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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -43.602260 0.0000000) to (21.799589 43.602260 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.4879342 3.4879342 3.0829274 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -43.602260 0.0000000) to (21.799589 43.602260 3.0829274) create_atoms CPU = 0.000 seconds 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.4879342 3.4879342 3.0829274 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -43.602260 0.0000000) to (21.799589 43.602260 3.0829274) create_atoms CPU = 0.000 seconds 202 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 27 1 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 8 atoms, new total = 396 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.834 | 4.834 | 4.834 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2542.2452 0 -2542.2452 5263.9389 60 0 -2569.6867 0 -2569.6867 -16028.254 Loop time of 6.2494 on 1 procs for 60 steps with 396 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 = -2542.24519776973 -2569.68451311808 -2569.68670949829 Force two-norm initial, final = 32.749355 0.21408047 Force max component initial, final = 10.328400 0.049049455 Final line search alpha, max atom move = 1.0000000 0.049049455 Iterations, force evaluations = 60 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2452 | 6.2452 | 6.2452 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002634 | 0.002634 | 0.002634 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001566 | | | 0.03 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3304.00 ave 3304 max 3304 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: 25616.0 ave 25616 max 25616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25616 Ave neighs/atom = 64.686869 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.216 | 5.216 | 5.216 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -2569.6867 0 -2569.6867 -16028.254 5860.7148 72 0 -2570.0351 0 -2570.0351 565.65772 5812.051 Loop time of 0.73451 on 1 procs for 12 steps with 396 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 = -2569.68670949829 -2570.03451628191 -2570.03508901602 Force two-norm initial, final = 88.086458 2.7036873 Force max component initial, final = 72.580576 2.2624098 Final line search alpha, max atom move = 0.00056270723 0.0012730743 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7334 | 0.7334 | 0.7334 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002505 | 0.0002505 | 0.0002505 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000859 | | | 0.12 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3299.00 ave 3299 max 3299 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: 28720.0 ave 28720 max 28720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28720 Ave neighs/atom = 72.525253 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.354 | 5.354 | 5.354 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2570.0351 0 -2570.0351 565.65772 Loop time of 2.2e-06 on 1 procs for 0 steps with 396 atoms 136.4% 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 | | 2.2e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3289.00 ave 3289 max 3289 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: 29004.0 ave 29004 max 29004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29004 Ave neighs/atom = 73.242424 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.354 | 5.354 | 5.354 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 -2570.0351 -2570.0351 21.864543 87.20452 3.0482461 565.65772 565.65772 -379.6438 2693.2673 -616.65029 2.5841894 684.36541 Loop time of 2e-06 on 1 procs for 0 steps with 396 atoms 150.0% 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 | | 2e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3289.00 ave 3289 max 3289 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14502.0 ave 14502 max 14502 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29004.0 ave 29004 max 29004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29004 Ave neighs/atom = 73.242424 Neighbor list builds = 0 Dangerous builds = 0 396 -2570.03508901602 eV 2.58418940721954 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07