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 -36.918071 0.0000000) to (45.215218 36.918071 8.6222038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7546642 5.3699013 5.7481359 Created 1316 atoms using lattice units in orthogonal box = (0.0000000 -36.918071 0.0000000) to (45.215218 36.918071 8.6222038) create_atoms CPU = 0.002 seconds 1316 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7546642 5.3699013 5.7481359 Created 1322 atoms using lattice units in orthogonal box = (0.0000000 -36.918071 0.0000000) to (45.215218 36.918071 8.6222038) create_atoms CPU = 0.002 seconds 1322 atoms in group lower Displacing atoms ... Reading adp potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXX8LR3Er/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 = 13 21 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 = 2638 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 = 13 21 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) = 8.095 | 8.095 | 8.095 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11556.132 0 -11556.132 8130.1633 63 0 -11674.453 0 -11674.453 7869.3722 Loop time of 2.331 on 1 procs for 63 steps with 2638 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11556.1319741698 -11674.4417099018 -11674.4525538933 Force two-norm initial, final = 51.178829 0.35730904 Force max component initial, final = 4.4320943 0.049326948 Final line search alpha, max atom move = 1.0000000 0.049326948 Iterations, force evaluations = 63 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2856 | 2.2856 | 2.2856 | 0.0 | 98.05 Neigh | 0.021245 | 0.021245 | 0.021245 | 0.0 | 0.91 Comm | 0.010393 | 0.010393 | 0.010393 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01373 | | | 0.59 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8375.00 ave 8375 max 8375 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 184040.0 ave 184040 max 184040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184040 Ave neighs/atom = 69.764973 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.095 | 8.095 | 8.095 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -11674.453 0 -11674.453 7869.3722 28785.377 68 0 -11674.951 0 -11674.951 -9.8132409 28914.248 Loop time of 0.164332 on 1 procs for 5 steps with 2638 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 = -11674.4525538933 -11674.9505169235 -11674.9509212455 Force two-norm initial, final = 268.85749 1.2161226 Force max component initial, final = 225.90607 1.0223753 Final line search alpha, max atom move = 0.00014363710 0.00014685102 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16103 | 0.16103 | 0.16103 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049239 | 0.00049239 | 0.00049239 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002809 | | | 1.71 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8263.00 ave 8263 max 8263 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 184088.0 ave 184088 max 184088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184088 Ave neighs/atom = 69.783169 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 = 13 21 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) = 7.725 | 7.725 | 7.725 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11674.951 0 -11674.951 -9.8132409 Loop time of 2.159e-06 on 1 procs for 0 steps with 2638 atoms 185.3% 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 | | 2.159e-06 | | |100.00 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8298.00 ave 8298 max 8298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 183960.0 ave 183960 max 183960 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 = 183960 Ave neighs/atom = 69.734647 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) = 7.725 | 7.725 | 7.725 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 -11674.951 -11674.951 45.26005 74.135682 8.6172676 -9.8132409 -9.8132409 -56.707329 4.7255057 22.542101 2.1845723 1408.8088 Loop time of 1.992e-06 on 1 procs for 0 steps with 2638 atoms 251.0% 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 | | 1.992e-06 | | |100.00 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8298.00 ave 8298 max 8298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 183960.0 ave 183960 max 183960 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 367920.0 ave 367920 max 367920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 367920 Ave neighs/atom = 139.46929 Neighbor list builds = 0 Dangerous builds = 0 2638 -11674.9509212455 eV 2.18457229737468 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02