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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -43.680213 0.0000000) to (53.497117 43.680213 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1298605 5.3852318 5.9032705 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -43.680213 0.0000000) to (53.497117 43.680213 8.8549058) create_atoms CPU = 0.007 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1298605 5.3852318 5.9032705 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -43.680213 0.0000000) to (53.497117 43.680213 8.8549058) create_atoms CPU = 0.006 seconds 1756 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 14 23 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 3480 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 7.375 | 7.375 | 7.375 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11946.137 0 -11946.137 4854.9231 91 0 -12281.013 0 -12281.013 -4602.8608 Loop time of 8.30098 on 1 procs for 91 steps with 3480 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 = -11946.137492938 -12281.0011069592 -12281.0132885364 Force two-norm initial, final = 96.012313 0.31574859 Force max component initial, final = 9.8369235 0.027042195 Final line search alpha, max atom move = 1.0000000 0.027042195 Iterations, force evaluations = 91 159 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.9536 | 7.9536 | 7.9536 | 0.0 | 95.82 Neigh | 0.24878 | 0.24878 | 0.24878 | 0.0 | 3.00 Comm | 0.04229 | 0.04229 | 0.04229 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05628 | | | 0.68 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10943.0 ave 10943 max 10943 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: 568088.0 ave 568088 max 568088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 568088 Ave neighs/atom = 163.24368 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.992 | 6.992 | 6.992 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -12281.013 0 -12281.013 -4602.8608 41383.676 95 0 -12281.297 0 -12281.297 100.16665 41240.701 Loop time of 0.299566 on 1 procs for 4 steps with 3480 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 = -12281.0132885364 -12281.2958614793 -12281.2965934991 Force two-norm initial, final = 216.75560 5.6611049 Force max component initial, final = 164.26719 5.3954668 Final line search alpha, max atom move = 0.00011223616 0.00060556646 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29212 | 0.29212 | 0.29212 | 0.0 | 97.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013291 | 0.0013291 | 0.0013291 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006113 | | | 2.04 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10656.0 ave 10656 max 10656 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: 561978.0 ave 561978 max 561978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 561978 Ave neighs/atom = 161.48793 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 7.130 | 7.130 | 7.130 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12281.297 0 -12281.297 100.16665 Loop time of 6.536e-06 on 1 procs for 0 steps with 3480 atoms 0.0% 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 | | 6.536e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10679.0 ave 10679 max 10679 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: 578932.0 ave 578932 max 578932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578932 Ave neighs/atom = 166.35977 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 7.130 | 7.130 | 7.130 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 -12281.297 -12281.297 53.438114 87.109085 8.8595459 100.16665 100.16665 209.37947 38.884029 52.23646 2.3681664 1421.992 Loop time of 6.606e-06 on 1 procs for 0 steps with 3480 atoms 257.3% 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 | | 6.606e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10679.0 ave 10679 max 10679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 289466.0 ave 289466 max 289466 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 578932.0 ave 578932 max 578932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578932 Ave neighs/atom = 166.35977 Neighbor list builds = 0 Dangerous builds = 0 3480 -12281.2965934991 eV 2.36816644409896 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09