2015-02-05 0:40 GMT-07:00 Vikram Reddy <[email protected]>: > Thank you very much for your response. > In the settings.xml, I had to add <command>lmp_mpi</command> to the lammps > section, to tell votca what command to use in order to run lammps on my > machine. Thanks, I wasn't able to reproduce your problem with the latest version of VOTCA ~/votca/src/csg-tutorials/spce/ibi_lammps $ csg_stat --options settings.xml --top topol.xml --trj 1.dump --begin 0 --first-frame 0 begin to calculate distribution functions # of bonded interactions: 0 # of non-bonded interactions: 1 Reading frame, timestep 0 WARNING: topology created from .dump file, masses, charges, types, residue names are wrong! I have 2180 beads in 2180 molecules Reading frame, timestep 0 written CG-CG.dist.new
The file "1.dump" was your frame below. What version of VOTCA are you using? I remember that in 1.2.* the lammps reader wasn't as robust as the current one. However in 1.2 you would have gotten the following error: begin to calculate distribution functions # of bonded interactions: 0 # of non-bonded interactions: 1 Reading frame, timestep 0 an error occurred: unknown item lammps file : BOX BOUNDS pp pp pp So, please update your tools, csg and csg-tutorial version to the latest development version <https://code.google.com/p/votca/wiki/Installing#Development_Version> and try again! Christoph > > Here is my first frame from traj.dump (step_001) > ITEM: TIMESTEP > 0 > ITEM: NUMBER OF ATOMS > 2180 > ITEM: BOX BOUNDS pp pp pp > 0 4.031 > 0 4.031 > 0 4.031 > ITEM: ATOMS id type xs ys zs > 285 1 0.0300174 0.122302 0.119821 <snip> > > Cheers, > Vikram > > On Wednesday, February 4, 2015 at 9:18:33 PM UTC+1, Vikram Reddy wrote: >> >> Dear Votca users, I am just starting to use votca with lammps. I tried >> running the example 'csg-tutorials/spce/ibi_lammps'. I didn't change >> anything in the given script (except for the lammps command). I get the >> following error and I don't seem to understand why. Please help. Thanks in >> advance. >> >> Running critical command 'csg_stat --nt 64 --options >> /home/va83ruvu/votca/src/csg-tutorials/spce/ibi_lammps/settings.xml --top >> topol.xml --trj traj.dump --begin 0 --first-frame 0' >> an error occurred: >> boost::bad_any_cast: failed conversion using boost::any_cast >> >> Callstack: >> /home/va83ruvu/votca/share/votca/scripts/inverse/inverse.sh - linenumber >> 263 >> do_external - linenumber 175 in >> /home/va83ruvu/votca/share/votca/scripts/inverse/functions_common.sh >> /home/va83ruvu/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') >> >> /home/va83ruvu/votca/share/votca/scripts/inverse/calc_rdf_generic.sh - >> linenumber 73 >> critical - linenumber 4 (see 'csg_call --cat >> function critical') >> die - linenumber 2 (see 'csg_call --cat >> function die') >> >> ############################################################################################################################################################################### >> # >> # >> # ERROR: >> # >> # critical: 'csg_stat --nt 64 --options >> /home/va83ruvu/votca/src/csg-tutorials/spce/ibi_lammps/settings.xml --top >> topol.xml --trj traj.dump --begin 0 --first-frame 0' failed # >> # For details see the logfile >> /home/va83ruvu/votca/src/csg-tutorials/spce/ibi_lammps/inverse.log >> # >> # >> # >> >> ############################################################################################################################################################################### >> die: (called from 48760) CSG_MASTER_PID is 46956 >> die: pids to kill: 46956 48524 48745 48760 >> >> >> Cheers, >> Vikram > > -- > 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 post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
