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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -80.822023 0.0000000) to (46.662617 80.822023 6.9819593) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2681127 6.4335938 6.9819593 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -80.822023 0.0000000) to (46.662617 80.822023 6.9819593) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2681127 6.4335938 6.9819593 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -80.822023 0.0000000) to (46.662617 80.822023 6.9819593) create_atoms CPU = 0.004 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 43 2 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 6 atoms, new total = 3212 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_699137396381_005#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 = 13 43 2 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) = 6.629 | 6.629 | 6.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10630.961 0 -10630.961 4332.3141 107 0 -10770.206 0 -10770.206 1119.1732 Loop time of 3.49291 on 1 procs for 107 steps with 3212 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10630.960792765 -10770.1979802568 -10770.2064675311 Force two-norm initial, final = 52.268336 0.26371799 Force max component initial, final = 7.2179298 0.044613761 Final line search alpha, max atom move = 1.0000000 0.044613761 Iterations, force evaluations = 107 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3142 | 3.3142 | 3.3142 | 0.0 | 94.88 Neigh | 0.12226 | 0.12226 | 0.12226 | 0.0 | 3.50 Comm | 0.023732 | 0.023732 | 0.023732 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03274 | | | 0.94 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10849.0 ave 10849 max 10849 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: 423836.0 ave 423836 max 423836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423836 Ave neighs/atom = 131.95392 Neighbor list builds = 5 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 = 13 43 2 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 : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.629 | 6.629 | 6.629 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -10770.206 0 -10770.206 1119.1732 52663.063 111 0 -10770.354 0 -10770.354 -11.688709 52742.021 Loop time of 0.111711 on 1 procs for 4 steps with 3212 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 = -10770.2064675311 -10770.3522785014 -10770.3536313897 Force two-norm initial, final = 95.442661 1.4263803 Force max component initial, final = 93.784550 1.2916810 Final line search alpha, max atom move = 7.6357621e-05 9.8629691e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10786 | 0.10786 | 0.10786 | 0.0 | 96.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053338 | 0.00053338 | 0.00053338 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003315 | | | 2.97 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10885.0 ave 10885 max 10885 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: 423824.0 ave 423824 max 423824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423824 Ave neighs/atom = 131.95019 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 = 13 43 2 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) = 6.767 | 6.767 | 6.767 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10770.354 0 -10770.354 -11.688709 Loop time of 2.491e-06 on 1 procs for 0 steps with 3212 atoms 160.6% 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 | | 2.491e-06 | | |100.00 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10899.0 ave 10899 max 10899 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: 423632.0 ave 423632 max 423632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423632 Ave neighs/atom = 131.89041 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 = 13 43 2 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) = 6.767 | 6.767 | 6.767 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 -10770.354 -10770.354 46.641114 162.16115 6.9733432 -11.688709 -11.688709 -39.220101 13.069233 -8.9152606 2.5980804 1629.9659 Loop time of 2.793e-06 on 1 procs for 0 steps with 3212 atoms 358.0% 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 | | 2.793e-06 | | |100.00 Nlocal: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10899.0 ave 10899 max 10899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 211816.0 ave 211816 max 211816 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 423632.0 ave 423632 max 423632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423632 Ave neighs/atom = 131.89041 Neighbor list builds = 0 Dangerous builds = 0 3212 -10770.3536313897 eV 2.59808042890435 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04