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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -79.810443 0.0000000) to (48.873715 79.810443 9.8739816) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6520623 5.7007459 6.5826544 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -79.810443 0.0000000) to (48.873715 79.810443 9.8739816) create_atoms CPU = 0.003 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6520623 5.7007459 6.5826544 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -79.810443 0.0000000) to (48.873715 79.810443 9.8739816) create_atoms CPU = 0.003 seconds 2357 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 42 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 4708 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_699137396381_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 11.41 | 11.41 | 11.41 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15541.442 0 -15541.442 6831.5101 96 0 -15788.368 0 -15788.368 3043.2391 Loop time of 4.48072 on 1 procs for 96 steps with 4708 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15541.441998237 -15788.35288458 -15788.3683134596 Force two-norm initial, final = 72.324137 0.35865446 Force max component initial, final = 5.4039419 0.10946298 Final line search alpha, max atom move = 1.0000000 0.10946298 Iterations, force evaluations = 96 174 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3302 | 4.3302 | 4.3302 | 0.0 | 96.64 Neigh | 0.083813 | 0.083813 | 0.083813 | 0.0 | 1.87 Comm | 0.026133 | 0.026133 | 0.026133 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04055 | | | 0.91 Nlocal: 4708.00 ave 4708 max 4708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12716.0 ave 12716 max 12716 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: 621228.0 ave 621228 max 621228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621228 Ave neighs/atom = 131.95157 Neighbor list builds = 2 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.40 | 11.40 | 11.40 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -15788.368 0 -15788.368 3043.2391 77029.555 102 0 -15788.973 0 -15788.973 -26.574434 77345.795 Loop time of 0.188711 on 1 procs for 6 steps with 4708 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 = -15788.3683134596 -15788.9731522433 -15788.9733209198 Force two-norm initial, final = 285.83127 2.3643865 Force max component initial, final = 249.86637 1.7193286 Final line search alpha, max atom move = 0.00035781375 0.00061519943 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18264 | 0.18264 | 0.18264 | 0.0 | 96.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007603 | 0.0007603 | 0.0007603 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005307 | | | 2.81 Nlocal: 4708.00 ave 4708 max 4708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12277.0 ave 12277 max 12277 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: 621872.0 ave 621872 max 621872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621872 Ave neighs/atom = 132.08836 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 10.91 | 10.91 | 10.91 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15788.973 0 -15788.973 -26.574434 Loop time of 2.061e-06 on 1 procs for 0 steps with 4708 atoms 194.1% 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 | | 2.061e-06 | | |100.00 Nlocal: 4708.00 ave 4708 max 4708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12264.0 ave 12264 max 12264 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: 621394.0 ave 621394 max 621394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621394 Ave neighs/atom = 131.98683 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 10.91 | 10.91 | 10.91 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 -15788.973 -15788.973 48.885422 160.43233 9.8620102 -26.574434 -26.574434 -35.623498 -17.138706 -26.961098 2.5640349 2395.9954 Loop time of 2.633e-06 on 1 procs for 0 steps with 4708 atoms 303.8% 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 | | 2.633e-06 | | |100.00 Nlocal: 4708.00 ave 4708 max 4708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12264.0 ave 12264 max 12264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 310697.0 ave 310697 max 310697 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 621394.0 ave 621394 max 621394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621394 Ave neighs/atom = 131.98683 Neighbor list builds = 0 Dangerous builds = 0 4708 -15788.9733209198 eV 2.56403491189333 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05