LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.52 3.52 3.52 Created orthogonal box = (0 -55.4365 0) to (33.9457 55.4365 8.6222) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4751 5.36449 5.74814 Created 1493 atoms create_atoms CPU = 0.00068903 secs 1493 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4751 5.36449 5.74814 Created 1493 atoms create_atoms CPU = 0.000520945 secs 1493 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 8 26 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 2963 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 7.876 | 7.876 | 7.876 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13092.873 0 -13092.873 3615.0483 23 0 -13145.648 0 -13145.648 -1250.418 Loop time of 0.634087 on 1 procs for 23 steps with 2963 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13092.8729426 -13145.6354283 -13145.6479004 Force two-norm initial, final = 34.8765 0.38072 Force max component initial, final = 5.30699 0.0446458 Final line search alpha, max atom move = 1 0.0446458 Iterations, force evaluations = 23 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62766 | 0.62766 | 0.62766 | 0.0 | 98.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0037506 | 0.0037506 | 0.0037506 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002678 | | | 0.42 Nlocal: 2963 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13073 ave 13073 max 13073 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 732840 ave 732840 max 732840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 732840 Ave neighs/atom = 247.33 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.876 | 7.876 | 7.876 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -13145.648 0 -13145.648 -1250.418 32451.032 25 0 -13145.669 0 -13145.669 -1258.4064 32451.243 Loop time of 0.069838 on 1 procs for 2 steps with 2963 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13145.6479004 -13145.6686582 -13145.6686682 Force two-norm initial, final = 42.4955 0.404228 Force max component initial, final = 30.3704 0.094245 Final line search alpha, max atom move = 0.00116253 0.000109562 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068518 | 0.068518 | 0.068518 | 0.0 | 98.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036407 | 0.00036407 | 0.00036407 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009561 | | | 1.37 Nlocal: 2963 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13052 ave 13052 max 13052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 732718 ave 732718 max 732718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 732718 Ave neighs/atom = 247.289 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13145.669 0 -13145.669 -1258.4064 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2963 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.907e-06 | | |100.00 Nlocal: 2963 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13052 ave 13052 max 13052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 732690 ave 732690 max 732690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 732690 Ave neighs/atom = 247.28 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -13145.669 -13145.669 33.969225 110.87307 8.6162762 -1258.4064 -1258.4064 -4.4454684 -3766.1238 -4.6498461 2.1883526 1096.9117 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2963 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.192e-06 | | |100.00 Nlocal: 2963 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13052 ave 13052 max 13052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 366345 ave 366345 max 366345 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 732690 ave 732690 max 732690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 732690 Ave neighs/atom = 247.28 Neighbor list builds = 0 Dangerous builds = 0 2963 -13078.8540548213 eV 2.18835260391567 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01