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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -77.481064 0.0000000) to (44.733713 77.481064 7.0148059) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6000560 5.9275131 7.0148059 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -77.481064 0.0000000) to (44.733713 77.481064 7.0148059) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6000560 5.9275131 7.0148059 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -77.481064 0.0000000) to (44.733713 77.481064 7.0148059) create_atoms CPU = 0.003 seconds 1466 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 41 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.200 | 6.200 | 6.200 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9604.4943 0 -9604.4943 10193.692 102 0 -9821.3772 0 -9821.3772 3818.9875 Loop time of 2.82816 on 1 procs for 102 steps with 2926 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 = -9604.49433011669 -9821.37060882174 -9821.37716252853 Force two-norm initial, final = 136.62002 0.19106707 Force max component initial, final = 23.415810 0.048246117 Final line search alpha, max atom move = 1.0000000 0.048246117 Iterations, force evaluations = 102 172 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6655 | 2.6655 | 2.6655 | 0.0 | 94.25 Neigh | 0.11533 | 0.11533 | 0.11533 | 0.0 | 4.08 Comm | 0.022365 | 0.022365 | 0.022365 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.025 | | | 0.88 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11424.0 ave 11424 max 11424 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: 384504.0 ave 384504 max 384504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 384504 Ave neighs/atom = 131.40943 Neighbor list builds = 5 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.199 | 6.199 | 6.199 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -9821.3772 0 -9821.3772 3818.9875 48626.854 109 0 -9821.9515 0 -9821.9515 94.931212 48856.043 Loop time of 0.173823 on 1 procs for 7 steps with 2926 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 = -9821.37716252851 -9821.95028374589 -9821.95145929991 Force two-norm initial, final = 226.34519 5.2628658 Force max component initial, final = 200.57909 4.1955557 Final line search alpha, max atom move = 0.00022725949 0.00095347983 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1435 | 0.1435 | 0.1435 | 0.0 | 82.55 Neigh | 0.023589 | 0.023589 | 0.023589 | 0.0 | 13.57 Comm | 0.001222 | 0.001222 | 0.001222 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005513 | | | 3.17 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11421.0 ave 11421 max 11421 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: 383684.0 ave 383684 max 383684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383684 Ave neighs/atom = 131.12919 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.337 | 6.337 | 6.337 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9821.9515 0 -9821.9515 94.931212 Loop time of 2.359e-06 on 1 procs for 0 steps with 2926 atoms 212.0% 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 | | 2.359e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11421.0 ave 11421 max 11421 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: 383672.0 ave 383672 max 383672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383672 Ave neighs/atom = 131.12509 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.337 | 6.337 | 6.337 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 -9821.9515 -9821.9515 44.718722 155.92171 7.0068417 94.931212 94.931212 68.097531 138.44032 78.255786 2.5845595 1312.8061 Loop time of 2.383e-06 on 1 procs for 0 steps with 2926 atoms 209.8% 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 | | 2.383e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11421.0 ave 11421 max 11421 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 191836.0 ave 191836 max 191836 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 383672.0 ave 383672 max 383672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383672 Ave neighs/atom = 131.12509 Neighbor list builds = 0 Dangerous builds = 0 2926 -9821.95145929991 eV 2.58455947916869 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03