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 -57.690356 0.0000000) to (40.793242 57.690356 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0885436 5.5968256 4.9836877 Created 1071 atoms using lattice units in orthogonal box = (0.0000000 -57.690356 0.0000000) to (40.793242 57.690356 4.9836877) create_atoms CPU = 0.003 seconds 1071 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0885436 5.5968256 4.9836877 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -57.690356 0.0000000) to (40.793242 57.690356 4.9836877) create_atoms CPU = 0.003 seconds 1079 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 = 10 26 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 6 atoms, new total = 2144 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 = 10 26 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) = 8.561 | 8.561 | 8.561 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8076.3061 0 -8076.3061 136849.12 96 0 -9497.7573 0 -9497.7573 4404.0342 Loop time of 7.76867 on 1 procs for 96 steps with 2144 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8076.30609950911 -9497.74873156417 -9497.75734294755 Force two-norm initial, final = 1634.2500 0.31619676 Force max component initial, final = 217.96341 0.033769517 Final line search alpha, max atom move = 1.0000000 0.033769517 Iterations, force evaluations = 96 176 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6723 | 7.6723 | 7.6723 | 0.0 | 98.76 Neigh | 0.029712 | 0.029712 | 0.029712 | 0.0 | 0.38 Comm | 0.0381 | 0.0381 | 0.0381 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02858 | | | 0.37 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13846.0 ave 13846 max 13846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271568.0 ave 271568 max 271568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271568 Ave neighs/atom = 126.66418 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 : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.563 | 8.563 | 8.563 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -9497.7573 0 -9497.7573 4404.0342 23456.989 99 0 -9497.8749 0 -9497.8749 3.4895247 23512.772 Loop time of 0.25938 on 1 procs for 3 steps with 2144 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 = -9497.75734294754 -9497.8721925593 -9497.87487161644 Force two-norm initial, final = 124.61070 1.7762695 Force max component initial, final = 105.02529 1.4738757 Final line search alpha, max atom move = 5.5997282e-05 8.2533031e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2554 | 0.2554 | 0.2554 | 0.0 | 98.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069829 | 0.00069829 | 0.00069829 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003285 | | | 1.27 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13867.0 ave 13867 max 13867 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271559.0 ave 271559 max 271559 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271559 Ave neighs/atom = 126.65998 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 = 10 26 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) = 8.192 | 8.192 | 8.192 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9497.8749 0 -9497.8749 3.4895247 Loop time of 2.519e-06 on 1 procs for 0 steps with 2144 atoms 158.8% 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 | | 2.519e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13813.0 ave 13813 max 13813 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271067.0 ave 271067 max 271067 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 = 271067 Ave neighs/atom = 126.43050 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) = 8.192 | 8.192 | 8.192 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 -9497.8749 -9497.8749 40.868896 115.47043 4.9824181 3.4895247 3.4895247 -49.147796 100.50899 -40.892621 2.3334225 981.40292 Loop time of 2.948e-06 on 1 procs for 0 steps with 2144 atoms 237.4% 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 | | 2.948e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13813.0 ave 13813 max 13813 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271067.0 ave 271067 max 271067 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 542134.0 ave 542134 max 542134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 542134 Ave neighs/atom = 252.86101 Neighbor list builds = 0 Dangerous builds = 0 2144 -9497.87487161644 eV 2.33342245329774 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08