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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -45.875803 0.0000000) to (32.439092 45.875803 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0072392 6.2300473 5.0973115 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -45.875803 0.0000000) to (32.439092 45.875803 5.0973115) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0072392 6.2300473 5.0973115 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -45.875803 0.0000000) to (32.439092 45.875803 5.0973115) create_atoms CPU = 0.001 seconds 650 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 0 atoms, new total = 1298 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_492310898779_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) = 5.032 | 5.032 | 5.032 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5238.1159 0 -5238.1159 71571.25 246 0 -5511.1583 0 -5511.1583 -1930.3953 Loop time of 21.1504 on 1 procs for 246 steps with 1298 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5238.11589637399 -5511.1531717184 -5511.15827394122 Force two-norm initial, final = 720.69167 0.21274887 Force max component initial, final = 146.50695 0.056497246 Final line search alpha, max atom move = 1.0000000 0.056497246 Iterations, force evaluations = 246 477 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.049 | 21.049 | 21.049 | 0.0 | 99.52 Neigh | 0.043864 | 0.043864 | 0.043864 | 0.0 | 0.21 Comm | 0.028783 | 0.028783 | 0.028783 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02856 | | | 0.14 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5489.00 ave 5489 max 5489 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: 90002.0 ave 90002 max 90002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90002 Ave neighs/atom = 69.338983 Neighbor list builds = 6 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 : 246 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.652 | 4.652 | 4.652 Mbytes Step Temp E_pair E_mol TotEng Press Volume 246 0 -5511.1583 0 -5511.1583 -1930.3953 15171.326 278 0 -5525.502 0 -5525.502 -5.8378705 15130.448 Loop time of 1.52089 on 1 procs for 32 steps with 1298 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 = -5511.15827394121 -5525.49804098899 -5525.50204850739 Force two-norm initial, final = 686.16429 1.8478899 Force max component initial, final = 505.79134 0.47751080 Final line search alpha, max atom move = 0.00010769517 5.1425607e-05 Iterations, force evaluations = 32 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5034 | 1.5034 | 1.5034 | 0.0 | 98.85 Neigh | 0.0072793 | 0.0072793 | 0.0072793 | 0.0 | 0.48 Comm | 0.0017211 | 0.0017211 | 0.0017211 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008478 | | | 0.56 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5609.00 ave 5609 max 5609 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: 88084.0 ave 88084 max 88084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88084 Ave neighs/atom = 67.861325 Neighbor list builds = 1 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 = 12 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) = 4.791 | 4.791 | 4.791 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5525.502 0 -5525.502 -5.8378705 Loop time of 1.719e-06 on 1 procs for 0 steps with 1298 atoms 174.5% 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 | | 1.719e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5574.00 ave 5574 max 5574 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: 87930.0 ave 87930 max 87930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87930 Ave neighs/atom = 67.742681 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 = 12 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) = 4.791 | 4.791 | 4.791 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 -5525.502 -5525.502 33.46412 91.039863 4.9663895 -5.8378705 -5.8378705 -31.391227 -35.387712 49.265328 2.3294416 1502.3909 Loop time of 1.897e-06 on 1 procs for 0 steps with 1298 atoms 158.1% 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 | | 1.897e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5574.00 ave 5574 max 5574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43965.0 ave 43965 max 43965 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87930.0 ave 87930 max 87930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87930 Ave neighs/atom = 67.742681 Neighbor list builds = 0 Dangerous builds = 0 1298 -5525.50204850739 eV 2.3294415679365 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23