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? 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.
