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_XuWangQian_2022_NiPd__SM_559286646876_000 # For Simulator : LAMMPS 29 Sep 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created orthogonal box = (0.0000000 -45.132736 0.0000000) to (22.564606 45.132736 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9532062 4.9532062 3.5239994 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -45.132736 0.0000000) to (22.564606 45.132736 3.5239994) create_atoms CPU = 0.002 seconds 329 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9532062 4.9532062 3.5239994 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -45.132736 0.0000000) to (22.564606 45.132736 3.5239994) create_atoms CPU = 0.001 seconds 329 atoms in group lower Displacing atoms ... 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 6 21 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 6 atoms, new total = 652 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_559286646876_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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 6 21 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) = 7.221 | 7.221 | 7.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2853.9096 0 -2853.9096 24342.74 63 0 -2886.1928 0 -2886.1928 -4221.0409 Loop time of 2.9432 on 1 procs for 63 steps with 652 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2853.90956003269 -2886.19035393713 -2886.19279202945 Force two-norm initial, final = 47.782471 0.17712319 Force max component initial, final = 13.634008 0.053195094 Final line search alpha, max atom move = 1.0000000 0.053195094 Iterations, force evaluations = 63 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9002 | 2.9002 | 2.9002 | 0.0 | 98.54 Neigh | 0.0095449 | 0.0095449 | 0.0095449 | 0.0 | 0.32 Comm | 0.020867 | 0.020867 | 0.020867 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01263 | | | 0.43 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8449.00 ave 8449 max 8449 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82517.0 ave 82517 max 82517 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82517 Ave neighs/atom = 126.55982 Neighbor list builds = 1 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) = 7.221 | 7.221 | 7.221 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -2886.1928 0 -2886.1928 -4221.0409 7177.6989 65 0 -2886.2055 0 -2886.2055 -1489.4351 7166.9945 Loop time of 0.135551 on 1 procs for 2 steps with 652 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2886.19279202945 -2886.20525737173 -2886.20550983971 Force two-norm initial, final = 22.150258 0.17945032 Force max component initial, final = 18.750497 0.048872186 Final line search alpha, max atom move = 0.00070552383 3.4480492e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13238 | 0.13238 | 0.13238 | 0.0 | 97.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00087921 | 0.00087921 | 0.00087921 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00229 | | | 1.69 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8422.00 ave 8422 max 8422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82184.0 ave 82184 max 82184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82184 Ave neighs/atom = 126.04908 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 6 21 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) = 6.852 | 6.852 | 6.852 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2886.2055 0 -2886.2055 -1489.4351 Loop time of 6.124e-06 on 1 procs for 0 steps with 652 atoms 179.6% 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 | | 6.124e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8429.00 ave 8429 max 8429 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82278.0 ave 82278 max 82278 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 = 82278 Ave neighs/atom = 126.19325 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) = 6.852 | 6.852 | 6.852 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 -2886.2055 -2886.2055 22.539318 90.265472 3.5226917 -1489.4351 -1489.4351 2.1079961 -4468.671 -1.7423165 2.2516587 148.78064 Loop time of 6.535e-06 on 1 procs for 0 steps with 652 atoms 260.1% 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 | | 6.535e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8429.00 ave 8429 max 8429 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82278.0 ave 82278 max 82278 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 164556.0 ave 164556 max 164556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164556 Ave neighs/atom = 252.38650 Neighbor list builds = 0 Dangerous builds = 0 652 -2886.20550983971 eV 2.25165868715681 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03