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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -41.746968 0.0000000) to (25.562766 41.746968 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6477756 4.7436161 5.1383093 Created 531 atoms using lattice units in orthogonal box = (0.0000000 -41.746968 0.0000000) to (25.562766 41.746968 7.7074639) create_atoms CPU = 0.003 seconds 531 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6477756 4.7436161 5.1383093 Created 531 atoms using lattice units in orthogonal box = (0.0000000 -41.746968 0.0000000) to (25.562766 41.746968 7.7074639) create_atoms CPU = 0.002 seconds 531 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 1053 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.523 | 4.523 | 4.523 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7045.3521 0 -7045.3521 20923.818 57 0 -7130.1411 0 -7130.1411 4465.3338 Loop time of 5.84929 on 1 procs for 57 steps with 1053 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 = -7045.35213728647 -7130.1358589751 -7130.14108390712 Force two-norm initial, final = 54.342856 0.39763585 Force max component initial, final = 6.6260402 0.089167815 Final line search alpha, max atom move = 1.0000000 0.089167815 Iterations, force evaluations = 57 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.828 | 5.828 | 5.828 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0084363 | 0.0084363 | 0.0084363 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01286 | | | 0.22 Nlocal: 1053.00 ave 1053 max 1053 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3286.00 ave 3286 max 3286 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: 60458.0 ave 60458 max 60458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60458 Ave neighs/atom = 57.415005 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.524 | 4.524 | 4.524 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -7130.1411 0 -7130.1411 4465.3338 16450.317 58 0 -7130.1448 0 -7130.1448 5677.266 16442.786 Loop time of 0.167176 on 1 procs for 1 steps with 1053 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7130.14108390711 -7130.14108390711 -7130.14479180293 Force two-norm initial, final = 19.899953 6.0989005 Force max component initial, final = 19.162985 5.8520029 Final line search alpha, max atom move = 5.2183936e-05 0.00030538055 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16606 | 0.16606 | 0.16606 | 0.0 | 99.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021554 | 0.00021554 | 0.00021554 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008982 | | | 0.54 Nlocal: 1053.00 ave 1053 max 1053 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3302.00 ave 3302 max 3302 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: 60330.0 ave 60330 max 60330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60330 Ave neighs/atom = 57.293447 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.661 | 4.661 | 4.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7130.1448 0 -7130.1448 5677.266 Loop time of 6.685e-06 on 1 procs for 0 steps with 1053 atoms 179.5% 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 | | 6.685e-06 | | |100.00 Nlocal: 1053.00 ave 1053 max 1053 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3306.00 ave 3306 max 3306 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: 60330.0 ave 60330 max 60330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60330 Ave neighs/atom = 57.293447 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.661 | 4.661 | 4.661 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 -7130.1448 -7130.1448 25.553617 83.493937 7.7066936 5677.266 5677.266 -162.86563 16624.504 570.15912 2.051958 901.52193 Loop time of 6.986e-06 on 1 procs for 0 steps with 1053 atoms 300.6% 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 | | 6.986e-06 | | |100.00 Nlocal: 1053.00 ave 1053 max 1053 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3306.00 ave 3306 max 3306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30165.0 ave 30165 max 30165 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 60330.0 ave 60330 max 60330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60330 Ave neighs/atom = 57.293447 Neighbor list builds = 0 Dangerous builds = 0 1053 -7130.14479180293 eV 2.0519579834106 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06