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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -37.528199 0.0000000) to (26.536444 37.528199 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8969875 4.8647665 5.1069410 Created 431 atoms using lattice units in orthogonal box = (0.0000000 -37.528199 0.0000000) to (26.536444 37.528199 5.1069410) create_atoms CPU = 0.001 seconds 431 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8969875 4.8647665 5.1069410 Created 439 atoms using lattice units in orthogonal box = (0.0000000 -37.528199 0.0000000) to (26.536444 37.528199 5.1069410) create_atoms CPU = 0.001 seconds 439 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 29 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 870 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_137964310702_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.305 | 5.305 | 5.305 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3419.3163 0 -3419.3163 71285.736 55 0 -3678.8104 0 -3678.8104 17632.182 Loop time of 4.18652 on 1 procs for 55 steps with 870 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 = -3419.31627824937 -3678.80674573308 -3678.81040208648 Force two-norm initial, final = 212.84403 0.21332240 Force max component initial, final = 57.356365 0.043933747 Final line search alpha, max atom move = 1.0000000 0.043933747 Iterations, force evaluations = 55 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1616 | 4.1616 | 4.1616 | 0.0 | 99.40 Neigh | 0.01651 | 0.01651 | 0.01651 | 0.0 | 0.39 Comm | 0.0038558 | 0.0038558 | 0.0038558 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004573 | | | 0.11 Nlocal: 870.000 ave 870 max 870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3597.00 ave 3597 max 3597 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: 47006.0 ave 47006 max 47006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47006 Ave neighs/atom = 54.029885 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.923 | 4.923 | 4.923 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -3678.8104 0 -3678.8104 17632.182 10171.647 64 0 -3679.5448 0 -3679.5448 400.18149 10275.216 Loop time of 0.491056 on 1 procs for 9 steps with 870 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 = -3678.81040208648 -3679.54261808077 -3679.54478356595 Force two-norm initial, final = 199.64511 4.6042682 Force max component initial, final = 146.09849 3.4747677 Final line search alpha, max atom move = 0.00026845436 0.00093281654 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48874 | 0.48874 | 0.48874 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032683 | 0.00032683 | 0.00032683 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001994 | | | 0.41 Nlocal: 870.000 ave 870 max 870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3579.00 ave 3579 max 3579 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: 46988.0 ave 46988 max 46988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46988 Ave neighs/atom = 54.009195 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.061 | 5.061 | 5.061 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3679.5448 0 -3679.5448 400.18149 Loop time of 2.082e-06 on 1 procs for 0 steps with 870 atoms 192.1% 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 | | 2.082e-06 | | |100.00 Nlocal: 870.000 ave 870 max 870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3583.00 ave 3583 max 3583 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: 46916.0 ave 46916 max 46916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46916 Ave neighs/atom = 53.926437 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.061 | 5.061 | 5.061 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 -3679.5448 -3679.5448 26.596678 75.692301 5.104014 400.18149 400.18149 341.84102 546.39807 312.30536 2.3128599 508.46666 Loop time of 1.753e-06 on 1 procs for 0 steps with 870 atoms 171.1% 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 | | 1.753e-06 | | |100.00 Nlocal: 870.000 ave 870 max 870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3583.00 ave 3583 max 3583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23458.0 ave 23458 max 23458 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46916.0 ave 46916 max 46916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46916 Ave neighs/atom = 53.926437 Neighbor list builds = 0 Dangerous builds = 0 870 -3679.54478356595 eV 2.31285985072285 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05