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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -43.286871 0.0000000) to (53.010893 43.286871 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0583878 5.5649845 5.9736509 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -43.286871 0.0000000) to (53.010893 43.286871 8.9604763) create_atoms CPU = 0.003 seconds 1687 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0583878 5.5649845 5.9736509 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -43.286871 0.0000000) to (53.010893 43.286871 8.9604763) create_atoms CPU = 0.003 seconds 1687 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 3343 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.524 | 6.524 | 6.524 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12854.962 0 -12854.962 8281.3744 1010 0 -13188.901 0 -13188.901 -71594.092 Loop time of 43.6242 on 1 procs for 1010 steps with 3343 atoms 96.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12854.9615035447 -13188.8898119214 -13188.9009276785 Force two-norm initial, final = 90.021566 0.32032433 Force max component initial, final = 7.9325799 0.049424358 Final line search alpha, max atom move = 1.0000000 0.049424358 Iterations, force evaluations = 1010 1921 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 42.409 | 42.409 | 42.409 | 0.0 | 97.21 Neigh | 0.76071 | 0.76071 | 0.76071 | 0.0 | 1.74 Comm | 0.18094 | 0.18094 | 0.18094 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2736 | | | 0.63 Nlocal: 3343.00 ave 3343 max 3343 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9848.00 ave 9848 max 9848 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: 459938.0 ave 459938 max 459938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459938 Ave neighs/atom = 137.58241 Neighbor list builds = 24 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1010 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.527 | 6.527 | 6.527 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1010 0 -13188.901 0 -13188.901 -71594.092 41122.774 1055 0 -13241.977 0 -13241.977 -33212.691 40228.856 Loop time of 1.09107 on 1 procs for 45 steps with 3343 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 = -13188.9009276785 -13241.9666823905 -13241.9774359908 Force two-norm initial, final = 2498.4712 4.8763283 Force max component initial, final = 2497.9458 0.73492932 Final line search alpha, max atom move = 4.6693870e-05 3.4316694e-05 Iterations, force evaluations = 45 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9977 | 0.9977 | 0.9977 | 0.0 | 91.44 Neigh | 0.060119 | 0.060119 | 0.060119 | 0.0 | 5.51 Comm | 0.0042867 | 0.0042867 | 0.0042867 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02897 | | | 2.66 Nlocal: 3343.00 ave 3343 max 3343 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9812.00 ave 9812 max 9812 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: 468324.0 ave 468324 max 468324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468324 Ave neighs/atom = 140.09094 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 14 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.664 | 6.664 | 6.664 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13241.977 0 -13241.977 -33212.691 Loop time of 1.575e-06 on 1 procs for 0 steps with 3343 atoms 127.0% 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 | | 1.575e-06 | | |100.00 Nlocal: 3343.00 ave 3343 max 3343 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9790.00 ave 9790 max 9790 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: 469468.0 ave 469468 max 469468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 469468 Ave neighs/atom = 140.43314 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 14 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.664 | 6.664 | 6.664 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 -13241.977 -13241.977 50.768233 86.573742 9.1529153 -33212.691 -33212.691 19.160458 -99627.337 -29.898307 2.3059984 2579.9031 Loop time of 2.03e-06 on 1 procs for 0 steps with 3343 atoms 197.0% 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 | | 2.03e-06 | | |100.00 Nlocal: 3343.00 ave 3343 max 3343 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9790.00 ave 9790 max 9790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 234734.0 ave 234734 max 234734 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 469468.0 ave 469468 max 469468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 469468 Ave neighs/atom = 140.43314 Neighbor list builds = 0 Dangerous builds = 0 3343 -12769.2049472488 eV 2.30599843604031 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:45