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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -63.091457 0.0000000) to (36.424053 63.091457 5.4500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8927833 5.0219551 5.4500000 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -63.091457 0.0000000) to (36.424053 63.091457 5.4500000) create_atoms CPU = 0.008 seconds 806 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8927833 5.0219551 5.4500000 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -63.091457 0.0000000) to (36.424053 63.091457 5.4500000) create_atoms CPU = 0.007 seconds 806 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 13 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1608 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 13 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.716 | 4.716 | 4.716 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10843.703 0 -10843.703 14668.269 29 0 -10907.805 0 -10907.805 6457.288 Loop time of 4.72365 on 1 procs for 29 steps with 1608 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 = -10843.7033197575 -10907.7960392336 -10907.8047262498 Force two-norm initial, final = 48.136949 0.31029919 Force max component initial, final = 8.3852655 0.064995461 Final line search alpha, max atom move = 0.80587174 0.052378005 Iterations, force evaluations = 29 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7064 | 4.7064 | 4.7064 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0076588 | 0.0076588 | 0.0076588 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009563 | | | 0.20 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5732.00 ave 5732 max 5732 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: 92788.0 ave 92788 max 92788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92788 Ave neighs/atom = 57.703980 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 13 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.716 | 4.716 | 4.716 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -10907.805 0 -10907.805 6457.288 25048.708 31 0 -10907.918 0 -10907.918 568.84554 25104.161 Loop time of 0.354821 on 1 procs for 2 steps with 1608 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 = -10907.8047262498 -10907.9126274239 -10907.9178049972 Force two-norm initial, final = 144.89757 9.6729681 Force max component initial, final = 114.92474 9.3503814 Final line search alpha, max atom move = 3.6220598e-05 0.00033867640 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35239 | 0.35239 | 0.35239 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050941 | 0.00050941 | 0.00050941 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001917 | | | 0.54 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5716.00 ave 5716 max 5716 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: 92836.0 ave 92836 max 92836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92836 Ave neighs/atom = 57.733831 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 13 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.853 | 4.853 | 4.853 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10907.918 0 -10907.918 568.84554 Loop time of 5.943e-06 on 1 procs for 0 steps with 1608 atoms 168.3% 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 | | 5.943e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5715.00 ave 5715 max 5715 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: 92828.0 ave 92828 max 92828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92828 Ave neighs/atom = 57.728856 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 13 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.853 | 4.853 | 4.853 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 -10907.918 -10907.918 36.455455 126.18291 5.4573605 568.84554 568.84554 -597.26657 2147.2273 156.57587 2.4312458 895.44562 Loop time of 7.297e-06 on 1 procs for 0 steps with 1608 atoms 260.4% 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 | | 7.297e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5715.00 ave 5715 max 5715 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46414.0 ave 46414 max 46414 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 92828.0 ave 92828 max 92828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92828 Ave neighs/atom = 57.728856 Neighbor list builds = 0 Dangerous builds = 0 1608 -10907.9178049972 eV 2.43124581007608 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05