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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -41.247506 0.0000000) to (35.721388 41.247506 7.0055406) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4115313 6.3457702 7.0055406 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -41.247506 0.0000000) to (35.721388 41.247506 7.0055406) create_atoms CPU = 0.002 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4115313 6.3457702 7.0055406 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.247506 0.0000000) to (35.721388 41.247506 7.0055406) create_atoms CPU = 0.001 seconds 629 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1250 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_618133763375_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.587 | 4.587 | 4.587 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3878.3777 0 -3878.3777 37539.25 100 0 -4179.7577 0 -4179.7577 7008.6839 Loop time of 8.15006 on 1 procs for 100 steps with 1250 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 = -3878.37774752239 -4179.75383333421 -4179.75768729168 Force two-norm initial, final = 338.60248 0.15613073 Force max component initial, final = 98.481891 0.037749576 Final line search alpha, max atom move = 1.0000000 0.037749576 Iterations, force evaluations = 100 177 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.0889 | 8.0889 | 8.0889 | 0.0 | 99.25 Neigh | 0.037742 | 0.037742 | 0.037742 | 0.0 | 0.46 Comm | 0.0096023 | 0.0096023 | 0.0096023 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01386 | | | 0.17 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4096.00 ave 4096 max 4096 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: 96856.0 ave 96856 max 96856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96856 Ave neighs/atom = 77.484800 Neighbor list builds = 5 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -4179.7577 0 -4179.7577 7008.6839 20644.182 111 0 -4180.4986 0 -4180.4986 20.998525 20824.82 Loop time of 0.593882 on 1 procs for 11 steps with 1250 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 = -4179.75768729171 -4180.49699560379 -4180.49855748847 Force two-norm initial, final = 173.91685 0.64102911 Force max component initial, final = 151.50652 0.38030924 Final line search alpha, max atom move = 0.00025518737 9.7050117e-05 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59004 | 0.59004 | 0.59004 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048957 | 0.00048957 | 0.00048957 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003349 | | | 0.56 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4092.00 ave 4092 max 4092 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: 96886.0 ave 96886 max 96886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96886 Ave neighs/atom = 77.508800 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.724 | 4.724 | 4.724 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4180.4986 0 -4180.4986 20.998525 Loop time of 1.686e-06 on 1 procs for 0 steps with 1250 atoms 177.9% 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 | | 1.686e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4094.00 ave 4094 max 4094 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: 96746.0 ave 96746 max 96746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96746 Ave neighs/atom = 77.396800 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.724 | 4.724 | 4.724 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 -4180.4986 -4180.4986 35.72326 83.362232 6.9929565 20.998525 20.998525 14.07617 19.712525 29.20688 2.5098402 1046.4926 Loop time of 1.624e-06 on 1 procs for 0 steps with 1250 atoms 184.7% 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 | | 1.624e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4094.00 ave 4094 max 4094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48373.0 ave 48373 max 48373 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 96746.0 ave 96746 max 96746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96746 Ave neighs/atom = 77.396800 Neighbor list builds = 0 Dangerous builds = 0 1250 -4180.49855748847 eV 2.50984019132917 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09