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 = 4.0816549 4.0816549 4.0816549 Created orthogonal box = (0.0000000 -59.987831 0.0000000) to (21.208901 59.987831 5.7723318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4986040 6.6653146 5.7723318 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -59.987831 0.0000000) to (21.208901 59.987831 5.7723318) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4986040 6.6653146 5.7723318 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -59.987831 0.0000000) to (21.208901 59.987831 5.7723318) create_atoms CPU = 0.001 seconds 434 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 20 1 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 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 866 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_049243498555_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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.875 | 5.875 | 5.875 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3032.5049 0 -3032.5049 13908.399 59 0 -3094.1684 0 -3094.1684 6363.8571 Loop time of 2.01 on 1 procs for 59 steps with 866 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 = -3032.50485922924 -3094.1653879525 -3094.16835589294 Force two-norm initial, final = 50.221845 0.11486764 Force max component initial, final = 13.822822 0.023075810 Final line search alpha, max atom move = 1.0000000 0.023075810 Iterations, force evaluations = 59 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9385 | 1.9385 | 1.9385 | 0.0 | 96.45 Neigh | 0.055928 | 0.055928 | 0.055928 | 0.0 | 2.78 Comm | 0.010054 | 0.010054 | 0.010054 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005471 | | | 0.27 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10852.0 ave 10852 max 10852 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: 370404.0 ave 370404 max 370404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 370404 Ave neighs/atom = 427.71824 Neighbor list builds = 3 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.875 | 5.875 | 5.875 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -3094.1684 0 -3094.1684 6363.8571 14687.998 67 0 -3094.471 0 -3094.471 12.631365 14786.676 Loop time of 0.226389 on 1 procs for 8 steps with 866 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 = -3094.16835589294 -3094.47053306556 -3094.47098271546 Force two-norm initial, final = 107.66125 0.80612023 Force max component initial, final = 88.029539 0.62823108 Final line search alpha, max atom move = 0.00024654772 0.00015488894 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22263 | 0.22263 | 0.22263 | 0.0 | 98.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076378 | 0.00076378 | 0.00076378 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00299 | | | 1.32 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10850.0 ave 10850 max 10850 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: 370508.0 ave 370508 max 370508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 370508 Ave neighs/atom = 427.83834 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 6.013 | 6.013 | 6.013 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3094.471 0 -3094.471 12.631365 Loop time of 1.583e-06 on 1 procs for 0 steps with 866 atoms 126.3% 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 | | 1.583e-06 | | |100.00 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10850.0 ave 10850 max 10850 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: 369928.0 ave 369928 max 369928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369928 Ave neighs/atom = 427.16859 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 6.013 | 6.013 | 6.013 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 -3094.471 -3094.471 21.217116 120.81948 5.7682923 12.631365 12.631365 -47.672929 17.544116 68.022909 2.5784888 567.56535 Loop time of 1.909e-06 on 1 procs for 0 steps with 866 atoms 209.5% 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 | | 1.909e-06 | | |100.00 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10850.0 ave 10850 max 10850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 184964.0 ave 184964 max 184964 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 369928.0 ave 369928 max 369928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369928 Ave neighs/atom = 427.16859 Neighbor list builds = 0 Dangerous builds = 0 866 -3094.47098271546 eV 2.57848884729279 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02