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 = 4.0496966 4.0496966 4.0496966 Created orthogonal box = (0.0000000 -48.932670 0.0000000) to (59.930036 48.932670 9.9196902) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7467158 6.0327949 6.6131268 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -48.932670 0.0000000) to (59.930036 48.932670 9.9196902) create_atoms CPU = 0.007 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7467158 6.0327949 6.6131268 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -48.932670 0.0000000) to (59.930036 48.932670 9.9196902) create_atoms CPU = 0.006 seconds 1755 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 16 26 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 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 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_284963179498_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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.489 | 6.489 | 6.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11108.028 0 -11108.028 37838.379 78 0 -11782.572 0 -11782.572 4147.4931 Loop time of 5.40505 on 1 procs for 78 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 = -11108.0282712296 -11782.5606726663 -11782.5722817405 Force two-norm initial, final = 590.76084 0.27278646 Force max component initial, final = 140.79989 0.034794678 Final line search alpha, max atom move = 1.0000000 0.034794678 Iterations, force evaluations = 78 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0674 | 5.0674 | 5.0674 | 0.0 | 93.75 Neigh | 0.25781 | 0.25781 | 0.25781 | 0.0 | 4.77 Comm | 0.03204 | 0.03204 | 0.03204 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04777 | | | 0.88 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9534.00 ave 9534 max 9534 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: 439182.0 ave 439182 max 439182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 439182 Ave neighs/atom = 125.33733 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.491 | 6.491 | 6.491 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -11782.572 0 -11782.572 4147.4931 58179.711 87 0 -11783.649 0 -11783.649 12.014212 58494.972 Loop time of 0.42988 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 = -11782.5722817405 -11783.6395962407 -11783.6488209745 Force two-norm initial, final = 308.58749 1.1538562 Force max component initial, final = 284.21373 0.93569995 Final line search alpha, max atom move = 6.6676840e-05 6.2389515e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4158 | 0.4158 | 0.4158 | 0.0 | 96.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023922 | 0.0023922 | 0.0023922 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01168 | | | 2.72 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9534.00 ave 9534 max 9534 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: 439816.0 ave 439816 max 439816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 439816 Ave neighs/atom = 125.51826 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.629 | 6.629 | 6.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11783.649 0 -11783.649 12.014212 Loop time of 6.766e-06 on 1 procs for 0 steps with 3504 atoms 192.1% 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 | | 6.766e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9494.00 ave 9494 max 9494 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: 434958.0 ave 434958 max 434958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434958 Ave neighs/atom = 124.13185 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.629 | 6.629 | 6.629 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 -11783.649 -11783.649 59.852902 98.728463 9.8989914 12.014212 12.014212 -1.2266496 11.693955 25.575331 2.5846205 2082.0253 Loop time of 6.976e-06 on 1 procs for 0 steps with 3504 atoms 272.4% 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 | | 6.976e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9494.00 ave 9494 max 9494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 217479.0 ave 217479 max 217479 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 434958.0 ave 434958 max 434958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434958 Ave neighs/atom = 124.13185 Neighbor list builds = 0 Dangerous builds = 0 3504 -11783.6488209745 eV 2.58462052144181 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06