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 = 3.61493 3.61493 3.61493 Created orthogonal box = (0 -53.4996 0) to (43.6793 53.4996 8.85472) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.38512 5.12975 5.90315 Created 1758 atoms create_atoms CPU = 0.000725985 secs 1758 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.38512 5.12975 5.90315 Created 1758 atoms create_atoms CPU = 0.000581026 secs 1758 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 29 3 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 44 atoms, new total = 3472 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.648 | 6.648 | 6.648 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12175.135 0 -12175.135 4086.7525 64 0 -12247.005 0 -12247.005 -6565.0108 Loop time of 1.14345 on 1 procs for 64 steps with 3472 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12175.135325 -12246.9937916 -12247.0049255 Force two-norm initial, final = 69.3101 0.319757 Force max component initial, final = 10.0379 0.0418807 Final line search alpha, max atom move = 1 0.0418807 Iterations, force evaluations = 64 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1152 | 1.1152 | 1.1152 | 0.0 | 97.53 Neigh | 0.011315 | 0.011315 | 0.011315 | 0.0 | 0.99 Comm | 0.0082943 | 0.0082943 | 0.0082943 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008608 | | | 0.75 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11205 ave 11205 max 11205 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: 490568 ave 490568 max 490568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 490568 Ave neighs/atom = 141.293 Neighbor list builds = 1 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.03 | 7.03 | 7.03 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -12247.005 0 -12247.005 -6565.0108 41383.894 67 0 -12247.335 0 -12247.335 -875.52811 41212.677 Loop time of 0.055124 on 1 procs for 3 steps with 3472 atoms 90.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12247.0049255 -12247.3297872 -12247.3348046 Force two-norm initial, final = 227.605 10.0956 Force max component initial, final = 170.131 9.90885 Final line search alpha, max atom move = 4.10451e-05 0.00040671 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053374 | 0.053374 | 0.053374 | 0.0 | 96.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034261 | 0.00034261 | 0.00034261 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001407 | | | 2.55 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11194 ave 11194 max 11194 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: 489552 ave 489552 max 489552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489552 Ave neighs/atom = 141 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.786 | 6.786 | 6.786 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12247.335 0 -12247.335 -875.52811 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3472 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 | | 9.537e-07 | | |100.00 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11209 ave 11209 max 11209 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: 490076 ave 490076 max 490076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 490076 Ave neighs/atom = 141.151 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) = 6.786 | 6.786 | 6.786 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 -12247.335 -12247.335 43.574608 106.99924 8.8392748 -875.52811 -875.52811 -73.675378 -2937.4515 384.54251 2.2952332 1534.8823 Loop time of 2.14577e-06 on 1 procs for 0 steps with 3472 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 | | 2.146e-06 | | |100.00 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11209 ave 11209 max 11209 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 245038 ave 245038 max 245038 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 490076 ave 490076 max 490076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 490076 Ave neighs/atom = 141.151 Neighbor list builds = 0 Dangerous builds = 0 3472 -12247.3521645757 eV 2.29523321743412 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01