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 -39.287075 0) to (27.780157 39.287075 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9023807 6.1626784 5.5012908 Created 408 atoms using lattice units in orthogonal box = (0 -39.287075 0) to (27.780157 39.287075 5.5012908) create_atoms CPU = 0.000 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9023807 6.1626784 5.5012908 Created 410 atoms using lattice units in orthogonal box = (0 -39.287075 0) to (27.780157 39.287075 5.5012908) create_atoms CPU = 0.000 seconds 410 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 = 7 18 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 0 atoms, new total = 818 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 = 7 18 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) = 7.245 | 7.245 | 7.245 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2667.6794 0 -2667.6794 181117.01 101 0 -3163.283 0 -3163.283 17591.381 Loop time of 0.855799 on 1 procs for 101 steps with 818 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 = -2667.679420057 -3163.28031308176 -3163.28297452008 Force two-norm initial, final = 642.75597 0.19665715 Force max component initial, final = 158.18878 0.050363528 Final line search alpha, max atom move = 1 0.050363528 Iterations, force evaluations = 101 195 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84723 | 0.84723 | 0.84723 | 0.0 | 99.00 Neigh | 0.0018773 | 0.0018773 | 0.0018773 | 0.0 | 0.22 Comm | 0.0042671 | 0.0042671 | 0.0042671 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002429 | | | 0.28 Nlocal: 818 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6181 ave 6181 max 6181 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 = 99.442543 Neighbor list builds = 1 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 : 101 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.247 | 7.247 | 7.247 Mbytes Step Temp E_pair E_mol TotEng Press Volume 101 0 -3163.283 0 -3163.283 17591.381 12008.23 109 0 -3164.0483 0 -3164.0483 -406.99175 12113.924 Loop time of 0.0461184 on 1 procs for 8 steps with 818 atoms 97.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3163.28297452008 -3164.04674181496 -3164.04833432918 Force two-norm initial, final = 238.93463 6.3223299 Force max component initial, final = 185.36347 4.8570965 Final line search alpha, max atom move = 0.00012644898 0.0006141749 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.044986 | 0.044986 | 0.044986 | 0.0 | 97.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025288 | 0.00025288 | 0.00025288 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008793 | | | 1.91 Nlocal: 818 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6205 ave 6205 max 6205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81330 ave 81330 max 81330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81330 Ave neighs/atom = 99.425428 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 = 7 18 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) = 6.879 | 6.879 | 6.879 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3164.0483 0 -3164.0483 -406.99175 Loop time of 4.91e-07 on 1 procs for 0 steps with 818 atoms 203.7% 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: 818 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6187 ave 6187 max 6187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81180 ave 81180 max 81180 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 = 81180 Ave neighs/atom = 99.242054 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) = 6.879 | 6.879 | 6.879 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 -3164.0483 -3164.0483 27.834404 79.155705 5.4982022 -406.99175 -406.99175 -643.64955 -48.156311 -529.1694 2.5464033 814.61568 Loop time of 5e-07 on 1 procs for 0 steps with 818 atoms 400.0% 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 | | 5e-07 | | |100.00 Nlocal: 818 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6187 ave 6187 max 6187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81180 ave 81180 max 81180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 162360 ave 162360 max 162360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162360 Ave neighs/atom = 198.48411 Neighbor list builds = 0 Dangerous builds = 0 818 -3164.04833432918 eV 2.54640332489594 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00