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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -46.828677 0.0000000) to (33.110852 46.828677 4.0451344) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9419183 4.5428031 4.0451344 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.828677 0.0000000) to (33.110852 46.828677 4.0451344) create_atoms CPU = 0.002 seconds 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9419183 4.5428031 4.0451344 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.828677 0.0000000) to (33.110852 46.828677 4.0451344) create_atoms CPU = 0.001 seconds 538 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 25 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 1067 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.034 | 5.034 | 5.034 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4511.4112 0 -4511.4112 10004.148 299 0 -4666.7457 0 -4666.7457 -5868.3564 Loop time of 4.48502 on 1 procs for 299 steps with 1067 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 = -4511.41119055872 -4666.74134728438 -4666.74568682717 Force two-norm initial, final = 107.53890 0.36526925 Force max component initial, final = 38.512152 0.15389360 Final line search alpha, max atom move = 0.85169976 0.13107114 Iterations, force evaluations = 299 532 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3336 | 4.3336 | 4.3336 | 0.0 | 96.62 Neigh | 0.092867 | 0.092867 | 0.092867 | 0.0 | 2.07 Comm | 0.032692 | 0.032692 | 0.032692 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02581 | | | 0.58 Nlocal: 1067.00 ave 1067 max 1067 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8073.00 ave 8073 max 8073 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: 167828.0 ave 167828 max 167828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167828 Ave neighs/atom = 157.28960 Neighbor list builds = 9 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 299 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.034 | 5.034 | 5.034 Mbytes Step Temp E_pair E_mol TotEng Press Volume 299 0 -4666.7457 0 -4666.7457 -5868.3564 12544.265 316 0 -4668.5784 0 -4668.5784 2336.3767 12442.095 Loop time of 0.166815 on 1 procs for 17 steps with 1067 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 = -4666.74568682718 -4668.57684217239 -4668.5784286591 Force two-norm initial, final = 202.87435 4.3567127 Force max component initial, final = 186.19889 3.4517144 Final line search alpha, max atom move = 0.00015311566 0.00052851152 Iterations, force evaluations = 17 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16047 | 0.16047 | 0.16047 | 0.0 | 96.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010952 | 0.0010952 | 0.0010952 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005254 | | | 3.15 Nlocal: 1067.00 ave 1067 max 1067 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8078.00 ave 8078 max 8078 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: 167828.0 ave 167828 max 167828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167828 Ave neighs/atom = 157.28960 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.172 | 5.172 | 5.172 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4668.5784 0 -4668.5784 2336.3767 Loop time of 1.595e-06 on 1 procs for 0 steps with 1067 atoms 125.4% 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 | | 1.595e-06 | | |100.00 Nlocal: 1067.00 ave 1067 max 1067 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8133.00 ave 8133 max 8133 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: 170084.0 ave 170084 max 170084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170084 Ave neighs/atom = 159.40394 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.172 | 5.172 | 5.172 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 -4668.5784 -4668.5784 32.579878 93.657354 4.0775769 2336.3767 2336.3767 268.41879 6292.667 448.04426 2.279852 6286.2682 Loop time of 1.893e-06 on 1 procs for 0 steps with 1067 atoms 158.5% 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 | | 1.893e-06 | | |100.00 Nlocal: 1067.00 ave 1067 max 1067 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8133.00 ave 8133 max 8133 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85042.0 ave 85042 max 85042 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 170084.0 ave 170084 max 170084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170084 Ave neighs/atom = 159.40394 Neighbor list builds = 0 Dangerous builds = 0 1067 -4668.5784286591 eV 2.27985199188611 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05