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 = 4.0415970 4.0415970 4.0415970 Created orthogonal box = (0.0000000 -69.534264 0.0000000) to (34.767132 69.534264 4.0415970) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6379133 5.6379133 4.0415970 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -69.534264 0.0000000) to (34.767132 69.534264 4.0415970) create_atoms CPU = 0.001 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6379133 5.6379133 4.0415970 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -69.534264 0.0000000) to (34.767132 69.534264 4.0415970) create_atoms CPU = 0.001 seconds 594 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 12 47 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 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 1184 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_736419017411_000#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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 12 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 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) = 5.380 | 5.380 | 5.380 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3926.6294 0 -3926.6294 10627.915 39 0 -3980.0868 0 -3980.0868 10582.828 Loop time of 6.89377 on 1 procs for 39 steps with 1184 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 = -3926.6293658738 -3980.08314259094 -3980.0867908981 Force two-norm initial, final = 78.437632 0.15450153 Force max component initial, final = 25.537794 0.027674110 Final line search alpha, max atom move = 1.0000000 0.027674110 Iterations, force evaluations = 39 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.884 | 6.884 | 6.884 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0044568 | 0.0044568 | 0.0044568 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00534 | | | 0.08 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4898.00 ave 4898 max 4898 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: 63996.0 ave 63996 max 63996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63996 Ave neighs/atom = 54.050676 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 12 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.380 | 5.380 | 5.380 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -3980.0868 0 -3980.0868 10582.828 19541.178 48 0 -3980.7971 0 -3980.7971 -1.2163436 19679.092 Loop time of 1.33037 on 1 procs for 9 steps with 1184 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 = -3980.08679089809 -3980.79710170108 -3980.79713832749 Force two-norm initial, final = 265.13403 0.52792946 Force max component initial, final = 211.13240 0.21728772 Final line search alpha, max atom move = 0.00086974806 0.00018898557 Iterations, force evaluations = 9 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3036 | 1.3036 | 1.3036 | 0.0 | 97.99 Neigh | 0.022643 | 0.022643 | 0.022643 | 0.0 | 1.70 Comm | 0.00070927 | 0.00070927 | 0.00070927 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003409 | | | 0.26 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4856.00 ave 4856 max 4856 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: 63648.0 ave 63648 max 63648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63648 Ave neighs/atom = 53.756757 Neighbor list builds = 1 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 12 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 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) = 5.518 | 5.518 | 5.518 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3980.7971 0 -3980.7971 -1.2163436 Loop time of 2.234e-06 on 1 procs for 0 steps with 1184 atoms 223.8% 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 | | 2.234e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4856.00 ave 4856 max 4856 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: 63648.0 ave 63648 max 63648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63648 Ave neighs/atom = 53.756757 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 12 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 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) = 5.518 | 5.518 | 5.518 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 -3980.7971 -3980.7971 34.799058 140.05817 4.0376541 -1.2163436 -1.2163436 -7.6874655 -13.634822 17.673257 2.4448567 419.00494 Loop time of 2.221e-06 on 1 procs for 0 steps with 1184 atoms 180.1% 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 | | 2.221e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4856.00 ave 4856 max 4856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31824.0 ave 31824 max 31824 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63648.0 ave 63648 max 63648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63648 Ave neighs/atom = 53.756757 Neighbor list builds = 0 Dangerous builds = 0 1184 -3980.79713832749 eV 2.44485670960574 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08