LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -41.226620 0.0000000) to (29.151622 41.226620 4.4455807) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4235576 5.2731723 4.4455807 Created 343 atoms using lattice units in orthogonal box = (0.0000000 -41.226620 0.0000000) to (29.151622 41.226620 4.4455807) create_atoms CPU = 0.001 seconds 343 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4235576 5.2731723 4.4455807 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -41.226620 0.0000000) to (29.151622 41.226620 4.4455807) create_atoms CPU = 0.001 seconds 345 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 17 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 683 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_534363225491_004#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.963 | 4.963 | 4.963 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3876.0055 0 -3876.0055 135531.13 459 0 -4591.4344 0 -4591.4344 -19691.904 Loop time of 6.82168 on 1 procs for 459 steps with 683 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3876.00550191997 -4591.43026779039 -4591.43440596208 Force two-norm initial, final = 1246.4461 0.40487297 Force max component initial, final = 419.63116 0.13241202 Final line search alpha, max atom move = 0.74068680 0.098075833 Iterations, force evaluations = 459 846 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5398 | 6.5398 | 6.5398 | 0.0 | 95.87 Neigh | 0.19591 | 0.19591 | 0.19591 | 0.0 | 2.87 Comm | 0.054121 | 0.054121 | 0.054121 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03186 | | | 0.47 Nlocal: 683.000 ave 683 max 683 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7205.00 ave 7205 max 7205 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: 182918.0 ave 182918 max 182918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182918 Ave neighs/atom = 267.81552 Neighbor list builds = 19 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 459 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.963 | 4.963 | 4.963 Mbytes Step Temp E_pair E_mol TotEng Press Volume 459 0 -4591.4344 0 -4591.4344 -19691.904 10685.601 488 0 -4611.2012 0 -4611.2012 -47.767574 10591.667 Loop time of 0.26079 on 1 procs for 29 steps with 683 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 = -4591.43440596206 -4611.19907883727 -4611.20122448622 Force two-norm initial, final = 1018.1608 7.8301502 Force max component initial, final = 701.36844 5.0118292 Final line search alpha, max atom move = 0.00024832201 0.0012445475 Iterations, force evaluations = 29 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24955 | 0.24955 | 0.24955 | 0.0 | 95.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018955 | 0.0018955 | 0.0018955 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009346 | | | 3.58 Nlocal: 683.000 ave 683 max 683 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7205.00 ave 7205 max 7205 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: 183080.0 ave 183080 max 183080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183080 Ave neighs/atom = 268.05271 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.101 | 5.101 | 5.101 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4611.2012 0 -4611.2012 -47.767574 Loop time of 1.786e-06 on 1 procs for 0 steps with 683 atoms 168.0% 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 | | 1.786e-06 | | |100.00 Nlocal: 683.000 ave 683 max 683 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7205.00 ave 7205 max 7205 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: 186816.0 ave 186816 max 186816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186816 Ave neighs/atom = 273.52269 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.101 | 5.101 | 5.101 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 -4611.2012 -4611.2012 28.328861 82.042032 4.5572072 -47.767574 -47.767574 276.06569 -754.34671 334.9783 2.4185754 3747.7482 Loop time of 2.139e-06 on 1 procs for 0 steps with 683 atoms 187.0% 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 | | 2.139e-06 | | |100.00 Nlocal: 683.000 ave 683 max 683 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7205.00 ave 7205 max 7205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93408.0 ave 93408 max 93408 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186816.0 ave 186816 max 186816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186816 Ave neighs/atom = 273.52269 Neighbor list builds = 0 Dangerous builds = 0 683 -4611.20122448622 eV 2.41857540658405 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07