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 = 4.0445274 4.0445274 4.0445274 Created orthogonal box = (0.0000000 -77.380409 0.0000000) to (44.673265 77.380409 7.0053269) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5911374 5.9195033 7.0053269 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -77.380409 0.0000000) to (44.673265 77.380409 7.0053269) create_atoms CPU = 0.003 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5911374 5.9195033 7.0053269 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -77.380409 0.0000000) to (44.673265 77.380409 7.0053269) create_atoms CPU = 0.003 seconds 1466 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2900 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_722733117926_000#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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 11.71 | 11.71 | 11.71 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9566.3196 0 -9566.3196 -1636.886 40 0 -9585.6339 0 -9585.6339 -3277.8469 Loop time of 2.89089 on 1 procs for 40 steps with 2900 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9566.31958197408 -9585.62542926842 -9585.63388293408 Force two-norm initial, final = 18.991645 0.22390700 Force max component initial, final = 4.2847539 0.041068080 Final line search alpha, max atom move = 1.0000000 0.041068080 Iterations, force evaluations = 40 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7809 | 2.7809 | 2.7809 | 0.0 | 96.19 Neigh | 0.085864 | 0.085864 | 0.085864 | 0.0 | 2.97 Comm | 0.013047 | 0.013047 | 0.013047 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01112 | | | 0.38 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16000.0 ave 16000 max 16000 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: 713596.0 ave 713596 max 713596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 713596 Ave neighs/atom = 246.06759 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.71 | 11.71 | 11.71 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -9585.6339 0 -9585.6339 -3277.8469 48432.525 43 0 -9585.8064 0 -9585.8064 -408.37829 48268.026 Loop time of 0.242343 on 1 procs for 3 steps with 2900 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 = -9585.63388293396 -9585.80548703922 -9585.80635768643 Force two-norm initial, final = 140.11707 0.25426603 Force max component initial, final = 107.85432 0.034662758 Final line search alpha, max atom move = 0.00021752830 7.5401308e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23853 | 0.23853 | 0.23853 | 0.0 | 98.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069191 | 0.00069191 | 0.00069191 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003124 | | | 1.29 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16000.0 ave 16000 max 16000 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: 713540.0 ave 713540 max 713540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 713540 Ave neighs/atom = 246.04828 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 11.22 | 11.22 | 11.22 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9585.8064 0 -9585.8064 -408.37829 Loop time of 1.886e-06 on 1 procs for 0 steps with 2900 atoms 212.1% 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 | | 1.886e-06 | | |100.00 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16000.0 ave 16000 max 16000 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: 713892.0 ave 713892 max 713892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 713892 Ave neighs/atom = 246.16966 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 11.22 | 11.22 | 11.22 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 -9585.8064 -9585.8064 44.615764 154.76082 6.9905314 -408.37829 -408.37829 -0.91617299 -1224.6445 0.42578731 2.6116662 1310.8925 Loop time of 2.137e-06 on 1 procs for 0 steps with 2900 atoms 234.0% 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 | | 2.137e-06 | | |100.00 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16000.0 ave 16000 max 16000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 356946.0 ave 356946 max 356946 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 713892.0 ave 713892 max 713892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 713892 Ave neighs/atom = 246.16966 Neighbor list builds = 0 Dangerous builds = 0 2900 -9585.80635768643 eV 2.61166620528445 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03