Understood. I've put the new votca you committed in my votca/lammps bilder toolchain and will test soon.
Cheers, Scott On 9/6/13 3:13 PM, "Christoph Junghans" <[email protected]> wrote: >2013/9/6 Scott Sides <[email protected]>: >> After I changed the name of my lammps executable to 'lmp' this problem >>went >> away. >How is lammps named by default? >You can also change what VOTCA is calling in the lammps block of your >settings.xml file: ><cg> >... > <inverse> > <lammps> > <command>lammps</command> > </lammps> > </inverse> ><cg> >That might become handy later, if you want to call >"mpirun -np 99 lmp_mpi" instead. > >> I tried running lammps at the top level and the CG_CG.pot files are >>created >> in the 'step_...' >> directories. However, now I get a different error at the analysis step >> >> >>######################################################################### >>######################################################################### >>################################### >> # >> # >> # ERROR: >> # >> # critical: 'csg_stat --nt 8 --options >> >>/Users/ssides/csg-tutorials.votca-8d845530808b/spce/ibi_lammps/settings.x >>ml >> --top topol.xml --trj traj.xyz --begin 0 --first-frame 0' failed # >> # For details see the logfile >> >>/Users/ssides/csg-tutorials.votca-8d845530808b/spce/ibi_lammps/inverse.lo >>g >> # >> # >> # >> >>######################################################################### >>######################################################################### >>################################### >> die: (called from 64638) CSG_MASTER_PID is 62128 >> die: pids to kill: 62128 64517 64623 64638 >> >> >> I've attached complete inverse.log file for reference. >I had a look at error in the log file and this is somewhat more >complicated. > >As lammps has no topology file, we are using an xml topology ( >topol.xml ) however this one is base on a pdb file (1st line: ><topology base="spce.pdb">), but the pbd reader is based on libgmx and >hence if VOTCA is compiled without gromacs it cannot reads pdb. (We >should fix that: https://code.google.com/p/votca/issues/detail?id=137) > >An easy solution would to use gro file as base topology, as the gro >reader is implemented independently from gromacs even though gro is a >gromacs format. >However for some reason the gro reader was not built, when gromacs >support is disabled, I fixed that: ><https://code.google.com/p/votca/source/detail?r=2d04b7aa845de20964053c53b >8bc6aa402d264e2&repo=csg> >and the tutorial, too: ><https://code.google.com/p/votca/source/detail?r=02ef40cb993fa2e1d6eb92c2b >fbfdcf1b1dee931&repo=csg-tutorials> > >Please update your code: ><https://code.google.com/p/votca/wiki/Installing#Update> > >Cheers, > >Christoph > > > > >> >> Scott >> >> On Friday, September 6, 2013 12:10:00 PM UTC-6, Scott Sides wrote: >>> >>> I'm running the tutorial for inverse boltzmann on spce water for >>>lammps. >>> I've got >>> a lammps build that I know is running. >>> >>> The files are in 'csg-tutorials.votca-8d845530808b/spce/ibi_lammps' >>> >>> When I run csg_inverse --options settings.xml I get >>> >>> >>> >>>######################################################################## >>>################################## >>> # >>> # >>> # ERROR: >>> # >>> # critical: 'lmp -in spce.in' failed >>> # >>> # For details see the logfile >>> >>>/Users/ssides/csg-tutorials.votca-8d845530808b/spce/ibi_lammps/inverse.l >>>og # >>> # >>> # >>> >>> >>>######################################################################## >>>################################## >>> >>> When I simply try 'lmp -in spce.in' I get >>> >>> LAMMPS (14 Aug 2013) >>> Reading data file ... >>> orthogonal box = (0 0 0) to (4.031 4.031 4.031) >>> 1 by 1 by 1 MPI processor grid >>> 2180 atoms >>> ERROR on proc 0: Cannot open file CG_CG.pot (../pair_table.cpp:350) >>> >>> Clearly from the spce.in file >>> >>> # coarse-grained spce water >>> >>> units lj >>> atom_style atomic >>> >>> read_data spce.data >>> >>> velocity all create 2.49 87287 >>> >>> pair_style table linear 1000 >>> pair_coeff 1 1 CG_CG.pot VOTCA 0.9 >>> >>> timestep 0.001 >>> fix 1 all nve >>> fix 2 all langevin 2.49 2.49 0.2 545454 >>> >>> dump 1 all xyz 50 traj.xyz >>> >>> thermo 50 >>> run 2500 >>> ########################################################### >>> >>> It needs a CG_CG.pot file. However, I dont know where this file is. Do >>>I >>> need to copy from somewhere? >>> >>> Scott Sides >>> NREL >> >> -- >> 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/groups/opt_out. > > > >-- >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/groups/opt_out. -- 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/groups/opt_out.
