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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -43.620617 0.0000000) to (21.808876 43.620617 2.8636458) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7601511 3.7601511 2.8636458 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -43.620617 0.0000000) to (21.808876 43.620617 2.8636458) create_atoms CPU = 0.002 seconds 234 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7601511 3.7601511 2.8636458 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -43.620617 0.0000000) to (21.808876 43.620617 2.8636458) create_atoms CPU = 0.001 seconds 234 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 7 28 1 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 460 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1955.1282 0 -1955.1282 1932.6801 15 0 -1963.9487 0 -1963.9487 -6857.1423 Loop time of 2.6612 on 1 procs for 15 steps with 460 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 = -1955.12822112657 -1963.9468122843 -1963.94866054896 Force two-norm initial, final = 21.878529 0.12611361 Force max component initial, final = 7.3989305 0.029746040 Final line search alpha, max atom move = 1.0000000 0.029746040 Iterations, force evaluations = 15 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6563 | 2.6563 | 2.6563 | 0.0 | 99.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026933 | 0.0026933 | 0.0026933 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002242 | | | 0.08 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4147.00 ave 4147 max 4147 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: 40252.0 ave 40252 max 40252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40252 Ave neighs/atom = 87.504348 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -1963.9487 0 -1963.9487 -6857.1423 5448.4678 21 0 -1964.0508 0 -1964.0508 1826.4212 5420.5773 Loop time of 1.0192 on 1 procs for 6 steps with 460 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 = -1963.94866054895 -1964.05044063852 -1964.05084746809 Force two-norm initial, final = 47.098442 0.15722342 Force max component initial, final = 40.288926 0.027920776 Final line search alpha, max atom move = 0.00029290511 8.1781379e-06 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0151 | 1.0151 | 1.0151 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089891 | 0.00089891 | 0.00089891 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003247 | | | 0.32 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4131.00 ave 4131 max 4131 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: 43604.0 ave 43604 max 43604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43604 Ave neighs/atom = 94.791304 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.611 | 4.611 | 4.611 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1964.0508 0 -1964.0508 1826.4212 Loop time of 7.598e-06 on 1 procs for 0 steps with 460 atoms 157.9% 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 | | 7.598e-06 | | |100.00 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4131.00 ave 4131 max 4131 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: 46496.0 ave 46496 max 46496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46496 Ave neighs/atom = 101.07826 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.611 | 4.611 | 4.611 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 -1964.0508 -1964.0508 21.8046 87.241233 2.8495456 1826.4212 1826.4212 -2.5197614 5480.9376 0.84556877 2.2872732 246.39692 Loop time of 9.753e-06 on 1 procs for 0 steps with 460 atoms 205.1% 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 | | 9.753e-06 | | |100.00 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4131.00 ave 4131 max 4131 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23248.0 ave 23248 max 23248 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46496.0 ave 46496 max 46496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46496 Ave neighs/atom = 101.07826 Neighbor list builds = 0 Dangerous builds = 0 460 -1964.05084746809 eV 2.28727321868407 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04