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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -55.604755 0.0000000) to (15.133697 55.604755 9.9073306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4858703 6.1783061 6.6048871 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -55.604755 0.0000000) to (15.133697 55.604755 9.9073306) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4858703 6.1783061 6.6048871 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -55.604755 0.0000000) to (15.133697 55.604755 9.9073306) create_atoms CPU = 0.001 seconds 507 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 33 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1008 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_618133763375_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.566 | 4.566 | 4.566 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2976.6108 0 -2976.6108 44644.467 84 0 -3376.3582 0 -3376.3582 3753.655 Loop time of 5.39687 on 1 procs for 84 steps with 1008 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 = -2976.61083296426 -3376.35588638383 -3376.35821431875 Force two-norm initial, final = 460.42164 0.11796540 Force max component initial, final = 99.138198 0.021669934 Final line search alpha, max atom move = 1.0000000 0.021669934 Iterations, force evaluations = 84 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3616 | 5.3616 | 5.3616 | 0.0 | 99.35 Neigh | 0.018434 | 0.018434 | 0.018434 | 0.0 | 0.34 Comm | 0.0075613 | 0.0075613 | 0.0075613 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009313 | | | 0.17 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4212.00 ave 4212 max 4212 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: 78232.0 ave 78232 max 78232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78232 Ave neighs/atom = 77.611111 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.565 | 4.565 | 4.565 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -3376.3582 0 -3376.3582 3753.655 16674.147 92 0 -3376.6324 0 -3376.6324 -5.0590792 16752.578 Loop time of 0.367958 on 1 procs for 8 steps with 1008 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 = -3376.35821431874 -3376.62911577873 -3376.63240256161 Force two-norm initial, final = 82.874055 0.25362638 Force max component initial, final = 77.822171 0.062004905 Final line search alpha, max atom move = 0.00019506338 1.2094886e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36535 | 0.36535 | 0.36535 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003786 | 0.0003786 | 0.0003786 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002227 | | | 0.61 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4176.00 ave 4176 max 4176 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: 78256.0 ave 78256 max 78256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78256 Ave neighs/atom = 77.634921 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.703 | 4.703 | 4.703 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3376.6324 0 -3376.6324 -5.0590792 Loop time of 2.324e-06 on 1 procs for 0 steps with 1008 atoms 172.1% 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 | | 2.324e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4176.00 ave 4176 max 4176 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: 78184.0 ave 78184 max 78184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78184 Ave neighs/atom = 77.563492 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.703 | 4.703 | 4.703 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 -3376.6324 -3376.6324 15.120453 112.08326 9.8849869 -5.0590792 -5.0590792 -3.87328 -5.9765917 -5.3273659 2.5688822 499.55341 Loop time of 2.621e-06 on 1 procs for 0 steps with 1008 atoms 228.9% 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 | | 2.621e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4176.00 ave 4176 max 4176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39092.0 ave 39092 max 39092 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78184.0 ave 78184 max 78184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78184 Ave neighs/atom = 77.563492 Neighbor list builds = 0 Dangerous builds = 0 1008 -3376.63240256161 eV 2.56888222866982 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06