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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -28.603420 0.0000000) to (2.8603420 28.603420 2.8603420) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 2.8603420 2.8603420 2.8603420 Created 20 atoms using lattice units in orthogonal box = (0.0000000 -28.603420 0.0000000) to (2.8603420 28.603420 2.8603420) create_atoms CPU = 0.001 seconds 20 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 2.8603420 2.8603420 2.8603420 Created 21 atoms using lattice units in orthogonal box = (0.0000000 -28.603420 0.0000000) to (2.8603420 28.603420 2.8603420) create_atoms CPU = 0.000 seconds 21 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 1 15 1 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 41 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 1 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.394 | 4.394 | 4.394 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 38.501007 0 38.501007 1126720.3 52 0 -175.09846 0 -175.09846 65728.063 Loop time of 0.0957951 on 1 procs for 52 steps with 41 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 = 38.5010072654382 -175.098307173863 -175.098456539632 Force two-norm initial, final = 1966.4399 0.053370977 Force max component initial, final = 1390.4418 0.015847183 Final line search alpha, max atom move = 1.0000000 0.015847183 Iterations, force evaluations = 52 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.089801 | 0.089801 | 0.089801 | 0.0 | 93.74 Neigh | 0.0010381 | 0.0010381 | 0.0010381 | 0.0 | 1.08 Comm | 0.0037798 | 0.0037798 | 0.0037798 | 0.0 | 3.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001176 | | | 1.23 Nlocal: 41.0000 ave 41 max 41 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2169.00 ave 2169 max 2169 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: 6988.00 ave 6988 max 6988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6988 Ave neighs/atom = 170.43902 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 1 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.394 | 4.394 | 4.394 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -175.09846 0 -175.09846 65728.063 468.04098 410 0 -179.71805 0 -179.71805 -912.83679 471.37845 Loop time of 0.552428 on 1 procs for 358 steps with 41 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 = -175.098456539632 -179.717919548995 -179.718051446407 Force two-norm initial, final = 33.432267 0.58246349 Force max component initial, final = 21.461145 0.50875573 Final line search alpha, max atom move = 0.0033361435 0.0016972821 Iterations, force evaluations = 358 405 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4744 | 0.4744 | 0.4744 | 0.0 | 85.88 Neigh | 0.0084822 | 0.0084822 | 0.0084822 | 0.0 | 1.54 Comm | 0.019117 | 0.019117 | 0.019117 | 0.0 | 3.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05043 | | | 9.13 Nlocal: 41.0000 ave 41 max 41 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2117.00 ave 2117 max 2117 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: 7102.00 ave 7102 max 7102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7102 Ave neighs/atom = 173.21951 Neighbor list builds = 8 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 1 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -179.71805 0 -179.71805 -912.83679 Loop time of 6.104e-06 on 1 procs for 0 steps with 41 atoms 196.6% 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 | | 6.104e-06 | | |100.00 Nlocal: 41.0000 ave 41 max 41 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2117.00 ave 2117 max 2117 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: 6930.00 ave 6930 max 6930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6930 Ave neighs/atom = 169.02439 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 1 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.542 | 4.542 | 4.542 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 -179.71805 -179.71805 3.7016855 51.165127 2.4888352 -912.83679 -912.83679 -512.67285 -721.213 -1504.6245 2.3744887 20.91231 Loop time of 6.785e-06 on 1 procs for 0 steps with 41 atoms 206.3% 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 | | 6.785e-06 | | |100.00 Nlocal: 41.0000 ave 41 max 41 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2117.00 ave 2117 max 2117 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3465.00 ave 3465 max 3465 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6930.00 ave 6930 max 6930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6930 Ave neighs/atom = 169.02439 Neighbor list builds = 0 Dangerous builds = 0 41 -179.718051446407 eV 2.37448872469882 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01