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 -52.091243 0.0000000) to (42.532322 52.091243 8.6222038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2437109 4.9950507 5.7481359 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -52.091243 0.0000000) to (42.532322 52.091243 8.6222038) create_atoms CPU = 0.003 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2437109 4.9950507 5.7481359 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -52.091243 0.0000000) to (42.532322 52.091243 8.6222038) create_atoms CPU = 0.002 seconds 1757 atoms in group lower Displacing atoms ... Reading adp potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXdxdMO5/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 30 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 5 atoms, new total = 3501 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 30 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) = 8.732 | 8.732 | 8.732 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15321.721 0 -15321.721 3750.3106 76 0 -15513.289 0 -15513.289 7689.0822 Loop time of 3.77352 on 1 procs for 76 steps with 3501 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 = -15321.7214905556 -15513.2747763909 -15513.2889475381 Force two-norm initial, final = 44.658480 0.41835162 Force max component initial, final = 4.8606405 0.029614744 Final line search alpha, max atom move = 1.0000000 0.029614744 Iterations, force evaluations = 76 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.669 | 3.669 | 3.669 | 0.0 | 97.23 Neigh | 0.062534 | 0.062534 | 0.062534 | 0.0 | 1.66 Comm | 0.017226 | 0.017226 | 0.017226 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02481 | | | 0.66 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10660.0 ave 10660 max 10660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 244053.0 ave 244053 max 244053 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 244053 Ave neighs/atom = 69.709512 Neighbor list builds = 4 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 : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.732 | 8.732 | 8.732 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -15513.289 0 -15513.289 7689.0822 38206.046 82 0 -15514.137 0 -15514.137 -187.70255 38374.953 Loop time of 0.242259 on 1 procs for 6 steps with 3501 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 = -15513.2889475381 -15514.1348382609 -15514.1367121012 Force two-norm initial, final = 374.51877 10.056102 Force max component initial, final = 343.69275 9.4184979 Final line search alpha, max atom move = 7.6323707e-05 0.00071885468 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23651 | 0.23651 | 0.23651 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073099 | 0.00073099 | 0.00073099 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005017 | | | 2.07 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10643.0 ave 10643 max 10643 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 244011.0 ave 244011 max 244011 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 244011 Ave neighs/atom = 69.697515 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 30 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) = 8.362 | 8.362 | 8.362 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15514.137 0 -15514.137 -187.70255 Loop time of 2.45e-06 on 1 procs for 0 steps with 3501 atoms 367.3% 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 | | 2.45e-06 | | |100.00 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10643.0 ave 10643 max 10643 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243869.0 ave 243869 max 243869 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 = 243869 Ave neighs/atom = 69.656955 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) = 8.362 | 8.362 | 8.362 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 -15514.137 -15514.137 42.517154 104.7222 8.6187629 -187.70255 -187.70255 -393.08751 -28.042804 -141.97735 2.1827247 1626.4901 Loop time of 2.873e-06 on 1 procs for 0 steps with 3501 atoms 243.6% 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 | | 2.873e-06 | | |100.00 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10643.0 ave 10643 max 10643 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243869.0 ave 243869 max 243869 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 487738.0 ave 487738 max 487738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 487738 Ave neighs/atom = 139.31391 Neighbor list builds = 0 Dangerous builds = 0 3501 -15514.1367121012 eV 2.18272471136096 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04