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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -29.203689 0.0000000) to (25.291137 29.203689 4.9600000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5394348 4.4928752 4.9600000 Created 311 atoms using lattice units in orthogonal box = (0.0000000 -29.203689 0.0000000) to (25.291137 29.203689 4.9600000) create_atoms CPU = 0.002 seconds 311 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5394348 4.4928752 4.9600000 Created 317 atoms using lattice units in orthogonal box = (0.0000000 -29.203689 0.0000000) to (25.291137 29.203689 4.9600000) create_atoms CPU = 0.002 seconds 317 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 = 9 20 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 2 atoms, new total = 626 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_179158257180_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 = 9 20 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) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2437.9982 0 -2437.9982 80514.036 128 0 -2667.4822 0 -2667.4822 15085.164 Loop time of 10.9805 on 1 procs for 128 steps with 626 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 = -2437.99822637135 -2667.47978657664 -2667.48218650103 Force two-norm initial, final = 481.71176 0.16522300 Force max component initial, final = 168.76479 0.040782803 Final line search alpha, max atom move = 1.0000000 0.040782803 Iterations, force evaluations = 128 233 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.916 | 10.916 | 10.916 | 0.0 | 99.41 Neigh | 0.02373 | 0.02373 | 0.02373 | 0.0 | 0.22 Comm | 0.020128 | 0.020128 | 0.020128 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02086 | | | 0.19 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3081.00 ave 3081 max 3081 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: 40830.0 ave 40830 max 40830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40830 Ave neighs/atom = 65.223642 Neighbor list builds = 3 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 = 9 20 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 : 128 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press Volume 128 0 -2667.4822 0 -2667.4822 15085.164 7326.8573 136 0 -2667.8885 0 -2667.8885 -6.9090525 7390.3309 Loop time of 0.487899 on 1 procs for 8 steps with 626 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 = -2667.48218650103 -2667.88831617543 -2667.88854587548 Force two-norm initial, final = 127.36939 0.33995769 Force max component initial, final = 103.31868 0.097325434 Final line search alpha, max atom move = 0.00035588550 3.4636710e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48409 | 0.48409 | 0.48409 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079231 | 0.00079231 | 0.00079231 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003016 | | | 0.62 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3081.00 ave 3081 max 3081 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: 40718.0 ave 40718 max 40718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40718 Ave neighs/atom = 65.044728 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 = 9 20 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) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2667.8885 0 -2667.8885 -6.9090525 Loop time of 5.914e-06 on 1 procs for 0 steps with 626 atoms 186.0% 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 | | 5.914e-06 | | |100.00 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3081.00 ave 3081 max 3081 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: 40582.0 ave 40582 max 40582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40582 Ave neighs/atom = 64.827476 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 = 9 20 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) = 4.631 | 4.631 | 4.631 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 -2667.8885 -2667.8885 25.284732 58.803603 4.9705174 -6.9090525 -6.9090525 -21.094189 -18.125585 18.492616 2.3117788 682.83365 Loop time of 6.525e-06 on 1 procs for 0 steps with 626 atoms 275.9% 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 | | 6.525e-06 | | |100.00 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3081.00 ave 3081 max 3081 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20291.0 ave 20291 max 20291 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40582.0 ave 40582 max 40582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40582 Ave neighs/atom = 64.827476 Neighbor list builds = 0 Dangerous builds = 0 626 -2667.88854587548 eV 2.31177878153232 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12