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 = 3.6149251 3.6149251 3.6149251 Created orthogonal box = (0.0000000 -43.679306 0.0000000) to (53.496006 43.679306 8.8547219) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1297540 5.3851199 5.9031479 Created 1752 atoms using lattice units in orthogonal box = (0.0000000 -43.679306 0.0000000) to (53.496006 43.679306 8.8547219) create_atoms CPU = 0.007 seconds 1752 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1297540 5.3851199 5.9031479 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -43.679306 0.0000000) to (53.496006 43.679306 8.8547219) create_atoms CPU = 0.006 seconds 1758 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 = 15 23 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 3492 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 = 15 23 3 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) = 6.958 | 6.958 | 6.958 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10598.844 0 -10598.844 118116.67 64 0 -12323.562 0 -12323.562 44.819657 Loop time of 5.768 on 1 procs for 64 steps with 3492 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 = -10598.8439047114 -12323.5511486099 -12323.5620547645 Force two-norm initial, final = 2432.7102 0.31481581 Force max component initial, final = 350.67591 0.022872027 Final line search alpha, max atom move = 1.0000000 0.022872027 Iterations, force evaluations = 64 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6213 | 5.6213 | 5.6213 | 0.0 | 97.46 Neigh | 0.077056 | 0.077056 | 0.077056 | 0.0 | 1.34 Comm | 0.029692 | 0.029692 | 0.029692 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03996 | | | 0.69 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10558.0 ave 10558 max 10558 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: 499980.0 ave 499980 max 499980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 499980 Ave neighs/atom = 143.17869 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 15 23 3 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.961 | 6.961 | 6.961 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -12323.562 0 -12323.562 44.819657 41381.098 65 0 -12323.572 0 -12323.572 -103.92087 41385.445 Loop time of 0.143699 on 1 procs for 1 steps with 3492 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12323.5620547645 -12323.5620547645 -12323.5720070633 Force two-norm initial, final = 25.627484 4.6794415 Force max component initial, final = 21.655166 3.0212832 Final line search alpha, max atom move = 4.6178358e-05 0.00013951790 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14046 | 0.14046 | 0.14046 | 0.0 | 97.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068511 | 0.00068511 | 0.00068511 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00255 | | | 1.77 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10933.0 ave 10933 max 10933 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: 498480.0 ave 498480 max 498480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498480 Ave neighs/atom = 142.74914 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 = 15 23 3 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) = 7.099 | 7.099 | 7.099 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12323.572 0 -12323.572 -103.92087 Loop time of 6.595e-06 on 1 procs for 0 steps with 3492 atoms 182.0% 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 | | 6.595e-06 | | |100.00 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10948.0 ave 10948 max 10948 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: 498456.0 ave 498456 max 498456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498456 Ave neighs/atom = 142.74227 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 = 15 23 3 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) = 7.099 | 7.099 | 7.099 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 -12323.572 -12323.572 53.475822 87.343396 8.8605378 -103.92087 -103.92087 -116.92039 -100.26119 -94.581036 2.371949 1430.9063 Loop time of 7.006e-06 on 1 procs for 0 steps with 3492 atoms 285.5% 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 | | 7.006e-06 | | |100.00 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10948.0 ave 10948 max 10948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 249228.0 ave 249228 max 249228 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 498456.0 ave 498456 max 498456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498456 Ave neighs/atom = 142.74227 Neighbor list builds = 0 Dangerous builds = 0 3492 -12323.5894670633 eV 2.37194904093371 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07