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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -59.452934 0.0000000) to (21.019786 59.452934 5.7208612) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4495743 6.6058816 5.7208612 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -59.452934 0.0000000) to (21.019786 59.452934 5.7208612) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4495743 6.6058816 5.7208612 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -59.452934 0.0000000) to (21.019786 59.452934 5.7208612) create_atoms CPU = 0.001 seconds 434 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 862 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_106969701023_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.999 | 4.999 | 4.999 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2724.2541 0 -2724.2541 34418.783 75 0 -2932.2044 0 -2932.2044 3492.4921 Loop time of 1.23398 on 1 procs for 75 steps with 862 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2724.25405838431 -2932.20171224016 -2932.20442204498 Force two-norm initial, final = 436.12184 0.11474478 Force max component initial, final = 117.15881 0.031378074 Final line search alpha, max atom move = 1.0000000 0.031378074 Iterations, force evaluations = 75 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1932 | 1.1932 | 1.1932 | 0.0 | 96.70 Neigh | 0.024906 | 0.024906 | 0.024906 | 0.0 | 2.02 Comm | 0.0087963 | 0.0087963 | 0.0087963 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00706 | | | 0.57 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6202.00 ave 6202 max 6202 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: 121776.0 ave 121776 max 121776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121776 Ave neighs/atom = 141.27146 Neighbor list builds = 3 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.999 | 4.999 | 4.999 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -2932.2044 0 -2932.2044 3492.4921 14298.583 82 0 -2932.3807 0 -2932.3807 -80.48677 14360.53 Loop time of 0.138223 on 1 procs for 7 steps with 862 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 = -2932.20442204497 -2932.37991362901 -2932.38074016923 Force two-norm initial, final = 65.321710 1.3093273 Force max component initial, final = 61.175241 0.98773635 Final line search alpha, max atom move = 0.00039444657 0.00038960922 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13367 | 0.13367 | 0.13367 | 0.0 | 96.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085697 | 0.00085697 | 0.00085697 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003695 | | | 2.67 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6266.00 ave 6266 max 6266 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: 121796.0 ave 121796 max 121796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121796 Ave neighs/atom = 141.29466 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.137 | 5.137 | 5.137 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2932.3807 0 -2932.3807 -80.48677 Loop time of 3.037e-06 on 1 procs for 0 steps with 862 atoms 164.6% 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 | | 3.037e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6266.00 ave 6266 max 6266 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: 121452.0 ave 121452 max 121452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121452 Ave neighs/atom = 140.89559 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.137 | 5.137 | 5.137 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 -2932.3807 -2932.3807 20.986535 119.67253 5.7178829 -80.48677 -80.48677 -110.0255 -77.0104 -54.424407 2.5407223 552.45618 Loop time of 3e-06 on 1 procs for 0 steps with 862 atoms 166.7% 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 | | 3e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6266.00 ave 6266 max 6266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60726.0 ave 60726 max 60726 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121452.0 ave 121452 max 121452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121452 Ave neighs/atom = 140.89559 Neighbor list builds = 0 Dangerous builds = 0 862 -2932.38074016922 eV 2.54072234712642 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01