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 # Using KIM Simulator Model : Sim_LAMMPS_ADP_MishinMehlPapaconstantopoulos_2005_Ni__SM_477692857359_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -69.692444 0.0000000) to (42.677732 69.692444 8.6222038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9355200 4.9780317 5.7481359 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -69.692444 0.0000000) to (42.677732 69.692444 8.6222038) create_atoms CPU = 0.004 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9355200 4.9780317 5.7481359 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.692444 0.0000000) to (42.677732 69.692444 8.6222038) create_atoms CPU = 0.003 seconds 2358 atoms in group lower Displacing atoms ... Reading adp potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXW3VZeu/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 bin: standard Deleted 18 atoms, new total = 4692 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/SM_477692857359_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 = 7.168 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 bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 15.85 | 15.85 | 15.85 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20713.709 0 -20713.709 2123.672 70 0 -20812.762 0 -20812.762 2876.9464 Loop time of 4.60363 on 1 procs for 70 steps with 4692 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 = -20713.7094853356 -20812.7416943705 -20812.7621153514 Force two-norm initial, final = 40.444591 0.49614888 Force max component initial, final = 4.5373848 0.018963161 Final line search alpha, max atom move = 1.0000000 0.018963161 Iterations, force evaluations = 70 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5215 | 4.5215 | 4.5215 | 0.0 | 98.22 Neigh | 0.036756 | 0.036756 | 0.036756 | 0.0 | 0.80 Comm | 0.018362 | 0.018362 | 0.018362 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02704 | | | 0.59 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13639.0 ave 13639 max 13639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 326796.0 ave 326796 max 326796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 326796 Ave neighs/atom = 69.649616 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.85 | 15.85 | 15.85 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -20812.762 0 -20812.762 2876.9464 51290.308 73 0 -20812.915 0 -20812.915 -105.50237 51376.174 Loop time of 0.208647 on 1 procs for 3 steps with 4692 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 = -20812.7621153514 -20812.9141782173 -20812.9154852378 Force two-norm initial, final = 185.02762 8.4531753 Force max component initial, final = 165.84418 7.8722213 Final line search alpha, max atom move = 7.5576554e-05 0.00059495535 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20453 | 0.20453 | 0.20453 | 0.0 | 98.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060472 | 0.00060472 | 0.00060472 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00351 | | | 1.68 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13655.0 ave 13655 max 13655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 327204.0 ave 327204 max 327204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327204 Ave neighs/atom = 69.736573 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 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) = 14.73 | 14.73 | 14.73 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20812.915 0 -20812.915 -105.50237 Loop time of 1.811e-06 on 1 procs for 0 steps with 4692 atoms 220.9% 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 | | 1.811e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13669.0 ave 13669 max 13669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 327126.0 ave 327126 max 327126 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327126 Ave neighs/atom = 69.719949 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) = 14.73 | 14.73 | 14.73 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 -20812.915 -20812.915 42.679375 139.65573 8.6195572 -105.50237 -105.50237 -245.50628 -92.408113 21.407298 2.1802467 1698.3075 Loop time of 2.199e-06 on 1 procs for 0 steps with 4692 atoms 227.4% 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 | | 2.199e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13669.0 ave 13669 max 13669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 327126.0 ave 327126 max 327126 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 654252.0 ave 654252 max 654252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654252 Ave neighs/atom = 139.43990 Neighbor list builds = 0 Dangerous builds = 0 4692 -20812.9154852378 eV 2.18024671951421 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05