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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -69.983557 0.0000000) to (40.405026 69.983557 6.3360136) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9613972 5.3539334 6.3360136 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -69.983557 0.0000000) to (40.405026 69.983557 6.3360136) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9613972 5.3539334 6.3360136 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -69.983557 0.0000000) to (40.405026 69.983557 6.3360136) create_atoms CPU = 0.002 seconds 1465 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 2925 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.213 | 6.213 | 6.213 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10380.205 0 -10380.205 73441.075 927 0 -11555.273 0 -11555.273 -66210.252 Loop time of 37.2753 on 1 procs for 927 steps with 2925 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 = -10380.2047867907 -11555.2647134665 -11555.2732001534 Force two-norm initial, final = 1875.0107 0.38967082 Force max component initial, final = 468.22553 0.13838915 Final line search alpha, max atom move = 0.74869236 0.10361090 Iterations, force evaluations = 927 1807 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 36.363 | 36.363 | 36.363 | 0.0 | 97.55 Neigh | 0.46309 | 0.46309 | 0.46309 | 0.0 | 1.24 Comm | 0.22657 | 0.22657 | 0.22657 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2225 | | | 0.60 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11597.0 ave 11597 max 11597 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: 395890.0 ave 395890 max 395890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 395890 Ave neighs/atom = 135.34701 Neighbor list builds = 19 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 927 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.593 | 6.593 | 6.593 Mbytes Step Temp E_pair E_mol TotEng Press Volume 927 0 -11555.273 0 -11555.273 -66210.252 35832.532 959 0 -11597.109 0 -11597.109 -168.82052 34241.298 Loop time of 0.806953 on 1 procs for 32 steps with 2925 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 = -11555.2732001534 -11597.1053759723 -11597.1086422456 Force two-norm initial, final = 2648.0634 10.645344 Force max component initial, final = 1810.9394 8.3879276 Final line search alpha, max atom move = 4.9402810e-05 0.00041438720 Iterations, force evaluations = 32 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70315 | 0.70315 | 0.70315 | 0.0 | 87.14 Neigh | 0.08006 | 0.08006 | 0.08006 | 0.0 | 9.92 Comm | 0.0040421 | 0.0040421 | 0.0040421 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01971 | | | 2.44 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11712.0 ave 11712 max 11712 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: 412950.0 ave 412950 max 412950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412950 Ave neighs/atom = 141.17949 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.730 | 6.730 | 6.730 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11597.109 0 -11597.109 -168.82052 Loop time of 2.461e-06 on 1 procs for 0 steps with 2925 atoms 162.5% 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 | | 2.461e-06 | | |100.00 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11705.0 ave 11705 max 11705 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: 412598.0 ave 412598 max 412598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412598 Ave neighs/atom = 141.05915 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.730 | 6.730 | 6.730 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 -11597.109 -11597.109 39.51855 136.35965 6.3542361 -168.82052 -168.82052 84.370753 -382.36195 -208.47037 2.202725 10343.647 Loop time of 2.244e-06 on 1 procs for 0 steps with 2925 atoms 222.8% 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 | | 2.244e-06 | | |100.00 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11705.0 ave 11705 max 11705 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 206299.0 ave 206299 max 206299 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 412598.0 ave 412598 max 412598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412598 Ave neighs/atom = 141.05915 Neighbor list builds = 0 Dangerous builds = 0 2925 -11183.4503922994 eV 2.20272504480042 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:38