Re: [Ifeffit] Conflicting FEFF calculation

2017-04-04 Thread Ashis Biswas
Dear Bruce,
In the new pre-release version of Artemis I am getting similar paths for TAA 
regardless of the order of import. Therefore, the problem does not exist 
anymore. Thank you very much for your time and help.
With regards,
Ashis

From: Ifeffit <ifeffit-boun...@millenia.cars.aps.anl.gov> on behalf of Robert 
Gordon <ragor...@alumni.sfu.ca>
Sent: Tuesday, April 4, 2017 17:58
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Conflicting FEFF calculation

Hi Bruce,

Issues with the pre-release. Log file attached.

Seems to be looking for gnuplot in the wrong location. Gnuplot was
installed to:
C:\Users\ragordon\AppData\Roaming\DemeterPerl\c\bin\gnuplot
not
C:\Strawberry...


also, log has this:
C:/Users/ragordon/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm
line 26

Which has the slashes in the wrong direction for windows...just
something from the log writing
or a linux-typo in the program somewhere?


-R.


On 4/4/2017 7:07 AM, Bruce Ravel wrote:
>
>
> Robert, thanks for doing so much work to verify what Ashis is seeing.
>
> That said, I am still not seeing this problem.  My working notion is
> that it is a problem that somehow got fixed while I was doing some
> other work a few months ago.
>
> This morning, I prepared and uploaded a new installer package as a
> pre-release of the upcoming version.  Here's the direct link.
>
> https://s3.amazonaws.com/demeter4xas/Demeter_0.9.26_with_Strawberry_Perl_(64)_pre2.exe
>
>
> If one or both of you could install this and let me know if the
> problem persists, I would be grateful.
>
>
> I did uncover a bunch of of problems with Demeter's crystallography
> bits while I was working on
>
>https://github.com/bruceravel/WebAtoms,
>http://millenia.cars.aps.anl.gov/webatoms
>
> I don't really see the value of sifting through all that work to
> figure out what had an impact on Ashis' issue.  If the newer code
> works -- that seems good enough to me.
>
> B
>
>
> On 04/03/2017 06:08 PM, Robert Gordon wrote:
>> Hi Ashis,
>>
>> I can reproduce what you are seeing.
>> I exported the atoms.inp's for your two structures.
>>
>> If I import TAA first and run atoms, it looks ok. I then import TPA and
>> run - ok.
>> I re-run Atoms on TAA, it changes.
>>
>> In fact, from a clean start of Artemis 0.9.25 on win10pro/AMD64, if I
>> import TAA's inp and run it, it looks ok.
>> I added it again, it still looks ok, even if I re-run Atoms. I add TPA
>> and run it, it looks ok, but if I rerun
>> either of the TAA, they have changed. Changes persist even if TPA
>> discarded.
>>
>> From another clean start of Artemis, I import TAA and run Atoms - ok.
>> I import a different inp (ni metal) and run it - ok. Re-run TAA and it
>> is ok.
>>
>> From another clean start, I import Ni metal and run it...ok
>> Import TPA and run it...ok...Rerun Ni and Ni changes...definite symmetry
>> change.
>> This symmetry change persists even if I discard TPA and import another
>> copy of Ni.
>>
>> Clean start, import Ni and run, then import another Rhombohedral
>> structure (B phase)
>> and same problem...symmetry changes and I don't seem to be able to get
>> it to change back,
>> even when I deliberately change the space group for Ni and it is the
>> only calculation remaining.
>>
>> Clean start...import Ni...okadd rhombohedral structure (B) but don't
>> run it..rerun Ni and Ni changes.
>>
>> Clean start, import hexagonal structure (in P6)...ok...import
>> Ni...okchange hex to Rhomb indexed on hex
>> and Ni changes when rerun...
>>
>> So...problem seems to be related to the symmetry - stuck in Rhombohedral
>> once a R-structure
>> is added...or symmetry changed to R.
>>
>> Haven't tried on Linux yet.
>>
>> -R.
>>
>>
>>
>>
>>
>> On 4/3/2017 1:46 PM, Ashis Biswas wrote:
>>>
>>> Dear Bruce,
>>>
>>> Sorry for late reply. I wanted to test in another computer before
>>> replying. Unfortunately, this time also I got different results for
>>> TAA. Following is the click by click description of what I am doing to
>>> arrive in this state:
>>>
>>> Double click on “Atemis” shortcut on desktop => Click “add” in the
>>> Feff calculation tab => Open “TPP” Atom input file from desktop=>
>>> Click “Run Atom” => Click “Run Feff” => Click “add” in the Feff
>>> calculation tab => Open “TAA” CIF file from desktop=> Click “Run Atom”
>>> => Click “Run Feff”
>>>
>>> I am 

Re: [Ifeffit] Conflicting FEFF calculation

2017-04-04 Thread Ashis Biswas

Dear Robert and Bruce,

Thank you very much for your explanation and time; I am grateful for 
that. I will test the problem with new version and report back as soon 
as possible.


With regards,

Ashis


On 2017-04-04 16:07, Bruce Ravel wrote:



Robert, thanks for doing so much work to verify what Ashis is seeing.

That said, I am still not seeing this problem.  My working notion is 
that it is a problem that somehow got fixed while I was doing some 
other work a few months ago.


This morning, I prepared and uploaded a new installer package as a 
pre-release of the upcoming version.  Here's the direct link.


https://s3.amazonaws.com/demeter4xas/Demeter_0.9.26_with_Strawberry_Perl_(64)_pre2.exe 



If one or both of you could install this and let me know if the 
problem persists, I would be grateful.



I did uncover a bunch of of problems with Demeter's crystallography 
bits while I was working on


   https://github.com/bruceravel/WebAtoms,
   http://millenia.cars.aps.anl.gov/webatoms

I don't really see the value of sifting through all that work to 
figure out what had an impact on Ashis' issue.  If the newer code 
works -- that seems good enough to me.


B


On 04/03/2017 06:08 PM, Robert Gordon wrote:

Hi Ashis,

I can reproduce what you are seeing.
I exported the atoms.inp's for your two structures.

If I import TAA first and run atoms, it looks ok. I then import TPA and
run - ok.
I re-run Atoms on TAA, it changes.

In fact, from a clean start of Artemis 0.9.25 on win10pro/AMD64, if I
import TAA's inp and run it, it looks ok.
I added it again, it still looks ok, even if I re-run Atoms. I add TPA
and run it, it looks ok, but if I rerun
either of the TAA, they have changed. Changes persist even if TPA 
discarded.


From another clean start of Artemis, I import TAA and run Atoms - ok.
I import a different inp (ni metal) and run it - ok. Re-run TAA and it
is ok.

From another clean start, I import Ni metal and run it...ok
Import TPA and run it...ok...Rerun Ni and Ni changes...definite symmetry
change.
This symmetry change persists even if I discard TPA and import another
copy of Ni.

Clean start, import Ni and run, then import another Rhombohedral
structure (B phase)
and same problem...symmetry changes and I don't seem to be able to get
it to change back,
even when I deliberately change the space group for Ni and it is the
only calculation remaining.

Clean start...import Ni...okadd rhombohedral structure (B) but don't
run it..rerun Ni and Ni changes.

Clean start, import hexagonal structure (in P6)...ok...import
Ni...okchange hex to Rhomb indexed on hex
and Ni changes when rerun...

So...problem seems to be related to the symmetry - stuck in Rhombohedral
once a R-structure
is added...or symmetry changed to R.

Haven't tried on Linux yet.

-R.





On 4/3/2017 1:46 PM, Ashis Biswas wrote:


Dear Bruce,

Sorry for late reply. I wanted to test in another computer before
replying. Unfortunately, this time also I got different results for
TAA. Following is the click by click description of what I am doing to
arrive in this state:

Double click on “Atemis” shortcut on desktop => Click “add” in the
Feff calculation tab => Open “TPP” Atom input file from desktop=>
Click “Run Atom” => Click “Run Feff” => Click “add” in the Feff
calculation tab => Open “TAA” CIF file from desktop=> Click “Run Atom”
=> Click “Run Feff”

I am sorry for killing your time. Actually, I am very much new in this
field and therefore I really want to be sure that what I am doing for
importing object for feff calculation is correct or not. Thank you
very much for your support.

With regards,

Ashis


On 2017-03-28 16:13, Bruce Ravel wrote:

On 03/27/2017 11:02 AM, Ashis Biswas wrote:

Thank you very much for your reply. Here I am attaching two Artemis
projects files (TAA_TPA and TPA_TAA), named according to their 
order of
import. In my computer the paths for *TAA* are different in two 
project

files. For example, i) in TAA_TPA project the Reff for three single
scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to
that in
TPA_TAA project, ii) the single scattering path @C5.1 (path number
6) at
Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, 
and

so on.

I am also attaching the papers from where the coordinates for TAA and
TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) 
and

TPA (Pappalardo et al., 1983: Table 1; Fig. 1).



I agree that the TPA_TAA.fpj project file that you sent me has
incorrect data in the Feff tab for TAA.

I have not, however, been able to reproduce that here.  And not for
want of trying -- I spent the last half hour trying to find a way to
replicate what you are showing in the TPA_TAA file. Regardless of
the order in which I import the two structures and regardless of
whether I have discarded and reimported Feff calculations, when I
click the "Run Atoms" button on the TAA cif file, I /always/ get the
structure from T

Re: [Ifeffit] Conflicting FEFF calculation

2017-04-03 Thread Ashis Biswas

Dear Bruce,

Sorry for late reply. I wanted to test in another computer before 
replying. Unfortunately, this time also I got different results for TAA. 
Following is the click by click description of what I am doing to arrive 
in this state:


Double click on “Atemis” shortcut on desktop => Click “add” in the Feff 
calculation tab => Open “TPP” Atom input file from desktop=> Click “Run 
Atom” => Click “Run Feff” => Click “add” in the Feff calculation tab => 
Open “TAA” CIF file from desktop=> Click “Run Atom” => Click “Run Feff”


I am sorry for killing your time. Actually, I am very much new in this 
field and therefore I really want to be sure that what I am doing for 
importing object for feff calculation is correct or not. Thank you very 
much for your support.


With regards,

Ashis


On 2017-03-28 16:13, Bruce Ravel wrote:

On 03/27/2017 11:02 AM, Ashis Biswas wrote:

Thank you very much for your reply. Here I am attaching two Artemis
projects files (TAA_TPA and TPA_TAA), named according to their order of
import. In my computer the paths for *TAA* are different in two project
files. For example, i) in TAA_TPA project the Reff for three single
scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to that in
TPA_TAA project, ii) the single scattering path @C5.1 (path number 6) at
Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and
so on.

I am also attaching the papers from where the coordinates for TAA and
TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and
TPA (Pappalardo et al., 1983: Table 1; Fig. 1).



I agree that the TPA_TAA.fpj project file that you sent me has 
incorrect data in the Feff tab for TAA.


I have not, however, been able to reproduce that here.  And not for 
want of trying -- I spent the last half hour trying to find a way to 
replicate what you are showing in the TPA_TAA file. Regardless of the 
order in which I import the two structures and regardless of whether I 
have discarded and reimported Feff calculations, when I click the "Run 
Atoms" button on the TAA cif file, I /always/ get the structure from 
Table 4 in the Kamenar paper.  I cannot reproduce the Feff tab that 
you show in your TPA_TAA project file.


I have no idea how you got into the state you show in the TPA_TAA 
project.  It is clear that something went awry, but I don't know if it 
is an error of the program or of the user.  I can't fix a problem I 
can't observe.


I understand that this is not the answer you were looking for.  I am 
simply not seeing the problem you are reporting.


B





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[Ifeffit] Conflicting FEFF calculation

2017-03-21 Thread Ashis Biswas

Dear All,

I have a problem of conflicting FEFF calculation for 
tris(acetate-O)arsenic [As(OCOCH3)3] (TAA) and tris(phenyl thio)arsenic 
[As(SC6H5)3] (TPA); respective cif and atom input files are attached. In 
Artemis, when I import TAA after TPA, the paths obtained for TAA from 
FEFF calculation are different compared to the scenario when I import 
and calculate the path for TAA at first. The problem is similar in both 
computers with Windows 7 home premium 64 bit operating system and 0.9.24 
version of Demeter and Windows 7 professional 32 bit operating system 
and 0.9.25 version of Demeter.


I have even tried a scenario, where I discarded both FEFF objects after 
getting inconsistent results for TAA and then imported TAA at first 
without restarting Artemis and I got wrong paths again, indicating 
software can remember from last calculation. Any explanation for this 
problem will be deeply appreciated.


With regards,

Ashis

--

Dr. Ashis Biswas
Alexander von Humboldt Postdoctoral Fellow
Environmental Geochemistry Group
University of Bayreuth
Room: 211, Geo III
Universitätsstraße 30, 95447 Bayreuth, Germany
Ph. No.: +49 921 553991; Fax:+49 921 552334



Tris_acetato_arsenic.cif
Description: CIF chemical test
## This Atoms file was generated by Demeter 0.9.24
## Demeter written by and copyright (c) Bruce Ravel, 2006-2015

title = Tris_Phenylthio_arsine
title = Pappalardo et al., 1983_C39_P_1618_1620
space = R -3
a =   9.70600b=   9.70600c =   9.70600
alpha =  82.27000beta =  82.27000gamma =  82.27000
rmax  =   8.0core  = As1
# polarization = 0.0  0.0  0.0
shift = 0.00.00.0
atoms
# el. x   y   ztag
  As 0.10460 0.10460 0.10460   As1   
  S  0.03998 0.33298 0.12177   S1
  C  0.85464 0.33110 0.14979   C1
  C  0.77915 0.34183 0.03628   C2
  C  0.63528 0.34838 0.05761   C3
  C  0.56520 0.34237 0.19082   C4
  C  0.64109 0.33011 0.30441   C5
  C  0.21472 0.32388 0.28415   C6
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