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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -81.107206 0.0000000) to (46.827267 81.107206 7.0065955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2902300 6.4562950 7.0065955 Created 1607 atoms using lattice units in orthogonal box = (0.0000000 -81.107206 0.0000000) to (46.827267 81.107206 7.0065955) create_atoms CPU = 0.010 seconds 1607 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2902300 6.4562950 7.0065955 Created 1609 atoms using lattice units in orthogonal box = (0.0000000 -81.107206 0.0000000) to (46.827267 81.107206 7.0065955) create_atoms CPU = 0.011 seconds 1609 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 39 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3216 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_106969701023_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.666 | 6.666 | 6.666 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10753.017 0 -10753.017 12786.344 119 0 -10946.254 0 -10946.254 3638.3393 Loop time of 11.857 on 1 procs for 119 steps with 3216 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 = -10753.0171943118 -10946.2433935137 -10946.2542339958 Force two-norm initial, final = 165.71991 0.22291418 Force max component initial, final = 25.386232 0.040019100 Final line search alpha, max atom move = 1.0000000 0.040019100 Iterations, force evaluations = 119 191 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.317 | 11.317 | 11.317 | 0.0 | 95.44 Neigh | 0.40163 | 0.40163 | 0.40163 | 0.0 | 3.39 Comm | 0.068377 | 0.068377 | 0.068377 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07037 | | | 0.59 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12906.0 ave 12906 max 12906 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: 453098.0 ave 453098 max 453098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 453098 Ave neighs/atom = 140.88868 Neighbor list builds = 6 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.666 | 6.666 | 6.666 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -10946.254 0 -10946.254 3638.3393 53222.503 125 0 -10946.788 0 -10946.788 -165.5966 53473.364 Loop time of 0.472831 on 1 procs for 6 steps with 3216 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 = -10946.2542339958 -10946.7842459851 -10946.7875720526 Force two-norm initial, final = 235.66593 10.922581 Force max component initial, final = 208.75083 7.9574634 Final line search alpha, max atom move = 6.6898150e-05 0.00053233958 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46137 | 0.46137 | 0.46137 | 0.0 | 97.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024115 | 0.0024115 | 0.0024115 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00905 | | | 1.91 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12902.0 ave 12902 max 12902 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: 452870.0 ave 452870 max 452870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452870 Ave neighs/atom = 140.81779 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.803 | 6.803 | 6.803 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10946.788 0 -10946.788 -165.5966 Loop time of 6.706e-06 on 1 procs for 0 steps with 3216 atoms 208.8% 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 | | 6.706e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12902.0 ave 12902 max 12902 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: 452178.0 ave 452178 max 452178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452178 Ave neighs/atom = 140.60261 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.803 | 6.803 | 6.803 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 -10946.788 -10946.788 46.822682 163.09722 7.0022024 -165.5966 -165.5966 -238.3993 -37.702759 -220.68775 2.4877481 1279.2778 Loop time of 6.786e-06 on 1 procs for 0 steps with 3216 atoms 294.7% 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 | | 6.786e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12902.0 ave 12902 max 12902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 226089.0 ave 226089 max 226089 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 452178.0 ave 452178 max 452178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452178 Ave neighs/atom = 140.60261 Neighbor list builds = 0 Dangerous builds = 0 3216 -10946.7875720526 eV 2.48774810093286 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13