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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -36.998211 0.0000000) to (13.079753 36.998211 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3599177 5.1382123 4.3599177 Created 146 atoms using lattice units in orthogonal box = (0.0000000 -36.998211 0.0000000) to (13.079753 36.998211 4.3599177) create_atoms CPU = 0.001 seconds 146 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3599177 5.1382123 4.3599177 Created 146 atoms using lattice units in orthogonal box = (0.0000000 -36.998211 0.0000000) to (13.079753 36.998211 4.3599177) create_atoms CPU = 0.000 seconds 146 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 3 atoms, new total = 289 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.802 | 4.802 | 4.802 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1671.6636 0 -1671.6636 174209.19 75 0 -1869.0704 0 -1869.0704 22024.265 Loop time of 11.0264 on 1 procs for 75 steps with 289 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 = -1671.66356363657 -1869.06850478518 -1869.0703518041 Force two-norm initial, final = 473.95330 0.20504449 Force max component initial, final = 108.76326 0.065885784 Final line search alpha, max atom move = 1.0000000 0.065885784 Iterations, force evaluations = 75 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.007 | 11.007 | 11.007 | 0.0 | 99.82 Neigh | 0.013898 | 0.013898 | 0.013898 | 0.0 | 0.13 Comm | 0.0030097 | 0.0030097 | 0.0030097 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002549 | | | 0.02 Nlocal: 289.000 ave 289 max 289 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2479.00 ave 2479 max 2479 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: 21272.0 ave 21272 max 21272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21272 Ave neighs/atom = 73.605536 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.802 | 4.802 | 4.802 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -1869.0704 0 -1869.0704 22024.265 4219.7679 78 0 -1869.0847 0 -1869.0847 18873.814 4226.0657 Loop time of 0.406662 on 1 procs for 3 steps with 289 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 = -1869.0703518041 -1869.08459887455 -1869.08471897767 Force two-norm initial, final = 15.147014 0.81965650 Force max component initial, final = 14.578637 0.76327763 Final line search alpha, max atom move = 0.00071115915 0.00054281187 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40614 | 0.40614 | 0.40614 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010284 | 0.00010284 | 0.00010284 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004159 | | | 0.10 Nlocal: 289.000 ave 289 max 289 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2443.00 ave 2443 max 2443 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: 21624.0 ave 21624 max 21624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21624 Ave neighs/atom = 74.823529 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.940 | 4.940 | 4.940 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1869.0847 0 -1869.0847 18873.814 Loop time of 2.157e-06 on 1 procs for 0 steps with 289 atoms 139.1% 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 | | 2.157e-06 | | |100.00 Nlocal: 289.000 ave 289 max 289 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2439.00 ave 2439 max 2439 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: 21540.0 ave 21540 max 21540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21540 Ave neighs/atom = 74.532872 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.940 | 4.940 | 4.940 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 -1869.0847 -1869.0847 13.106189 73.996423 4.3576173 18873.814 18873.814 289.95696 56276.969 54.515999 2.4603649 618.38531 Loop time of 1.814e-06 on 1 procs for 0 steps with 289 atoms 165.4% 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 | | 1.814e-06 | | |100.00 Nlocal: 289.000 ave 289 max 289 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2439.00 ave 2439 max 2439 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10770.0 ave 10770 max 10770 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21540.0 ave 21540 max 21540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21540 Ave neighs/atom = 74.532872 Neighbor list builds = 0 Dangerous builds = 0 289 -1869.08471897767 eV 2.46036490679691 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11