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 = 3.6149590 3.6149590 3.6149590 Created orthogonal box = (0.0000000 -42.157305 0.0000000) to (14.904858 42.157305 5.1123241) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1372944 6.1996036 5.1123241 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.157305 0.0000000) to (14.904858 42.157305 5.1123241) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1372944 6.1996036 5.1123241 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.157305 0.0000000) to (14.904858 42.157305 5.1123241) create_atoms CPU = 0.001 seconds 274 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 4 22 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 7.715752124786377 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_127245782811_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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 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) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1857.4911 0 -1857.4911 32182.479 67 0 -1920.3563 0 -1920.3563 12653.224 Loop time of 0.7242 on 1 procs for 67 steps with 544 atoms 94.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1857.49106443197 -1920.35445941546 -1920.3563206882 Force two-norm initial, final = 133.55736 0.13684522 Force max component initial, final = 41.575452 0.022950475 Final line search alpha, max atom move = 1.0000000 0.022950475 Iterations, force evaluations = 67 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71294 | 0.71294 | 0.71294 | 0.0 | 98.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0064053 | 0.0064053 | 0.0064053 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004854 | | | 0.67 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4672.00 ave 4672 max 4672 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: 95004.0 ave 95004 max 95004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95004 Ave neighs/atom = 174.63971 Neighbor list builds = 0 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -1920.3563 0 -1920.3563 12653.224 6424.6437 73 0 -1920.6057 0 -1920.6057 22.285669 6483.3876 Loop time of 0.0378674 on 1 procs for 6 steps with 544 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 = -1920.3563206882 -1920.60559896186 -1920.60568709911 Force two-norm initial, final = 89.054354 0.40611915 Force max component initial, final = 60.409175 0.31666866 Final line search alpha, max atom move = 0.00098247758 0.00031111985 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.036212 | 0.036212 | 0.036212 | 0.0 | 95.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033008 | 0.00033008 | 0.00033008 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001325 | | | 3.50 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4672.00 ave 4672 max 4672 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: 92492.0 ave 92492 max 92492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92492 Ave neighs/atom = 170.02206 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 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) = 4.666 | 4.666 | 4.666 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1920.6057 0 -1920.6057 22.285669 Loop time of 2.444e-06 on 1 procs for 0 steps with 544 atoms 122.7% 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 | | 2.444e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4656.00 ave 4656 max 4656 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: 91608.0 ave 91608 max 91608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91608 Ave neighs/atom = 168.39706 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 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) = 4.666 | 4.666 | 4.666 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 -1920.6057 -1920.6057 14.978252 84.596491 5.1166828 22.285669 22.285669 24.546404 78.516869 -36.206266 2.4201932 368.5814 Loop time of 2.35e-06 on 1 procs for 0 steps with 544 atoms 212.8% 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 | | 2.35e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4656.00 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45804.0 ave 45804 max 45804 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91608.0 ave 91608 max 91608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91608 Ave neighs/atom = 168.39706 Neighbor list builds = 0 Dangerous builds = 0 544 -1920.60568709911 eV 2.4201932417163 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01