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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -50.582273 0.0000000) to (29.203689 50.582273 4.9600000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4928752 4.5394348 4.9600000 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -50.582273 0.0000000) to (29.203689 50.582273 4.9600000) create_atoms CPU = 0.005 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4928752 4.5394348 4.9600000 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -50.582273 0.0000000) to (29.203689 50.582273 4.9600000) create_atoms CPU = 0.004 seconds 627 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 = 10 34 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 1 atoms, new total = 1248 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_179158257180_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 = 10 34 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) = 4.647 | 4.647 | 4.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4915.8523 0 -4915.8523 64832.111 65 0 -5333.8457 0 -5333.8457 5424.2197 Loop time of 9.22683 on 1 procs for 65 steps with 1248 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 = -4915.85234416771 -5333.8411958936 -5333.84569019492 Force two-norm initial, final = 650.42283 0.21736827 Force max component initial, final = 157.25257 0.045420752 Final line search alpha, max atom move = 1.0000000 0.045420752 Iterations, force evaluations = 65 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.1781 | 9.1781 | 9.1781 | 0.0 | 99.47 Neigh | 0.015631 | 0.015631 | 0.015631 | 0.0 | 0.17 Comm | 0.016164 | 0.016164 | 0.016164 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01698 | | | 0.18 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5424.00 ave 5424 max 5424 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: 80702.0 ave 80702 max 80702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80702 Ave neighs/atom = 64.665064 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 ghost atom cutoff = 6 binsize = 3, bins = 10 34 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.647 | 4.647 | 4.647 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -5333.8457 0 -5333.8457 5424.2197 14653.715 68 0 -5333.9391 0 -5333.9391 -2.5256627 14699.724 Loop time of 0.482688 on 1 procs for 3 steps with 1248 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 = -5333.84569019492 -5333.93627680993 -5333.93907598431 Force two-norm initial, final = 89.117399 0.27344188 Force max component initial, final = 65.610200 0.14262922 Final line search alpha, max atom move = 9.8085376e-05 1.3989840e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47936 | 0.47936 | 0.47936 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072449 | 0.00072449 | 0.00072449 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002599 | | | 0.54 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5299.00 ave 5299 max 5299 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: 80478.0 ave 80478 max 80478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80478 Ave neighs/atom = 64.485577 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 = 10 34 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) = 4.785 | 4.785 | 4.785 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5333.9391 0 -5333.9391 -2.5256627 Loop time of 6.375e-06 on 1 procs for 0 steps with 1248 atoms 172.5% 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 | | 6.375e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5299.00 ave 5299 max 5299 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: 80440.0 ave 80440 max 80440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80440 Ave neighs/atom = 64.455128 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 = 10 34 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) = 4.785 | 4.785 | 4.785 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 -5333.9391 -5333.9391 29.205662 101.36319 4.9654871 -2.5256627 -2.5256627 3.4367617 4.5491264 -15.562876 2.317002 764.62197 Loop time of 6.746e-06 on 1 procs for 0 steps with 1248 atoms 252.0% 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 | | 6.746e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5299.00 ave 5299 max 5299 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40220.0 ave 40220 max 40220 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80440.0 ave 80440 max 80440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80440 Ave neighs/atom = 64.455128 Neighbor list builds = 0 Dangerous builds = 0 1248 -5333.93907598431 eV 2.31700200821785 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10