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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -59.128172 0.0000000) to (12.069488 59.128172 8.9139073) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4861307 5.3752883 5.9426049 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -59.128172 0.0000000) to (12.069488 59.128172 8.9139073) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4861307 5.3752883 5.9426049 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -59.128172 0.0000000) to (12.069488 59.128172 8.9139073) create_atoms CPU = 0.001 seconds 530 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 25 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_609260676108_000#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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.972 | 5.972 | 5.972 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2488.6242 0 -2488.6242 182743.95 133 0 -3454.5408 0 -3454.5408 5092.4009 Loop time of 4.417 on 1 procs for 133 steps with 1056 atoms 95.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2488.62417638286 -3454.53748305434 -3454.54083532631 Force two-norm initial, final = 2208.2542 0.16065658 Force max component initial, final = 650.55661 0.011002728 Final line search alpha, max atom move = 1.0000000 0.011002728 Iterations, force evaluations = 133 232 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3011 | 4.3011 | 4.3011 | 0.0 | 97.38 Neigh | 0.078005 | 0.078005 | 0.078005 | 0.0 | 1.77 Comm | 0.022492 | 0.022492 | 0.022492 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01542 | | | 0.35 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8822.00 ave 8822 max 8822 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: 335868.0 ave 335868 max 335868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335868 Ave neighs/atom = 318.05682 Neighbor list builds = 4 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 133 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.971 | 5.971 | 5.971 Mbytes Step Temp E_pair E_mol TotEng Press Volume 133 0 -3454.5408 0 -3454.5408 5092.4009 12722.762 139 0 -3454.7171 0 -3454.7171 55.900172 12767.334 Loop time of 0.165772 on 1 procs for 6 steps with 1056 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 = -3454.54083532637 -3454.71692047308 -3454.71706938661 Force two-norm initial, final = 84.054878 0.81334051 Force max component initial, final = 77.241287 0.55421880 Final line search alpha, max atom move = 0.00066198788 0.00036688613 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16218 | 0.16218 | 0.16218 | 0.0 | 97.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065164 | 0.00065164 | 0.00065164 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002936 | | | 1.77 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8655.00 ave 8655 max 8655 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: 335720.0 ave 335720 max 335720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335720 Ave neighs/atom = 317.91667 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.109 | 6.109 | 6.109 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3454.7171 0 -3454.7171 55.900172 Loop time of 2.166e-06 on 1 procs for 0 steps with 1056 atoms 184.7% 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 | | 2.166e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8663.00 ave 8663 max 8663 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: 335532.0 ave 335532 max 335532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335532 Ave neighs/atom = 317.73864 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.109 | 6.109 | 6.109 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 -3454.7171 -3454.7171 12.064601 118.83959 8.9048396 55.900172 55.900172 45.36113 52.861056 69.478329 2.2057608 422.99924 Loop time of 2.364e-06 on 1 procs for 0 steps with 1056 atoms 296.1% 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 | | 2.364e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8663.00 ave 8663 max 8663 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167766.0 ave 167766 max 167766 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 335532.0 ave 335532 max 335532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335532 Ave neighs/atom = 317.73864 Neighbor list builds = 0 Dangerous builds = 0 1056 -3454.71706938661 eV 2.20576083419004 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05