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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -78.546973 0.0000000) to (45.346854 78.546973 6.7850866) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0913685 6.2521835 6.7850866 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -78.546973 0.0000000) to (45.346854 78.546973 6.7850866) create_atoms CPU = 0.011 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0913685 6.2521835 6.7850866 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -78.546973 0.0000000) to (45.346854 78.546973 6.7850866) create_atoms CPU = 0.011 seconds 1610 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 49 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 3192 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.832 | 5.832 | 5.832 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18266.487 0 -18266.487 4593.7033 48 0 -18350.384 0 -18350.384 -4295.4237 Loop time of 9.31943 on 1 procs for 48 steps with 3192 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 = -18266.4867986662 -18350.3705977093 -18350.384362806 Force two-norm initial, final = 85.263576 0.49215643 Force max component initial, final = 16.745562 0.098346865 Final line search alpha, max atom move = 0.94608073 0.093044073 Iterations, force evaluations = 48 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.2738 | 9.2738 | 9.2738 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018905 | 0.018905 | 0.018905 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02672 | | | 0.29 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10068.0 ave 10068 max 10068 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: 246880.0 ave 246880 max 246880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 246880 Ave neighs/atom = 77.343358 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.833 | 5.833 | 5.833 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -18350.384 0 -18350.384 -4295.4237 48335.032 50 0 -18350.468 0 -18350.468 -1643.8325 48261.445 Loop time of 0.567908 on 1 procs for 2 steps with 3192 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 = -18350.384362806 -18350.466635608 -18350.4677923757 Force two-norm initial, final = 143.04775 0.50505417 Force max component initial, final = 124.12481 0.096116961 Final line search alpha, max atom move = 9.4521107e-05 9.0850815e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56261 | 0.56261 | 0.56261 | 0.0 | 99.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001121 | 0.001121 | 0.001121 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004178 | | | 0.74 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10101.0 ave 10101 max 10101 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: 247144.0 ave 247144 max 247144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 247144 Ave neighs/atom = 77.426065 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.970 | 5.970 | 5.970 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18350.468 0 -18350.468 -1643.8325 Loop time of 6.425e-06 on 1 procs for 0 steps with 3192 atoms 186.8% 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 | | 6.425e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10101.0 ave 10101 max 10101 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: 247172.0 ave 247172 max 247172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 247172 Ave neighs/atom = 77.434837 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.970 | 5.970 | 5.970 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 -18350.468 -18350.468 45.3277 157.09395 6.7776197 -1643.8325 -1643.8325 -1.8207693 -4931.181 1.5042634 2.4609106 1243.2869 Loop time of 6.796e-06 on 1 procs for 0 steps with 3192 atoms 264.9% 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 | | 6.796e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10101.0 ave 10101 max 10101 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 123586.0 ave 123586 max 123586 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 247172.0 ave 247172 max 247172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 247172 Ave neighs/atom = 77.434837 Neighbor list builds = 0 Dangerous builds = 0 3192 -18350.4677923757 eV 2.46091055133109 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10