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 = 3.63909 3.63909 3.63909 Created orthogonal box = (0 -39.8678 0) to (8.13724 39.8678 8.9139) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.88234 5.31522 5.9426 Created 242 atoms create_atoms CPU = 0.000240088 secs 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.88234 5.31522 5.9426 Created 242 atoms create_atoms CPU = 0.000117064 secs 242 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 2 17 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 472 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 2 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.028 | 5.028 | 5.028 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1535.7735 0 -1535.7735 -6094.8475 60 0 -1541.1538 0 -1541.1538 -14127.091 Loop time of 0.398429 on 1 procs for 60 steps with 472 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1535.77349376 -1541.15241755 -1541.15384711 Force two-norm initial, final = 4.95067 0.0988041 Force max component initial, final = 0.947034 0.00954598 Final line search alpha, max atom move = 1 0.00954598 Iterations, force evaluations = 60 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39239 | 0.39239 | 0.39239 | 0.0 | 98.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043304 | 0.0043304 | 0.0043304 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001705 | | | 0.43 Nlocal: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5617 ave 5617 max 5617 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: 147960 ave 147960 max 147960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147960 Ave neighs/atom = 313.475 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.028 | 5.028 | 5.028 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1541.1538 0 -1541.1538 -14127.091 5783.5904 66 0 -1541.3892 0 -1541.3892 -1104.4074 5732.4618 Loop time of 0.0259171 on 1 procs for 6 steps with 472 atoms 115.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1541.15384711 -1541.38873394 -1541.38920037 Force two-norm initial, final = 74.3452 0.178771 Force max component initial, final = 54.3921 0.0347752 Final line search alpha, max atom move = 0.000599388 2.08438e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.024997 | 0.024997 | 0.024997 | 0.0 | 96.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023961 | 0.00023961 | 0.00023961 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00068 | | | 2.62 Nlocal: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5612 ave 5612 max 5612 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: 148876 ave 148876 max 148876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148876 Ave neighs/atom = 315.415 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 2 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.166 | 5.166 | 5.166 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1541.3892 0 -1541.3892 -1104.4074 Loop time of 9.53674e-07 on 1 procs for 0 steps with 472 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: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5636 ave 5636 max 5636 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: 149004 ave 149004 max 149004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149004 Ave neighs/atom = 315.686 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) = 5.166 | 5.166 | 5.166 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 -1541.3892 -1541.3892 8.0950689 79.735638 8.8811283 -1104.4074 -1104.4074 4.979677 -3316.7938 -1.4082518 2.2497735 295.47992 Loop time of 9.53674e-07 on 1 procs for 0 steps with 472 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: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5636 ave 5636 max 5636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74502 ave 74502 max 74502 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 149004 ave 149004 max 149004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149004 Ave neighs/atom = 315.686 Neighbor list builds = 0 Dangerous builds = 0 472 -1541.38920037148 eV 2.24977349646938 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00