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 = 3.5937292 3.5937292 3.5937292 Created orthogonal box = (0.0000000 -46.025783 0.0000000) to (23.011094 46.025783 3.5937292) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0512159 5.0512159 3.5937292 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -46.025783 0.0000000) to (23.011094 46.025783 3.5937292) create_atoms CPU = 0.002 seconds 330 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0512159 5.0512159 3.5937292 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -46.025783 0.0000000) to (23.011094 46.025783 3.5937292) create_atoms CPU = 0.001 seconds 330 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 655 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.529 | 4.529 | 4.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2699.9545 0 -2699.9545 71859.377 78 0 -2791.2453 0 -2791.2453 1994.621 Loop time of 12.9488 on 1 procs for 78 steps with 655 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 = -2699.95452149826 -2791.24302448592 -2791.24529259622 Force two-norm initial, final = 129.84375 0.20762542 Force max component initial, final = 48.644528 0.085676515 Final line search alpha, max atom move = 1.0000000 0.085676515 Iterations, force evaluations = 78 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.896 | 12.896 | 12.896 | 0.0 | 99.59 Neigh | 0.022321 | 0.022321 | 0.022321 | 0.0 | 0.17 Comm | 0.016669 | 0.016669 | 0.016669 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0136 | | | 0.11 Nlocal: 655.000 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5380.00 ave 5380 max 5380 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: 87326.0 ave 87326 max 87326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87326 Ave neighs/atom = 133.32214 Neighbor list builds = 2 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.529 | 4.529 | 4.529 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -2791.2453 0 -2791.2453 1994.621 7612.2632 84 0 -2791.3408 0 -2791.3408 80.171227 7621.0422 Loop time of 0.783724 on 1 procs for 6 steps with 655 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 = -2791.24529259622 -2791.34075270092 -2791.34077262109 Force two-norm initial, final = 30.146298 0.58875965 Force max component initial, final = 26.575041 0.44867935 Final line search alpha, max atom move = 0.0045922683 0.0020604560 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77969 | 0.77969 | 0.77969 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008654 | 0.0008654 | 0.0008654 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003165 | | | 0.40 Nlocal: 655.000 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5380.00 ave 5380 max 5380 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: 87314.0 ave 87314 max 87314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87314 Ave neighs/atom = 133.30382 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.667 | 4.667 | 4.667 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2791.3408 0 -2791.3408 80.171227 Loop time of 7.657e-06 on 1 procs for 0 steps with 655 atoms 352.6% 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 | | 7.657e-06 | | |100.00 Nlocal: 655.000 ave 655 max 655 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: 87322.0 ave 87322 max 87322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87322 Ave neighs/atom = 133.31603 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.667 | 4.667 | 4.667 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 -2791.3408 -2791.3408 22.922486 92.051565 3.6117815 80.171227 80.171227 93.962925 91.951727 54.599029 2.3057211 156.16754 Loop time of 7.116e-06 on 1 procs for 0 steps with 655 atoms 267.0% 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 | | 7.116e-06 | | |100.00 Nlocal: 655.000 ave 655 max 655 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: 43661.0 ave 43661 max 43661 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87322.0 ave 87322 max 87322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87322 Ave neighs/atom = 133.31603 Neighbor list builds = 0 Dangerous builds = 0 655 -2791.34077262109 eV 2.30572105824684 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14