LAMMPS (1 Jul 2012) dimension 3 units lj atom_style hybrid bond ellipsoid #special_bonds fene neighbor 0.8 multi read_data NPinmeltDilute1 Scanning data file ... 1 = max bonds/atom Reading data file ... orthogonal box = (0 0 0) to (40 40 40) 1 by 2 by 2 MPI processor grid 1000 atoms 1000 ellipsoids 810 bonds Finding 1-2 1-3 1-4 neighbors ... 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors group sol type 2 900 atoms in group sol group np type 1 100 atoms in group np set group np mass 1.571 Setting atom values ... 100 settings made for mass set group sol mass 0.526 Setting atom values ... 900 settings made for mass compute sys all temp/asphere variable dof1 equal count(sol) variable dof equal ${dof1}*3 variable dof equal 900*3 compute_modify sys extra ${dof} compute_modify sys extra 2700 compute q all property/atom quatw quati quatj quatk bond_style fene bond_coeff 1 30 1.5 0.0 0.0 pair_style gayberne 1.0 3.0 1.0 6.0 pair_coeff 1 1 2.0 1.0 1 1 0.2 1 1 0.2 pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 #pair_modify shift yes pair_coeff 1 2 1.0 1.0 1 1 0.2 1 1 1 fix 1 all npt/asphere temp 1.0 1.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 compute_modify 1_temp extra ${dof} compute_modify 1_temp extra 2700 thermo_style custom step c_sys epair etotal press vol thermo 100 timestep 0.002 dump 1 all custom 100 dump.shrink id type x y z c_q[1] c_q[2] c_q[3] c_q[4] run 10000 WARNING: Use special bonds = 0,1,1 with bond style fene (bond_fene.cpp:187) Setting up run ...