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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -45.077995 0.0000000) to (31.874956 45.077995 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4420656 6.0470481 4.9780318 Created 655 atoms using lattice units in orthogonal box = (0.0000000 -45.077995 0.0000000) to (31.874956 45.077995 4.9780318) create_atoms CPU = 0.002 seconds 655 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4420656 6.0470481 4.9780318 Created 659 atoms using lattice units in orthogonal box = (0.0000000 -45.077995 0.0000000) to (31.874956 45.077995 4.9780318) create_atoms CPU = 0.001 seconds 659 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 = 11 31 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1311 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_937008984446_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 = 11 31 2 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) = 5.037 | 5.037 | 5.037 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5370.6975 0 -5370.6975 119424.15 82 0 -5816.3276 0 -5816.3276 7056.1511 Loop time of 7.52548 on 1 procs for 82 steps with 1311 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5370.69753436517 -5816.32278659195 -5816.32764261434 Force two-norm initial, final = 1101.3843 0.20598384 Force max component initial, final = 235.93369 0.050374360 Final line search alpha, max atom move = 1.0000000 0.050374360 Iterations, force evaluations = 82 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.4917 | 7.4917 | 7.4917 | 0.0 | 99.55 Neigh | 0.0081618 | 0.0081618 | 0.0081618 | 0.0 | 0.11 Comm | 0.012036 | 0.012036 | 0.012036 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01356 | | | 0.18 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5316.00 ave 5316 max 5316 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: 102456.0 ave 102456 max 102456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102456 Ave neighs/atom = 78.151030 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 ghost atom cutoff = 6 binsize = 3, bins = 11 31 2 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 : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.037 | 5.037 | 5.037 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -5816.3276 0 -5816.3276 7056.1511 14305.461 87 0 -5816.6082 0 -5816.6082 273.35378 14356.449 Loop time of 0.345776 on 1 procs for 5 steps with 1311 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 = -5816.32764261434 -5816.6048467726 -5816.60824391365 Force two-norm initial, final = 138.13034 4.7384600 Force max component initial, final = 131.94753 3.7285480 Final line search alpha, max atom move = 0.00010224793 0.00038123630 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34349 | 0.34349 | 0.34349 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003375 | 0.0003375 | 0.0003375 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001948 | | | 0.56 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5330.00 ave 5330 max 5330 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: 102310.0 ave 102310 max 102310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102310 Ave neighs/atom = 78.039664 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 = 11 31 2 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) = 5.175 | 5.175 | 5.175 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5816.6082 0 -5816.6082 273.35378 Loop time of 2.31e-06 on 1 procs for 0 steps with 1311 atoms 173.2% 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 | | 2.31e-06 | | |100.00 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5330.00 ave 5330 max 5330 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: 102190.0 ave 102190 max 102190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102190 Ave neighs/atom = 77.948131 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 = 11 31 2 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) = 5.175 | 5.175 | 5.175 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 -5816.6082 -5816.6082 31.848494 90.544353 4.9784801 273.35378 273.35378 91.828592 312.09015 416.14259 2.3147479 599.46516 Loop time of 2.69e-06 on 1 procs for 0 steps with 1311 atoms 223.0% 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 | | 2.69e-06 | | |100.00 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5330.00 ave 5330 max 5330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51095.0 ave 51095 max 51095 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102190.0 ave 102190 max 102190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102190 Ave neighs/atom = 77.948131 Neighbor list builds = 0 Dangerous builds = 0 1311 -5816.60824391365 eV 2.3147479482255 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08