September 2018 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9
by Abhinav Prabhakar 05 Aug '20

05 Aug '20

Hello, Thank you for your reply. Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. However, the structure has partial occupancy and it is modified to include full occupancy. The modified CIF file shows a space group of B11b (and cannot be recognized by Artemis). I tried a C1c1 space group (it works) but it shows the same structural values as a P11b. Regards, AP On Tue, Mar 14, 2017 at 1:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > 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. Re: Space group type in Artemis (Bruce Ravel) > 2. Data export and coordination number (Abhinav Prabhakar) > 3. Re: Data export and coordination number (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Mar 2017 09:20:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Space group type in Artemis > Message-ID: <3853f1f7-61fd-6886-306f-040c540ecae1(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: > > Hello, > > > > I have a question about the working of Artemis as a new user. > > > > Artemis does not recognize the space group B11b. When importing a cif > > file of a crystal with this symmetry, it sends a prompt message that the > > space group symbol cannot be recognized. As a result, I changed it to > > P11b and it works. But would this change any crystal information (for > > eg. Degen, Reff values) significantly? > > I am not a crystallography expert in any sense. When I wrote Artemis, I > meticulously followed what I found in the fourth edition of the > International Tables for Crystallography, Volume A. Every symbol > defined in there is recognized by Artemis. (Well, I guess I should say > that every symbol is /supposed to be/ recognized by Artemis. If one is > missing, that's a bug and should be reported.) > > "B11b" is not a symbol that I found in my copy of ITC volume A. As > Robert suggested, there may be a way to rotate group 9 so that "B11b" is > an interpretable symbol in the abstract. But Artemis does not know how > to do that. (Nor do I.) > > "P11b" is a setting for space group #7. If, as Robert suggests, your > CIF file is for space group #9, then the answer to your last question is > yes. It is plainly obvious that using a different space group will > change the degeneracies and distances. > > > Of course, you did not bother to include a copy of the CIF file in > question to your original email, so it is not actually possible for > Robert or I or anyone else to actually help you effectively. > > At the risk of sounding like an annoyingly broken record, everyone > should take the time to ask a good question or write an actionable bug > report: > > http://bruceravel.github.io/demeter/documents/SinglePage/help.html > http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Mar 2017 21:48:31 +0800 > From: Abhinav Prabhakar <abhi.prabhakar(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data export and coordination number > Message-ID: > <CA+nbL85FJReunY1Am1oeNTMtFskXMd8FmH_OgaO00mnmew2c-g(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > As a new user, I have some questions related to the use of Athena and > Artemis: > > i) Is it possible to extract the normalized/background corrected data from > Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? > > ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' > parameters (Artemis allows only numerical values for N)? > > Thank you. > > Regards, > > Abhinav Prabhakar (Mr.) >

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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>

1 0