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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -42.532322 0.0000000) to (52.091243 42.532322 8.6222039) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950507 5.2437109 5.7481359 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -42.532322 0.0000000) to (52.091243 42.532322 8.6222039) create_atoms CPU = 0.003 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950507 5.2437109 5.7481359 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -42.532322 0.0000000) to (52.091243 42.532322 8.6222039) create_atoms CPU = 0.002 seconds 1754 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 16 25 3 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 3494 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_800536961967_003#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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.527 | 6.527 | 6.527 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15068.681 0 -15068.681 14239.783 129 0 -15500.519 0 -15500.519 6653.8431 Loop time of 4.51003 on 1 procs for 129 steps with 3494 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15068.6811496129 -15500.5051859317 -15500.5186902796 Force two-norm initial, final = 94.839750 0.42791489 Force max component initial, final = 10.495429 0.095386380 Final line search alpha, max atom move = 1.0000000 0.095386380 Iterations, force evaluations = 129 222 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3428 | 4.3428 | 4.3428 | 0.0 | 96.29 Neigh | 0.10112 | 0.10112 | 0.10112 | 0.0 | 2.24 Comm | 0.024615 | 0.024615 | 0.024615 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04151 | | | 0.92 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9812.00 ave 9812 max 9812 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: 462618.0 ave 462618 max 462618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462618 Ave neighs/atom = 132.40355 Neighbor list builds = 3 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 129 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.528 | 6.528 | 6.528 Mbytes Step Temp E_pair E_mol TotEng Press Volume 129 0 -15500.519 0 -15500.519 6653.8431 38206.046 136 0 -15501.536 0 -15501.536 -110.11233 38354.28 Loop time of 0.180552 on 1 procs for 7 steps with 3494 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15500.5186902795 -15501.5329423285 -15501.5358209834 Force two-norm initial, final = 361.39795 4.6643943 Force max component initial, final = 349.99600 2.9355527 Final line search alpha, max atom move = 7.9925035e-05 0.00023462415 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17442 | 0.17442 | 0.17442 | 0.0 | 96.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007637 | 0.0007637 | 0.0007637 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005371 | | | 2.97 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9826.00 ave 9826 max 9826 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: 462620.0 ave 462620 max 462620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462620 Ave neighs/atom = 132.40412 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.667 | 6.667 | 6.667 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15501.536 0 -15501.536 -110.11233 Loop time of 2.416e-06 on 1 procs for 0 steps with 3494 atoms 165.6% 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 | | 2.416e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9886.00 ave 9886 max 9886 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: 462044.0 ave 462044 max 462044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462044 Ave neighs/atom = 132.23927 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.667 | 6.667 | 6.667 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 -15501.536 -15501.536 52.018839 85.603044 8.6131889 -110.11233 -110.11233 -122.45664 -87.172242 -120.7081 2.2132024 1543.6049 Loop time of 3.081e-06 on 1 procs for 0 steps with 3494 atoms 227.2% 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 | | 3.081e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9886.00 ave 9886 max 9886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231022.0 ave 231022 max 231022 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 462044.0 ave 462044 max 462044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462044 Ave neighs/atom = 132.23927 Neighbor list builds = 0 Dangerous builds = 0 3494 -15501.5358209834 eV 2.21320239665604 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05