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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -44.667491 0.0000000) to (21.056457 44.667491 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1930757 6.1308321 5.1069410 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -44.667491 0.0000000) to (21.056457 44.667491 5.1069410) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1930757 6.1308321 5.1069410 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -44.667491 0.0000000) to (21.056457 44.667491 5.1069410) create_atoms CPU = 0.001 seconds 412 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 34 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 820 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_137964310702_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.921 | 4.921 | 4.921 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3229.7472 0 -3229.7472 61076.747 53 0 -3473.6914 0 -3473.6914 11359.383 Loop time of 3.94723 on 1 procs for 53 steps with 820 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 = -3229.74719845378 -3473.68866523657 -3473.69135485444 Force two-norm initial, final = 382.39944 0.20736681 Force max component initial, final = 110.20080 0.024151408 Final line search alpha, max atom move = 1.0000000 0.024151408 Iterations, force evaluations = 53 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.925 | 3.925 | 3.925 | 0.0 | 99.44 Neigh | 0.014592 | 0.014592 | 0.014592 | 0.0 | 0.37 Comm | 0.0032777 | 0.0032777 | 0.0032777 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004344 | | | 0.11 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3362.00 ave 3362 max 3362 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: 44312.0 ave 44312 max 44312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44312 Ave neighs/atom = 54.039024 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.921 | 4.921 | 4.921 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -3473.6914 0 -3473.6914 11359.383 9606.5556 59 0 -3473.9762 0 -3473.9762 -22.462326 9671.3136 Loop time of 0.37926 on 1 procs for 6 steps with 820 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 = -3473.69135485444 -3473.97588965264 -3473.97624521434 Force two-norm initial, final = 123.32446 0.82720570 Force max component initial, final = 97.033497 0.49830435 Final line search alpha, max atom move = 0.00026693741 0.00013301607 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37748 | 0.37748 | 0.37748 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026002 | 0.00026002 | 0.00026002 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00152 | | | 0.40 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3407.00 ave 3407 max 3407 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: 44456.0 ave 44456 max 44456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44456 Ave neighs/atom = 54.214634 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.059 | 5.059 | 5.059 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3473.9762 0 -3473.9762 -22.462326 Loop time of 1.627e-06 on 1 procs for 0 steps with 820 atoms 184.4% 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 | | 1.627e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3389.00 ave 3389 max 3389 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: 44416.0 ave 44416 max 44416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44416 Ave neighs/atom = 54.165854 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.059 | 5.059 | 5.059 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 -3473.9762 -3473.9762 21.088486 89.764019 5.1090221 -22.462326 -22.462326 71.458906 -56.261769 -82.584114 2.3376857 482.57561 Loop time of 1.687e-06 on 1 procs for 0 steps with 820 atoms 177.8% 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 | | 1.687e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3389.00 ave 3389 max 3389 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22208.0 ave 22208 max 22208 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44416.0 ave 44416 max 44416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44416 Ave neighs/atom = 54.165854 Neighbor list builds = 0 Dangerous builds = 0 820 -3473.97624521434 eV 2.3376857420639 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04