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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -37.117241 0.0000000) to (21.429649 37.117241 4.9600000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5920677 4.4187192 4.9600000 Created 336 atoms using lattice units in orthogonal box = (0.0000000 -37.117241 0.0000000) to (21.429649 37.117241 4.9600000) create_atoms CPU = 0.003 seconds 336 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5920677 4.4187192 4.9600000 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -37.117241 0.0000000) to (21.429649 37.117241 4.9600000) create_atoms CPU = 0.002 seconds 339 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 ghost atom cutoff = 6 binsize = 3, bins = 8 25 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 672 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_179158257180_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 ghost atom cutoff = 6 binsize = 3, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2821.0341 0 -2821.0341 28224.168 46 0 -2868.5193 0 -2868.5193 7181.1258 Loop time of 4.20012 on 1 procs for 46 steps with 672 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 = -2821.03414001956 -2868.51687436863 -2868.51932958694 Force two-norm initial, final = 71.378434 0.15201953 Force max component initial, final = 16.184706 0.017843556 Final line search alpha, max atom move = 1.0000000 0.017843556 Iterations, force evaluations = 46 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1836 | 4.1836 | 4.1836 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0081916 | 0.0081916 | 0.0081916 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008337 | | | 0.20 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3619.00 ave 3619 max 3619 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: 43716.0 ave 43716 max 43716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43716 Ave neighs/atom = 65.053571 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 ghost atom cutoff = 6 binsize = 3, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.513 | 4.513 | 4.513 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -2868.5193 0 -2868.5193 7181.1258 7890.4617 49 0 -2868.6041 0 -2868.6041 45.049768 7923.0436 Loop time of 0.227263 on 1 procs for 3 steps with 672 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2868.51932958694 -2868.60133587496 -2868.60408510136 Force two-norm initial, final = 63.002096 0.45066180 Force max component initial, final = 45.162542 0.33283808 Final line search alpha, max atom move = 0.00015964484 5.3135882e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22538 | 0.22538 | 0.22538 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003866 | 0.0003866 | 0.0003866 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001494 | | | 0.66 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3469.00 ave 3469 max 3469 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: 43558.0 ave 43558 max 43558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43558 Ave neighs/atom = 64.818452 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 ghost atom cutoff = 6 binsize = 3, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.651 | 4.651 | 4.651 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2868.6041 0 -2868.6041 45.049768 Loop time of 6.354e-06 on 1 procs for 0 steps with 672 atoms 188.9% 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 | | 6.354e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3434.00 ave 3434 max 3434 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: 43520.0 ave 43520 max 43520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43520 Ave neighs/atom = 64.761905 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 ghost atom cutoff = 6 binsize = 3, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.651 | 4.651 | 4.651 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 -2868.6041 -2868.6041 21.434286 74.41526 4.9673071 45.049768 45.049768 45.691567 67.469523 21.988214 2.329618 480.30707 Loop time of 6.906e-06 on 1 procs for 0 steps with 672 atoms 260.6% 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 | | 6.906e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3434.00 ave 3434 max 3434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21760.0 ave 21760 max 21760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43520.0 ave 43520 max 43520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43520 Ave neighs/atom = 64.761905 Neighbor list builds = 0 Dangerous builds = 0 672 -2868.60408510136 eV 2.32961796216926 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04