[ase-users] ase-gui related issues
Jens Jørgen Mortensen
jjmo at dtu.dk
Mon Jul 31 09:32:00 CEST 2017
On 07/30/2017 05:08 PM, Iyemperumal, Satish Kumar via ase-users wrote:
>
> 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.
>
Could you try to install the latest version of ASE (3.14.1) and check if
the issues are still there?
https://wiki.fysik.dtu.dk/ase/install.html
Jens Jørgen
> 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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