LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_ADP_MishinMehlPapaconstantopoulos_2005_Ni__SM_477692857359_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 7 Aug 2019 # Lattice spacing in x,y,z = 3.52 3.52 3.52 Created orthogonal box = (0 -69.696 0) to (42.6777 69.696 8.6222) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.93552 4.97803 5.74814 Created 2358 atoms create_atoms CPU = 0.000736952 secs 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.93552 4.97803 5.74814 Created 2358 atoms create_atoms CPU = 0.000553846 secs 2358 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXQmKQ0Q/Ni.adp with DATE: 2011-06-20 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 = 7.168 ghost atom cutoff = 7.168 binsize = 3.584, bins = 12 39 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 adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Deleted 48 atoms, new total = 4668 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.168 ghost atom cutoff = 7.168 binsize = 3.584, bins = 12 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 15.79 | 15.79 | 15.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20660.118 0 -20660.118 2.9335493 56 0 -20705.877 0 -20705.877 -6186.7447 Loop time of 2.06158 on 1 procs for 56 steps with 4668 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 = -20660.117942 -20705.8625153 -20705.8770615 Force two-norm initial, final = 28.7605 0.373294 Force max component initial, final = 4.36168 0.0182199 Final line search alpha, max atom move = 1 0.0182199 Iterations, force evaluations = 56 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.042 | 2.042 | 2.042 | 0.0 | 99.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0092268 | 0.0092268 | 0.0092268 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01037 | | | 0.50 Nlocal: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13119 ave 13119 max 13119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 324432 ave 324432 max 324432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324432 Ave neighs/atom = 69.5013 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.79 | 15.79 | 15.79 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -20705.877 0 -20705.877 -6186.7447 51292.898 58 0 -20706.087 0 -20706.087 -1681.8465 51162.564 Loop time of 0.0865681 on 1 procs for 2 steps with 4668 atoms 92.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20705.8770615 -20706.0754711 -20706.0866451 Force two-norm initial, final = 233.513 7.83651 Force max component initial, final = 168.314 6.47227 Final line search alpha, max atom move = 2.25366e-05 0.000145863 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.084845 | 0.084845 | 0.084845 | 0.0 | 98.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034952 | 0.00034952 | 0.00034952 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001374 | | | 1.59 Nlocal: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13536 ave 13536 max 13536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 325218 ave 325218 max 325218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 325218 Ave neighs/atom = 69.6697 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 = 7.168 ghost atom cutoff = 7.168 binsize = 3.584, bins = 12 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton 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, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 14.68 | 14.68 | 14.68 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20706.087 0 -20706.087 -1681.8465 Loop time of 9.53674e-07 on 1 procs for 0 steps with 4668 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13604 ave 13604 max 13604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 325266 ave 325266 max 325266 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 325266 Ave neighs/atom = 69.6799 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 14.68 | 14.68 | 14.68 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 -20706.087 -20706.087 42.620117 139.39193 8.6119209 -1681.8465 -1681.8465 -137.58659 -5110.3931 202.44017 2.1889279 1697.0262 Loop time of 9.53674e-07 on 1 procs for 0 steps with 4668 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13604 ave 13604 max 13604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 325266 ave 325266 max 325266 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 650532 ave 650532 max 650532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 650532 Ave neighs/atom = 139.36 Neighbor list builds = 0 Dangerous builds = 0 4668 -20706.0866451404 eV 2.18892791324487 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02