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 = 3.5937292 3.5937292 3.5937292 Created orthogonal box = (0.0000000 -35.940886 0.0000000) to (17.968646 35.940886 3.5937292) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0312209 5.0312209 3.5937292 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -35.940886 0.0000000) to (17.968646 35.940886 3.5937292) create_atoms CPU = 0.001 seconds 201 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0312209 5.0312209 3.5937292 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -35.940886 0.0000000) to (17.968646 35.940886 3.5937292) create_atoms CPU = 0.001 seconds 201 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 398 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1639.2428 0 -1639.2428 70190.107 65 0 -1694.1762 0 -1694.1762 -1422.2419 Loop time of 7.58479 on 1 procs for 65 steps with 398 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 = -1639.24279005573 -1694.17474940558 -1694.17618216174 Force two-norm initial, final = 97.633746 0.15286708 Force max component initial, final = 37.177045 0.049586959 Final line search alpha, max atom move = 1.0000000 0.049586959 Iterations, force evaluations = 65 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5572 | 7.5572 | 7.5572 | 0.0 | 99.64 Neigh | 0.0066222 | 0.0066222 | 0.0066222 | 0.0 | 0.09 Comm | 0.011627 | 0.011627 | 0.011627 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009313 | | | 0.12 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3827.00 ave 3827 max 3827 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: 52766.0 ave 52766 max 52766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52766 Ave neighs/atom = 132.57789 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -1694.1762 0 -1694.1762 -1422.2419 4641.7256 71 0 -1694.2391 0 -1694.2391 -1129.1173 4640.7561 Loop time of 0.468552 on 1 procs for 6 steps with 398 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1694.17618216174 -1694.23896770949 -1694.23911439649 Force two-norm initial, final = 19.469687 0.39296688 Force max component initial, final = 17.300190 0.21779215 Final line search alpha, max atom move = 0.0014022446 0.00030539785 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4657 | 0.4657 | 0.4657 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065633 | 0.00065633 | 0.00065633 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002199 | | | 0.47 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3827.00 ave 3827 max 3827 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: 52818.0 ave 52818 max 52818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52818 Ave neighs/atom = 132.70854 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1694.2391 0 -1694.2391 -1129.1173 Loop time of 6.405e-06 on 1 procs for 0 steps with 398 atoms 171.7% 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 | | 6.405e-06 | | |100.00 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3842.00 ave 3842 max 3842 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: 52842.0 ave 52842 max 52842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52842 Ave neighs/atom = 132.76884 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.594 | 4.594 | 4.594 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 -1694.2391 -1694.2391 17.882797 71.881771 3.6102272 -1129.1173 -1129.1173 -67.27889 -3244.5371 -75.535832 2.3064242 156.19912 Loop time of 8.048e-06 on 1 procs for 0 steps with 398 atoms 0.0% 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 | | 8.048e-06 | | |100.00 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3842.00 ave 3842 max 3842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26421.0 ave 26421 max 26421 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52842.0 ave 52842 max 52842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52842 Ave neighs/atom = 132.76884 Neighbor list builds = 0 Dangerous builds = 0 398 -1694.23911439649 eV 2.30642421113718 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08