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 = 4.0333018 4.0333018 4.0333018 Created orthogonal box = (0.0000000 -53.507796 0.0000000) to (32.766699 53.507796 9.8795315) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9575817 6.0804313 6.5863543 Created 1042 atoms using lattice units in orthogonal box = (0.0000000 -53.507796 0.0000000) to (32.766699 53.507796 9.8795315) create_atoms CPU = 0.002 seconds 1042 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9575817 6.0804313 6.5863543 Created 1066 atoms using lattice units in orthogonal box = (0.0000000 -53.507796 0.0000000) to (32.766699 53.507796 9.8795315) create_atoms CPU = 0.002 seconds 1066 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 = 8 26 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 0 atoms, new total = 2108 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_577453891941_005#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 = 8 26 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) = 5.959 | 5.959 | 5.959 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7000.1329 0 -7000.1329 8498.088 85 0 -7093.2283 0 -7093.2283 1217.0887 Loop time of 2.5836 on 1 procs for 85 steps with 2108 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7000.13290912547 -7093.22222696399 -7093.2283051803 Force two-norm initial, final = 189.57349 0.17521710 Force max component initial, final = 74.454834 0.010309181 Final line search alpha, max atom move = 1.0000000 0.010309181 Iterations, force evaluations = 85 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.454 | 2.454 | 2.454 | 0.0 | 94.98 Neigh | 0.10029 | 0.10029 | 0.10029 | 0.0 | 3.88 Comm | 0.0122 | 0.0122 | 0.0122 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0171 | | | 0.66 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7686.00 ave 7686 max 7686 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: 296998.0 ave 296998 max 296998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296998 Ave neighs/atom = 140.89089 Neighbor list builds = 4 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 = 8 26 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 : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.959 | 5.959 | 5.959 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -7093.2283 0 -7093.2283 1217.0887 34643.048 89 0 -7093.3472 0 -7093.3472 -204.07207 34705.628 Loop time of 0.111297 on 1 procs for 4 steps with 2108 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7093.22830518025 -7093.34392502295 -7093.34720637659 Force two-norm initial, final = 68.710611 8.4794681 Force max component initial, final = 68.249781 6.0986504 Final line search alpha, max atom move = 8.9088046e-05 0.00054331685 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10835 | 0.10835 | 0.10835 | 0.0 | 97.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043225 | 0.00043225 | 0.00043225 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002515 | | | 2.26 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7666.00 ave 7666 max 7666 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: 296084.0 ave 296084 max 296084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296084 Ave neighs/atom = 140.45731 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 = 8 26 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) = 6.097 | 6.097 | 6.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7093.3472 0 -7093.3472 -204.07207 Loop time of 2.455e-06 on 1 procs for 0 steps with 2108 atoms 162.9% 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 | | 2.455e-06 | | |100.00 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7666.00 ave 7666 max 7666 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: 295590.0 ave 295590 max 295590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295590 Ave neighs/atom = 140.22296 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 = 8 26 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) = 6.097 | 6.097 | 6.097 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 -7093.3472 -7093.3472 32.73325 107.39756 9.8722548 -204.07207 -204.07207 -281.25525 -67.876837 -263.08413 2.6849976 997.64772 Loop time of 2.236e-06 on 1 procs for 0 steps with 2108 atoms 268.3% 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 | | 2.236e-06 | | |100.00 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7666.00 ave 7666 max 7666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147795.0 ave 147795 max 147795 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 295590.0 ave 295590 max 295590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295590 Ave neighs/atom = 140.22296 Neighbor list builds = 0 Dangerous builds = 0 2108 -7093.34720637659 eV 2.68499762432672 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03