Re: Fwd: parseFEP domain error

From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Mon Mar 05 2018 - 17:25:57 CST

Hello Francesco,

thank you for your message and for pointing this issue to our attention.
ParseFEP has undergone a number of important changes recently, and in
the process, the link to XMGrace and ImageMagick has been broken. Sorry
for the trouble it has created. The problem has now been fixed, and a
revised version of the code should be available in the next nightly
build of VMD.

Cheers,

Chris Chipot

On 3/6/18 5:17 AM, Francesco Pietra wrote:
> At this point, I would appreciate very much receiving frwd.fepout and
> back.fepout couple of files from whatever system. Just to check
> whether there is anything wrong with grace/imagemgick from debian
> amd64, or with namd creating those .fepout for my system.
>
> Thanks
>
> francesco
> ---------- Forwarded message ----------
> From: *Francesco Pietra* <chiendarret_at_gmail.com
> <mailto:chiendarret_at_gmail.com>>
> Date: Sat, Mar 3, 2018 at 6:44 PM
> Subject: Fwd: parseFEP domain error
> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>>,
> NAMD <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>>
>
>
> Hello
> As, in my hands, parseFEP fails to call imagemagick when both frwd and
> back PEF are submitted (while it works when frwd alone is submitted),
> is there any described way to reconstruct from the log files all
> graphics ? From what I could do to this regard, grace plots from
> ParseFep. do match.
>
> Thanks for help
>
> francesco pietra
>
> ---------- Forwarded message ----------
> From: *Francesco Pietra* <chiendarret_at_gmail.com
> <mailto:chiendarret_at_gmail.com>>
> Date: Fri, Mar 2, 2018 at 4:47 PM
> Subject: parseFEP domain error
> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>>,
> namd_at_ks.uiuc.edu <mailto:namd_at_ks.uiuc.edu>
>
>
> Hello:
> With frwd.fepout parseFEP invokes imagemagick, providing graphics
> besides tables.
>
> With frwd.fepout + back.fepout imagemagic only provides
> entropy.log
> gc.log
> ParseFEP.log
>
> not invoking imagemagick, while reporting the error:
> domain error: argument not in valid range
> domain error: argument not in valid range
>     while executing
> "expr  $nSample * $var / ($sigma_factor ** 2) "
>     (procedure "::ParseFEP::FEP_formula" line 95)
>     invoked from within
> "::ParseFEP::FEP_formula $file    $file_entropy $window $mean_xi
> $fororback"
>     (procedure "::ParseFEP::normal_parse_log" line 55)
>     invoked from within
> "::ParseFEP::normal_parse_log $::ParseFEP::fepbofile backward    "
>     (procedure "namdparse" line 158)
>     invoked from within
> "namdparse"
>     (in namespace inscope "::ParseFEP" script line 16)
>     invoked from within
> "::namespace inscope ::ParseFEP {
>
>         if { [string length $::ParseFEP::fepofile] < 1 } {
>             tk_dialog .errmsg {NamdPlot Error} "No FEP (inward)
> logfile ..."
>     invoked from within
> ".parseFEP.runbutton invoke"
>     ("uplevel" body line 1)
>     invoked from within
> "uplevel #0 [list $w invoke]"
>     (procedure "tk::ButtonUp" line 22)
>     invoked from within
> "tk::ButtonUp .parseFEP.runbutton"
>     (command bound to event)
>
> SOFTWARE USED: VMD 1.9.3 on debian 9 (stretch) amd64 with XFCE
>
> all imagemagic programs are on the path:
> francesco_at_vaio64:~$ which animate
> /usr/bin/animate
> francesco_at_vaio64:~$ which compare
> /usr/bin/compare
> francesco_at_vaio64:~$ which composite
> /usr/bin/composite
> francesco_at_vaio64:~$ which conjure
> /usr/bin/conjure
> francesco_at_vaio64:~$ which convert
> /usr/bin/convert
> francesco_at_vaio64:~$ which display
> /usr/bin/display
> francesco_at_vaio64:~$ which identify
> /usr/bin/identify
> francesco_at_vaio64:~$ which import
> /usr/bin/import
> francesco_at_vaio64:~$ which mogrify
> /usr/bin/mogrify
> francesco_at_vaio64:~$ which montage
> /usr/bin/montage
> francesco_at_vaio64:~$ which stream
> /usr/bin/stream
>
> Incidentally, I was surprised that the following command ($ or #) did
> not show /usr/bin with the various programs
> francesco_at_vaio64:~$ dpkg -L imagemagick
> /.
> /usr
> /usr/share
> /usr/share/bug
> /usr/share/doc
> /usr/share/doc/imagemagick
> /usr/share/doc/imagemagick/NEWS.Debian.gz
> /usr/share/doc/imagemagick/changelog.Debian.gz
> /usr/share/doc/imagemagick/changelog.gz
> /usr/share/doc/imagemagick/copyright
> /usr/share/bug/imagemagick
>
>
> Thanks for advice
> francesco pietra
>
>
>

-- 
Chris Chipot
CNRS research director, University of Lorraine
Adjunct professor of physics, University of Illinois, Urbana-Champaign
_______________________________________________________________________
Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
3165 Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
405 North Mathews
Urbana, Illinois 61801                            Phone: (217) 300-0380
                              E-mail: chipot_at_ks.uiuc.edu
                                      Christophe.Chipot_at_Univ-Lorraine.fr
                              Web:    http://www.ks.uiuc.edu/~chipot
                                      http://www.lia-uiuc.cnrs.fr
      It is hard for France to maintain a thirty-five-hour workweek when
      China and India have invented a thirty-five-hour workday.
                                                      Thomas L. Friedman
_______________________________________________________________________

This archive was generated by hypermail 2.1.6 : Sun Sep 15 2019 - 23:19:28 CDT