Re: [Ifeffit] P K-edge EXAFS

[Mangold, Stefan (IPS)]

some additional comments:

- it is a bit tricky to operate ionisation chambers at this low energies (low 
pressure)
- some Beamlines have issues with higher harmonics (high angles of mirrors to 
get low cut off energies)
- preparation of good sample is tricky


best regards

Stefan Mangold

Am 14.09.2023 um 06:09 schrieb Mike Massey 
mailto:mmas...@gmail.com>>:

The other difficulty I have experienced with P EXAFS is that a lot of the 
second-shell backscatterers are fairly weak, so picking that signal out is 
pretty difficult.

I have some spectra of minerals and that's where I've wanted to start with P 
EXAFS (since the structures are well-constrained). But as has been mentioned, 
low-frequency oscillations and background subtraction have massive impacts on 
the P K-edge EXAFS function (tested this by taking spectra of the same sample 
during different runs and getting different EXAFS due to slightly different 
background).

I don't think it's necessarily impossible, I just personally put it in the 
not-right-now basket.





On Sep 14, 2023, at 07:42, Mike Massey 
mailto:mmas...@gmail.com>> wrote:


In my experience the main difficulties with EXAFS on P (phosphate) come from 
two factors (not signal to noise, it's not hard to get a nice smooth line, but):

1) You've got 4 O atoms, guaranteed, so any other signal will be small and on 
top of that very strong signal generated from the first-neighbor O

Unfortunately,

2) You have very limited data range, either due to instrumental limitations, or 
due to interference from sulfur

Don't get me wrong I still have some data sitting around and I'd love to try P 
EXAFS analysis on it just to try and grasp that brass ring but...It's not the 
easiest task ever.

If you want good data quality "scan longer" is always an option. Some might 
think it's crazy but I do think I have some P XAS data where I took 30 or 60 
scans, maybe overnight or something. The scans are so short that repeats are 
easy.


Hope this commentary is helpful.



Mike




On Sep 14, 2023, at 07:04, Marcelo Eduardo Alves 
mailto:meal...@gmail.com>> wrote:


Hi there,
I begin by examining phosphorus adsorption by goethite, hematite, and gibbsite.
Why is it difficult, if not impossible, to obtain EXAFS spectra at the P-K edge 
that can be properly used, i.e., spectra with a high signal-to-noise ratio, 
especially for dilute samples?
Would it be possible to use arsenic as a phosphorus proxy to get conclusions 
from As K-edge EXAFS data that could be extended to P?
Thank you.

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[Ifeffit] Larch and calculation of theoretical EXAFS via cif -files part 2

[Mangold, Stefan (IPS)]

Dear all,

i have another set of cif files, which also don't work on larch. They work with 
Artemis, except that they hit the 500 atoms limit per cluster. This won't be a 
problem in larch, because of the option to exclude the H-atoms.

One problem seems to occur on the line

_chemical_formula_moiety
;
2(C18 H36 K1 N2 O6 1+),Bi2 2-
;

which I rewrote to

_chemical_formula_moiety '2(C18 H36 K1 N2 O6 1+),Bi2 2-'


but still I got the message

Error reading CIF File: 
/Users/stefanmangold/Documents/eigene_Daten/Messdaten/PrepMessungen/XPS-Proben/Bi2-crypt-222_e.cif
Traceback (most recent calls last):
  File 
"/Users/stefanmangold/xraylarch/lib/python3.10/site-packages/larch/wxlib/cif_browser.py",
 line 618, in onImportCIF
cif_data = parse_cif_file(path)
  File 
"/Users/stefanmangold/xraylarch/lib/python3.10/site-packages/larch/xrd/amcsd.py",
 line 142, in parse_cif_file
raise ValueError(f'Cannot read symmetries from file {filename:s}')
ValueError: Cannot read symmetries from file 
/Users/stefanmangold/Documents/eigene_Daten/Messdaten/PrepMessungen/XPS-Proben/Bi2-crypt-222_e.cif


Anybody an idea, I attached the unchanged file (Bi2-crypt-222.cif) and the 
edited file (Bi2-crypt-222_e.cif). Any idea what’s wrong?




best regards

Stefan


Bi2-crypt-222_e.cif
Description: Bi2-crypt-222_e.cif


Bi2-crypt-222.cif
Description: Bi2-crypt-222.cif
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Re: [Ifeffit] Larch and calculation of theoretical EXAFS via cif -files

[Mangold, Stefan (IPS)]

Thanks for the support, will do the quick fix to proceed with my work, Thanks 
for the fast feedback.

Am 09.08.2023 um 20:17 schrieb Matt Newville :

Hi Stefan,

OK, yes I see that too.  I have this fixed in the code.  For a quick 
workaround, changing

_chemical_name_common 'Bismuth potassium (2/1)'

to

_chemical_name_common 'Bismuth potassium'

will fix the problem.


On Wed, Aug 9, 2023 at 11:25 AM Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> wrote:



Am 09.08.2023 um 17:17 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Stefan,

Can you send a CIF file that is not working? I tried the one for BiK3 from the 
built-in AmMin database, and it worked for me.  But, for sure it is possible to 
come up with a CIF file that doesn't work!  They are surprisingly tricky.

On Wed, Aug 9, 2023 at 9:51 AM Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> wrote:
Dear all,

i have some cif files, which doesn’t work on larch. One example is KBi2, which 
works well on Artmenis with feff6. The same file (and also the cifs found in 
the database) won't work on larch (not with feff 6 nor feff8). There is no 
error message displayed -> just, that feff is started.


###
# Run Feff in folder: 
/Users/Name/.larch/feff/Bi1_L3_Bismuth_potassium__2_1__cif200012_13
###
###

no result even after hours.

Any ideas?

Best regards

Stefan



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Re: [Ifeffit] Larch and calculation of theoretical EXAFS via cif -files

[Mangold, Stefan (IPS)]

Am 09.08.2023 um 17:17 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Stefan,

Can you send a CIF file that is not working? I tried the one for BiK3 from the 
built-in AmMin database, and it worked for me.  But, for sure it is possible to 
come up with a CIF file that doesn't work!  They are surprisingly tricky.

On Wed, Aug 9, 2023 at 9:51 AM Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> wrote:
Dear all,

i have some cif files, which doesn’t work on larch. One example is KBi2, which 
works well on Artmenis with feff6. The same file (and also the cifs found in 
the database) won't work on larch (not with feff 6 nor feff8). There is no 
error message displayed -> just, that feff is started.


###
# Run Feff in folder: 
/Users/Name/.larch/feff/Bi1_L3_Bismuth_potassium__2_1__cif200012_13
###
###

no result even after hours.

Any ideas?

Best regards

Stefan



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KBi2.cif
Description: KBi2.cif
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Re: [Ifeffit] Larch and calculation of theoretical EXAFS via cif -files

[Mangold, Stefan (IPS)]

calculations are done on a Macbook-Air with the current uptodate OS. 

best regards 

Stefan

> Am 09.08.2023 um 16:51 schrieb Mangold, Stefan (IPS) :
> 
> Dear all,
> 
> i have some cif files, which doesn’t work on larch. One example is KBi2, 
> which works well on Artmenis with feff6. The same file (and also the cifs 
> found in the database) won't work on larch (not with feff 6 nor feff8). There 
> is no error message displayed -> just, that feff is started. 
> 
> 
> ###
> # Run Feff in folder: 
> /Users/Name/.larch/feff/Bi1_L3_Bismuth_potassium__2_1__cif200012_13
> ###
> ###   
> 
> no result even after hours. 
> 
> Any ideas?
> 
> Best regards
> 
> Stefan
> 
> 
> 
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[Ifeffit] Larch and calculation of theoretical EXAFS via cif -files

[Mangold, Stefan (IPS)]

Dear all,

i have some cif files, which doesn’t work on larch. One example is KBi2, which 
works well on Artmenis with feff6. The same file (and also the cifs found in 
the database) won't work on larch (not with feff 6 nor feff8). There is no 
error message displayed -> just, that feff is started. 


###
# Run Feff in folder: 
/Users/Name/.larch/feff/Bi1_L3_Bismuth_potassium__2_1__cif200012_13
###
###   

no result even after hours. 

Any ideas?

Best regards

Stefan



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Re: [Ifeffit] Not possible to install larch on actual system and Mac M1 system

[Mangold, Stefan (IPS)]

Dear all, Dear Matt


found the reason:

- you need command line developer tools installed

- these have to be up to date

If this is the case, the install via script works also on ARM Macs ….; the 
Intel-Mac, which I tested, had an updated version installed.

best regards

Stefan

Am 16.05.2023 um 16:31 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Stefan,

Sorry for the trouble.  As it turns out, I am writing this on a Macbook M1 
running 13.3.1.

I think the "GetLarch.sh" script should work (downloading 
https://raw.githubusercontent.com/xraypy/xraylarch/master/installers/GetLarch.sh
and running with `sh GetLarch.sh` in a Terminal).

For me, that is using fabio version 2023.4.1.

Does that work for you?  If not, can you send the log file (GetLarch.log)?

--Matt

On Tue, May 16, 2023 at 9:19 AM Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> wrote:
Dear all,

from binary package:
can’t write to system partition

by script and by anaconda I got the following message back:

Collecting fabio
  Using cached fabio-2023.4.1.tar.gz (724 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error

System ist 13.3.1, tried to install the newest version completely from scratch, 
because the update killed my larch version ….

best regards

Stefan
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Re: [Ifeffit] Not possible to install larch on actual system and Mac M1 system

[Mangold, Stefan (IPS)]

I used chmod, but wit your command the same result ….


Collecting fabio
  Using cached fabio-2023.4.1.tar.gz (724 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'error'
  error: subprocess-exited-with-error



  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1


put it into GitHub
best regards

Stefan

Am 16.05.2023 um 16:31 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Stefan,

Sorry for the trouble.  As it turns out, I am writing this on a Macbook M1 
running 13.3.1.

I think the "GetLarch.sh" script should work (downloading 
https://raw.githubusercontent.com/xraypy/xraylarch/master/installers/GetLarch.sh
and running with `sh GetLarch.sh` in a Terminal).

For me, that is using fabio version 2023.4.1.

Does that work for you?  If not, can you send the log file (GetLarch.log)?

--Matt

On Tue, May 16, 2023 at 9:19 AM Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> wrote:
Dear all,

from binary package:
can’t write to system partition

by script and by anaconda I got the following message back:

Collecting fabio
  Using cached fabio-2023.4.1.tar.gz (724 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error

System ist 13.3.1, tried to install the newest version completely from scratch, 
because the update killed my larch version ….

best regards

Stefan
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[Ifeffit] Not possible to install larch on actual system and Mac M1 system

[Mangold, Stefan (IPS)]

Dear all,

from binary package:
can’t write to system partition

by script and by anaconda I got the following message back:

Collecting fabio
  Using cached fabio-2023.4.1.tar.gz (724 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error

System ist 13.3.1, tried to install the newest version completely from scratch, 
because the update killed my larch version ….

best regards

Stefan
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Re: [Ifeffit] found some issues found in larch (read-in issues)

[Mangold, Stefan (IPS)]

Dear Mauro,

> Am 26.10.2022 um 13:19 schrieb Mauro ROVEZZI :
> 
> Dear Stefan,
> 
> Thanks for reporting these issues. Some of them are already known to us, but 
> require time for fixing and implementing new features.
> 
> I take the occasion to say that anybody with Python programming skills is 
> welcome to contribute and help with the development of Larch. Having a 
> community of developers instead of always asking to one single person should 
> be strongly considered.

There are still to much limitation in some parts of the code in larch for my 
data evaluation. I would need to quite some code into the project and I#m not a 
python programmer (yet).

> 
> Going back to your specific questions, here my two cents contribution.
> 
> On 26/10/2022 11:46, Mangold, Stefan (IPS) wrote:
>> Dear All, dear Matt,
>> all tests were done on Macs (one M1 & one Intel) with the latest version 
>> your software & latest OS.
>> 1. Read-In of spec files works, but only one file at once. Even if multiple 
>> files are selected
> >
>> 2. If one tries to load text-files it is possible to load data form multiple 
>> files as long as you don’t try to load also the reference spectra. If you 
>> load the reference  also the read-in stopps at the transmission/fluorescence 
>> spectrum of the second file selected.
> 
> These are related to:
> 
> https://github.com/xraypy/xraylarch/issues/367


we create 3 different files in one go:

- one spec like file 
- one simple text file with only a view columns 
- one hdf5 file (also all fluorescence data of all detector channels available)

we don't write multiple scans in one file, because in the beginning hdf5 file 
access was limited to one program, so we were not able to write multiple scans 
during in-situ experiments and make online data evaluation 

best regards

Stefan

> 
> Furthermore, with respect to an ASCII file, a Spec file may contain multiple 
> scans, so it is impossible to know in advance which scan to select if one 
> selects multiple Spec files to load.
> 
> To my opinion, when you need to read multiple data from many files, the 
> simplest approach is to write a small python script (or Jupyter notebook) 
> that reads the data and save them in an Athena project file or Larch session 
> that you can then easily read back with xas_viewer.
> 
> I can further help with that.
> 
>> 3. Trouble, that I sometimes can’t unmount network volumes after reading 
>> from them, larch saved on local discs. MacOS claims that python has files 
>> open; no other python program running
> 
> I let Matt or somebody else reply on this point.
> 
>> 4. unable to save the data of one XAS-viewer while having two xas-viewer 
>> open.
> 
> This is related to:
> 
> https://github.com/xraypy/xraylarch/issues/410
> 
> Best,
> Mauro
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[Ifeffit] found some issues found in larch (read-in issues)

[Mangold, Stefan (IPS)]

Dear All, dear Matt,

all tests were done on Macs (one M1 & one Intel) with the latest version your 
software & latest OS. 

1. Read-In of spec files works, but only one file at once. Even if multiple 
files are selected

2. If one tries to load text-files it is possible to load data form multiple 
files as long as you don’t try to load also the reference spectra. If you load 
the reference  also the read-in stopps at the transmission/fluorescence 
spectrum of the second file selected.

3. Trouble, that I sometimes can’t unmount network volumes after reading from 
them, larch saved on local discs. MacOS claims that python has files open; no 
other python program running 

4. unable to save the data of one XAS-viewer while having two xas-viewer open. 

best regards

Stefan Mangold

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Re: [Ifeffit] Using larch for feff Fitting -> simple 4 parameter fit

[Mangold, Stefan (IPS)]

Thanks for the feedback:

> Am 18.08.2022 um 13:55 schrieb Christopher Patridge :
> 
> Stefan,
> 
> The simple 4 parameter fit typically involves just a single path such as the 
> first coordination shell.  Do you have multiple paths or multiple unique 
> scatterers inside the first coordination?

Artemis allows to do a fit with one structure with the for parameter:

amp and enot (aka So2 and e0 in larch)

and 

fit also with one delr (difference to structure) and one ss (aka sigma2 in 
larch)

This is not really perfect, but a nice and fast check of your structure 

best regards

Stefan Mangold  

> 
> Chris  
> 
>> On Aug 18, 2022, at 7:50 AM, Mangold, Stefan (IPS)  
>> wrote:
>> 
>> Dear all,
>> 
>> I try to use larch for Feff Fitting. For a first start, I liked the option 
>> of Artemis with the „simple 4 parameter fit“. Larch produces for every path 
>> an independent dear and sigma2. Is there a simple way to make this simple 4 
>> parameter fit also in larch?
>> 
>> best regards
>> 
>> Stefan Mangold
>> 
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[Ifeffit] Using larch for feff Fitting -> simple 4 parameter fit

[Mangold, Stefan (IPS)]

Dear all,

I try to use larch for Feff Fitting. For a first start, I liked the option of 
Artemis with the „simple 4 parameter fit“. Larch produces for every path an 
independent dear and sigma2. Is there a simple way to make this simple 4 
parameter fit also in larch?

best regards

Stefan Mangold

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Re: [Ifeffit] data plotting

[Mangold, Stefan (IPS)]

Yepp,


well known bug in Athena ->

- either patch Athena

- save the files in eV

- or use larch as Mat showed

best regards

Stefan

Am 28.06.2022 um 09:33 schrieb Gleb Pokrovski 
mailto:gleb.pokrov...@get.omp.eu>>:

Hi,
If I'm not mistaken, it is a bug of athena 026,
you may easily fix it yourself as Bruce nicely explained below.
don't need to downgrade to 025, I think.
best regards,
Gleb



 Forwarded Message 
Subject:Re: [Ifeffit] Import Error
Date:   Sat, 6 Apr 2019 14:16:35 +
From:   Ravel, Bruce 
Reply-To:   XAFS Analysis using Ifeffit 

To: 
ifeffit@millenia.cars.aps.anl.gov 




I did not remember when you asked the other day, but it occurred to me that 
your data-in-keV problem was reported a few months ago.

https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2019-January/009688.html

I have not yet made a new Windows release with the fix. However, it is not too 
hard to apply the fix by editing a small amount of Athena's source code.


I think this is the easiest way to explain the small changes. Find the
file "lib/Demeter/Data.pm" underneath the location on your computer that
the software was installed. Look at this link:

https://github.com/bruceravel/demeter/commit/1b586b88d36336cad00b13d73913ebdb48b1d132#diff-74dd62af0fb82fb27595c1edcf73041f

Make the indicated change at line 22 (i.e. add $EPSILON6 to the argument
list of qw().)

Make the indicated changes around 885 (i.e. add the two lines before the
while block and alter the argument of the greater-than comparison in the
first line of the while block).

The change at line 871 is irrelevant and has no impact on Athena's operations.

That should do it. You can then drop the edited file into place on any
other computer.

B



On 04/05/2019 10:33 AM, Clark Adam Hugh (PSI) wrote:
Dear Bruce and Lucy

Thanks for your work around Lucy, it works perfectly but still doesn't explain 
the behavior I am observing.

Bruce what other information would be useful to diagnose the problem I am 
currently having? I have attached two figures, one showing the import window 
with the setting I have been using, specifically that I am not using the rebin 
feature. The second figure shows the difference in the pre-edge region between 
importing the data with eV and keV units for the energy column to demonstrate 
clearly that resampling is occurring when importing with data that has an 
energy column of KeV.

Many Thanks
Adam Clark

__
Paul Scherrer Institut
Adam Hugh Clark
WLGA/129
Forschungsstrasse 111
5232 Villigen PSI
Schweiz

Telefon: +41 56 310 41 51
E-Mail: adam.cl...@psi.ch
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Sent: Freitag, 5. April 2019 15:20
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 194, Issue 4

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Today's Topics:

1. Data Import Bug (Athena 0.9.26) (Clark Adam Hugh (PSI))
2. Re: Data Import Bug (Athena 0.9.26) (Ravel, Bruce)
3. Re: Data Import Bug (Athena 0.9.26) (Lucy M Mottram)


--

Message: 1
Date: Fri, 5 Apr 2019 11:33:13 +
From: "Clark Adam Hugh (PSI)" 
To: 
"ifeffit@millenia.cars.aps.anl.gov"

Subject: [Ifeffit] Data Import Bug (Athena 0.9.26)
Message-ID:

Content-Type: text/plain; charset="us-ascii"

Dear Mailing List

I have recently come across a data import error when using Athena version 
0.9.26. When importing data there appears to be a resampling which 
significantly reduces the resolution of the data. Attached is an example 
dataset with an energy step of 0.5 eV on the Cu K edge. When importing with 
Athena 0.9.26 this data is significantly resampled resulting in an energy 
resolution on the edge of 1.5 eV which can either be seen by plotting or by 
exporting and inspecting the datafile. Using 

[Ifeffit] Larch 0.9.59, problems with PCA

[Mangold, Stefan (IPS)]

Dear all,

on 2 computers (Mac, Intel and ARM, newest version operating system) the PCA 
does not work. If I press "Build Model with selected groups“ on both computers 
and several different datasets, I only get „training model“ and nothing else 
happens. Absolutely nothing else changes within this tab inside XAS viewer.

Best regards

Stefan Mangold

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Re: [Ifeffit] Larch install error on MacOS 12.2

[Mangold, Stefan (IPS)]

Dear Matt and Jeff


I checked again the binary installer and there is no xas_viewer in 
~/xraylarch/bin/

so the installer seemed to work only partially.

all installers go through the process (binary installer and script) with 
telling everything is fine, no error message.

If you are clicking on the icon (XAS Viewer) after script installer succeeded 
just 3 bumps on the icon in the dock end no message.
all other Application in the folder work now, but not XAS Viewer

The script seemed to work,
~/xraylarch/bin/xas_viewer is created and starts up by terminal, not per 
clicking on the icon (also option click doesn’t, system don’t ask for access 
privileges).

Do you have any idea to get the XAS Viewer working? No error messages in the 
sys-log. Even after the starting from terminal, it doesn’t work.

best regards

Stefan


Am 10.02.2022 um 14:22 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Stefan,

I hope it's kind of obvious,  but telling us "it doesn't work" is not going to 
ever get a reply other than "follow the instructions and report back any errors 
you may get".  You have not given us any error messages.

What do you mean by 'larch -m' did not work?  Did it give any error messages?  
If so, what were they?  If not, why didn't you say that?
When you installed with 'GetLarch.sh', what does the log file say about its 
installation?

Did you try opening a Terminal and running
 ~/xraylarch/bin/xas_viewer

? If so, what does that report?

On Thu, Feb 10, 2022, 4:26 AM Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> wrote:
Dear Matt,

sorry for the delayed feedback, my time for testing is pretty limited.

1. tried to start the old installation, but XAS viewer didn’t start
2. installed binary installer and tried to create new ICONs, didn’t work (used 
all command described on the webpage)
3. Install via script on the web page, installer said everything fine, start-up 
icons (XAS-viewer) created, but they didn’t start up.

so next thing I will do is to install anaconda again, and try it via the 
instruction Jeff Terry pointed to

——

# Create new environment
conda config --add channels conda-forge
conda create -n exafs python=3.7
conda activate exafs

# Install Conda Dependencies
conda install -y "numpy=>1.20" "scipy=>1.5" "matplotlib=>3.0" scikit-learn 
pandas
conda install -y pyparsing pytest pytest-cov coverage
conda install -y h5py pillow  sqlalchemy psutil pyyaml
conda install -y psycopg2-binary numdifftools emcee
conda install -y wxpython
conda install -y pymatgen
conda install -y cython

# Install lmfits and Xraylarch using Pip
pip install lmfit peakutils pyepics pyshortcuts termcolor sphinx dill 
pycifrw xraydb wxmplot wxutils
pip install xraylarch

larch -m





more testing probably this evening …

best regards

Stefan Mangold


> Am 09.02.2022 um 22:59 schrieb Matt Newville 
> mailto:newvi...@cars.uchicago.edu>>:
>
> Hi Stefan,
>
> Sorry for the trouble.  I would definitely recommend deleting and starting 
> over with the binary installer.  If you run into trouble with that, running 
> the "GetLarch.sh" in a Terminal would probably be the most helpful, as it 
> will create a log file that might have some clues about what went wrong.  
> And, like Jeff said, if you don't get the Larch folder of Apps, typing
>    ~/xraylarch/bin/larch -m
>
> in a Terminal should remake those.



>
>
> On Wed, Feb 9, 2022 at 2:05 AM Mangold, Stefan (IPS) 
> mailto:stefan.mang...@kit.edu>> wrote:
> Dear all,
>
> I upgraded a machine to 12.2 (MacPro), Larch was installed via binary 
> installer. Afterwards Larch didn’t launch. I did a re-install with the binary 
> installer and this didn’t work, because already installed. deleted it, but 
> this also didn’t work
>
> tried
>
> pip install xraylarch
>
> stopped
> with
> ERROR: Failed building wheel for fabio
> Failed to build fabio
>
> also no director with XAS viewer created.
>
>
> best regards
>
> Stefan Mangold
>
>
> --
> --Matt Newville http://cars.uchicago.edu/>> 
> 630-327-7411


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Re: [Ifeffit] Larch install error on MacOS 12.2

[Mangold, Stefan (IPS)]

Dear Matt,

sorry for the delayed feedback, my time for testing is pretty limited. 

1. tried to start the old installation, but XAS viewer didn’t start 
2. installed binary installer and tried to create new ICONs, didn’t work (used 
all command described on the webpage)
3. Install via script on the web page, installer said everything fine, start-up 
icons (XAS-viewer) created, but they didn’t start up.

so next thing I will do is to install anaconda again, and try it via the 
instruction Jeff Terry pointed to 

——

# Create new environment
conda config --add channels conda-forge
conda create -n exafs python=3.7
conda activate exafs

# Install Conda Dependencies
conda install -y "numpy=>1.20" "scipy=>1.5" "matplotlib=>3.0" scikit-learn 
pandas
conda install -y pyparsing pytest pytest-cov coverage
conda install -y h5py pillow  sqlalchemy psutil pyyaml
conda install -y psycopg2-binary numdifftools emcee
conda install -y wxpython
conda install -y pymatgen
conda install -y cython

# Install lmfits and Xraylarch using Pip
pip install lmfit peakutils pyepics pyshortcuts termcolor sphinx dill 
pycifrw xraydb wxmplot wxutils
pip install xraylarch

larch -m





more testing probably this evening …

best regards

Stefan Mangold


> Am 09.02.2022 um 22:59 schrieb Matt Newville :
> 
> Hi Stefan,
> 
> Sorry for the trouble.  I would definitely recommend deleting and starting 
> over with the binary installer.  If you run into trouble with that, running 
> the "GetLarch.sh" in a Terminal would probably be the most helpful, as it 
> will create a log file that might have some clues about what went wrong.  
> And, like Jeff said, if you don't get the Larch folder of Apps, typing   
>~/xraylarch/bin/larch -m 
> 
> in a Terminal should remake those.



> 
> 
> On Wed, Feb 9, 2022 at 2:05 AM Mangold, Stefan (IPS)  
> wrote:
> Dear all,
> 
> I upgraded a machine to 12.2 (MacPro), Larch was installed via binary 
> installer. Afterwards Larch didn’t launch. I did a re-install with the binary 
> installer and this didn’t work, because already installed. deleted it, but 
> this also didn’t work 
> 
> tried
> 
> pip install xraylarch
> 
> stopped 
> with
> ERROR: Failed building wheel for fabio
> Failed to build fabio
> 
> also no director with XAS viewer created.
> 
> 
> best regards
> 
> Stefan Mangold
> 
> 
> -- 
> --Matt Newville  630-327-7411


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[Ifeffit] Larch install error on MacOS 12.2

[Mangold, Stefan (IPS)]

Dear all,

I upgraded a machine to 12.2 (MacPro), Larch was installed via binary 
installer. Afterwards Larch didn’t launch. I did a re-install with the binary 
installer and this didn’t work, because already installed. deleted it, but this 
also didn’t work 

tried

pip install xraylarch

stopped 
with
ERROR: Failed building wheel for fabio
Failed to build fabio

also no director with XAS viewer created.


best regards

Stefan Mangold

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Re: [Ifeffit] Larch R plot

[Mangold, Stefan (IPS)]

Dear Chris,

seen similar issues with Larch. The data (edge Jump 0.25), 200.k counts per 
channel. Used Fluorescence signal for Athena and Larch. Used the same parameter 
and got different result. Very similar to yours …

best regards

Stefan Mangold

Am 25.10.2021 um 14:41 schrieb Christopher Patridge 
mailto:patri...@buffalo.edu>>:

Hello,

I am using Larch and Athena together and I just have a question about the 
magnitude plots and its effect (if any) on EXAFS modeling.  Below are plots of 
the same merged samples using the same setting values.  I noted that the plot 
in Larch begins below 0 and just want to make sure this is not a setting I 
missed in Larch?


Thank you,

Chris

**
Dr Christopher Patridge
Associate Professor
Dept of Chemistry
SASE 315
716-829-8096 | patri...@dyc.edu
www.dyc.edu

Social: Twitter



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Re: [Ifeffit] Larch 0.9.56

[Mangold, Stefan (IPS)]

Dear Matt,


update on Mac doesn’t work. 9.55 is up to date is the feedback. I did the 
standard binary install and the other updates worked well

best regards

Stefan


Am 20.10.2021 um 20:22 schrieb Matthew Newville 
mailto:matt.newvi...@gmail.com>>:

Hi Folks,

Larch version 0.9.56 is now available on PyPI 
(https://pypi.org/project/xraylarch) and should now be installed by default 
using most installation mechanisms.

This really represents a collection of small improvements and bug fixes but 
includes one emergency bug fix that many people have seen with the latest 
version of `lmfit` (which was released recently).  I believe that this will now 
work, but please let me know if you continue to have installation problems.
Cheers,

--Matt Newville
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Re: [Ifeffit] Question about CsNO3 L3 edge

[Mangold, Stefan (IPS)]

the plot from researchgate is transmission data, your data is fluorescence;

best regards

Stefan Mangold

Am 01.07.2021 um 10:17 schrieb 田能全 
mailto:tien.nengch...@gmail.com>>:

Hi Stefan,
Thanks for the response. I am confusing about the two plots. Could you please 
explain more about the difference?

https://www.researchgate.net/publication/231097049_Cs_L-edge_EXAFS_atomic_absorption_background/figures?lo=1






Kind regards,

N. C. Tien



Mangold, Stefan (IPS) mailto:stefan.mang...@kit.edu>> 於 
2021年7月1日 週四 下午3:38寫道：
normal for every element,

the higher the energy, the larger is the penetration depth —

regards

Stefan Mangold

Am 01.07.2021 um 06:13 schrieb 田能全 
mailto:tien.nengch...@gmail.com>>:


Hi everyone,
My colleague sent me data of liquid CsNO3 sample measured using fluorescence 
model. According to the attached figure, I don't understand why mu(E) increased 
with increasing energy before and after the L3 edge. Does it make sense for 
cesium?  Thanks.

Nengchuan

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Re: [Ifeffit] Question about CsNO3 L3 edge

[Mangold, Stefan (IPS)]

normal for every element,

the higher the energy, the larger is the penetration depth —

regards

Stefan Mangold

Am 01.07.2021 um 06:13 schrieb 田能全 
mailto:tien.nengch...@gmail.com>>:


Hi everyone,
My colleague sent me data of liquid CsNO3 sample measured using fluorescence 
model. According to the attached figure, I don't understand why mu(E) increased 
with increasing energy before and after the L3 edge. Does it make sense for 
cesium?  Thanks.

Nengchuan

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Re: [Ifeffit] Larch 0.9.51

[Mangold, Stefan (IPS)]

Dear all,

tested the latest version on two Macs:

M1 on Big Sur
XAS viewer starts up, but the open dialog doesn’t work, it doesn’t open at all

old MacPro an 10.12.6
XAS viewer starts up, but the open dialog starts up, but I get a message, the 
he can’t read in the file or files. These file worked with the older version.

In both cases I started with an anaconda installation and made the update.

Matt, I can sent you more information.

Best regards

Stefan


Am 23.04.2021 um 18:12 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Folks,

Larch 0.9.51 is now available for download and use.   It's been several months 
since the last release, and there have been some important improvements to XAFS 
data processing and to the XAS Viewer application:

 - Parameters saved in an Athena Project File are now correctly saved and read 
into XAS Viewer (thanks Tyler Valentine!)

 - There is now a simple "Apply to all marked groups" feature for pre-edge peak 
fitting. That is, you can define a pre-edge peak model with one data set and 
then apply it to many others, either inspecting the individual fits or saving a 
CSV file with all the parameters and uncertainties for each fit to each data 
set.

 - XAS Viewer can now import multiple scans from a Spec file (thanks Mauro 
Rovezzi for help with this).  It may seem that Specfiles are "legacy", but the 
reader should also be able to handle the ESRF Bliss HDF5 files (as read in with 
the silx package, from ESRF), which is their way of efficiently stacking 
multiple scans into a single binary file.  While support for this here should 
be considered "beta" (or maybe "alpha"!), it is also reasonable to expect that 
this or a similar HDF5 format file will become a common way to collect and 
store XAFS data.

 - There are binary installers for Windows, MacOSX, and Linux. There are also 
now "GetLarch.sh" and "GetLarch.bat" scripts (that are very short) that can be 
run to do the download and install, essentially mimicking what the binary 
installer does.  This may be useful for folks wanting to install Larch on 
multi-user servers or in existing (or "other") Python environments.
This might also be useful for those who run into permissions issues, especially 
on MacOS, where installing a package from an untrusted source is often blocked 
by default.  With the installer script, the unprivileged user is simply running 
a script that downloads a bunch of files and places them in the home folder.
These scripts might also be useful for those who run into problems downloading 
very large files from 
millenia.cars.aps.anl.gov, as the installer 
scripts will use Anaconda and PyPI resources that are better distributed 
throughout the world.

... which brings me to a final note (I'll send out another message next week):  
The APS will have a planned power outage from April 30 to May 4 . This will 
take millenia.cars.aps.anl.gov off-line for 
those 5 +/- 1 days.  That machine hosts the binary installers and also this 
mailing list.   Mail sent to this list during that time will likely be lost 
(email routing servers can handle destination servers being down for a few 
hours, but not days).   So, if you're planning on sending announcements here, 
either do it before April 29 or wait until May 5.

If you have any questions, problems, or suggestions, please let me know.

--Matt

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Re: [Ifeffit] Not possible to install Larch MacOS X 10.12.6 via anaconda (see report)

[Mangold, Stefan (IPS)]

Hi Matt,

here is the output. I work directly on this machine and not via remote login

bash-3.2$ xas_viewer
Traceback (most recent call last):
  File "/Users/myloginname/opt/anaconda3/bin/xas_viewer", line 8, in 
sys.exit(run_xas_viewer())
  File 
"/Users/myloginname/opt/anaconda3/lib/python3.8/site-packages/larch/apps.py", 
line 146, in run_xas_viewer
from larch.wxxas import XASViewer
  File 
"/Users/myloginname/opt/anaconda3/lib/python3.8/site-packages/larch/wxxas/__init__.py",
 line 1, in 
from .taskpanel  import TaskPanel, FONTSIZE
  File 
"/Users/myloginname/opt/anaconda3/lib/python3.8/site-packages/larch/wxxas/taskpanel.py",
 line 10, in 
import wx
ModuleNotFoundError: No module named ‚wx‘




Am 16.03.2021 um 03:23 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Stefan,


Sorry, my earlier suggestions were automatically for Windows.  On MacOS, it 
would be pretty similar, but "open a Terminal" and then make sure that 
/Users/USERNAME/xraylarch exists and is in your path.

To launch xas_viewer, you *should* be able to do

 %>  xas_viewer

but you might need (note "pythonw", not "python"!)

 %> pythonw ~/xraylarch/bin/xas_viewer

The rest of the advice is basically the same:  try to do a conda update and/or 
report what error messages you get.

On MacOS, if you get

 This program needs access to the screen. Please run with a Framework build 
of python,
 and only when you are logged in on the main display of your Mac.
then you need to make sure you're running with "pythonw", not "python".



On Mon, Mar 15, 2021 at 5:32 PM Matt Newville 
mailto:newvi...@cars.uchicago.edu>> wrote:
Hi Stefan,

Sorry for the trouble.  It's always a little tricky to diagnose a problem of 
"it doesn't work", but here are a couple of things to try:

If you can open the Anaconda Prompt (from Start Menu it may be under "Anaconda3 
(64-bit) and then "Anaconda Prompt (xraylarch)") where you ran 'larch -m" from, 
try running

C:>   xas_viewer

That is supposed to run, but I suspect that it might print out some error 
messages.  If I had to guess, some package is not correctly installed.

Second, it might be helpful just to run (from the same prompt):

C:> conda update --all


and see if that installs some updates or spins forever.  If it finishes, then 
try running "xas_viewer" again.

Third, you could just try reinstalling from scratch.  That might be "easiest", 
but if you have the patience to try the other approaches above it would help 
identify what the problem is.

--Matt


On Mon, Mar 15, 2021 at 7:59 AM Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> wrote:
Thanks Matt,

installation worked. But still have the problem, that I can’t start XAS Viewer. 
I executed also larch -m (no error message).

regards

Stefan

Am 13.03.2021 um 16:35 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Stefan, Morgane, All,

Yeah, sorry for the trouble with this.   I should admit I've had increasing 
struggles over the past year or two with maintaining packages for Anaconda 
Python, running into many painful claims of incompatible packages.Most of 
the "core scientific python packages" are well-maintained by 
Anaconda.com<http://anaconda.com/> -- it's hard to complain about this free 
distribution and all of the work that goes into it.   But the 
"non-Anaconda-provided" packages make Larch more complicated, and the xraylarch 
"conda" package is out-of-date.

The semi-good news on this front is that almost everything, including Larch, is 
actually available from the PyPI packaging system and can be installed with 
"pip".  Anaconda and its "conda" package-manager will regularly say to not mix 
"conda" and "pip", but this mostly applies to cases where C code is going to be 
compiled on installation, which we don't do.

What I'm now doing for building the binary distributions, and what I recommend 
for updating is:
   1. install a basic Anaconda distribution - this can be from the Larch binary 
installers.
   2. install or update the Larch code with  "pip install --upgrade xraylarch".

I should probably take another look at adding xraylarch to the 
large-and-diverse "conda_forge" channel for the "conda" system.

Hope that helps, and suggestions on how to handle this better would be most 
welcome,

--Matt


On Fri, Mar 12, 2021 at 10:07 AM Morgane Desmau 
mailto:morgane.des...@gmail.com>> wrote:
Hello,

I already had this issue and it was related to the python version (6/7 months 
ago with python 3.8, and then it worked with Python 3.7, but I was thinking it 
was fixed since).

Best,
Morgane Desmau

Le ven. 12 mars 2021 à 16:55, Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit

Re: [Ifeffit] Not possible to install Larch MacOS X 10.12.6 via anaconda (see report)

[Mangold, Stefan (IPS)]

Thanks Matt,

installation worked. But still have the problem, that I can’t start XAS Viewer. 
I executed also larch -m (no error message).

regards

Stefan

Am 13.03.2021 um 16:35 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Stefan, Morgane, All,

Yeah, sorry for the trouble with this.   I should admit I've had increasing 
struggles over the past year or two with maintaining packages for Anaconda 
Python, running into many painful claims of incompatible packages.Most of 
the "core scientific python packages" are well-maintained by 
Anaconda.com<http://Anaconda.com> -- it's hard to complain about this free 
distribution and all of the work that goes into it.   But the 
"non-Anaconda-provided" packages make Larch more complicated, and the xraylarch 
"conda" package is out-of-date.

The semi-good news on this front is that almost everything, including Larch, is 
actually available from the PyPI packaging system and can be installed with 
"pip".  Anaconda and its "conda" package-manager will regularly say to not mix 
"conda" and "pip", but this mostly applies to cases where C code is going to be 
compiled on installation, which we don't do.

What I'm now doing for building the binary distributions, and what I recommend 
for updating is:
   1. install a basic Anaconda distribution - this can be from the Larch binary 
installers.
   2. install or update the Larch code with  "pip install --upgrade xraylarch".

I should probably take another look at adding xraylarch to the 
large-and-diverse "conda_forge" channel for the "conda" system.

Hope that helps, and suggestions on how to handle this better would be most 
welcome,

--Matt


On Fri, Mar 12, 2021 at 10:07 AM Morgane Desmau 
mailto:morgane.des...@gmail.com>> wrote:
Hello,

I already had this issue and it was related to the python version (6/7 months 
ago with python 3.8, and then it worked with Python 3.7, but I was thinking it 
was fixed since).

Best,
Morgane Desmau

Le ven. 12 mars 2021 à 16:55, Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> a écrit :
Dear all,

I tried to reinstall; before I updated and couldn’t open larch anymore


conda install -yc GSECARS xraylarch
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible 
solve.
Solving environment: failed with repodata from current_repodata.json, will 
retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible 
solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible 
with each other:


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[Ifeffit] Not possible to install Larch MacOS X 10.12.6 via anaconda (see report)

[Mangold, Stefan (IPS)]

Dear all,

I tried to reinstall; before I updated and couldn’t open larch anymore 


conda install -yc GSECARS xraylarch
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible 
solve.
Solving environment: failed with repodata from current_repodata.json, will 
retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible 
solve.
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed  

 

UnsatisfiableError: The following specifications were found to be incompatible 
with each other:


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Re: [Ifeffit] Normalization of LCF coefficients when fitting experimental spectra with theoretical spectra

[Mangold, Stefan (IPS)]

Dear Patricia,


Linear combination fits are a nice tool, but one should handle them with great 
care

- the background subtraction process can introduce significant errors. You have 
to fine tune the parameters by hand if you are using Athena to get reasonable 
results

- sometimes PCA (principle component analysis) helps to find a reasonable 
number of components

- Athena only shows the fitting errors: please keep in mind, that the error of 
the complete measurement and data evaluation process is much larger. It makes 
sense to test the process with known mixtures.

- the variation of the of the sum of all components between 98 and 105 % (even 
with choosing -> sum coefficients to 1) is a problem somewhere inside of 
Athena. I think only Bruce Ravel can help you there.

best regards

Stefan


> Am 08.03.2021 um 19:27 schrieb Patricia Poths :
> 
> Hi,
> 
> I am a theoretical chemistry PhD student working on fitting experimental 
> spectra with computed spectra in order to get a better understanding of the 
> composition. In the LCF process with athena, I have found that when I allow 
> "sum coefficients to 1", I get an unphysical negative coefficient of the last 
> standard- after reading through the mailing list I understood why, and so no 
> longer use that. The sum of my coefficients during the fitting now is close 
> to 1- generally within the range of 0.95-1.1 at the absolute extremes, but 
> more often around ~0.98- ~1.05. 
> 
> In order to compare these coefficients, I renormalize them to 1, so they can 
> represent the fractions of each component present. However, to test this I 
> took the new normalized coefficients and summed up the standards with their 
> respective weights to create this normalized "fit", and found that it is 
> worse than the initial one. Is this something I should be concerned about 
> when reporting the qualitative trends in how the composition changes? And if 
> so, is there a better way to do the fits in a more normalized way?
> 
> Many thanks,
> Patricia
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Re: [Ifeffit] Re. Larch Energy Calibration

[Mangold, Stefan (IPS)]

Dear Valerie,


The reason why I'm currently not using Larch for my data-evaluation chain is, 
that I didn’t found some features (like energy calibration; not as I use it; 
like Calibration of references, absorption and fluorescence spectra in one 
group) in Larch, which I need for my data evaluation process. They might be 
there, but I didn’t found them.

for the XANES data evaluation your energy region might be a bit to short to fit 
a good background to the data. Anyway you have to fine-tune the parameters to 
reach a good background fit in the XANES region. While the automatic process in 
Athena produces quite good results for a lot of absorption edges, one has to be 
careful not add artefacts to the data in the XANES.

Best regards

Stefan


> Am 08.03.2021 um 14:17 schrieb Schoepfer, Valerie 
> :
> 
> Hi Chris and Adam,
> 
> I'm actually looking at Mo, so the energy range is from about 19800 through 
> 20200 eV on a Si(220) monochromator.  (But thank you for your Fe offer!)
> The standards seem to be all from the Canadian Light Source, but going as far 
> back as 2013...
> I'm not looking to make the LCF perfect at this point, but it does seem like 
> the deeper I go, the less confident I am that I have the correct standards. 
> 
> I'm doing alright in Athena with respect to the process, its just that I 
> can't get Larch to align properly. I'll probably just use Athena for data 
> prep, Larch just seemed nice to learn.  
> But then in Athena I run into trouble with incorrect standards. One thing 
> after another, you know?
> 
> Thanks-
> Valerie
> 
> -Original Message-
> From: Ifeffit  On Behalf Of 
> ifeffit-requ...@millenia.cars.aps.anl.gov
> Sent: Thursday, March 4, 2021 12:00 PM
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: Ifeffit Digest, Vol 217, Issue 3
> 
> CAUTION: External to USask. Verify sender and use caution with links and 
> attachments. Forward suspicious emails to phish...@usask.ca
> 
> 
> Send Ifeffit mailing list submissions to
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> To subscribe or unsubscribe via the World Wide Web, visit
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> When replying, please edit your Subject line so it is more specific than "Re: 
> Contents of Ifeffit digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: Larch energy calibration (Matt Newville)
> 
> 
> --
> 
> Message: 1
> Date: Wed, 3 Mar 2021 18:38:24 -0600
> From: Matt Newville 
> To: XAFS Analysis using Ifeffit 
> Subject: Re: [Ifeffit] Larch energy calibration
> Message-ID:
>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Valerie,
> 
> On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < 
> valerie.schoep...@usask.ca> wrote:
> 
>> Hi,
>> 
>> 
>> 
>> I am using Larch XAS Viewer for the first time to analyze some Mo 
>> XANES data. It is fairly straightforward, however I am running into 
>> problems with energy calibration, which leads to problems with Linear 
>> Combination Fitting.
>> 
>> 
>> 
>> Right now, which is likely wrong, I?m calibrating the energy of a 
>> standard to the theoretical edge, then auto-aligning the samples to the 
>> standard.
>> But how do reference foils fit in here? Reference foils don?t seem to 
>> be tied to the sample like they are in Athena. Should I be manually aligning?
>> 
>> 
>> 
>> Is there a general guidance or work flow?
>> 
> 
> It's possible that I do not fully understand the question or that this answer 
> will veer a bit off the topic of your question.
> 
> For sure, energies need to be aligned properly for any multi-spectra 
> comparison or linear method to work well. But it should be that you will have 
> groups of spectra that all share a consistent energy calibration, say from 
> the same beamline/beamtime.
> 
> If you do have a reference channel for every measurement, you can compare 
> those reference channels.  Ideally, these will not vary for every
> measurement - that would indicate a serious problem.   So, I think you
> should be able to group spectra together as uniformly calibrated (hopefully 
> all data from a day or more of beamtime at a particular beamline) and then 
> make sure that the different groups of spectra.  Does that seem reasonable?
> 
> I have to admit that at my beamline I don't often have the luxury or need to 
> run a reference foil for every scan, so we calibrate consistently ahead
> of time.  I'm sure that leads to a bias in the software.   I guess I forgot
> that Athena had the ability to read and tie a second spectrum as a 
> "reference" and use that to auto-apply calibration.
> 
> Is it generally necessary to calibrate many spectra individually, or do 
> people find that doing them in a few large groups 

Re: [Ifeffit] P K-edge XANES spectrum question

[Mangold, Stefan (IPS)]

My2Cents,

strange features in spectra can be also induced by mixtures of different 
species (especially from different oxidation states, especially at low energies)

best regards

Stefan Mangold


Karlsruhe Institute of Technology (KIT)


Am 16.10.2020 um 07:26 schrieb Ganga Hettiarachchi 
mailto:ga...@ksu.edu>>:

All,
Can anyone provide some insight into the pre-edge “features” in this P XANES 
spectrum?
This is the P XANES spectrum we got for a recovered P-product (rich in Fe and 
Al) from wastewater using the AnMBR technology. During the coagulation process, 
our collaborators (environmental engineers) used stock solutions of aluminum 
chlorohydrate (ACH) and FeCl3.

Thanks very much.

Best regards,

Ganga



Ganga M. Hettiarachchi, Ph.D.
Professor of Soil and Environmental Chemistry
Department of Agronomy
2107 Throckmorton Plant Sciences Center
1712 Claflin Road
Kansas State University
Manhattan, KS 66506 USA

785-532-7209 (office)
785-532-6094 (FAX)

http://www.agronomy.k-state.edu/research/soil-and-environment/soil-environment-chem/
http://www.agronomy.k-state.edu/people/faculty/hettiarachchi-ganga/index.html

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Re: [Ifeffit] Larch 0.9.47

[Mangold, Stefan (IPS)]

Dear all,

tried the upgrade under anaconda3, on MacOs10.12.6. after the upgrade nothing 
worked any more

did the following steps:

conda update --all
conda install -yc GSECARS xraylarch
larch -m

and
pip install pyshortcuts==1.4
larch -m

nothing worked anymore. It worked again after a complete delete and re-install 
of the actual version of anaconda3

Best regards

Stefan Mangold

Am 28.02.2020 um 21:53 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Everyone,

Larch 0.9.47 is now available, with installers and source code at  
https://xraypy.github.io/xraylarch/installation.html.   For python users, there 
is a plain python package available on PyPI and conda packages for Anaconda 
Python.  See the installation docs for more details.

There have been several improvements and bug fixes, especially for the XAS 
Viewer application and for XRF modeling in the nearly six months since the last 
release.  In particular, there have been two improvements to basic XAFS and 
XANES data processing, both based on user reports and comparisons to older 
versions of Ifeffit/Athena and give a noticeable change in XAFS and XANES 
processing.

First, the ranges used in by the pre_edge() function for finding the edge step 
for normalization are now better determined from the actual data range rather 
than simply being hard-wired numbers.  These improvements were long over-due 
and give noticeably better default results for XANES data, especially for 
relatively low-energy edges such as S and Cl K edges.

When reading Athena Project files (say, to import into XAS Viewer), the 
pre-edge and normalization ranges from the Athena Project file will be 
preserved.  When reading in new raw data, or if you select the "Use Default 
Setting" button on the Normalization Panel for any group in XAS Viewer, the 
newer defaults will be used.   You can always alter these values, but in 
playing around with this with a range of datasets, the new defaults seem to 
give a noticeable improvement in almost all cases and rarely bad.

Second, as a few users have pointed out or gently hinted at over many months, 
there were sometimes significant differences in the background removals between 
classic Autobk/Ifeffit/Athena and Larch, with Larch sometimes being noticeably 
and inexplicably worse. I believe this involved two different problems.  One 
was introduced a while back when implementing an estimate of delta_chi - the 
variance in chi due to the background subtraction. This estimate is important, 
but I botched some of the configurations of the number of knots, fit range, and 
Rbkg. The other problem was that "spline clamps" were just done too differently 
in Larch and Ifeffit/Athena.

I believe this is now working much better: the background results are much more 
consistent, and do not occasionally get "very bad".  They also happen to be 
generally closer to Autobk/Ifeffit/Athena, and perhaps slightly better because 
the fit range in R-space is now more consistently determined (instead of 
wandering +/- a few R data points around Rbkg where the misfit will often be 
the largest). In addition, `delta_chi` (never calculated in Ifeffit/Athena) is 
now also more consistent.  One consequence of this change is that a very small 
change in Rbkg (of say 0.01 to 0.05 Ang) may actually give no difference at all 
in mu0(E) or in chi(k).

I bring these changes up because I think they will be noticeable.  I think they 
are both improvements, but let me know if you find cases for which you think 
are now made worse.   Possibly related: one thing that I definitely noticed in 
going through several example data sets was that I tended to favor a k-weight 
of 2 instead of 1 for background subtraction -- so much so that it seemed like 
this might be a better default.  I did not change this default yet, but if you 
have a strong opinion on this, that might be a good topic for discussion here.

There are some documentation improvements, but this is an ongoing process and 
never complete.  It is also one area where help and feedback would greatly be 
appreciated.  If you or your students have time to work through the larch 
examples and/or documentation and make improvements or even suggestions for 
improvements in readability or completeness, it would be greatly appreciated.

Thanks,

--Matt Newville
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Re: [Ifeffit] Larch install error

[Mangold, Stefan (IPS)]

Thanks, your feedback helped. Shortcuts are now created and XAS-viewer works as 
before...

Best regards
Stefan

Von: Matt Newville 
Gesendet: Donnerstag, 3. Oktober 2019 18:46:13
An: Mangold, Stefan (IPS)
Cc: XAFS Analysis using Ifeffit
Betreff: Re: Larch install error

Hi Stefan,



On Wed, Oct 2, 2019 at 12:08 PM Mangold, Stefan (IPS) 
mailto:stefan.mang...@kit.edu>> wrote:
Dear Matt,


I tried to install larch via Anaconda. Install of Anaconda and larch seems to 
work fine, but I couldn't create the Links via

larch -m
[numexpr.utils] INFO : NumExpr defaulting to 8 threads.
Warning: could not create shortcut to  /Users/myaccount/anaconda3/bin/larch
Warning: could not create shortcut to  /Users/myaccount/anaconda3/bin/larch 
--wxgui
Warning: could not create shortcut to  /Users/myaccount/anaconda3/bin/xas_viewer
Warning: could not create shortcut to  
/Users/myaccount/anaconda3/bin/gse_mapviewer
Warning: could not create shortcut to  
/Users/myaccount/anaconda3/bin/gse_dtcorrect
Warning: could not create shortcut to  /Users/myaccount/anaconda3/bin/xrfdisplay
Warning: could not create shortcut to  
/Users/myaccount/anaconda3/bin/dioptas_larch
Warning: could not create shortcut to  
/Users/myaccount/anaconda3/bin/xrd2d_viewer
Warning: could not create shortcut to  
/Users/myaccount/anaconda3/bin/xrd1d_viewer

I have MacOS Sierra installed

On a similar system I installed larch half a year ago without any issues.

Oh very sorry.  I can reproduce this. I believe that an update to `pyshortcuts` 
 (which *will* be a good thing for the next release of Larch) has broken the 
current release.  (ah progress!).
I also believe that this means that Larch did get installed correctly, but that 
the Desktop Apps/Icons did not get made.

You should be able to do this from a Terminal command line:

  pip install pyshortcuts==1.4
  larch -m

Let me know whether that fixes it or not.
Cheers,

--Matt

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[Ifeffit] Larch install error

[Mangold, Stefan (IPS)]

Dear Matt,


I tried to install larch via Anaconda. Install of Anaconda and larch seems to 
work fine, but I couldn’t create the Links via

larch -m
[numexpr.utils] INFO : NumExpr defaulting to 8 threads.
Warning: could not create shortcut to  /Users/myaccount/anaconda3/bin/larch
Warning: could not create shortcut to  /Users/myaccount/anaconda3/bin/larch 
--wxgui
Warning: could not create shortcut to  /Users/myaccount/anaconda3/bin/xas_viewer
Warning: could not create shortcut to  
/Users/myaccount/anaconda3/bin/gse_mapviewer
Warning: could not create shortcut to  
/Users/myaccount/anaconda3/bin/gse_dtcorrect
Warning: could not create shortcut to  /Users/myaccount/anaconda3/bin/xrfdisplay
Warning: could not create shortcut to  
/Users/myaccount/anaconda3/bin/dioptas_larch
Warning: could not create shortcut to  
/Users/myaccount/anaconda3/bin/xrd2d_viewer
Warning: could not create shortcut to  
/Users/myaccount/anaconda3/bin/xrd1d_viewer

I have MacOS Sierra installed

On a similar system I installed larch half a year ago without any issues. 

best regards
Stefan Mangold

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Re: [Ifeffit] Larch 0.9.43

[Mangold, Stefan (IPS)]

Dear Matt,


conda update —all
does not help. I think re-install anaconda is the only option. I testet this on 
a Mac (10.12.6).

best regards
Stefan

Am 02.05.2019 um 19:08 schrieb Matt Newville 
mailto:newvi...@cars.uchicago.edu>>:

Hi Garret,


On Thu, May 2, 2019 at 8:33 AM Garret Bland 
mailto:gbl...@andrew.cmu.edu>> wrote:
Hi Matt,
I just want everyone to know that for Windows, I tried to update larch to 
0.9.43 from my existing Anaconda environment, but wasn't able to because of the 
Python version (3.6.8).

Ah, OK.  I  saw that "update" did not work from an older version using Python 
2.7 too.   I guess it will not update python versions, though I am not sure of 
that  Hopefully the ability to do a conda update will be useful until we 
switch to Python 3.8, which is probably at least a year away.

We did notice yesterday that - at least on Windows - the Warning that things 
may not work correctly if there is a space in the installation path is a 
correct warning.  Some of the things that we saw not work correctly include 
making the desktop icons or launching the applications from the auto-generated 
'.exe'  files.   I think this is not specific to Larch, and not something I'm 
going to be able to fix or work around easily.  For people who have a space in 
their username, I believe you will need to install to another folder.

I just recreated a new environment with Python 3.7.3 and I was able to update 
to the current version. And thanks for fixing up the import statements! Can't 
wait to use larch on jupyter notebook :).

Great, I'd be interested to see what you use these for.  That is, it might be 
nice to have some example notebooks.

--Matt Newville

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