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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -76.318363 0.0000000) to (38.157159 76.318363 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5735177 5.5735177 4.0446508 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -76.318363 0.0000000) to (38.157159 76.318363 4.0446508) create_atoms CPU = 0.003 seconds 714 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5735177 5.5735177 4.0446508 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -76.318363 0.0000000) to (38.157159 76.318363 4.0446508) create_atoms CPU = 0.002 seconds 714 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 12 46 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 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1416 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_127847080751_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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 12 46 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.069 | 5.069 | 5.069 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4730.6846 0 -4730.6846 2260.144 69 0 -4747.5528 0 -4747.5528 -1754.7815 Loop time of 14.7548 on 1 procs for 69 steps with 1416 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 = -4730.68458877216 -4747.54820467434 -4747.55276925448 Force two-norm initial, final = 19.320692 0.17417431 Force max component initial, final = 4.8407891 0.035015690 Final line search alpha, max atom move = 1.0000000 0.035015690 Iterations, force evaluations = 69 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.696 | 14.696 | 14.696 | 0.0 | 99.60 Neigh | 0.015861 | 0.015861 | 0.015861 | 0.0 | 0.11 Comm | 0.021085 | 0.021085 | 0.021085 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02156 | | | 0.15 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6908.00 ave 6908 max 6908 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: 109684.0 ave 109684 max 109684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109684 Ave neighs/atom = 77.460452 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 12 46 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.069 | 5.069 | 5.069 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -4747.5528 0 -4747.5528 -1754.7815 23556.79 71 0 -4747.5875 0 -4747.5875 81.813204 23501.676 Loop time of 0.450893 on 1 procs for 2 steps with 1416 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 = -4747.55276925448 -4747.58542677947 -4747.58746615904 Force two-norm initial, final = 41.899756 2.9823237 Force max component initial, final = 32.771989 2.7834316 Final line search alpha, max atom move = 0.00011101572 0.00030900467 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44832 | 0.44832 | 0.44832 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060636 | 0.00060636 | 0.00060636 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001966 | | | 0.44 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6880.00 ave 6880 max 6880 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: 109612.0 ave 109612 max 109612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109612 Ave neighs/atom = 77.409605 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 12 46 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.207 | 5.207 | 5.207 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4747.5875 0 -4747.5875 81.813204 Loop time of 6.044e-06 on 1 procs for 0 steps with 1416 atoms 182.0% 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 | | 6.044e-06 | | |100.00 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6880.00 ave 6880 max 6880 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: 109624.0 ave 109624 max 109624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109624 Ave neighs/atom = 77.418079 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 12 46 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.207 | 5.207 | 5.207 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 -4747.5875 -4747.5875 38.121113 152.63673 4.0390035 81.813204 81.813204 189.57524 127.81996 -71.955591 2.5263706 568.62061 Loop time of 6.706e-06 on 1 procs for 0 steps with 1416 atoms 298.2% 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: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6880.00 ave 6880 max 6880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54812.0 ave 54812 max 54812 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109624.0 ave 109624 max 109624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109624 Ave neighs/atom = 77.418079 Neighbor list builds = 0 Dangerous builds = 0 1416 -4747.58746615904 eV 2.52637058815435 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16