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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -42.836039 0.0000000) to (52.458786 42.836039 8.8671532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9952898 5.5070253 5.9114354 Created 1693 atoms using lattice units in orthogonal box = (0.0000000 -42.836039 0.0000000) to (52.458786 42.836039 8.8671532) create_atoms CPU = 0.002 seconds 1693 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9952898 5.5070253 5.9114354 Created 1693 atoms using lattice units in orthogonal box = (0.0000000 -42.836039 0.0000000) to (52.458786 42.836039 8.8671532) create_atoms CPU = 0.002 seconds 1693 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 74 atoms, new total = 3312 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.977 | 6.977 | 6.977 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11592.728 0 -11592.728 1206.6087 58 0 -11685.365 0 -11685.365 -11787.798 Loop time of 2.75681 on 1 procs for 58 steps with 3312 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 = -11592.7284583399 -11685.3547655331 -11685.3653699844 Force two-norm initial, final = 49.813973 0.27934005 Force max component initial, final = 5.1676586 0.027747836 Final line search alpha, max atom move = 1.0000000 0.027747836 Iterations, force evaluations = 58 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6968 | 2.6968 | 2.6968 | 0.0 | 97.82 Neigh | 0.033042 | 0.033042 | 0.033042 | 0.0 | 1.20 Comm | 0.010821 | 0.010821 | 0.010821 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01619 | | | 0.59 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10582.0 ave 10582 max 10582 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: 571012.0 ave 571012 max 571012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 571012 Ave neighs/atom = 172.40700 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.979 | 6.979 | 6.979 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -11685.365 0 -11685.365 -11787.798 39851.231 63 0 -11686.329 0 -11686.329 -2357.8669 39566.13 Loop time of 0.204232 on 1 procs for 5 steps with 3312 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 = -11685.3653699843 -11686.3269475452 -11686.3293486666 Force two-norm initial, final = 376.95337 2.2187538 Force max component initial, final = 286.28072 1.7797990 Final line search alpha, max atom move = 9.6041619e-05 0.00017093477 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1991 | 0.1991 | 0.1991 | 0.0 | 97.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067353 | 0.00067353 | 0.00067353 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004463 | | | 2.19 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10850.0 ave 10850 max 10850 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: 574272.0 ave 574272 max 574272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 574272 Ave neighs/atom = 173.39130 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.118 | 7.118 | 7.118 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11686.329 0 -11686.329 -2357.8669 Loop time of 2.274e-06 on 1 procs for 0 steps with 3312 atoms 175.9% 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 | | 2.274e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10972.0 ave 10972 max 10972 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: 574528.0 ave 574528 max 574528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 574528 Ave neighs/atom = 173.46860 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.118 | 7.118 | 7.118 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 -11686.329 -11686.329 52.308711 85.672078 8.8289743 -2357.8669 -2357.8669 71.864353 -7196.5935 51.128557 2.432107 1472.8248 Loop time of 2.586e-06 on 1 procs for 0 steps with 3312 atoms 270.7% 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 | | 2.586e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10972.0 ave 10972 max 10972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 287264.0 ave 287264 max 287264 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 574528.0 ave 574528 max 574528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 574528 Ave neighs/atom = 173.46860 Neighbor list builds = 0 Dangerous builds = 0 3312 -11686.3293486666 eV 2.43210702771102 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03