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 -39.959306 0.0000000) to (23.070516 39.959306 5.3397869) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9436820 4.7570602 5.3397869 Created 336 atoms using lattice units in orthogonal box = (0.0000000 -39.959306 0.0000000) to (23.070516 39.959306 5.3397869) create_atoms CPU = 0.001 seconds 336 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9436820 4.7570602 5.3397869 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -39.959306 0.0000000) to (23.070516 39.959306 5.3397869) create_atoms CPU = 0.001 seconds 339 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 24 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 0 atoms, new total = 675 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_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 24 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) = 5.278 | 5.278 | 5.278 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4046.449 0 -4046.449 129564.17 107 0 -4380.3788 0 -4380.3788 17560.819 Loop time of 40.6495 on 1 procs for 107 steps with 675 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 = -4046.44896938644 -4380.37516464395 -4380.37878765224 Force two-norm initial, final = 503.20472 0.31388067 Force max component initial, final = 157.43091 0.13631139 Final line search alpha, max atom move = 1.0000000 0.13631139 Iterations, force evaluations = 107 202 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 40.575 | 40.575 | 40.575 | 0.0 | 99.82 Neigh | 0.050671 | 0.050671 | 0.050671 | 0.0 | 0.12 Comm | 0.012604 | 0.012604 | 0.012604 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.011 | | | 0.03 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3667.00 ave 3667 max 3667 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: 52048.0 ave 52048 max 52048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52048 Ave neighs/atom = 77.108148 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 24 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 : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.278 | 5.278 | 5.278 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -4380.3788 0 -4380.3788 17560.819 9845.3047 114 0 -4380.9164 0 -4380.9164 -9.109331 9923.7888 Loop time of 2.02255 on 1 procs for 7 steps with 675 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 = -4380.37878765225 -4380.91587836811 -4380.91643998841 Force two-norm initial, final = 196.47068 0.64792218 Force max component initial, final = 155.17360 0.13225024 Final line search alpha, max atom move = 0.00016425535 2.1722809e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0202 | 2.0202 | 2.0202 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038413 | 0.00038413 | 0.00038413 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00197 | | | 0.10 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3667.00 ave 3667 max 3667 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: 51364.0 ave 51364 max 51364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51364 Ave neighs/atom = 76.094815 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 25 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) = 5.417 | 5.417 | 5.417 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4380.9164 0 -4380.9164 -9.109331 Loop time of 2.144e-06 on 1 procs for 0 steps with 675 atoms 186.6% 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 | | 2.144e-06 | | |100.00 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3663.00 ave 3663 max 3663 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: 50730.0 ave 50730 max 50730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50730 Ave neighs/atom = 75.155556 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 25 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) = 5.417 | 5.417 | 5.417 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 -4380.9164 -4380.9164 23.078964 80.359964 5.3508339 -9.109331 -9.109331 -19.506387 -21.469459 13.647853 2.4735061 1789.4201 Loop time of 2.492e-06 on 1 procs for 0 steps with 675 atoms 200.6% 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 | | 2.492e-06 | | |100.00 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3663.00 ave 3663 max 3663 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25365.0 ave 25365 max 25365 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50730.0 ave 50730 max 50730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50730 Ave neighs/atom = 75.155556 Neighbor list builds = 0 Dangerous builds = 0 675 -4380.91643998841 eV 2.47350608343653 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:43