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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -42.836037 0.0000000) to (52.458783 42.836037 8.8671528) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9952895 5.5070251 5.9114352 Created 1691 atoms using lattice units in orthogonal box = (0.0000000 -42.836037 0.0000000) to (52.458783 42.836037 8.8671528) create_atoms CPU = 0.008 seconds 1691 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9952895 5.5070251 5.9114352 Created 1691 atoms using lattice units in orthogonal box = (0.0000000 -42.836037 0.0000000) to (52.458783 42.836037 8.8671528) create_atoms CPU = 0.007 seconds 1691 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 35 atoms, new total = 3347 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_313717476091_001#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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.670 | 5.670 | 5.670 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11619.766 0 -11619.766 13512.809 15 0 -11783.409 0 -11783.409 969.31845 Loop time of 3.50393 on 1 procs for 15 steps with 3347 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 = -11619.7663634279 -11783.4070127797 -11783.4094311746 Force two-norm initial, final = 112.72904 3.4739902 Force max component initial, final = 9.8369067 0.70261395 Final line search alpha, max atom move = 0.28683738 0.20153595 Iterations, force evaluations = 15 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4893 | 3.4893 | 3.4893 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0056098 | 0.0056098 | 0.0056098 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008975 | | | 0.26 Nlocal: 3347.00 ave 3347 max 3347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7961.00 ave 7961 max 7961 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: 259354.0 ave 259354 max 259354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259354 Ave neighs/atom = 77.488497 Neighbor list builds = 0 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.670 | 5.670 | 5.670 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -11783.409 0 -11783.409 969.31845 39851.226 18 0 -11783.507 0 -11783.507 2605.7649 39803.723 Loop time of 0.855526 on 1 procs for 3 steps with 3347 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11783.4094311746 -11783.5010364521 -11783.5066895248 Force two-norm initial, final = 85.890644 29.439403 Force max component initial, final = 79.387435 21.594847 Final line search alpha, max atom move = 0.0034972710 0.075523031 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84714 | 0.84714 | 0.84714 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012556 | 0.0012556 | 0.0012556 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007132 | | | 0.83 Nlocal: 3347.00 ave 3347 max 3347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7940.00 ave 7940 max 7940 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: 258502.0 ave 258502 max 258502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258502 Ave neighs/atom = 77.233941 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.807 | 5.807 | 5.807 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11783.507 0 -11783.507 2605.7649 Loop time of 6.114e-06 on 1 procs for 0 steps with 3347 atoms 212.6% 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 | | 6.114e-06 | | |100.00 Nlocal: 3347.00 ave 3347 max 3347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7926.00 ave 7926 max 7926 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: 258506.0 ave 258506 max 258506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258506 Ave neighs/atom = 77.235136 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.807 | 5.807 | 5.807 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 -11783.507 -11783.507 52.504934 85.672075 8.8487983 2605.7649 2605.7649 869.99888 6154.5136 792.78225 2.2718826 1888.4985 Loop time of 7.488e-06 on 1 procs for 0 steps with 3347 atoms 293.8% 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 | | 7.488e-06 | | |100.00 Nlocal: 3347.00 ave 3347 max 3347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7926.00 ave 7926 max 7926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129253.0 ave 129253 max 129253 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258506.0 ave 258506 max 258506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258506 Ave neighs/atom = 77.235136 Neighbor list builds = 0 Dangerous builds = 0 3347 -11783.5066895248 eV 2.2718825646493 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05