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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -68.302026 0.0000000) to (34.151013 68.302026 3.6200001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9883502 4.9883502 3.6200001 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -68.302026 0.0000000) to (34.151013 68.302026 3.6200001) create_atoms CPU = 0.001 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9883502 4.9883502 3.6200001 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -68.302026 0.0000000) to (34.151013 68.302026 3.6200001) create_atoms CPU = 0.001 seconds 714 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 = 9 36 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 2 atoms, new total = 1424 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 = 9 36 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) = 5.545 | 5.545 | 5.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4633.034 0 -4633.034 51368.471 108 0 -5029.1246 0 -5029.1246 4261.4431 Loop time of 2.70392 on 1 procs for 108 steps with 1424 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4633.03403706568 -5029.12073808046 -5029.12461340008 Force two-norm initial, final = 838.55573 0.19803946 Force max component initial, final = 232.14983 0.047513020 Final line search alpha, max atom move = 1.0000000 0.047513020 Iterations, force evaluations = 108 196 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6256 | 2.6256 | 2.6256 | 0.0 | 97.10 Neigh | 0.042305 | 0.042305 | 0.042305 | 0.0 | 1.56 Comm | 0.020906 | 0.020906 | 0.020906 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01508 | | | 0.56 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11280.0 ave 11280 max 11280 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: 248548.0 ave 248548 max 248548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248548 Ave neighs/atom = 174.54213 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 = 9 36 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 : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.544 | 5.544 | 5.544 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -5029.1246 0 -5029.1246 4261.4431 16887.904 113 0 -5029.3031 0 -5029.3031 -619.56343 16948.987 Loop time of 0.0975637 on 1 procs for 5 steps with 1424 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5029.12461340002 -5029.29840913925 -5029.30307591701 Force two-norm initial, final = 92.215939 12.952046 Force max component initial, final = 85.254453 11.642501 Final line search alpha, max atom move = 0.00012454632 0.0014500308 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.094209 | 0.094209 | 0.094209 | 0.0 | 96.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063587 | 0.00063587 | 0.00063587 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002719 | | | 2.79 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11276.0 ave 11276 max 11276 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: 248512.0 ave 248512 max 248512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248512 Ave neighs/atom = 174.51685 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 = 9 36 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) = 5.682 | 5.682 | 5.682 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5029.3031 0 -5029.3031 -619.56343 Loop time of 1.961e-06 on 1 procs for 0 steps with 1424 atoms 204.0% 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 | | 1.961e-06 | | |100.00 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11259.0 ave 11259 max 11259 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: 248360.0 ave 248360 max 248360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248360 Ave neighs/atom = 174.41011 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 = 9 36 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) = 5.682 | 5.682 | 5.682 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 -5029.3031 -5029.3031 34.157579 137.22921 3.6158474 -619.56343 -619.56343 -371.76706 -387.62776 -1099.2955 2.3113385 414.53886 Loop time of 2.346e-06 on 1 procs for 0 steps with 1424 atoms 255.8% 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 | | 2.346e-06 | | |100.00 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11259.0 ave 11259 max 11259 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124180.0 ave 124180 max 124180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 248360.0 ave 248360 max 248360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248360 Ave neighs/atom = 174.41011 Neighbor list builds = 0 Dangerous builds = 0 1424 -5029.30307591701 eV 2.3113385251381 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03