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 = 3.5618363 3.5618363 3.5618363 Created orthogonal box = (0.0000000 -43.623408 0.0000000) to (6.1692815 43.623408 5.0371973) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1692815 5.8164544 5.0371973 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -43.623408 0.0000000) to (6.1692815 43.623408 5.0371973) create_atoms CPU = 0.003 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1692815 5.8164544 5.0371973 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -43.623408 0.0000000) to (6.1692815 43.623408 5.0371973) create_atoms CPU = 0.002 seconds 122 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 2 21 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, cut 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 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_322509103239_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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 2 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 4.496 | 4.496 | 4.496 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -923.99585 0 -923.99585 22775.397 68 0 -941.27518 0 -941.27518 2541.2943 Loop time of 0.786379 on 1 procs for 68 steps with 240 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 = -923.995850114888 -941.274338988951 -941.275182360097 Force two-norm initial, final = 41.404141 0.12355652 Force max component initial, final = 13.383865 0.016743476 Final line search alpha, max atom move = 1.0000000 0.016743476 Iterations, force evaluations = 68 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75917 | 0.75917 | 0.75917 | 0.0 | 96.54 Neigh | 0.0074525 | 0.0074525 | 0.0074525 | 0.0 | 0.95 Comm | 0.012537 | 0.012537 | 0.012537 | 0.0 | 1.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007222 | | | 0.92 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4476.00 ave 4476 max 4476 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: 53804.0 ave 53804 max 53804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53804 Ave neighs/atom = 224.18333 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 2 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.498 | 4.498 | 4.498 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -941.27518 0 -941.27518 2541.2943 2711.2723 72 0 -941.31219 0 -941.31219 128.77052 2714.6329 Loop time of 0.0372803 on 1 procs for 4 steps with 240 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 = -941.275182360097 -941.31163312851 -941.3121913197 Force two-norm initial, final = 20.044750 0.55004176 Force max component initial, final = 18.816935 0.50593138 Final line search alpha, max atom move = 0.00050485730 0.00025542315 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035137 | 0.035137 | 0.035137 | 0.0 | 94.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058379 | 0.00058379 | 0.00058379 | 0.0 | 1.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001559 | | | 4.18 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4800.00 ave 4800 max 4800 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: 53916.0 ave 53916 max 53916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53916 Ave neighs/atom = 224.65000 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 2 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 4.636 | 4.636 | 4.636 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -941.31219 0 -941.31219 128.77052 Loop time of 6.505e-06 on 1 procs for 0 steps with 240 atoms 169.1% 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 | | 6.505e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4737.00 ave 4737 max 4737 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: 53912.0 ave 53912 max 53912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53912 Ave neighs/atom = 224.63333 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 2 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 4.636 | 4.636 | 4.636 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 -941.31219 -941.31219 6.1891061 87.074909 5.0372111 128.77052 128.77052 83.995209 3.7148021 298.60155 2.3615829 196.2221 Loop time of 7.027e-06 on 1 procs for 0 steps with 240 atoms 284.6% 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 | | 7.027e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4737.00 ave 4737 max 4737 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26956.0 ave 26956 max 26956 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53912.0 ave 53912 max 53912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53912 Ave neighs/atom = 224.63333 Neighbor list builds = 0 Dangerous builds = 0 240 -941.3121913197 eV 2.36158287250496 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01