, 72)
ValueError: Expected 3-dimensional array, got 1
----------------------------------------------------------------------
Ran 138 tests in 72.423s
FAILED (errors=1)
Thank you!
Best,
Thang
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