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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -53.975220 0.0000000) to (44.070583 53.975220 8.9340421) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4333595 5.1757061 5.9560280 Created 1752 atoms using lattice units in orthogonal box = (0.0000000 -53.975220 0.0000000) to (44.070583 53.975220 8.9340421) create_atoms CPU = 0.002 seconds 1752 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4333595 5.1757061 5.9560280 Created 1760 atoms using lattice units in orthogonal box = (0.0000000 -53.975220 0.0000000) to (44.070583 53.975220 8.9340421) create_atoms CPU = 0.002 seconds 1760 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 = 17 41 4 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 = 3512 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 = 17 41 4 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) = 6.333 | 6.333 | 6.333 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14145.722 0 -14145.722 32617.326 34 0 -14514.313 0 -14514.313 9775.4136 Loop time of 11.7146 on 1 procs for 34 steps with 3512 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 = -14145.7223502548 -14514.2995699142 -14514.3126527372 Force two-norm initial, final = 297.25382 0.48928692 Force max component initial, final = 37.589878 0.075929260 Final line search alpha, max atom move = 1.0000000 0.075929260 Iterations, force evaluations = 34 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.696 | 11.696 | 11.696 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0061436 | 0.0061436 | 0.0061436 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01221 | | | 0.10 Nlocal: 3512.00 ave 3512 max 3512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6868.00 ave 6868 max 6868 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: 189552.0 ave 189552 max 189552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189552 Ave neighs/atom = 53.972665 Neighbor list builds = 0 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 = 17 41 4 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 : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.333 | 6.333 | 6.333 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -14514.313 0 -14514.313 9775.4136 42503.159 39 0 -14515.183 0 -14515.183 -44.947658 42751.193 Loop time of 1.60104 on 1 procs for 5 steps with 3512 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 = -14514.3126527372 -14515.181810033 -14515.1828743989 Force two-norm initial, final = 460.63068 4.9750922 Force max component initial, final = 341.05728 4.2985607 Final line search alpha, max atom move = 6.9028382e-05 0.00029672269 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5961 | 1.5961 | 1.5961 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052497 | 0.00052497 | 0.00052497 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004419 | | | 0.28 Nlocal: 3512.00 ave 3512 max 3512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6867.00 ave 6867 max 6867 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: 188928.0 ave 188928 max 188928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188928 Ave neighs/atom = 53.794989 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 = 17 41 4 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) = 6.471 | 6.471 | 6.471 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14515.183 0 -14515.183 -44.947658 Loop time of 2.324e-06 on 1 procs for 0 steps with 3512 atoms 172.1% 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 | | 2.324e-06 | | |100.00 Nlocal: 3512.00 ave 3512 max 3512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6867.00 ave 6867 max 6867 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: 188848.0 ave 188848 max 188848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188848 Ave neighs/atom = 53.772210 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 = 17 41 4 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) = 6.471 | 6.471 | 6.471 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 -14515.183 -14515.183 44.122886 108.36359 8.9413061 -44.947658 -44.947658 -161.28735 -47.463956 73.90833 2.3057285 851.06512 Loop time of 2.559e-06 on 1 procs for 0 steps with 3512 atoms 234.5% 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 | | 2.559e-06 | | |100.00 Nlocal: 3512.00 ave 3512 max 3512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6867.00 ave 6867 max 6867 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94424.0 ave 94424 max 94424 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188848.0 ave 188848 max 188848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188848 Ave neighs/atom = 53.772210 Neighbor list builds = 0 Dangerous builds = 0 3512 -14515.1828743989 eV 2.3057285171089 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14