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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -47.176520 0.0000000) to (16.679419 47.176520 5.7209934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8679959 6.9377236 5.7209934 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -47.176520 0.0000000) to (16.679419 47.176520 5.7209934) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8679959 6.9377236 5.7209934 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -47.176520 0.0000000) to (16.679419 47.176520 5.7209934) create_atoms CPU = 0.001 seconds 274 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 6 31 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_461927113651_000#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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.487 | 4.487 | 4.487 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1776.4605 0 -1776.4605 13422.516 94 0 -1822.9371 0 -1822.9371 2818.9218 Loop time of 3.06584 on 1 procs for 94 steps with 544 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1776.46051025695 -1822.9358486803 -1822.93709539515 Force two-norm initial, final = 94.072793 0.080687590 Force max component initial, final = 32.669252 0.0064895992 Final line search alpha, max atom move = 1.0000000 0.0064895992 Iterations, force evaluations = 94 174 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0516 | 3.0516 | 3.0516 | 0.0 | 99.53 Neigh | 0.0025605 | 0.0025605 | 0.0025605 | 0.0 | 0.08 Comm | 0.0056948 | 0.0056948 | 0.0056948 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006015 | | | 0.20 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2764.00 ave 2764 max 2764 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: 29704.0 ave 29704 max 29704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29704 Ave neighs/atom = 54.602941 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.485 | 4.485 | 4.485 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -1822.9371 0 -1822.9371 2818.9218 9003.4355 100 0 -1823.006 0 -1823.006 -69.161213 9038.5061 Loop time of 0.144466 on 1 procs for 6 steps with 544 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 = -1822.93709539515 -1823.00593454511 -1823.00604284241 Force two-norm initial, final = 31.763317 0.75169541 Force max component initial, final = 28.866946 0.56269781 Final line search alpha, max atom move = 0.0010069364 0.00056660090 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14324 | 0.14324 | 0.14324 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018363 | 0.00018363 | 0.00018363 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001039 | | | 0.72 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2654.00 ave 2654 max 2654 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: 29620.0 ave 29620 max 29620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29620 Ave neighs/atom = 54.448529 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.623 | 4.623 | 4.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1823.006 0 -1823.006 -69.161213 Loop time of 1.969e-06 on 1 procs for 0 steps with 544 atoms 152.4% 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 | | 1.969e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2654.00 ave 2654 max 2654 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: 29576.0 ave 29576 max 29576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29576 Ave neighs/atom = 54.367647 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.623 | 4.623 | 4.623 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 -1823.006 -1823.006 16.674019 94.844119 5.7153912 -69.161213 -69.161213 -82.31911 -25.517709 -99.64682 2.6371898 352.8137 Loop time of 1.77e-06 on 1 procs for 0 steps with 544 atoms 169.5% 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 | | 1.77e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2654.00 ave 2654 max 2654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14788.0 ave 14788 max 14788 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29576.0 ave 29576 max 29576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29576 Ave neighs/atom = 54.367647 Neighbor list builds = 0 Dangerous builds = 0 544 -1823.00604284241 eV 2.63718984692899 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03