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 = 4.0496966 4.0496966 4.0496966 Created orthogonal box = (0.0000000 -49.099961 0.0000000) to (40.089951 49.099961 9.9196902) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7271358 5.6782268 6.6131268 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -49.099961 0.0000000) to (40.089951 49.099961 9.9196902) create_atoms CPU = 0.005 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7271358 5.6782268 6.6131268 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -49.099961 0.0000000) to (40.089951 49.099961 9.9196902) create_atoms CPU = 0.004 seconds 1184 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 11 26 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 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2336 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_284963179498_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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 5.949 | 5.949 | 5.949 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7455.1523 0 -7455.1523 29453.76 89 0 -7850.5993 0 -7850.5993 451.15603 Loop time of 4.50581 on 1 procs for 89 steps with 2336 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 = -7455.15229476982 -7850.5921567073 -7850.59934188675 Force two-norm initial, final = 448.31979 0.19260916 Force max component initial, final = 71.033849 0.016077164 Final line search alpha, max atom move = 1.0000000 0.016077164 Iterations, force evaluations = 89 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.351 | 4.351 | 4.351 | 0.0 | 96.57 Neigh | 0.086123 | 0.086123 | 0.086123 | 0.0 | 1.91 Comm | 0.029291 | 0.029291 | 0.029291 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03935 | | | 0.87 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7235.00 ave 7235 max 7235 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: 296864.0 ave 296864 max 296864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296864 Ave neighs/atom = 127.08219 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.947 | 5.947 | 5.947 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -7850.5993 0 -7850.5993 451.15603 39052.135 93 0 -7850.7016 0 -7850.7016 139.35905 39070.417 Loop time of 0.156811 on 1 procs for 4 steps with 2336 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 = -7850.59934188673 -7850.70012036929 -7850.70160022188 Force two-norm initial, final = 52.817036 6.5767214 Force max component initial, final = 50.093760 5.7005103 Final line search alpha, max atom move = 0.00019511461 0.0011122528 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15182 | 0.15182 | 0.15182 | 0.0 | 96.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091356 | 0.00091356 | 0.00091356 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00408 | | | 2.60 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6944.00 ave 6944 max 6944 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: 299264.0 ave 299264 max 299264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 299264 Ave neighs/atom = 128.10959 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.085 | 6.085 | 6.085 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7850.7016 0 -7850.7016 139.35905 Loop time of 6.014e-06 on 1 procs for 0 steps with 2336 atoms 182.9% 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 | | 6.014e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6944.00 ave 6944 max 6944 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: 298800.0 ave 298800 max 298800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298800 Ave neighs/atom = 127.91096 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.085 | 6.085 | 6.085 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 -7850.7016 -7850.7016 40.054441 98.512064 9.9016587 139.35905 139.35905 68.870038 234.5062 114.70092 2.5929844 1866.4568 Loop time of 7.037e-06 on 1 procs for 0 steps with 2336 atoms 270.0% 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 | | 7.037e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6944.00 ave 6944 max 6944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 149400.0 ave 149400 max 149400 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 298800.0 ave 298800 max 298800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298800 Ave neighs/atom = 127.91096 Neighbor list builds = 0 Dangerous builds = 0 2336 -7850.70160022188 eV 2.59298442792889 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05