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 = 3.6390299 3.6390299 3.6390299 Created orthogonal box = (0.0000000 -42.124816 0.0000000) to (29.786743 42.124816 5.1463654) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7795174 6.2872860 5.1463654 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -42.124816 0.0000000) to (29.786743 42.124816 5.1463654) create_atoms CPU = 0.004 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7795174 6.2872860 5.1463654 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -42.124816 0.0000000) to (29.786743 42.124816 5.1463654) create_atoms CPU = 0.004 seconds 538 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 22 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1074 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_748636486270_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.028 | 5.028 | 5.028 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3492.0568 0 -3492.0568 61498.41 49 0 -3666.8796 0 -3666.8796 6182.7775 Loop time of 2.05751 on 1 procs for 49 steps with 1074 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 = -3492.05681427855 -3666.87611503843 -3666.87963470821 Force two-norm initial, final = 339.05196 0.15398895 Force max component initial, final = 86.622477 0.013379260 Final line search alpha, max atom move = 1.0000000 0.013379260 Iterations, force evaluations = 49 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0304 | 2.0304 | 2.0304 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014529 | 0.014529 | 0.014529 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0126 | | | 0.61 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6766.00 ave 6766 max 6766 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: 189436.0 ave 189436 max 189436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189436 Ave neighs/atom = 176.38361 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.028 | 5.028 | 5.028 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -3666.8796 0 -3666.8796 6182.7775 12914.918 57 0 -3667.2781 0 -3667.2781 -71.907791 12969.708 Loop time of 0.248805 on 1 procs for 8 steps with 1074 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 = -3666.87963470821 -3667.27803560639 -3667.2781264219 Force two-norm initial, final = 123.69882 1.1646304 Force max component initial, final = 121.93570 0.86069087 Final line search alpha, max atom move = 0.00063532021 0.00054681431 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24162 | 0.24162 | 0.24162 | 0.0 | 97.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015403 | 0.0015403 | 0.0015403 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005644 | | | 2.27 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6774.00 ave 6774 max 6774 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: 188924.0 ave 188924 max 188924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188924 Ave neighs/atom = 175.90689 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.166 | 5.166 | 5.166 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3667.2781 0 -3667.2781 -71.907791 Loop time of 6.455e-06 on 1 procs for 0 steps with 1074 atoms 170.4% 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 | | 6.455e-06 | | |100.00 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6774.00 ave 6774 max 6774 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: 188576.0 ave 188576 max 188576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188576 Ave neighs/atom = 175.58287 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.166 | 5.166 | 5.166 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 -3667.2781 -3667.2781 29.726247 84.826128 5.1435207 -71.907791 -71.907791 -106.10709 -90.005459 -19.610825 2.3579344 541.04858 Loop time of 7.107e-06 on 1 procs for 0 steps with 1074 atoms 225.1% 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 | | 7.107e-06 | | |100.00 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6774.00 ave 6774 max 6774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94288.0 ave 94288 max 94288 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188576.0 ave 188576 max 188576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188576 Ave neighs/atom = 175.58287 Neighbor list builds = 0 Dangerous builds = 0 1074 -3667.2781264219 eV 2.35793438241429 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02