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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -58.563650 0.0000000) to (20.705377 58.563650 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6469210 6.2112962 5.0973115 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.563650 0.0000000) to (20.705377 58.563650 5.0973115) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6469210 6.2112962 5.0973115 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.563650 0.0000000) to (20.705377 58.563650 5.0973115) create_atoms CPU = 0.002 seconds 530 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 ghost atom cutoff = 6 binsize = 3, bins = 7 40 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1058 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.621 | 4.621 | 4.621 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4209.5647 0 -4209.5647 82784.199 474 0 -4512.1298 0 -4512.1298 -7880.36 Loop time of 32.4443 on 1 procs for 474 steps with 1058 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 = -4209.56469318919 -4512.12558743614 -4512.12984964055 Force two-norm initial, final = 866.27022 0.18842658 Force max component initial, final = 298.67255 0.035700538 Final line search alpha, max atom move = 1.0000000 0.035700538 Iterations, force evaluations = 474 854 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 32.247 | 32.247 | 32.247 | 0.0 | 99.39 Neigh | 0.10982 | 0.10982 | 0.10982 | 0.0 | 0.34 Comm | 0.045907 | 0.045907 | 0.045907 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04169 | | | 0.13 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5068.00 ave 5068 max 5068 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: 68548.0 ave 68548 max 68548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68548 Ave neighs/atom = 64.790170 Neighbor list builds = 19 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 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 474 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.622 | 4.622 | 4.622 Mbytes Step Temp E_pair E_mol TotEng Press Volume 474 0 -4512.1298 0 -4512.1298 -7880.36 12361.821 506 0 -4523.0689 0 -4523.0689 -7.6193756 12289.648 Loop time of 1.20182 on 1 procs for 32 steps with 1058 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 = -4512.12984964055 -4523.06882503449 -4523.06892775758 Force two-norm initial, final = 590.63817 1.3016735 Force max component initial, final = 535.00233 0.73445170 Final line search alpha, max atom move = 0.0021430530 0.0015739689 Iterations, force evaluations = 32 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1874 | 1.1874 | 1.1874 | 0.0 | 98.80 Neigh | 0.0053717 | 0.0053717 | 0.0053717 | 0.0 | 0.45 Comm | 0.0015537 | 0.0015537 | 0.0015537 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007467 | | | 0.62 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5133.00 ave 5133 max 5133 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: 68476.0 ave 68476 max 68476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68476 Ave neighs/atom = 64.722117 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 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.761 | 4.761 | 4.761 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4523.0689 0 -4523.0689 -7.6193756 Loop time of 1.691e-06 on 1 procs for 0 steps with 1058 atoms 118.3% 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 | | 1.691e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5138.00 ave 5138 max 5138 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: 68460.0 ave 68460 max 68460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68460 Ave neighs/atom = 64.706994 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 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.761 | 4.761 | 4.761 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 -4523.0689 -4523.0689 20.943033 118.78839 4.9399879 -7.6193756 -7.6193756 91.4369 -97.10688 -17.188147 2.3653777 2560.6055 Loop time of 1.682e-06 on 1 procs for 0 steps with 1058 atoms 178.4% 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 | | 1.682e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5138.00 ave 5138 max 5138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34230.0 ave 34230 max 34230 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68460.0 ave 68460 max 68460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68460 Ave neighs/atom = 64.706994 Neighbor list builds = 0 Dangerous builds = 0 1058 -4523.06892775758 eV 2.36537769732967 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:33