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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -39.087598 0.0000000) to (13.027995 39.087598 3.6133156) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0107672 5.0107672 3.6133156 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.087598 0.0000000) to (13.027995 39.087598 3.6133156) create_atoms CPU = 0.002 seconds 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0107672 5.0107672 3.6133156 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.087598 0.0000000) to (13.027995 39.087598 3.6133156) create_atoms CPU = 0.001 seconds 158 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 23 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 308 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_694335101831_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.437 | 4.437 | 4.437 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1080.478 0 -1080.478 -61.367197 41 0 -1085.6442 0 -1085.6442 -9316.4166 Loop time of 2.07396 on 1 procs for 41 steps with 308 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1080.47798070349 -1085.64337631785 -1085.644168556 Force two-norm initial, final = 12.178429 0.078893460 Force max component initial, final = 4.6367865 0.018088997 Final line search alpha, max atom move = 1.0000000 0.018088997 Iterations, force evaluations = 41 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0632 | 2.0632 | 2.0632 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.005809 | 0.005809 | 0.005809 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004971 | | | 0.24 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3063.00 ave 3063 max 3063 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: 40240.0 ave 40240 max 40240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40240 Ave neighs/atom = 130.64935 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.437 | 4.437 | 4.437 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -1085.6442 0 -1085.6442 -9316.4166 3680.0393 46 0 -1085.7051 0 -1085.7051 -1613.6373 3659.4825 Loop time of 0.188555 on 1 procs for 5 steps with 308 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1085.644168556 -1085.70408354997 -1085.70514938964 Force two-norm initial, final = 28.570648 0.95845255 Force max component initial, final = 21.571483 0.85070185 Final line search alpha, max atom move = 0.00035941200 0.00030575245 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18657 | 0.18657 | 0.18657 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044992 | 0.00044992 | 0.00044992 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001536 | | | 0.81 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3000.00 ave 3000 max 3000 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: 39000.0 ave 39000 max 39000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39000 Ave neighs/atom = 126.62338 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.575 | 4.575 | 4.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1085.7051 0 -1085.7051 -1613.6373 Loop time of 6.385e-06 on 1 procs for 0 steps with 308 atoms 172.3% 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 | | 6.385e-06 | | |100.00 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3000.00 ave 3000 max 3000 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: 39272.0 ave 39272 max 39272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39272 Ave neighs/atom = 127.50649 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.575 | 4.575 | 4.575 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 -1085.7051 -1085.7051 13.012368 78.175196 3.5974466 -1613.6373 -1613.6373 -185.76595 -4284.3317 -370.81434 2.3169492 162.22744 Loop time of 6.666e-06 on 1 procs for 0 steps with 308 atoms 300.0% 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 | | 6.666e-06 | | |100.00 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3000.00 ave 3000 max 3000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19636.0 ave 19636 max 19636 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39272.0 ave 39272 max 39272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39272 Ave neighs/atom = 127.50649 Neighbor list builds = 0 Dangerous builds = 0 308 -1085.70514938964 eV 2.31694921774933 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02