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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -62.328863 0.0000000) to (31.162608 62.328863 3.6473074) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6957355 4.6957355 3.6473074 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -62.328863 0.0000000) to (31.162608 62.328863 3.6473074) create_atoms CPU = 0.002 seconds 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6957355 4.6957355 3.6473074 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -62.328863 0.0000000) to (31.162608 62.328863 3.6473074) create_atoms CPU = 0.002 seconds 586 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 12 atoms, new total = 1160 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_608695023236_000#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.376 | 5.376 | 5.376 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4775.2395 0 -4775.2395 380.29237 44 0 -4795.8556 0 -4795.8556 -5281.4703 Loop time of 13.0506 on 1 procs for 44 steps with 1160 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 = -4775.23952786774 -4795.85270963562 -4795.85563893528 Force two-norm initial, final = 33.287201 0.21173488 Force max component initial, final = 8.6870202 0.044628015 Final line search alpha, max atom move = 1.0000000 0.044628015 Iterations, force evaluations = 44 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.03 | 13.03 | 13.03 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0091582 | 0.0091582 | 0.0091582 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01114 | | | 0.09 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4772.00 ave 4772 max 4772 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: 62128.0 ave 62128 max 62128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62128 Ave neighs/atom = 53.558621 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.376 | 5.376 | 5.376 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -4795.8556 0 -4795.8556 -5281.4703 14168.549 47 0 -4795.9095 0 -4795.9095 -1584.4558 14135.936 Loop time of 0.933924 on 1 procs for 3 steps with 1160 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 = -4795.85563893529 -4795.90633812581 -4795.90948817327 Force two-norm initial, final = 55.140737 0.23103599 Force max component initial, final = 47.115038 0.053788519 Final line search alpha, max atom move = 0.00016013330 8.6133331e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.93093 | 0.93093 | 0.93093 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063849 | 0.00063849 | 0.00063849 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002357 | | | 0.25 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4762.00 ave 4762 max 4762 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: 62172.0 ave 62172 max 62172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62172 Ave neighs/atom = 53.596552 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.514 | 5.514 | 5.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4795.9095 0 -4795.9095 -1584.4558 Loop time of 6.194e-06 on 1 procs for 0 steps with 1160 atoms 177.6% 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 | | 6.194e-06 | | |100.00 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4768.00 ave 4768 max 4768 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: 62172.0 ave 62172 max 62172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62172 Ave neighs/atom = 53.596552 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.514 | 5.514 | 5.514 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 -4795.9095 -4795.9095 31.092627 124.65773 3.6471023 -1584.4558 -1584.4558 0.0492746 -4752.8854 -0.53143303 2.309615 192.29016 Loop time of 6.976e-06 on 1 procs for 0 steps with 1160 atoms 258.0% 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 | | 6.976e-06 | | |100.00 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4768.00 ave 4768 max 4768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31086.0 ave 31086 max 31086 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62172.0 ave 62172 max 62172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62172 Ave neighs/atom = 53.596552 Neighbor list builds = 0 Dangerous builds = 0 1160 -4795.90948817327 eV 2.30961502182394 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15