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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -72.829637 0.0000000) to (44.598862 72.829637 9.0103308) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1576915 5.2021169 6.0068872 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -72.829637 0.0000000) to (44.598862 72.829637 9.0103308) create_atoms CPU = 0.009 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1576915 5.2021169 6.0068872 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -72.829637 0.0000000) to (44.598862 72.829637 9.0103308) create_atoms CPU = 0.008 seconds 2357 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 15 48 3 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 4692 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 15 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 6.214 | 6.214 | 6.214 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19274.924 0 -19274.924 14851.268 96 0 -19771.305 0 -19771.305 -3271.2248 Loop time of 5.42416 on 1 procs for 96 steps with 4692 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 = -19274.9243570944 -19771.2852901643 -19771.3047415389 Force two-norm initial, final = 322.39241 0.63250566 Force max component initial, final = 41.424642 0.082396095 Final line search alpha, max atom move = 0.93534112 0.077068456 Iterations, force evaluations = 96 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1111 | 5.1111 | 5.1111 | 0.0 | 94.23 Neigh | 0.18036 | 0.18036 | 0.18036 | 0.0 | 3.33 Comm | 0.050412 | 0.050412 | 0.050412 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08229 | | | 1.52 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10538.0 ave 10538 max 10538 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: 364696.0 ave 364696 max 364696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 364696 Ave neighs/atom = 77.727195 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 15 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.214 | 6.214 | 6.214 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -19771.305 0 -19771.305 -3271.2248 58533.252 103 0 -19772.399 0 -19772.399 -7.4504292 58357.423 Loop time of 0.260833 on 1 procs for 7 steps with 4692 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 = -19771.3047415389 -19772.3965607511 -19772.3987952447 Force two-norm initial, final = 347.30494 3.7821293 Force max component initial, final = 307.35400 3.0181388 Final line search alpha, max atom move = 9.7552096e-05 0.00029442576 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24713 | 0.24713 | 0.24713 | 0.0 | 94.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022226 | 0.0022226 | 0.0022226 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01148 | | | 4.40 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10491.0 ave 10491 max 10491 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: 364540.0 ave 364540 max 364540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 364540 Ave neighs/atom = 77.693947 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 15 47 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 6.351 | 6.351 | 6.351 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19772.399 0 -19772.399 -7.4504292 Loop time of 6.716e-06 on 1 procs for 0 steps with 4692 atoms 208.5% 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 | | 6.716e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10501.0 ave 10501 max 10501 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: 364600.0 ave 364600 max 364600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 364600 Ave neighs/atom = 77.706735 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 15 47 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 6.351 | 6.351 | 6.351 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 -19772.399 -19772.399 44.596279 144.76972 9.0389868 -7.4504292 -7.4504292 1.9135802 -82.355584 58.090716 2.2531258 2515.2667 Loop time of 6.825e-06 on 1 procs for 0 steps with 4692 atoms 293.0% 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 | | 6.825e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10501.0 ave 10501 max 10501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 182300.0 ave 182300 max 182300 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 364600.0 ave 364600 max 364600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 364600 Ave neighs/atom = 77.706735 Neighbor list builds = 0 Dangerous builds = 0 4692 -19772.3983260447 eV 2.25312577272935 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06