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 = 4.0499990 4.0499990 4.0499990 Created orthogonal box = (0.0000000 -49.270364 0.0000000) to (24.635182 49.270364 4.0499990) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6607101 4.6607101 4.0499990 Created 296 atoms using lattice units in orthogonal box = (0.0000000 -49.270364 0.0000000) to (24.635182 49.270364 4.0499990) create_atoms CPU = 0.001 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6607101 4.6607101 4.0499990 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -49.270364 0.0000000) to (24.635182 49.270364 4.0499990) create_atoms CPU = 0.000 seconds 298 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 ghost atom cutoff = 8 binsize = 4, bins = 7 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, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 592 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_093637366498_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.518 | 4.518 | 4.518 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1780.3234 0 -1780.3234 37172.495 80 0 -1981.6054 0 -1981.6054 4071.2689 Loop time of 7.55337 on 1 procs for 80 steps with 592 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1780.32343966089 -1981.60399500745 -1981.60538239838 Force two-norm initial, final = 262.13709 0.094347973 Force max component initial, final = 76.260833 0.017661948 Final line search alpha, max atom move = 1.0000000 0.017661948 Iterations, force evaluations = 80 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5307 | 7.5307 | 7.5307 | 0.0 | 99.70 Neigh | 0.0048552 | 0.0048552 | 0.0048552 | 0.0 | 0.06 Comm | 0.0099312 | 0.0099312 | 0.0099312 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007933 | | | 0.11 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5073.00 ave 5073 max 5073 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: 78828.0 ave 78828 max 78828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78828 Ave neighs/atom = 133.15541 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -1981.6054 0 -1981.6054 4071.2689 9831.6513 88 0 -1981.7707 0 -1981.7707 48.56936 9880.555 Loop time of 0.500494 on 1 procs for 8 steps with 592 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 = -1981.60538239838 -1981.7692992768 -1981.77074933848 Force two-norm initial, final = 50.856843 0.55759972 Force max component initial, final = 45.721901 0.32156348 Final line search alpha, max atom move = 0.00042128994 0.00013547146 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49794 | 0.49794 | 0.49794 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041372 | 0.00041372 | 0.00041372 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002144 | | | 0.43 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5068.00 ave 5068 max 5068 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: 78832.0 ave 78832 max 78832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78832 Ave neighs/atom = 133.16216 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 ghost atom cutoff = 8 binsize = 4, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.655 | 4.655 | 4.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1981.7707 0 -1981.7707 48.56936 Loop time of 2.464e-06 on 1 procs for 0 steps with 592 atoms 162.3% 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 | | 2.464e-06 | | |100.00 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5068.00 ave 5068 max 5068 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: 78728.0 ave 78728 max 78728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78728 Ave neighs/atom = 132.98649 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 ghost atom cutoff = 8 binsize = 4, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.655 | 4.655 | 4.655 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 -1981.7707 -1981.7707 24.642496 99.299398 4.0378485 48.56936 48.56936 41.489775 52.231773 51.986532 2.6158246 244.16777 Loop time of 2.748e-06 on 1 procs for 0 steps with 592 atoms 145.6% 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 | | 2.748e-06 | | |100.00 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5068.00 ave 5068 max 5068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39364.0 ave 39364 max 39364 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78728.0 ave 78728 max 78728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78728 Ave neighs/atom = 132.98649 Neighbor list builds = 0 Dangerous builds = 0 592 -1981.77074933848 eV 2.61582463437541 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08