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 -43.337443 0.0000000) to (15.320823 43.337443 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1069410 6.0185877 5.1069410 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -43.337443 0.0000000) to (15.320823 43.337443 5.1069410) create_atoms CPU = 0.001 seconds 292 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1069410 6.0185877 5.1069410 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -43.337443 0.0000000) to (15.320823 43.337443 5.1069410) create_atoms CPU = 0.001 seconds 292 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 = 6 33 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 8 atoms, new total = 576 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 = 6 33 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) = 4.872 | 4.872 | 4.872 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2400.1528 0 -2400.1528 16321.309 22 0 -2435.8078 0 -2435.8078 6565.9233 Loop time of 1.07315 on 1 procs for 22 steps with 576 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 = -2400.15281385734 -2435.80570122417 -2435.80784547279 Force two-norm initial, final = 50.177035 0.20261323 Force max component initial, final = 9.2463019 0.033549446 Final line search alpha, max atom move = 1.0000000 0.033549446 Iterations, force evaluations = 22 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0713 | 1.0713 | 1.0713 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085298 | 0.00085298 | 0.00085298 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009949 | | | 0.09 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2694.00 ave 2694 max 2694 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: 31104.0 ave 31104 max 31104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31104 Ave neighs/atom = 54.000000 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 33 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.872 | 4.872 | 4.872 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -2435.8078 0 -2435.8078 6565.9233 6781.6632 25 0 -2435.8334 0 -2435.8334 2660.6546 6797.4063 Loop time of 0.157966 on 1 procs for 3 steps with 576 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 = -2435.80784547279 -2435.83213107003 -2435.83338790568 Force two-norm initial, final = 27.118661 0.24632574 Force max component initial, final = 22.794389 0.035298494 Final line search alpha, max atom move = 0.00025788960 9.1031145e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1573 | 0.1573 | 0.1573 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011466 | 0.00011466 | 0.00011466 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005478 | | | 0.35 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2694.00 ave 2694 max 2694 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: 30880.0 ave 30880 max 30880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30880 Ave neighs/atom = 53.611111 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 = 6 33 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) = 5.010 | 5.010 | 5.010 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2435.8334 0 -2435.8334 2660.6546 Loop time of 1.521e-06 on 1 procs for 0 steps with 576 atoms 131.5% 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 | | 1.521e-06 | | |100.00 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2694.00 ave 2694 max 2694 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: 30880.0 ave 30880 max 30880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30880 Ave neighs/atom = 53.611111 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 = 6 33 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) = 5.010 | 5.010 | 5.010 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 -2435.8334 -2435.8334 15.353018 86.674885 5.1080625 2660.6546 2660.6546 -3.0608727 7986.1256 -1.1007825 2.2920007 133.75131 Loop time of 1.451e-06 on 1 procs for 0 steps with 576 atoms 137.8% 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 | | 1.451e-06 | | |100.00 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2694.00 ave 2694 max 2694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15440.0 ave 15440 max 15440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30880.0 ave 30880 max 30880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30880 Ave neighs/atom = 53.611111 Neighbor list builds = 0 Dangerous builds = 0 576 -2435.83338790568 eV 2.29200069306031 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01