- Ifeffit - millenia.cars.aps.anl.gov

restraints in larch
by Barbara Etschmann 12 Oct '18

12 Oct '18

Hello I'm trying to use larch to refine the coordination of Y in solution. I need to use 2xO paths to fit the first shell and would like to restrain the total coordination to be between 5.5 and 8. I can apply the constraint to each nO, but not the total, i.e. nO1 = param(7.0, min=5, max=7, vary=True), nO2 = param(1, vary=True), but ntot1 = param(expr='nO1+nO2', min=5.0, max=8.5) does not work. How can I restrain the total coordination? Also, having some problems with the gofs and errors - the chi square is rather small and often the errors are not reported and it is not clear why. Thanks Barb

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Better late than never
by Anatoly Frenkel 10 Oct '18

10 Oct '18

After 15 years or so of using Athena, I just accidentally learned that the vertical scale of the plot can be changed by simply turning the scroll wheel of the mouse! Anatoly

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Larch: GSE Mapviewer export error
by Naomi Intrator 06 Oct '18

06 Oct '18

Hello I made correlation plots in the GSE Mapviewer and am trying to export the data. When I click file, export data. I get an error that says 'Export Data to ASCII: Export Data not available" I have tried to do this on both a Mac and Windows. Has anyone else encountered this and know a way around it? Thank you, Naomi

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Re: [Ifeffit] Port p5.26-ifeffit not installing via MacPorts on Yosemite
by Fowler, Joseph W. (Assoc) 17 Sep '18

17 Sep '18

Dear Sergio, Thanks for the alert. I’m the official MacPorts maintainer of ifeffit, but I must make my usual warning: I am very experienced with Unix and Linux in general, but I know practically nothing about Perl and don’t really understand MacPorts. (If anyone reading this has the qualifications and the willingness to replace me as maintainer of ifeffit and demeter, we need to talk!) I have been trying for months—and failing—to get Demeter version 0.9.26 to build on my Mac, which gives you a sense of my competence for this job. Anyway, to the topic at hand. Thank you for including the log file. It looks clear to me that your linker is not finding a gfortran run-time library. You might lack the library on your system, or the library is simply not listed among the link options in your compile command. fowlerj@817jfmac:~$ port installed g95 The following ports are currently installed: g95 @0.93_5 (active) fowlerj@817jfmac:~$ port installed gcc7 The following ports are currently installed: gcc7 @7.3.0_3 (active) fowlerj@817jfmac:~$ port installed p5.26-ifeffit The following ports are currently installed: p5.26-ifeffit @1.2.13_0+gcc7 (active) fowlerj@817jfmac:~$ port installed ifeffit The following ports are currently installed: ifeffit @1.2.13_5+gcc7 (active) fowlerj@817jfmac:~$ port ech depof:ifeffit gcc7 libgcc libgcc7 libpng ncurses pgplot xorg-libX11 Do you have the package g95 (a FORTRAN compiler) installed? You can see (above) that I have it, but it’s not a listed dependency of ifeffit. Why don’t you try installing it (“sudo port install g95”) and then clean and install first the package ifeffit, then p5.26-ifeffit. If that works, then it means we should add g95 as a dependency for ifeffit (or p5.26-ifeffit). If it doesn’t work, then at least you might gather more clues. Best wishes, Joe Fowler On Sep 16, 2018, at 3:42 PM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.ca… or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Port p5.26-ifeffit not installing via MacPorts on Yosemite (Sergio Tatay) From: Sergio Tatay <sergio.tatay(a)uv.es> Subject: [Ifeffit] Port p5.26-ifeffit not installing via MacPorts on Yosemite Date: September 16, 2018 at 3:12:52 PM MDT To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Hi everybody, I’ve been trying to install Demeter package on MacOS using MacPorts. All the dependencies seem to install smoothly but for p5.26-iffefit. During port install I’ve got the following error: ---> Computing dependencies for demeter The following dependencies will be installed: p5.26-ifeffit Continue? [Y/n]: Y ---> Building p5.26-ifeffit Error: Failed to build p5.26-ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port demeter failed I've pasted below an extract of the log file and attached the complete file to this mail. I’m completely newbie and I will be very grateful if someone could help me to get the problem solved. Thanks very much in advance, Sergio -LOG FILE- version:1 :debug:sysinfo OS X 10.10 (darwin/14.5.0) arch i386 :debug:sysinfo MacPorts 2.5.3 :debug:sysinfo Xcode 7.2.1 :debug:sysinfo SDK 10.10 :debug:sysinfo MACOSX_DEPLOYMENT_TARGET: 10.10 … …. :info:build /opt/local/lib/perl5/5.26/darwin-thread-multi-2level/CORE/libperl.dylib -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl/../../src/lib -L/opt/local/lib -Wl,-headerpad_max_install_names -lifeffit -L/opt/local/lib -lpgplot -lpng -lX11 -L/opt/local/lib -lSystem -lm \ :info:build :info:build Undefined symbols for architecture x86_64: :info:build "__gfortran_compare_string", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _settxt_ in libifeffit.a(misc_vars.o) :info:build ... :info:build "__gfortran_concat_string", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _set_array_index_ in libifeffit.a(misc_arr.o) :info:build _getsca_ in libifeffit.a(misc_vars.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build ... :info:build "__gfortran_getenv", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build "__gfortran_st_close", referenced from: :info:build _close_echofile_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_history_ in libifeffit.a(iff_history.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_log_ in libifeffit.a(iff_log.o) :info:build _iff_rddata_ in libifeffit.a(iff_rddata.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build ... :info:build "__gfortran_st_inquire", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build _fefinp_ in libifeffit.a(fefinp.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build _newfil_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_open", referenced from: :info:build _rcldat_ in libifeffit.a(clcalc.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_read", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_read_done", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_write", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.1 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_st_write_done", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.1 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_stop_string", referenced from: :info:build _fstop_ in libifeffit.a(echo.o) :info:build "__gfortran_string_index", referenced from: :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _isvnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _hexcol_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_string_len_trim", referenced from: :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _fixarr_ in libifeffit.a(misc_arr.o) :info:build _iofarr_ in libifeffit.a(misc_arr.o) :info:build ... :info:build "__gfortran_transfer_character", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_transfer_character_write", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_transfer_integer_write", referenced from: :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_getpath_ in libifeffit.a(iff_getpath.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_macro_do_ in libifeffit.a(iff_macro.o) :info:build ... :info:build "__gfortran_transfer_real", referenced from: :info:build _str2dp_ in libifeffit.a(str.o) :info:build "__gfortran_transfer_real_write", referenced from: :info:build _iff_correl_s_.part.0 in libifeffit.a(iff_correl.o) :info:build _iff_cursor_ in libifeffit.a(iff_cursor.o) :info:build _iff_zoom_ in libifeffit.a(iff_cursor.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_print_ in libifeffit.a(iff_print.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build _ishsca_ in libifeffit.a(iff_show.o) :info:build ... :info:build ld: symbol(s) not found for architecture x86_64 :info:build clang: error: linker command failed with exit code 1 (use -v to see invocation) :info:build make: *** [blib/arch/auto/Ifeffit/Ifeffit.bundle] Error 1 :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl' :info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl" && /usr/bin/make -j4 -w all :info:build Exit code: 2 :error:build Failed to build p5.26-ifeffit: command execution failed :debug:build Error code: CHILDSTATUS 42934 2 :debug:build Backtrace: command execution failed :debug:build while executing :debug:build "system {*}$notty {*}$nice $fullcmdstring" :debug:build invoked from within :debug:build "command_exec build" :debug:build (procedure "portbuild::build_main" line 8) :debug:build invoked from within :debug:build "$procedure $targetname" :error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details. <main.log> _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.ca… Unsubscribe: https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.ca…

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Port p5.26-ifeffit not installing via MacPorts on Yosemite
by Sergio Tatay 16 Sep '18

16 Sep '18

Hi everybody, I’ve been trying to install Demeter package on MacOS using MacPorts. All the dependencies seem to install smoothly but for p5.26-iffefit. During port install I’ve got the following error: ---> Computing dependencies for demeter The following dependencies will be installed: p5.26-ifeffit Continue? [Y/n]: Y ---> Building p5.26-ifeffit Error: Failed to build p5.26-ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port demeter failed I've pasted below an extract of the log file and attached the complete file to this mail. I’m completely newbie and I will be very grateful if someone could help me to get the problem solved. Thanks very much in advance, Sergio -LOG FILE- version:1 :debug:sysinfo OS X 10.10 (darwin/14.5.0) arch i386 :debug:sysinfo MacPorts 2.5.3 :debug:sysinfo Xcode 7.2.1 :debug:sysinfo SDK 10.10 :debug:sysinfo MACOSX_DEPLOYMENT_TARGET: 10.10 … …. :info:build /opt/local/lib/perl5/5.26/darwin-thread-multi-2level/CORE/libperl.dylib -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl/../../src/lib -L/opt/local/lib -Wl,-headerpad_max_install_names -lifeffit -L/opt/local/lib -lpgplot -lpng -lX11 -L/opt/local/lib -lSystem -lm \ :info:build :info:build Undefined symbols for architecture x86_64: :info:build "__gfortran_compare_string", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _settxt_ in libifeffit.a(misc_vars.o) :info:build ... :info:build "__gfortran_concat_string", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _set_array_index_ in libifeffit.a(misc_arr.o) :info:build _getsca_ in libifeffit.a(misc_vars.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build ... :info:build "__gfortran_getenv", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build "__gfortran_st_close", referenced from: :info:build _close_echofile_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_history_ in libifeffit.a(iff_history.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_log_ in libifeffit.a(iff_log.o) :info:build _iff_rddata_ in libifeffit.a(iff_rddata.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build ... :info:build "__gfortran_st_inquire", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build _fefinp_ in libifeffit.a(fefinp.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build _newfil_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_open", referenced from: :info:build _rcldat_ in libifeffit.a(clcalc.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_read", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_read_done", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_write", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.1 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_st_write_done", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.1 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_stop_string", referenced from: :info:build _fstop_ in libifeffit.a(echo.o) :info:build "__gfortran_string_index", referenced from: :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _isvnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _hexcol_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_string_len_trim", referenced from: :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _fixarr_ in libifeffit.a(misc_arr.o) :info:build _iofarr_ in libifeffit.a(misc_arr.o) :info:build ... :info:build "__gfortran_transfer_character", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_transfer_character_write", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_transfer_integer_write", referenced from: :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_getpath_ in libifeffit.a(iff_getpath.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_macro_do_ in libifeffit.a(iff_macro.o) :info:build ... :info:build "__gfortran_transfer_real", referenced from: :info:build _str2dp_ in libifeffit.a(str.o) :info:build "__gfortran_transfer_real_write", referenced from: :info:build _iff_correl_s_.part.0 in libifeffit.a(iff_correl.o) :info:build _iff_cursor_ in libifeffit.a(iff_cursor.o) :info:build _iff_zoom_ in libifeffit.a(iff_cursor.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_print_ in libifeffit.a(iff_print.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build _ishsca_ in libifeffit.a(iff_show.o) :info:build ... :info:build ld: symbol(s) not found for architecture x86_64 :info:build clang: error: linker command failed with exit code 1 (use -v to see invocation) :info:build make: *** [blib/arch/auto/Ifeffit/Ifeffit.bundle] Error 1 :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl' :info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl" && /usr/bin/make -j4 -w all :info:build Exit code: 2 :error:build Failed to build p5.26-ifeffit: command execution failed :debug:build Error code: CHILDSTATUS 42934 2 :debug:build Backtrace: command execution failed :debug:build while executing :debug:build "system {*}$notty {*}$nice $fullcmdstring" :debug:build invoked from within :debug:build "command_exec build" :debug:build (procedure "portbuild::build_main" line 8) :debug:build invoked from within :debug:build "$procedure $targetname" :error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details.

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Data import issue on Ubuntu 18.04
by Joshua Wright 14 Sep '18

14 Sep '18

I am having some difficulty importing both .prj files and regular data files. I have included here two data files that open just fine on my Windows machine. When I try to import the raw data I get the following two popups: 1) Demeter::UI::Athena Warning Unquoted string "to" may clash with future reserved word at (eval 2479) line 1 2) Import warning Could not read "/path/to/file/Th_GWB.001" as either data or a project file. Do you need to enable a plugin? Selecting continue importing does nothing except close the dialogue box. When I import the project file the normal import window comes up, allowing me to select the data I want to import. Then a warning pops up: Warning! /path/to/file/ThoriumData.prj could not be read correctly. OK to continue importing data, cancel to quit importing data. Pressing OK just closes the dialogue box and nothing gets imported. Any ideas on what to do to fix this? Joshua

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Job Posting
by Frejka, Jean M 12 Sep '18

12 Sep '18

Brookhaven National Laboratory currently has three post-doc positions in Material Characterizations available. Can you please post and/or upload the attached job postings? There are two pdf files per position: (1) short version for posting on a bulletin board and (2) a longer version to upload or email. If you have any questions, please contact me. Thank you for your assistance. Jeannie ************************************* Jean Marie Frejka Brookhaven National Laboratory Nuclear Science and Technology Department Building 817, 33 North Renaissance Road Upton, NY 11973 Phone: 631-344-2349 Fax: 631-344-2806 frejka(a)bnl.gov<mailto:frejka@bnl.gov>

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XANES simulation
by Motta Meira, Debora 30 Aug '18

30 Aug '18

Good morning everyone, I'm trying to simulate XANES spectra for a material used for batteries. In the Figure, my experimental data are the blue (pristine material) and the red (charged state) curves. When I apply my EXAFS results to the original structure, to simulate using Feff, (I contracted the distances proportionally to what I found in the EXAFS fit) the XANES shifts accordantly, as you can see in the green and purple curves. However, the intensity is completely different. To fix this I changed S02 to 0.4. Additionally, I also correct the vr0 (found a value of -8.4) and I'm using Rpath = 5. The simulation using these parameters is the yellow curve. My problem is: using these parameters the simulation matches the experimental data, for the intensity and position, however, I'm missing the pre-edge and I also have a bump in the white line (yellow curve)... Does anyone know how to fix it, please? [cid:image003.jpg@01D44050.C0ECC210] Thank you, Debora

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Constraining values in Artemis fit
by Thomas, Andrew (AGW) 23 Aug '18

23 Aug '18

Hello, Does anyone have any suggestions for breaking the correlation between the coordination number and sigma^2? Specifically, is there a way to set a maximum or minimum value for parameters in a fit? Andrew Thomas

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32ビット版アプリケーションの申請
by 天田雄大 23 Aug '18

23 Aug '18

Ifeffit管理者様 32ビット版アプリケーションを使用したいので、 32ビット版のインストールアプリを添付していただけませんか？よろしくお願いします。

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