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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -65.277437 0.0000000) to (23.079059 65.277437 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1919427 5.5724642 5.0973115 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -65.277437 0.0000000) to (23.079059 65.277437 5.0973115) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1919427 5.5724642 5.0973115 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -65.277437 0.0000000) to (23.079059 65.277437 5.0973115) create_atoms CPU = 0.001 seconds 658 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 43 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1314 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5413.9925 0 -5413.9925 43867.804 448 0 -5581.4181 0 -5581.4181 3048.5193 Loop time of 44.1093 on 1 procs for 448 steps with 1314 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 = -5413.99253251453 -5581.41279809098 -5581.41814310012 Force two-norm initial, final = 459.84814 0.19811935 Force max component initial, final = 100.51527 0.058309577 Final line search alpha, max atom move = 0.97502012 0.056853010 Iterations, force evaluations = 448 871 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 43.858 | 43.858 | 43.858 | 0.0 | 99.43 Neigh | 0.11083 | 0.11083 | 0.11083 | 0.0 | 0.25 Comm | 0.073869 | 0.073869 | 0.073869 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06675 | | | 0.15 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6135.00 ave 6135 max 6135 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: 102572.0 ave 102572 max 102572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102572 Ave neighs/atom = 78.060883 Neighbor list builds = 13 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 448 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.063 | 5.063 | 5.063 Mbytes Step Temp E_pair E_mol TotEng Press Volume 448 0 -5581.4181 0 -5581.4181 3048.5193 15358.626 453 0 -5581.6074 0 -5581.6074 -226.73866 15389.55 Loop time of 0.369748 on 1 procs for 5 steps with 1314 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 = -5581.41814310012 -5581.60199083715 -5581.60737606238 Force two-norm initial, final = 80.950567 3.9396181 Force max component initial, final = 77.639162 3.0356145 Final line search alpha, max atom move = 0.00010347456 0.00031410887 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36724 | 0.36724 | 0.36724 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038756 | 0.00038756 | 0.00038756 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002124 | | | 0.57 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6093.00 ave 6093 max 6093 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: 102548.0 ave 102548 max 102548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102548 Ave neighs/atom = 78.042618 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.202 | 5.202 | 5.202 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5581.6074 0 -5581.6074 -226.73866 Loop time of 2.476e-06 on 1 procs for 0 steps with 1314 atoms 201.9% 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 | | 2.476e-06 | | |100.00 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6093.00 ave 6093 max 6093 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: 102460.0 ave 102460 max 102460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102460 Ave neighs/atom = 77.975647 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.202 | 5.202 | 5.202 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 -5581.6074 -5581.6074 23.030332 131.18816 5.0936733 -226.73866 -226.73866 -164.82542 -199.58412 -315.80643 2.3696152 3658.6157 Loop time of 2.785e-06 on 1 procs for 0 steps with 1314 atoms 251.3% 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 | | 2.785e-06 | | |100.00 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6093.00 ave 6093 max 6093 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51230.0 ave 51230 max 51230 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102460.0 ave 102460 max 102460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102460 Ave neighs/atom = 77.975647 Neighbor list builds = 0 Dangerous builds = 0 1314 -5581.60737606238 eV 2.36961515982034 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:44