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 -46.216819 0.0000000) to (32.680226 46.216819 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0800420 5.9114536 4.9836877 Created 685 atoms using lattice units in orthogonal box = (0.0000000 -46.216819 0.0000000) to (32.680226 46.216819 4.9836877) create_atoms CPU = 0.002 seconds 685 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0800420 5.9114536 4.9836877 Created 693 atoms using lattice units in orthogonal box = (0.0000000 -46.216819 0.0000000) to (32.680226 46.216819 4.9836877) create_atoms CPU = 0.002 seconds 693 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 = 8 21 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 2 atoms, new total = 1376 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 = 8 21 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) = 7.886 | 7.886 | 7.886 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5483.7267 0 -5483.7267 149042.01 62 0 -6090.1619 0 -6090.1619 6161.4377 Loop time of 3.24319 on 1 procs for 62 steps with 1376 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5483.72672292999 -6090.15622898749 -6090.16185545428 Force two-norm initial, final = 874.70042 0.25365740 Force max component initial, final = 129.67838 0.038266085 Final line search alpha, max atom move = 1.0000000 0.038266085 Iterations, force evaluations = 62 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2066 | 3.2066 | 3.2066 | 0.0 | 98.87 Neigh | 0.0098364 | 0.0098364 | 0.0098364 | 0.0 | 0.30 Comm | 0.015565 | 0.015565 | 0.015565 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01123 | | | 0.35 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10045.0 ave 10045 max 10045 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173976.0 ave 173976 max 173976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173976 Ave neighs/atom = 126.43605 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.886 | 7.886 | 7.886 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -6090.1619 0 -6090.1619 6161.4377 15054.485 65 0 -6090.276 0 -6090.276 -1.2332767 15104.802 Loop time of 0.163001 on 1 procs for 3 steps with 1376 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 = -6090.16185545428 -6090.2729646464 -6090.27598765624 Force two-norm initial, final = 103.94282 0.82589869 Force max component initial, final = 79.457750 0.61200147 Final line search alpha, max atom move = 0.00010370170 6.3465596e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16014 | 0.16014 | 0.16014 | 0.0 | 98.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051075 | 0.00051075 | 0.00051075 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002355 | | | 1.44 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9991.00 ave 9991 max 9991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173622.0 ave 173622 max 173622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173622 Ave neighs/atom = 126.17878 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 = 8 21 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) = 7.517 | 7.517 | 7.517 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6090.276 0 -6090.276 -1.2332767 Loop time of 2.039e-06 on 1 procs for 0 steps with 1376 atoms 196.2% 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 | | 2.039e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9991.00 ave 9991 max 9991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173319.0 ave 173319 max 173319 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 = 173319 Ave neighs/atom = 125.95858 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) = 7.517 | 7.517 | 7.517 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 -6090.276 -6090.276 32.709437 92.630011 4.9852882 -1.2332767 -1.2332767 64.97343 -23.361397 -45.311863 2.3442754 950.64534 Loop time of 2.483e-06 on 1 procs for 0 steps with 1376 atoms 362.5% 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 | | 2.483e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9991.00 ave 9991 max 9991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173319.0 ave 173319 max 173319 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 346638.0 ave 346638 max 346638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346638 Ave neighs/atom = 251.91715 Neighbor list builds = 0 Dangerous builds = 0 1376 -6090.27598765624 eV 2.34427539230543 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03