LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -53.475802 0.0000000) to (43.659859 53.475802 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3827223 5.1274701 5.9005197 Created 1757 atoms create_atoms CPU = 0.001 seconds 1757 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3827223 5.1274701 5.9005197 Created 1757 atoms create_atoms CPU = 0.001 seconds 1757 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 50 atoms, new total = 3464 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.687 | 5.687 | 5.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12124.995 0 -12124.995 4451.4096 68 0 -12215.192 0 -12215.192 -8827.3592 Loop time of 3.87784 on 1 procs for 68 steps with 3464 atoms 92.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12124.9945104039 -12215.1820557018 -12215.1924520997 Force two-norm initial, final = 88.377454 0.31966410 Force max component initial, final = 10.723652 0.068267787 Final line search alpha, max atom move = 1.0000000 0.068267787 Iterations, force evaluations = 68 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8617 | 3.8617 | 3.8617 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0069356 | 0.0069356 | 0.0069356 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009189 | | | 0.24 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8399.00 ave 8399 max 8399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 266940.0 ave 266940 max 266940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266940 Ave neighs/atom = 77.061201 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.687 | 5.687 | 5.687 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -12215.192 0 -12215.192 -8827.3592 41328.644 72 0 -12215.756 0 -12215.756 -1602.6714 41113.163 Loop time of 0.160315 on 1 procs for 4 steps with 3464 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12215.1924520996 -12215.7512093732 -12215.755642395 Force two-norm initial, final = 298.01498 0.74155704 Force max component initial, final = 225.13177 0.45774968 Final line search alpha, max atom move = 7.7194678e-05 3.5335839e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15867 | 0.15867 | 0.15867 | 0.0 | 98.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003052 | 0.0003052 | 0.0003052 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001335 | | | 0.83 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8130.00 ave 8130 max 8130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267872.0 ave 267872 max 267872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267872 Ave neighs/atom = 77.330254 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.824 | 5.824 | 5.824 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12215.756 0 -12215.756 -1602.6714 Loop time of 2.10002e-06 on 1 procs for 0 steps with 3464 atoms 238.1% 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 | | 2.1e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8155.00 ave 8155 max 8155 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267902.0 ave 267902 max 267902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267902 Ave neighs/atom = 77.338915 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) = 5.824 | 5.824 | 5.824 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 -12215.756 -12215.756 43.513645 106.9516 8.8342183 -1602.6714 -1602.6714 -17.778727 -4774.7259 -15.509525 2.2613889 1794.2782 Loop time of 2.60002e-06 on 1 procs for 0 steps with 3464 atoms 192.3% 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 | | 2.6e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8155.00 ave 8155 max 8155 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133951.0 ave 133951 max 133951 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267902.0 ave 267902 max 267902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267902 Ave neighs/atom = 77.338915 Neighbor list builds = 0 Dangerous builds = 0 3464 -12215.755642395 eV 2.26138892632684 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04