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 = 3.6584036 3.6584036 3.6584036 Created orthogonal box = (0.0000000 -47.979513 0.0000000) to (33.926639 47.979513 5.1737640) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3119329 6.1369145 5.1737640 Created 686 atoms using lattice units in orthogonal box = (0.0000000 -47.979513 0.0000000) to (33.926639 47.979513 5.1737640) create_atoms CPU = 0.002 seconds 686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3119329 6.1369145 5.1737640 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -47.979513 0.0000000) to (33.926639 47.979513 5.1737640) create_atoms CPU = 0.002 seconds 694 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 27 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1380 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_143977152728_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.081 | 5.081 | 5.081 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4864.4162 0 -4864.4162 102504.56 941 0 -5455.0339 0 -5455.0339 -60708.295 Loop time of 19.2607 on 1 procs for 941 steps with 1380 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 = -4864.41617526222 -5455.02993170879 -5455.03394958222 Force two-norm initial, final = 752.79703 0.21027199 Force max component initial, final = 113.16208 0.091289762 Final line search alpha, max atom move = 0.79609746 0.072675548 Iterations, force evaluations = 941 1805 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.706 | 18.706 | 18.706 | 0.0 | 97.12 Neigh | 0.25593 | 0.25593 | 0.25593 | 0.0 | 1.33 Comm | 0.15647 | 0.15647 | 0.15647 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1421 | | | 0.74 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7325.00 ave 7325 max 7325 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: 186846.0 ave 186846 max 186846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186846 Ave neighs/atom = 135.39565 Neighbor list builds = 20 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 941 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.086 | 5.086 | 5.086 Mbytes Step Temp E_pair E_mol TotEng Press Volume 941 0 -5455.0339 0 -5455.0339 -60708.295 16843.537 986 0 -5484.0702 0 -5484.0702 -30.060243 16125.429 Loop time of 0.513122 on 1 procs for 45 steps with 1380 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 = -5455.03394958228 -5484.06764755235 -5484.07015491678 Force two-norm initial, final = 1266.3251 3.3903014 Force max component initial, final = 1126.1958 1.3510792 Final line search alpha, max atom move = 0.00012986398 0.00017545653 Iterations, force evaluations = 45 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4928 | 0.4928 | 0.4928 | 0.0 | 96.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002964 | 0.002964 | 0.002964 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01736 | | | 3.38 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7335.00 ave 7335 max 7335 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: 186540.0 ave 186540 max 186540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186540 Ave neighs/atom = 135.17391 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.227 | 5.227 | 5.227 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5484.0702 0 -5484.0702 -30.060243 Loop time of 3.922e-06 on 1 procs for 0 steps with 1380 atoms 204.0% 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 | | 3.922e-06 | | |100.00 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7646.00 ave 7646 max 7646 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: 193026.0 ave 193026 max 193026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193026 Ave neighs/atom = 139.87391 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.227 | 5.227 | 5.227 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 -5484.0702 -5484.0702 33.748837 96.627563 4.9448309 -30.060243 -30.060243 -133.53584 -65.73193 109.08705 2.2498455 4923.4255 Loop time of 2.572e-06 on 1 procs for 0 steps with 1380 atoms 311.0% 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 | | 2.572e-06 | | |100.00 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7646.00 ave 7646 max 7646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96513.0 ave 96513 max 96513 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 193026.0 ave 193026 max 193026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193026 Ave neighs/atom = 139.87391 Neighbor list builds = 0 Dangerous builds = 0 1380 -5484.07015491678 eV 2.24984547616934 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20