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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -44.121590 0.0000000) to (36.025127 44.121590 8.9139073) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1464468 5.1024968 5.9426049 Created 1174 atoms using lattice units in orthogonal box = (0.0000000 -44.121590 0.0000000) to (36.025127 44.121590 8.9139073) create_atoms CPU = 0.002 seconds 1174 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1464468 5.1024968 5.9426049 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -44.121590 0.0000000) to (36.025127 44.121590 8.9139073) create_atoms CPU = 0.002 seconds 1182 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 19 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 2336 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_609260676108_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.712 | 7.712 | 7.712 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6745.942 0 -6745.942 88917.186 79 0 -7628.7694 0 -7628.7694 -1882.5711 Loop time of 5.02739 on 1 procs for 79 steps with 2336 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 = -6745.94196588436 -7628.76329142754 -7628.7693679171 Force two-norm initial, final = 1318.0455 0.19725456 Force max component initial, final = 229.39832 0.0090819072 Final line search alpha, max atom move = 1.0000000 0.0090819072 Iterations, force evaluations = 79 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9164 | 4.9164 | 4.9164 | 0.0 | 97.79 Neigh | 0.076335 | 0.076335 | 0.076335 | 0.0 | 1.52 Comm | 0.018293 | 0.018293 | 0.018293 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01641 | | | 0.33 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11488.0 ave 11488 max 11488 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: 740364.0 ave 740364 max 740364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 740364 Ave neighs/atom = 316.93664 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.712 | 7.712 | 7.712 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -7628.7694 0 -7628.7694 -1882.5711 28337.06 82 0 -7628.8446 0 -7628.8446 228.13877 28295.838 Loop time of 0.173136 on 1 procs for 3 steps with 2336 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 = -7628.76936791711 -7628.84231446369 -7628.84464641059 Force two-norm initial, final = 74.818345 9.5017979 Force max component initial, final = 64.992977 9.0778913 Final line search alpha, max atom move = 9.0934741e-05 0.00082549569 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17069 | 0.17069 | 0.17069 | 0.0 | 98.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041524 | 0.00041524 | 0.00041524 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002026 | | | 1.17 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11068.0 ave 11068 max 11068 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: 739542.0 ave 739542 max 739542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 739542 Ave neighs/atom = 316.58476 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.850 | 7.850 | 7.850 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7628.8446 0 -7628.8446 228.13877 Loop time of 1.819e-06 on 1 procs for 0 steps with 2336 atoms 219.9% 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 | | 1.819e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11081.0 ave 11081 max 11081 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: 739552.0 ave 739552 max 739552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 739552 Ave neighs/atom = 316.58904 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.850 | 7.850 | 7.850 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 -7628.8446 -7628.8446 35.995267 88.340296 8.8985309 228.13877 228.13877 12.14976 514.57713 157.68941 2.2558788 1436.4188 Loop time of 2.277e-06 on 1 procs for 0 steps with 2336 atoms 307.4% 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 | | 2.277e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11081.0 ave 11081 max 11081 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 369776.0 ave 369776 max 369776 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 739552.0 ave 739552 max 739552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 739552 Ave neighs/atom = 316.58904 Neighbor list builds = 0 Dangerous builds = 0 2336 -7628.84464641059 eV 2.25587878533842 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06