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 = 2.8509989 2.8509989 2.8509989 Created orthogonal box = (0.0000000 -41.514021 0.0000000) to (20.755585 41.514021 2.8509989) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5245333 3.5245333 2.8509989 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.514021 0.0000000) to (20.755585 41.514021 2.8509989) create_atoms CPU = 0.001 seconds 213 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5245333 3.5245333 2.8509989 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.514021 0.0000000) to (20.755585 41.514021 2.8509989) create_atoms CPU = 0.001 seconds 213 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 1 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 418 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.469 | 4.469 | 4.469 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1756.1199 0 -1756.1199 15431.772 74 0 -1782.1236 0 -1782.1236 -15888.043 Loop time of 8.32566 on 1 procs for 74 steps with 418 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 = -1756.11986244162 -1782.12207026188 -1782.12364722926 Force two-norm initial, final = 100.91827 0.12645080 Force max component initial, final = 45.712220 0.027454159 Final line search alpha, max atom move = 1.0000000 0.027454159 Iterations, force evaluations = 74 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2898 | 8.2898 | 8.2898 | 0.0 | 99.57 Neigh | 0.0088822 | 0.0088822 | 0.0088822 | 0.0 | 0.11 Comm | 0.015697 | 0.015697 | 0.015697 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01132 | | | 0.14 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4451.00 ave 4451 max 4451 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: 52760.0 ave 52760 max 52760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52760 Ave neighs/atom = 126.22010 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.467 | 4.467 | 4.467 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -1782.1236 0 -1782.1236 -15888.043 4913.1139 83 0 -1782.444 0 -1782.444 1274.0782 4861.6268 Loop time of 0.65446 on 1 procs for 9 steps with 418 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 = -1782.12364722926 -1782.44341545588 -1782.44401151999 Force two-norm initial, final = 81.065496 1.8639898 Force max component initial, final = 64.129052 1.8341660 Final line search alpha, max atom move = 0.00037599396 0.00068963536 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65029 | 0.65029 | 0.65029 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00098112 | 0.00098112 | 0.00098112 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003187 | | | 0.49 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4075.00 ave 4075 max 4075 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: 52922.0 ave 52922 max 52922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52922 Ave neighs/atom = 126.60766 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.605 | 4.605 | 4.605 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1782.444 0 -1782.444 1274.0782 Loop time of 6.656e-06 on 1 procs for 0 steps with 418 atoms 180.3% 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 | | 6.656e-06 | | |100.00 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4075.00 ave 4075 max 4075 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: 54230.0 ave 54230 max 54230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54230 Ave neighs/atom = 129.73684 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.605 | 4.605 | 4.605 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 -1782.444 -1782.444 20.70756 83.028043 2.8276646 1274.0782 1274.0782 603.06111 3156.8047 62.368758 2.3346488 278.01941 Loop time of 7.257e-06 on 1 procs for 0 steps with 418 atoms 261.8% 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 | | 7.257e-06 | | |100.00 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4075.00 ave 4075 max 4075 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27115.0 ave 27115 max 27115 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54230.0 ave 54230 max 54230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54230 Ave neighs/atom = 129.73684 Neighbor list builds = 0 Dangerous builds = 0 418 -1782.44401151999 eV 2.33464878701759 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09