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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -50.037232 0.0000000) to (16.679077 50.037232 4.0452705) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9056110 4.9056110 4.0452705 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -50.037232 0.0000000) to (16.679077 50.037232 4.0452705) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9056110 4.9056110 4.0452705 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -50.037232 0.0000000) to (16.679077 50.037232 4.0452705) create_atoms CPU = 0.000 seconds 206 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 4 22 1 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_658278549784_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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 4 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 4.511 | 4.511 | 4.511 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1358.437 0 -1358.437 15856.806 47 0 -1387.1021 0 -1387.1021 4971.0747 Loop time of 0.486158 on 1 procs for 47 steps with 408 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 = -1358.43699127877 -1387.10079274039 -1387.10214647254 Force two-norm initial, final = 65.237577 0.077978088 Force max component initial, final = 20.773138 0.015180034 Final line search alpha, max atom move = 1.0000000 0.015180034 Iterations, force evaluations = 47 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4736 | 0.4736 | 0.4736 | 0.0 | 97.42 Neigh | 0.0054135 | 0.0054135 | 0.0054135 | 0.0 | 1.11 Comm | 0.0045803 | 0.0045803 | 0.0045803 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002563 | | | 0.53 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5324.00 ave 5324 max 5324 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: 89696.0 ave 89696 max 89696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89696 Ave neighs/atom = 219.84314 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 4 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.511 | 4.511 | 4.511 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1387.1021 0 -1387.1021 4971.0747 6752.1622 57 0 -1387.2475 0 -1387.2475 -11.796745 6793.1807 Loop time of 0.0730707 on 1 procs for 10 steps with 408 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 = -1387.10214647254 -1387.2475002626 -1387.24750749788 Force two-norm initial, final = 41.525943 0.17859172 Force max component initial, final = 37.366186 0.066357868 Final line search alpha, max atom move = 0.0051336431 0.00034065761 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.069874 | 0.069874 | 0.069874 | 0.0 | 95.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057313 | 0.00057313 | 0.00057313 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002624 | | | 3.59 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5334.00 ave 5334 max 5334 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: 89924.0 ave 89924 max 89924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89924 Ave neighs/atom = 220.40196 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 4 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 4.649 | 4.649 | 4.649 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1387.2475 0 -1387.2475 -11.796745 Loop time of 1.76e-06 on 1 procs for 0 steps with 408 atoms 227.3% 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 | | 1.76e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5279.00 ave 5279 max 5279 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: 89432.0 ave 89432 max 89432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89432 Ave neighs/atom = 219.19608 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 4 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 4.649 | 4.649 | 4.649 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 -1387.2475 -1387.2475 16.667588 100.97733 4.0362358 -11.796745 -11.796745 -5.4665225 -14.308117 -15.615596 2.6045584 235.31127 Loop time of 2.706e-06 on 1 procs for 0 steps with 408 atoms 221.7% 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 | | 2.706e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5279.00 ave 5279 max 5279 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 44716.0 ave 44716 max 44716 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 89432.0 ave 89432 max 89432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89432 Ave neighs/atom = 219.19608 Neighbor list builds = 0 Dangerous builds = 0 408 -1387.24750749788 eV 2.60455840173503 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00