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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -44.266132 0.0000000) to (9.0357863 44.266132 9.8982079) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4214718 5.9021509 6.5988053 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -44.266132 0.0000000) to (9.0357863 44.266132 9.8982079) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4214718 5.9021509 6.5988053 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.266132 0.0000000) to (9.0357863 44.266132 9.8982079) create_atoms CPU = 0.000 seconds 242 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 2 18 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 2 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.005 | 5.005 | 5.005 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1829.6652 0 -1829.6652 18621.689 42 0 -1868.7503 0 -1868.7503 6983.4589 Loop time of 0.654662 on 1 procs for 42 steps with 480 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1829.66518854227 -1868.74935827716 -1868.75032208676 Force two-norm initial, final = 67.262361 0.064204705 Force max component initial, final = 20.474080 0.010734514 Final line search alpha, max atom move = 1.0000000 0.010734514 Iterations, force evaluations = 42 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64841 | 0.64841 | 0.64841 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0035825 | 0.0035825 | 0.0035825 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002671 | | | 0.41 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5184.00 ave 5184 max 5184 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: 119284.0 ave 119284 max 119284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119284 Ave neighs/atom = 248.50833 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 2 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.007 | 5.007 | 5.007 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -1868.7503 0 -1868.7503 6983.4589 7918.1567 54 0 -1869.0625 0 -1869.0625 39.253327 7984.0642 Loop time of 0.124401 on 1 procs for 12 steps with 480 atoms 97.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1868.75032208676 -1869.06249025212 -1869.06251151901 Force two-norm initial, final = 69.061639 0.40840465 Force max component initial, final = 62.225677 0.22682128 Final line search alpha, max atom move = 0.0037257870 0.00084508779 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12047 | 0.12047 | 0.12047 | 0.0 | 96.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067536 | 0.00067536 | 0.00067536 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003257 | | | 2.62 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5425.00 ave 5425 max 5425 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: 118152.0 ave 118152 max 118152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118152 Ave neighs/atom = 246.15000 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 2 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.145 | 5.145 | 5.145 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1869.0625 0 -1869.0625 39.253327 Loop time of 1.911e-06 on 1 procs for 0 steps with 480 atoms 209.3% 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 | | 1.911e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5443.00 ave 5443 max 5443 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: 117768.0 ave 117768 max 117768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117768 Ave neighs/atom = 245.35000 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 2 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.145 | 5.145 | 5.145 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 -1869.0625 -1869.0625 9.0312813 89.50424 9.8771361 39.253327 39.253327 45.493941 35.785855 36.480184 2.5506541 382.94282 Loop time of 1.983e-06 on 1 procs for 0 steps with 480 atoms 201.7% 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 | | 1.983e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5443.00 ave 5443 max 5443 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58884.0 ave 58884 max 58884 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117768.0 ave 117768 max 117768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117768 Ave neighs/atom = 245.35000 Neighbor list builds = 0 Dangerous builds = 0 480 -1869.06251151901 eV 2.55065409940796 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01