Re: [Ifeffit] LCF on Larch - EXAFS Region
Thanks for the reply Matt! I mostly do linear combinations in the XANES region as well, but with Hg, I also do first derivative of XANES and EXAFS regions to confirm my fits. Garret On Thu, Aug 9, 2018 at 3:57 PM Matt Newville wrote: > Hi Garret, > > On Thu, Aug 9, 2018 at 12:27 PM Garret Bland > wrote: > >> Hello! >> >> I've recently been trying to use Larch instead of Athena for EXAFS >> analysis, and I mainly do linear combination fitting for my samples. It >> seems that the XANES fitting is doing just fine requesting a specified >> region to fit (-25 to +75 eV). When I try to fit in the k-space however, >> Larch does not request a specific region in k space. I try to input the eV >> values corresponding to the k value I want to fit, but it is still plotting >> in mu rather than k . Is there anyway I can change this and/or do it >> manually on the larch GUI? Any help would be appreciated! >> > > You're right that linear combinations in k-space are not really working in > Larch's XAS Viewer, including that the range can only be set in energy. > Much of XAS Viewer is fairly new -- I think it is fairly complete, but > there are a few missing parts. I don't ever do linear combinations of > chi(k) myself and am slightly skeptical that they are robust, so they've > haven't surfaced to the top of the ToDo list yet. Any help would be > greatly appreciated. > > --Matt > > ___ > 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 > -- Garret Bland Graduate Student Carnegie Mellon University Civil and Environmental Engineering Porter Hall 207C Pittsburgh, PA, 15213 ___ 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
Re: [Ifeffit] LCF on Larch - EXAFS Region
This is interesting. Could you say more about your skepticism of the robustness of EXAFS LCF, Matt? To be fair, it suffers from many of the same drawbacks of XANES LCF, plus others. But I'm curious about your thoughts on it since yours seems to be what amounts to a "strong opinion" on the subject. > On Aug 9, 2018, at 12:56 PM, Matt Newville wrote: > > Hi Garret, > >> On Thu, Aug 9, 2018 at 12:27 PM Garret Bland wrote: >> Hello! >> >> I've recently been trying to use Larch instead of Athena for EXAFS analysis, >> and I mainly do linear combination fitting for my samples. It seems that the >> XANES fitting is doing just fine requesting a specified region to fit (-25 >> to +75 eV). When I try to fit in the k-space however, Larch does not request >> a specific region in k space. I try to input the eV values corresponding to >> the k value I want to fit, but it is still plotting in mu rather than k . Is >> there anyway I can change this and/or do it manually on the larch GUI? Any >> help would be appreciated! > > You're right that linear combinations in k-space are not really working in > Larch's XAS Viewer, including that the range can only be set in energy. Much > of XAS Viewer is fairly new -- I think it is fairly complete, but there are a > few missing parts. I don't ever do linear combinations of chi(k) myself and > am slightly skeptical that they are robust, so they've haven't surfaced to > the top of the ToDo list yet. Any help would be greatly appreciated. > > --Matt > > ___ > 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
Re: [Ifeffit] LCF on Larch - EXAFS Region
Hi Garret, On Thu, Aug 9, 2018 at 12:27 PM Garret Bland wrote: > Hello! > > I've recently been trying to use Larch instead of Athena for EXAFS > analysis, and I mainly do linear combination fitting for my samples. It > seems that the XANES fitting is doing just fine requesting a specified > region to fit (-25 to +75 eV). When I try to fit in the k-space however, > Larch does not request a specific region in k space. I try to input the eV > values corresponding to the k value I want to fit, but it is still plotting > in mu rather than k . Is there anyway I can change this and/or do it > manually on the larch GUI? Any help would be appreciated! > You're right that linear combinations in k-space are not really working in Larch's XAS Viewer, including that the range can only be set in energy. Much of XAS Viewer is fairly new -- I think it is fairly complete, but there are a few missing parts. I don't ever do linear combinations of chi(k) myself and am slightly skeptical that they are robust, so they've haven't surfaced to the top of the ToDo list yet. Any help would be greatly appreciated. --Matt ___ 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] LCF on Larch - EXAFS Region
Hello! I've recently been trying to use Larch instead of Athena for EXAFS analysis, and I mainly do linear combination fitting for my samples. It seems that the XANES fitting is doing just fine requesting a specified region to fit (-25 to +75 eV). When I try to fit in the k-space however, Larch does not request a specific region in k space. I try to input the eV values corresponding to the k value I want to fit, but it is still plotting in mu rather than k . Is there anyway I can change this and/or do it manually on the larch GUI? Any help would be appreciated! Thanks, Garret -- Garret Bland Graduate Student Carnegie Mellon University Civil and Environmental Engineering Porter Hall 207C Pittsburgh, PA, 15213 ___ 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
Re: [Ifeffit] Demeter on ubuntu 14.04
... Okay, now on ubuntu 16.04. it worked including larch. Not completely without some pain, but almost. I installed it as user. It was missing wx and my attempts to install it from cpan were failing. Installing from repositories solved the issue and Demeter build without problems after that. Cheers, Edmund On 09.08.2018 11:49, Edmund Welter wrote: Dear Bruce, Robert, thanks for the hints. I just installed Larch, it is running (meaning I can start the larch_gui) and the last error message, the one concerning Larch disappeared. All the others are still there. Anyway, I am just now upgrading to 16.04. I do not think that the problem is caused by Demeter or by 14.04 (Demeter was running on 14.04). I think I broke something in my ubuntu. Several packages which are vital for Demeter are reported as broken in /var/log/dist-upgrade/apt.log The last entry way "libalien-wxwidgets-perl". This broken package actually blocked the distribution upgrade and I had to remove it before i could continue. Well let's see, the next step will be a fresh install of 16.04 Cheers, Edmund On 08.08.2018 17:11, Bruce Ravel wrote: Is larch up to date? Or even installed? It would seem that $larch_exe is not being evaluated properly and is undefined when you get to line 288 in Larch.pm. B On 08/08/2018 10:07 AM, Edmund Welter wrote: Dear all, I am hitting a wall trying to install the latest Demeter version on my ubuntu laptop. System: Ubuntu 14.04 Demeter: 0.9.26 perl: 5.18.2 pdl and pdl::stats from repositories. (I tried a newer versions from cpan, but ot no avail) moose: initially from repositories, than vs. 2.2011 from cpan I did follow the installation instructions on https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.html and tried to install demeter in ~/perl5 and also the instructions in: https://bruceravel.github.io/demeter/documents/SinglePage/installation.html to install Demeter as sudo Both attempts ended with the same result when I start dathena in a terminal the image of the goddess appears briefly and I get the following error messages in the terminal: - Invalid version format (non-numeric data) at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Moose.pm line 15, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose.pm line 15, line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, line 90. Compilation failed in require at /usr/local/bin/dathena line 31, line 90. BEGIN failed--compilation aborted at /usr/local/bin/dathena line 31, line 90. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288, line 90. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288, line 90. When i try to start denv to create the nice overview of installed components I only get the following errors: [PDL->Version: 10 PDL_CORE_VERSION: 8 XS_VERSION: ] PDL::Stats::Distr needs to be recompiled against the newly installed PDL at /usr/lib/perl/5.18/DynaLoader.pm line 207. Compilation failed in require at (eval 1130) line 5. BEGIN failed--compilation aborted at (eval 1130) line 5. BEGIN failed--compilation aborted at /usr/local/bin/denv line 24. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288. -- This is insofar interesting as I got the same error about PDL when I tried to start dathena before I installed the pdl::stats module from cpan, that means when both, pdl and pdl::stats were installed from repositories. Any hint would be welcome, upgrading ubuntu to a newer LTS version might be useful (It is absolutely possible that something is weird with this installation after a lot of playing around) but I am currently reluctant to do so, because it will for sure break other things... Best regards, Edmund ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe:
Re: [Ifeffit] Artemis problem
Please reply solution of problem. Regards, Parasmani On Sun, Aug 5, 2018 at 4:28 AM, ParasMani Rajput wrote: > Dear All, > > I am using windows 8 and running ARTEMIS (1.2.11) in my leptop. Today I > found that Artemis not working properly. When I am opening my project > files in Artemis then showing an error massage "Artemis trapped one or > more errors! Error message dumped to the screen" where i fitted and saved > the project file the day before. > > Please let me know if some has seen this problem and how to resolve it. > > Regards, > > Parasmani > > --- > Dr. Parasmani Rajput > > Atomic & Molecular Physics Division BL-09, INDUS-2 complex > Bhabha Atomic Research Centre Raja Ramanna Centre for Advanced > Technology > Trombay, Mumbai-85, India Indore, Madhya Pradesh 452013, > India > > E-mail: parasmaniraj...@gmail.com > Phone: (+91) 731-2442509 > > Web page :https://sites.google.com/site/parasmanirajput/ > orcid.org/-0003-0694-6756 > http://www.researcherid.com/rid/E-4783-2011 > > --- > ___ 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
Re: [Ifeffit] Demeter on ubuntu 14.04
Dear Bruce, Robert, thanks for the hints. I just installed Larch, it is running (meaning I can start the larch_gui) and the last error message, the one concerning Larch disappeared. All the others are still there. Anyway, I am just now upgrading to 16.04. I do not think that the problem is caused by Demeter or by 14.04 (Demeter was running on 14.04). I think I broke something in my ubuntu. Several packages which are vital for Demeter are reported as broken in /var/log/dist-upgrade/apt.log The last entry way "libalien-wxwidgets-perl". This broken package actually blocked the distribution upgrade and I had to remove it before i could continue. Well let's see, the next step will be a fresh install of 16.04 Cheers, Edmund On 08.08.2018 17:11, Bruce Ravel wrote: Is larch up to date? Or even installed? It would seem that $larch_exe is not being evaluated properly and is undefined when you get to line 288 in Larch.pm. B On 08/08/2018 10:07 AM, Edmund Welter wrote: Dear all, I am hitting a wall trying to install the latest Demeter version on my ubuntu laptop. System: Ubuntu 14.04 Demeter: 0.9.26 perl: 5.18.2 pdl and pdl::stats from repositories. (I tried a newer versions from cpan, but ot no avail) moose: initially from repositories, than vs. 2.2011 from cpan I did follow the installation instructions on https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.html and tried to install demeter in ~/perl5 and also the instructions in: https://bruceravel.github.io/demeter/documents/SinglePage/installation.html to install Demeter as sudo Both attempts ended with the same result when I start dathena in a terminal the image of the goddess appears briefly and I get the following error messages in the terminal: - Invalid version format (non-numeric data) at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Moose.pm line 15, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose.pm line 15, line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, line 90. Compilation failed in require at /usr/local/bin/dathena line 31, line 90. BEGIN failed--compilation aborted at /usr/local/bin/dathena line 31, line 90. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288, line 90. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288, line 90. When i try to start denv to create the nice overview of installed components I only get the following errors: [PDL->Version: 10 PDL_CORE_VERSION: 8 XS_VERSION: ] PDL::Stats::Distr needs to be recompiled against the newly installed PDL at /usr/lib/perl/5.18/DynaLoader.pm line 207. Compilation failed in require at (eval 1130) line 5. BEGIN failed--compilation aborted at (eval 1130) line 5. BEGIN failed--compilation aborted at /usr/local/bin/denv line 24. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288. -- This is insofar interesting as I got the same error about PDL when I tried to start dathena before I installed the pdl::stats module from cpan, that means when both, pdl and pdl::stats were installed from repositories. Any hint would be welcome, upgrading ubuntu to a newer LTS version might be useful (It is absolutely possible that something is weird with this installation after a lot of playing around) but I am currently reluctant to do so, because it will for sure break other things... Best regards, Edmund ___ 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
