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 = 3.5618363 3.5618363 3.5618363 Created orthogonal box = (0.0000000 -38.030005 0.0000000) to (26.891275 38.030005 5.0371973) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1330977 6.0047377 5.0371973 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.030005 0.0000000) to (26.891275 38.030005 5.0371973) create_atoms CPU = 0.004 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1330977 6.0047377 5.0371973 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.030005 0.0000000) to (26.891275 38.030005 5.0371973) create_atoms CPU = 0.003 seconds 458 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 18 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 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 914 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_322509103239_004#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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.393 | 5.393 | 5.393 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3380.1121 0 -3380.1121 50660.187 88 0 -3581.8935 0 -3581.8935 5215.5171 Loop time of 3.44512 on 1 procs for 88 steps with 914 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 = -3380.11205274236 -3581.89006351609 -3581.89351826863 Force two-norm initial, final = 273.85749 0.25234372 Force max component initial, final = 85.960192 0.030642164 Final line search alpha, max atom move = 1.0000000 0.030642164 Iterations, force evaluations = 88 168 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3683 | 3.3683 | 3.3683 | 0.0 | 97.77 Neigh | 0.027438 | 0.027438 | 0.027438 | 0.0 | 0.80 Comm | 0.028071 | 0.028071 | 0.028071 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02127 | | | 0.62 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7209.00 ave 7209 max 7209 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: 206204.0 ave 206204 max 206204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206204 Ave neighs/atom = 225.60613 Neighbor list builds = 1 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.395 | 5.395 | 5.395 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -3581.8935 0 -3581.8935 5215.5171 10302.835 94 0 -3582.2012 0 -3582.2012 36.668579 10331.835 Loop time of 0.1822 on 1 procs for 6 steps with 914 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 = -3581.89351826863 -3582.20112357739 -3582.20116285363 Force two-norm initial, final = 117.05514 0.62547455 Force max component initial, final = 110.52214 0.43474417 Final line search alpha, max atom move = 0.0010613113 0.00046139888 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17652 | 0.17652 | 0.17652 | 0.0 | 96.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012955 | 0.0012955 | 0.0012955 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00438 | | | 2.40 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7154.00 ave 7154 max 7154 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: 206660.0 ave 206660 max 206660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206660 Ave neighs/atom = 226.10503 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.533 | 5.533 | 5.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3582.2012 0 -3582.2012 36.668579 Loop time of 6.345e-06 on 1 procs for 0 steps with 914 atoms 173.4% 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 | | 6.345e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7105.00 ave 7105 max 7105 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: 206464.0 ave 206464 max 206464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206464 Ave neighs/atom = 225.89059 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.533 | 5.533 | 5.533 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 -3582.2012 -3582.2012 27.019831 75.874726 5.039619 36.668579 36.668579 9.7350608 32.821695 67.448982 2.3609331 1084.2905 Loop time of 6.735e-06 on 1 procs for 0 steps with 914 atoms 252.4% 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 | | 6.735e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7105.00 ave 7105 max 7105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103232.0 ave 103232 max 103232 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206464.0 ave 206464 max 206464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206464 Ave neighs/atom = 225.89059 Neighbor list builds = 0 Dangerous builds = 0 914 -3582.20116285363 eV 2.36093309893818 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04