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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -41.266734 0.0000000) to (29.179987 41.266734 4.4499064) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4288349 5.2783032 4.4499064 Created 344 atoms using lattice units in orthogonal box = (0.0000000 -41.266734 0.0000000) to (29.179987 41.266734 4.4499064) create_atoms CPU = 0.001 seconds 344 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4288349 5.2783032 4.4499064 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -41.266734 0.0000000) to (29.179987 41.266734 4.4499064) create_atoms CPU = 0.001 seconds 346 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 ghost atom cutoff = 8 binsize = 4, bins = 8 21 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 690 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_380272712420_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.530 | 4.530 | 4.530 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4146.833 0 -4146.833 195341.57 61 0 -4675.3033 0 -4675.3033 15532.232 Loop time of 5.86341 on 1 procs for 61 steps with 690 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4146.83298189762 -4675.29898672572 -4675.30326700663 Force two-norm initial, final = 530.49649 0.39420781 Force max component initial, final = 172.65113 0.094430685 Final line search alpha, max atom move = 1.0000000 0.094430685 Iterations, force evaluations = 61 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.85 | 5.85 | 5.85 | 0.0 | 99.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0072133 | 0.0072133 | 0.0072133 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006224 | | | 0.11 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5052.00 ave 5052 max 5052 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: 94236.0 ave 94236 max 94236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94236 Ave neighs/atom = 136.57391 Neighbor list builds = 0 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 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.530 | 4.530 | 4.530 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -4675.3033 0 -4675.3033 15532.232 10716.823 67 0 -4675.7109 0 -4675.7109 -7.2514155 10779.483 Loop time of 0.475186 on 1 procs for 6 steps with 690 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 = -4675.30326700663 -4675.70927051755 -4675.71093050292 Force two-norm initial, final = 189.32673 0.65572528 Force max component initial, final = 150.82486 0.38538659 Final line search alpha, max atom move = 7.4743667e-05 2.8805207e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4729 | 0.4729 | 0.4729 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003811 | 0.0003811 | 0.0003811 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001903 | | | 0.40 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5042.00 ave 5042 max 5042 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: 94516.0 ave 94516 max 94516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94516 Ave neighs/atom = 136.97971 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 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.668 | 4.668 | 4.668 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4675.7109 0 -4675.7109 -7.2514155 Loop time of 3.467e-06 on 1 procs for 0 steps with 690 atoms 144.2% 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 | | 3.467e-06 | | |100.00 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5029.00 ave 5029 max 5029 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: 94344.0 ave 94344 max 94344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94344 Ave neighs/atom = 136.73043 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 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.668 | 4.668 | 4.668 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 -4675.7109 -4675.7109 29.209141 82.93362 4.4498823 -7.2514155 -7.2514155 -57.338022 1.0606688 34.523106 2.4849219 480.46431 Loop time of 2.183e-06 on 1 procs for 0 steps with 690 atoms 183.2% 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 | | 2.183e-06 | | |100.00 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5029.00 ave 5029 max 5029 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47172.0 ave 47172 max 47172 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94344.0 ave 94344 max 94344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94344 Ave neighs/atom = 136.73043 Neighbor list builds = 0 Dangerous builds = 0 690 -4675.71093050292 eV 2.4849218630059 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06