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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -32.919740 0.0000000) to (19.004441 32.919740 5.3397869) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0011686 4.6198817 5.3397869 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -32.919740 0.0000000) to (19.004441 32.919740 5.3397869) create_atoms CPU = 0.000 seconds 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0011686 4.6198817 5.3397869 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -32.919740 0.0000000) to (19.004441 32.919740 5.3397869) create_atoms CPU = 0.000 seconds 230 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 456 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.843 | 4.843 | 4.843 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2748.7806 0 -2748.7806 118643.88 135 0 -2955.9287 0 -2955.9287 7765.4724 Loop time of 12.6367 on 1 procs for 135 steps with 456 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 = -2748.78055176517 -2955.92582074191 -2955.92873165499 Force two-norm initial, final = 344.16898 0.25880818 Force max component initial, final = 81.199755 0.054398724 Final line search alpha, max atom move = 1.0000000 0.054398724 Iterations, force evaluations = 135 256 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.614 | 12.614 | 12.614 | 0.0 | 99.82 Neigh | 0.014599 | 0.014599 | 0.014599 | 0.0 | 0.12 Comm | 0.0058508 | 0.0058508 | 0.0058508 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002612 | | | 0.02 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2813.00 ave 2813 max 2813 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: 34582.0 ave 34582 max 34582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34582 Ave neighs/atom = 75.837719 Neighbor list builds = 2 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 135 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.843 | 4.843 | 4.843 Mbytes Step Temp E_pair E_mol TotEng Press Volume 135 0 -2955.9287 0 -2955.9287 7765.4724 6681.3682 142 0 -2956.2398 0 -2956.2398 3911.4853 6692.5108 Loop time of 0.494978 on 1 procs for 7 steps with 456 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 = -2955.92873165499 -2956.23892468017 -2956.23976657721 Force two-norm initial, final = 93.775608 5.8722710 Force max component initial, final = 88.250356 4.3918421 Final line search alpha, max atom move = 0.014508046 0.063717050 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49438 | 0.49438 | 0.49438 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001383 | 0.0001383 | 0.0001383 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004618 | | | 0.09 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2813.00 ave 2813 max 2813 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: 34308.0 ave 34308 max 34308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34308 Ave neighs/atom = 75.236842 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.981 | 4.981 | 4.981 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2956.2398 0 -2956.2398 3911.4853 Loop time of 2e-06 on 1 procs for 0 steps with 456 atoms 150.0% 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 | | 2e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2809.00 ave 2809 max 2809 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: 34450.0 ave 34450 max 34450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34450 Ave neighs/atom = 75.548246 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.981 | 4.981 | 4.981 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 -2956.2398 -2956.2398 18.930401 65.83948 5.3696118 3911.4853 3911.4853 913.19983 9763.9835 1057.2726 2.5353413 1030.1165 Loop time of 1.9e-06 on 1 procs for 0 steps with 456 atoms 105.3% 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 | | 1.9e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2809.00 ave 2809 max 2809 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17225.0 ave 17225 max 17225 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34450.0 ave 34450 max 34450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34450 Ave neighs/atom = 75.548246 Neighbor list builds = 0 Dangerous builds = 0 456 -2956.23976657721 eV 2.53534126481176 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13