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 = 3.5200010 3.5200010 3.5200010 Created orthogonal box = (0.0000000 -62.175614 0.0000000) to (35.897108 62.175614 6.0968206) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5226319 5.5798628 6.0968206 Created 1248 atoms using lattice units in orthogonal box = (0.0000000 -62.175614 0.0000000) to (35.897108 62.175614 6.0968206) create_atoms CPU = 0.008 seconds 1248 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5226319 5.5798628 6.0968206 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -62.175614 0.0000000) to (35.897108 62.175614 6.0968206) create_atoms CPU = 0.008 seconds 1252 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2492 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_469343973171_005#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.521 | 6.521 | 6.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10752.049 0 -10752.049 43111.678 77 0 -11055.23 0 -11055.23 6900.2938 Loop time of 7.15677 on 1 procs for 77 steps with 2492 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 = -10752.0488260711 -11055.2192245333 -11055.2295141408 Force two-norm initial, final = 345.36913 0.43518705 Force max component initial, final = 61.514165 0.057587383 Final line search alpha, max atom move = 1.0000000 0.057587383 Iterations, force evaluations = 77 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9022 | 6.9022 | 6.9022 | 0.0 | 96.44 Neigh | 0.17559 | 0.17559 | 0.17559 | 0.0 | 2.45 Comm | 0.040966 | 0.040966 | 0.040966 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03802 | | | 0.53 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10748.0 ave 10748 max 10748 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: 434800.0 ave 434800 max 434800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434800 Ave neighs/atom = 174.47833 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.521 | 6.521 | 6.521 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -11055.23 0 -11055.23 6900.2938 27215.289 82 0 -11055.685 0 -11055.685 -41.407844 27319.741 Loop time of 0.330449 on 1 procs for 5 steps with 2492 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 = -11055.2295141408 -11055.6849045923 -11055.6853143336 Force two-norm initial, final = 243.93931 1.3698847 Force max component initial, final = 220.65828 0.86706391 Final line search alpha, max atom move = 0.00025514198 0.00022122440 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32235 | 0.32235 | 0.32235 | 0.0 | 97.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017452 | 0.0017452 | 0.0017452 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006356 | | | 1.92 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10751.0 ave 10751 max 10751 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: 434656.0 ave 434656 max 434656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434656 Ave neighs/atom = 174.42055 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.659 | 6.659 | 6.659 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11055.685 0 -11055.685 -41.407844 Loop time of 6.405e-06 on 1 procs for 0 steps with 2492 atoms 171.7% 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 | | 6.405e-06 | | |100.00 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10745.0 ave 10745 max 10745 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: 434448.0 ave 434448 max 434448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434448 Ave neighs/atom = 174.33708 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.659 | 6.659 | 6.659 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 -11055.685 -11055.685 35.914853 124.85512 6.0925083 -41.407844 -41.407844 -50.874427 -26.580138 -46.768968 2.2701469 1030.789 Loop time of 6.906e-06 on 1 procs for 0 steps with 2492 atoms 318.6% 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 | | 6.906e-06 | | |100.00 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10745.0 ave 10745 max 10745 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 217224.0 ave 217224 max 217224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 434448.0 ave 434448 max 434448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434448 Ave neighs/atom = 174.33708 Neighbor list builds = 0 Dangerous builds = 0 2492 -10964.8463906853 eV 2.27014688867303 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08