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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -38.852378 0.0000000) to (19.426189 38.852378 3.6073527) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6890801 4.6890801 3.6073527 Created 231 atoms using lattice units in orthogonal box = (0.0000000 -38.852378 0.0000000) to (19.426189 38.852378 3.6073527) create_atoms CPU = 0.001 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6890801 4.6890801 3.6073527 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -38.852378 0.0000000) to (19.426189 38.852378 3.6073527) create_atoms CPU = 0.000 seconds 233 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 13 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 464 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_151002396060_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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.364 | 5.364 | 5.364 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1528.9589 0 -1528.9589 43393.881 47 0 -1625.0166 0 -1625.0166 9059.1219 Loop time of 1.27525 on 1 procs for 47 steps with 464 atoms 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1528.95888008541 -1625.01522954306 -1625.01664830198 Force two-norm initial, final = 161.16765 0.15539489 Force max component initial, final = 37.022323 0.029506800 Final line search alpha, max atom move = 1.0000000 0.029506800 Iterations, force evaluations = 47 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2477 | 1.2477 | 1.2477 | 0.0 | 97.84 Neigh | 0.014381 | 0.014381 | 0.014381 | 0.0 | 1.13 Comm | 0.0091381 | 0.0091381 | 0.0091381 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004065 | | | 0.32 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9804.00 ave 9804 max 9804 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: 292594.0 ave 292594 max 292594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292594 Ave neighs/atom = 630.59052 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.364 | 5.364 | 5.364 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1625.0166 0 -1625.0166 9059.1219 5445.3251 55 0 -1625.2219 0 -1625.2219 153.16474 5480.0687 Loop time of 0.146464 on 1 procs for 8 steps with 464 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 = -1625.01664830199 -1625.22157663885 -1625.22191669663 Force two-norm initial, final = 62.236258 0.96544508 Force max component initial, final = 52.287418 0.55194053 Final line search alpha, max atom move = 0.0011846295 0.00065384504 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14274 | 0.14274 | 0.14274 | 0.0 | 97.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086449 | 0.00086449 | 0.00086449 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00286 | | | 1.95 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9788.00 ave 9788 max 9788 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: 292598.0 ave 292598 max 292598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292598 Ave neighs/atom = 630.59914 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.502 | 5.502 | 5.502 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1625.2219 0 -1625.2219 153.16474 Loop time of 1.961e-06 on 1 procs for 0 steps with 464 atoms 153.0% 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 | | 1.961e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9786.00 ave 9786 max 9786 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: 290138.0 ave 290138 max 290138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290138 Ave neighs/atom = 625.29741 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.502 | 5.502 | 5.502 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 -1625.2219 -1625.2219 19.364744 78.176385 3.6199174 153.16474 153.16474 160.85731 138.98887 159.64806 2.2941595 290.4787 Loop time of 2.417e-06 on 1 procs for 0 steps with 464 atoms 206.9% 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 | | 2.417e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9786.00 ave 9786 max 9786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145069.0 ave 145069 max 145069 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 290138.0 ave 290138 max 290138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290138 Ave neighs/atom = 625.29741 Neighbor list builds = 0 Dangerous builds = 0 464 -1625.22191669663 eV 2.29415949528903 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01