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 = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -57.212805 0.0000000) to (35.035545 57.212805 8.8990373) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6508943 5.5367231 5.9326915 Created 1485 atoms using lattice units in orthogonal box = (0.0000000 -57.212805 0.0000000) to (35.035545 57.212805 8.8990373) create_atoms CPU = 0.003 seconds 1485 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6508943 5.5367231 5.9326915 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -57.212805 0.0000000) to (35.035545 57.212805 8.8990373) create_atoms CPU = 0.002 seconds 1491 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 3 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2976 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.902 | 6.902 | 6.902 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12261.851 0 -12261.851 43293.056 75 0 -12690.621 0 -12690.621 2977.6989 Loop time of 2.84349 on 1 procs for 75 steps with 2976 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12261.8506094167 -12690.608099947 -12690.6205388795 Force two-norm initial, final = 429.04731 0.47223609 Force max component initial, final = 108.53674 0.054311265 Final line search alpha, max atom move = 1.0000000 0.054311265 Iterations, force evaluations = 75 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7442 | 2.7442 | 2.7442 | 0.0 | 96.51 Neigh | 0.063004 | 0.063004 | 0.063004 | 0.0 | 2.22 Comm | 0.015849 | 0.015849 | 0.015849 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0204 | | | 0.72 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10205.0 ave 10205 max 10205 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: 488876.0 ave 488876 max 488876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 488876 Ave neighs/atom = 164.27285 Neighbor list builds = 2 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/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) = 6.904 | 6.904 | 6.904 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -12690.621 0 -12690.621 2977.6989 35675.917 78 0 -12690.764 0 -12690.764 31.228045 35743.667 Loop time of 0.107163 on 1 procs for 3 steps with 2976 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 = -12690.6205388795 -12690.7605866149 -12690.7636839981 Force two-norm initial, final = 145.24170 2.9940436 Force max component initial, final = 136.31514 1.9166750 Final line search alpha, max atom move = 6.0755139e-05 0.00011644786 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10405 | 0.10405 | 0.10405 | 0.0 | 97.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047463 | 0.00047463 | 0.00047463 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002643 | | | 2.47 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10370.0 ave 10370 max 10370 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: 490916.0 ave 490916 max 490916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 490916 Ave neighs/atom = 164.95833 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.661 | 6.661 | 6.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12690.764 0 -12690.764 31.228045 Loop time of 2.485e-06 on 1 procs for 0 steps with 2976 atoms 120.7% 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 | | 2.485e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10370.0 ave 10370 max 10370 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: 469138.0 ave 469138 max 469138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 469138 Ave neighs/atom = 157.64046 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.661 | 6.661 | 6.661 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 -12690.764 -12690.764 35.107623 114.44678 8.8959858 31.228045 31.228045 75.03182 -67.231394 85.883708 2.3426839 1008.9698 Loop time of 2.759e-06 on 1 procs for 0 steps with 2976 atoms 253.7% 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 | | 2.759e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10370.0 ave 10370 max 10370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 234569.0 ave 234569 max 234569 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 469138.0 ave 469138 max 469138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 469138 Ave neighs/atom = 157.64046 Neighbor list builds = 0 Dangerous builds = 0 2976 -12690.7636839981 eV 2.34268388737093 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03