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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -40.902736 0.0000000) to (14.460211 40.902736 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2582586 4.6476879 4.3599177 Created 177 atoms using lattice units in orthogonal box = (0.0000000 -40.902736 0.0000000) to (14.460211 40.902736 4.3599177) create_atoms CPU = 0.001 seconds 177 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2582586 4.6476879 4.3599177 Created 177 atoms using lattice units in orthogonal box = (0.0000000 -40.902736 0.0000000) to (14.460211 40.902736 4.3599177) create_atoms CPU = 0.000 seconds 177 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 352 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_152208847456_001#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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.823 | 4.823 | 4.823 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2117.2403 0 -2117.2403 115633.5 95 0 -2280.9005 0 -2280.9005 7409.5843 Loop time of 16.091 on 1 procs for 95 steps with 352 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 = -2117.24033154965 -2280.89834091565 -2280.90048471816 Force two-norm initial, final = 417.10925 0.21420200 Force max component initial, final = 134.51436 0.075697904 Final line search alpha, max atom move = 1.0000000 0.075697904 Iterations, force evaluations = 95 180 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.07 | 16.07 | 16.07 | 0.0 | 99.87 Neigh | 0.013358 | 0.013358 | 0.013358 | 0.0 | 0.08 Comm | 0.0040758 | 0.0040758 | 0.0040758 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003269 | | | 0.02 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2788.00 ave 2788 max 2788 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: 25864.0 ave 25864 max 25864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25864 Ave neighs/atom = 73.477273 Neighbor list builds = 1 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.822 | 4.822 | 4.822 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -2280.9005 0 -2280.9005 7409.5843 5157.4531 102 0 -2281.1829 0 -2281.1829 1036.55 5171.8918 Loop time of 0.806891 on 1 procs for 7 steps with 352 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 = -2280.90048471816 -2281.18099608852 -2281.18288432365 Force two-norm initial, final = 79.790299 0.88779092 Force max component initial, final = 76.209310 0.28163082 Final line search alpha, max atom move = 0.00021172433 5.9628096e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.80591 | 0.80591 | 0.80591 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019714 | 0.00019714 | 0.00019714 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007849 | | | 0.10 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2780.00 ave 2780 max 2780 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: 26504.0 ave 26504 max 26504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26504 Ave neighs/atom = 75.295455 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.960 | 4.960 | 4.960 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2281.1829 0 -2281.1829 1036.55 Loop time of 1.62e-06 on 1 procs for 0 steps with 352 atoms 123.5% 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 | | 1.62e-06 | | |100.00 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2772.00 ave 2772 max 2772 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: 26516.0 ave 26516 max 26516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26516 Ave neighs/atom = 75.329545 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.960 | 4.960 | 4.960 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 -2281.1829 -2281.1829 14.55247 81.805473 4.3444056 1036.55 1036.55 59.755795 2962.9596 86.934703 2.4959804 803.40484 Loop time of 1.412e-06 on 1 procs for 0 steps with 352 atoms 212.5% 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 | | 1.412e-06 | | |100.00 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2772.00 ave 2772 max 2772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13258.0 ave 13258 max 13258 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26516.0 ave 26516 max 26516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26516 Ave neighs/atom = 75.329545 Neighbor list builds = 0 Dangerous builds = 0 352 -2281.18288432365 eV 2.49598044676777 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17