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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -57.625105 0.0000000) to (40.747102 57.625105 4.9780508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0816571 5.5904952 4.9780508 Created 1071 atoms using lattice units in orthogonal box = (0.0000000 -57.625105 0.0000000) to (40.747102 57.625105 4.9780508) create_atoms CPU = 0.003 seconds 1071 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0816571 5.5904952 4.9780508 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -57.625105 0.0000000) to (40.747102 57.625105 4.9780508) create_atoms CPU = 0.002 seconds 1079 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 = 10 28 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 6 atoms, new total = 2144 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 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) = 6.486 | 6.486 | 6.486 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9419.3535 0 -9419.3535 3727.1113 74 0 -9515.723 0 -9515.723 4807.5593 Loop time of 3.2692 on 1 procs for 74 steps with 2144 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9419.35351092763 -9515.71487010787 -9515.72300618543 Force two-norm initial, final = 31.421343 0.28841092 Force max component initial, final = 4.4240421 0.037402993 Final line search alpha, max atom move = 1.0000000 0.037402993 Iterations, force evaluations = 74 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1718 | 3.1718 | 3.1718 | 0.0 | 97.02 Neigh | 0.058807 | 0.058807 | 0.058807 | 0.0 | 1.80 Comm | 0.021137 | 0.021137 | 0.021137 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01745 | | | 0.53 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13507.0 ave 13507 max 13507 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: 481780.0 ave 481780 max 481780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 481780 Ave neighs/atom = 224.71082 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 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 : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.486 | 6.486 | 6.486 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -9515.723 0 -9515.723 4807.5593 23377.485 76 0 -9515.8239 0 -9515.8239 -203.87791 23443.024 Loop time of 0.101977 on 1 procs for 2 steps with 2144 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 = -9515.72300618541 -9515.82057693987 -9515.82394111224 Force two-norm initial, final = 123.66209 7.3954550 Force max component initial, final = 88.649210 6.2433483 Final line search alpha, max atom move = 5.2459425e-05 0.00032752246 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.09957 | 0.09957 | 0.09957 | 0.0 | 97.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042425 | 0.00042425 | 0.00042425 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001983 | | | 1.94 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13516.0 ave 13516 max 13516 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: 482788.0 ave 482788 max 482788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 482788 Ave neighs/atom = 225.18097 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 = 10 28 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) = 6.624 | 6.624 | 6.624 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9515.8239 0 -9515.8239 -203.87791 Loop time of 2.516e-06 on 1 procs for 0 steps with 2144 atoms 159.0% 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 | | 2.516e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13516.0 ave 13516 max 13516 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: 482242.0 ave 482242 max 482242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 482242 Ave neighs/atom = 224.92631 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 = 10 28 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) = 6.624 | 6.624 | 6.624 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 -9515.8239 -9515.8239 40.801454 115.32705 4.9820354 -203.87791 -203.87791 75.096396 -426.97628 -259.75386 2.3227637 861.12345 Loop time of 2.649e-06 on 1 procs for 0 steps with 2144 atoms 226.5% 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 | | 2.649e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13516.0 ave 13516 max 13516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 241121.0 ave 241121 max 241121 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 482242.0 ave 482242 max 482242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 482242 Ave neighs/atom = 224.92631 Neighbor list builds = 0 Dangerous builds = 0 2144 -9457.375495756 eV 2.32276368229965 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04