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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -52.578389 0.0000000) to (26.289194 52.578389 3.6110986) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4642028 4.4642028 3.6110986 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -52.578389 0.0000000) to (26.289194 52.578389 3.6110986) create_atoms CPU = 0.001 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4642028 4.4642028 3.6110986 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -52.578389 0.0000000) to (26.289194 52.578389 3.6110986) create_atoms CPU = 0.000 seconds 426 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 ghost atom cutoff = 6 binsize = 3, bins = 9 36 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 850 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_912636107108_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 ghost atom cutoff = 6 binsize = 3, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.556 | 4.556 | 4.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3456.5597 0 -3456.5597 43123.855 42 0 -3592.4187 0 -3592.4187 11615.59 Loop time of 2.31809 on 1 procs for 42 steps with 850 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 = -3456.55968524325 -3592.41608607617 -3592.41867414332 Force two-norm initial, final = 248.43381 0.15055559 Force max component initial, final = 80.157656 0.025529903 Final line search alpha, max atom move = 1.0000000 0.025529903 Iterations, force evaluations = 42 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.309 | 2.309 | 2.309 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.004632 | 0.004632 | 0.004632 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004412 | | | 0.19 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5348.00 ave 5348 max 5348 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: 66460.0 ave 66460 max 66460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66460 Ave neighs/atom = 78.188235 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 ghost atom cutoff = 6 binsize = 3, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.556 | 4.556 | 4.556 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -3592.4187 0 -3592.4187 11615.59 9982.8348 49 0 -3592.7278 0 -3592.7278 -504.1423 10052.808 Loop time of 0.3005 on 1 procs for 7 steps with 850 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 = -3592.41867414333 -3592.72466225434 -3592.72783813896 Force two-norm initial, final = 127.17649 6.3713027 Force max component initial, final = 84.596714 4.6808883 Final line search alpha, max atom move = 8.8417639e-05 0.00041387309 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29782 | 0.29782 | 0.29782 | 0.0 | 99.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004314 | 0.0004314 | 0.0004314 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002252 | | | 0.75 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5348.00 ave 5348 max 5348 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: 65972.0 ave 65972 max 65972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65972 Ave neighs/atom = 77.614118 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 ghost atom cutoff = 6 binsize = 3, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.694 | 4.694 | 4.694 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3592.7278 0 -3592.7278 -504.1423 Loop time of 1.913e-06 on 1 procs for 0 steps with 850 atoms 156.8% 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 | | 1.913e-06 | | |100.00 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5352.00 ave 5352 max 5352 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: 65928.0 ave 65928 max 65928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65928 Ave neighs/atom = 77.562353 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 ghost atom cutoff = 6 binsize = 3, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.694 | 4.694 | 4.694 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 -3592.7278 -3592.7278 26.238591 105.44478 3.633472 -504.1423 -504.1423 -744.5853 -684.50632 -83.335292 2.2940547 357.90936 Loop time of 1.965e-06 on 1 procs for 0 steps with 850 atoms 254.5% 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 | | 1.965e-06 | | |100.00 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5352.00 ave 5352 max 5352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32964.0 ave 32964 max 32964 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 65928.0 ave 65928 max 65928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65928 Ave neighs/atom = 77.562353 Neighbor list builds = 0 Dangerous builds = 0 850 -3592.72783813896 eV 2.29405469054302 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03