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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -37.421777 0.0000000) to (37.418257 37.421777 3.5200135) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9670253 4.9670253 3.5200135 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -37.421777 0.0000000) to (37.418257 37.421777 3.5200135) create_atoms CPU = 0.001 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9670253 4.9670253 3.5200135 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -37.421777 0.0000000) to (37.418257 37.421777 3.5200135) create_atoms CPU = 0.000 seconds 454 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 18 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 902 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.398 | 5.398 | 5.398 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3955.01 0 -3955.01 12727.938 57 0 -4002.1188 0 -4002.1188 103.78429 Loop time of 0.987349 on 1 procs for 57 steps with 902 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 = -3955.00996938448 -4002.11574874205 -4002.1188131423 Force two-norm initial, final = 24.291467 0.18816440 Force max component initial, final = 5.1437817 0.018255177 Final line search alpha, max atom move = 1.0000000 0.018255177 Iterations, force evaluations = 57 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96435 | 0.96435 | 0.96435 | 0.0 | 97.67 Neigh | 0.011682 | 0.011682 | 0.011682 | 0.0 | 1.18 Comm | 0.0067644 | 0.0067644 | 0.0067644 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004551 | | | 0.46 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8794.00 ave 8794 max 8794 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: 203876.0 ave 203876 max 203876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203876 Ave neighs/atom = 226.02661 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.398 | 5.398 | 5.398 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -4002.1188 0 -4002.1188 103.78429 9857.8518 61 0 -4002.1631 0 -4002.1631 -40.934342 9858.5899 Loop time of 0.070927 on 1 procs for 4 steps with 902 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 = -4002.1188131423 -4002.16295914259 -4002.16310363706 Force two-norm initial, final = 27.312776 0.20394217 Force max component initial, final = 23.427958 0.031228511 Final line search alpha, max atom move = 0.00039198226 1.2241023e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068801 | 0.068801 | 0.068801 | 0.0 | 97.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043759 | 0.00043759 | 0.00043759 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001689 | | | 2.38 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8758.00 ave 8758 max 8758 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: 203024.0 ave 203024 max 203024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203024 Ave neighs/atom = 225.08204 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.536 | 5.536 | 5.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4002.1631 0 -4002.1631 -40.934342 Loop time of 1.567e-06 on 1 procs for 0 steps with 902 atoms 127.6% 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 | | 1.567e-06 | | |100.00 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8782.00 ave 8782 max 8782 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: 202984.0 ave 202984 max 202984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202984 Ave neighs/atom = 225.03769 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.536 | 5.536 | 5.536 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 -4002.1631 -4002.1631 37.331299 74.843554 3.528477 -40.934342 -40.934342 -3.7414621 -116.94828 -2.1132815 2.2299428 134.30342 Loop time of 1.944e-06 on 1 procs for 0 steps with 902 atoms 205.8% 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 | | 1.944e-06 | | |100.00 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8782.00 ave 8782 max 8782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101492.0 ave 101492 max 101492 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 202984.0 ave 202984 max 202984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202984 Ave neighs/atom = 225.03769 Neighbor list builds = 0 Dangerous builds = 0 902 -3977.57331925678 eV 2.22994283889521 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01