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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -41.488985 0.0000000) to (29.337143 41.488985 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4450216 5.6575889 5.1069410 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.488985 0.0000000) to (29.337143 41.488985 5.1069410) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4450216 5.6575889 5.1069410 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.488985 0.0000000) to (29.337143 41.488985 5.1069410) create_atoms CPU = 0.001 seconds 532 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 32 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 1060 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.349 | 5.349 | 5.349 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4234.9734 0 -4234.9734 52855.801 36 0 -4482.588 0 -4482.588 12595.272 Loop time of 3.49043 on 1 procs for 36 steps with 1060 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 = -4234.97343398171 -4482.58405625706 -4482.58799251074 Force two-norm initial, final = 294.14547 0.22804030 Force max component initial, final = 54.630842 0.026760162 Final line search alpha, max atom move = 1.0000000 0.026760162 Iterations, force evaluations = 36 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4836 | 3.4836 | 3.4836 | 0.0 | 99.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026282 | 0.0026282 | 0.0026282 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00418 | | | 0.12 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3848.00 ave 3848 max 3848 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: 57496.0 ave 57496 max 57496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57496 Ave neighs/atom = 54.241509 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.349 | 5.349 | 5.349 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -4482.588 0 -4482.588 12595.272 12432.013 47 0 -4483.4393 0 -4483.4393 328.56482 12524.437 Loop time of 0.732334 on 1 procs for 11 steps with 1060 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 = -4482.58799251075 -4483.43807140053 -4483.4393471926 Force two-norm initial, final = 203.35741 4.7105613 Force max component initial, final = 189.28503 3.4872859 Final line search alpha, max atom move = 0.00021793451 0.00075999995 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72877 | 0.72877 | 0.72877 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046427 | 0.00046427 | 0.00046427 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003102 | | | 0.42 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3830.00 ave 3830 max 3830 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: 57192.0 ave 57192 max 57192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57192 Ave neighs/atom = 53.954717 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.487 | 5.487 | 5.487 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4483.4393 0 -4483.4393 328.56482 Loop time of 2.144e-06 on 1 procs for 0 steps with 1060 atoms 186.6% 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 | | 2.144e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3842.00 ave 3842 max 3842 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: 57168.0 ave 57168 max 57168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57168 Ave neighs/atom = 53.932075 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.487 | 5.487 | 5.487 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 -4483.4393 -4483.4393 29.250277 83.787088 5.110356 328.56482 328.56482 182.13412 450.45765 353.10269 2.330169 516.74654 Loop time of 2.109e-06 on 1 procs for 0 steps with 1060 atoms 237.1% 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 | | 2.109e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3842.00 ave 3842 max 3842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28584.0 ave 28584 max 28584 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57168.0 ave 57168 max 57168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57168 Ave neighs/atom = 53.932075 Neighbor list builds = 0 Dangerous builds = 0 1060 -4483.4393471926 eV 2.33016900591179 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04