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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -36.470854 0.0000000) to (25.788788 36.470854 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5509626 5.7209182 5.1069410 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -36.470854 0.0000000) to (25.788788 36.470854 5.1069410) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5509626 5.7209182 5.1069410 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.470854 0.0000000) to (25.788788 36.470854 5.1069410) create_atoms CPU = 0.001 seconds 410 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 28 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 818 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.909 | 4.909 | 4.909 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3198.9903 0 -3198.9903 69298.12 56 0 -3456.0763 0 -3456.0763 10873.231 Loop time of 3.95719 on 1 procs for 56 steps with 818 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 = -3198.99028672585 -3456.07302809351 -3456.07631000382 Force two-norm initial, final = 299.20783 0.27567513 Force max component initial, final = 60.800779 0.040754605 Final line search alpha, max atom move = 1.0000000 0.040754605 Iterations, force evaluations = 56 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9384 | 3.9384 | 3.9384 | 0.0 | 99.52 Neigh | 0.012177 | 0.012177 | 0.012177 | 0.0 | 0.31 Comm | 0.002919 | 0.002919 | 0.002919 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003705 | | | 0.09 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3163.00 ave 3163 max 3163 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: 44068.0 ave 44068 max 44068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44068 Ave neighs/atom = 53.872861 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.909 | 4.909 | 4.909 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -3456.0763 0 -3456.0763 10873.231 9606.5556 66 0 -3456.633 0 -3456.633 248.89029 9667.5572 Loop time of 0.46809 on 1 procs for 10 steps with 818 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 = -3456.07631000382 -3456.63009990688 -3456.63297537393 Force two-norm initial, final = 139.55599 2.7507747 Force max component initial, final = 132.11907 1.9497672 Final line search alpha, max atom move = 0.00020227294 0.00039438516 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46616 | 0.46616 | 0.46616 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029619 | 0.00029619 | 0.00029619 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001636 | | | 0.35 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3155.00 ave 3155 max 3155 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: 44060.0 ave 44060 max 44060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44060 Ave neighs/atom = 53.863081 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3456.633 0 -3456.633 248.89029 Loop time of 1.671e-06 on 1 procs for 0 steps with 818 atoms 119.7% 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 | | 1.671e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3155.00 ave 3155 max 3155 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: 44008.0 ave 44008 max 44008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44008 Ave neighs/atom = 53.799511 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.047 | 5.047 | 5.047 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 -3456.633 -3456.633 25.687467 73.596783 5.1137164 248.89029 248.89029 219.64852 326.03129 200.99106 2.2767513 395.53361 Loop time of 1.452e-06 on 1 procs for 0 steps with 818 atoms 206.6% 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 | | 1.452e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3155.00 ave 3155 max 3155 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22004.0 ave 22004 max 22004 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44008.0 ave 44008 max 44008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44008 Ave neighs/atom = 53.799511 Neighbor list builds = 0 Dangerous builds = 0 818 -3456.63297537393 eV 2.27675133155559 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04