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 -48.940391 0.0000000) to (59.934533 48.940391 9.9204345) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7471470 6.0332475 6.6136230 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -48.940391 0.0000000) to (59.934533 48.940391 9.9204345) create_atoms CPU = 0.002 seconds 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7471470 6.0332475 6.6136230 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -48.940391 0.0000000) to (59.934533 48.940391 9.9204345) create_atoms CPU = 0.002 seconds 1756 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 26 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 80 atoms, new total = 3432 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 26 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) = 6.541 | 6.541 | 6.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11455.233 0 -11455.233 -1278.505 38 0 -11507.769 0 -11507.769 -10344.63 Loop time of 1.26158 on 1 procs for 38 steps with 3432 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 = -11455.2328882643 -11507.7591669664 -11507.7694588395 Force two-norm initial, final = 18.328539 0.24398489 Force max component initial, final = 3.1944518 0.013736529 Final line search alpha, max atom move = 1.0000000 0.013736529 Iterations, force evaluations = 38 60 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2185 | 1.2185 | 1.2185 | 0.0 | 96.58 Neigh | 0.027107 | 0.027107 | 0.027107 | 0.0 | 2.15 Comm | 0.0060861 | 0.0060861 | 0.0060861 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009899 | | | 0.78 Nlocal: 3432.00 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9529.00 ave 9529 max 9529 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: 448740.0 ave 448740 max 448740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448740 Ave neighs/atom = 130.75175 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 16 26 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 : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.541 | 6.541 | 6.541 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -11507.769 0 -11507.769 -10344.63 58197.623 45 0 -11509.454 0 -11509.454 -2290.4972 57622.483 Loop time of 0.191929 on 1 procs for 7 steps with 3432 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 = -11507.7694588394 -11509.4453039637 -11509.454141844 Force two-norm initial, final = 465.33769 11.470604 Force max component initial, final = 376.86002 10.220646 Final line search alpha, max atom move = 4.8938923e-05 0.00050018743 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18619 | 0.18619 | 0.18619 | 0.0 | 97.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074651 | 0.00074651 | 0.00074651 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004993 | | | 2.60 Nlocal: 3432.00 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9526.00 ave 9526 max 9526 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: 448872.0 ave 448872 max 448872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448872 Ave neighs/atom = 130.79021 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 26 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) = 6.679 | 6.679 | 6.679 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11509.454 0 -11509.454 -2290.4972 Loop time of 2.238e-06 on 1 procs for 0 steps with 3432 atoms 178.7% 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 | | 2.238e-06 | | |100.00 Nlocal: 3432.00 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9529.00 ave 9529 max 9529 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: 449520.0 ave 449520 max 449520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449520 Ave neighs/atom = 130.97902 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 26 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) = 6.679 | 6.679 | 6.679 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 -11509.454 -11509.454 59.741448 97.880782 9.8541416 -2290.4972 -2290.4972 283.2666 -7297.7938 143.03566 2.6565064 2474.4828 Loop time of 2.512e-06 on 1 procs for 0 steps with 3432 atoms 199.0% 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 | | 2.512e-06 | | |100.00 Nlocal: 3432.00 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9529.00 ave 9529 max 9529 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 224760.0 ave 224760 max 224760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 449520.0 ave 449520 max 449520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449520 Ave neighs/atom = 130.97902 Neighbor list builds = 0 Dangerous builds = 0 3432 -11509.454141844 eV 2.65650639472155 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02