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 = 3.5273294 3.5273294 3.5273294 Created orthogonal box = (0.0000000 -57.312319 0.0000000) to (20.262965 57.312319 4.9883971) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5262631 6.0785793 4.9883971 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.312319 0.0000000) to (20.262965 57.312319 4.9883971) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5262631 6.0785793 4.9883971 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.312319 0.0000000) to (20.262965 57.312319 4.9883971) create_atoms CPU = 0.002 seconds 530 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 4 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 10.13295 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_758825945924_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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 4 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.315 | 6.315 | 6.315 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4230.5697 0 -4230.5697 35241.014 67 0 -4415.4197 0 -4415.4197 3921.3626 Loop time of 2.08031 on 1 procs for 67 steps with 1056 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 = -4230.56970659045 -4415.41567091342 -4415.41968246471 Force two-norm initial, final = 324.69605 0.27970914 Force max component initial, final = 104.83383 0.037348269 Final line search alpha, max atom move = 1.0000000 0.037348269 Iterations, force evaluations = 67 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0376 | 2.0376 | 2.0376 | 0.0 | 97.95 Neigh | 0.022544 | 0.022544 | 0.022544 | 0.0 | 1.08 Comm | 0.012081 | 0.012081 | 0.012081 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008113 | | | 0.39 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11388.0 ave 11388 max 11388 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: 402984.0 ave 402984 max 402984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 402984 Ave neighs/atom = 381.61364 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 4 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.315 | 6.315 | 6.315 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -4415.4197 0 -4415.4197 3921.3626 11586.226 74 0 -4415.9097 0 -4415.9097 -43.970693 11610.407 Loop time of 0.165123 on 1 procs for 7 steps with 1056 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 = -4415.4196824647 -4415.90913001189 -4415.90966149076 Force two-norm initial, final = 146.29596 0.73674721 Force max component initial, final = 136.98405 0.32737816 Final line search alpha, max atom move = 0.00024912847 8.1559220e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16069 | 0.16069 | 0.16069 | 0.0 | 97.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008286 | 0.0008286 | 0.0008286 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003605 | | | 2.18 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11354.0 ave 11354 max 11354 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: 402668.0 ave 402668 max 402668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 402668 Ave neighs/atom = 381.31439 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 4 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.454 | 6.454 | 6.454 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4415.9097 0 -4415.9097 -43.970693 Loop time of 2.079e-06 on 1 procs for 0 steps with 1056 atoms 336.7% 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 | | 2.079e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11404.0 ave 11404 max 11404 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: 402112.0 ave 402112 max 402112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 402112 Ave neighs/atom = 380.78788 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 4 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.454 | 6.454 | 6.454 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 -4415.9097 -4415.9097 20.184598 115.27843 4.9897556 -43.970693 -43.970693 -42.096143 -44.62713 -45.188807 2.286609 411.22456 Loop time of 2.938e-06 on 1 procs for 0 steps with 1056 atoms 238.3% 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 | | 2.938e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11404.0 ave 11404 max 11404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 201056.0 ave 201056 max 201056 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 402112.0 ave 402112 max 402112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 402112 Ave neighs/atom = 380.78788 Neighbor list builds = 0 Dangerous builds = 0 1056 -4415.90966149076 eV 2.28660898619852 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02