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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -71.219995 0.0000000) to (41.118883 71.219995 6.9836950) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3259820 6.3915380 6.9836950 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -71.219995 0.0000000) to (41.118883 71.219995 6.9836950) create_atoms CPU = 0.003 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3259820 6.3915380 6.9836950 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -71.219995 0.0000000) to (41.118883 71.219995 6.9836950) create_atoms CPU = 0.002 seconds 1250 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 10 33 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2496 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 6.521 | 6.521 | 6.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8224.8717 0 -8224.8717 7261.9064 151 0 -8366.6846 0 -8366.6846 4221.4539 Loop time of 5.94644 on 1 procs for 151 steps with 2496 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8224.87171105018 -8366.6772715103 -8366.68462032774 Force two-norm initial, final = 60.481770 0.22170515 Force max component initial, final = 9.3594499 0.035653247 Final line search alpha, max atom move = 1.0000000 0.035653247 Iterations, force evaluations = 151 279 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7683 | 5.7683 | 5.7683 | 0.0 | 97.00 Neigh | 0.11958 | 0.11958 | 0.11958 | 0.0 | 2.01 Comm | 0.028628 | 0.028628 | 0.028628 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02992 | | | 0.50 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10769.0 ave 10769 max 10769 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: 434528.0 ave 434528 max 434528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434528 Ave neighs/atom = 174.08974 Neighbor list builds = 5 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 151 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.520 | 6.520 | 6.520 Mbytes Step Temp E_pair E_mol TotEng Press Volume 151 0 -8366.6846 0 -8366.6846 4221.4539 40903.315 159 0 -8367.3737 0 -8367.3737 69.512171 41102.042 Loop time of 0.270518 on 1 procs for 8 steps with 2496 atoms 97.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8366.68462032774 -8367.3729902729 -8367.37372649078 Force two-norm initial, final = 225.73615 3.2121208 Force max component initial, final = 208.24534 2.3899368 Final line search alpha, max atom move = 0.00028681522 0.00068547027 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2362 | 0.2362 | 0.2362 | 0.0 | 87.31 Neigh | 0.026714 | 0.026714 | 0.026714 | 0.0 | 9.88 Comm | 0.0013462 | 0.0013462 | 0.0013462 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006262 | | | 2.31 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10727.0 ave 10727 max 10727 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: 434200.0 ave 434200 max 434200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434200 Ave neighs/atom = 173.95833 Neighbor list builds = 1 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 6.658 | 6.658 | 6.658 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8367.3737 0 -8367.3737 69.512171 Loop time of 2.436e-06 on 1 procs for 0 steps with 2496 atoms 205.3% 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 | | 2.436e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10721.0 ave 10721 max 10721 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: 434192.0 ave 434192 max 434192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434192 Ave neighs/atom = 173.95513 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 6.658 | 6.658 | 6.658 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 -8367.3737 -8367.3737 41.114972 143.46256 6.9682674 69.512171 69.512171 49.748019 93.829637 64.958858 2.6044707 1282.7264 Loop time of 3.078e-06 on 1 procs for 0 steps with 2496 atoms 259.9% 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 | | 3.078e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10721.0 ave 10721 max 10721 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 217096.0 ave 217096 max 217096 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 434192.0 ave 434192 max 434192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434192 Ave neighs/atom = 173.95513 Neighbor list builds = 0 Dangerous builds = 0 2496 -8367.3737264908 eV 2.60447073478769 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06