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.
