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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -42.850502 0.0000000) to (42.850502 42.850502 4.0310361) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6881197 5.6881197 4.0310361 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -42.850502 0.0000000) to (42.850502 42.850502 4.0310361) create_atoms CPU = 0.001 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6881197 5.6881197 4.0310361 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -42.850502 0.0000000) to (42.850502 42.850502 4.0310361) create_atoms CPU = 0.001 seconds 454 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 12 23 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 906 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_699137396381_005#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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 12 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2929.1185 0 -2929.1185 18696.24 75 0 -3037.6581 0 -3037.6581 3064.695 Loop time of 0.768987 on 1 procs for 75 steps with 906 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 = -2929.11853089938 -3037.65522650274 -3037.65810178985 Force two-norm initial, final = 51.635921 0.15560973 Force max component initial, final = 7.0470139 0.045449761 Final line search alpha, max atom move = 1.0000000 0.045449761 Iterations, force evaluations = 75 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74367 | 0.74367 | 0.74367 | 0.0 | 96.71 Neigh | 0.012981 | 0.012981 | 0.012981 | 0.0 | 1.69 Comm | 0.0066161 | 0.0066161 | 0.0066161 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005718 | | | 0.74 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5619.00 ave 5619 max 5619 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: 119108.0 ave 119108 max 119108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119108 Ave neighs/atom = 131.46578 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 12 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.949 | 4.949 | 4.949 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -3037.6581 0 -3037.6581 3064.695 14803.299 82 0 -3037.8364 0 -3037.8364 3.0372541 14862.47 Loop time of 0.0582533 on 1 procs for 7 steps with 906 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 = -3037.65810178985 -3037.83636874233 -3037.83642157933 Force two-norm initial, final = 62.941007 0.26881894 Force max component initial, final = 55.372631 0.17174191 Final line search alpha, max atom move = 0.00084370740 0.00014489992 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055592 | 0.055592 | 0.055592 | 0.0 | 95.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045028 | 0.00045028 | 0.00045028 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002211 | | | 3.80 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5606.00 ave 5606 max 5606 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: 119508.0 ave 119508 max 119508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119508 Ave neighs/atom = 131.90728 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 12 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.087 | 5.087 | 5.087 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3037.8364 0 -3037.8364 3.0372541 Loop time of 2.25e-06 on 1 procs for 0 steps with 906 atoms 177.8% 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 | | 2.25e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5615.00 ave 5615 max 5615 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: 119300.0 ave 119300 max 119300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119300 Ave neighs/atom = 131.67770 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 12 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.087 | 5.087 | 5.087 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 -3037.8364 -3037.8364 42.710903 86.175101 4.0380382 3.0372541 3.0372541 -1.9022997 -7.531901 18.545963 2.5957782 199.63178 Loop time of 4.375e-06 on 1 procs for 0 steps with 906 atoms 205.7% 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 | | 4.375e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5615.00 ave 5615 max 5615 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59650.0 ave 59650 max 59650 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119300.0 ave 119300 max 119300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119300 Ave neighs/atom = 131.67770 Neighbor list builds = 0 Dangerous builds = 0 906 -3037.83642157933 eV 2.5957782375636 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01