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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -40.851619 0.0000000) to (20.425809 40.851619 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.2681295 3.2681295 2.8886457 Created 200 atoms using lattice units in orthogonal box = (0.0000000 -40.851619 0.0000000) to (20.425809 40.851619 2.8886457) create_atoms CPU = 0.001 seconds 200 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.2681295 3.2681295 2.8886457 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -40.851619 0.0000000) to (20.425809 40.851619 2.8886457) create_atoms CPU = 0.001 seconds 202 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 31 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 402 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_608695023236_000#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.811 | 4.811 | 4.811 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1582.2862 0 -1582.2862 66384.307 60 0 -1671.9192 0 -1671.9192 12803.934 Loop time of 8.1462 on 1 procs for 60 steps with 402 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 = -1582.28618395862 -1671.9176084939 -1671.9191737883 Force two-norm initial, final = 124.07983 0.14377590 Force max component initial, final = 41.314603 0.020781665 Final line search alpha, max atom move = 1.0000000 0.020781665 Iterations, force evaluations = 60 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.131 | 8.131 | 8.131 | 0.0 | 99.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.007781 | 0.007781 | 0.007781 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007414 | | | 0.09 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2718.00 ave 2718 max 2718 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: 23252.0 ave 23252 max 23252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23252 Ave neighs/atom = 57.840796 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard 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) = 4.811 | 4.811 | 4.811 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1671.9192 0 -1671.9192 12803.934 4820.7301 74 0 -1672.3398 0 -1672.3398 -19.909114 4855.3258 Loop time of 1.18293 on 1 procs for 14 steps with 402 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 = -1671.9191737883 -1672.33913175579 -1672.33978322274 Force two-norm initial, final = 79.409218 0.77290506 Force max component initial, final = 73.516871 0.33653929 Final line search alpha, max atom move = 0.00087433885 0.00029424938 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1568 | 1.1568 | 1.1568 | 0.0 | 97.79 Neigh | 0.020995 | 0.020995 | 0.020995 | 0.0 | 1.77 Comm | 0.0011541 | 0.0011541 | 0.0011541 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003952 | | | 0.33 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704.00 ave 2704 max 2704 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: 23172.0 ave 23172 max 23172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23172 Ave neighs/atom = 57.641791 Neighbor list builds = 1 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.949 | 4.949 | 4.949 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1672.3398 0 -1672.3398 -19.909114 Loop time of 6.225e-06 on 1 procs for 0 steps with 402 atoms 176.7% 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 | | 6.225e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704.00 ave 2704 max 2704 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: 23172.0 ave 23172 max 23172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23172 Ave neighs/atom = 57.641791 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.949 | 4.949 | 4.949 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 -1672.3398 -1672.3398 20.362221 82.804576 2.8796447 -19.909114 -19.909114 22.756992 -112.54931 30.064974 2.4090507 208.43387 Loop time of 6.866e-06 on 1 procs for 0 steps with 402 atoms 218.5% 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 | | 6.866e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704.00 ave 2704 max 2704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11586.0 ave 11586 max 11586 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23172.0 ave 23172 max 23172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23172 Ave neighs/atom = 57.641791 Neighbor list builds = 0 Dangerous builds = 0 402 -1672.33978322274 eV 2.40905069417688 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09