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...ok....add rhombohedral structure (B) but don't >> run it..rerun Ni and Ni changes. >> >> Clean start, import hexagonal structure (in P6)...ok...import >> Ni...ok....change 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 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 >>>> >>>> >>>> >>> >>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit@millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit@millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> > > _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit