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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -42.552660 0.0000000) to (52.111839 42.552660 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9970257 5.2457842 5.7504086 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.552660 0.0000000) to (52.111839 42.552660 8.6256130) create_atoms CPU = 0.002 seconds 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9970257 5.2457842 5.7504086 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.552660 0.0000000) to (52.111839 42.552660 8.6256130) create_atoms CPU = 0.002 seconds 1756 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 28 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 3456 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 6.071 | 6.071 | 6.071 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15242.356 0 -15242.356 -825.6153 66 0 -15324.252 0 -15324.252 -16972.255 Loop time of 13.428 on 1 procs for 66 steps with 3456 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 = -15242.3563704947 -15324.2377866823 -15324.2518692215 Force two-norm initial, final = 58.518071 0.47548683 Force max component initial, final = 9.5677877 0.078835373 Final line search alpha, max atom move = 1.0000000 0.078835373 Iterations, force evaluations = 66 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.352 | 13.352 | 13.352 | 0.0 | 99.44 Neigh | 0.042375 | 0.042375 | 0.042375 | 0.0 | 0.32 Comm | 0.012469 | 0.012469 | 0.012469 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02099 | | | 0.16 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8370.00 ave 8370 max 8370 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: 296220.0 ave 296220 max 296220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296220 Ave neighs/atom = 85.711806 Neighbor list builds = 2 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.078 | 6.078 | 6.078 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -15324.252 0 -15324.252 -16972.255 38254.548 71 0 -15325.422 0 -15325.422 -4653.044 37995.222 Loop time of 0.855968 on 1 procs for 5 steps with 3456 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 = -15324.2518692215 -15325.4220439972 -15325.4221211726 Force two-norm initial, final = 485.16323 0.74260894 Force max component initial, final = 349.14096 0.20571605 Final line search alpha, max atom move = 0.00053239213 0.00010952160 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85191 | 0.85191 | 0.85191 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053466 | 0.00053466 | 0.00053466 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003523 | | | 0.41 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8370.00 ave 8370 max 8370 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: 296184.0 ave 296184 max 296184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296184 Ave neighs/atom = 85.701389 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 6.216 | 6.216 | 6.216 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15325.422 0 -15325.422 -4653.044 Loop time of 1.858e-06 on 1 procs for 0 steps with 3456 atoms 161.5% 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 | | 1.858e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8390.00 ave 8390 max 8390 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: 296316.0 ave 296316 max 296316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296316 Ave neighs/atom = 85.739583 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 6.216 | 6.216 | 6.216 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 -15325.422 -15325.422 51.933577 85.10532 8.5965469 -4653.044 -4653.044 2.628019 -13953.115 -8.6453706 2.2064061 1454.121 Loop time of 1.942e-06 on 1 procs for 0 steps with 3456 atoms 257.5% 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 | | 1.942e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8390.00 ave 8390 max 8390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 148158.0 ave 148158 max 148158 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 296316.0 ave 296316 max 296316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296316 Ave neighs/atom = 85.739583 Neighbor list builds = 0 Dangerous builds = 0 3456 -15325.4221211726 eV 2.20640606575361 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15