Dear All,
I am experiencing some problem with the latest version of lib/colvars (2016). This problem can be reproduced with the example files provided with lammps: examples/USER/colvars.
To reproduce the problem, I add an additional block to the peptide.colvars file:
colvar {
name three
gyration {
atoms {
atomNumbers 2 4 5 6
}
}
upperBoundary 10
upperWall 10
upperWallConstant 5
}
With the modified file, the following error appeared after running lammps: lmp_openmpi < in.peptide-colvars
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
colvars: Re-initialized atom group three:0/0. 4 atoms: total mass = 4.
colvars: The restart output state file will be “rest.colvars.state”.
colvars: The final output state file will be “out.colvars.state”.
colvars: Writing to colvar trajectory file “out.colvars.traj”.
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group three:0/0. 4 atoms: total mass = 15.035.
[eofe4:mpi_rank_0][error_sighandler] Caught error: Segmentation fault (signal 11)
Segmentation fault
I appreciate any comment on the possible issue here.
Best regards,
Bin