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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -51.275759 0.0000000) to (25.636119 51.275759 3.5213917) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3533032 4.3533032 3.5213917 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -51.275759 0.0000000) to (25.636119 51.275759 3.5213917) create_atoms CPU = 0.002 seconds 426 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3533032 4.3533032 3.5213917 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -51.275759 0.0000000) to (25.636119 51.275759 3.5213917) create_atoms CPU = 0.001 seconds 426 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, 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, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 840 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_131642768288_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.959 | 4.959 | 4.959 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3710.0449 0 -3710.0449 2205.8346 20 0 -3721.0566 0 -3721.0566 -6452.2712 Loop time of 4.77825 on 1 procs for 20 steps with 840 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 = -3710.04491744826 -3721.05411728436 -3721.05664912227 Force two-norm initial, final = 26.760695 0.17573285 Force max component initial, final = 8.6454918 0.040651539 Final line search alpha, max atom move = 1.0000000 0.040651539 Iterations, force evaluations = 20 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7679 | 4.7679 | 4.7679 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0056625 | 0.0056625 | 0.0056625 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004664 | | | 0.10 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6420.00 ave 6420 max 6420 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: 110784.0 ave 110784 max 110784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110784 Ave neighs/atom = 131.88571 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.959 | 4.959 | 4.959 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -3721.0566 0 -3721.0566 -6452.2712 9257.8196 23 0 -3721.1112 0 -3721.1112 -1151.8263 9231.086 Loop time of 0.774136 on 1 procs for 3 steps with 840 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3721.05664912227 -3721.10891640837 -3721.11117295782 Force two-norm initial, final = 48.747981 0.19944333 Force max component initial, final = 39.612384 0.048567880 Final line search alpha, max atom move = 0.00021142529 1.0268478e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77055 | 0.77055 | 0.77055 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081611 | 0.00081611 | 0.00081611 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002766 | | | 0.36 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6420.00 ave 6420 max 6420 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: 110848.0 ave 110848 max 110848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110848 Ave neighs/atom = 131.96190 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3721.1112 0 -3721.1112 -1151.8263 Loop time of 6.074e-06 on 1 procs for 0 steps with 840 atoms 181.1% 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 | | 6.074e-06 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6420.00 ave 6420 max 6420 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: 110896.0 ave 110896 max 110896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110896 Ave neighs/atom = 132.01905 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.097 | 5.097 | 5.097 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 -3721.1112 -3721.1112 25.623197 102.55152 3.5129938 -1151.8263 -1151.8263 -2.174161 -3454.1103 0.80544796 2.282391 336.98715 Loop time of 9.833e-06 on 1 procs for 0 steps with 840 atoms 223.7% 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 | | 9.833e-06 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6420.00 ave 6420 max 6420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55448.0 ave 55448 max 55448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 110896.0 ave 110896 max 110896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110896 Ave neighs/atom = 132.01905 Neighbor list builds = 0 Dangerous builds = 0 840 -3721.11117295782 eV 2.28239098282806 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06