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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -58.709431 0.0000000) to (11.984012 58.709431 8.8507797) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4472783 5.3372210 5.9005198 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.709431 0.0000000) to (11.984012 58.709431 8.8507797) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4472783 5.3372210 5.9005198 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.709431 0.0000000) to (11.984012 58.709431 8.8507797) create_atoms CPU = 0.001 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 37 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_353393547686_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3331.3405 0 -3331.3405 76321.451 101 0 -3725.4669 0 -3725.4669 5716.4191 Loop time of 5.58716 on 1 procs for 101 steps with 1056 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 = -3331.34049767462 -3725.46326124112 -3725.46685095346 Force two-norm initial, final = 533.18160 0.17841635 Force max component initial, final = 153.71955 0.037253503 Final line search alpha, max atom move = 1.0000000 0.037253503 Iterations, force evaluations = 101 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5598 | 5.5598 | 5.5598 | 0.0 | 99.51 Neigh | 0.0081458 | 0.0081458 | 0.0081458 | 0.0 | 0.15 Comm | 0.0092434 | 0.0092434 | 0.0092434 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009998 | | | 0.18 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4932.00 ave 4932 max 4932 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: 91064.0 ave 91064 max 91064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91064 Ave neighs/atom = 86.234848 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 101 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press Volume 101 0 -3725.4669 0 -3725.4669 5716.4191 12454.366 106 0 -3725.6188 0 -3725.6188 -211.44343 12506.295 Loop time of 0.211425 on 1 procs for 5 steps with 1056 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 = -3725.46685095347 -3725.61702553763 -3725.61881465974 Force two-norm initial, final = 83.788503 3.9470923 Force max component initial, final = 69.940574 3.7404870 Final line search alpha, max atom move = 0.00012194911 0.00045614906 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20952 | 0.20952 | 0.20952 | 0.0 | 99.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030343 | 0.00030343 | 0.00030343 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0016 | | | 0.76 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4835.00 ave 4835 max 4835 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: 91040.0 ave 91040 max 91040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91040 Ave neighs/atom = 86.212121 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.744 | 4.744 | 4.744 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3725.6188 0 -3725.6188 -211.44343 Loop time of 1.862e-06 on 1 procs for 0 steps with 1056 atoms 214.8% 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 | | 1.862e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4839.00 ave 4839 max 4839 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: 90952.0 ave 90952 max 90952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90952 Ave neighs/atom = 86.128788 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.744 | 4.744 | 4.744 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 -3725.6188 -3725.6188 11.972447 117.89709 8.8601822 -211.44343 -211.44343 -478.72986 2.3601789 -157.96062 2.2732833 441.15799 Loop time of 1.894e-06 on 1 procs for 0 steps with 1056 atoms 211.2% 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 | | 1.894e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4839.00 ave 4839 max 4839 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45476.0 ave 45476 max 45476 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90952.0 ave 90952 max 90952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90952 Ave neighs/atom = 86.128788 Neighbor list builds = 0 Dangerous builds = 0 1056 -3725.61881465974 eV 2.27328331552433 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06