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 -47.232299 0.0000000) to (28.921578 47.232299 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2584687 5.3669021 5.8134559 Created 1071 atoms using lattice units in orthogonal box = (0.0000000 -47.232299 0.0000000) to (28.921578 47.232299 8.7201838) create_atoms CPU = 0.002 seconds 1071 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2584687 5.3669021 5.8134559 Created 1071 atoms using lattice units in orthogonal box = (0.0000000 -47.232299 0.0000000) to (28.921578 47.232299 8.7201838) create_atoms CPU = 0.001 seconds 1071 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 = 8 25 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 78 atoms, new total = 2064 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_803527979660_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 = 8 25 3 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) = 6.010 | 6.010 | 6.010 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8973.0562 0 -8973.0562 -16400.496 85 0 -9065.1257 0 -9065.1257 -27763.912 Loop time of 2.64781 on 1 procs for 85 steps with 2064 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 = -8973.05616209718 -9065.11694702072 -9065.12573806555 Force two-norm initial, final = 10.766775 0.35427251 Force max component initial, final = 1.2027937 0.066377171 Final line search alpha, max atom move = 1.0000000 0.066377171 Iterations, force evaluations = 85 159 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6045 | 2.6045 | 2.6045 | 0.0 | 98.36 Neigh | 0.020327 | 0.020327 | 0.020327 | 0.0 | 0.77 Comm | 0.010208 | 0.010208 | 0.010208 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0128 | | | 0.48 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8143.00 ave 8143 max 8143 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: 357770.0 ave 357770 max 357770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 357770 Ave neighs/atom = 173.33818 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 = 8 25 3 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 : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.011 | 6.011 | 6.011 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -9065.1257 0 -9065.1257 -27763.912 23824.111 97 0 -9069.2402 0 -9069.2402 469.6391 23480.269 Loop time of 0.249063 on 1 procs for 12 steps with 2064 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 = -9065.12573806561 -9069.23964171963 -9069.24024226171 Force two-norm initial, final = 695.84023 0.61445677 Force max component initial, final = 577.13975 0.14865566 Final line search alpha, max atom move = 0.00010268625 1.5264893e-05 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.243 | 0.243 | 0.243 | 0.0 | 97.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090152 | 0.00090152 | 0.00090152 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005165 | | | 2.07 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8191.00 ave 8191 max 8191 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: 360754.0 ave 360754 max 360754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 360754 Ave neighs/atom = 174.78391 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 = 8 25 3 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) = 6.149 | 6.149 | 6.149 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9069.2402 0 -9069.2402 469.6391 Loop time of 1.611e-06 on 1 procs for 0 steps with 2064 atoms 124.1% 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 | | 1.611e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8260.00 ave 8260 max 8260 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: 361164.0 ave 361164 max 361164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361164 Ave neighs/atom = 174.98256 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 = 8 25 3 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) = 6.149 | 6.149 | 6.149 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 -9069.2402 -9069.2402 28.613432 94.464597 8.6868844 469.6391 469.6391 -5.8431746 1424.8653 -10.104787 2.3945797 594.30395 Loop time of 2.594e-06 on 1 procs for 0 steps with 2064 atoms 192.8% 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 | | 2.594e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8260.00 ave 8260 max 8260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 180582.0 ave 180582 max 180582 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 361164.0 ave 361164 max 361164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361164 Ave neighs/atom = 174.98256 Neighbor list builds = 0 Dangerous builds = 0 2064 -9069.24024226171 eV 2.39457965689402 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03