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 = 3.6336621 3.6336621 3.6336621 Created orthogonal box = (0.0000000 -51.130158 0.0000000) to (12.051494 51.130158 5.1387742) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4779517 6.1975949 5.1387742 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -51.130158 0.0000000) to (12.051494 51.130158 5.1387742) create_atoms CPU = 0.001 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4779517 6.1975949 5.1387742 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -51.130158 0.0000000) to (12.051494 51.130158 5.1387742) create_atoms CPU = 0.001 seconds 266 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 5 36 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 526 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_529419924683_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 5 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2120.2011 0 -2120.2011 7904.1921 42 0 -2151.9557 0 -2151.9557 1296.1221 Loop time of 12.8637 on 1 procs for 42 steps with 526 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 = -2120.20114616459 -2151.95362117328 -2151.95569046361 Force two-norm initial, final = 29.234409 0.11814059 Force max component initial, final = 8.1930223 0.030868600 Final line search alpha, max atom move = 1.0000000 0.030868600 Iterations, force evaluations = 42 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.852 | 12.852 | 12.852 | 0.0 | 99.91 Neigh | 0.0026327 | 0.0026327 | 0.0026327 | 0.0 | 0.02 Comm | 0.0045303 | 0.0045303 | 0.0045303 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004458 | | | 0.03 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3102.00 ave 3102 max 3102 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: 29888.0 ave 29888 max 29888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29888 Ave neighs/atom = 56.821293 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 5 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -2151.9557 0 -2151.9557 1296.1221 6332.9716 47 0 -2152.0166 0 -2152.0166 64.946719 6338.2112 Loop time of 1.30073 on 1 procs for 5 steps with 526 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 = -2151.95569046361 -2152.01639198759 -2152.0165548921 Force two-norm initial, final = 26.611222 0.54322557 Force max component initial, final = 24.815157 0.40532622 Final line search alpha, max atom move = 0.0010392269 0.00042122593 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2989 | 1.2989 | 1.2989 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026858 | 0.00026858 | 0.00026858 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001563 | | | 0.12 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3076.00 ave 3076 max 3076 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: 29836.0 ave 29836 max 29836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29836 Ave neighs/atom = 56.722433 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 5 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2152.0166 0 -2152.0166 64.946719 Loop time of 1.883e-06 on 1 procs for 0 steps with 526 atoms 106.2% 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 | | 1.883e-06 | | |100.00 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3076.00 ave 3076 max 3076 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: 29752.0 ave 29752 max 29752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29752 Ave neighs/atom = 56.562738 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 5 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.633 | 4.633 | 4.633 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 -2152.0166 -2152.0166 12.014132 102.63272 5.1403001 64.946719 64.946719 16.534831 102.83171 75.473619 2.3873083 269.79388 Loop time of 1.402e-06 on 1 procs for 0 steps with 526 atoms 142.7% 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 | | 1.402e-06 | | |100.00 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3076.00 ave 3076 max 3076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14876.0 ave 14876 max 14876 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29752.0 ave 29752 max 29752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29752 Ave neighs/atom = 56.562738 Neighbor list builds = 0 Dangerous builds = 0 526 -1344.48293456768 eV 2.38730831162063 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15