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 = 3.4921275 3.4921275 3.4921275 Created orthogonal box = (0.0000000 -66.808334 0.0000000) to (38.571809 66.808334 6.0485423) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6909227 5.1110201 6.0485423 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -66.808334 0.0000000) to (38.571809 66.808334 6.0485423) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6909227 5.1110201 6.0485423 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -66.808334 0.0000000) to (38.571809 66.808334 6.0485423) create_atoms CPU = 0.003 seconds 1466 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 10 34 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 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2924 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_270337113239_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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 7.012 | 7.012 | 7.012 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9482.5777 0 -9482.5777 21880.451 67 0 -9692.4557 0 -9692.4557 1325.3239 Loop time of 3.2578 on 1 procs for 67 steps with 2924 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9482.57768008377 -9692.44613319086 -9692.4556636308 Force two-norm initial, final = 318.39992 0.27673695 Force max component initial, final = 71.965468 0.031884575 Final line search alpha, max atom move = 1.0000000 0.031884575 Iterations, force evaluations = 67 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.113 | 3.113 | 3.113 | 0.0 | 95.55 Neigh | 0.10112 | 0.10112 | 0.10112 | 0.0 | 3.10 Comm | 0.022339 | 0.022339 | 0.022339 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02139 | | | 0.66 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12863.0 ave 12863 max 12863 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: 582820.0 ave 582820 max 582820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582820 Ave neighs/atom = 199.32285 Neighbor list builds = 3 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.013 | 7.013 | 7.013 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -9692.4557 0 -9692.4557 1325.3239 31173.199 69 0 -9692.4765 0 -9692.4765 -16.111295 31213.628 Loop time of 0.143722 on 1 procs for 2 steps with 2924 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 = -9692.45566363069 -9692.47419256958 -9692.47651753079 Force two-norm initial, final = 46.232594 0.79152459 Force max component initial, final = 35.070230 0.54508154 Final line search alpha, max atom move = 0.00015384985 8.3860713e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14031 | 0.14031 | 0.14031 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055904 | 0.00055904 | 0.00055904 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002853 | | | 1.99 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12742.0 ave 12742 max 12742 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: 583012.0 ave 583012 max 583012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583012 Ave neighs/atom = 199.38851 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 7.151 | 7.151 | 7.151 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9692.4765 0 -9692.4765 -16.111295 Loop time of 2.568e-06 on 1 procs for 0 steps with 2924 atoms 155.8% 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 | | 2.568e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12714.0 ave 12714 max 12714 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: 582896.0 ave 582896 max 582896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582896 Ave neighs/atom = 199.34884 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 7.151 | 7.151 | 7.151 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 -9692.4765 -9692.4765 38.570394 133.75235 6.0504651 -16.111295 -16.111295 -25.346239 -28.007114 5.0194685 2.2424264 814.57251 Loop time of 2.302e-06 on 1 procs for 0 steps with 2924 atoms 304.1% 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 | | 2.302e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12714.0 ave 12714 max 12714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291448.0 ave 291448 max 291448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 582896.0 ave 582896 max 582896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582896 Ave neighs/atom = 199.34884 Neighbor list builds = 0 Dangerous builds = 0 2924 -9569.01461724116 eV 2.24242638767492 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04