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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -47.936049 0.0000000) to (29.354715 47.936049 8.8507797) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3372210 5.4472783 5.9005198 Created 1045 atoms using lattice units in orthogonal box = (0.0000000 -47.936049 0.0000000) to (29.354715 47.936049 8.8507797) create_atoms CPU = 0.002 seconds 1045 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3372210 5.4472783 5.9005198 Created 1069 atoms using lattice units in orthogonal box = (0.0000000 -47.936049 0.0000000) to (29.354715 47.936049 8.8507797) create_atoms CPU = 0.001 seconds 1069 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 24 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 2109 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 24 3 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) = 6.042 | 6.042 | 6.042 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7413.6335 0 -7413.6335 6970.3922 62 0 -7453.4343 0 -7453.4343 1968.6094 Loop time of 12.7206 on 1 procs for 62 steps with 2109 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 = -7413.63349142535 -7453.42772695153 -7453.43426347968 Force two-norm initial, final = 63.988769 0.20461357 Force max component initial, final = 19.045228 0.045878917 Final line search alpha, max atom move = 1.0000000 0.045878917 Iterations, force evaluations = 62 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.67 | 12.67 | 12.67 | 0.0 | 99.60 Neigh | 0.023238 | 0.023238 | 0.023238 | 0.0 | 0.18 Comm | 0.012958 | 0.012958 | 0.012958 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01452 | | | 0.11 Nlocal: 2109.00 ave 2109 max 2109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8700.00 ave 8700 max 8700 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: 370868.0 ave 370868 max 370868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 370868 Ave neighs/atom = 175.85017 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 24 3 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.042 | 6.042 | 6.042 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -7453.4343 0 -7453.4343 1968.6094 24908.733 66 0 -7453.5707 0 -7453.5707 -221.07999 24946.824 Loop time of 0.645891 on 1 procs for 4 steps with 2109 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 = -7453.43426347968 -7453.56874936341 -7453.57073613919 Force two-norm initial, final = 82.028545 7.9898023 Force max component initial, final = 81.670338 6.4415219 Final line search alpha, max atom move = 8.3019508e-05 0.00053477198 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64335 | 0.64335 | 0.64335 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041522 | 0.00041522 | 0.00041522 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002128 | | | 0.33 Nlocal: 2109.00 ave 2109 max 2109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8700.00 ave 8700 max 8700 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: 369992.0 ave 369992 max 369992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369992 Ave neighs/atom = 175.43480 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 25 3 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) = 6.180 | 6.180 | 6.180 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7453.5707 0 -7453.5707 -221.07999 Loop time of 2.431e-06 on 1 procs for 0 steps with 2109 atoms 205.7% 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 | | 2.431e-06 | | |100.00 Nlocal: 2109.00 ave 2109 max 2109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8700.00 ave 8700 max 8700 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: 369768.0 ave 369768 max 369768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369768 Ave neighs/atom = 175.32859 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 25 3 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) = 6.180 | 6.180 | 6.180 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 -7453.5707 -7453.5707 29.327339 96.189979 8.8432676 -221.07999 -221.07999 -413.31234 48.944399 -298.87203 2.4074607 756.9028 Loop time of 2.495e-06 on 1 procs for 0 steps with 2109 atoms 240.5% 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 | | 2.495e-06 | | |100.00 Nlocal: 2109.00 ave 2109 max 2109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8700.00 ave 8700 max 8700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 184884.0 ave 184884 max 184884 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 369768.0 ave 369768 max 369768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369768 Ave neighs/atom = 175.32859 Neighbor list builds = 0 Dangerous builds = 0 2109 -7453.57073613919 eV 2.40746065379157 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14