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 -52.832658 0.0000000) to (37.355857 52.832658 4.9479041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8982931 6.0243778 4.9479041 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -52.832658 0.0000000) to (37.355857 52.832658 4.9479041) create_atoms CPU = 0.002 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8982931 6.0243778 4.9479041 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -52.832658 0.0000000) to (37.355857 52.832658 4.9479041) create_atoms CPU = 0.002 seconds 916 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 28 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 = 1816 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 28 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) = 5.972 | 5.972 | 5.972 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7360.976 0 -7360.976 30604.526 42 0 -7459.6648 0 -7459.6648 -3617.5167 Loop time of 1.15512 on 1 procs for 42 steps with 1816 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 = -7360.97596980246 -7459.65751023039 -7459.66484182258 Force two-norm initial, final = 167.50019 0.37003453 Force max component initial, final = 47.071527 0.050636288 Final line search alpha, max atom move = 1.0000000 0.050636288 Iterations, force evaluations = 42 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1255 | 1.1255 | 1.1255 | 0.0 | 97.44 Neigh | 0.016961 | 0.016961 | 0.016961 | 0.0 | 1.47 Comm | 0.0064997 | 0.0064997 | 0.0064997 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006142 | | | 0.53 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9840.00 ave 9840 max 9840 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: 317256.0 ave 317256 max 317256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317256 Ave neighs/atom = 174.70044 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 28 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.972 | 5.972 | 5.972 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -7459.6648 0 -7459.6648 -3617.5167 19530.458 43 0 -7459.6695 0 -7459.6695 -2873.3513 19518.311 Loop time of 0.0463137 on 1 procs for 1 steps with 1816 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 = -7459.66484182258 -7459.66484182258 -7459.66947161502 Force two-norm initial, final = 17.825149 3.3446206 Force max component initial, final = 17.345517 3.2232973 Final line search alpha, max atom move = 5.7651783e-05 0.00018582884 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.045291 | 0.045291 | 0.045291 | 0.0 | 97.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002165 | 0.0002165 | 0.0002165 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000806 | | | 1.74 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9904.00 ave 9904 max 9904 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: 317856.0 ave 317856 max 317856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317856 Ave neighs/atom = 175.03084 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 = 10 28 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) = 6.110 | 6.110 | 6.110 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7459.6695 0 -7459.6695 -2873.3513 Loop time of 1.64e-06 on 1 procs for 0 steps with 1816 atoms 182.9% 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 | | 1.64e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9904.00 ave 9904 max 9904 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: 317888.0 ave 317888 max 317888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317888 Ave neighs/atom = 175.04846 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 = 10 28 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) = 6.110 | 6.110 | 6.110 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 -7459.6695 -7459.6695 37.337055 105.66532 4.9473168 -2873.3513 -2873.3513 -66.564763 -8818.0448 264.55559 2.3097611 635.61335 Loop time of 2.262e-06 on 1 procs for 0 steps with 1816 atoms 221.0% 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 | | 2.262e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9904.00 ave 9904 max 9904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 158944.0 ave 158944 max 158944 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 317888.0 ave 317888 max 317888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317888 Ave neighs/atom = 175.04846 Neighbor list builds = 0 Dangerous builds = 0 1816 -7459.66947161502 eV 2.30976113891269 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01