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 = 4.0320000 4.0320000 4.0320000 Created orthogonal box = (0.0000000 -59.668151 0.0000000) to (48.718841 59.668151 9.8763426) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0064325 5.7216035 6.5842284 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -59.668151 0.0000000) to (48.718841 59.668151 9.8763426) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0064325 5.7216035 6.5842284 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -59.668151 0.0000000) to (48.718841 59.668151 9.8763426) create_atoms CPU = 0.002 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 11 27 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 8.875 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_519613893196_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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 11 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 7.439 | 7.439 | 7.439 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11077.39 0 -11077.39 24826.963 70 0 -11743.282 0 -11743.282 3958.5427 Loop time of 3.58006 on 1 procs for 70 steps with 3504 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 = -11077.3904873535 -11743.2706926941 -11743.2820703308 Force two-norm initial, final = 497.83710 0.26485781 Force max component initial, final = 67.164227 0.033511343 Final line search alpha, max atom move = 1.0000000 0.033511343 Iterations, force evaluations = 70 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4336 | 3.4336 | 3.4336 | 0.0 | 95.91 Neigh | 0.10968 | 0.10968 | 0.10968 | 0.0 | 3.06 Comm | 0.015751 | 0.015751 | 0.015751 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02105 | | | 0.59 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12070.0 ave 12070 max 12070 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: 614788.0 ave 614788 max 614788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614788 Ave neighs/atom = 175.45320 Neighbor list builds = 3 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 11 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.438 | 7.438 | 7.438 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -11743.282 0 -11743.282 3958.5427 57420.328 77 0 -11744.007 0 -11744.007 -24.146436 57700.502 Loop time of 0.258859 on 1 procs for 7 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 = -11743.2820703308 -11744.0039838971 -11744.0070182221 Force two-norm initial, final = 279.77759 1.6948406 Force max component initial, final = 250.56605 1.1784352 Final line search alpha, max atom move = 0.00012010380 0.00014153455 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25318 | 0.25318 | 0.25318 | 0.0 | 97.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000809 | 0.000809 | 0.000809 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004873 | | | 1.88 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12037.0 ave 12037 max 12037 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: 614662.0 ave 614662 max 614662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614662 Ave neighs/atom = 175.41724 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 11 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 7.576 | 7.576 | 7.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11744.007 0 -11744.007 -24.146436 Loop time of 2.168e-06 on 1 procs for 0 steps with 3504 atoms 138.4% 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 | | 2.168e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11970.0 ave 11970 max 11970 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: 614114.0 ave 614114 max 614114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614114 Ave neighs/atom = 175.26084 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 11 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 7.576 | 7.576 | 7.576 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 -11744.007 -11744.007 48.673452 120.10189 9.8704651 -24.146436 -24.146436 -32.691261 -30.372401 -9.3756459 2.5672135 2143.461 Loop time of 2.242e-06 on 1 procs for 0 steps with 3504 atoms 267.6% 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 | | 2.242e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11970.0 ave 11970 max 11970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 307057.0 ave 307057 max 307057 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 614114.0 ave 614114 max 614114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614114 Ave neighs/atom = 175.26084 Neighbor list builds = 0 Dangerous builds = 0 3504 -11744.0070182221 eV 2.56721352964669 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04