Some questions regarding running Larch code in Python
Hello everyone, I'm trying to find radial distribution functions for materials with known concentrations of individual atoms by running Larch code through Python, but am having some difficulties with creating feffpaths: 1. I'm not quite understanding the feff.inp files stuff. Calling FeffRunner().run() with a input file that works with Atoms always throws the "rdinp not found exception". From what I'm understanding, feffrunner().run() calls the different modules to create a feffpath() group, but where are the rdinp, pot, xsph, etc codes/files? 2. Somewhat on the same line of thought, can someone give me an example of a valid feffNNNN.dat file to generate a feffpath() group? I went through feffdat.py and the parsing code in lines 88-102 (under __read()) looks like it only accepts very specific input formats. 3. What does "ipot" stand for in the "geom" variable? I understand that if I did pass in a valid file, I'd probably not have to know this, but I was just curious... Also, this might be a overly-general question, but is this the best way to approach the problem? The basic idea now is to get chi(k) values for a bunch of different paths/RDFs, and figure out which ones match experimental values the best. This is also the main reason I want to get past the Demeter GUI and Larch-specific interface: eventually I might throw the code on a supercomputer of some sort and have it crunch the numbers. The details still have to be worked out on my end, but I was wondering if there was a faster or better way to go about finding the RDF for compound materials with known concentrations of individual atoms. I've attached some of my Python code (with more specific versions of questions 1 and 2 inserted as comments) and the feff.inp file I've been testing with. (Simple file from http://cars9.uchicago.edu/~ newville/adb/search.html) I'm currently an undergrad exploring the field of XAFS, so sorry in advance if there is something obvious that I'm missing... Also, let me know if any clarifications are needed. Thank you for your time and sorry about the email being so long, Alice ---------- Hanyu (Alice) Zhang CWRU Class of 2018 | Engineering Physics major BS/MS program | Materials science *Minors:* Mathematics | Materials science *Honors societies:* National Society of Collegiate Scholars | Tau Beta Pi | Pi Mu Epsilon *Active Clubs:* Case Origami Circle | Case Rocket Team | CWRUbotix | Case Physics and Astronomy club | Math club
Hi Hanyu, Sorry for the confusion. The 'Co.inp' file you attached is actually an Atoms.inp file, not a Feff6 or Feff8 input file. If you run that file through WebAtoms, http://cars9.uchicago.edu/webatoms?url=http://cars9.uchicago.edu/atomsdb/Co.... you'll get a Feff6l input file -- running this with larch> feff6l('feff_Co.inp') will generate `feffNNNN.dat` files that you can use to define Feff Paths, as the examples show... To run Feff8l, you'll have to generate a Feff8 file from WebAtoms (see attached for your Co.inp) To use that to create feffNNNN.dat files, use larch> feff8l('feff8_Co.inp') or, using feffrunner for Feff8 inputs and from python, use: import larch from pylab import loadtxt from larch import Group from larch import Interpreter from larch_plugins.xafs import autobk from larch_plugins.xafs import feffrunner from larch_plugins.xafs import feffdat session = Interpreter() feff = feffrunner.feffrunner('feff8_Co.inp',_larch=session) # run Fef8: feff.run() # OR explicitly run all Feff8 modules in order feff.run(exe='rdinp') feff.run(exe='pot') feff.run(exe='xsph') feff.run(exe='pathfinder') feff.run(exe='genfmt') feff.run(exe='ff2x') # create a Path from a feffNNNN.dat file: testPath = feffdat.FeffPathGroup(filename='feff0001.dat', _larch=session) feffdat._path2chi(testPath,_larch = session) print(testPath) print(dir(testPath)) #### Hope that helps.... --Matt
Thanks Matt!
I'll go play with more. I think this is the missing link that I needed.
----------
Hanyu (Alice) Zhang
CWRU Class of 2018 | Engineering Physics major
BS/MS program | Materials science
*Minors:* Mathematics | Materials science
*Honors societies:* National Society of Collegiate Scholars | Tau Beta Pi | Pi
Mu Epsilon
*Active Clubs:* Case Origami Circle | Case Rocket Team | CWRUbotix | Case
Physics and Astronomy club | Math club
On Tue, Jan 9, 2018 at 1:26 PM, Matt Newville
Hi Hanyu,
Sorry for the confusion. The 'Co.inp' file you attached is actually an Atoms.inp file, not a Feff6 or Feff8 input file.
If you run that file through WebAtoms, http://cars9.uchicago.edu/ webatoms?url=http://cars9.uchicago.edu/atomsdb/Co.inp you'll get a Feff6l input file -- running this with
larch> feff6l('feff_Co.inp')
will generate `feffNNNN.dat` files that you can use to define Feff Paths, as the examples show...
To run Feff8l, you'll have to generate a Feff8 file from WebAtoms (see attached for your Co.inp)
To use that to create feffNNNN.dat files, use
larch> feff8l('feff8_Co.inp')
or, using feffrunner for Feff8 inputs and from python, use:
import larch
from pylab import loadtxt from larch import Group from larch import Interpreter from larch_plugins.xafs import autobk from larch_plugins.xafs import feffrunner from larch_plugins.xafs import feffdat
session = Interpreter() feff = feffrunner.feffrunner('feff8_Co.inp',_larch=session)
# run Fef8: feff.run()
# OR explicitly run all Feff8 modules in order feff.run(exe='rdinp') feff.run(exe='pot') feff.run(exe='xsph') feff.run(exe='pathfinder') feff.run(exe='genfmt') feff.run(exe='ff2x')
# create a Path from a feffNNNN.dat file:
testPath = feffdat.FeffPathGroup(filename='feff0001.dat', _larch=session) feffdat._path2chi(testPath,_larch = session)
print(testPath) print(dir(testPath)) ####
Hope that helps....
--Matt
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Matt Newville