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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -60.971942 0.0000000) to (24.890254 60.971942 8.6222370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9736610 5.2839299 5.7481580 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -60.971942 0.0000000) to (24.890254 60.971942 8.6222370) create_atoms CPU = 0.002 seconds 1205 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9736610 5.2839299 5.7481580 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -60.971942 0.0000000) to (24.890254 60.971942 8.6222370) create_atoms CPU = 0.002 seconds 1205 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 29 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2384 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.962 | 6.962 | 6.962 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10550.08 0 -10550.08 1287.8529 24 0 -10579.211 0 -10579.211 -8369.9195 Loop time of 1.01151 on 1 procs for 24 steps with 2384 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10550.0800613144 -10579.2004274592 -10579.2108919007 Force two-norm initial, final = 23.225464 0.33769968 Force max component initial, final = 3.0224811 0.030107510 Final line search alpha, max atom move = 1.0000000 0.030107510 Iterations, force evaluations = 24 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96934 | 0.96934 | 0.96934 | 0.0 | 95.83 Neigh | 0.032882 | 0.032882 | 0.032882 | 0.0 | 3.25 Comm | 0.0043408 | 0.0043408 | 0.0043408 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004944 | | | 0.49 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11021.0 ave 11021 max 11021 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: 534108.0 ave 534108 max 534108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 534108 Ave neighs/atom = 224.03859 Neighbor list builds = 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.962 | 6.962 | 6.962 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -10579.211 0 -10579.211 -8369.9195 26170.337 27 0 -10579.412 0 -10579.412 -2324.8229 26080.963 Loop time of 0.138604 on 1 procs for 3 steps with 2384 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 = -10579.2108919007 -10579.412226343 -10579.4123779306 Force two-norm initial, final = 166.03594 0.35915275 Force max component initial, final = 119.92423 0.069625972 Final line search alpha, max atom move = 0.00041351713 2.8791532e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13586 | 0.13586 | 0.13586 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046737 | 0.00046737 | 0.00046737 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00228 | | | 1.65 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11064.0 ave 11064 max 11064 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: 534864.0 ave 534864 max 534864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 534864 Ave neighs/atom = 224.35570 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.100 | 7.100 | 7.100 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10579.412 0 -10579.412 -2324.8229 Loop time of 1.943e-06 on 1 procs for 0 steps with 2384 atoms 154.4% 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 | | 1.943e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11087.0 ave 11087 max 11087 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: 535034.0 ave 535034 max 535034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 535034 Ave neighs/atom = 224.42701 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.100 | 7.100 | 7.100 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 -10579.412 -10579.412 24.850922 121.94388 8.6063913 -2324.8229 -2324.8229 -4.2704258 -6968.9586 -1.2398077 2.3210843 746.96543 Loop time of 2.086e-06 on 1 procs for 0 steps with 2384 atoms 239.7% 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 | | 2.086e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11087.0 ave 11087 max 11087 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 267517.0 ave 267517 max 267517 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 535034.0 ave 535034 max 535034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 535034 Ave neighs/atom = 224.42701 Neighbor list builds = 0 Dangerous builds = 0 2384 -10514.4211961539 eV 2.32108431360929 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01