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 = 3.5200010 3.5200010 3.5200010 Created orthogonal box = (0.0000000 -55.433031 0.0000000) to (33.945660 55.433031 8.6222063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4751065 5.3644869 5.7481376 Created 1487 atoms using lattice units in orthogonal box = (0.0000000 -55.433031 0.0000000) to (33.945660 55.433031 8.6222063) create_atoms CPU = 0.002 seconds 1487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4751065 5.3644869 5.7481376 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -55.433031 0.0000000) to (33.945660 55.433031 8.6222063) create_atoms CPU = 0.002 seconds 1493 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2976 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_469343973171_005#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.968 | 6.968 | 6.968 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10904.333 0 -10904.333 135793.51 81 0 -13206.505 0 -13206.505 8526.6991 Loop time of 3.69938 on 1 procs for 81 steps with 2976 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10904.3327114025 -13206.4923229935 -13206.5051867912 Force two-norm initial, final = 2234.1585 0.46822313 Force max component initial, final = 361.33908 0.10145465 Final line search alpha, max atom move = 1.0000000 0.10145465 Iterations, force evaluations = 81 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5961 | 3.5961 | 3.5961 | 0.0 | 97.21 Neigh | 0.065449 | 0.065449 | 0.065449 | 0.0 | 1.77 Comm | 0.016079 | 0.016079 | 0.016079 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02172 | | | 0.59 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10470.0 ave 10470 max 10470 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: 518374.0 ave 518374 max 518374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518374 Ave neighs/atom = 174.18481 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.964 | 6.964 | 6.964 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -13206.505 0 -13206.505 8526.6991 32448.998 86 0 -13207.161 0 -13207.161 -132.04318 32604.508 Loop time of 0.1732 on 1 procs for 5 steps with 2976 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 = -13206.5051867911 -13207.1601265643 -13207.1609796379 Force two-norm initial, final = 330.81074 5.9280026 Force max component initial, final = 266.47945 4.5943203 Final line search alpha, max atom move = 9.7791187e-05 0.00044928404 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16946 | 0.16946 | 0.16946 | 0.0 | 97.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057051 | 0.00057051 | 0.00057051 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003174 | | | 1.83 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10460.0 ave 10460 max 10460 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: 518476.0 ave 518476 max 518476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518476 Ave neighs/atom = 174.21909 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.102 | 7.102 | 7.102 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13207.161 0 -13207.161 -132.04318 Loop time of 2.047e-06 on 1 procs for 0 steps with 2976 atoms 195.4% 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 | | 2.047e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10460.0 ave 10460 max 10460 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: 517932.0 ave 517932 max 517932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 517932 Ave neighs/atom = 174.03629 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.102 | 7.102 | 7.102 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 -13207.161 -13207.161 34.001278 111.31727 8.6142974 -132.04318 -132.04318 -226.13352 11.768818 -181.76482 2.2638556 908.29351 Loop time of 2.382e-06 on 1 procs for 0 steps with 2976 atoms 209.9% 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 | | 2.382e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10460.0 ave 10460 max 10460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 258966.0 ave 258966 max 258966 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 517932.0 ave 517932 max 517932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 517932 Ave neighs/atom = 174.03629 Neighbor list builds = 0 Dangerous builds = 0 2976 -13098.6791831783 eV 2.26385557862979 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04