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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -44.125349 0.0000000) to (20.800889 44.125349 5.0449566) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1179085 6.0564204 5.0449566 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -44.125349 0.0000000) to (20.800889 44.125349 5.0449566) create_atoms CPU = 0.002 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1179085 6.0564204 5.0449566 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -44.125349 0.0000000) to (20.800889 44.125349 5.0449566) create_atoms CPU = 0.001 seconds 412 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 32 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 816 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_058735400462_001#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.543 | 4.543 | 4.543 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3337.7341 0 -3337.7341 39853.485 179 0 -3444.6751 0 -3444.6751 47670.977 Loop time of 8.41989 on 1 procs for 179 steps with 816 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3337.73411027458 -3444.67205059688 -3444.67514526609 Force two-norm initial, final = 161.30893 0.21758268 Force max component initial, final = 37.179575 0.018812527 Final line search alpha, max atom move = 1.0000000 0.018812527 Iterations, force evaluations = 179 351 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.3844 | 8.3844 | 8.3844 | 0.0 | 99.58 Neigh | 0.0042477 | 0.0042477 | 0.0042477 | 0.0 | 0.05 Comm | 0.015055 | 0.015055 | 0.015055 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01614 | | | 0.19 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3828.00 ave 3828 max 3828 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: 47536.0 ave 47536 max 47536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47536 Ave neighs/atom = 58.254902 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 179 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.544 | 4.544 | 4.544 Mbytes Step Temp E_pair E_mol TotEng Press Volume 179 0 -3444.6751 0 -3444.6751 47670.977 9260.9911 188 0 -3446.7955 0 -3446.7955 -561.80377 9403.0006 Loop time of 0.243859 on 1 procs for 9 steps with 816 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 = -3444.67514526609 -3446.79242629113 -3446.79549324247 Force two-norm initial, final = 480.56543 6.9178242 Force max component initial, final = 313.99328 6.0168677 Final line search alpha, max atom move = 8.9958166e-05 0.00054126638 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24173 | 0.24173 | 0.24173 | 0.0 | 99.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033873 | 0.00033873 | 0.00033873 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001792 | | | 0.73 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3845.00 ave 3845 max 3845 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: 47592.0 ave 47592 max 47592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47592 Ave neighs/atom = 58.323529 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.682 | 4.682 | 4.682 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3446.7955 0 -3446.7955 -561.80377 Loop time of 1.87e-06 on 1 procs for 0 steps with 816 atoms 107.0% 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 | | 1.87e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3823.00 ave 3823 max 3823 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: 46496.0 ave 46496 max 46496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46496 Ave neighs/atom = 56.980392 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.682 | 4.682 | 4.682 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 -3446.7955 -3446.7955 20.965125 88.42509 5.0721665 -561.80377 -561.80377 -238.21622 -1027.2395 -419.95556 2.3994301 1024.3705 Loop time of 1.767e-06 on 1 procs for 0 steps with 816 atoms 169.8% 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 | | 1.767e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3823.00 ave 3823 max 3823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23248.0 ave 23248 max 23248 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46496.0 ave 46496 max 46496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46496 Ave neighs/atom = 56.980392 Neighbor list builds = 0 Dangerous builds = 0 816 -3446.79549324247 eV 2.39943013105324 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08