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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -53.593983 0.0000000) to (32.819478 53.593983 9.8954449) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9671778 6.0902253 6.5969632 Created 1051 atoms using lattice units in orthogonal box = (0.0000000 -53.593983 0.0000000) to (32.819478 53.593983 9.8954449) create_atoms CPU = 0.002 seconds 1051 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9671778 6.0902253 6.5969632 Created 1075 atoms using lattice units in orthogonal box = (0.0000000 -53.593983 0.0000000) to (32.819478 53.593983 9.8954449) create_atoms CPU = 0.002 seconds 1075 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 6 19 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2112 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_279544746097_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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 6 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 8.489 | 8.489 | 8.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6069.6693 0 -6069.6693 2310.4028 19 0 -6086.9951 0 -6086.9951 1029.9858 Loop time of 1.17785 on 1 procs for 19 steps with 2112 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6069.66926060597 -6086.98952671436 -6086.9950527206 Force two-norm initial, final = 21.487684 0.21651523 Force max component initial, final = 4.8613856 0.011433825 Final line search alpha, max atom move = 1.0000000 0.011433825 Iterations, force evaluations = 19 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.167 | 1.167 | 1.167 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058102 | 0.0058102 | 0.0058102 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00499 | | | 0.42 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12553.0 ave 12553 max 12553 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: 902066.0 ave 902066 max 902066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 902066 Ave neighs/atom = 427.11458 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 6 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 8.490 | 8.490 | 8.490 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -6086.9951 0 -6086.9951 1029.9858 34810.721 25 0 -6087.2824 0 -6087.2824 6.9755099 34856.375 Loop time of 0.304297 on 1 procs for 6 steps with 2112 atoms 95.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6086.99505272059 -6087.28243876524 -6087.28244438134 Force two-norm initial, final = 103.37490 0.38987417 Force max component initial, final = 94.114085 0.19465468 Final line search alpha, max atom move = 0.0020690047 0.00040274145 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29914 | 0.29914 | 0.29914 | 0.0 | 98.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089803 | 0.00089803 | 0.00089803 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00426 | | | 1.40 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12583.0 ave 12583 max 12583 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: 886786.0 ave 886786 max 886786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 886786 Ave neighs/atom = 419.87973 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 8.246 | 8.246 | 8.246 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6087.2824 0 -6087.2824 6.9755099 Loop time of 2.173e-06 on 1 procs for 0 steps with 2112 atoms 184.1% 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 | | 2.173e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12613.0 ave 12613 max 12613 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: 869518.0 ave 869518 max 869518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 869518 Ave neighs/atom = 411.70360 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 8.246 | 8.246 | 8.246 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 -6087.2824 -6087.2824 32.714387 107.69743 9.8932294 6.9755099 6.9755099 8.9186705 7.1899772 4.8178821 2.7271797 556.89752 Loop time of 2.274e-06 on 1 procs for 0 steps with 2112 atoms 307.8% 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 | | 2.274e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12613.0 ave 12613 max 12613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 434759.0 ave 434759 max 434759 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 869518.0 ave 869518 max 869518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 869518 Ave neighs/atom = 411.70360 Neighbor list builds = 0 Dangerous builds = 0 2112 -6087.28244438134 eV 2.7271797494122 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02