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 -42.532322 0.0000000) to (52.091243 42.532322 8.6222038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950507 5.2437109 5.7481359 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -42.532322 0.0000000) to (52.091243 42.532322 8.6222038) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950507 5.2437109 5.7481359 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.532322 0.0000000) to (52.091243 42.532322 8.6222038) create_atoms CPU = 0.002 seconds 1756 atoms in group lower Displacing atoms ... Reading adp potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXlyOwUJ/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 = 15 24 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 3 atoms, new total = 3503 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 = 15 24 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) = 8.709 | 8.709 | 8.709 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15272.775 0 -15272.775 7039.8663 89 0 -15529.718 0 -15529.718 8184.4304 Loop time of 4.40043 on 1 procs for 89 steps with 3503 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15272.774529744 -15529.7038040782 -15529.7180748621 Force two-norm initial, final = 51.240963 0.41555904 Force max component initial, final = 3.5244105 0.091810912 Final line search alpha, max atom move = 1.0000000 0.091810912 Iterations, force evaluations = 89 162 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.317 | 4.317 | 4.317 | 0.0 | 98.10 Neigh | 0.040073 | 0.040073 | 0.040073 | 0.0 | 0.91 Comm | 0.018189 | 0.018189 | 0.018189 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02519 | | | 0.57 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10261.0 ave 10261 max 10261 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243986.0 ave 243986 max 243986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 243986 Ave neighs/atom = 69.650585 Neighbor list builds = 3 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 : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.709 | 8.709 | 8.709 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -15529.718 0 -15529.718 8184.4304 38206.046 95 0 -15530.564 0 -15530.564 -85.842203 38383.628 Loop time of 0.213652 on 1 procs for 6 steps with 3503 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 = -15529.7180748621 -15530.5626412142 -15530.5641244171 Force two-norm initial, final = 382.37980 6.7388998 Force max component initial, final = 339.07879 6.3137262 Final line search alpha, max atom move = 7.0488894e-05 0.00044504757 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20926 | 0.20926 | 0.20926 | 0.0 | 97.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060265 | 0.00060265 | 0.00060265 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00379 | | | 1.77 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10240.0 ave 10240 max 10240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243902.0 ave 243902 max 243902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 243902 Ave neighs/atom = 69.626606 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 = 15 24 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) = 8.339 | 8.339 | 8.339 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15530.564 0 -15530.564 -85.842203 Loop time of 1.876e-06 on 1 procs for 0 steps with 3503 atoms 159.9% 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 | | 1.876e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10236.0 ave 10236 max 10236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243666.0 ave 243666 max 243666 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 = 243666 Ave neighs/atom = 69.559235 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) = 8.339 | 8.339 | 8.339 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 -15530.564 -15530.564 52.088381 85.501746 8.61847 -85.842203 -85.842203 -263.52767 70.808443 -64.807379 2.1661027 1490.0403 Loop time of 2.292e-06 on 1 procs for 0 steps with 3503 atoms 218.2% 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 | | 2.292e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10236.0 ave 10236 max 10236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243666.0 ave 243666 max 243666 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 487332.0 ave 487332 max 487332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 487332 Ave neighs/atom = 139.11847 Neighbor list builds = 0 Dangerous builds = 0 3503 -15530.5641244171 eV 2.16610272437159 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05