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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -63.750352 0.0000000) to (22.539153 63.750352 4.9780662) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0470899 5.4421033 4.9780662 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -63.750352 0.0000000) to (22.539153 63.750352 4.9780662) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0470899 5.4421033 4.9780662 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.750352 0.0000000) to (22.539153 63.750352 4.9780662) 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 6 31 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.541 | 5.541 | 5.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4931.2505 0 -4931.2505 166530.61 106 0 -5826.2897 0 -5826.2897 4236.1014 Loop time of 2.88161 on 1 procs for 106 steps with 1312 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4931.25047979387 -5826.28507094964 -5826.28972224057 Force two-norm initial, final = 2421.8143 0.22667796 Force max component initial, final = 535.53858 0.027339898 Final line search alpha, max atom move = 1.0000000 0.027339898 Iterations, force evaluations = 106 194 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7963 | 2.7963 | 2.7963 | 0.0 | 97.04 Neigh | 0.051827 | 0.051827 | 0.051827 | 0.0 | 1.80 Comm | 0.019481 | 0.019481 | 0.019481 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01404 | | | 0.49 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10400.0 ave 10400 max 10400 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: 293432.0 ave 293432 max 293432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293432 Ave neighs/atom = 223.65244 Neighbor list builds = 3 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.546 | 5.546 | 5.546 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -5826.2897 0 -5826.2897 4236.1014 14305.757 108 0 -5826.3361 0 -5826.3361 -0.65413739 14339.563 Loop time of 0.0736908 on 1 procs for 2 steps with 1312 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5826.28972224055 -5826.33554524995 -5826.33606615572 Force two-norm initial, final = 66.100131 0.47520196 Force max component initial, final = 44.223814 0.33395481 Final line search alpha, max atom move = 0.00027682370 9.2446606e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071608 | 0.071608 | 0.071608 | 0.0 | 97.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040802 | 0.00040802 | 0.00040802 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001675 | | | 2.27 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10424.0 ave 10424 max 10424 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: 293328.0 ave 293328 max 293328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293328 Ave neighs/atom = 223.57317 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.684 | 5.684 | 5.684 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5826.3361 0 -5826.3361 -0.65413739 Loop time of 1.86e-06 on 1 procs for 0 steps with 1312 atoms 161.3% 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 | | 1.86e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10415.0 ave 10415 max 10415 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: 293220.0 ave 293220 max 293220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293220 Ave neighs/atom = 223.49085 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.684 | 5.684 | 5.684 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 -5826.3361 -5826.3361 22.563322 127.60077 4.9805761 -0.65413739 -0.65413739 -21.203194 37.342453 -18.101672 2.3135084 426.36545 Loop time of 1.901e-06 on 1 procs for 0 steps with 1312 atoms 210.4% 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 | | 1.901e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10415.0 ave 10415 max 10415 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146610.0 ave 146610 max 146610 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 293220.0 ave 293220 max 293220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293220 Ave neighs/atom = 223.49085 Neighbor list builds = 0 Dangerous builds = 0 1312 -5790.56910699412 eV 2.31350840246258 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03