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 -48.3955 0) to (13.1706 48.3955 8.6222) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.64456 5.37689 5.74814 Created 507 atoms create_atoms CPU = 0.00027895 secs 507 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.64456 5.37689 5.74814 Created 507 atoms create_atoms CPU = 0.000195026 secs 507 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX2N4VGW/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 = 4 28 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 15 atoms, new total = 999 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 = 4 28 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) = 7.303 | 7.303 | 7.303 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4404.541 0 -4404.541 2713.5984 51 0 -4426.9378 0 -4426.9378 -7160.7358 Loop time of 0.33587 on 1 procs for 51 steps with 999 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4404.54099784 -4426.9342313 -4426.93775219 Force two-norm initial, final = 21.4101 0.20101 Force max component initial, final = 4.43785 0.0337262 Final line search alpha, max atom move = 1 0.0337262 Iterations, force evaluations = 51 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33095 | 0.33095 | 0.33095 | 0.0 | 98.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026996 | 0.0026996 | 0.0026996 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002223 | | | 0.66 Nlocal: 999 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5226 ave 5226 max 5226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69351 ave 69351 max 69351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69351 Ave neighs/atom = 69.4204 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 : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.303 | 7.303 | 7.303 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -4426.9378 0 -4426.9378 -7160.7358 10991.58 54 0 -4426.9916 0 -4426.9916 -2418.4268 10962.056 Loop time of 0.0261619 on 1 procs for 3 steps with 999 atoms 76.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4426.93775219 -4426.99138917 -4426.99159212 Force two-norm initial, final = 54.7807 0.216719 Force max component initial, final = 44.152 0.0455065 Final line search alpha, max atom move = 0.000489925 2.22948e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.025292 | 0.025292 | 0.025292 | 0.0 | 96.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017738 | 0.00017738 | 0.00017738 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006926 | | | 2.65 Nlocal: 999 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5313 ave 5313 max 5313 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69593 ave 69593 max 69593 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69593 Ave neighs/atom = 69.6627 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 = 4 28 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) = 6.935 | 6.935 | 6.935 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4426.9916 0 -4426.9916 -2418.4268 Loop time of 9.53674e-07 on 1 procs for 0 steps with 999 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: 999 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5313 ave 5313 max 5313 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69595 ave 69595 max 69595 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 = 69595 Ave neighs/atom = 69.6647 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) = 6.935 | 6.935 | 6.935 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 -4426.9916 -4426.9916 13.158004 96.791038 8.6072981 -2418.4268 -2418.4268 -4.4915294 -7249.8662 -0.92270195 2.1910311 400.42743 Loop time of 1.90735e-06 on 1 procs for 0 steps with 999 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 | | 1.907e-06 | | |100.00 Nlocal: 999 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5313 ave 5313 max 5313 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69595 ave 69595 max 69595 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139190 ave 139190 max 139190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139190 Ave neighs/atom = 139.329 Neighbor list builds = 0 Dangerous builds = 0 999 -4426.99159211539 eV 2.19103110633905 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00