[gpaw-users] Plotting error

Varadharajan Srinivasan varadharajan.srinivasan at gmail.com
Wed Apr 27 08:46:33 CEST 2016 

Dear Jens,

I modified the script and ran python setup.py install again. The plot looks
like the example online now.
Thanks a lot for your help.

Best,
Vardha.

On Wed, Apr 27, 2016 at 10:02 AM, Varadharajan Srinivasan <
varadharajan.srinivasan at gmail.com> wrote:

> Thanks. I will modify the script accordingly.
>
> Best,
> Vardha.
>
> On Wed, Apr 27, 2016 at 9:53 AM, Jens Jørgen Mortensen <jensj at fysik.dtu.dk
> > wrote:
>
>> 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>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> 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>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 listgpaw-users at listserv.fysik.dtu.dkhttps://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>>
>
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