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 -60.968188 0.0000000) to (24.890159 60.968188 8.6222038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9736381 5.2839096 5.7481359 Created 1195 atoms using lattice units in orthogonal box = (0.0000000 -60.968188 0.0000000) to (24.890159 60.968188 8.6222038) create_atoms CPU = 0.002 seconds 1195 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9736381 5.2839096 5.7481359 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -60.968188 0.0000000) to (24.890159 60.968188 8.6222038) create_atoms CPU = 0.002 seconds 1203 atoms in group lower Displacing atoms ... Reading adp potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXCGmbS4/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 = 7 35 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 0 atoms, new total = 2398 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 = 7 35 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) = 8.112 | 8.112 | 8.112 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10543.385 0 -10543.385 6433.9533 80 0 -10641.695 0 -10641.695 1745.786 Loop time of 2.60976 on 1 procs for 80 steps with 2398 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10543.3849705609 -10641.684706136 -10641.6948775618 Force two-norm initial, final = 42.892935 0.35594297 Force max component initial, final = 4.8926521 0.050827135 Final line search alpha, max atom move = 1.0000000 0.050827135 Iterations, force evaluations = 80 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5526 | 2.5526 | 2.5526 | 0.0 | 97.81 Neigh | 0.027248 | 0.027248 | 0.027248 | 0.0 | 1.04 Comm | 0.013866 | 0.013866 | 0.013866 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01604 | | | 0.61 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8806.00 ave 8806 max 8806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167719.0 ave 167719 max 167719 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167719 Ave neighs/atom = 69.941201 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 : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.113 | 8.113 | 8.113 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -10641.695 0 -10641.695 1745.786 26168.524 83 0 -10641.844 0 -10641.844 240.00098 26190.482 Loop time of 0.0935434 on 1 procs for 3 steps with 2398 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 = -10641.6948775618 -10641.8343206945 -10641.8439719829 Force two-norm initial, final = 109.01687 7.2160446 Force max component initial, final = 105.73987 4.9174461 Final line search alpha, max atom move = 5.4392276e-05 0.00026747108 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091448 | 0.091448 | 0.091448 | 0.0 | 97.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034153 | 0.00034153 | 0.00034153 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001754 | | | 1.88 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8896.00 ave 8896 max 8896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167673.0 ave 167673 max 167673 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167673 Ave neighs/atom = 69.922018 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 = 7 35 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) = 7.744 | 7.744 | 7.744 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10641.844 0 -10641.844 240.00098 Loop time of 3.607e-06 on 1 procs for 0 steps with 2398 atoms 166.3% 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 | | 3.607e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8896.00 ave 8896 max 8896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167661.0 ave 167661 max 167661 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 = 167661 Ave neighs/atom = 69.917014 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) = 7.744 | 7.744 | 7.744 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 -10641.844 -10641.844 24.861831 122.24412 8.6175222 240.00098 240.00098 300.47747 299.88836 119.63712 2.2737934 809.61792 Loop time of 2.263e-06 on 1 procs for 0 steps with 2398 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 | | 2.263e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8896.00 ave 8896 max 8896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167661.0 ave 167661 max 167661 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 335322.0 ave 335322 max 335322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335322 Ave neighs/atom = 139.83403 Neighbor list builds = 0 Dangerous builds = 0 2398 -10641.8439719829 eV 2.27379340682812 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03