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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -59.864378 0.0000000) to (48.879060 59.864378 9.9088223) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0261855 5.7404198 6.6058816 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -59.864378 0.0000000) to (48.879060 59.864378 9.9088223) create_atoms CPU = 0.007 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0261855 5.7404198 6.6058816 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -59.864378 0.0000000) to (48.879060 59.864378 9.9088223) create_atoms CPU = 0.006 seconds 1757 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 29 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3504 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_106969701023_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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 -11007.003 0 -11007.003 36598.793 82 0 -11918.155 0 -11918.155 4496.2604 Loop time of 7.59093 on 1 procs for 82 steps with 3504 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 = -11007.0026604091 -11918.1449416127 -11918.1554448112 Force two-norm initial, final = 860.87743 0.22323042 Force max component initial, final = 124.08507 0.022749985 Final line search alpha, max atom move = 1.0000000 0.022749985 Iterations, force evaluations = 82 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2034 | 7.2034 | 7.2034 | 0.0 | 94.90 Neigh | 0.30683 | 0.30683 | 0.30683 | 0.0 | 4.04 Comm | 0.032884 | 0.032884 | 0.032884 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04776 | | | 0.63 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10842.0 ave 10842 max 10842 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: 494788.0 ave 494788 max 494788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 494788 Ave neighs/atom = 141.20662 Neighbor list builds = 4 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.977 | 6.977 | 6.977 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -11918.155 0 -11918.155 4496.2604 57988.698 91 0 -11919.242 0 -11919.242 51.13982 58304.766 Loop time of 0.762766 on 1 procs for 9 steps with 3504 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 = -11918.1554448112 -11919.2416276583 -11919.2419398436 Force two-norm initial, final = 330.41861 3.6670687 Force max component initial, final = 303.30680 3.1651153 Final line search alpha, max atom move = 0.00025298726 0.00080073383 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67035 | 0.67035 | 0.67035 | 0.0 | 87.88 Neigh | 0.075996 | 0.075996 | 0.075996 | 0.0 | 9.96 Comm | 0.003432 | 0.003432 | 0.003432 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01299 | | | 1.70 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10857.0 ave 10857 max 10857 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: 493154.0 ave 493154 max 493154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 493154 Ave neighs/atom = 140.74030 Neighbor list builds = 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.115 | 7.115 | 7.115 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11919.242 0 -11919.242 51.13982 Loop time of 6.465e-06 on 1 procs for 0 steps with 3504 atoms 170.1% 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 | | 6.465e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10857.0 ave 10857 max 10857 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: 493036.0 ave 493036 max 493036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 493036 Ave neighs/atom = 140.70662 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.115 | 7.115 | 7.115 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 -11919.242 -11919.242 48.789948 120.69277 9.9013051 51.13982 51.13982 20.027877 87.675574 45.716009 2.5286512 2126.4112 Loop time of 6.876e-06 on 1 procs for 0 steps with 3504 atoms 261.8% 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 | | 6.876e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10857.0 ave 10857 max 10857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 246518.0 ave 246518 max 246518 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 493036.0 ave 493036 max 493036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 493036 Ave neighs/atom = 140.70662 Neighbor list builds = 0 Dangerous builds = 0 3504 -11919.2419398436 eV 2.52865116443303 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09