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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -40.049157 0.0000000) to (9.4396769 40.049157 4.4499064) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2442650 4.4499064 4.4499064 Created 108 atoms using lattice units in orthogonal box = (0.0000000 -40.049157 0.0000000) to (9.4396769 40.049157 4.4499064) create_atoms CPU = 0.001 seconds 108 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2442650 4.4499064 4.4499064 Created 110 atoms using lattice units in orthogonal box = (0.0000000 -40.049157 0.0000000) to (9.4396769 40.049157 4.4499064) create_atoms CPU = 0.000 seconds 110 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 25 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 218 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_356501945107_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.404 | 4.404 | 4.404 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -923.54908 0 -923.54908 394247.63 71 0 -1473.2754 0 -1473.2754 39355.93 Loop time of 0.999624 on 1 procs for 71 steps with 218 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 = -923.549075369113 -1473.27397217242 -1473.27544271022 Force two-norm initial, final = 1187.7447 0.24450062 Force max component initial, final = 470.87371 0.046010218 Final line search alpha, max atom move = 0.77113096 0.035479904 Iterations, force evaluations = 71 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99338 | 0.99338 | 0.99338 | 0.0 | 99.37 Neigh | 0.0013264 | 0.0013264 | 0.0013264 | 0.0 | 0.13 Comm | 0.0025802 | 0.0025802 | 0.0025802 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002342 | | | 0.23 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1885.00 ave 1885 max 1885 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: 14052.0 ave 14052 max 14052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14052 Ave neighs/atom = 64.458716 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.404 | 4.404 | 4.404 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -1473.2754 0 -1473.2754 39355.93 3364.584 96 0 -1474.5839 0 -1474.5839 -74.906269 3414.0158 Loop time of 0.247289 on 1 procs for 25 steps with 218 atoms 93.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1473.27544271022 -1474.58370047011 -1474.5838958171 Force two-norm initial, final = 168.10153 1.2741380 Force max component initial, final = 154.56513 1.0017284 Final line search alpha, max atom move = 0.0030768922 0.0030822103 Iterations, force evaluations = 25 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24292 | 0.24292 | 0.24292 | 0.0 | 98.23 Neigh | 0.0012396 | 0.0012396 | 0.0012396 | 0.0 | 0.50 Comm | 0.00060298 | 0.00060298 | 0.00060298 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002528 | | | 1.02 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1885.00 ave 1885 max 1885 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: 13936.0 ave 13936 max 13936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13936 Ave neighs/atom = 63.926606 Neighbor list builds = 1 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1474.5839 0 -1474.5839 -74.906269 Loop time of 1.752e-06 on 1 procs for 0 steps with 218 atoms 171.2% 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 | | 1.752e-06 | | |100.00 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1893.00 ave 1893 max 1893 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: 13932.0 ave 13932 max 13932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13932 Ave neighs/atom = 63.908257 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.542 | 4.542 | 4.542 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 -1474.5839 -1474.5839 9.4252793 81.551109 4.4416203 -74.906269 -74.906269 202.19142 -478.63154 51.72131 2.4895283 224.53357 Loop time of 2.044e-06 on 1 procs for 0 steps with 218 atoms 146.8% 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 | | 2.044e-06 | | |100.00 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1893.00 ave 1893 max 1893 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6966.00 ave 6966 max 6966 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13932.0 ave 13932 max 13932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13932 Ave neighs/atom = 63.908257 Neighbor list builds = 0 Dangerous builds = 0 218 -1474.5838958171 eV 2.48952834520162 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01