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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -33.883114 0.0000000) to (41.498170 33.883114 7.0144710) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7426480 4.3564003 4.6763140 Created 835 atoms using lattice units in orthogonal box = (0.0000000 -33.883114 0.0000000) to (41.498170 33.883114 7.0144710) create_atoms CPU = 0.002 seconds 835 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7426480 4.3564003 4.6763140 Created 841 atoms using lattice units in orthogonal box = (0.0000000 -33.883114 0.0000000) to (41.498170 33.883114 7.0144710) create_atoms CPU = 0.001 seconds 841 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 13 22 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1669 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 13 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.090 | 5.090 | 5.090 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6442.6939 0 -6442.6939 71278.558 98 0 -7117.9142 0 -7117.9142 -1409.652 Loop time of 23.9701 on 1 procs for 98 steps with 1669 atoms 85.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6442.69387991607 -7117.90797421092 -7117.91421834508 Force two-norm initial, final = 782.35873 0.27331474 Force max component initial, final = 146.51491 0.074030610 Final line search alpha, max atom move = 1.0000000 0.074030610 Iterations, force evaluations = 98 172 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.904 | 23.904 | 23.904 | 0.0 | 99.72 Neigh | 0.036846 | 0.036846 | 0.036846 | 0.0 | 0.15 Comm | 0.01191 | 0.01191 | 0.01191 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01716 | | | 0.07 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5685.00 ave 5685 max 5685 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: 161090.0 ave 161090 max 161090 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161090 Ave neighs/atom = 96.518874 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 13 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.090 | 5.090 | 5.090 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -7117.9142 0 -7117.9142 -1409.652 19725.916 101 0 -7117.9808 0 -7117.9808 15.571599 19709.345 Loop time of 1.34721 on 1 procs for 3 steps with 1669 atoms 50.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7117.91421834508 -7117.98043688301 -7117.98076204511 Force two-norm initial, final = 59.836811 1.1822281 Force max component initial, final = 56.423734 0.70164775 Final line search alpha, max atom move = 0.00021427949 0.00015034872 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3454 | 1.3454 | 1.3454 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027646 | 0.00027646 | 0.00027646 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001581 | | | 0.12 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5662.00 ave 5662 max 5662 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: 159240.0 ave 159240 max 159240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159240 Ave neighs/atom = 95.410425 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 13 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.228 | 5.228 | 5.228 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7117.9808 0 -7117.9808 15.571599 Loop time of 1.97e-06 on 1 procs for 0 steps with 1669 atoms 203.0% 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 | | 1.97e-06 | | |100.00 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5662.00 ave 5662 max 5662 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: 163736.0 ave 163736 max 163736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163736 Ave neighs/atom = 98.104254 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 13 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.228 | 5.228 | 5.228 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 -7117.9808 -7117.9808 41.493849 67.850713 7.0005805 15.571599 15.571599 -57.031145 54.886836 48.859107 2.2854178 1634.7491 Loop time of 1.951e-06 on 1 procs for 0 steps with 1669 atoms 205.0% 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 | | 1.951e-06 | | |100.00 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5662.00 ave 5662 max 5662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81868.0 ave 81868 max 81868 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163736.0 ave 163736 max 163736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163736 Ave neighs/atom = 98.104254 Neighbor list builds = 0 Dangerous builds = 0 1669 -7117.98076204511 eV 2.28541777984404 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:26