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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -39.439895 0.0000000) to (10.734180 39.439895 7.0271702) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6003628 4.3822106 4.6847802 Created 252 atoms using lattice units in orthogonal box = (0.0000000 -39.439895 0.0000000) to (10.734180 39.439895 7.0271702) create_atoms CPU = 0.001 seconds 252 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6003628 4.3822106 4.6847802 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -39.439895 0.0000000) to (10.734180 39.439895 7.0271702) create_atoms CPU = 0.001 seconds 254 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 16 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 504 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.006 | 5.006 | 5.006 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1818.918 0 -1818.918 73284.664 70 0 -2068.3717 0 -2068.3717 7223.9298 Loop time of 1.06781 on 1 procs for 70 steps with 504 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1818.91798205042 -2068.36991744787 -2068.37170404843 Force two-norm initial, final = 479.33480 0.18469554 Force max component initial, final = 153.98552 0.034474897 Final line search alpha, max atom move = 1.0000000 0.034474897 Iterations, force evaluations = 70 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0432 | 1.0432 | 1.0432 | 0.0 | 97.69 Neigh | 0.011539 | 0.011539 | 0.011539 | 0.0 | 1.08 Comm | 0.0083749 | 0.0083749 | 0.0083749 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004701 | | | 0.44 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6871.00 ave 6871 max 6871 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: 195176.0 ave 195176 max 195176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195176 Ave neighs/atom = 387.25397 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.006 | 5.006 | 5.006 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -2068.3717 0 -2068.3717 7223.9298 5949.9743 75 0 -2068.4723 0 -2068.4723 33.476346 5975.0528 Loop time of 0.0544655 on 1 procs for 5 steps with 504 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 = -2068.37170404843 -2068.47225584081 -2068.47231646759 Force two-norm initial, final = 53.226928 0.37786848 Force max component initial, final = 46.500704 0.20630883 Final line search alpha, max atom move = 0.0012940259 0.00026696897 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.052546 | 0.052546 | 0.052546 | 0.0 | 96.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038244 | 0.00038244 | 0.00038244 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001537 | | | 2.82 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6832.00 ave 6832 max 6832 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: 195816.0 ave 195816 max 195816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195816 Ave neighs/atom = 388.52381 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.144 | 5.144 | 5.144 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2068.4723 0 -2068.4723 33.476346 Loop time of 2.168e-06 on 1 procs for 0 steps with 504 atoms 184.5% 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 | | 2.168e-06 | | |100.00 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6836.00 ave 6836 max 6836 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: 193724.0 ave 193724 max 193724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193724 Ave neighs/atom = 384.37302 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.144 | 5.144 | 5.144 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 -2068.4723 -2068.4723 10.742601 79.200661 7.0226897 33.476346 33.476346 55.363943 42.857603 2.2074915 2.2954926 493.95765 Loop time of 1.591e-06 on 1 procs for 0 steps with 504 atoms 188.6% 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 | | 1.591e-06 | | |100.00 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6836.00 ave 6836 max 6836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96862.0 ave 96862 max 96862 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 193724.0 ave 193724 max 193724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193724 Ave neighs/atom = 384.37302 Neighbor list builds = 0 Dangerous builds = 0 504 -2068.47231646759 eV 2.29549263396065 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01