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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -57.308406 0.0000000) to (35.094088 57.308406 8.9139073) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6603368 5.5459748 5.9426049 Created 1488 atoms using lattice units in orthogonal box = (0.0000000 -57.308406 0.0000000) to (35.094088 57.308406 8.9139073) create_atoms CPU = 0.002 seconds 1488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6603368 5.5459748 5.9426049 Created 1494 atoms using lattice units in orthogonal box = (0.0000000 -57.308406 0.0000000) to (35.094088 57.308406 8.9139073) create_atoms CPU = 0.002 seconds 1494 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 24 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 2964 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_609260676108_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.53 | 12.53 | 12.53 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7200.9074 0 -7200.9074 158330.28 103 0 -9701.0344 0 -9701.0344 -698.28644 Loop time of 8.88538 on 1 procs for 103 steps with 2964 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7200.90738526308 -9701.02505453137 -9701.03438966648 Force two-norm initial, final = 3825.1253 0.24184923 Force max component initial, final = 771.15147 0.0087569288 Final line search alpha, max atom move = 1.0000000 0.0087569288 Iterations, force evaluations = 103 187 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.6735 | 8.6735 | 8.6735 | 0.0 | 97.62 Neigh | 0.1507 | 0.1507 | 0.1507 | 0.0 | 1.70 Comm | 0.031994 | 0.031994 | 0.031994 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02914 | | | 0.33 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13884.0 ave 13884 max 13884 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: 941208.0 ave 941208 max 941208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 941208 Ave neighs/atom = 317.54656 Neighbor list builds = 3 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.53 | 12.53 | 12.53 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -9701.0344 0 -9701.0344 -698.28644 35855.055 105 0 -9701.0671 0 -9701.0671 -8.4420487 35837.726 Loop time of 0.240254 on 1 procs for 2 steps with 2964 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9701.03438966656 -9701.05915964033 -9701.06713892726 Force two-norm initial, final = 49.638162 3.0137140 Force max component initial, final = 37.349890 2.4321845 Final line search alpha, max atom move = 2.8622234e-05 6.9614555e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23685 | 0.23685 | 0.23685 | 0.0 | 98.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056225 | 0.00056225 | 0.00056225 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002837 | | | 1.18 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13517.0 ave 13517 max 13517 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: 941832.0 ave 941832 max 941832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 941832 Ave neighs/atom = 317.75709 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.04 | 12.04 | 12.04 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9701.0671 0 -9701.0671 -8.4420487 Loop time of 2.164e-06 on 1 procs for 0 steps with 2964 atoms 138.6% 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 | | 2.164e-06 | | |100.00 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13535.0 ave 13535 max 13535 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: 941808.0 ave 941808 max 941808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 941808 Ave neighs/atom = 317.74899 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.04 | 12.04 | 12.04 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 -9701.0671 -9701.0671 35.127947 114.54952 8.9062402 -8.4420487 -8.4420487 4.7831175 -108.67043 78.561166 2.2206535 1151.0399 Loop time of 4.481e-06 on 1 procs for 0 steps with 2964 atoms 245.5% 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 | | 4.481e-06 | | |100.00 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13535.0 ave 13535 max 13535 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 470904.0 ave 470904 max 470904 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 941808.0 ave 941808 max 941808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 941808 Ave neighs/atom = 317.74899 Neighbor list builds = 0 Dangerous builds = 0 2964 -9701.06713892726 eV 2.22065352436737 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10