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 = 3.1409628 3.1409628 3.1409628 Created orthogonal box = (0.0000000 -47.427498 0.0000000) to (33.536306 47.427498 4.4419922) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2952062 5.4083989 4.4419922 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -47.427498 0.0000000) to (33.536306 47.427498 4.4419922) create_atoms CPU = 0.002 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2952062 5.4083989 4.4419922 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -47.427498 0.0000000) to (33.536306 47.427498 4.4419922) create_atoms CPU = 0.001 seconds 458 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 6 17 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 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_666830945336_004#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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 6 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 5.841 | 5.841 | 5.841 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4517.6627 0 -4517.6627 223855.03 82 0 -6120.6088 0 -6120.6088 12889.718 Loop time of 2.93779 on 1 procs for 82 steps with 912 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4517.66268499823 -6120.60310447788 -6120.60883117362 Force two-norm initial, final = 2685.6898 0.44574096 Force max component initial, final = 754.30837 0.075257267 Final line search alpha, max atom move = 1.0000000 0.075257267 Iterations, force evaluations = 82 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8404 | 2.8404 | 2.8404 | 0.0 | 96.68 Neigh | 0.067717 | 0.067717 | 0.067717 | 0.0 | 2.31 Comm | 0.018931 | 0.018931 | 0.018931 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01074 | | | 0.37 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11473.0 ave 11473 max 11473 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: 373628.0 ave 373628 max 373628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373628 Ave neighs/atom = 409.67982 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 6 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.841 | 5.841 | 5.841 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -6120.6088 0 -6120.6088 12889.718 14130.36 85 0 -6120.9024 0 -6120.9024 -394.31915 14195.315 Loop time of 0.0933643 on 1 procs for 3 steps with 912 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 = -6120.60883117359 -6120.89635530641 -6120.90239401854 Force two-norm initial, final = 205.62815 6.9969529 Force max component initial, final = 153.31253 5.8373900 Final line search alpha, max atom move = 5.8566942e-05 0.00034187808 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.09123 | 0.09123 | 0.09123 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045034 | 0.00045034 | 0.00045034 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001683 | | | 1.80 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11494.0 ave 11494 max 11494 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: 373728.0 ave 373728 max 373728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373728 Ave neighs/atom = 409.78947 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 5.979 | 5.979 | 5.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6120.9024 0 -6120.9024 -394.31915 Loop time of 2.382e-06 on 1 procs for 0 steps with 912 atoms 209.9% 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 | | 2.382e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11480.0 ave 11480 max 11480 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: 373084.0 ave 373084 max 373084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373084 Ave neighs/atom = 409.08333 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 5.979 | 5.979 | 5.979 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 -6120.9024 -6120.9024 33.594487 95.0809 4.4440989 -394.31915 -394.31915 -103.12036 -420.6784 -659.15868 2.5697741 974.14426 Loop time of 2.877e-06 on 1 procs for 0 steps with 912 atoms 243.3% 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 | | 2.877e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11480.0 ave 11480 max 11480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 186542.0 ave 186542 max 186542 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 373084.0 ave 373084 max 373084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373084 Ave neighs/atom = 409.08333 Neighbor list builds = 0 Dangerous builds = 0 912 -6120.90239401854 eV 2.56977413662292 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03