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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -46.631982 0.0000000) to (9.5187134 46.631982 7.0300358) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3266879 4.2392711 4.6866905 Created 263 atoms using lattice units in orthogonal box = (0.0000000 -46.631982 0.0000000) to (9.5187134 46.631982 7.0300358) create_atoms CPU = 0.002 seconds 263 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3266879 4.2392711 4.6866905 Created 265 atoms using lattice units in orthogonal box = (0.0000000 -46.631982 0.0000000) to (9.5187134 46.631982 7.0300358) create_atoms CPU = 0.001 seconds 265 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 = 4 31 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 0 atoms, new total = 528 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 = 4 31 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) = 4.492 | 4.492 | 4.492 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2127.2424 0 -2127.2424 42304.43 61 0 -2248.0442 0 -2248.0442 10607.384 Loop time of 0.462833 on 1 procs for 61 steps with 528 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2127.24244431377 -2248.04233761861 -2248.04416243472 Force two-norm initial, final = 136.30498 0.14469072 Force max component initial, final = 45.456059 0.032743630 Final line search alpha, max atom move = 1.0000000 0.032743630 Iterations, force evaluations = 61 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43383 | 0.43383 | 0.43383 | 0.0 | 93.73 Neigh | 0.013429 | 0.013429 | 0.013429 | 0.0 | 2.90 Comm | 0.0074002 | 0.0074002 | 0.0074002 | 0.0 | 1.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008172 | | | 1.77 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3172.00 ave 3172 max 3172 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: 34676.0 ave 34676 max 34676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34676 Ave neighs/atom = 65.674242 Neighbor list builds = 2 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 = 4 31 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.491 | 4.491 | 4.491 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -2248.0442 0 -2248.0442 10607.384 6240.9349 69 0 -2248.2889 0 -2248.2889 -48.377901 6280.428 Loop time of 0.0508492 on 1 procs for 8 steps with 528 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2248.04416243472 -2248.28880257237 -2248.28886924098 Force two-norm initial, final = 82.384567 0.57212138 Force max component initial, final = 74.520201 0.40844877 Final line search alpha, max atom move = 0.00086566086 0.00035357812 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.047169 | 0.047169 | 0.047169 | 0.0 | 92.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085253 | 0.00085253 | 0.00085253 | 0.0 | 1.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002828 | | | 5.56 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3109.00 ave 3109 max 3109 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: 34590.0 ave 34590 max 34590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34590 Ave neighs/atom = 65.511364 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 = 4 31 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) = 4.629 | 4.629 | 4.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2248.2889 0 -2248.2889 -48.377901 Loop time of 6.405e-06 on 1 procs for 0 steps with 528 atoms 203.0% 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 | | 6.405e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3101.00 ave 3101 max 3101 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: 34462.0 ave 34462 max 34462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34462 Ave neighs/atom = 65.268939 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 = 4 31 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) = 4.629 | 4.629 | 4.629 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 -2248.2889 -2248.2889 9.5149962 93.899252 7.0294038 -48.377901 -48.377901 -104.15715 -72.673722 31.697166 2.3174236 325.58363 Loop time of 6.354e-06 on 1 procs for 0 steps with 528 atoms 267.5% 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 | | 6.354e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3101.00 ave 3101 max 3101 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17231.0 ave 17231 max 17231 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34462.0 ave 34462 max 34462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34462 Ave neighs/atom = 65.268939 Neighbor list builds = 0 Dangerous builds = 0 528 -2248.28881644098 eV 2.31742355015755 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00