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 = 3.6149590 3.6149590 3.6149590 Created orthogonal box = (0.0000000 -53.128829 0.0000000) to (18.783878 53.128829 5.1123240) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8698942 5.9032033 5.1123240 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -53.128829 0.0000000) to (18.783878 53.128829 5.1123240) create_atoms CPU = 0.004 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8698942 5.9032033 5.1123240 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -53.128829 0.0000000) to (18.783878 53.128829 5.1123240) create_atoms CPU = 0.003 seconds 434 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 5 28 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 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 858 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_759493141826_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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 5.000 | 5.000 | 5.000 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2956.5331 0 -2956.5331 17405.274 71 0 -3028.0531 0 -3028.0531 1092.9004 Loop time of 2.15461 on 1 procs for 71 steps with 858 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 = -2956.53312359325 -3028.05020871284 -3028.05308617474 Force two-norm initial, final = 156.34843 0.16150137 Force max component initial, final = 50.284007 0.039975896 Final line search alpha, max atom move = 1.0000000 0.039975896 Iterations, force evaluations = 71 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0784 | 2.0784 | 2.0784 | 0.0 | 96.46 Neigh | 0.040152 | 0.040152 | 0.040152 | 0.0 | 1.86 Comm | 0.020171 | 0.020171 | 0.020171 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01592 | | | 0.74 Nlocal: 858.000 ave 858 max 858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6290.00 ave 6290 max 6290 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: 147004.0 ave 147004 max 147004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147004 Ave neighs/atom = 171.33333 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.001 | 5.001 | 5.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -3028.0531 0 -3028.0531 1092.9004 10203.845 74 0 -3028.088 0 -3028.088 -549.38465 10215.998 Loop time of 0.0800905 on 1 procs for 3 steps with 858 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 = -3028.05308617473 -3028.08518723081 -3028.08804375693 Force two-norm initial, final = 24.388491 6.4447878 Force max component initial, final = 23.978819 5.2328643 Final line search alpha, max atom move = 0.00023361942 0.0012224987 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07707 | 0.07707 | 0.07707 | 0.0 | 96.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068958 | 0.00068958 | 0.00068958 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002331 | | | 2.91 Nlocal: 858.000 ave 858 max 858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6342.00 ave 6342 max 6342 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: 147412.0 ave 147412 max 147412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147412 Ave neighs/atom = 171.80886 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 5.139 | 5.139 | 5.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3028.088 0 -3028.088 -549.38465 Loop time of 6.545e-06 on 1 procs for 0 steps with 858 atoms 183.3% 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 | | 6.545e-06 | | |100.00 Nlocal: 858.000 ave 858 max 858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6366.00 ave 6366 max 6366 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: 147196.0 ave 147196 max 147196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147196 Ave neighs/atom = 171.55711 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 5.139 | 5.139 | 5.139 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 -3028.088 -3028.088 18.752523 106.53741 5.1135087 -549.38465 -549.38465 -819.30096 -461.03514 -367.81786 2.3508857 486.54941 Loop time of 7.508e-06 on 1 procs for 0 steps with 858 atoms 239.7% 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 | | 7.508e-06 | | |100.00 Nlocal: 858.000 ave 858 max 858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6366.00 ave 6366 max 6366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73598.0 ave 73598 max 73598 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 147196.0 ave 147196 max 147196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147196 Ave neighs/atom = 171.55711 Neighbor list builds = 0 Dangerous builds = 0 858 -3028.08804375693 eV 2.35088574438517 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02