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 -35.200000 0.0000000) to (17.600000 35.200000 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9280000 4.9280000 3.5200000 Created 200 atoms using lattice units in orthogonal box = (0.0000000 -35.200000 0.0000000) to (17.600000 35.200000 3.5200000) create_atoms CPU = 0.001 seconds 200 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9280000 4.9280000 3.5200000 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -35.200000 0.0000000) to (17.600000 35.200000 3.5200000) create_atoms CPU = 0.000 seconds 202 atoms in group lower Displacing atoms ... Reading adp potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXX9yPqb8/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 = 5 20 1 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 2 atoms, new total = 400 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 = 5 20 1 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) = 7.052 | 7.052 | 7.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1752.878 0 -1752.878 11213.296 37 0 -1771.8072 0 -1771.8072 8900.387 Loop time of 0.253851 on 1 procs for 37 steps with 400 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1752.87798117178 -1771.80602630658 -1771.8072410479 Force two-norm initial, final = 20.681034 0.10845951 Force max component initial, final = 5.0741064 0.016601505 Final line search alpha, max atom move = 1.0000000 0.016601505 Iterations, force evaluations = 37 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24946 | 0.24946 | 0.24946 | 0.0 | 98.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026403 | 0.0026403 | 0.0026403 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001747 | | | 0.69 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4373.00 ave 4373 max 4373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28004.0 ave 28004 max 28004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28004 Ave neighs/atom = 70.010000 Neighbor list builds = 0 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.052 | 7.052 | 7.052 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -1771.8072 0 -1771.8072 8900.387 4361.4207 43 0 -1771.9674 0 -1771.9674 212.0716 4382.6233 Loop time of 0.0295469 on 1 procs for 6 steps with 400 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 = -1771.8072410479 -1771.96581323401 -1771.96744270911 Force two-norm initial, final = 55.565708 1.0952891 Force max component initial, final = 49.403481 0.88598905 Final line search alpha, max atom move = 0.00025252779 0.00022373686 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028015 | 0.028015 | 0.028015 | 0.0 | 94.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027899 | 0.00027899 | 0.00027899 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001253 | | | 4.24 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4428.00 ave 4428 max 4428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27900.0 ave 27900 max 27900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27900 Ave neighs/atom = 69.750000 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 = 5 20 1 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) = 6.684 | 6.684 | 6.684 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1771.9674 0 -1771.9674 212.0716 Loop time of 1.871e-06 on 1 procs for 0 steps with 400 atoms 160.3% 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 | | 1.871e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4428.00 ave 4428 max 4428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27868.0 ave 27868 max 27868 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 = 27868 Ave neighs/atom = 69.670000 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) = 6.684 | 6.684 | 6.684 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 -1771.9674 -1771.9674 17.557656 70.778132 3.5266999 212.0716 212.0716 124.03957 187.6635 324.51173 2.2227196 150.82324 Loop time of 1.84e-06 on 1 procs for 0 steps with 400 atoms 108.7% 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 | | 1.84e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4428.00 ave 4428 max 4428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27868.0 ave 27868 max 27868 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55736.0 ave 55736 max 55736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55736 Ave neighs/atom = 139.34000 Neighbor list builds = 0 Dangerous builds = 0 400 -1771.96744270911 eV 2.22271956542333 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00