this is not (still) mdout file.
(example:
http://ambermd.org/tutorials/basic/tutorial1/files/output_files/polyAT_vac_md1_12Acut.out
)
Hai
On Mon, Feb 1, 2016 at 2:27 PM, Jean-Patrick Francoia <
jeanpatrick.francoia.gmail.com> wrote:
> Sorry, I misunderstood. Here you are (again).
>
>
> Le 01/02/2016 15:52, Jean-Patrick Francoia a écrit :
>
>> Here you are
>>
>> Le 01/02/2016 15:36, Jason Swails a écrit :
>>
>>> Can you provide the mdout file that failed here?
>>>
>>> On Mon, Feb 1, 2016 at 9:32 AM, Jean-Patrick Francoia <
>>> jeanpatrick.francoia.gmail.com> wrote:
>>>
>>> Cool.
>>>>
>>>> It's buggy however:
>>>>
>>>> Traceback (most recent call last):
>>>> File "/home/djipey/SOFT/amber14/bin/mdout_analyzer.py", line 63, in
>>>> <module>
>>>> mdout = MdoutClass(f)
>>>> File
>>>>
>>>> "/home/djipey/SOFT/amber14/lib/python2.7/site-packages/mdoutanalyzer/mdout.py",
>>>>
>>>> line 82, in __init__
>>>> if self.properties['imin'] == 5:
>>>> KeyError: 'imin'
>>>>
>>>> Le 01/02/2016 15:05, Jason Swails a écrit :
>>>>
>>>>> If you're trying to plot data from mdout files, you can always try
>>>>> "mdout_analyzer.py". It's built on top of matplotlib and doesn't
>>>>> require
>>>>> any pre-processing step for mdout files (i.e., you can just type:
>>>>>
>>>>> mdout_analyzer.py mdout1 mdout2 ... mdoutN
>>>>> )
>>>>>
>>>>> HTH,
>>>>> Jason
>>>>>
>>>>> On Mon, Feb 1, 2016 at 8:57 AM, Jean-Patrick Francoia <
>>>>> jeanpatrick.francoia.gmail.com> wrote:
>>>>>
>>>>> "Plots generally look good"...Yeah maybe with a little formatting as
>>>>>> you
>>>>>> suggested. Actually xmgrace has an old look on my platform, a bit like
>>>>>> xleap. That's why I will go for gnuplot.
>>>>>>
>>>>>> I had a bit of spare time, so I wrote a quick script:
>>>>>>
>>>>>> #!/usr/bin/python
>>>>>> # coding: utf-8
>>>>>>
>>>>>> help = """Plot.py
>>>>>>
>>>>>> Script to plot (x, y) data from files
>>>>>>
>>>>>> Usage:
>>>>>> plot.py <files>...
>>>>>>
>>>>>> Options:
>>>>>> -h --help Display help
>>>>>> """
>>>>>>
>>>>>>
>>>>>> from docopt import docopt
>>>>>> import matplotlib.pyplot as plt
>>>>>>
>>>>>> plt.style.use('ggplot')
>>>>>> plt.style.use('seaborn-poster')
>>>>>> plt.tick_params(left='off', bottom='off', top='off', right='off')
>>>>>>
>>>>>>
>>>>>> arguments = docopt(help)
>>>>>>
>>>>>> for arg in arguments['<files>']:
>>>>>> pts_x = []
>>>>>> pts_y = []
>>>>>>
>>>>>> with open(arg, 'r') as f:
>>>>>> for line in f.readlines():
>>>>>> res = [float(value.strip()) for value in line.split('
>>>>>> ')
>>>>>> if value.strip() != '']
>>>>>> if res:
>>>>>> pts_x.append(res[0])
>>>>>> pts_y.append(res[1])
>>>>>>
>>>>>> plt.plot(pts_x, pts_y, label=arg)
>>>>>>
>>>>>> plt.legend()
>>>>>> plt.show()
>>>>>>
>>>>>> Just to try docopt and the new version of matplotlib (which includes
>>>>>> styles). The graph formatting is clearly R-inspired (the devs of
>>>>>> matplotlib finally underestood...).
>>>>>>
>>>>>> Usage:
>>>>>> ./plot.py summary.EPTOT summary.ETOT
>>>>>>
>>>>>> Result:
>>>>>> http://i.imgur.com/FPdBfsz.png
>>>>>>
>>>>>> Le 01/02/2016 14:08, David A Case a écrit :
>>>>>>
>>>>>>> On Mon, Feb 01, 2016, Lorenzo Gontrani wrote:
>>>>>>>
>>>>>>> xmgrace is great..and lightweight.
>>>>>>>>
>>>>>>> Just some (off-topic) comments about why I like xmgrace:
>>>>>>>
>>>>>>> 1. Plots generally look good and can be interactively edited if they
>>>>>>>
>>>>>> don't.
>>>>>>
>>>>>>> Consider modifying your ~/.grace/templates/Default.agr file to
>>>>>>> specify
>>>>>>> Helvetica as "font 0" (the default) and change 'xaxis label char
>>>>>>> size'
>>>>>>>
>>>>>> to 1.25
>>>>>>
>>>>>>> (from 1.0); same for yaxis.
>>>>>>>
>>>>>>> 2. A single .agr file has both the data and the formatting in a
>>>>>>> single
>>>>>>>
>>>>>> file.
>>>>>>
>>>>>>> This is good if you come back months or years later and don't
>>>>>>> remember
>>>>>>>
>>>>>> your
>>>>>>
>>>>>>> file naming conventions.
>>>>>>>
>>>>>>> 3. You can also write simple scripts to systematically modify lots of
>>>>>>> files, to replace the data but keep the formatting, etc. Once you
>>>>>>> grok
>>>>>>>
>>>>>> the
>>>>>>
>>>>>>> file syntax (which is pretty straightforward), it's about as easy to
>>>>>>>
>>>>>> write
>>>>>>
>>>>>>> scripts to create or manipulate xmgrace files as it is to write
>>>>>>> gnuplot
>>>>>>>
>>>>>> or
>>>>>>
>>>>>>> matplotlib scripts.
>>>>>>>
>>>>>>> 4. Consider aliasing xmgrace to 'xmgrace -hdevice PDF'. This means
>>>>>>>
>>>>>> that
>>>>
>>>>> "print" will create a PDF file (rather than the default PostScript).
>>>>>>>
>>>>>> This is
>>>>>>
>>>>>>> likely to be what most people want.
>>>>>>>
>>>>>>> ....dac
>>>>>>>
>>>>>>> (OK: I realize I've probably started a flame war here... Next up: why
>>>>>>>
>>>>>> you
>>>>
>>>>> should write all your code in LISP.)
>>>>>>>
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>>>>>>>
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>>>>>> AMBER mailing list
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>>>>>>
>>>>>>
>>>>>
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>>>
>>>
>>
>
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Received on Mon Feb 01 2016 - 12:00:03 PST
