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 = 3.6461252 3.6461252 3.6461252 Created orthogonal box = (0.0000000 -64.403412 0.0000000) to (37.183327 64.403412 6.3152742) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7205119 5.7797934 6.3152742 Created 1247 atoms using lattice units in orthogonal box = (0.0000000 -64.403412 0.0000000) to (37.183327 64.403412 6.3152742) create_atoms CPU = 0.003 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7205119 5.7797934 6.3152742 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -64.403412 0.0000000) to (37.183327 64.403412 6.3152742) create_atoms CPU = 0.002 seconds 1251 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 9 30 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 2495 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_331285495617_004#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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 6.938 | 6.938 | 6.938 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9389.4834 0 -9389.4834 26130.196 65 0 -9698.5175 0 -9698.5175 3371.0663 Loop time of 2.17835 on 1 procs for 65 steps with 2495 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 = -9389.48338372782 -9698.50823324553 -9698.5175073395 Force two-norm initial, final = 345.79870 0.42230390 Force max component initial, final = 91.958203 0.082653106 Final line search alpha, max atom move = 1.0000000 0.082653106 Iterations, force evaluations = 65 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0653 | 2.0653 | 2.0653 | 0.0 | 94.81 Neigh | 0.072815 | 0.072815 | 0.072815 | 0.0 | 3.34 Comm | 0.022043 | 0.022043 | 0.022043 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01821 | | | 0.84 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12745.0 ave 12745 max 12745 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: 556490.0 ave 556490 max 556490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556490 Ave neighs/atom = 223.04208 Neighbor list builds = 2 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.939 | 6.939 | 6.939 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -9698.5175 0 -9698.5175 3371.0663 30246.793 68 0 -9698.632 0 -9698.632 23.662293 30307.548 Loop time of 0.112757 on 1 procs for 3 steps with 2495 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 = -9698.51750733951 -9698.63062066121 -9698.63203870673 Force two-norm initial, final = 130.72561 2.8317006 Force max component initial, final = 114.57589 2.0265082 Final line search alpha, max atom move = 9.3436409e-05 0.00018934965 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1085 | 0.1085 | 0.1085 | 0.0 | 96.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071243 | 0.00071243 | 0.00071243 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003547 | | | 3.15 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12781.0 ave 12781 max 12781 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: 556824.0 ave 556824 max 556824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556824 Ave neighs/atom = 223.17595 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 7.077 | 7.077 | 7.077 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9698.632 0 -9698.632 23.662293 Loop time of 2.583e-06 on 1 procs for 0 steps with 2495 atoms 154.9% 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 | | 2.583e-06 | | |100.00 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12785.0 ave 12785 max 12785 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: 556556.0 ave 556556 max 556556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556556 Ave neighs/atom = 223.06854 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 7.077 | 7.077 | 7.077 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 -9698.632 -9698.632 37.202111 129.03449 6.3136051 23.662293 23.662293 -87.79071 51.676687 107.1009 2.2983717 1058.8726 Loop time of 3.04e-06 on 1 procs for 0 steps with 2495 atoms 230.3% 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 | | 3.04e-06 | | |100.00 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12785.0 ave 12785 max 12785 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 278278.0 ave 278278 max 278278 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 556556.0 ave 556556 max 556556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556556 Ave neighs/atom = 223.06854 Neighbor list builds = 0 Dangerous builds = 0 2495 -9698.63203870673 eV 2.29837169665983 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02