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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -32.041804 0.0000000) to (22.654797 32.041804 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0343993 4.1531676 4.3599177 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -32.041804 0.0000000) to (22.654797 32.041804 4.3599177) create_atoms CPU = 0.000 seconds 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0343993 4.1531676 4.3599177 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -32.041804 0.0000000) to (22.654797 32.041804 4.3599177) create_atoms CPU = 0.000 seconds 218 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 434 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.827 | 4.827 | 4.827 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2550.1158 0 -2550.1158 160049.5 50 0 -2804.672 0 -2804.672 23695.718 Loop time of 5.27293 on 1 procs for 50 steps with 434 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 = -2550.11579121877 -2804.66937335218 -2804.67200189192 Force two-norm initial, final = 514.56704 0.23732083 Force max component initial, final = 145.53634 0.057711296 Final line search alpha, max atom move = 1.0000000 0.057711296 Iterations, force evaluations = 50 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2608 | 5.2608 | 5.2608 | 0.0 | 99.77 Neigh | 0.0089567 | 0.0089567 | 0.0089567 | 0.0 | 0.17 Comm | 0.0019053 | 0.0019053 | 0.0019053 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001276 | | | 0.02 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2898.00 ave 2898 max 2898 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: 32470.0 ave 32470 max 32470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32470 Ave neighs/atom = 74.815668 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.209 | 5.209 | 5.209 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -2804.672 0 -2804.672 23695.718 6329.7334 62 0 -2805.5589 0 -2805.5589 2888.5947 6387.6491 Loop time of 0.895289 on 1 procs for 12 steps with 434 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 = -2804.67200189192 -2805.55863883089 -2805.55887028286 Force two-norm initial, final = 167.44985 2.0559029 Force max component initial, final = 166.87962 1.2842460 Final line search alpha, max atom move = 0.00075601493 0.00097090914 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.89407 | 0.89407 | 0.89407 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002549 | 0.0002549 | 0.0002549 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009613 | | | 0.11 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2902.00 ave 2902 max 2902 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: 33070.0 ave 33070 max 33070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33070 Ave neighs/atom = 76.198157 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.966 | 4.966 | 4.966 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2805.5589 0 -2805.5589 2888.5947 Loop time of 2.3e-06 on 1 procs for 0 steps with 434 atoms 130.4% 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 | | 2.3e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2902.00 ave 2902 max 2902 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: 32360.0 ave 32360 max 32360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32360 Ave neighs/atom = 74.562212 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.966 | 4.966 | 4.966 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 -2805.5589 -2805.5589 22.901863 64.083608 4.3523447 2888.5947 2888.5947 171.50063 8172.7231 321.56037 2.4703657 1123.2243 Loop time of 2.4e-06 on 1 procs for 0 steps with 434 atoms 125.0% 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 | | 2.4e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2902.00 ave 2902 max 2902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16180.0 ave 16180 max 16180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32360.0 ave 32360 max 32360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32360 Ave neighs/atom = 74.562212 Neighbor list builds = 0 Dangerous builds = 0 434 -2805.55887028286 eV 2.47036569081125 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06