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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -55.433228 0.0000000) to (33.945781 55.433228 8.6222370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4751260 5.3645060 5.7481580 Created 1487 atoms using lattice units in orthogonal box = (0.0000000 -55.433228 0.0000000) to (33.945781 55.433228 8.6222370) create_atoms CPU = 0.003 seconds 1487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4751260 5.3645060 5.7481580 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -55.433228 0.0000000) to (33.945781 55.433228 8.6222370) create_atoms CPU = 0.002 seconds 1493 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 2964 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.450 | 7.450 | 7.450 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13039.991 0 -13039.991 1970.7648 97 0 -13147.579 0 -13147.579 -831.32326 Loop time of 6.0553 on 1 procs for 97 steps with 2964 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13039.991103031 -13147.5689921177 -13147.5792179328 Force two-norm initial, final = 35.673811 0.32924208 Force max component initial, final = 3.7810947 0.050628742 Final line search alpha, max atom move = 1.0000000 0.050628742 Iterations, force evaluations = 97 178 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8728 | 5.8728 | 5.8728 | 0.0 | 96.99 Neigh | 0.12368 | 0.12368 | 0.12368 | 0.0 | 2.04 Comm | 0.027508 | 0.027508 | 0.027508 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03135 | | | 0.52 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12084.0 ave 12084 max 12084 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: 665436.0 ave 665436 max 665436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 665436 Ave neighs/atom = 224.50607 Neighbor list builds = 3 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.447 | 7.447 | 7.447 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -13147.579 0 -13147.579 -831.32326 32449.344 100 0 -13147.668 0 -13147.668 2.2846896 32433.847 Loop time of 0.194749 on 1 procs for 3 steps with 2964 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 = -13147.5792179328 -13147.6650430315 -13147.6682185434 Force two-norm initial, final = 84.216109 1.8546599 Force max component initial, final = 68.506257 1.5278331 Final line search alpha, max atom move = 4.1060129e-05 6.2733024e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19049 | 0.19049 | 0.19049 | 0.0 | 97.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006297 | 0.0006297 | 0.0006297 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003629 | | | 1.86 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12015.0 ave 12015 max 12015 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: 665314.0 ave 665314 max 665314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 665314 Ave neighs/atom = 224.46491 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.585 | 7.585 | 7.585 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13147.668 0 -13147.668 2.2846896 Loop time of 2.229e-06 on 1 procs for 0 steps with 2964 atoms 179.5% 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 | | 2.229e-06 | | |100.00 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12020.0 ave 12020 max 12020 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: 665518.0 ave 665518 max 665518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 665518 Ave neighs/atom = 224.53374 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.585 | 7.585 | 7.585 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 -13147.668 -13147.668 33.993741 110.68452 8.6201061 2.2846896 2.2846896 -37.474894 -31.124726 75.453689 2.1962428 1110.3086 Loop time of 2.699e-06 on 1 procs for 0 steps with 2964 atoms 259.4% 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 | | 2.699e-06 | | |100.00 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12020.0 ave 12020 max 12020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 332759.0 ave 332759 max 332759 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 665518.0 ave 665518 max 665518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 665518 Ave neighs/atom = 224.53374 Neighbor list builds = 0 Dangerous builds = 0 2964 -13066.8654237505 eV 2.19624277273878 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06