[gpaw-users] [ase-users] having 'pylab' problem in STM study

Fri Apr 15 15:03:32 CEST 2011

On Fri, 2011-04-15 at 12:02 +0200, sudip chakraborty wrote:
> yeah dateutil is coming from opensuse...i tries with yast..but it
> doesnt work out...should i check with any other version of ASE?
> Also,I tried to install ASE on my mac10.6.6..it has been installed as
> well as numpy,matplotlib...when i want to visualize, it shows pygtk
> problem..

Try to ask on the ASE mailing list - and include the error message you
get.

Jens Jørgen

> Regards
> SC
> 
> On Fri, Apr 15, 2011 at 10:12 AM, Marcin Dulak
> <Marcin.Dulak at fysik.dtu.dk> wrote:
> > Hi,
> >
> > sudip chakraborty wrote:
> >>
> >> I have Linux Suse and dateutil I have is of version 2.0...
> >> my queries are specifcally following:
> >> 1. the script dat i wrote is that correct fully for calculating the stm ?
> >> 2. Can I do  STM as well as NEB as without installing Gpaw with my
> >> ASE-3.41 or I need to install something else?
> >>
> >
> > maybe someone on gpaw-users will answer these two questions
> >>
> >> 3. why the script doesnt work in spite of having numpy,dateutil and
> >> matplotlib ?
> >>  I will be really happy if these will get solved.
> >>
> >
> > does python-dateutil-2.0 come from the openSUSE?
> > Please use the package provided by the distribution, remove the manually
> > installed dateutil and:
> > yast -i python-dateutil
> >
> > Best regards,
> >
> > Marcin
> >>
> >> Thanx in advance...
> >> Regards
> >> SC
> >>
> >> On Thu, Apr 14, 2011 at 5:37 PM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
> >> wrote:
> >>
> >>>
> >>> Hi,
> >>>
> >>> sudip chakraborty wrote:
> >>>
> >>>>
> >>>> Thanx Marcin for the kind reply.I have installed ASE-3.4.1 and I have
> >>>> Python-2.6 and also numpy1.5.1. Do you suggest me to install different
> >>>> version of ASE??can you please elaborate the problem concerning
> >>>> dateutil..
> >>>>
> >>>>
> >>>
> >>> no, i'm saying there is a problem with the python dateutil package.
> >>> The first question is: what is your Linux distribution, the second: if
> >>> there
> >>> are
> >>> dateutil, numpy, etc. packages available for this distribution - please
> >>> use
> >>> them instead of installing by hand
> >>> (i guess you did the latter).
> >>>
> >>> Best regards,
> >>>
> >>> Marcin
> >>>
> >>>>
> >>>> Regards
> >>>> SC
> >>>>
> >>>> On Thu, Apr 14, 2011 at 9:55 AM, Marcin Dulak
> >>>> <Marcin.Dulak at fysik.dtu.dk>
> >>>> wrote:
> >>>>
> >>>>
> >>>>>
> >>>>> Hi,
> >>>>>
> >>>>> it's seems that you have installed dateutil package that requires
> >>>>> python
> >>>>>
> >>>>>>
> >>>>>> =
> >>>>>>
> >>>>>
> >>>>> 3.0 (http://niemeyer.net/python-dateutil), or it's just a bug in
> >>>>> dateutil.
> >>>>> It's always better to use the package that comes with you Linux
> >>>>> distribution, and as a rule to never install packages manually
> >>>>> (from tarballs or python eggs) as root.
> >>>>>
> >>>>> Best regards,
> >>>>>
> >>>>> Marcin
> >>>>>
> >>>>> sudip chakraborty wrote:
> >>>>>
> >>>>>
> >>>>>>
> >>>>>> Hello everybody
> >>>>>>  I am a new user in ASE and it's really optimum according to my
> >>>>>> requirement. I have a question regarding the STM study. For getting
> >>>>>> stm image can we do without having Gpaw code? I have installed ase
> >>>>>> 3.4.1. along with numpy and matplotlib also. But while running the
> >>>>>> following script I am getting some unusual error of pylab. As a
> >>>>>> beginner of Python I am not getting what exactly the problem is. I
> >>>>>> will be reall grateful if somebody can illuminate me in this problem.
> >>>>>>
> >>>>>> 같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같컈y
> >>>>>> script같같같같같같같같같같같같같같같같같같같같같같같�>
> >>>>>> from ase.calculators.test import make_test_dft_calculation
> >>>>>> from ase.dft.stm import STM
> >>>>>> import matplotlib
> >>>>>> import pylab as p
> >>>>>> #from ase.io import view
> >>>>>> from ase.visualize import primiplotter as p
> >>>>>> atoms = make_test_dft_calculation()
> >>>>>> stm = STM(atoms, [0, 1, 2])
> >>>>>> c = stm.get_averaged_current(4.5)
> >>>>>> h = stm.scan(c)
> >>>>>> plot.contourf()
> >>>>>> p.hot()
> >>>>>> p.colorbar()
> >>>>>> p.view()
> >>>>>>
> >>>>>> 같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같캞rror I
> >>>>>> am getting같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같�>
> >>>>>> Traceback (most recent call last):
> >>>>>>  File "stm_line2.py", line 4, in <module>
> >>>>>>  import pylab as p
> >>>>>>  File "/usr/local/lib64/python2.6/site-packages/pylab.py", line 1, in
> >>>>>> <module>
> >>>>>>  from matplotlib.pylab import *
> >>>>>>  File "/usr/local/lib64/python2.6/site-packages/matplotlib/pylab.py",
> >>>>>> line 220, in <module>
> >>>>>>  from matplotlib import mpl  # pulls in most modules
> >>>>>>  File "/usr/local/lib64/python2.6/site-packages/matplotlib/mpl.py",
> >>>>>> line 3, in <module>
> >>>>>>  from matplotlib import axes
> >>>>>>  File "/usr/local/lib64/python2.6/site-packages/matplotlib/axes.py",
> >>>>>> line 19, in <module>
> >>>>>>  import matplotlib.dates as mdates
> >>>>>>  File "/usr/local/lib64/python2.6/site-packages/matplotlib/dates.py",
> >>>>>> line 119, in <module>
> >>>>>>  from dateutil.rrule import rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY,
> >>>>>> \
> >>>>>>  File
> >>>>>>
> >>>>>>
> >>>>>> "/usr/local/lib64/python2.6/site-packages/python_dateutil-2.0-py2.6.egg/dateutil/rrule.py",
> >>>>>> line 13, in <module>
> >>>>>>  import _thread
> >>>>>> ImportError: No module named _thread
> >>>>>> 같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같�>
> >>>>>> cheers
> >>>>>> SC
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> ase-users mailing list
> >>>>>> ase-users at listserv.fysik.dtu.dk
> >>>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>> --
> >>>>> ***********************************
> >>>>>
> >>>>> Marcin Dulak
> >>>>> Technical University of Denmark
> >>>>> Department of Physics
> >>>>> Building 307, Room 229
> >>>>> DK-2800 Kongens Lyngby
> >>>>> Denmark
> >>>>> Tel.: (+45) 4525 3157
> >>>>> Fax.: (+45) 4593 2399
> >>>>> email: Marcin.Dulak at fysik.dtu.dk
> >>>>>
> >>>>> ***********************************
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>> --
> >>> ***********************************
> >>>
> >>> Marcin Dulak
> >>> Technical University of Denmark
> >>> Department of Physics
> >>> Building 307, Room 229
> >>> DK-2800 Kongens Lyngby
> >>> Denmark
> >>> Tel.: (+45) 4525 3157
> >>> Fax.: (+45) 4593 2399
> >>> email: Marcin.Dulak at fysik.dtu.dk
> >>>
> >>> ***********************************
> >>>
> >>>
> >>>
> >>
> >>
> >>
> >>
> >
> > --
> > ***********************************
> >
> > Marcin Dulak
> > Technical University of Denmark
> > Department of Physics
> > Building 307, Room 229
> > DK-2800 Kongens Lyngby
> > Denmark
> > Tel.: (+45) 4525 3157
> > Fax.: (+45) 4593 2399
> > email: Marcin.Dulak at fysik.dtu.dk
> >
> > ***********************************
> >
> >
> 
> 
> 
> -- 
> Sudip Chakraborty
> Post Doctoral Fellow
> Atomistic Modelling Group
> Max-Planck-Institut für Eisenforschung GmbH
> Max-Planck-Straße 1
> 40237 Düsseldorf
>                &
> Lehrstuhl für Anorganische Chemie II
> Organometallics and Materials Chemistry
> Ruhr-Universität Bochum,
> 44780 Bochum
> Germany
> 
> http://electronics.unipune.ac.in/sudip/home.html
> 
> _______________________________________________
> gpaw-users mailing list
> gpaw-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users