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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -36.595377 0.0000000) to (25.876839 36.595377 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7504086 4.7438451 4.9800000 Created 431 atoms using lattice units in orthogonal box = (0.0000000 -36.595377 0.0000000) to (25.876839 36.595377 4.9800000) create_atoms CPU = 0.002 seconds 431 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7504086 4.7438451 4.9800000 Created 439 atoms using lattice units in orthogonal box = (0.0000000 -36.595377 0.0000000) to (25.876839 36.595377 4.9800000) create_atoms CPU = 0.001 seconds 439 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 23 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 864 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_008996216289_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.563 | 4.563 | 4.563 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3614.1409 0 -3614.1409 74787.561 46 0 -3825.3641 0 -3825.3641 12624.531 Loop time of 3.93556 on 1 procs for 46 steps with 864 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3614.14091453206 -3825.36135735713 -3825.36407044342 Force two-norm initial, final = 317.05047 0.16130253 Force max component initial, final = 51.783065 0.025065577 Final line search alpha, max atom move = 1.0000000 0.025065577 Iterations, force evaluations = 46 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9161 | 3.9161 | 3.9161 | 0.0 | 99.51 Neigh | 0.0064495 | 0.0064495 | 0.0064495 | 0.0 | 0.16 Comm | 0.0067731 | 0.0067731 | 0.0067731 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006215 | | | 0.16 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4851.00 ave 4851 max 4851 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: 77742.0 ave 77742 max 77742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77742 Ave neighs/atom = 89.979167 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.566 | 4.566 | 4.566 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -3825.3641 0 -3825.3641 12624.531 9431.8477 62 0 -3826.4753 0 -3826.4753 7.479788 9494.029 Loop time of 0.992883 on 1 procs for 16 steps with 864 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3825.3640704434 -3826.47415210992 -3826.475250364 Force two-norm initial, final = 182.60822 0.36327747 Force max component initial, final = 169.54416 0.083280407 Final line search alpha, max atom move = 0.00022464133 1.8708221e-05 Iterations, force evaluations = 16 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.97957 | 0.97957 | 0.97957 | 0.0 | 98.66 Neigh | 0.0065651 | 0.0065651 | 0.0065651 | 0.0 | 0.66 Comm | 0.0011976 | 0.0011976 | 0.0011976 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005554 | | | 0.56 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4879.00 ave 4879 max 4879 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: 75296.0 ave 75296 max 75296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75296 Ave neighs/atom = 87.148148 Neighbor list builds = 1 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.704 | 4.704 | 4.704 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3826.4753 0 -3826.4753 7.479788 Loop time of 2.663e-06 on 1 procs for 0 steps with 864 atoms 150.2% 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 | | 2.663e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4879.00 ave 4879 max 4879 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: 75296.0 ave 75296 max 75296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75296 Ave neighs/atom = 87.148148 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.704 | 4.704 | 4.704 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 -3826.4753 -3826.4753 25.729662 74.153545 4.976048 7.479788 7.479788 3.3815507 14.238962 4.8188509 2.3702803 688.31709 Loop time of 2.409e-06 on 1 procs for 0 steps with 864 atoms 207.6% 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 | | 2.409e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4879.00 ave 4879 max 4879 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37648.0 ave 37648 max 37648 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75296.0 ave 75296 max 75296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75296 Ave neighs/atom = 87.148148 Neighbor list builds = 0 Dangerous builds = 0 864 -3826.475250364 eV 2.37028025826192 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05