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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -47.325887 0.0000000) to (28.981069 47.325887 8.7381210) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2692852 5.3779417 5.8254140 Created 1054 atoms using lattice units in orthogonal box = (0.0000000 -47.325887 0.0000000) to (28.981069 47.325887 8.7381210) create_atoms CPU = 0.002 seconds 1054 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2692852 5.3779417 5.8254140 Created 1078 atoms using lattice units in orthogonal box = (0.0000000 -47.325887 0.0000000) to (28.981069 47.325887 8.7381210) create_atoms CPU = 0.001 seconds 1078 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 34 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 2112 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 34 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8901.4336 0 -8901.4336 5421.2424 5 0 -8911.8523 0 -8911.8523 12491.372 Loop time of 0.60115 on 1 procs for 5 steps with 2112 atoms 95.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8901.43359709989 -8911.84968343645 -8911.85227338357 Force two-norm initial, final = 20.792939 5.3227223 Force max component initial, final = 2.1328080 0.41328624 Final line search alpha, max atom move = 0.24432448 0.10097595 Iterations, force evaluations = 5 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59946 | 0.59946 | 0.59946 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061825 | 0.00061825 | 0.00061825 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001076 | | | 0.18 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5565.00 ave 5565 max 5565 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: 114532.0 ave 114532 max 114532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114532 Ave neighs/atom = 54.229167 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 34 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 5 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press Volume 5 0 -8911.8523 0 -8911.8523 12491.372 23969.624 43 0 -8920.5275 0 -8920.5275 802.97439 24465.728 Loop time of 1.97309 on 1 procs for 38 steps with 2112 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8911.85227338357 -8920.52401913419 -8920.52752555613 Force two-norm initial, final = 392.67845 21.933987 Force max component initial, final = 368.34823 13.457608 Final line search alpha, max atom move = 8.8525499e-05 0.0011913414 Iterations, force evaluations = 38 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9242 | 1.9242 | 1.9242 | 0.0 | 97.52 Neigh | 0.032558 | 0.032558 | 0.032558 | 0.0 | 1.65 Comm | 0.0023014 | 0.0023014 | 0.0023014 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01403 | | | 0.71 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5452.00 ave 5452 max 5452 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: 120364.0 ave 120364 max 120364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120364 Ave neighs/atom = 56.990530 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 36 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.203 | 5.203 | 5.203 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8920.5275 0 -8920.5275 802.97439 Loop time of 2.206e-06 on 1 procs for 0 steps with 2112 atoms 181.3% 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 | | 2.206e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5452.00 ave 5452 max 5452 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: 123348.0 ave 123348 max 123348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123348 Ave neighs/atom = 58.403409 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 36 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.203 | 5.203 | 5.203 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 -8920.5275 -8920.5275 28.700448 98.184494 8.6821357 802.97439 802.97439 872.75903 774.30795 761.8562 2.4539488 601.93025 Loop time of 2.333e-06 on 1 procs for 0 steps with 2112 atoms 214.3% 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 | | 2.333e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5452.00 ave 5452 max 5452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61674.0 ave 61674 max 61674 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 123348.0 ave 123348 max 123348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123348 Ave neighs/atom = 58.403409 Neighbor list builds = 0 Dangerous builds = 0 2112 -8920.52752555613 eV 2.45394875687583 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03