[gpaw-users] Plotting error
Jens Jørgen Mortensen
jensj at fysik.dtu.dk
Wed Apr 27 06:23:59 CEST 2016
Den 27-04-2016 kl. 06:19 skrev Varadharajan Srinivasan:
> I was using the development version gpaw-1.0.1b1. Does this also have
> the bug? I will the latest one.
It was fixed here:
https://gitlab.com/gpaw/gpaw/commit/680d003505
Jens Jørgen
>
> Best,
> Vardha.
>
> On Wed, Apr 27, 2016 at 9:38 AM, Jens Jørgen Mortensen
> <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>> wrote:
>
> Den 27-04-2016 kl. 06:00 skrev Varadharajan Srinivasan:
>> Dear Jens,
>>
>> I think I solved the problem. The issue was with the location on
>> latex. I had to do the following to get it to work
>>
>> 1. Make a link for the latex binaries (since in El Capitan
>> /usr/texbin is no longer the path for these).
>> sudo ln -s
>> /Library/TeX/Distributions/.DefaultTeX/Contents/Programs/texbin
>> /Library/TeX/texbin
>> 2. Add the following lines in the python script for plotting :
>>
>> import os
>> os.environ['PATH'] = os.environ['PATH'] + ':/Library/TeX/texbin'
>>
>> With these the script proceeded to give me a png file. However,
>> the spin-dependent colour scheme in the plot is now messed up as
>> compared to the example. I will look into this a little and
>> further and let you know if I continue to have problems.
>
> Unfortunately there is a bug in the spinorbit.py that was in
> GPAW-1.0. Maybe you are being hit by that. Try latest master from
> gitlab.
>
> Jens Jørgen
>
>
>>
>> Best,
>> Vardha.
>>
>> On Tue, Apr 26, 2016 at 10:22 PM, Varadharajan Srinivasan
>> <varadharajan.srinivasan at gmail.com
>> <mailto:varadharajan.srinivasan at gmail.com>> wrote:
>>
>> Dear Jens,
>>
>> I did an upgrade install and still got an error (below).
>>
>> Traceback (most recent call last):
>> File "MoS2_bands_plot.py", line 37, in <module>
>> plt.savefig('MoS2_bands.png')
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/pyplot.py", line
>> 688, in savefig
>> res = fig.savefig(*args, **kwargs)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/figure.py", line
>> 1565, in savefig
>> self.canvas.print_figure(*args, **kwargs)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/backend_bases.py",
>> line 2232, in print_figure
>> **kwargs)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py",
>> line 527, in print_png
>> FigureCanvasAgg.draw(self)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py",
>> line 474, in draw
>> self.figure.draw(self.renderer)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/artist.py", line
>> 61, in draw_wrapper
>> draw(artist, renderer, *args, **kwargs)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/figure.py", line
>> 1159, in draw
>> func(*args)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/artist.py", line
>> 61, in draw_wrapper
>> draw(artist, renderer, *args, **kwargs)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/axes/_base.py",
>> line 2324, in draw
>> a.draw(renderer)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/artist.py", line
>> 61, in draw_wrapper
>> draw(artist, renderer, *args, **kwargs)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/axis.py",
>> line 1108, in draw
>> renderer)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/axis.py",
>> line 1058, in _get_tick_bboxes
>> extent = tick.label1.get_window_extent(renderer)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/text.py",
>> line 961, in get_window_extent
>> bbox, info, descent = self._get_layout(self._renderer)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/text.py",
>> line 352, in _get_layout
>> ismath=False)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py",
>> line 229, in get_text_width_height_descent
>> renderer=self)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/texmanager.py",
>> line 675, in get_text_width_height_descent
>> dvifile = self.make_dvi(tex, fontsize)
>> File
>> "/usr/local/lib/python2.7/site-packages/matplotlib/texmanager.py",
>> line 422, in make_dvi
>> report))
>> RuntimeError: LaTeX was not able to process the following string:
>> 'lp'
>> Here is the full report generated by LaTeX:
>>
>>
>>
>>
>> On Tue, Apr 26, 2016 at 3:54 PM, Jens Jørgen Mortensen
>> <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>> wrote:
>>
>> On 04/26/2016 09:27 AM, Varadharajan Srinivasan via
>> gpaw-users wrote:
>>> Dear all,
>>>
>>> I was trying out a tutorial calculation on WS2 band
>>> structure with spin-orbit coupling. I modified the
>>> system to MoS2 and tried out the python scripts given in
>>> the tutorial. At the plotting stage I get the following
>>> error :
>>
>> What version of matplotlib do you have? You could try to
>> a "pip install -U --user matplotlib" and see if that helps.
>>
>> Jens Jørgen
>>
>>>
>>> plt.savefig('MoS2_bands.png')
>>>
>>> Traceback (most recent call last):
>>> File "<stdin>", line 1, in <module>
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/pyplot.py",
>>> line 688, in savefig
>>> res = fig.savefig(*args, **kwargs)
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/figure.py",
>>> line 1565, in savefig
>>> self.canvas.print_figure(*args, **kwargs)
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/backend_bases.py",
>>> line 2232, in print_figure
>>> **kwargs)
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py",
>>> line 527, in print_png
>>> FigureCanvasAgg.draw(self)
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py",
>>> line 474, in draw
>>> self.figure.draw(self.renderer)
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/artist.py",
>>> line 61, in draw_wrapper
>>> draw(artist, renderer, *args, **kwargs)
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/figure.py",
>>> line 1159, in draw
>>> func(*args)
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/artist.py",
>>> line 61, in draw_wrapper
>>> draw(artist, renderer, *args, **kwargs)
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/axes/_base.py",
>>> line 2324, in draw
>>> a.draw(renderer)
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/artist.py",
>>> line 61, in draw_wrapper
>>> draw(artist, renderer, *args, **kwargs)
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/lines.py",
>>> line 739, in draw
>>> ln_color_rgba = self._get_rgba_ln_color()
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/lines.py",
>>> line 1251, in _get_rgba_ln_color
>>> return colorConverter.to_rgba(self._color, self._alpha)
>>> File
>>> "/usr/local/lib/python2.7/site-packages/matplotlib/colors.py",
>>> line 376, in to_rgba
>>> 'to_rgba: Invalid rgba arg "%s"\n%s' % (str(arg), exc))
>>> ValueError: to_rgba: Invalid rgba arg "0.5"
>>> to_rgb: Invalid rgb arg "0.5"
>>> cannot convert argument to rgb sequence
>>>
>>>
>>> Have I missed installing some libraries? I am working on
>>> a brew-based installation of ase and gpaw on El Capitan
>>> Mac OS X.
>>>
>>> Thanks,
>>> Vardha.
>>>
>>>
>>>
>>> _______________________________________________
>>> gpaw-users mailing list
>>> gpaw-users at listserv.fysik.dtu.dk
>>> <mailto:gpaw-users at listserv.fysik.dtu.dk>
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>
>>
>>
>
>
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