On Wed, May 27, 2020 at 7:33 AM sandip khan <[email protected]> wrote: > > Thank you for your reply. Now I changed the bead type from Bead1 to F1 in the > setting file and it is working. Please find the version below that I am > using. That is a good workaround.
One last thing, can you post the output of "uname -a"? Christoph > > ws7@ws7:/usr/local/share/votca/csg-tutorials/spce/ibi_lammps$ csg_call > --version > csg_call, version 1.6 gitid: d8d9ab8 > > > > > On Wednesday, May 27, 2020 at 6:25:09 PM UTC+5:30, Christoph Junghans wrote: >> >> 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/8ff3935e-2b30-491f-938d-ea16e7c45e5b%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/CAHG27e5UFTCk1vhkfgFAH_uixaZieWAOv1eFpdV4Lx8mvU2rhg%40mail.gmail.com.
