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 = 3.6084290 3.6084290 3.6084290 Created orthogonal box = (0.0000000 -46.774194 0.0000000) to (27.003010 46.774194 6.2499824) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7863594 5.5679269 6.2499824 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -46.774194 0.0000000) to (27.003010 46.774194 6.2499824) create_atoms CPU = 0.004 seconds 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7863594 5.5679269 6.2499824 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -46.774194 0.0000000) to (27.003010 46.774194 6.2499824) create_atoms CPU = 0.004 seconds 676 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 = 10 32 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 24 atoms, new total = 1328 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_549900287421_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 = 10 32 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) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5592.8887 0 -5592.8887 -1425.7971 60 0 -5634.1573 0 -5634.1573 -15728.049 Loop time of 12.3395 on 1 procs for 60 steps with 1328 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 = -5592.88867444907 -5634.15222447656 -5634.15732125415 Force two-norm initial, final = 26.793794 0.23039385 Force max component initial, final = 6.1457777 0.023335116 Final line search alpha, max atom move = 1.0000000 0.023335116 Iterations, force evaluations = 60 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.276 | 12.276 | 12.276 | 0.0 | 99.48 Neigh | 0.033038 | 0.033038 | 0.033038 | 0.0 | 0.27 Comm | 0.013551 | 0.013551 | 0.013551 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01721 | | | 0.14 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5128.00 ave 5128 max 5128 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: 101744.0 ave 101744 max 101744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101744 Ave neighs/atom = 76.614458 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 = 10 32 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.048 | 5.048 | 5.048 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -5634.1573 0 -5634.1573 -15728.049 15788.006 66 0 -5634.5523 0 -5634.5523 -6178.7327 15696.172 Loop time of 0.984224 on 1 procs for 6 steps with 1328 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 = -5634.15732125414 -5634.55056878405 -5634.55232818347 Force two-norm initial, final = 159.52253 4.0891668 Force max component initial, final = 140.04602 4.0558949 Final line search alpha, max atom move = 0.00010633498 0.00043128351 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.97892 | 0.97892 | 0.97892 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092029 | 0.00092029 | 0.00092029 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004387 | | | 0.45 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5140.00 ave 5140 max 5140 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: 101784.0 ave 101784 max 101784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101784 Ave neighs/atom = 76.644578 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 = 9 32 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) = 5.185 | 5.185 | 5.185 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5634.5523 0 -5634.5523 -6178.7327 Loop time of 8.329e-06 on 1 procs for 0 steps with 1328 atoms 180.1% 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 | | 8.329e-06 | | |100.00 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5158.00 ave 5158 max 5158 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: 101864.0 ave 101864 max 101864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101864 Ave neighs/atom = 76.704819 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 = 9 32 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) = 5.185 | 5.185 | 5.185 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 -5634.5523 -5634.5523 26.867086 93.548389 6.2450638 -6178.7327 -6178.7327 -411.91886 -18083.671 -40.608118 2.2425467 982.37516 Loop time of 8.75e-06 on 1 procs for 0 steps with 1328 atoms 262.9% 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 | | 8.75e-06 | | |100.00 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5158.00 ave 5158 max 5158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50932.0 ave 50932 max 50932 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101864.0 ave 101864 max 101864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101864 Ave neighs/atom = 76.704819 Neighbor list builds = 0 Dangerous builds = 0 1328 -5634.55232818347 eV 2.24254671543449 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14