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 -40.855528 0.0000000) to (17.690963 40.855528 6.2546998) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8969875 5.1069410 6.2546998 Created 384 atoms using lattice units in orthogonal box = (0.0000000 -40.855528 0.0000000) to (17.690963 40.855528 6.2546998) create_atoms CPU = 0.001 seconds 384 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8969875 5.1069410 6.2546998 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.855528 0.0000000) to (17.690963 40.855528 6.2546998) create_atoms CPU = 0.001 seconds 396 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 = 7 31 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 776 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 = 7 31 3 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) = 4.884 | 4.884 | 4.884 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3055.6637 0 -3055.6637 82044.548 36 0 -3279.8771 0 -3279.8771 23216.545 Loop time of 2.34134 on 1 procs for 36 steps with 776 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 = -3055.66365987057 -3279.87479760148 -3279.87706203925 Force two-norm initial, final = 164.40905 0.18801332 Force max component initial, final = 20.773347 0.028745016 Final line search alpha, max atom move = 1.0000000 0.028745016 Iterations, force evaluations = 36 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3379 | 2.3379 | 2.3379 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014962 | 0.0014962 | 0.0014962 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001946 | | | 0.08 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3058.00 ave 3058 max 3058 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: 42632.0 ave 42632 max 42632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42632 Ave neighs/atom = 54.938144 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 31 3 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.884 | 4.884 | 4.884 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -3279.8771 0 -3279.8771 23216.545 9041.4641 48 0 -3281.083 0 -3281.083 -185.31955 9164.8357 Loop time of 0.502568 on 1 procs for 12 steps with 776 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 = -3279.87706203925 -3281.08249397481 -3281.08304196111 Force two-norm initial, final = 240.98998 1.9875237 Force max component initial, final = 197.06065 1.3814760 Final line search alpha, max atom move = 0.00034439056 0.00047576729 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50042 | 0.50042 | 0.50042 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032597 | 0.00032597 | 0.00032597 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001826 | | | 0.36 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3046.00 ave 3046 max 3046 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: 42048.0 ave 42048 max 42048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42048 Ave neighs/atom = 54.185567 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 = 7 31 3 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) = 5.022 | 5.022 | 5.022 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3281.083 0 -3281.083 -185.31955 Loop time of 1.386e-06 on 1 procs for 0 steps with 776 atoms 144.3% 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 | | 1.386e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3046.00 ave 3046 max 3046 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: 41976.0 ave 41976 max 41976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41976 Ave neighs/atom = 54.092784 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 = 7 31 3 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) = 5.022 | 5.022 | 5.022 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 -3281.083 -3281.083 17.696546 82.632482 6.2673707 -185.31955 -185.31955 -241.58282 -118.46421 -195.91163 2.2322231 464.38217 Loop time of 1.456e-06 on 1 procs for 0 steps with 776 atoms 137.4% 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 | | 1.456e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3046.00 ave 3046 max 3046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20988.0 ave 20988 max 20988 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41976.0 ave 41976 max 41976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41976 Ave neighs/atom = 54.092784 Neighbor list builds = 0 Dangerous builds = 0 776 -3281.08304196111 eV 2.23222307028906 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03