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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -33.438491 0.0000000) to (23.644584 33.438491 4.0851619) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5877551 4.9908196 4.0851619 Created 268 atoms using lattice units in orthogonal box = (0.0000000 -33.438491 0.0000000) to (23.644584 33.438491 4.0851619) create_atoms CPU = 0.001 seconds 268 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5877551 4.9908196 4.0851619 Created 270 atoms using lattice units in orthogonal box = (0.0000000 -33.438491 0.0000000) to (23.644584 33.438491 4.0851619) create_atoms CPU = 0.001 seconds 270 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 26 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 538 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.840 | 4.840 | 4.840 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2061.1909 0 -2061.1909 83716.475 136 0 -2232.0291 0 -2232.0291 15983.191 Loop time of 9.139 on 1 procs for 136 steps with 538 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 = -2061.19094554012 -2232.02749734161 -2232.02910861126 Force two-norm initial, final = 264.85978 0.18767600 Force max component initial, final = 84.946365 0.030219033 Final line search alpha, max atom move = 1.0000000 0.030219033 Iterations, force evaluations = 136 260 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.1148 | 9.1148 | 9.1148 | 0.0 | 99.74 Neigh | 0.010835 | 0.010835 | 0.010835 | 0.0 | 0.12 Comm | 0.0066252 | 0.0066252 | 0.0066252 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006707 | | | 0.07 Nlocal: 538.000 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2642.00 ave 2642 max 2642 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: 30880.0 ave 30880 max 30880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30880 Ave neighs/atom = 57.397770 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 136 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.840 | 4.840 | 4.840 Mbytes Step Temp E_pair E_mol TotEng Press Volume 136 0 -2232.0291 0 -2232.0291 15983.191 6459.7784 149 0 -2232.9684 0 -2232.9684 -84.17629 6515.9462 Loop time of 0.553093 on 1 procs for 13 steps with 538 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 = -2232.02910861125 -2232.96809469326 -2232.96838587687 Force two-norm initial, final = 164.06214 1.6016238 Force max component initial, final = 162.38171 1.1091176 Final line search alpha, max atom move = 0.0011324910 0.0012560657 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55095 | 0.55095 | 0.55095 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033085 | 0.00033085 | 0.00033085 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001813 | | | 0.33 Nlocal: 538.000 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2633.00 ave 2633 max 2633 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: 30868.0 ave 30868 max 30868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30868 Ave neighs/atom = 57.375465 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.978 | 4.978 | 4.978 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2232.9684 0 -2232.9684 -84.17629 Loop time of 1.814e-06 on 1 procs for 0 steps with 538 atoms 165.4% 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 | | 1.814e-06 | | |100.00 Nlocal: 538.000 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2624.00 ave 2624 max 2624 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: 30852.0 ave 30852 max 30852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30852 Ave neighs/atom = 57.345725 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.978 | 4.978 | 4.978 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 -2232.9684 -2232.9684 23.57828 67.680441 4.0832144 -84.17629 -84.17629 72.866658 -52.80963 -272.5859 2.2971973 537.04543 Loop time of 1.593e-06 on 1 procs for 0 steps with 538 atoms 251.1% 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 | | 1.593e-06 | | |100.00 Nlocal: 538.000 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2624.00 ave 2624 max 2624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15426.0 ave 15426 max 15426 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30852.0 ave 30852 max 30852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30852 Ave neighs/atom = 57.345725 Neighbor list builds = 0 Dangerous builds = 0 538 -2232.96838587687 eV 2.29719734610625 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10