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 = 2.8147787 2.8147787 2.8147787 Created orthogonal box = (0.0000000 -36.483702 0.0000000) to (21.063875 36.483702 4.8753398) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5136876 4.3432979 4.8753398 Created 336 atoms using lattice units in orthogonal box = (0.0000000 -36.483702 0.0000000) to (21.063875 36.483702 4.8753398) create_atoms CPU = 0.002 seconds 336 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5136876 4.3432979 4.8753398 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -36.483702 0.0000000) to (21.063875 36.483702 4.8753398) create_atoms CPU = 0.002 seconds 339 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 672 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.925 | 4.925 | 4.925 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2591.0255 0 -2591.0255 73555.01 66 0 -2756.7892 0 -2756.7892 1850.3771 Loop time of 1.86298 on 1 procs for 66 steps with 672 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2591.02550022918 -2756.78661021374 -2756.78917924413 Force two-norm initial, final = 306.89977 0.25901901 Force max component initial, final = 67.877627 0.044296108 Final line search alpha, max atom move = 1.0000000 0.044296108 Iterations, force evaluations = 66 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8347 | 1.8347 | 1.8347 | 0.0 | 98.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015685 | 0.015685 | 0.015685 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01257 | | | 0.67 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4888.00 ave 4888 max 4888 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: 112224.0 ave 112224 max 112224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112224 Ave neighs/atom = 167.00000 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.926 | 4.926 | 4.926 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -2756.7892 0 -2756.7892 1850.3771 7493.2817 69 0 -2756.8042 0 -2756.8042 -1.469613 7500.2167 Loop time of 0.0994839 on 1 procs for 3 steps with 672 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2756.78917924413 -2756.80400887095 -2756.80416485492 Force two-norm initial, final = 21.366956 0.35054164 Force max component initial, final = 20.998244 0.13735438 Final line search alpha, max atom move = 0.00035629239 4.8938319e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.096606 | 0.096606 | 0.096606 | 0.0 | 97.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067707 | 0.00067707 | 0.00067707 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002201 | | | 2.21 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4941.00 ave 4941 max 4941 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: 111714.0 ave 111714 max 111714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111714 Ave neighs/atom = 166.24107 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.064 | 5.064 | 5.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2756.8042 0 -2756.8042 -1.469613 Loop time of 6.145e-06 on 1 procs for 0 steps with 672 atoms 179.0% 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 | | 6.145e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4941.00 ave 4941 max 4941 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: 111688.0 ave 111688 max 111688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111688 Ave neighs/atom = 166.20238 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.064 | 5.064 | 5.064 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 -2756.8042 -2756.8042 21.059471 73.076052 4.8736156 -1.469613 -1.469613 -24.085343 -9.6543986 29.330903 2.2763171 432.99685 Loop time of 6.706e-06 on 1 procs for 0 steps with 672 atoms 238.6% 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 | | 6.706e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4941.00 ave 4941 max 4941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55844.0 ave 55844 max 55844 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 111688.0 ave 111688 max 111688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111688 Ave neighs/atom = 166.20238 Neighbor list builds = 0 Dangerous builds = 0 672 -2756.80416485492 eV 2.27631705528095 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03