LAMMPS (17 Feb 2016-ICMS) WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:90) using 1 OpenMP thread(s) per MPI task atom_style full units real dimension 3 boundary p p p variable Ctype equal 1 variable CLtype equal 2 variable Htype equal 3 variable Otype equal 5 variable pistontype equal 6 variable NAtype equal 4 variable seed equal 1 variable pressure equal 0.02 variable 1atm equal -0.000041 variable waterbond equal 1 variable waterangle equal 1 read_data pristine.dat Reading data file ... orthogonal box = (-0.5 -0.5 -0.5) to (0.5 0.5 0.5) 1 by 1 by 1 MPI processor grid reading atoms ... 6405 atoms scanning bonds ... 3 = max bonds/atom reading bonds ... 5216 bonds Finding 1-2 1-3 1-4 neighbors ... Special bond factors lj: 0 0 0 Special bond factors coul: 0 0 0 3 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors variable natoms equal "count(all)" # Define interaction parameters pair_style hybrid lj/cut/tip4p/long ${Otype} ${Htype} ${waterbond} ${waterangle} 0.1546 13.0 airebo 3.0 0 1 pair_style hybrid lj/cut/tip4p/long 5 ${Htype} ${waterbond} ${waterangle} 0.1546 13.0 airebo 3.0 0 1 pair_style hybrid lj/cut/tip4p/long 5 3 ${waterbond} ${waterangle} 0.1546 13.0 airebo 3.0 0 1 pair_style hybrid lj/cut/tip4p/long 5 3 1 ${waterangle} 0.1546 13.0 airebo 3.0 0 1 pair_style hybrid lj/cut/tip4p/long 5 3 1 1 0.1546 13.0 airebo 3.0 0 1 pair_modify tail yes bond_style harmonic angle_style harmonic dihedral_style none # ------------- Regions and Groups ---------------- group carbon type ${Ctype} ${pistontype} # all carbon atoms group carbon type 1 ${pistontype} group carbon type 1 6 1248 atoms in group carbon group ox type ${Otype} group ox type 5 1711 atoms in group ox group hy type ${Htype} group hy type 3 3422 atoms in group hy group na type ${NAtype} group na type 4 12 atoms in group na group cl type ${CLtype} group cl type 2 12 atoms in group cl # Defining the positions of all four carbon planes variable zpiston1 equal -50 variable zmembrane1 equal 0 variable zpiston2 equal "20" # Defining the piston and the membrane carbons variable zmin equal ${zpiston1}-1.0 variable zmin equal -50-1.0 variable zmax equal ${zpiston1}+1.0 variable zmax equal -50+1.0 region piston1zone block INF INF INF INF ${zmin} ${zmax} units box region piston1zone block INF INF INF INF -51 ${zmax} units box region piston1zone block INF INF INF INF -51 -49 units box variable zmin equal ${zmembrane1}-1.0 variable zmin equal 0-1.0 variable zmax equal ${zmembrane1}+1.0 variable zmax equal 0+1.0 region membrane1zone block INF INF INF INF ${zmin} ${zmax} units box region membrane1zone block INF INF INF INF -1 ${zmax} units box region membrane1zone block INF INF INF INF -1 1 units box variable zmin equal ${zpiston2}-1.0 variable zmin equal 20-1.0 variable zmax equal ${zpiston2}+1.0 variable zmax equal 20+1.0 region piston2zone block INF INF INF INF ${zmin} ${zmax} units box region piston2zone block INF INF INF INF 19 ${zmax} units box region piston2zone block INF INF INF INF 19 21 units box group piston1 region piston1zone # whole piston1 (carbon) 0 atoms in group piston1 group piston2 region piston2zone # whole piston1 (carbon) 0 atoms in group piston2 group bothpistons union piston1 piston2 0 atoms in group bothpistons group membrane1_atoms region membrane1zone 6405 atoms in group membrane1_atoms group totalmembrane union membrane1_atoms 6405 atoms in group totalmembrane group not_hy subtract all hy 2983 atoms in group not_hy region rigidmembrane1_zone cylinder z 15.0 15.0 15.0 INF INF group in_rigidmembrane_1zone region rigidmembrane1_zone 0 atoms in group in_rigidmembrane_1zone group membrane1_free subtract membrane1_atoms in_rigidmembrane_1zone 6405 atoms in group membrane1_free # defining water groups group water union ox hy 5133 atoms in group water group saltwater union water na cl 5157 atoms in group saltwater group notsaltwater subtract all saltwater 1248 atoms in group notsaltwater group thermostat_target union saltwater membrane1_free piston1 piston2 6405 atoms in group thermostat_target set group ox charge -1.0484 Setting atom values ... 1711 settings made for charge set group hy charge 0.5242 Setting atom values ... 3422 settings made for charge set group na charge 1. Setting atom values ... 12 settings made for charge set group cl charge -1. Setting atom values ... 12 settings made for charge # ------------- Coefficients ---------------- # AIREBO: pair_coeff * * airebo CH.airebo_real C NULL NULL NULL NULL NULL C H ERROR: Incorrect args for pair coefficients (../pair_airebo.cpp:161)