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 = 3.14096 3.14096 3.14096 Created orthogonal box = (0 -31.7253 0) to (22.431 31.7253 4.44199) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9584 4.97603 4.44199 Created 206 atoms create_atoms CPU = 0.000258207 secs 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9584 4.97603 4.44199 Created 206 atoms create_atoms CPU = 0.000111103 secs 206 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 4 11 1 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 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 411 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 4 11 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 4.911 | 4.911 | 4.911 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2335.6119 0 -2335.6119 228733.38 147 0 -2776.7886 0 -2776.7886 40602.005 Loop time of 1.03526 on 1 procs for 147 steps with 411 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2335.61187378 -2776.78607948 -2776.78862664 Force two-norm initial, final = 509.258 0.263632 Force max component initial, final = 142.748 0.0383001 Final line search alpha, max atom move = 1 0.0383001 Iterations, force evaluations = 147 252 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99919 | 0.99919 | 0.99919 | 0.0 | 96.52 Neigh | 0.022728 | 0.022728 | 0.022728 | 0.0 | 2.20 Comm | 0.0097797 | 0.0097797 | 0.0097797 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003564 | | | 0.34 Nlocal: 411 ave 411 max 411 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6609 ave 6609 max 6609 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: 169810 ave 169810 max 169810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169810 Ave neighs/atom = 413.163 Neighbor list builds = 6 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 : 147 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.913 | 4.913 | 4.913 Mbytes Step Temp E_pair E_mol TotEng Press Volume 147 0 -2776.7886 0 -2776.7886 40602.005 6322.1027 176 0 -2783.8932 0 -2783.8932 -12781.493 6429.3309 Loop time of 0.126955 on 1 procs for 29 steps with 411 atoms 102.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2776.78862664 -2783.89298119 -2783.89317931 Force two-norm initial, final = 574.564 2.2922 Force max component initial, final = 574.011 1.24945 Final line search alpha, max atom move = 0.00178458 0.00222974 Iterations, force evaluations = 29 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12284 | 0.12284 | 0.12284 | 0.0 | 96.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011077 | 0.0011077 | 0.0011077 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003005 | | | 2.37 Nlocal: 411 ave 411 max 411 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6657 ave 6657 max 6657 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: 168028 ave 168028 max 168028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168028 Ave neighs/atom = 408.827 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 4 11 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2783.8932 0 -2783.8932 -12781.493 Loop time of 0 on 1 procs for 0 steps with 411 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 | | 0 | | | 0.00 Nlocal: 411 ave 411 max 411 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6657 ave 6657 max 6657 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: 168652 ave 168652 max 168652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168652 Ave neighs/atom = 410.345 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) = 5.051 | 5.051 | 5.051 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 -2783.8932 -2783.8932 22.257353 63.450621 4.5525675 -12781.493 -12781.493 -308.95074 -37726.832 -308.69527 2.6298118 3205.5929 Loop time of 1.90735e-06 on 1 procs for 0 steps with 411 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: 411 ave 411 max 411 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6657 ave 6657 max 6657 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84326 ave 84326 max 84326 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 168652 ave 168652 max 168652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168652 Ave neighs/atom = 410.345 Neighbor list builds = 0 Dangerous builds = 0 411 -2783.89317930885 eV 2.62981183656475 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01