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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -42.532485 0.0000000) to (52.091443 42.532485 8.6222370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950699 5.2437310 5.7481580 Created 1752 atoms using lattice units in orthogonal box = (0.0000000 -42.532485 0.0000000) to (52.091443 42.532485 8.6222370) create_atoms CPU = 0.002 seconds 1752 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950699 5.2437310 5.7481580 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -42.532485 0.0000000) to (52.091443 42.532485 8.6222370) create_atoms CPU = 0.002 seconds 1758 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3504 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.286 | 8.286 | 8.286 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15399.709 0 -15399.709 7793.2895 20 0 -15533.863 0 -15533.863 9057.7741 Loop time of 1.33908 on 1 procs for 20 steps with 3504 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15399.7085000359 -15533.8523971517 -15533.8634495891 Force two-norm initial, final = 50.124983 0.35947956 Force max component initial, final = 4.8354101 0.014322511 Final line search alpha, max atom move = 1.0000000 0.014322511 Iterations, force evaluations = 20 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3266 | 1.3266 | 1.3266 | 0.0 | 99.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.005177 | 0.005177 | 0.005177 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007352 | | | 0.55 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12799.0 ave 12799 max 12799 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: 788520.0 ave 788520 max 788520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 788520 Ave neighs/atom = 225.03425 Neighbor list builds = 0 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.286 | 8.286 | 8.286 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -15533.863 0 -15533.863 9057.7741 38206.486 28 0 -15535.176 0 -15535.176 25.098284 38400.098 Loop time of 0.41653 on 1 procs for 8 steps with 3504 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 = -15533.863449589 -15535.1760570781 -15535.1761783133 Force two-norm initial, final = 447.68917 1.8729508 Force max component initial, final = 414.67143 1.7104030 Final line search alpha, max atom move = 0.00022355550 0.00038236999 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40749 | 0.40749 | 0.40749 | 0.0 | 97.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001216 | 0.001216 | 0.001216 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007828 | | | 1.88 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12757.0 ave 12757 max 12757 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: 787740.0 ave 787740 max 787740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 787740 Ave neighs/atom = 224.81164 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.424 | 8.424 | 8.424 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15535.176 0 -15535.176 25.098284 Loop time of 2.339e-06 on 1 procs for 0 steps with 3504 atoms 0.0% 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 | | 2.339e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12763.0 ave 12763 max 12763 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: 786432.0 ave 786432 max 786432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 786432 Ave neighs/atom = 224.43836 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.424 | 8.424 | 8.424 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 -15535.176 -15535.176 52.051469 85.647841 8.6135646 25.098284 25.098284 -11.024812 15.02789 71.291775 2.1952555 1539.6326 Loop time of 2.828e-06 on 1 procs for 0 steps with 3504 atoms 318.2% 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 | | 2.828e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12763.0 ave 12763 max 12763 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 393216.0 ave 393216 max 393216 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 786432.0 ave 786432 max 786432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 786432 Ave neighs/atom = 224.43836 Neighbor list builds = 0 Dangerous builds = 0 3504 -15439.6522265744 eV 2.19525551275384 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02