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 = 2.8669658 2.8669658 2.8669658 Created orthogonal box = (0.0000000 -42.430086 0.0000000) to (34.641679 42.430086 7.0226033) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2708920 4.0683635 4.6817355 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -42.430086 0.0000000) to (34.641679 42.430086 7.0226033) create_atoms CPU = 0.001 seconds 878 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2708920 4.0683635 4.6817355 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -42.430086 0.0000000) to (34.641679 42.430086 7.0226033) create_atoms CPU = 0.001 seconds 878 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 23 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1740 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.572 | 5.572 | 5.572 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6746.5887 0 -6746.5887 44866.684 252 0 -6995.4512 0 -6995.4512 -71307.007 Loop time of 5.94181 on 1 procs for 252 steps with 1740 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 = -6746.58866291488 -6995.44428209617 -6995.45124841117 Force two-norm initial, final = 338.33518 0.28761095 Force max component initial, final = 72.505321 0.054518181 Final line search alpha, max atom move = 0.91368111 0.049812232 Iterations, force evaluations = 252 495 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8632 | 5.8632 | 5.8632 | 0.0 | 98.68 Neigh | 0.015559 | 0.015559 | 0.015559 | 0.0 | 0.26 Comm | 0.030867 | 0.030867 | 0.030867 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03213 | | | 0.54 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7656.00 ave 7656 max 7656 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: 275496.0 ave 275496 max 275496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275496 Ave neighs/atom = 158.33103 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 252 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.572 | 5.572 | 5.572 Mbytes Step Temp E_pair E_mol TotEng Press Volume 252 0 -6995.4512 0 -6995.4512 -71307.007 20644.339 414 0 -7055.6473 0 -7055.6473 -4966.9724 18754.16 Loop time of 2.33212 on 1 procs for 162 steps with 1740 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 = -6995.45124841118 -7055.64509457762 -7055.64734388422 Force two-norm initial, final = 1483.3180 10.960242 Force max component initial, final = 1074.8488 6.9813572 Final line search alpha, max atom move = 0.00024067607 0.0016802456 Iterations, force evaluations = 162 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2465 | 2.2465 | 2.2465 | 0.0 | 96.33 Neigh | 0.016597 | 0.016597 | 0.016597 | 0.0 | 0.71 Comm | 0.010572 | 0.010572 | 0.010572 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05847 | | | 2.51 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7830.00 ave 7830 max 7830 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: 283512.0 ave 283512 max 283512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283512 Ave neighs/atom = 162.93793 Neighbor list builds = 1 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.712 | 5.712 | 5.712 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7055.6473 0 -7055.6473 -4966.9724 Loop time of 1.636e-06 on 1 procs for 0 steps with 1740 atoms 122.2% 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 | | 1.636e-06 | | |100.00 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8001.00 ave 8001 max 8001 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: 289844.0 ave 289844 max 289844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289844 Ave neighs/atom = 166.57701 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.712 | 5.712 | 5.712 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 -7055.6473 -7055.6473 32.922612 84.860172 6.7127338 -4966.9724 -4966.9724 385.63706 -15856.658 570.10374 2.2808621 7501.0635 Loop time of 1.765e-06 on 1 procs for 0 steps with 1740 atoms 170.0% 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 | | 1.765e-06 | | |100.00 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8001.00 ave 8001 max 8001 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144922.0 ave 144922 max 144922 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 289844.0 ave 289844 max 289844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289844 Ave neighs/atom = 166.57701 Neighbor list builds = 0 Dangerous builds = 0 1740 -7055.64734388422 eV 2.28086206092289 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08