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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -58.376981 0.0000000) to (29.188491 58.376981 3.6203867) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9395907 4.9395907 3.6203867 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.376981 0.0000000) to (29.188491 58.376981 3.6203867) create_atoms CPU = 0.003 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9395907 4.9395907 3.6203867 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.376981 0.0000000) to (29.188491 58.376981 3.6203867) create_atoms CPU = 0.002 seconds 522 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 ghost atom cutoff = 6 binsize = 3, bins = 10 39 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1042 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_390178379548_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 ghost atom cutoff = 6 binsize = 3, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.607 | 4.607 | 4.607 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3518.8722 0 -3518.8722 43441.317 66 0 -3677.4765 0 -3677.4765 9323.0616 Loop time of 5.28126 on 1 procs for 66 steps with 1042 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 = -3518.87224946456 -3677.4728773127 -3677.47649352599 Force two-norm initial, final = 193.63614 0.19328494 Force max component initial, final = 38.001708 0.037189526 Final line search alpha, max atom move = 1.0000000 0.037189526 Iterations, force evaluations = 66 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2465 | 5.2465 | 5.2465 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018575 | 0.018575 | 0.018575 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01616 | | | 0.31 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6229.00 ave 6229 max 6229 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: 81312.0 ave 81312 max 81312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81312 Ave neighs/atom = 78.034549 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 ghost atom cutoff = 6 binsize = 3, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.601 | 4.601 | 4.601 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -3677.4765 0 -3677.4765 9323.0616 12337.814 76 0 -3677.9886 0 -3677.9886 -69.623954 12417.771 Loop time of 0.516924 on 1 procs for 10 steps with 1042 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 = -3677.47649352599 -3677.98769719984 -3677.9886428288 Force two-norm initial, final = 144.68835 1.7761789 Force max component initial, final = 130.69398 1.2739911 Final line search alpha, max atom move = 0.00045976518 0.00058573675 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49744 | 0.49744 | 0.49744 | 0.0 | 96.23 Neigh | 0.01194 | 0.01194 | 0.01194 | 0.0 | 2.31 Comm | 0.0017791 | 0.0017791 | 0.0017791 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005761 | | | 1.11 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5442.00 ave 5442 max 5442 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: 80576.0 ave 80576 max 80576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80576 Ave neighs/atom = 77.328215 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.739 | 4.739 | 4.739 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3677.9886 0 -3677.9886 -69.623954 Loop time of 6.445e-06 on 1 procs for 0 steps with 1042 atoms 186.2% 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 | | 6.445e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5442.00 ave 5442 max 5442 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: 80572.0 ave 80572 max 80572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80572 Ave neighs/atom = 77.324376 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 ghost atom cutoff = 6 binsize = 3, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.739 | 4.739 | 4.739 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 -3677.9886 -3677.9886 29.178925 117.78016 3.6132849 -69.623954 -69.623954 -164.32012 80.317292 -124.86903 2.3127067 455.37905 Loop time of 6.906e-06 on 1 procs for 0 steps with 1042 atoms 246.2% 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 | | 6.906e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5442.00 ave 5442 max 5442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40286.0 ave 40286 max 40286 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80572.0 ave 80572 max 80572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80572 Ave neighs/atom = 77.324376 Neighbor list builds = 0 Dangerous builds = 0 1042 -3677.9886428288 eV 2.31270671456544 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06