LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -63.682046 0) to (45.030006 63.682046 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7208965 6.1781089 5.5012908 Created 1072 atoms using lattice units in orthogonal box = (0 -63.682046 0) to (45.030006 63.682046 5.5012908) create_atoms CPU = 0.001 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7208965 6.1781089 5.5012908 Created 1080 atoms using lattice units in orthogonal box = (0 -63.682046 0) to (45.030006 63.682046 5.5012908) create_atoms CPU = 0.001 seconds 1080 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 = 11 29 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 8 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:187) 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 = 11 29 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) = 8.497 | 8.497 | 8.497 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5866.7155 0 -5866.7155 150272.21 98 0 -8318.9657 0 -8318.9657 4131.531 Loop time of 2.01757 on 1 procs for 98 steps with 2144 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 = -5866.7154794081 -8318.95835971587 -8318.96567073422 Force two-norm initial, final = 2048.7693 0.28334648 Force max component initial, final = 291.28293 0.029973602 Final line search alpha, max atom move = 1 0.029973602 Iterations, force evaluations = 98 180 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9936 | 1.9936 | 1.9936 | 0.0 | 98.81 Neigh | 0.0091285 | 0.0091285 | 0.0091285 | 0.0 | 0.45 Comm | 0.0084466 | 0.0084466 | 0.0084466 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006442 | | | 0.32 Nlocal: 2144 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12324 ave 12324 max 12324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 213512 ave 213512 max 213512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213512 Ave neighs/atom = 99.585821 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.497 | 8.497 | 8.497 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -8318.9657 0 -8318.9657 4131.531 31551.035 101 0 -8319.1162 0 -8319.1162 165.98902 31614.018 Loop time of 0.0558761 on 1 procs for 3 steps with 2144 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8318.96567073422 -8319.11417809345 -8319.11619128476 Force two-norm initial, final = 153.52741 9.5270452 Force max component initial, final = 122.91788 6.7274676 Final line search alpha, max atom move = 5.7419156e-05 0.00038628552 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.054945 | 0.054945 | 0.054945 | 0.0 | 98.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019402 | 0.00019402 | 0.00019402 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007368 | | | 1.32 Nlocal: 2144 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11494 ave 11494 max 11494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 213728 ave 213728 max 213728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213728 Ave neighs/atom = 99.686567 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 = 11 29 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) = 8.122 | 8.122 | 8.122 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8319.1162 0 -8319.1162 165.98902 Loop time of 6.61e-07 on 1 procs for 0 steps with 2144 atoms 151.3% 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 | | 6.61e-07 | | |100.00 Nlocal: 2144 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11484 ave 11484 max 11484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 213672 ave 213672 max 213672 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213672 Ave neighs/atom = 99.660448 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.122 | 8.122 | 8.122 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 -8319.1162 -8319.1162 45.118451 127.46722 5.4970158 165.98902 165.98902 341.61305 306.82363 -150.46961 2.5807299 1152.6068 Loop time of 4.91e-07 on 1 procs for 0 steps with 2144 atoms 407.3% 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 | | 4.91e-07 | | |100.00 Nlocal: 2144 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11484 ave 11484 max 11484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 213672 ave 213672 max 213672 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 427344 ave 427344 max 427344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 427344 Ave neighs/atom = 199.3209 Neighbor list builds = 0 Dangerous builds = 0 2144 -8319.11619128476 eV 2.58072989594252 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02