[Ifeffit] Larch python instructions

[Imad Ahmed]

Dear Matt,

Thank you so much for your feedback. I’ve tested both the python and Larch scripts and they work absolutely fine. Although, I am able to work with the python route, I do like the Larch way! 
By the way, for a Larch script, how would you create plots in different windows? display = get_display(win=i); i = 1..n, following plot(), does not seem to work?

Out of interest how would you create the different paths from a cif file? e.g., similar to *.dat files in  ../xraylarch/examples/Feff_Cu. This does not seem possible using Atoms?

Best wishes,
Imad

 


From: Matt Newville <newville at cars.uchicago.edu>
Reply: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Date: 16 April 2018 at 03:57:27
To: Imad Ahmed <imad.ahmed at earth.ox.ac.uk>, XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject:  Re: [Ifeffit] Larch python instructions  

Hi Imad,


On Sun, Apr 15, 2018 at 7:15 PM, Imad Ahmed <imad.ahmed at earth.ox.ac.uk> wrote:
Dear Matt,

I am looking for some proper instructions on how to use Larch from python. 
I have larch installed on Anaconda2 and trying to run the /examples/feffit/doc_feffdat1.lar script from python. 
I tried the python code below but still having issues to run it, especially with Feffpath and some larch plugins. Could you please help?

Best wishes, Imad



import
sys, os

import
numpy as
np

from
scipy.optimize import leastsq
as
scipy_leastsq

import
larch

from
larch import Group,
Parameter

from
larch_plugins.io import
read_ascii

from
larch_plugins.xafs import
FeffPathGroup

from
larch_plugins.xafs.feffit import
(TransformGroup, FeffitDataSet,feffit, feffit_report)

fname  
= ‘~/xraylarch/examples/feffit/feff0001.dat'

path1 =
FeffPathGroup(fname)

path2chi(path1)

show(path1)

newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$',

ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True,

title=r'$\chi(k)$ from %s' % fname)

path1.sigma2 = 0.002

path2chi(path1)

plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$')
 


Well, there are some differences between Larch and Python.

With some small modifications, your scaript can become a valid Larch script like this:
      # larch
from
os.path import join, expanduser

fname  
= join(expanduser(‘~'),
'/xraylarch/examples/feffit/feff0001.dat')

path1 =
feffpath(fname)



 path2chi(path1)

show(path1)

newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$',

ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True,

title=r'$\chi(k)$ from %s' % fname)

path1.sigma2 = 0.002

path2chi(path1)

plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$')
 

To do that from Python is a bit more involved.

Each of the functions "feffpath", "path2chi", "show", "newplot", and "plot"  need to be translated.  As you probably say, "feffpath" is effectively `FeffPathGroup'.   The others are less obvious, and many of the larch functions really want to be passed a "larch session" so that they can find other larch function or data sources.  For example, FeffPathGroup needs a larch session in order to be able to look up atomic information.

So in pure python that would be approximately:

    import os
    import os.path
    import matplotlib.pyplot as plt   # using pyplot instead of build in plot commmands

    from larch import Interpreter
    from larch_plugins.xafs.feffdat import FeffPathGroup, _path2chi

   # need to create a Larch interpreter for each "session"
   _larch = Interpreter()

    fname = os.path.join(os.path.expanduser("~"), "Codes/xraylarch/examples/feffit/feff0001.dat")
  
    # note that many of the Larch functions will want a `_larch` instance passed in.
    path1 = FeffPathGroup(fname, _larch=_larch)

   _path2chi(path1, _larch=_larch)

    # show, approximately
    for attr in dir(path1):
        print(attr, getattr(path1, attr))

    # plot, approximately
    plt.plot(path1.k, path1.chi*path1.k**2, label= r'$\sigma^2 = 0$')

    path1.sigma2 = 0.002
   _path2chi(path1, _larch=_larch)

    plt.plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$')

    plt.xlabel(r' $ k \rm\, (\AA^{-1})$')
    plt.ylabel(r'$ k^2\chi(k)$')
    plt.title(r'$\chi(k)$ from %s' % fname)

    plt.legend()
    plt.show()


But also, since you have to build a Larch Interpreter, you could simply use it to execute the previous Larch script:


    from larch import Interpreter

   text = '''
      # larch
from
os.path import join, expanduser

fname  
= join(expanduser(‘~'),
'/xraylarch/examples/feffit/feff0001.dat')

path1 =
feffpath(fname)



 path2chi(path1)

show(path1)

newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$',

ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True,

title=r'$\chi(k)$ from %s' % fname)

path1.sigma2 = 0.002

path2chi(path1)

plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$')
'''
    _larch = Interpreter()
    _larch.run(text)

The latter approach is highly recommended.

--Matt Newville
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