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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -40.445241 0.0000000) to (28.596615 40.445241 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3328205 5.5147802 4.9780318 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.445241 0.0000000) to (28.596615 40.445241 4.9780318) create_atoms CPU = 0.003 seconds 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3328205 5.5147802 4.9780318 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.445241 0.0000000) to (28.596615 40.445241 4.9780318) create_atoms CPU = 0.003 seconds 532 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.433 | 5.433 | 5.433 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4600.6174 0 -4600.6174 16733.339 42 0 -4642.7816 0 -4642.7816 -1071.2658 Loop time of 1.8633 on 1 procs for 42 steps with 1048 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 = -4600.61744825821 -4642.7775046926 -4642.78158772621 Force two-norm initial, final = 65.015065 0.20906301 Force max component initial, final = 15.239972 0.014444940 Final line search alpha, max atom move = 1.0000000 0.014444940 Iterations, force evaluations = 42 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8083 | 1.8083 | 1.8083 | 0.0 | 97.05 Neigh | 0.030898 | 0.030898 | 0.030898 | 0.0 | 1.66 Comm | 0.013461 | 0.013461 | 0.013461 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01063 | | | 0.57 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7538.00 ave 7538 max 7538 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: 234040.0 ave 234040 max 234040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234040 Ave neighs/atom = 223.32061 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.433 | 5.433 | 5.433 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -4642.7816 0 -4642.7816 -1071.2658 11515.153 44 0 -4642.7959 0 -4642.7959 1372.4641 11499.358 Loop time of 0.124528 on 1 procs for 2 steps with 1048 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 = -4642.78158772622 -4642.79530306065 -4642.79592275 Force two-norm initial, final = 28.933275 0.22156575 Force max component initial, final = 21.427237 0.044515722 Final line search alpha, max atom move = 0.00037928661 1.6884217e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12123 | 0.12123 | 0.12123 | 0.0 | 97.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081085 | 0.00081085 | 0.00081085 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002487 | | | 2.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7514.00 ave 7514 max 7514 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: 233856.0 ave 233856 max 233856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233856 Ave neighs/atom = 223.14504 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.571 | 5.571 | 5.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4642.7959 0 -4642.7959 1372.4641 Loop time of 6.826e-06 on 1 procs for 0 steps with 1048 atoms 161.1% 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 | | 6.826e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7514.00 ave 7514 max 7514 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: 233872.0 ave 233872 max 233872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233872 Ave neighs/atom = 223.16031 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.571 | 5.571 | 5.571 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 -4642.7959 -4642.7959 28.56882 80.890483 4.97604 1372.4641 1372.4641 -1.2416163 4124.8336 -6.1997815 2.251822 516.24753 Loop time of 6.966e-06 on 1 procs for 0 steps with 1048 atoms 244.0% 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 | | 6.966e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7514.00 ave 7514 max 7514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116936.0 ave 116936 max 116936 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 233872.0 ave 233872 max 233872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233872 Ave neighs/atom = 223.16031 Neighbor list builds = 0 Dangerous builds = 0 1048 -4614.2575031628 eV 2.25182196853755 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02