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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -44.682831 0.0000000) to (22.339985 44.682831 2.8603420) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0285219 4.0285219 2.8603420 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -44.682831 0.0000000) to (22.339985 44.682831 2.8603420) create_atoms CPU = 0.001 seconds 245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0285219 4.0285219 2.8603420 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -44.682831 0.0000000) to (22.339985 44.682831 2.8603420) create_atoms CPU = 0.000 seconds 245 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 23 1 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 484 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.501 | 4.501 | 4.501 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2055.2534 0 -2055.2534 -1734.5431 294 0 -2092.1494 0 -2092.1494 3001.2096 Loop time of 2.40899 on 1 procs for 294 steps with 484 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2055.25337439496 -2092.14751369441 -2092.14941824081 Force two-norm initial, final = 30.860442 0.19329610 Force max component initial, final = 10.350928 0.051653768 Final line search alpha, max atom move = 1.0000000 0.051653768 Iterations, force evaluations = 294 578 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3553 | 2.3553 | 2.3553 | 0.0 | 97.77 Neigh | 0.014351 | 0.014351 | 0.014351 | 0.0 | 0.60 Comm | 0.024974 | 0.024974 | 0.024974 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01437 | | | 0.60 Nlocal: 484.000 ave 484 max 484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5777.00 ave 5777 max 5777 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: 80720.0 ave 80720 max 80720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80720 Ave neighs/atom = 166.77686 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 294 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.501 | 4.501 | 4.501 Mbytes Step Temp E_pair E_mol TotEng Press Volume 294 0 -2092.1494 0 -2092.1494 3001.2096 5710.4656 382 0 -2109.1891 0 -2109.1891 46105.981 5587.049 Loop time of 0.45037 on 1 procs for 88 steps with 484 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2092.14941824081 -2109.18813203877 -2109.18908333193 Force two-norm initial, final = 402.23352 2.3296378 Force max component initial, final = 372.25095 0.76749086 Final line search alpha, max atom move = 0.00023094830 0.00017725071 Iterations, force evaluations = 88 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42862 | 0.42862 | 0.42862 | 0.0 | 95.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.004138 | 0.004138 | 0.004138 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01761 | | | 3.91 Nlocal: 484.000 ave 484 max 484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5770.00 ave 5770 max 5770 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: 80782.0 ave 80782 max 80782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80782 Ave neighs/atom = 166.90496 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.641 | 4.641 | 4.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2109.1891 0 -2109.1891 46105.981 Loop time of 1.502e-06 on 1 procs for 0 steps with 484 atoms 133.2% 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 | | 1.502e-06 | | |100.00 Nlocal: 484.000 ave 484 max 484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6105.00 ave 6105 max 6105 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: 80298.0 ave 80298 max 80298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80298 Ave neighs/atom = 165.90496 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.641 | 4.641 | 4.641 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 -2109.1891 -2109.1891 23.180548 89.365661 2.6970445 46105.981 46105.981 228.3715 137948.22 141.35012 2.3353205 2052.8689 Loop time of 1.558e-06 on 1 procs for 0 steps with 484 atoms 192.6% 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 | | 1.558e-06 | | |100.00 Nlocal: 484.000 ave 484 max 484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6105.00 ave 6105 max 6105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40149.0 ave 40149 max 40149 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80298.0 ave 80298 max 80298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80298 Ave neighs/atom = 165.90496 Neighbor list builds = 0 Dangerous builds = 0 484 -2109.18908333193 eV 2.33532051416756 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03