Re: [Ifeffit] Installing Larch without installing Anaconda

2022-12-12 Thread Uma Mahendra Kumar K 
Dear Laurent Tranchant,


   I may not be the best guy to answer yet I have a simple answer.

On MAC-OS the existing python is made by apple.

The following is about Apple Python


Apple: Mac OS X comes with a pre-installation of Python, usually one or two 
years old. This can be sufficient for some needs, but the 
MacPython community recommends 
installing a newer, more capable, version. Don't get rid of the Apple version, 
though! It's used by some system utilities.
copied from https://wiki.python.org/moin/MacPython/PythonDistributionsForMac


Larch don't want to disturb this native python on MAC.


So the ANACONDA method is best to install LARCH and keep your apple created 
python safe.

When you don't want ANACONDA, just delete the anaconda folder. That's it no 
questions asked.


Mahendra



Dr. K Uma Mahendra Kumar
Asst  Professor of Physics
Dept of Physics - SAS
Vellore Institute of Technology - Vellore,TN 632 014
Bharat
https://sites.google.com/view/umamahendrakumar/home


From: Ifeffit  on behalf of 
TRANCHANT Laurent 
Sent: Monday, December 12, 2022 9:43:46 PM
To: ifeffit
Subject: Re: [Ifeffit] Installing Larch without installing Anaconda

Dear Mr or Mrs,

I sent you this message about ten days ago but on my side I did not receive any 
answer.
I would like to avoid installing Anaconda during the installation of Larch on 
my MacOS computer. I would like to know if it is possible or not.

I thank you in advance for your help.

Best regards,

Laurent Tranchant


De: "TRANCHANT Laurent" 
À: "ifeffit" 
Envoyé: Mercredi 30 Novembre 2022 13:49:11
Objet: Installing Larch without installing Anaconda

Dear Mr or Mrs,

I am Laurent Tranchant, post-doctoral researcher working at the IPANEMA 
laboratory at the SOLEIL synchrotron in France.
I would like to install Larch (especially to use XAS Viewer to treat my XAS 
data) without installing Anaconda on MacOS. Do you know if it is possible or 
not ? For example by using MacPorts instead of Anaconda...
It seems that all the solutions proposed online to install Larch on MacOS 
require the installation of Anaconda Python environment.

I thank you in advance for your help.

Best regards,

Laurent Tranchant

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Re: [Ifeffit] How do I create a histogram based on R-space values

2020-12-10 Thread Uma Mahendra Kumar K 
Dear Deepak,


 First add your affiliation in your email signature. It is the 
right thing to do. Next, 


What do you mean by histogram?

What do you want to plot?


in other words


What do you want on the x-axis and what's on the y-axis?


Mahendra





Dr. Uma Mahendra Kumar
Asst  Professor of Physics
School of Advanced Sciences
VIT University-Vellore 632 014
Bharat
VIT-Recognized as an Institution of Eminence (IoE),

From: Ifeffit  on behalf of Deepak 
Varanasi 
Sent: Thursday, December 10, 2020 8:56:55 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] How do I create a histogram based on R-space values

Good evening

May I also know how to calculate the necessary ingredients in building a 
histogram such as R and N?

I suppose R is just the R-space stuff so how do I calculate N? Is it simply the 
number of peaks in my R-space graph or something else entirely?

I need to be able to construct the histogram to finish my thesis and graduate 
but I am still stuck on it. Hence, may I request your guidance on this please?

Yours sincerely
Deepak Varanasi



On Wed, Dec 9, 2020, 13:21 Robert Gordon 
mailto:ragor...@alumni.sfu.ca>> wrote:
When i look at the files you included, I see R-value in the first column, then 
what I am assuming are
the (magnitude of) Fourier transforms of different data sets selected for 
export, with vertical
displacements of 10 or 25 between each data set.

A histogram plot would involve extracting N and R values (and 
mean-square-relative-displacements and Eo-shift).

So, some questions:
Do these individual datasets comprise multiple scans for one sample?
If so, do you plan on merging this data (typically, I do this before removing 
background and extracting chi(k))?

else if they represent data that is to be kept separate (not to be merged)...

Have you fit this data to get N and R (and...)?

If you have a standard (e.g. only 1 target element), where you know N and R, 
and what a histogram
plot of N vs R would be, have you tried examining that first to get a feel for 
what you need to do
with your unknowns?



On 2020-12-09 10:38 a.m., Deepak Varanasi wrote:

Good afternoon

I hope that everyone is safe and healthy.

I am trying to create a histogram of Number of atoms vs. the radial distance 
between the central atoms and their neighbours  (in Angstroms). I have the 
R-space data for 3 of my “central atoms” but I do not know how to create a 
histogram using them as each of them has 8 columns of data and I do not know 
which one(s) to use.

Hence, may I ask for your guidance please?

Yours Sincerely
Deepak Varanasi

P.S.: I have appended an example file of an R-space reading to demonstrate what 
I mean .




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Re: [Ifeffit] About Athena

2019-09-30 Thread Uma Mahendra Kumar K 
Dear Pankaj Singh Rawat,


Its mostly because of wrong file or corrupted data file.

Does Athena plotted your data? If not, then there is an issue with your data 
file.


>From your screenshot, it looks like you have uploaded XAS data measured at 
>potassium  L3 edge.

And looking for Oxygen edge data.

K edge of oxygen is at 0.537 keV but your E0 is at 292.11 (unknown units)

Please check again the data file in a text editor like notepad or word-pad.

Before coming to athena, try plotting your data via some other plotting 
software like gnuplot.

Make sure the data file doesn't have any un-necessary characters.

See which columns are marked for energy and mu.

I am sure Athena could read wisely.


good luck

Mahendra


Dr. Uma Mahendra Kumar
Asst  Professor of Physics
School of Advanced Sciences
VIT University-Vellore 632 014
Bharat
VIT – Recognised as Institution of Eminence (IoE) by Government of India



From: Ifeffit  on behalf of Pankaj 
Singh Rawat 
Sent: Monday, September 30, 2019 10:50
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] About Athena

Hey There,
Good Morning.I am using Athena to analyse O-k edge XAS data. After uploading 
the data to the Athena, Fourier transform parameters are not showing.
attaching a screenshot of home page.

I'll be thankful to you for any suggestion.

Thank you. hoping to hear from you soon.
--
Pankaj Singh Rawat
PhD Research Scholar
GBPUA&T Pantnagar
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Re: [Ifeffit] LARCH installation issue in UBUNTU 18

2018-12-08 Thread Uma Mahendra Kumar K 
On 05/12/18 9:54 PM, Matt Newville wrote:
Hi Mahendra,

On Wed, Dec 5, 2018 at 6:28 AM Uma Mahendra Kumar K 
mailto:umamahen...@vit.ac.in>> wrote:

Dear All,

  I wanted to install LARCH on Ubuntu 18. And I could not.

I have tried several methods  (miniconda, Anaconda, from source and the Linux 
Binaries and even through pip).

 For several issues , I found answers in Ifeffit mailing list. This is new.

lmfit is not able to import 'ufloat'.

Actually "ufloat" belongs to "uncertainties". I could not able to link(port) 
them properly.

I need your help to install Larch.

the following is the error message

Traceback (most recent call last):
  File "/usr/local/bin/larch", line 58, in 
import larch
  File "/root/.local/lib/python2.7/site-packages/larch/__init__.py", line 25, 
in 
from .shell import shell
  File "/root/.local/lib/python2.7/site-packages/larch/shell.py", line 10, in 

from .interpreter import Interpreter
  File "/root/.local/lib/python2.7/site-packages/larch/interpreter.py", line 
18, in 
from . import builtins
  File "/root/.local/lib/python2.7/site-packages/larch/builtins.py", line 22, 
in 
from . import fitting
  File "/root/.local/lib/python2.7/site-packages/larch/fitting/__init__.py", 
line 20, in 
from lmfit import (Parameter, Parameters, Minimizer, conf_interval,
ImportError: cannot import name ufloat


Oh, very sorry for the trouble.  That is totally my fault, and something I 
realize is not very well tested.   Basically, lmfit (which I am at least partly 
responsible for) had a new release (0.9.12) that breaks larch 0.9.40, in 
exactly this place.  The unreleased, development version of larch does work 
with the latest version (so all the tests say everything is fine).   I'm 
working on getting 0.9.41 released soon (hopefully next week), but that doesn't 
solve the problem for you now.

The first thing to try is:
   pip install lmfit==0.9.11

I think that *should* work.  If there are still problems, I would forcibly 
remove .../python2.7/site-packages/lmfit* and then install lmfit version 0.9.11.

As an aside, I might recommend using a version of Python that is not installed 
as root and in the /root/.local.That seems slightly dangerous to me.

Hope that helps,

--Matt


Dear Dr Matt,

Finally I have fully functional larch on my ubuntu 18.04.

First I installed conda.

Then installed all the larch dependencies listed in the larch web-page via 
conda.

Later, xraylarch-0.9.40-Linux-x86_64.sh was installed using bash.

As you suggested i have forced lmfit==0.9.11, installation went very well and i 
got functional larch.


Thanks

Mahendra

VIT university-Bharat
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[Ifeffit] LARCH installation issue in UBUNTU 18

2018-12-05 Thread Uma Mahendra Kumar K 
Dear All,

  I wanted to install LARCH on Ubuntu 18. And I could not.

I have tried several methods  (miniconda, Anaconda, from source and the Linux 
Binaries and even through pip).

 For several issues , I found answers in Ifeffit mailing list. This is new.

lmfit is not able to import 'ufloat'.

Actually "ufloat" belongs to "uncertainties". I could not able to link(port) 
them properly.

I need your help to install Larch.

the following is the error message

Traceback (most recent call last):
  File "/usr/local/bin/larch", line 58, in 
import larch
  File "/root/.local/lib/python2.7/site-packages/larch/__init__.py", line 25, 
in 
from .shell import shell
  File "/root/.local/lib/python2.7/site-packages/larch/shell.py", line 10, in 

from .interpreter import Interpreter
  File "/root/.local/lib/python2.7/site-packages/larch/interpreter.py", line 
18, in 
from . import builtins
  File "/root/.local/lib/python2.7/site-packages/larch/builtins.py", line 22, 
in 
from . import fitting
  File "/root/.local/lib/python2.7/site-packages/larch/fitting/__init__.py", 
line 20, in 
from lmfit import (Parameter, Parameters, Minimizer, conf_interval,
ImportError: cannot import name ufloat


Mahendra

Asst Prof of Physics

VIT university -Bharat.
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