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 = 4.0500004 4.0500004 4.0500004 Created orthogonal box = (0.0000000 -47.924301 0.0000000) to (58.690082 47.924301 9.9204345) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7074379 6.1611751 6.6136230 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -47.924301 0.0000000) to (58.690082 47.924301 9.9204345) create_atoms CPU = 0.002 seconds 1688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7074379 6.1611751 6.6136230 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -47.924301 0.0000000) to (58.690082 47.924301 9.9204345) create_atoms CPU = 0.002 seconds 1688 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 = 16 25 3 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 56 atoms, new total = 3320 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_820335782779_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 = 16 25 3 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) = 6.524 | 6.524 | 6.524 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11009.692 0 -11009.692 5943.8984 40 0 -11121.918 0 -11121.918 -1819.0262 Loop time of 1.28936 on 1 procs for 40 steps with 3320 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 = -11009.6921311106 -11121.9098638572 -11121.9181437553 Force two-norm initial, final = 58.279691 0.26733487 Force max component initial, final = 6.4098512 0.052508206 Final line search alpha, max atom move = 1.0000000 0.052508206 Iterations, force evaluations = 40 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.275 | 1.275 | 1.275 | 0.0 | 98.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0055465 | 0.0055465 | 0.0055465 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008811 | | | 0.68 Nlocal: 3320.00 ave 3320 max 3320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9248.00 ave 9248 max 9248 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: 436352.0 ave 436352 max 436352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436352 Ave neighs/atom = 131.43133 Neighbor list builds = 0 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 = 16 25 3 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.524 | 6.524 | 6.524 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -11121.918 0 -11121.918 -1819.0262 55806.038 43 0 -11122.137 0 -11122.137 1173.891 55598.525 Loop time of 0.0928835 on 1 procs for 3 steps with 3320 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 = -11121.9181437553 -11122.1367309676 -11122.1371080021 Force two-norm initial, final = 166.03257 0.74974161 Force max component initial, final = 124.69737 0.50472815 Final line search alpha, max atom move = 0.00030868642 0.00015580272 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090569 | 0.090569 | 0.090569 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034022 | 0.00034022 | 0.00034022 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001974 | | | 2.13 Nlocal: 3320.00 ave 3320 max 3320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9270.00 ave 9270 max 9270 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: 435106.0 ave 435106 max 435106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 435106 Ave neighs/atom = 131.05602 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 = 16 25 3 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) = 6.662 | 6.662 | 6.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11122.137 0 -11122.137 1173.891 Loop time of 1.778e-06 on 1 procs for 0 steps with 3320 atoms 112.5% 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 | | 1.778e-06 | | |100.00 Nlocal: 3320.00 ave 3320 max 3320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9272.00 ave 9272 max 9272 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: 435302.0 ave 435302 max 435302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 435302 Ave neighs/atom = 131.11506 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 = 16 25 3 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) = 6.662 | 6.662 | 6.662 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 -11122.137 -11122.137 58.564842 95.848602 9.9046815 1173.891 1173.891 12.650337 3494.501 14.521599 2.6150941 2995.7857 Loop time of 2.014e-06 on 1 procs for 0 steps with 3320 atoms 198.6% 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 | | 2.014e-06 | | |100.00 Nlocal: 3320.00 ave 3320 max 3320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9272.00 ave 9272 max 9272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 217651.0 ave 217651 max 217651 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 435302.0 ave 435302 max 435302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 435302 Ave neighs/atom = 131.11506 Neighbor list builds = 0 Dangerous builds = 0 3320 -11122.1371080021 eV 2.61509410626628 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01