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 = 3.5200004 3.5200004 3.5200004 Created orthogonal box = (0.0000000 -42.532326 0.0000000) to (52.091248 42.532326 8.6222048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950512 5.2437115 5.7481365 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -42.532326 0.0000000) to (52.091248 42.532326 8.6222048) create_atoms CPU = 0.002 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950512 5.2437115 5.7481365 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -42.532326 0.0000000) to (52.091248 42.532326 8.6222048) create_atoms CPU = 0.002 seconds 1754 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 3494 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 7.381 | 7.381 | 7.381 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15068.946 0 -15068.946 14121.162 130 0 -15500.486 0 -15500.486 6622.7314 Loop time of 6.88784 on 1 procs for 130 steps with 3494 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 = -15068.9463752449 -15500.4724706287 -15500.4862337904 Force two-norm initial, final = 94.753271 0.42416347 Force max component initial, final = 10.483019 0.090521275 Final line search alpha, max atom move = 1.0000000 0.090521275 Iterations, force evaluations = 130 226 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6627 | 6.6627 | 6.6627 | 0.0 | 96.73 Neigh | 0.15678 | 0.15678 | 0.15678 | 0.0 | 2.28 Comm | 0.02677 | 0.02677 | 0.02677 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04156 | | | 0.60 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11508.0 ave 11508 max 11508 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: 608184.0 ave 608184 max 608184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 608184 Ave neighs/atom = 174.06525 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 130 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.384 | 7.384 | 7.384 Mbytes Step Temp E_pair E_mol TotEng Press Volume 130 0 -15500.486 0 -15500.486 6622.7314 38206.058 137 0 -15501.497 0 -15501.497 -100.60762 38353.087 Loop time of 0.270627 on 1 procs for 7 steps with 3494 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 = -15500.4862337904 -15501.494279278 -15501.4968388249 Force two-norm initial, final = 360.06392 4.2704947 Force max component initial, final = 348.80881 2.6895574 Final line search alpha, max atom move = 8.5532826e-05 0.00023004544 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26388 | 0.26388 | 0.26388 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008762 | 0.0008762 | 0.0008762 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005874 | | | 2.17 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11524.0 ave 11524 max 11524 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: 608340.0 ave 608340 max 608340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 608340 Ave neighs/atom = 174.10990 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 7.522 | 7.522 | 7.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15501.497 0 -15501.497 -100.60762 Loop time of 2.345e-06 on 1 procs for 0 steps with 3494 atoms 170.6% 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 | | 2.345e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11505.0 ave 11505 max 11505 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: 607508.0 ave 607508 max 607508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 607508 Ave neighs/atom = 173.87178 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 7.522 | 7.522 | 7.522 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 -15501.497 -15501.497 52.018472 85.60129 8.6131581 -100.60762 -100.60762 -109.90617 -79.679987 -112.23671 2.2138336 1543.1506 Loop time of 5.066e-06 on 1 procs for 0 steps with 3494 atoms 217.1% 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 | | 5.066e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11505.0 ave 11505 max 11505 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 303754.0 ave 303754 max 303754 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 607508.0 ave 607508 max 607508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 607508 Ave neighs/atom = 173.87178 Neighbor list builds = 0 Dangerous builds = 0 3494 -15501.4968388249 eV 2.21383362472642 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08