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 -37.359355 0.0000000) to (26.414579 37.359355 4.9479041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0243778 5.8982931 4.9479041 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.359355 0.0000000) to (26.414579 37.359355 4.9479041) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0243778 5.8982931 4.9479041 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.359355 0.0000000) to (26.414579 37.359355 4.9479041) create_atoms CPU = 0.001 seconds 458 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 = 7 20 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 12 atoms, new total = 904 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 = 7 20 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) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3639.1964 0 -3639.1964 39563.775 48 0 -3706.4653 0 -3706.4653 -9379.8342 Loop time of 0.670953 on 1 procs for 48 steps with 904 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 = -3639.19638695738 -3706.46212050898 -3706.46533696043 Force two-norm initial, final = 127.65577 0.28019705 Force max component initial, final = 43.556002 0.057142993 Final line search alpha, max atom move = 1.0000000 0.057142993 Iterations, force evaluations = 48 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65386 | 0.65386 | 0.65386 | 0.0 | 97.45 Neigh | 0.0093976 | 0.0093976 | 0.0093976 | 0.0 | 1.40 Comm | 0.0044034 | 0.0044034 | 0.0044034 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003295 | | | 0.49 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6356.00 ave 6356 max 6356 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: 157256.0 ave 157256 max 157256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157256 Ave neighs/atom = 173.95575 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 = 7 20 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 : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -3706.4653 0 -3706.4653 -9379.8342 9765.4968 51 0 -3706.5147 0 -3706.5147 -5483.0371 9734.0014 Loop time of 0.0472988 on 1 procs for 3 steps with 904 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 = -3706.46533696043 -3706.51467137034 -3706.51470046055 Force two-norm initial, final = 43.049158 0.38204400 Force max component initial, final = 32.707746 0.12339457 Final line search alpha, max atom move = 0.0019638775 0.00024233181 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.045916 | 0.045916 | 0.045916 | 0.0 | 97.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028106 | 0.00028106 | 0.00028106 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001102 | | | 2.33 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6372.00 ave 6372 max 6372 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: 157428.0 ave 157428 max 157428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157428 Ave neighs/atom = 174.14602 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 = 7 20 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) = 5.132 | 5.132 | 5.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3706.5147 0 -3706.5147 -5483.0371 Loop time of 1.706e-06 on 1 procs for 0 steps with 904 atoms 175.8% 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 | | 1.706e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6372.00 ave 6372 max 6372 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: 157480.0 ave 157480 max 157480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157480 Ave neighs/atom = 174.20354 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 = 7 20 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) = 5.132 | 5.132 | 5.132 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 -3706.5147 -3706.5147 26.370506 74.718711 4.9401892 -5483.0371 -5483.0371 -20.276348 -16448.906 20.071464 2.2685411 661.85436 Loop time of 2.035e-06 on 1 procs for 0 steps with 904 atoms 196.6% 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 | | 2.035e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6372.00 ave 6372 max 6372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78740.0 ave 78740 max 78740 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 157480.0 ave 157480 max 157480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157480 Ave neighs/atom = 174.20354 Neighbor list builds = 0 Dangerous builds = 0 904 -3706.51470046055 eV 2.26854105982078 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01