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 -44.888100 0.0000000) to (22.444050 44.888100 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8112538 3.8112538 3.0829274 Created 212 atoms using lattice units in orthogonal box = (0.0000000 -44.888100 0.0000000) to (22.444050 44.888100 3.0829274) create_atoms CPU = 0.001 seconds 212 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8112538 3.8112538 3.0829274 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -44.888100 0.0000000) to (22.444050 44.888100 3.0829274) create_atoms CPU = 0.000 seconds 213 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 = 7 27 1 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 0 atoms, new total = 425 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 = 7 27 1 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) = 5.223 | 5.223 | 5.223 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2474.1627 0 -2474.1627 146552.7 61 0 -2755.3571 0 -2755.3571 14786.621 Loop time of 12.9479 on 1 procs for 61 steps with 425 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2474.16274026715 -2755.35458466861 -2755.35710211546 Force two-norm initial, final = 874.46649 0.24480868 Force max component initial, final = 420.98598 0.087490914 Final line search alpha, max atom move = 1.0000000 0.087490914 Iterations, force evaluations = 61 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.94 | 12.94 | 12.94 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0047794 | 0.0047794 | 0.0047794 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003618 | | | 0.03 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3846.00 ave 3846 max 3846 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: 27916.0 ave 27916 max 27916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27916 Ave neighs/atom = 65.684706 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 27 1 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.223 | 5.223 | 5.223 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -2755.3571 0 -2755.3571 14786.621 6211.9184 89 0 -2756.7406 0 -2756.7406 1219.7898 6242.0731 Loop time of 3.51227 on 1 procs for 28 steps with 425 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 = -2755.35710211546 -2756.73902852066 -2756.74063221629 Force two-norm initial, final = 144.84833 8.4687786 Force max component initial, final = 142.35273 4.8556895 Final line search alpha, max atom move = 0.0014429940 0.0070067306 Iterations, force evaluations = 28 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4852 | 3.4852 | 3.4852 | 0.0 | 99.23 Neigh | 0.021399 | 0.021399 | 0.021399 | 0.0 | 0.61 Comm | 0.0010163 | 0.0010163 | 0.0010163 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004633 | | | 0.13 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3852.00 ave 3852 max 3852 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: 31692.0 ave 31692 max 31692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31692 Ave neighs/atom = 74.569412 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 28 1 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) = 5.361 | 5.361 | 5.361 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2756.7406 0 -2756.7406 1219.7898 Loop time of 2.159e-06 on 1 procs for 0 steps with 425 atoms 185.3% 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 | | 2.159e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3824.00 ave 3824 max 3824 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: 32426.0 ave 32426 max 32426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32426 Ave neighs/atom = 76.296471 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 = 7 28 1 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) = 5.361 | 5.361 | 5.361 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 -2756.7406 -2756.7406 22.433982 91.80764 3.030705 1219.7898 1219.7898 1245.7691 1240.8288 1172.7714 2.5792442 602.04174 Loop time of 2.936e-06 on 1 procs for 0 steps with 425 atoms 170.3% 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 | | 2.936e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3824.00 ave 3824 max 3824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16213.0 ave 16213 max 16213 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32426.0 ave 32426 max 32426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32426 Ave neighs/atom = 76.296471 Neighbor list builds = 0 Dangerous builds = 0 425 -2756.74063221629 eV 2.57924416868825 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17