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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -55.073134 0.0000000) to (38.942586 55.073134 5.1580716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1488294 6.2802697 5.1580716 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -55.073134 0.0000000) to (38.942586 55.073134 5.1580716) create_atoms CPU = 0.003 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1488294 6.2802697 5.1580716 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -55.073134 0.0000000) to (38.942586 55.073134 5.1580716) create_atoms CPU = 0.002 seconds 916 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 = 15 42 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 0 atoms, new total = 1828 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 15 42 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) = 5.897 | 5.897 | 5.897 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7295.882 0 -7295.882 39566.173 73 0 -7570.5193 0 -7570.5193 6331.9007 Loop time of 13.4982 on 1 procs for 73 steps with 1828 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7295.88203527277 -7570.51232777566 -7570.51926906556 Force two-norm initial, final = 324.34026 0.30655549 Force max component initial, final = 63.809696 0.032379021 Final line search alpha, max atom move = 1.0000000 0.032379021 Iterations, force evaluations = 73 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.477 | 13.477 | 13.477 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0083677 | 0.0083677 | 0.0083677 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01271 | | | 0.09 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5864.00 ave 5864 max 5864 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: 98880.0 ave 98880 max 98880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98880 Ave neighs/atom = 54.091904 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 = 15 42 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 : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.897 | 5.897 | 5.897 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -7570.5193 0 -7570.5193 6331.9007 22124.932 76 0 -7570.7176 0 -7570.7176 98.347013 22208.807 Loop time of 0.513375 on 1 procs for 3 steps with 1828 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7570.51926906556 -7570.71116676467 -7570.71760132796 Force two-norm initial, final = 156.71893 3.0004613 Force max component initial, final = 119.28761 2.6995069 Final line search alpha, max atom move = 7.1120317e-05 0.00019198979 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51139 | 0.51139 | 0.51139 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029454 | 0.00029454 | 0.00029454 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001691 | | | 0.33 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5886.00 ave 5886 max 5886 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: 98512.0 ave 98512 max 98512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98512 Ave neighs/atom = 53.890591 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 = 15 42 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) = 6.035 | 6.035 | 6.035 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7570.7176 0 -7570.7176 98.347013 Loop time of 4.255e-06 on 1 procs for 0 steps with 1828 atoms 164.5% 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 | | 4.255e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5886.00 ave 5886 max 5886 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: 98472.0 ave 98472 max 98472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98472 Ave neighs/atom = 53.868709 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 = 15 42 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) = 6.035 | 6.035 | 6.035 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 -7570.7176 -7570.7176 38.981071 110.4152 5.1599156 98.347013 98.347013 194.93891 91.000644 9.1014816 2.3532622 681.28171 Loop time of 2.268e-06 on 1 procs for 0 steps with 1828 atoms 220.5% 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 | | 2.268e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5886.00 ave 5886 max 5886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49236.0 ave 49236 max 49236 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 98472.0 ave 98472 max 98472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98472 Ave neighs/atom = 53.868709 Neighbor list builds = 0 Dangerous builds = 0 1828 -7570.71760132796 eV 2.35326221860969 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14