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 -42.062205 0.0000000) to (21.029658 42.062205 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5710740 3.5710740 2.8886457 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -42.062205 0.0000000) to (21.029658 42.062205 2.8886457) create_atoms CPU = 0.002 seconds 213 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5710740 3.5710740 2.8886457 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -42.062205 0.0000000) to (21.029658 42.062205 2.8886457) create_atoms CPU = 0.001 seconds 213 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 32 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 4 atoms, new total = 422 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 32 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) = 4.817 | 4.817 | 4.817 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1716.9434 0 -1716.9434 19926.75 53 0 -1754.1266 0 -1754.1266 -325.9089 Loop time of 8.78906 on 1 procs for 53 steps with 422 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 = -1716.94336573189 -1754.12514826316 -1754.12659827624 Force two-norm initial, final = 85.571419 0.21412955 Force max component initial, final = 26.151073 0.049500299 Final line search alpha, max atom move = 1.0000000 0.049500299 Iterations, force evaluations = 53 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.7743 | 8.7743 | 8.7743 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0074651 | 0.0074651 | 0.0074651 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007336 | | | 0.08 Nlocal: 422.000 ave 422 max 422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2790.00 ave 2790 max 2790 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: 24208.0 ave 24208 max 24208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24208 Ave neighs/atom = 57.364929 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 32 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 : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.817 | 4.817 | 4.817 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1754.1266 0 -1754.1266 -325.9089 5110.3249 56 0 -1754.1437 0 -1754.1437 3413.3074 5098.9232 Loop time of 0.510277 on 1 procs for 3 steps with 422 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 = -1754.12659827624 -1754.14253573058 -1754.1436847306 Force two-norm initial, final = 18.464564 0.22527045 Force max component initial, final = 15.361529 0.054555926 Final line search alpha, max atom move = 0.00029673356 1.6188574e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50813 | 0.50813 | 0.50813 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044353 | 0.00044353 | 0.00044353 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0017 | | | 0.33 Nlocal: 422.000 ave 422 max 422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2795.00 ave 2795 max 2795 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: 24228.0 ave 24228 max 24228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24228 Ave neighs/atom = 57.412322 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 32 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) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1754.1437 0 -1754.1437 3413.3074 Loop time of 6.245e-06 on 1 procs for 0 steps with 422 atoms 176.1% 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 | | 6.245e-06 | | |100.00 Nlocal: 422.000 ave 422 max 422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2795.00 ave 2795 max 2795 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: 24230.0 ave 24230 max 24230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24230 Ave neighs/atom = 57.417062 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 32 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) = 4.955 | 4.955 | 4.955 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 -1754.1437 -1754.1437 21.028803 84.124409 2.882318 3413.3074 3413.3074 -2.5811406 10239.9 2.6029391 2.3351421 220.59194 Loop time of 6.424e-06 on 1 procs for 0 steps with 422 atoms 264.6% 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 | | 6.424e-06 | | |100.00 Nlocal: 422.000 ave 422 max 422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2795.00 ave 2795 max 2795 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12115.0 ave 12115 max 12115 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24230.0 ave 24230 max 24230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24230 Ave neighs/atom = 57.417062 Neighbor list builds = 0 Dangerous builds = 0 422 -1754.1436847306 eV 2.33514212500244 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09