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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -40.959244 0.0000000) to (17.734306 40.959244 6.2700239) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9114352 5.1194531 6.2700239 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.959244 0.0000000) to (17.734306 40.959244 6.2700239) create_atoms CPU = 0.003 seconds 396 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9114352 5.1194531 6.2700239 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.959244 0.0000000) to (17.734306 40.959244 6.2700239) create_atoms CPU = 0.002 seconds 396 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 = 6 28 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 752 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_313717476091_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 = 6 28 3 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) = 4.559 | 4.559 | 4.559 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2636.4675 0 -2636.4675 -3983.6942 18 0 -2642.2554 0 -2642.2554 -9285.5927 Loop time of 0.994024 on 1 procs for 18 steps with 752 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2636.46751473222 -2642.25395745742 -2642.25544545005 Force two-norm initial, final = 9.5374061 0.69605139 Force max component initial, final = 1.9670421 0.17498264 Final line search alpha, max atom move = 1.0000000 0.17498264 Iterations, force evaluations = 18 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.98752 | 0.98752 | 0.98752 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029853 | 0.0029853 | 0.0029853 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003524 | | | 0.35 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3622.00 ave 3622 max 3622 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: 57424.0 ave 57424 max 57424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57424 Ave neighs/atom = 76.361702 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 28 3 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 : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.559 | 4.559 | 4.559 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -2642.2554 0 -2642.2554 -9285.5927 9108.887 22 0 -2642.3722 0 -2642.3722 -2497.4962 9062.6215 Loop time of 0.194206 on 1 procs for 4 steps with 752 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2642.25544545005 -2642.37196434032 -2642.37224945389 Force two-norm initial, final = 64.015645 1.9547188 Force max component initial, final = 48.382928 1.3774051 Final line search alpha, max atom move = 0.0042620818 0.0058706131 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19149 | 0.19149 | 0.19149 | 0.0 | 98.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057248 | 0.00057248 | 0.00057248 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002148 | | | 1.11 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3622.00 ave 3622 max 3622 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: 57584.0 ave 57584 max 57584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57584 Ave neighs/atom = 76.574468 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 = 6 28 3 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) = 4.697 | 4.697 | 4.697 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2642.3722 0 -2642.3722 -2497.4962 Loop time of 6.475e-06 on 1 procs for 0 steps with 752 atoms 169.9% 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 | | 6.475e-06 | | |100.00 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3622.00 ave 3622 max 3622 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: 57584.0 ave 57584 max 57584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57584 Ave neighs/atom = 76.574468 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 = 6 28 3 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) = 4.697 | 4.697 | 4.697 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 -2642.3722 -2642.3722 17.696143 81.918489 6.2516305 -2497.4962 -2497.4962 -242.98676 -7455.6669 206.16505 2.3991795 607.29292 Loop time of 6.736e-06 on 1 procs for 0 steps with 752 atoms 282.1% 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 | | 6.736e-06 | | |100.00 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3622.00 ave 3622 max 3622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28792.0 ave 28792 max 28792 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57584.0 ave 57584 max 57584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57584 Ave neighs/atom = 76.574468 Neighbor list builds = 0 Dangerous builds = 0 752 -2642.37224945389 eV 2.39917948367949 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01