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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -38.775057 0.0000000) to (38.771409 38.775057 3.6473074) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1466473 5.1466473 3.6473074 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.775057 0.0000000) to (38.771409 38.775057 3.6473074) create_atoms CPU = 0.002 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1466473 5.1466473 3.6473074 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.775057 0.0000000) to (38.771409 38.775057 3.6473074) create_atoms CPU = 0.002 seconds 454 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 = 15 29 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 5 atoms, new total = 903 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 15 29 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) = 5.306 | 5.306 | 5.306 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3653.6939 0 -3653.6939 31199.23 87 0 -3737.6376 0 -3737.6376 1425.2878 Loop time of 19.3818 on 1 procs for 87 steps with 903 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 = -3653.69387585052 -3737.63398079068 -3737.63757742596 Force two-norm initial, final = 62.492464 0.20942314 Force max component initial, final = 16.063086 0.031412162 Final line search alpha, max atom move = 1.0000000 0.031412162 Iterations, force evaluations = 87 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.304 | 19.304 | 19.304 | 0.0 | 99.60 Neigh | 0.043117 | 0.043117 | 0.043117 | 0.0 | 0.22 Comm | 0.01618 | 0.01618 | 0.01618 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0181 | | | 0.09 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4321.00 ave 4321 max 4321 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: 48642.0 ave 48642 max 48642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48642 Ave neighs/atom = 53.867110 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 15 29 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 : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.306 | 5.306 | 5.306 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -3737.6376 0 -3737.6376 1425.2878 10966.458 93 0 -3737.7906 0 -3737.7906 -436.68702 10978.952 Loop time of 0.970357 on 1 procs for 6 steps with 903 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 = -3737.63757742597 -3737.79004675996 -3737.79059375831 Force two-norm initial, final = 45.099033 0.27606386 Force max component initial, final = 36.092159 0.044296037 Final line search alpha, max atom move = 0.00046820168 2.0739479e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96649 | 0.96649 | 0.96649 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078685 | 0.00078685 | 0.00078685 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003077 | | | 0.32 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4317.00 ave 4317 max 4317 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: 48640.0 ave 48640 max 48640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48640 Ave neighs/atom = 53.864895 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 = 15 29 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) = 5.444 | 5.444 | 5.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3737.7906 0 -3737.7906 -436.68702 Loop time of 6.425e-06 on 1 procs for 0 steps with 903 atoms 171.2% 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 | | 6.425e-06 | | |100.00 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4321.00 ave 4321 max 4321 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: 48644.0 ave 48644 max 48644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48644 Ave neighs/atom = 53.869324 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 = 15 29 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) = 5.444 | 5.444 | 5.444 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 -3737.7906 -3737.7906 38.610434 77.550114 3.6666866 -436.68702 -436.68702 4.3383749 -1314.5769 0.17746215 2.3237541 102.61801 Loop time of 7.016e-06 on 1 procs for 0 steps with 903 atoms 270.8% 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 | | 7.016e-06 | | |100.00 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4321.00 ave 4321 max 4321 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24322.0 ave 24322 max 24322 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48644.0 ave 48644 max 48644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48644 Ave neighs/atom = 53.869324 Neighbor list builds = 0 Dangerous builds = 0 903 -3737.79059375831 eV 2.32375409569233 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21