LAMMPS (30 Aug 2013) units lj lattice sc 1.0 Lattice spacing in x,y,z = 1 1 1 boundary p p p neighbor 1.0 bin neigh_modify every 5 delay 0 check yes atom_style full bond_style quartic #angle_style harmonic pair_style lj/cut 2.5 pair_modify table 0 special_bonds lj 1.0 1.0 1.0 read_data harmonic_bonds.init Scanning data file ... 6 = max bonds/atom Reading data file ... orthogonal box = (-6.54473 -6.54473 -6.54473) to (6.54473 6.54473 6.54473) 1 by 2 by 2 MPI processor grid 2100 atoms 2600 bonds Finding 1-2 1-3 1-4 neighbors ... 6 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 16 = max # of 1-4 neighbors 18 = max # of special neighbors # k b1 b2 rc U0 bond_coeff 1 1434.3 -0.7589 0.00 1.5 67.2234 pair_coeff * * 1.0 1.0 2.5 timestep 0.005 fix 1 all npt temp 0.3 0.3 1.0 iso 0.1 0.1 10.0 thermo_style custom step temp etotal evdwl ebond pxx pyy pzz lz thermo_modify flush yes thermo 100 reset_timestep 0 ######################################################################## variable l equal xhi #region MESH block xlo xhi ylo yhi zlo zhi region MESH block -$l $l -$l $l -$l $l region MESH block -6.5447300000000003806 $l -$l $l -$l $l region MESH block -6.5447300000000003806 6.5447300000000003806 -$l $l -$l $l region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 $l -$l $l region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -$l $l region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 $l region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 group MESH region MESH 2100 atoms in group MESH # ID group atc PhysicsType ParameterFile fix ATC all atc field ATC: constructing shape function field estimate ATC: version 2.0 ATC: peratom PE compute created with ID: 5 fix_modify ATC fields add mass_density energy stress heat_flux # ID part keywords nx ny nz region fix_modify ATC mesh create 4 4 1 MESH p p p ATC: created uniform mesh with 50 nodes, 16 unique nodes, and 16 elements fix_modify ATC bond_interactions on fix_modify ATC pair_interactions off fix_modify ATC output nodeset all average energy fix_modify ATC output nodeset all average stress fix_modify ATC output harmonic_bondsFE 100 full_text binary tensor_components ATC: Warning : text output can create _LARGE_ files ATC: output custom names: ######################################################################## dump d1 all custom 1000 config.dmp id type mol x y z ix iy iz run 1000 Setting up run ... WARNING: Inconsistent image flags (../domain.cpp:607) ATC: computing bond matrix ...........done Memory usage per processor = 22.5059 Mbytes Step Temp TotEng E_vdwl E_bond Pxx Pyy Pzz Lz 0 0 27.418101 -4.9222297 32.340331 -6.4375188 -5.3652966 -8.8338595 13.08946 ATC: computing bond matrix ...........done 100 2.2145029 25.770666 -4.6618339 27.112327 1.4701161 2.16737 2.7891188 13.107872 ATC: computing bond matrix ...........done 200 1.6441119 24.285276 -4.6100702 26.430353 -0.2111306 0.11829479 -0.34968383 13.21971 ATC: computing bond matrix ...........done 300 1.2519109 23.218023 -4.7073226 26.048373 -0.90980473 -0.55453672 -1.175576 13.280803 ATC: computing bond matrix ...........done 400 1.0087196 22.413664 -4.8800967 25.781401 -0.94622376 -0.72705532 -0.96132435 13.209446 ATC: computing bond matrix ...........done 500 0.85508692 21.781946 -5.1146958 25.614623 -0.25867636 0.45882845 -1.5464988 13.067112 ATC: computing bond matrix ...........done 600 0.72896043 21.277404 -5.3122654 25.496749 -0.23318524 -0.79102184 -0.28592714 12.940731 ATC: computing bond matrix ...........done 700 0.63573201 20.877991 -5.4819279 25.406775 -0.22930105 0.17264694 -0.13977843 12.838254 ATC: computing bond matrix ...........done 800 0.54900117 20.560582 -5.6107452 25.348218 -0.40709766 -0.32952441 -0.39623019 12.765768 ATC: computing bond matrix ...........done 900 0.4864295 20.309827 -5.7089607 25.289491 0.18995702 -0.4389685 0.32204857 12.716563 ATC: computing bond matrix ...........done 1000 0.43059305 20.104384 -5.8079042 25.266707 -0.0082532778 0.34329484 0.20699648 12.673678 Loop time of 2.37561 on 4 procs for 1000 steps with 2100 atoms Pair time (%) = 1.15772 (48.7335) Bond time (%) = 0.108688 (4.57518) Neigh time (%) = 0.317073 (13.347) Comm time (%) = 0.327571 (13.7889) Outpt time (%) = 0.0205073 (0.863244) Other time (%) = 0.444053 (18.6922) Nlocal: 525 ave 530 max 523 min Histogram: 2 1 0 0 0 0 0 0 0 1 Nghost: 3067.75 ave 3080 max 3059 min Histogram: 2 0 0 0 0 1 0 0 0 1 Neighs: 48006.5 ave 48692 max 47634 min Histogram: 1 1 1 0 0 0 0 0 0 1 FullNghs: 96013 ave 97189 max 95320 min Histogram: 2 0 0 1 0 0 0 0 0 1 Total # of neighbors = 384052 Ave neighs/atom = 182.882 Ave special neighs/atom = 13.3324 Neighbor list builds = 28 Dangerous builds = 0