Thanks Christoph. Here it is uname -a Linux ws7 4.4.0-179-generic #209-Ubuntu SMP Fri Apr 24 17:48:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
On Wednesday, May 27, 2020 at 7:36:53 PM UTC+5:30, Christoph Junghans wrote: > > On Wed, May 27, 2020 at 7:33 AM sandip khan <[email protected] > <javascript:>> 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] <javascript:>. > > 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/8c443228-cd5f-4e9b-a85a-72404325591c%40googlegroups.com.
