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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -43.540005 0.0000000) to (14.513335 43.540005 3.5200008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2686279 4.2686279 3.5200008 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -43.540005 0.0000000) to (14.513335 43.540005 3.5200008) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2686279 4.2686279 3.5200008 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -43.540005 0.0000000) to (14.513335 43.540005 3.5200008) create_atoms CPU = 0.000 seconds 206 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 23 1 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1724.11 0 -1724.11 42350.049 98 0 -1805.6931 0 -1805.6931 12551.492 Loop time of 0.737838 on 1 procs for 98 steps with 408 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1724.10997972821 -1805.69150787942 -1805.69306303899 Force two-norm initial, final = 222.95804 0.15318939 Force max component initial, final = 63.587655 0.026691693 Final line search alpha, max atom move = 1.0000000 0.026691693 Iterations, force evaluations = 98 190 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72374 | 0.72374 | 0.72374 | 0.0 | 98.09 Neigh | 0.0041215 | 0.0041215 | 0.0041215 | 0.0 | 0.56 Comm | 0.0061091 | 0.0061091 | 0.0061091 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003863 | | | 0.52 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4607.00 ave 4607 max 4607 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: 72592.0 ave 72592 max 72592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72592 Ave neighs/atom = 177.92157 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -1805.6931 0 -1805.6931 12551.492 4448.6521 104 0 -1805.8353 0 -1805.8353 -8.8041529 4478.5709 Loop time of 0.0388597 on 1 procs for 6 steps with 408 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 = -1805.69306303899 -1805.8338125154 -1805.83531137734 Force two-norm initial, final = 61.693107 0.70796081 Force max component initial, final = 45.235579 0.47583768 Final line search alpha, max atom move = 0.00013586702 6.4650648e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.037105 | 0.037105 | 0.037105 | 0.0 | 95.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031392 | 0.00031392 | 0.00031392 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00144 | | | 3.71 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4552.00 ave 4552 max 4552 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: 71936.0 ave 71936 max 71936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71936 Ave neighs/atom = 176.31373 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.630 | 4.630 | 4.630 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1805.8353 0 -1805.8353 -8.8041529 Loop time of 2.112e-06 on 1 procs for 0 steps with 408 atoms 142.0% 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 | | 2.112e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4512.00 ave 4512 max 4512 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: 71700.0 ave 71700 max 71700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71700 Ave neighs/atom = 175.73529 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.630 | 4.630 | 4.630 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 -1805.8353 -1805.8353 14.524164 87.562124 3.5215351 -8.8041529 -8.8041529 170.35452 -38.162897 -158.60408 2.3114625 178.25515 Loop time of 8.805e-06 on 1 procs for 0 steps with 408 atoms 124.9% 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 | | 8.805e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4512.00 ave 4512 max 4512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35850.0 ave 35850 max 35850 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71700.0 ave 71700 max 71700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71700 Ave neighs/atom = 175.73529 Neighbor list builds = 0 Dangerous builds = 0 408 -1805.83531137734 eV 2.31146252067825 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01