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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -69.274156 0.0000000) to (42.419441 69.274156 8.5700212) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9056496 4.9479041 5.7133475 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.274156 0.0000000) to (42.419441 69.274156 8.5700212) create_atoms CPU = 0.009 seconds 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9056496 4.9479041 5.7133475 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.274156 0.0000000) to (42.419441 69.274156 8.5700212) create_atoms CPU = 0.009 seconds 2358 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 = 12 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 4680 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 = 12 37 3 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) = 12.32 | 12.32 | 12.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19089.646 0 -19089.646 13244.732 49 0 -19208.059 0 -19208.059 -1335.5793 Loop time of 7.37958 on 1 procs for 49 steps with 4680 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -19089.645940618 -19208.0398470399 -19208.058695016 Force two-norm initial, final = 171.29360 0.48751068 Force max component initial, final = 29.193115 0.058009235 Final line search alpha, max atom move = 0.70743398 0.041037704 Iterations, force evaluations = 49 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3108 | 7.3108 | 7.3108 | 0.0 | 99.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.03024 | 0.03024 | 0.03024 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03854 | | | 0.52 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14701.0 ave 14701 max 14701 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: 818424.0 ave 818424 max 818424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 818424 Ave neighs/atom = 174.87692 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 37 3 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 : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.32 | 12.32 | 12.32 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -19208.059 0 -19208.059 -1335.5793 50367.231 51 0 -19208.118 0 -19208.118 499.10283 50288.102 Loop time of 0.316161 on 1 procs for 2 steps with 4680 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -19208.058695016 -19208.1179325894 -19208.1181931238 Force two-norm initial, final = 101.16658 0.53981587 Force max component initial, final = 86.857617 0.14177206 Final line search alpha, max atom move = 0.00024278085 3.4419541e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31021 | 0.31021 | 0.31021 | 0.0 | 98.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012536 | 0.0012536 | 0.0012536 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004693 | | | 1.48 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14739.0 ave 14739 max 14739 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: 817140.0 ave 817140 max 817140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 817140 Ave neighs/atom = 174.60256 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 = 12 37 3 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) = 11.83 | 11.83 | 11.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19208.118 0 -19208.118 499.10283 Loop time of 6.315e-06 on 1 procs for 0 steps with 4680 atoms 205.9% 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 | | 6.315e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14739.0 ave 14739 max 14739 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: 817224.0 ave 817224 max 817224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 817224 Ave neighs/atom = 174.62051 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 = 12 37 3 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) = 11.83 | 11.83 | 11.83 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 -19208.118 -19208.118 42.397689 138.54831 8.5609473 499.10283 499.10283 -4.5145348 1505.0869 -3.263856 2.2704525 1714.2338 Loop time of 6.716e-06 on 1 procs for 0 steps with 4680 atoms 312.7% 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 | | 6.716e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14739.0 ave 14739 max 14739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 408612.0 ave 408612 max 408612 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 817224.0 ave 817224 max 817224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 817224 Ave neighs/atom = 174.62051 Neighbor list builds = 0 Dangerous builds = 0 4680 -19208.1181931238 eV 2.27045254240825 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09