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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -55.436748 0.0000000) to (33.945781 55.436748 8.6222370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4751260 5.3645060 5.7481580 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -55.436748 0.0000000) to (33.945781 55.436748 8.6222370) create_atoms CPU = 0.002 seconds 1493 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4751260 5.3645060 5.7481580 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -55.436748 0.0000000) to (33.945781 55.436748 8.6222370) create_atoms CPU = 0.002 seconds 1493 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 2963 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.446 | 7.446 | 7.446 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13090.332 0 -13090.332 3611.3579 23 0 -13143.071 0 -13143.071 -1250.3286 Loop time of 1.05453 on 1 procs for 23 steps with 2963 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 = -13090.3317491273 -13143.0582900361 -13143.0707549615 Force two-norm initial, final = 34.848222 0.38044400 Force max component initial, final = 5.3024842 0.044662819 Final line search alpha, max atom move = 1.0000000 0.044662819 Iterations, force evaluations = 23 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0456 | 1.0456 | 1.0456 | 0.0 | 99.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0038831 | 0.0038831 | 0.0038831 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005025 | | | 0.48 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11988.0 ave 11988 max 11988 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: 662864.0 ave 662864 max 662864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 662864 Ave neighs/atom = 223.71380 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.446 | 7.446 | 7.446 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -13143.071 0 -13143.071 -1250.3286 32451.405 25 0 -13143.092 0 -13143.092 -1257.7596 32451.606 Loop time of 0.140656 on 1 procs for 2 steps with 2963 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 = -13143.0707549615 -13143.0914966683 -13143.0915068874 Force two-norm initial, final = 42.467379 0.40343585 Force max component initial, final = 30.362147 0.093052579 Final line search alpha, max atom move = 0.0011469336 0.00010672513 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13819 | 0.13819 | 0.13819 | 0.0 | 98.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042282 | 0.00042282 | 0.00042282 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002047 | | | 1.46 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11991.0 ave 11991 max 11991 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: 664996.0 ave 664996 max 664996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 664996 Ave neighs/atom = 224.43334 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.584 | 7.584 | 7.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13143.092 0 -13143.092 -1257.7596 Loop time of 2.197e-06 on 1 procs for 0 steps with 2963 atoms 136.5% 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 | | 2.197e-06 | | |100.00 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11991.0 ave 11991 max 11991 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: 664990.0 ave 664990 max 664990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 664990 Ave neighs/atom = 224.43132 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.584 | 7.584 | 7.584 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 -13143.092 -13143.092 33.969348 110.8735 8.6163085 -1257.7596 -1257.7596 -4.3867536 -3764.3011 -4.5909637 2.1883417 1096.9259 Loop time of 2.174e-06 on 1 procs for 0 steps with 2963 atoms 230.0% 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 | | 2.174e-06 | | |100.00 Nlocal: 2963.00 ave 2963 max 2963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11991.0 ave 11991 max 11991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 332495.0 ave 332495 max 332495 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 664990.0 ave 664990 max 664990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 664990 Ave neighs/atom = 224.43132 Neighbor list builds = 0 Dangerous builds = 0 2963 -13062.3159734963 eV 2.18834172992492 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01