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 -34.882425 0.0000000) to (15.103198 34.882425 5.3397869) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0343993 4.3599177 5.3397869 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -34.882425 0.0000000) to (15.103198 34.882425 5.3397869) create_atoms CPU = 0.000 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0343993 4.3599177 5.3397869 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -34.882425 0.0000000) to (15.103198 34.882425 5.3397869) create_atoms CPU = 0.000 seconds 204 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 21 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 24 atoms, new total = 384 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_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 21 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) = 4.844 | 4.844 | 4.844 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2487.6114 0 -2487.6114 2937.2745 27 0 -2494.872 0 -2494.872 1053.3371 Loop time of 2.35182 on 1 procs for 27 steps with 384 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 = -2487.61142308935 -2494.87029886708 -2494.87199013042 Force two-norm initial, final = 7.3022670 0.16492180 Force max component initial, final = 1.4710929 0.016782384 Final line search alpha, max atom move = 1.0000000 0.016782384 Iterations, force evaluations = 27 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3501 | 2.3501 | 2.3501 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012568 | 0.0012568 | 0.0012568 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005073 | | | 0.02 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2752.00 ave 2752 max 2752 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: 25184.0 ave 25184 max 25184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25184 Ave neighs/atom = 65.583333 Neighbor list builds = 0 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 21 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.844 | 4.844 | 4.844 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -2494.872 0 -2494.872 1053.3371 5626.3856 30 0 -2494.9037 0 -2494.9037 1485.9153 5625.1308 Loop time of 0.356489 on 1 procs for 3 steps with 384 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 = -2494.87199013042 -2494.90367474871 -2494.90368315632 Force two-norm initial, final = 25.471064 0.46805145 Force max component initial, final = 18.265595 0.31784047 Final line search alpha, max atom move = 0.0073489983 0.0023358091 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35609 | 0.35609 | 0.35609 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.5e-05 | 9.5e-05 | 9.5e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003044 | | | 0.09 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2731.00 ave 2731 max 2731 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: 29840.0 ave 29840 max 29840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29840 Ave neighs/atom = 77.708333 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 21 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) = 4.981 | 4.981 | 4.981 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2494.9037 0 -2494.9037 1485.9153 Loop time of 2.3e-06 on 1 procs for 0 steps with 384 atoms 130.4% 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 | | 2.3e-06 | | |100.00 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2731.00 ave 2731 max 2731 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: 30000.0 ave 30000 max 30000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30000 Ave neighs/atom = 78.125000 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 21 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) = 4.981 | 4.981 | 4.981 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 -2494.9037 -2494.9037 15.074924 69.764849 5.3486087 1485.9153 1485.9153 -65.553197 4613.9775 -90.678397 2.647913 389.48617 Loop time of 2.2e-06 on 1 procs for 0 steps with 384 atoms 136.4% 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 | | 2.2e-06 | | |100.00 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2731.00 ave 2731 max 2731 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15000.0 ave 15000 max 15000 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30000.0 ave 30000 max 30000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30000 Ave neighs/atom = 78.125000 Neighbor list builds = 0 Dangerous builds = 0 384 -2494.90368315632 eV 2.64791304075593 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02