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 (22.682403 48.116643 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6712951 6.6042452 5.5012908 Created 408 atoms using lattice units in orthogonal box = (0 -48.116643 0) to (22.682403 48.116643 5.5012908) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6712951 6.6042452 5.5012908 Created 412 atoms using lattice units in orthogonal box = (0 -48.116643 0) to (22.682403 48.116643 5.5012908) create_atoms CPU = 0.000 seconds 412 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 22 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 4 atoms, new total = 816 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 = 6 22 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) = 7.268 | 7.268 | 7.268 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1794.8687 0 -1794.8687 212153.42 41 0 -3162.6446 0 -3162.6446 6837.5612 Loop time of 0.289345 on 1 procs for 41 steps with 816 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 = -1794.8687445577 -3162.64230346998 -3162.64462313854 Force two-norm initial, final = 1556.69 0.1634741 Force max component initial, final = 325.89167 0.015755305 Final line search alpha, max atom move = 1 0.015755305 Iterations, force evaluations = 41 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28306 | 0.28306 | 0.28306 | 0.0 | 97.83 Neigh | 0.0036626 | 0.0036626 | 0.0036626 | 0.0 | 1.27 Comm | 0.0016338 | 0.0016338 | 0.0016338 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009855 | | | 0.34 Nlocal: 816 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6474 ave 6474 max 6474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81376 ave 81376 max 81376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81376 Ave neighs/atom = 99.72549 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.27 | 7.27 | 7.27 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -3162.6446 0 -3162.6446 6837.5612 12008.23 45 0 -3162.7675 0 -3162.7675 280.20008 12047.745 Loop time of 0.0256112 on 1 procs for 4 steps with 816 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 = -3162.64462313854 -3162.76668220157 -3162.76753838652 Force two-norm initial, final = 92.566111 3.8658597 Force max component initial, final = 69.484066 2.8263244 Final line search alpha, max atom move = 0.00022713833 0.0006419666 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.025024 | 0.025024 | 0.025024 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013078 | 0.00013078 | 0.00013078 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004561 | | | 1.78 Nlocal: 816 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6474 ave 6474 max 6474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81344 ave 81344 max 81344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81344 Ave neighs/atom = 99.686275 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 = 6 22 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) = 6.901 | 6.901 | 6.901 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3162.7675 0 -3162.7675 280.20008 Loop time of 6.62e-07 on 1 procs for 0 steps with 816 atoms 151.1% 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 | | 6.62e-07 | | |100.00 Nlocal: 816 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6474 ave 6474 max 6474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81244 ave 81244 max 81244 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 = 81244 Ave neighs/atom = 99.563725 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) = 6.901 | 6.901 | 6.901 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 -3162.7675 -3162.7675 22.711017 96.506427 5.4968381 280.20008 280.20008 318.3123 376.92723 145.3607 2.6269554 614.89326 Loop time of 4.6e-07 on 1 procs for 0 steps with 816 atoms 217.4% 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 | | 4.6e-07 | | |100.00 Nlocal: 816 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6474 ave 6474 max 6474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81244 ave 81244 max 81244 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 162488 ave 162488 max 162488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162488 Ave neighs/atom = 199.12745 Neighbor list builds = 0 Dangerous builds = 0 816 -3162.76753838652 eV 2.62695538228565 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00