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 = 3.6583664 3.6583664 3.6583664 Created orthogonal box = (0.0000000 -40.075396 0.0000000) to (8.1803559 40.075396 8.9611309) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9082136 5.3433861 5.9740873 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -40.075396 0.0000000) to (8.1803559 40.075396 8.9611309) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9082136 5.3433861 5.9740873 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -40.075396 0.0000000) to (8.1803559 40.075396 8.9611309) create_atoms CPU = 0.000 seconds 242 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 22 3 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 482 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_807997826449_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1780.6724 0 -1780.6724 96835.848 228 0 -1932.6296 0 -1932.6296 -76471.805 Loop time of 1.60294 on 1 procs for 228 steps with 482 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1780.67240588217 -1932.62853397586 -1932.6295726783 Force two-norm initial, final = 328.49857 0.094605881 Force max component initial, final = 100.93597 0.011459764 Final line search alpha, max atom move = 1.0000000 0.011459764 Iterations, force evaluations = 228 446 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5681 | 1.5681 | 1.5681 | 0.0 | 97.83 Neigh | 0.0096021 | 0.0096021 | 0.0096021 | 0.0 | 0.60 Comm | 0.014049 | 0.014049 | 0.014049 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01114 | | | 0.70 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3634.00 ave 3634 max 3634 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: 66336.0 ave 66336 max 66336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66336 Ave neighs/atom = 137.62656 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 228 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press Volume 228 0 -1932.6296 0 -1932.6296 -76471.805 5875.4731 275 0 -1941.6884 0 -1941.6884 156.76386 5560.0122 Loop time of 0.223005 on 1 procs for 47 steps with 482 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 = -1932.6295726783 -1941.68781008421 -1941.68836323264 Force two-norm initial, final = 492.51666 2.5778834 Force max component initial, final = 314.63359 1.6739765 Final line search alpha, max atom move = 0.00083005392 0.0013894907 Iterations, force evaluations = 47 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21279 | 0.21279 | 0.21279 | 0.0 | 95.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016709 | 0.0016709 | 0.0016709 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008549 | | | 3.83 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3641.00 ave 3641 max 3641 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: 66308.0 ave 66308 max 66308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66308 Ave neighs/atom = 137.56846 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.654 | 4.654 | 4.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1941.6884 0 -1941.6884 156.76386 Loop time of 1.744e-06 on 1 procs for 0 steps with 482 atoms 114.7% 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 | | 1.744e-06 | | |100.00 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3862.00 ave 3862 max 3862 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: 69332.0 ave 69332 max 69332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69332 Ave neighs/atom = 143.84232 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.654 | 4.654 | 4.654 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 -1941.6884 -1941.6884 7.9932913 79.953765 8.6998383 156.76386 156.76386 471.34337 -241.41734 240.36554 2.291168 2078.0851 Loop time of 2.16e-06 on 1 procs for 0 steps with 482 atoms 231.5% 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 | | 2.16e-06 | | |100.00 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3862.00 ave 3862 max 3862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34666.0 ave 34666 max 34666 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69332.0 ave 69332 max 69332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69332 Ave neighs/atom = 143.84232 Neighbor list builds = 0 Dangerous builds = 0 482 -1941.68836323264 eV 2.29116798679599 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02