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 = 3.1707 3.1707 3.1707 Created orthogonal box = (0 -32.3381 0) to (16.1675 32.3381 3.1707) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.73095 3.73095 3.1707 Created 105 atoms create_atoms CPU = 0.000170946 secs 105 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.73095 3.73095 3.1707 Created 105 atoms create_atoms CPU = 3.29018e-05 secs 105 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 5 20 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 208 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.398 | 4.398 | 4.398 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2225.981 0 -2225.981 13748.936 39 0 -2244.3461 0 -2244.3461 16829.797 Loop time of 2.31414 on 1 procs for 39 steps with 208 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2225.98095098 -2244.34492881 -2244.34606586 Force two-norm initial, final = 26.1149 0.0919453 Force max component initial, final = 7.8465 0.0121669 Final line search alpha, max atom move = 1 0.0121669 Iterations, force evaluations = 39 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3121 | 2.3121 | 2.3121 | 0.0 | 99.91 Neigh | 0.00051904 | 0.00051904 | 0.00051904 | 0.0 | 0.02 Comm | 0.0010312 | 0.0010312 | 0.0010312 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000524 | | | 0.02 Nlocal: 208 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2194 ave 2194 max 2194 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: 13396 ave 13396 max 13396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13396 Ave neighs/atom = 64.4038 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 : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.4 | 4.4 | 4.4 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -2244.3461 0 -2244.3461 16829.797 3315.4403 41 0 -2244.3644 0 -2244.3644 10488.453 3323.2341 Loop time of 0.127233 on 1 procs for 2 steps with 208 atoms 94.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2244.34606586 -2244.36318795 -2244.36441827 Force two-norm initial, final = 21.8972 0.934894 Force max component initial, final = 17.4748 0.839485 Final line search alpha, max atom move = 0.00020066 0.000168451 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12702 | 0.12702 | 0.12702 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.1498e-05 | 5.1498e-05 | 5.1498e-05 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001652 | | | 0.13 Nlocal: 208 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2327 ave 2327 max 2327 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: 13348 ave 13348 max 13348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13348 Ave neighs/atom = 64.1731 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.538 | 4.538 | 4.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2244.3644 0 -2244.3644 10488.453 Loop time of 9.53674e-07 on 1 procs for 0 steps with 208 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: 208 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2327 ave 2327 max 2327 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: 13340 ave 13340 max 13340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13340 Ave neighs/atom = 64.1346 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) = 4.538 | 4.538 | 4.538 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 -2244.3644 -2244.3644 16.182822 64.676178 3.175136 10488.453 10488.453 -405.11171 31678.155 192.31661 2.5144699 70.595832 Loop time of 0 on 1 procs for 0 steps with 208 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: 208 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2327 ave 2327 max 2327 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6670 ave 6670 max 6670 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13340 ave 13340 max 13340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13340 Ave neighs/atom = 64.1346 Neighbor list builds = 0 Dangerous builds = 0 208 -637.726520458574 eV 2.51446993278951 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02