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 -48.116643 0) to (16.038881 48.116643 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.717318 4.717318 3.8900001 Created 204 atoms using lattice units in orthogonal box = (0 -48.116643 0) to (16.038881 48.116643 3.8900001) create_atoms CPU = 0.000 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.717318 4.717318 3.8900001 Created 206 atoms using lattice units in orthogonal box = (0 -48.116643 0) to (16.038881 48.116643 3.8900001) create_atoms CPU = 0.000 seconds 206 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 = 4 22 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 = 408 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 = 4 22 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) = 7.097 | 7.097 | 7.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -983.31622 0 -983.31622 198434.1 53 0 -1578.7476 0 -1578.7476 11963.736 Loop time of 0.206982 on 1 procs for 53 steps with 408 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 = -983.316223276267 -1578.74654790052 -1578.74757938571 Force two-norm initial, final = 1002.8401 0.1197155 Force max component initial, final = 281.47251 0.027948745 Final line search alpha, max atom move = 1 0.027948745 Iterations, force evaluations = 53 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20212 | 0.20212 | 0.20212 | 0.0 | 97.65 Neigh | 0.0020625 | 0.0020625 | 0.0020625 | 0.0 | 1.00 Comm | 0.0020056 | 0.0020056 | 0.0020056 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007937 | | | 0.38 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5712 ave 5712 max 5712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40610 ave 40610 max 40610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40610 Ave neighs/atom = 99.534314 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 : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.097 | 7.097 | 7.097 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1578.7476 0 -1578.7476 11963.736 6004.1149 63 0 -1578.9711 0 -1578.9711 0.6340862 6040.0305 Loop time of 0.0310948 on 1 procs for 10 steps with 408 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 = -1578.74757938571 -1578.97097576176 -1578.971131118 Force two-norm initial, final = 80.929491 0.47691668 Force max component initial, final = 63.392054 0.18743563 Final line search alpha, max atom move = 0.0021631649 0.00040545417 Iterations, force evaluations = 10 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.029946 | 0.029946 | 0.029946 | 0.0 | 96.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002715 | 0.0002715 | 0.0002715 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008777 | | | 2.82 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5712 ave 5712 max 5712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40596 ave 40596 max 40596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40596 Ave neighs/atom = 99.5 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 = 4 22 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) = 6.728 | 6.728 | 6.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1578.9711 0 -1578.9711 0.6340862 Loop time of 4.31e-07 on 1 procs for 0 steps with 408 atoms 232.0% 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 | | 4.31e-07 | | |100.00 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5712 ave 5712 max 5712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40548 ave 40548 max 40548 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 = 40548 Ave neighs/atom = 99.382353 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) = 6.728 | 6.728 | 6.728 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 -1578.9711 -1578.9711 16.024185 97.063062 3.8833737 0.6340862 0.6340862 -49.673558 5.1418164 46.434 2.5505105 229.97551 Loop time of 3.81e-07 on 1 procs for 0 steps with 408 atoms 524.9% 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 | | 3.81e-07 | | |100.00 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5712 ave 5712 max 5712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40548 ave 40548 max 40548 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81096 ave 81096 max 81096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81096 Ave neighs/atom = 198.76471 Neighbor list builds = 0 Dangerous builds = 0 408 -1578.971131118 eV 2.55051050888303 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00