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 -57.521355 0.0000000) to (28.760677 57.521355 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8671915 4.8671915 3.5673230 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -57.521355 0.0000000) to (28.760677 57.521355 3.5673230) create_atoms CPU = 0.002 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8671915 4.8671915 3.5673230 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -57.521355 0.0000000) to (28.760677 57.521355 3.5673230) create_atoms CPU = 0.002 seconds 522 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 42 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1034 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 42 2 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4216.9299 0 -4216.9299 24554.964 61 0 -4352.4259 0 -4352.4259 20719.396 Loop time of 8.36732 on 1 procs for 61 steps with 1034 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4216.92987577254 -4352.42197233909 -4352.42593946341 Force two-norm initial, final = 281.15788 0.60683700 Force max component initial, final = 90.375844 0.20233649 Final line search alpha, max atom move = 0.62960889 0.12739286 Iterations, force evaluations = 61 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.325 | 8.325 | 8.325 | 0.0 | 99.49 Neigh | 0.011827 | 0.011827 | 0.011827 | 0.0 | 0.14 Comm | 0.014973 | 0.014973 | 0.014973 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0155 | | | 0.19 Nlocal: 1034.00 ave 1034 max 1034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5266.00 ave 5266 max 5266 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: 57520.0 ave 57520 max 57520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57520 Ave neighs/atom = 55.628627 Neighbor list builds = 1 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 42 2 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -4352.4259 0 -4352.4259 20719.396 11803.224 419 0 -4411.4533 0 -4411.4533 -375.62332 12205.401 Loop time of 25.9604 on 1 procs for 358 steps with 1034 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 = -4352.42593946341 -4411.44898650629 -4411.4533322048 Force two-norm initial, final = 316.37872 11.013658 Force max component initial, final = 233.79030 8.0345230 Final line search alpha, max atom move = 0.00010718374 0.00086117020 Iterations, force evaluations = 358 406 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.53 | 25.53 | 25.53 | 0.0 | 98.34 Neigh | 0.15666 | 0.15666 | 0.15666 | 0.0 | 0.60 Comm | 0.059465 | 0.059465 | 0.059465 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2146 | | | 0.83 Nlocal: 1034.00 ave 1034 max 1034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6486.00 ave 6486 max 6486 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: 59968.0 ave 59968 max 59968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59968 Ave neighs/atom = 57.996132 Neighbor list builds = 15 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 = 12 47 2 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) = 4.750 | 4.750 | 4.750 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4411.4533 0 -4411.4533 -375.62332 Loop time of 8.83e-06 on 1 procs for 0 steps with 1034 atoms 158.6% 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 | | 8.83e-06 | | |100.00 Nlocal: 1034.00 ave 1034 max 1034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6476.00 ave 6476 max 6476 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: 59932.0 ave 59932 max 59932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59932 Ave neighs/atom = 57.961315 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 = 12 47 2 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) = 4.750 | 4.750 | 4.750 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 -4411.4533 -4411.4533 32.69853 130.5107 2.8600769 -375.62332 -375.62332 -59.843795 -221.44817 -845.57801 2.2966919 1659.8317 Loop time of 8.801e-06 on 1 procs for 0 steps with 1034 atoms 238.6% 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 | | 8.801e-06 | | |100.00 Nlocal: 1034.00 ave 1034 max 1034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6476.00 ave 6476 max 6476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29966.0 ave 29966 max 29966 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59932.0 ave 59932 max 59932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59932 Ave neighs/atom = 57.961315 Neighbor list builds = 0 Dangerous builds = 0 1034 -4411.4533322048 eV 2.29669188796469 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:34