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 -67.341565 0.0000000) to (38.879671 67.341565 6.0968188) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7363448 5.1518137 6.0968188 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -67.341565 0.0000000) to (38.879671 67.341565 6.0968188) create_atoms CPU = 0.009 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7363448 5.1518137 6.0968188 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.341565 0.0000000) to (38.879671 67.341565 6.0968188) create_atoms CPU = 0.009 seconds 1466 atoms in group lower Displacing atoms ... Reading adp potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXB6cmEc/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 = 11 38 2 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 = 2930 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 = 11 38 2 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) = 8.740 | 8.740 | 8.740 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12896.521 0 -12896.521 6160.1463 63 0 -12996.999 0 -12996.999 5248.1989 Loop time of 5.40141 on 1 procs for 63 steps with 2930 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 = -12896.5211695313 -12996.9869073134 -12996.9987790842 Force two-norm initial, final = 42.561933 0.34711345 Force max component initial, final = 5.0543938 0.051909992 Final line search alpha, max atom move = 0.78853288 0.040932736 Iterations, force evaluations = 63 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2647 | 5.2647 | 5.2647 | 0.0 | 97.47 Neigh | 0.072211 | 0.072211 | 0.072211 | 0.0 | 1.34 Comm | 0.031626 | 0.031626 | 0.031626 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03285 | | | 0.61 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11867.0 ave 11867 max 11867 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 205074.0 ave 205074 max 205074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205074 Ave neighs/atom = 69.991126 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.740 | 8.740 | 8.740 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -12996.999 0 -12996.999 5248.1989 31925.6 66 0 -12997.187 0 -12997.187 3.2037858 32019.148 Loop time of 0.314137 on 1 procs for 3 steps with 2930 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 = -12996.9987790842 -12997.1833318201 -12997.1873889079 Force two-norm initial, final = 190.22794 2.6174485 Force max component initial, final = 145.43246 2.0312135 Final line search alpha, max atom move = 5.3871159e-05 0.00010942383 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30704 | 0.30704 | 0.30704 | 0.0 | 97.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015789 | 0.0015789 | 0.0015789 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005519 | | | 1.76 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11871.0 ave 11871 max 11871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 205084.0 ave 205084 max 205084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205084 Ave neighs/atom = 69.994539 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 = 11 38 2 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) = 8.371 | 8.371 | 8.371 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12997.187 0 -12997.187 3.2037858 Loop time of 6.575e-06 on 1 procs for 0 steps with 2930 atoms 167.3% 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 | | 6.575e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11871.0 ave 11871 max 11871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 205020.0 ave 205020 max 205020 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 = 205020 Ave neighs/atom = 69.972696 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) = 8.371 | 8.371 | 8.371 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 -12997.187 -12997.187 38.915312 134.93654 6.0976106 3.2037858 3.2037858 -101.73118 43.796746 67.545795 2.2148644 1010.686 Loop time of 6.996e-06 on 1 procs for 0 steps with 2930 atoms 271.6% 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 | | 6.996e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11871.0 ave 11871 max 11871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 205020.0 ave 205020 max 205020 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 410040.0 ave 410040 max 410040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 410040 Ave neighs/atom = 139.94539 Neighbor list builds = 0 Dangerous builds = 0 2930 -12997.1873889079 eV 2.21486439570769 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06