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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -42.753327 0.0000000) to (52.361918 42.753327 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9842192 5.4968564 5.9005197 Created 1664 atoms using lattice units in orthogonal box = (0.0000000 -42.753327 0.0000000) to (52.361918 42.753327 8.8507796) create_atoms CPU = 0.002 seconds 1664 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9842192 5.4968564 5.9005197 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -42.753327 0.0000000) to (52.361918 42.753327 8.8507796) create_atoms CPU = 0.002 seconds 1688 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 19 31 4 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3352 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.227 | 5.227 | 5.227 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11329.146 0 -11329.146 44751.451 194 0 -11811.259 0 -11811.259 4522.2453 Loop time of 19.2215 on 1 procs for 194 steps with 3352 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 = -11329.145803155 -11811.2507615635 -11811.2590789811 Force two-norm initial, final = 369.52651 0.25490690 Force max component initial, final = 43.869601 0.057135953 Final line search alpha, max atom move = 0.90025667 0.051437023 Iterations, force evaluations = 194 353 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.053 | 19.053 | 19.053 | 0.0 | 99.12 Neigh | 0.075007 | 0.075007 | 0.075007 | 0.0 | 0.39 Comm | 0.034279 | 0.034279 | 0.034279 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05966 | | | 0.31 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7459.00 ave 7459 max 7459 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: 206638.0 ave 206638 max 206638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206638 Ave neighs/atom = 61.646181 Neighbor list builds = 4 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 194 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.609 | 5.609 Mbytes Step Temp E_pair E_mol TotEng Press Volume 194 0 -11811.259 0 -11811.259 4522.2453 39627.529 198 0 -11811.657 0 -11811.657 -172.91634 39759.041 Loop time of 0.325165 on 1 procs for 4 steps with 3352 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 = -11811.2590789811 -11811.6465627355 -11811.6572705972 Force two-norm initial, final = 228.24966 7.7499730 Force max component initial, final = 177.90499 5.8146055 Final line search alpha, max atom move = 5.1988889e-05 0.00030229488 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32164 | 0.32164 | 0.32164 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037619 | 0.00037619 | 0.00037619 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003145 | | | 0.97 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7458.00 ave 7458 max 7458 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: 204920.0 ave 204920 max 204920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204920 Ave neighs/atom = 61.133652 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.747 | 5.747 | 5.747 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11811.657 0 -11811.657 -172.91634 Loop time of 2.734e-06 on 1 procs for 0 steps with 3352 atoms 182.9% 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 | | 2.734e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7458.00 ave 7458 max 7458 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: 197734.0 ave 197734 max 197734 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197734 Ave neighs/atom = 58.989857 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.747 | 5.747 | 5.747 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 -11811.657 -11811.657 52.457717 85.785895 8.835083 -172.91634 -172.91634 -234.74078 -109.64901 -174.35923 2.2822515 1806.8385 Loop time of 2.533e-06 on 1 procs for 0 steps with 3352 atoms 276.4% 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 | | 2.533e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7458.00 ave 7458 max 7458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98867.0 ave 98867 max 98867 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 197734.0 ave 197734 max 197734 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197734 Ave neighs/atom = 58.989857 Neighbor list builds = 0 Dangerous builds = 0 3352 -11811.6572705972 eV 2.28225149114626 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20