On Wed, Nov 18, 2020 at 7:29 AM sandipan c <[email protected]> wrote: > > Hi Chrristoph, > > Thank you for fixing the earlier issue. > > Now, no error as such is being thrown, but the process is getting stuck > forever. I am getting the following message: > csg_stat --nt 4 --options > /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/software/VOTCA/my_examples_custom_folder/spce/settings.xml > --top spce.data --trj traj.dump --begin 0 --first-frame 0 > > begin to calculate distribution functions > # of bonded interactions: 0 > # of non-bonded interactions: 1 > > WARNING: The votca lammps data reader is only able to read lammps files > formatted in the following styles: > angle > atom > bond > full > molecule > > These styles use the following formats in the atom block: > atom-ID molecule-ID atom-type charge x y z > atom-ID molecule-ID atom-type charge x y z nx ny nz > atom-ID molecule-ID atom-type x y z > atom-ID molecule-ID atom-type x y z nx ny nz > atom-ID atom-type x y z > atom-ID atom-type x y z nx ny nz > > Unable to associate mass 18.01540 with element assuming pseudo atom, > assigning name Bead1 . > ------------------------------------------------------------------------------------------------------------------------------------------------ > When I was running the spce example from > /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/software/VOTCA/my_examples_custom_folder/spce, > the job was getting stuck with the following message: > > csg_inverse --options settings.xml > Appending to existing logfile inverse.log > We are doing Method: ibi > Prepare (dir step_000) > Using initial guess from dist CG-CG.dist.tgt for CG-CG > step 0 done > Doing iteration 1 (dir step_001) > Simulation with lammps > Make update for ibi > Calculating rdfs with csg_stat using 4 tasks > ----------------------------------------------------------------------------- > The process was getting stuck after that. Nothing was being written in the > inverse.log file for a very long time (days). Could you please suggest how I > can resolve this issue?
I have no good idea, can you pack the input files (settings.xml spce.data traj.dump) in a zip, create an new issue for csg(https://github.com/votca/csg/issues/new) and attach them? Thanks, Christoph > > Thanks, > Sandipan > > On Tue, Nov 17, 2020 at 7:49 PM Christoph Junghans <[email protected]> wrote: >> >> On Tue, Nov 17, 2020 at 5:51 AM sandipan c <[email protected]> wrote: >> > >> > Thank you, Christoph. >> > >> > I used the command >> > $dos2unix spce.data >> > and the error regarding "unrecognized line in data file" is gone. >> FYI, we fixed that issue in the latest master and stable versions. >> > >> > Now, I am getting the following message in the inverse.log file: >> > Unable to associate mass 18.01540 with element assuming pseudo atom, >> > assigning name Bead1 >> This is usually just a warning. >> >> > >> > Could you please suggest why I am getting this? >> Can you run the last command by hand >> $ cd >> /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/software/VOTCA/my_examples_custom_folder/spce/step_001 >> $ csg_stat --nt 4 --options >> /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/software/VOTCA/my_examples_custom_folder/spce/settings.xml >> --top spce.data --trj traj.dump --begin 0 --first-frame 0 >> >> and see what the error is? >> >> Christoph >> > >> > As mentioned earlier, this is a tutorial example taken from: >> > https://github.com/votca/csg-tutorials/tree/master/spce/ibi_lammps >> > I am attaching the inverse.log and settings.xml files. >> > >> > Thanks, >> > Sandipan >> > >> > >> > >> > >> > >> > >> > On Sun, Nov 15, 2020 at 8:11 PM Christoph Junghans <[email protected]> >> > wrote: >> >> >> >> Ok, it seems your data file has windows line endings and the reader >> >> doesn't like that. >> >> >> >> You can fix the input file using do2unix: >> >> $ dos2unix spec.data >> >> or sed: >> >> sed -i 's/\r//g' spce.data >> >> (on mac you might need to do) >> >> sed 's/\r//g' spce.data > spce.data.new && mv spce.data.new spce.data >> >> >> >> I made an issue: https://github.com/votca/csg/issues/613 >> >> >> >> Christoph >> >> >> >> >> >> On Sun, Nov 15, 2020 at 12:22 AM sandipan c <[email protected]> >> >> wrote: >> >> > >> >> > Hi Everyone, >> >> > >> >> > I am trying to run the ibi_lammps example provided in VOTCA tutorials, >> >> > collected from this page: >> >> > https://github.com/votca/csg-tutorials/tree/master/spce/ibi_lammps >> >> > >> >> > I am getting the error: Unrecognized line in .data file. >> >> > >> >> > This error is coming after completion of 2 iterations. So, the LAMMPS >> >> > simulations run a couple of times before throwing this error. I am >> >> > attaching the inverse.log and spce.data files. >> >> > >> >> > Could you please suggest what could be the reason for getting this >> >> > error? >> >> > >> >> > Error details: >> >> > WARNING: The votca lammps data reader is only able to read lammps files >> >> > formatted in the following styles: >> >> > angle >> >> > atom >> >> > bond >> >> > full >> >> > molecule >> >> > >> >> > These styles use the following formats in the atom block: >> >> > atom-ID molecule-ID atom-type charge x y z >> >> > atom-ID molecule-ID atom-type charge x y z nx ny nz >> >> > atom-ID molecule-ID atom-type x y z >> >> > atom-ID molecule-ID atom-type x y z nx ny nz >> >> > atom-ID atom-type x y z >> >> > atom-ID atom-type x y z nx ny nz >> >> > >> >> > an error occurred: >> >> > Unrecognized line in lammps .data file: >> >> > 1 1 28.15 5.43 2.37 >> >> > >> >> > Callstack: >> >> > /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/VOTCA/share/votca/scripts/inverse/inverse.sh >> >> > - linenumber 266 >> >> > do_external - linenumber 177 in >> >> > /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/VOTCA/share/votca/scripts/inverse/functions_common.sh >> >> > >> >> > /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/VOTCA/share/votca/scripts/inverse/update_ibi.sh >> >> > - linenumber 31 >> >> > for_all - linenumber 22 (see 'csg_call --cat function >> >> > for_all') >> >> > do_external - linenumber 19 (see 'csg_call --cat >> >> > function do_external') >> >> > >> >> > /media/sandipan/124a8887-6d75-4321-bb42-1c9f00e06fcc/Sandipan/VOTCA/share/votca/scripts/inverse/calc_rdf_generic.sh >> >> > - linenumber 84 >> >> > critical - linenumber 4 (see 'csg_call >> >> > --cat function critical') >> >> > die - linenumber 2 (see 'csg_call --cat >> >> > function die') >> >> > ####################################################################### >> >> > >> >> > Thanks, >> >> > Sandipan >> >> > >> >> > -- >> >> > Join us on Slack: https://join.slack.com/t/votca/signup >> >> > --- >> >> > You received this message because you are subscribed to the Google >> >> > Groups "votca" group. >> >> > To unsubscribe from this group and stop receiving emails from it, send >> >> > an email to [email protected]. >> >> > To view this discussion on the web visit >> >> > https://groups.google.com/d/msgid/votca/CAB-cU%3D5O4G0kauzOt0eynCXZdiQwXbbhRfCtCav4OmMwoPEkcQ%40mail.gmail.com. >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> >> >> >> -- >> >> Join us on Slack: https://join.slack.com/t/votca/signup >> >> --- >> >> You received this message because you are subscribed to the Google Groups >> >> "votca" group. >> >> To unsubscribe from this group and stop receiving emails from it, send an >> >> email to [email protected]. >> >> To view this discussion on the web visit >> >> https://groups.google.com/d/msgid/votca/CAHG27e5ATbgQ%3Dy%2B4HqLdsu1M9q46A%3DmN2org3i9E1ODkpMGuZw%40mail.gmail.com. >> > >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > You received this message because you are subscribed to the Google Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to [email protected]. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/CAB-cU%3D47qhFJyrL6nUjbF0WJfM5p7d01UCMqTmZX33jKA8ViLA%40mail.gmail.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e6h%3DRArS7n9yOYgOqm21cS_6YvU4OYSVgFS4wsxFtWrCw%40mail.gmail.com. > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAB-cU%3D6yyzbOO4xwBoGRZnA9xNEWTV6__kZR5abu%2BpbOnT8v4A%40mail.gmail.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e75Mti%2Bodq-U8PNo-hSjZN15w1XDo-CcAsc-F8LPTzqew%40mail.gmail.com.
