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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -47.414384 0.0000000) to (27.374707 47.414384 6.3360136) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8660087 5.6445695 6.3360136 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -47.414384 0.0000000) to (27.374707 47.414384 6.3360136) create_atoms CPU = 0.002 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8660087 5.6445695 6.3360136 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -47.414384 0.0000000) to (27.374707 47.414384 6.3360136) create_atoms CPU = 0.001 seconds 676 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 26 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1344 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4412.3627 0 -4412.3627 128225.02 587 0 -5286.5222 0 -5286.5222 -55673.045 Loop time of 11.263 on 1 procs for 587 steps with 1344 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 = -4412.36273618853 -5286.51836502235 -5286.52216709086 Force two-norm initial, final = 1710.3570 0.21279892 Force max component initial, final = 406.78729 0.084765091 Final line search alpha, max atom move = 1.0000000 0.084765091 Iterations, force evaluations = 587 1146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.945 | 10.945 | 10.945 | 0.0 | 97.18 Neigh | 0.16116 | 0.16116 | 0.16116 | 0.0 | 1.43 Comm | 0.082425 | 0.082425 | 0.082425 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07404 | | | 0.66 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6466.00 ave 6466 max 6466 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: 182770.0 ave 182770 max 182770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182770 Ave neighs/atom = 135.98958 Neighbor list builds = 13 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 587 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.096 | 5.096 | 5.096 Mbytes Step Temp E_pair E_mol TotEng Press Volume 587 0 -5286.5222 0 -5286.5222 -55673.045 16447.72 627 0 -5304.3373 0 -5304.3373 704.70293 15796.97 Loop time of 0.473327 on 1 procs for 40 steps with 1344 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 = -5286.52216709086 -5304.33209359438 -5304.33734362987 Force two-norm initial, final = 1069.8767 12.806239 Force max component initial, final = 902.81173 7.9674982 Final line search alpha, max atom move = 0.00011587062 0.00092319892 Iterations, force evaluations = 40 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41949 | 0.41949 | 0.41949 | 0.0 | 88.62 Neigh | 0.037228 | 0.037228 | 0.037228 | 0.0 | 7.87 Comm | 0.0029134 | 0.0029134 | 0.0029134 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0137 | | | 2.89 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6547.00 ave 6547 max 6547 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: 190198.0 ave 190198 max 190198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190198 Ave neighs/atom = 141.51637 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.234 | 5.234 | 5.234 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5304.3373 0 -5304.3373 704.70293 Loop time of 2.47e-06 on 1 procs for 0 steps with 1344 atoms 161.9% 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 | | 2.47e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6528.00 ave 6528 max 6528 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: 190134.0 ave 190134 max 190134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190134 Ave neighs/atom = 141.46875 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.234 | 5.234 | 5.234 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 -5304.3373 -5304.3373 27.315851 91.39016 6.3279002 704.70293 704.70293 806.35035 706.11256 601.64588 2.2298814 4464.3077 Loop time of 2.959e-06 on 1 procs for 0 steps with 1344 atoms 202.8% 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 | | 2.959e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6528.00 ave 6528 max 6528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95067.0 ave 95067 max 95067 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 190134.0 ave 190134 max 190134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190134 Ave neighs/atom = 141.46875 Neighbor list builds = 0 Dangerous builds = 0 1344 -5114.26668109047 eV 2.22988143443656 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12