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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -45.593806 0.0000000) to (22.795123 45.593806 3.5600001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0038075 5.0038075 3.5600001 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -45.593806 0.0000000) to (22.795123 45.593806 3.5600001) create_atoms CPU = 0.001 seconds 329 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0038075 5.0038075 3.5600001 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -45.593806 0.0000000) to (22.795123 45.593806 3.5600001) create_atoms CPU = 0.000 seconds 329 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 = 6 24 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 10 atoms, new total = 648 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 = 6 24 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) = 4.940 | 4.940 | 4.940 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2803.2762 0 -2803.2762 -2669.5857 84 0 -2842.4779 0 -2842.4779 -4934.2459 Loop time of 0.960137 on 1 procs for 84 steps with 648 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 = -2803.27618767359 -2842.47531148533 -2842.47787644104 Force two-norm initial, final = 34.191810 0.26349293 Force max component initial, final = 7.2080672 0.086080110 Final line search alpha, max atom move = 1.0000000 0.086080110 Iterations, force evaluations = 84 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94003 | 0.94003 | 0.94003 | 0.0 | 97.91 Neigh | 0.0064806 | 0.0064806 | 0.0064806 | 0.0 | 0.67 Comm | 0.0080313 | 0.0080313 | 0.0080313 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005594 | | | 0.58 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6341.00 ave 6341 max 6341 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: 113186.0 ave 113186 max 113186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113186 Ave neighs/atom = 174.66975 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 = 6 24 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 : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.940 | 4.940 | 4.940 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -2842.4779 0 -2842.4779 -4934.2459 7399.9332 93 0 -2842.7069 0 -2842.7069 -396.41365 7387.5212 Loop time of 0.0681671 on 1 procs for 9 steps with 648 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 = -2842.47787644105 -2842.70508304851 -2842.70691627585 Force two-norm initial, final = 42.879895 0.59867612 Force max component initial, final = 41.508791 0.18099761 Final line search alpha, max atom move = 0.00034518927 6.2478433e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.065591 | 0.065591 | 0.065591 | 0.0 | 96.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050787 | 0.00050787 | 0.00050787 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002069 | | | 3.03 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6348.00 ave 6348 max 6348 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: 113140.0 ave 113140 max 113140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113140 Ave neighs/atom = 174.59877 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 = 6 24 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) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2842.7069 0 -2842.7069 -396.41365 Loop time of 1.791e-06 on 1 procs for 0 steps with 648 atoms 167.5% 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 | | 1.791e-06 | | |100.00 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6348.00 ave 6348 max 6348 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: 113072.0 ave 113072 max 113072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113072 Ave neighs/atom = 174.49383 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 = 6 24 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) = 5.078 | 5.078 | 5.078 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 -2842.7069 -2842.7069 22.949093 91.187612 3.5301843 -396.41365 -396.41365 -39.51919 -1129.942 -19.779735 2.3112239 160.14407 Loop time of 1.555e-06 on 1 procs for 0 steps with 648 atoms 192.9% 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 | | 1.555e-06 | | |100.00 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6348.00 ave 6348 max 6348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56536.0 ave 56536 max 56536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113072.0 ave 113072 max 113072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113072 Ave neighs/atom = 174.49383 Neighbor list builds = 0 Dangerous builds = 0 648 -2842.70691627585 eV 2.3112238668321 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01