[gpaw-users] Plotting error
Varadharajan Srinivasan
varadharajan.srinivasan at gmail.com
Wed Apr 27 06:32:06 CEST 2016
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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