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 -30.832357 0.0000000) to (4.3599177 30.832357 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3599177 3.0829274 4.3599177 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -30.832357 0.0000000) to (4.3599177 30.832357 4.3599177) create_atoms CPU = 0.000 seconds 42 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3599177 3.0829274 4.3599177 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -30.832357 0.0000000) to (4.3599177 30.832357 4.3599177) create_atoms CPU = 0.000 seconds 42 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 = 2 19 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 0 atoms, new total = 84 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_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 2 19 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) = 4.771 | 4.771 | 4.771 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -248.73513 0 -248.73513 965227.57 20 0 -542.98498 0 -542.98498 119291.38 Loop time of 0.435165 on 1 procs for 20 steps with 84 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 = -248.735130784895 -542.984874979409 -542.984980792451 Force two-norm initial, final = 591.22107 0.031690247 Force max component initial, final = 152.49416 0.0071967696 Final line search alpha, max atom move = 1.0000000 0.0071967696 Iterations, force evaluations = 20 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43452 | 0.43452 | 0.43452 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003899 | 0.0003899 | 0.0003899 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000255 | | | 0.06 Nlocal: 84.0000 ave 84 max 84 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1788.00 ave 1788 max 1788 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: 6080.00 ave 6080 max 6080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6080 Ave neighs/atom = 72.380952 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 = 2 19 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 : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.771 | 4.771 | 4.771 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -542.98498 0 -542.98498 119291.38 1172.1773 46 0 -545.05191 0 -545.05191 1475.2678 1230.571 Loop time of 0.497237 on 1 procs for 26 steps with 84 atoms 86.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -542.984980792451 -545.051880992893 -545.051913200507 Force two-norm initial, final = 123.08079 0.027934493 Force max component initial, final = 87.031255 0.0057437198 Final line search alpha, max atom move = 1.0000000 0.0057437198 Iterations, force evaluations = 26 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49558 | 0.49558 | 0.49558 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003766 | 0.0003766 | 0.0003766 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001286 | | | 0.26 Nlocal: 84.0000 ave 84 max 84 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1788.00 ave 1788 max 1788 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: 7392.00 ave 7392 max 7392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7392 Ave neighs/atom = 88.000000 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 = 2 19 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) = 4.524 | 4.524 | 4.524 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -545.05191 0 -545.05191 1475.2678 Loop time of 2.3e-06 on 1 procs for 0 steps with 84 atoms 130.4% 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 | | 2.3e-06 | | |100.00 Nlocal: 84.0000 ave 84 max 84 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1372.00 ave 1372 max 1372 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: 7392.00 ave 7392 max 7392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7392 Ave neighs/atom = 88.000000 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 = 2 19 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) = 4.524 | 4.524 | 4.524 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 -545.05191 -545.05191 4.4671958 61.664713 4.4671958 1475.2678 1475.2678 -6.2900592 4438.3837 -6.2900592 2.6723589 4.0428931e-05 Loop time of 2.4e-06 on 1 procs for 0 steps with 84 atoms 166.7% 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 | | 2.4e-06 | | |100.00 Nlocal: 84.0000 ave 84 max 84 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3696.00 ave 3696 max 3696 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7392.00 ave 7392 max 7392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7392 Ave neighs/atom = 88.000000 Neighbor list builds = 0 Dangerous builds = 0 84 -545.051913200507 eV 2.67235888295984 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01