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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -57.279629 0.0000000) to (40.500340 57.279629 4.9479041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0448269 5.5566395 4.9479041 Created 1077 atoms using lattice units in orthogonal box = (0.0000000 -57.279629 0.0000000) to (40.500340 57.279629 4.9479041) create_atoms CPU = 0.002 seconds 1077 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0448269 5.5566395 4.9479041 Created 1077 atoms using lattice units in orthogonal box = (0.0000000 -57.279629 0.0000000) to (40.500340 57.279629 4.9479041) create_atoms CPU = 0.002 seconds 1077 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 31 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2128 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.049 | 6.049 | 6.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8700.9732 0 -8700.9732 7382.9528 43 0 -8739.0342 0 -8739.0342 -6337.5493 Loop time of 1.40689 on 1 procs for 43 steps with 2128 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8700.9732180005 -8739.02602108295 -8739.03421171484 Force two-norm initial, final = 44.740543 0.31773947 Force max component initial, final = 11.278123 0.042644546 Final line search alpha, max atom move = 1.0000000 0.042644546 Iterations, force evaluations = 43 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3712 | 1.3712 | 1.3712 | 0.0 | 97.47 Neigh | 0.020185 | 0.020185 | 0.020185 | 0.0 | 1.43 Comm | 0.007975 | 0.007975 | 0.007975 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007503 | | | 0.53 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11040.0 ave 11040 max 11040 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: 371304.0 ave 371304 max 371304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 371304 Ave neighs/atom = 174.48496 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.049 | 6.049 | 6.049 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -8739.0342 0 -8739.0342 -6337.5493 22956.736 46 0 -8739.1319 0 -8739.1319 -3016.012 22889.047 Loop time of 0.0914036 on 1 procs for 3 steps with 2128 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 = -8739.03421171485 -8739.13123134361 -8739.13188838097 Force two-norm initial, final = 85.212754 0.43682001 Force max component initial, final = 75.095611 0.17776071 Final line search alpha, max atom move = 0.00020942605 3.7227722e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.089144 | 0.089144 | 0.089144 | 0.0 | 97.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040861 | 0.00040861 | 0.00040861 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001851 | | | 2.03 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11096.0 ave 11096 max 11096 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: 371876.0 ave 371876 max 371876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 371876 Ave neighs/atom = 174.75376 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.187 | 6.187 | 6.187 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8739.1319 0 -8739.1319 -3016.012 Loop time of 1.865e-06 on 1 procs for 0 steps with 2128 atoms 160.9% 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 | | 1.865e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11096.0 ave 11096 max 11096 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: 372080.0 ave 372080 max 372080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 372080 Ave neighs/atom = 174.84962 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.187 | 6.187 | 6.187 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 -8739.1319 -8739.1319 40.46831 114.55926 4.9372196 -3016.012 -3016.012 -12.432968 -9025.1692 -10.433758 2.2898163 725.05872 Loop time of 2.416e-06 on 1 procs for 0 steps with 2128 atoms 289.7% 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 | | 2.416e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11096.0 ave 11096 max 11096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 186040.0 ave 186040 max 186040 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 372080.0 ave 372080 max 372080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 372080 Ave neighs/atom = 174.84962 Neighbor list builds = 0 Dangerous builds = 0 2128 -8739.13188838097 eV 2.28981633951534 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01