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 = 3.4524642 3.4524642 3.4524642 Created orthogonal box = (0.0000000 -50.268637 0.0000000) to (25.134319 50.268637 3.4524642) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2680919 4.2680919 3.4524642 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -50.268637 0.0000000) to (25.134319 50.268637 3.4524642) create_atoms CPU = 0.002 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2680919 4.2680919 3.4524642 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -50.268637 0.0000000) to (25.134319 50.268637 3.4524642) create_atoms CPU = 0.001 seconds 426 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 26 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 846 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.016 | 5.016 | 5.016 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3689.9979 0 -3689.9979 32194.442 79 0 -3796.1125 0 -3796.1125 13636.353 Loop time of 2.95895 on 1 procs for 79 steps with 846 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 = -3689.99794874302 -3796.10901001266 -3796.11248463947 Force two-norm initial, final = 240.00636 0.20415514 Force max component initial, final = 81.778571 0.051169899 Final line search alpha, max atom move = 1.0000000 0.051169899 Iterations, force evaluations = 79 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8862 | 2.8862 | 2.8862 | 0.0 | 97.54 Neigh | 0.022159 | 0.022159 | 0.022159 | 0.0 | 0.75 Comm | 0.031745 | 0.031745 | 0.031745 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01888 | | | 0.64 Nlocal: 846.000 ave 846 max 846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8736.00 ave 8736 max 8736 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: 168552.0 ave 168552 max 168552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168552 Ave neighs/atom = 199.23404 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.016 | 5.016 | 5.016 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -3796.1125 0 -3796.1125 13636.353 8724.1557 86 0 -3796.5665 0 -3796.5665 528.41378 8752.8152 Loop time of 0.188556 on 1 procs for 7 steps with 846 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3796.11248463946 -3796.56445870234 -3796.56651349798 Force two-norm initial, final = 164.62225 5.0919528 Force max component initial, final = 157.81724 3.6185828 Final line search alpha, max atom move = 0.00016798818 0.00060787915 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18136 | 0.18136 | 0.18136 | 0.0 | 96.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017975 | 0.0017975 | 0.0017975 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005395 | | | 2.86 Nlocal: 846.000 ave 846 max 846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8742.00 ave 8742 max 8742 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: 168628.0 ave 168628 max 168628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168628 Ave neighs/atom = 199.32388 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.154 | 5.154 | 5.154 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3796.5665 0 -3796.5665 528.41378 Loop time of 6.034e-06 on 1 procs for 0 steps with 846 atoms 182.3% 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 | | 6.034e-06 | | |100.00 Nlocal: 846.000 ave 846 max 846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8754.00 ave 8754 max 8754 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: 168460.0 ave 168460 max 168460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168460 Ave neighs/atom = 199.12530 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.154 | 5.154 | 5.154 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 -3796.5665 -3796.5665 25.104029 101.17428 3.4461504 528.41378 528.41378 433.83383 666.56746 484.84006 2.2046524 366.6643 Loop time of 7.057e-06 on 1 procs for 0 steps with 846 atoms 269.2% 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 | | 7.057e-06 | | |100.00 Nlocal: 846.000 ave 846 max 846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8754.00 ave 8754 max 8754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84230.0 ave 84230 max 84230 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 168460.0 ave 168460 max 168460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168460 Ave neighs/atom = 199.12530 Neighbor list builds = 0 Dangerous builds = 0 846 -3796.56651350007 eV 2.20465244635836 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03