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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -46.564820 0.0000000) to (38.020017 46.564820 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6873993 4.4651197 5.1383093 Created 876 atoms using lattice units in orthogonal box = (0.0000000 -46.564820 0.0000000) to (38.020017 46.564820 7.7074639) create_atoms CPU = 0.002 seconds 876 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6873993 4.4651197 5.1383093 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -46.564820 0.0000000) to (38.020017 46.564820 7.7074639) create_atoms CPU = 0.001 seconds 878 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 33 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1752 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 5.037 | 5.037 | 5.037 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11748.605 0 -11748.605 25039.361 19 0 -13634.689 0 -13634.689 16811.937 Loop time of 7.70094 on 1 procs for 19 steps with 1752 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 = -11748.6048226159 -13634.6873470941 -13634.6888140126 Force two-norm initial, final = 46.374791 324.71879 Force max component initial, final = 5.7172542 102.35891 Final line search alpha, max atom move = 3.4216947e-08 3.5024095e-06 Iterations, force evaluations = 19 186 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6777 | 7.6777 | 7.6777 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010199 | 0.010199 | 0.010199 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01309 | | | 0.17 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4658.00 ave 4658 max 4658 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: 101108.0 ave 101108 max 101108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101108 Ave neighs/atom = 57.710046 Neighbor list builds = 0 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.037 | 5.037 | 5.037 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -13634.689 0 -13634.689 16811.937 27290.515 20 0 -13634.69 0 -13634.69 16636.796 27290.8 Loop time of 0.123788 on 1 procs for 1 steps with 1752 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 = -13634.6888140126 -13634.6888140126 -13634.6903803332 Force two-norm initial, final = 615.04441 1317.7859 Force max component initial, final = 415.74046 412.14895 Final line search alpha, max atom move = 2.4053468e-06 0.00099136117 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12293 | 0.12293 | 0.12293 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013162 | 0.00013162 | 0.00013162 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000726 | | | 0.59 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4667.00 ave 4667 max 4667 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: 100932.0 ave 100932 max 100932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100932 Ave neighs/atom = 57.609589 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 5.175 | 5.175 | 5.175 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13634.69 0 -13634.69 16636.796 Loop time of 2.468e-06 on 1 procs for 0 steps with 1752 atoms 202.6% 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 | | 2.468e-06 | | |100.00 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4667.00 ave 4667 max 4667 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: 100932.0 ave 100932 max 100932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100932 Ave neighs/atom = 57.609589 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 5.175 | 5.175 | 5.175 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 -13634.69 -13634.69 38.020106 93.130112 7.7074875 16636.796 16636.796 11220.881 24196.385 14493.12 0.0056880419 1157.4118 Loop time of 2.854e-06 on 1 procs for 0 steps with 1752 atoms 210.2% 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 | | 2.854e-06 | | |100.00 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50466.0 ave 50466 max 50466 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 100932.0 ave 100932 max 100932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100932 Ave neighs/atom = 57.609589 Neighbor list builds = 0 Dangerous builds = 0 1752 -13634.6903803332 eV 0.0056880419050223 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08