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 = 4.0499989 4.0499989 4.0499989 Created orthogonal box = (0.0000000 -76.419276 0.0000000) to (38.207613 76.419276 4.0499989) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5808873 5.5808873 4.0499989 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -76.419276 0.0000000) to (38.207613 76.419276 4.0499989) create_atoms CPU = 0.003 seconds 714 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5808873 5.5808873 4.0499989 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -76.419276 0.0000000) to (38.207613 76.419276 4.0499989) create_atoms CPU = 0.002 seconds 714 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 44 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1412 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_315820974149_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.082 | 5.082 | 5.082 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4718.6833 0 -4718.6833 1936.8471 29 0 -4732.6788 0 -4732.6788 -2667.0949 Loop time of 4.59853 on 1 procs for 29 steps with 1412 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4718.68326443777 -4732.67450685883 -4732.67884417643 Force two-norm initial, final = 24.584695 0.25374317 Force max component initial, final = 7.8545113 0.046366306 Final line search alpha, max atom move = 1.0000000 0.046366306 Iterations, force evaluations = 29 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5799 | 4.5799 | 4.5799 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0097995 | 0.0097995 | 0.0097995 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008878 | | | 0.19 Nlocal: 1412.00 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8029.00 ave 8029 max 8029 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: 109636.0 ave 109636 max 109636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109636 Ave neighs/atom = 77.645892 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.082 | 5.082 | 5.082 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -4732.6788 0 -4732.6788 -2667.0949 23650.358 32 0 -4732.7337 0 -4732.7337 -482.91532 23582.829 Loop time of 0.530777 on 1 procs for 3 steps with 1412 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4732.67884417642 -4732.7326042817 -4732.73370268342 Force two-norm initial, final = 52.325623 0.27366721 Force max component initial, final = 40.285393 0.058799119 Final line search alpha, max atom move = 0.00029183928 1.7159892e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52635 | 0.52635 | 0.52635 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009715 | 0.0009715 | 0.0009715 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003451 | | | 0.65 Nlocal: 1412.00 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8057.00 ave 8057 max 8057 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: 110408.0 ave 110408 max 110408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110408 Ave neighs/atom = 78.192635 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.220 | 5.220 | 5.220 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4732.7337 0 -4732.7337 -482.91532 Loop time of 6.144e-06 on 1 procs for 0 steps with 1412 atoms 179.0% 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 | | 6.144e-06 | | |100.00 Nlocal: 1412.00 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8057.00 ave 8057 max 8057 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: 110624.0 ave 110624 max 110624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110624 Ave neighs/atom = 78.345609 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.220 | 5.220 | 5.220 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 -4732.7337 -4732.7337 38.175734 152.83855 4.0418072 -482.91532 -482.91532 -3.0054105 -1445.7183 -0.022238838 2.5487796 559.51679 Loop time of 6.856e-06 on 1 procs for 0 steps with 1412 atoms 277.1% 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 | | 6.856e-06 | | |100.00 Nlocal: 1412.00 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8057.00 ave 8057 max 8057 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55312.0 ave 55312 max 55312 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 110624.0 ave 110624 max 110624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110624 Ave neighs/atom = 78.345609 Neighbor list builds = 0 Dangerous builds = 0 1412 -4732.73370268342 eV 2.54877959716022 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05