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 = 4.03204 4.03204 4.03204 Created orthogonal box = (0 -56.7398 0) to (13.3728 56.7398 5.70216) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.07853 6.87707 5.70216 Created 266 atoms create_atoms CPU = 0.000381947 secs 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.07853 6.87707 5.70216 Created 266 atoms create_atoms CPU = 0.000259161 secs 266 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 4 27 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 524 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 4 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1749.5091 0 -1749.5091 2930.7634 21 0 -1756.4157 0 -1756.4157 -2164.0268 Loop time of 0.089535 on 1 procs for 21 steps with 524 atoms 100.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1749.50908729 -1756.41412555 -1756.4157082 Force two-norm initial, final = 15.6883 0.112042 Force max component initial, final = 5.54965 0.0229289 Final line search alpha, max atom move = 1 0.0229289 Iterations, force evaluations = 21 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087615 | 0.087615 | 0.087615 | 0.0 | 97.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012922 | 0.0012922 | 0.0012922 | 0.0 | 1.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006275 | | | 0.70 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5204 ave 5204 max 5204 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: 91128 ave 91128 max 91128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91128 Ave neighs/atom = 173.908 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 : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -1756.4157 0 -1756.4157 -2164.0268 8653.2393 24 0 -1756.4397 0 -1756.4397 285.12239 8627.6746 Loop time of 0.015017 on 1 procs for 3 steps with 524 atoms 66.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1756.4157082 -1756.43929468 -1756.43972797 Force two-norm initial, final = 21.5535 0.127333 Force max component initial, final = 17.3946 0.0241868 Final line search alpha, max atom move = 0.000710062 1.71741e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.014275 | 0.014275 | 0.014275 | 0.0 | 95.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018167 | 0.00018167 | 0.00018167 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005603 | | | 3.73 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5180 ave 5180 max 5180 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: 90640 ave 90640 max 90640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90640 Ave neighs/atom = 172.977 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 4 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 4.691 | 4.691 | 4.691 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1756.4397 0 -1756.4397 285.12239 Loop time of 9.53674e-07 on 1 procs for 0 steps with 524 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: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5180 ave 5180 max 5180 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: 90728 ave 90728 max 90728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90728 Ave neighs/atom = 173.145 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) = 4.691 | 4.691 | 4.691 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 -1756.4397 -1756.4397 13.343962 113.47968 5.6975856 285.12239 285.12239 1.0967308 858.75836 -4.4879286 2.6780226 348.14094 Loop time of 9.53674e-07 on 1 procs for 0 steps with 524 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: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5180 ave 5180 max 5180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45364 ave 45364 max 45364 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90728 ave 90728 max 90728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90728 Ave neighs/atom = 173.145 Neighbor list builds = 0 Dangerous builds = 0 524 -1756.43972797324 eV 2.67802257086269 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00