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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -33.944457 0.0000000) to (41.573300 33.944457 7.0271702) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7512343 4.3642873 4.6847802 Created 836 atoms using lattice units in orthogonal box = (0.0000000 -33.944457 0.0000000) to (41.573300 33.944457 7.0271702) create_atoms CPU = 0.002 seconds 836 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7512343 4.3642873 4.6847802 Created 842 atoms using lattice units in orthogonal box = (0.0000000 -33.944457 0.0000000) to (41.573300 33.944457 7.0271702) create_atoms CPU = 0.001 seconds 842 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 14 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, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1666 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_984358344196_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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 7.173 | 7.173 | 7.173 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5950.4065 0 -5950.4065 71491.16 172 0 -6833.5505 0 -6833.5505 -6158.4355 Loop time of 7.57251 on 1 procs for 172 steps with 1666 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 = -5950.40653492288 -6833.54382425552 -6833.55054216954 Force two-norm initial, final = 889.12426 0.36119882 Force max component initial, final = 171.11928 0.048603001 Final line search alpha, max atom move = 1.0000000 0.048603001 Iterations, force evaluations = 172 312 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3298 | 7.3298 | 7.3298 | 0.0 | 96.79 Neigh | 0.17084 | 0.17084 | 0.17084 | 0.0 | 2.26 Comm | 0.040902 | 0.040902 | 0.040902 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03096 | | | 0.41 Nlocal: 1666.00 ave 1666 max 1666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11267.0 ave 11267 max 11267 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: 633072.0 ave 633072 max 633072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 633072 Ave neighs/atom = 379.99520 Neighbor list builds = 5 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 172 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.172 | 7.172 | 7.172 Mbytes Step Temp E_pair E_mol TotEng Press Volume 172 0 -6833.5505 0 -6833.5505 -6158.4355 19833.248 175 0 -6833.722 0 -6833.722 -2.4521488 19760.154 Loop time of 0.147333 on 1 procs for 3 steps with 1666 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 = -6833.55054216952 -6833.71961363213 -6833.72198636417 Force two-norm initial, final = 139.64826 0.63290877 Force max component initial, final = 103.99482 0.36393871 Final line search alpha, max atom move = 8.0270229e-05 2.9213444e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14403 | 0.14403 | 0.14403 | 0.0 | 97.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059889 | 0.00059889 | 0.00059889 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002703 | | | 1.83 Nlocal: 1666.00 ave 1666 max 1666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11255.0 ave 11255 max 11255 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: 634256.0 ave 634256 max 634256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 634256 Ave neighs/atom = 380.70588 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 7.310 | 7.310 | 7.310 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6833.722 0 -6833.722 -2.4521488 Loop time of 2.288e-06 on 1 procs for 0 steps with 1666 atoms 174.8% 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 | | 2.288e-06 | | |100.00 Nlocal: 1666.00 ave 1666 max 1666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11282.0 ave 11282 max 11282 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: 639340.0 ave 639340 max 639340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 639340 Ave neighs/atom = 383.75750 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 7.310 | 7.310 | 7.310 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 -6833.722 -6833.722 41.564989 67.791645 7.0127197 -2.4521488 -2.4521488 -15.549436 29.4663 -21.27331 2.3187193 2422.5844 Loop time of 2.669e-06 on 1 procs for 0 steps with 1666 atoms 262.3% 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 | | 2.669e-06 | | |100.00 Nlocal: 1666.00 ave 1666 max 1666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11282.0 ave 11282 max 11282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 319670.0 ave 319670 max 319670 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 639340.0 ave 639340 max 639340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 639340 Ave neighs/atom = 383.75750 Neighbor list builds = 0 Dangerous builds = 0 1666 -6833.72198636417 eV 2.31871931395485 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08