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 = 2.8599988 2.8599988 2.8599988 Created orthogonal box = (0.0000000 -40.243751 0.0000000) to (9.4855430 40.243751 4.0446491) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3116105 4.8780304 4.0446491 Created 132 atoms using lattice units in orthogonal box = (0.0000000 -40.243751 0.0000000) to (9.4855430 40.243751 4.0446491) create_atoms CPU = 0.001 seconds 132 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3116105 4.8780304 4.0446491 Created 134 atoms using lattice units in orthogonal box = (0.0000000 -40.243751 0.0000000) to (9.4855430 40.243751 4.0446491) create_atoms CPU = 0.001 seconds 134 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 3 23 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 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 264 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_763197941039_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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 3 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1087.8628 0 -1087.8628 61588.618 158 0 -1151.9615 0 -1151.9615 52434.897 Loop time of 0.634367 on 1 procs for 158 steps with 264 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1087.86280655615 -1151.9603483553 -1151.96147316978 Force two-norm initial, final = 93.778542 0.16208993 Force max component initial, final = 24.359082 0.035557499 Final line search alpha, max atom move = 1.0000000 0.035557499 Iterations, force evaluations = 158 301 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61623 | 0.61623 | 0.61623 | 0.0 | 97.14 Neigh | 0.0048949 | 0.0048949 | 0.0048949 | 0.0 | 0.77 Comm | 0.0082325 | 0.0082325 | 0.0082325 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005009 | | | 0.79 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3671.00 ave 3671 max 3671 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: 35456.0 ave 35456 max 35456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35456 Ave neighs/atom = 134.30303 Neighbor list builds = 2 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 3 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 158 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.443 | 4.443 | 4.443 Mbytes Step Temp E_pair E_mol TotEng Press Volume 158 0 -1151.9615 0 -1151.9615 52434.897 3087.9588 223 0 -1154.2835 0 -1154.2835 -259.02941 3174.5037 Loop time of 0.180104 on 1 procs for 65 steps with 264 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 = -1151.96147316978 -1154.28271374459 -1154.28346357491 Force two-norm initial, final = 188.53325 2.1931507 Force max component initial, final = 157.81248 1.4534784 Final line search alpha, max atom move = 0.00042705779 0.00062071926 Iterations, force evaluations = 65 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16744 | 0.16744 | 0.16744 | 0.0 | 92.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021868 | 0.0021868 | 0.0021868 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01047 | | | 5.82 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3641.00 ave 3641 max 3641 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: 35456.0 ave 35456 max 35456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35456 Ave neighs/atom = 134.30303 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 3 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.575 | 4.575 | 4.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1154.2835 0 -1154.2835 -259.02941 Loop time of 1.8627e-05 on 1 procs for 0 steps with 264 atoms 107.4% 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 | | 1.863e-05 | | |100.00 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2856.00 ave 2856 max 2856 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: 33860.0 ave 33860 max 33860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33860 Ave neighs/atom = 128.25758 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 3 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.575 | 4.575 | 4.575 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 -1154.2835 -1154.2835 9.515021 80.592028 4.1397489 -259.02941 -259.02941 -735.8523 -133.5346 92.298654 2.3773954 1461.6722 Loop time of 1.645e-06 on 1 procs for 0 steps with 264 atoms 182.4% 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 | | 1.645e-06 | | |100.00 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2856.00 ave 2856 max 2856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16930.0 ave 16930 max 16930 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33860.0 ave 33860 max 33860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33860 Ave neighs/atom = 128.25758 Neighbor list builds = 0 Dangerous builds = 0 264 -1154.28346357491 eV 2.37739538609298 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01