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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -43.633070 0.0000000) to (53.439379 43.633070 8.8453489) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1243240 5.3794196 5.8968993 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -43.633070 0.0000000) to (53.439379 43.633070 8.8453489) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1243240 5.3794196 5.8968993 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -43.633070 0.0000000) to (53.439379 43.633070 8.8453489) create_atoms CPU = 0.002 seconds 1755 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 ghost atom cutoff = 6 binsize = 3, bins = 18 30 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 3501 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_321233176498_001#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 ghost atom cutoff = 6 binsize = 3, bins = 18 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.668 | 5.668 | 5.668 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13817.475 0 -13817.475 57858.773 71 0 -14819.483 0 -14819.483 3815.7286 Loop time of 14.0755 on 1 procs for 71 steps with 3501 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 = -13817.4750662938 -14819.4693516548 -14819.4834705926 Force two-norm initial, final = 855.65662 0.40461016 Force max component initial, final = 112.13645 0.11841404 Final line search alpha, max atom move = 1.0000000 0.11841404 Iterations, force evaluations = 71 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.998 | 13.998 | 13.998 | 0.0 | 99.45 Neigh | 0.044489 | 0.044489 | 0.044489 | 0.0 | 0.32 Comm | 0.012253 | 0.012253 | 0.012253 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02106 | | | 0.15 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8171.00 ave 8171 max 8171 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: 269652.0 ave 269652 max 269652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269652 Ave neighs/atom = 77.021422 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 ghost atom cutoff = 6 binsize = 3, bins = 18 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.667 | 5.667 | 5.667 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -14819.483 0 -14819.483 3815.7286 41249.827 76 0 -14819.904 0 -14819.904 94.189059 41338.682 Loop time of 0.862696 on 1 procs for 5 steps with 3501 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 = -14819.4834705926 -14819.9017475472 -14819.903628429 Force two-norm initial, final = 220.02581 7.6840207 Force max component initial, final = 204.51286 7.4548375 Final line search alpha, max atom move = 5.1077072e-05 0.00038077127 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8583 | 0.8583 | 0.8583 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052653 | 0.00052653 | 0.00052653 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003869 | | | 0.45 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8174.00 ave 8174 max 8174 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: 269612.0 ave 269612 max 269612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269612 Ave neighs/atom = 77.009997 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 ghost atom cutoff = 6 binsize = 3, bins = 18 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.805 | 5.805 | 5.805 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14819.904 0 -14819.904 94.189059 Loop time of 2.388e-06 on 1 procs for 0 steps with 3501 atoms 125.6% 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 | | 2.388e-06 | | |100.00 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8168.00 ave 8168 max 8168 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: 269512.0 ave 269512 max 269512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269512 Ave neighs/atom = 76.981434 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 ghost atom cutoff = 6 binsize = 3, bins = 18 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.805 | 5.805 | 5.805 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 -14819.904 -14819.904 53.47262 87.057611 8.8801116 94.189059 94.189059 289.10924 -52.071247 45.529182 2.3321481 1683.0796 Loop time of 2.302e-06 on 1 procs for 0 steps with 3501 atoms 217.2% 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 | | 2.302e-06 | | |100.00 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8168.00 ave 8168 max 8168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134756.0 ave 134756 max 134756 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 269512.0 ave 269512 max 269512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269512 Ave neighs/atom = 76.981434 Neighbor list builds = 0 Dangerous builds = 0 3501 -14819.903628429 eV 2.33214813111423 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15