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 = 3.3901167 3.3901167 3.3901167 Created orthogonal box = (0.0000000 -41.933427 0.0000000) to (19.767607 41.933427 4.7943490) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8140021 5.7555684 4.7943490 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -41.933427 0.0000000) to (19.767607 41.933427 4.7943490) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8140021 5.7555684 4.7943490 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -41.933427 0.0000000) to (19.767607 41.933427 4.7943490) create_atoms CPU = 0.001 seconds 206 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 9 1 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 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_959249795837_003#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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 9 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 11.31 | 11.31 | 11.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 999094.14 0 999094.14 8.2080953e+08 245 0 -14902.623 0 -14902.623 -248651.12 Loop time of 4.6135 on 1 procs for 245 steps with 408 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 999094.139077257 -14902.6101832986 -14902.6231234699 Force two-norm initial, final = 6970456.8 1.9102750 Force max component initial, final = 2457895.7 0.46103021 Final line search alpha, max atom move = 0.16943888 0.078116444 Iterations, force evaluations = 245 453 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2302 | 4.2302 | 4.2302 | 0.0 | 91.69 Neigh | 0.27556 | 0.27556 | 0.27556 | 0.0 | 5.97 Comm | 0.08289 | 0.08289 | 0.08289 | 0.0 | 1.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02485 | | | 0.54 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17367.0 ave 17367 max 17367 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: 753510.0 ave 753510 max 753510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 753510 Ave neighs/atom = 1846.8382 Neighbor list builds = 8 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 9 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 245 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.31 | 11.31 | 11.31 Mbytes Step Temp E_pair E_mol TotEng Press Volume 245 0 -14902.623 0 -14902.623 -248651.12 7948.2972 273 0 -14981.378 0 -14981.378 27329.186 7832.1643 Loop time of 0.349731 on 1 procs for 28 steps with 408 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 = -14902.6231234699 -14981.3639541778 -14981.3779374342 Force two-norm initial, final = 5089.0830 254.75423 Force max component initial, final = 3862.3830 217.84235 Final line search alpha, max atom move = 2.8974607e-06 0.00063118967 Iterations, force evaluations = 28 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29726 | 0.29726 | 0.29726 | 0.0 | 85.00 Neigh | 0.032683 | 0.032683 | 0.032683 | 0.0 | 9.35 Comm | 0.0044759 | 0.0044759 | 0.0044759 | 0.0 | 1.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01531 | | | 4.38 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17517.0 ave 17517 max 17517 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: 762978.0 ave 762978 max 762978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 762978 Ave neighs/atom = 1870.0441 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 8 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 10.83 | 10.83 | 10.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14981.378 0 -14981.378 27329.186 Loop time of 2.108e-06 on 1 procs for 0 steps with 408 atoms 142.3% 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 | | 2.108e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17547.0 ave 17547 max 17547 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: 769690.0 ave 769690 max 769690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 769690 Ave neighs/atom = 1886.4951 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 8 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 10.83 | 10.83 | 10.83 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 -14981.378 -14981.378 19.607759 81.947549 4.8743629 27329.186 27329.186 15372.703 21308.503 45306.353 2.7902453 3577.5849 Loop time of 2.168e-06 on 1 procs for 0 steps with 408 atoms 276.8% 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 | | 2.168e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17547.0 ave 17547 max 17547 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 384845.0 ave 384845 max 384845 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 769690.0 ave 769690 max 769690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 769690 Ave neighs/atom = 1886.4951 Neighbor list builds = 0 Dangerous builds = 0 408 -14981.3779374343 eV 2.79024526391321 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05