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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -50.029567 0.0000000) to (16.676522 50.029567 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9048595 4.9048595 4.0446508 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -50.029567 0.0000000) to (16.676522 50.029567 4.0446508) create_atoms CPU = 0.002 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9048595 4.9048595 4.0446508 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -50.029567 0.0000000) to (16.676522 50.029567 4.0446508) create_atoms CPU = 0.001 seconds 206 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 31 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_616482358807_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1161.2827 0 -1161.2827 53448.5 65 0 -1365.8706 0 -1365.8706 4502.9785 Loop time of 3.97884 on 1 procs for 65 steps with 408 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 = -1161.28272039854 -1365.86977721698 -1365.87059068103 Force two-norm initial, final = 339.74179 0.065543354 Force max component initial, final = 118.30929 0.0070212623 Final line search alpha, max atom move = 1.0000000 0.0070212623 Iterations, force evaluations = 65 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9526 | 3.9526 | 3.9526 | 0.0 | 99.34 Neigh | 0.009163 | 0.009163 | 0.009163 | 0.0 | 0.23 Comm | 0.0087266 | 0.0087266 | 0.0087266 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008401 | | | 0.21 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2856.00 ave 2856 max 2856 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: 31284.0 ave 31284 max 31284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31284 Ave neighs/atom = 76.676471 Neighbor list builds = 2 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.448 | 4.448 | 4.448 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -1365.8706 0 -1365.8706 4502.9785 6749.0595 76 0 -1366.0383 0 -1366.0383 -45.371916 6787.3474 Loop time of 0.45578 on 1 procs for 11 steps with 408 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 = -1365.87059068103 -1366.0382462364 -1366.03827875818 Force two-norm initial, final = 40.054280 0.41222697 Force max component initial, final = 37.519836 0.29193388 Final line search alpha, max atom move = 0.0054009720 0.0015767267 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44685 | 0.44685 | 0.44685 | 0.0 | 98.04 Neigh | 0.0045382 | 0.0045382 | 0.0045382 | 0.0 | 1.00 Comm | 0.0010574 | 0.0010574 | 0.0010574 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003331 | | | 0.73 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2824.00 ave 2824 max 2824 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: 31232.0 ave 31232 max 31232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31232 Ave neighs/atom = 76.549020 Neighbor list builds = 1 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1366.0383 0 -1366.0383 -45.371916 Loop time of 3.8339e-05 on 1 procs for 0 steps with 408 atoms 31.3% 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 | | 3.834e-05 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2824.00 ave 2824 max 2824 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: 31240.0 ave 31240 max 31240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31240 Ave neighs/atom = 76.568627 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.586 | 4.586 | 4.586 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 -1366.0383 -1366.0383 16.657153 101.07389 4.0314411 -45.371916 -45.371916 -40.046017 -69.610864 -26.458866 2.6307638 236.93064 Loop time of 6.475e-06 on 1 procs for 0 steps with 408 atoms 262.5% 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 | | 6.475e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2824.00 ave 2824 max 2824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15620.0 ave 15620 max 15620 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31240.0 ave 31240 max 31240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31240 Ave neighs/atom = 76.568627 Neighbor list builds = 0 Dangerous builds = 0 408 -1366.03827875818 eV 2.63076382141885 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04