[gpaw-users] Plotting error
Jens Jørgen Mortensen
jensj at fysik.dtu.dk
Wed Apr 27 06:08:57 CEST 2016
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.
>>
>>
>>
>> _______________________________________________
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>
>
>
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