On Wed, May 27, 2020 at 2:41 AM sandip khan <[email protected]> wrote: > > Thanks Christoph for your prompt reply. I have installed either master or > stable version of Votca. I looked into the Cmakelists.txt and it is written > as project version 1.6 and I installed it under /usr/local/ > > I am using ubuntu 16.04 LTS > > Here is the output of "csg_dump --top spce.data" > > > 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 > > I have 2180 beads in 2180 molecules > Boundary Condition: orthorhombic > Box matix: 4.031 0 0 > 0 4.031 0 > 0 0 4.031 > > List of residues: > 0 name: DUM id: 0 > 1 name: DUM id: 1 > 2 name: DUM id: 2 > 3 name: DUM id: 3 > 4 name: DUM id: 4 > 5 name: DUM id: 5 > 6 name: DUM id: 6 > > --- > --- > --- > > List of molecules: > molecule: 1 F1 beads: 1 > 0 Name F1 Type F1 Mass 18.0154 Resnr 1 Resname DUM Charge 0 > molecule: 2 F1 beads: 1 > 1 Name F1 Type F1 Mass 18.0154 Resnr 2 Resname DUM Charge 0 > molecule: 3 F1 beads: 1 > 2 Name F1 Type F1 Mass 18.0154 Resnr 3 Resname DUM Charge 0 Using the latest stable version (1.6), I get: List of molecules: molecule: 1 Be1 beads: 1 0 Name Bead1 Type Bead1 Mass 18.0154 Resnr 1 Resname DUM Charge 0 molecule: 2 Be1 beads: 1 1 Name Bead1 Type Bead1 Mass 18.0154 Resnr 2 Resname DUM Charge 0
which has type "Bead1" (instead of "F1"). Please make sure you are using the latest version. Check your version by running: csg_call --version. Christoph > > Thanks, > Sandip > > > > > On Wednesday, May 27, 2020 at 12:29:57 AM UTC+5:30, sandip khan wrote: >> >> Dear All, >> >> I was running the ibi tutorial with lammps for spce water model. I >> got following error in the inverse.log file for step001. However lammps >> simulation done in folder "step-001" >> >> Topology does not have beads of type "Bead1" >> This was specified in type1 of interaction "CG-CG" >> >> Callstack: >> /usr/local/share/votca/scripts/inverse/inverse.sh - linenumber 266 >> do_external - linenumber 176 in >> /usr/local/share/votca/scripts/inverse/functions_common.sh >> /usr/local/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') >> >> /usr/local/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') >> ############################################################################################################################################################################# >> ######### >> # >> # >> # ERROR: >> # >> # critical: 'csg_stat --nt 20 --options >> /home/ws7/Downloads/share/votca/csg-tutorials/spce/ibi_lammps/settings.xml >> --top spce.data --trj traj.dump --begin 0 --first-frame 0' >> failed # >> # For details see the logfile >> /home/ws7/Downloads/share/votca/csg-tutorials/spce/ibi_lammps/inverse.log >> # >> # >> # >> ############################################################################################################################################################################# >> ######### >> die: (called from 19206) CSG_MASTER_PID is 16324 >> >> Any thought on this. >> >> Thanks, >> Sandip >> >> >> > -- > 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/d3a8c7ae-efce-4e10-9f63-8ee3c1ff0f70%40googlegroups.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/CAHG27e6M%2B%2B0C0cP%3DXrDO3EUG1pro96mROzUWrGHYRbgoeOym3A%40mail.gmail.com.
