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.xml > --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.log > # > # > # > ##################################################################################################################################################################################### > 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=2d04b7aa845de20964053c53b8bc6aa402d264e2&repo=csg> and the tutorial, too: <https://code.google.com/p/votca/source/detail?r=02ef40cb993fa2e1d6eb92c2bfbfdcf1b1dee931&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.log # >> # >> # >> >> ########################################################################################################## >> >> 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.
