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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -81.202248 0.0000000) to (46.882140 81.202248 7.0148058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2976008 6.4638605 7.0148058 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -81.202248 0.0000000) to (46.882140 81.202248 7.0148058) create_atoms CPU = 0.015 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2976008 6.4638605 7.0148058 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -81.202248 0.0000000) to (46.882140 81.202248 7.0148058) create_atoms CPU = 0.010 seconds 1610 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 11 38 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3218 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_664470114311_005#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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.052 | 7.052 | 7.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10685.707 0 -10685.707 4158.1322 51 0 -10791.685 0 -10791.685 3554.2658 Loop time of 4.99094 on 1 procs for 51 steps with 3218 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10685.707265224 -10791.6747924513 -10791.6854289237 Force two-norm initial, final = 59.743116 0.23169041 Force max component initial, final = 13.308284 0.023855550 Final line search alpha, max atom move = 1.0000000 0.023855550 Iterations, force evaluations = 51 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.714 | 4.714 | 4.714 | 0.0 | 94.45 Neigh | 0.22015 | 0.22015 | 0.22015 | 0.0 | 4.41 Comm | 0.02835 | 0.02835 | 0.02835 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02844 | | | 0.57 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13039.0 ave 13039 max 13039 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: 561808.0 ave 561808 max 561808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 561808 Ave neighs/atom = 174.58297 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.052 | 7.052 | 7.052 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -10791.685 0 -10791.685 3554.2658 53409.821 58 0 -10792.291 0 -10792.291 40.798697 53645.293 Loop time of 0.644496 on 1 procs for 7 steps with 3218 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10791.6854289241 -10792.2907932657 -10792.2911156093 Force two-norm initial, final = 237.85983 3.3393856 Force max component initial, final = 214.76997 3.2736392 Final line search alpha, max atom move = 0.00024299038 0.00079546283 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55661 | 0.55661 | 0.55661 | 0.0 | 86.36 Neigh | 0.073479 | 0.073479 | 0.073479 | 0.0 | 11.40 Comm | 0.0036416 | 0.0036416 | 0.0036416 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01076 | | | 1.67 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13062.0 ave 13062 max 13062 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: 561392.0 ave 561392 max 561392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 561392 Ave neighs/atom = 174.45370 Neighbor list builds = 1 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.190 | 7.190 | 7.190 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10792.291 0 -10792.291 40.798697 Loop time of 6.745e-06 on 1 procs for 0 steps with 3218 atoms 192.7% 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 | | 6.745e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13044.0 ave 13044 max 13044 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: 561304.0 ave 561304 max 561304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 561304 Ave neighs/atom = 174.42635 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.190 | 7.190 | 7.190 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 -10792.291 -10792.291 46.879194 163.38209 7.0040146 40.798697 40.798697 14.373671 98.359416 9.6630054 2.5297144 1316.7505 Loop time of 7.648e-06 on 1 procs for 0 steps with 3218 atoms 261.5% 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 | | 7.648e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13044.0 ave 13044 max 13044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 280652.0 ave 280652 max 280652 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 561304.0 ave 561304 max 561304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 561304 Ave neighs/atom = 174.42635 Neighbor list builds = 0 Dangerous builds = 0 3218 -10772.727559442 eV 2.52971443656354 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06