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 -46.680001 0) to (16.503873 46.680001 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5012908 6.4833334 5.5012908 Created 288 atoms using lattice units in orthogonal box = (0 -46.680001 0) to (16.503873 46.680001 5.5012908) create_atoms CPU = 0.000 seconds 288 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5012908 6.4833334 5.5012908 Created 292 atoms using lattice units in orthogonal box = (0 -46.680001 0) to (16.503873 46.680001 5.5012908) create_atoms CPU = 0.000 seconds 292 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 21 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 = 576 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 21 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) = 7.183 | 7.183 | 7.183 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1848.3556 0 -1848.3556 167326.92 59 0 -2230.3721 0 -2230.3721 10785.851 Loop time of 0.34255 on 1 procs for 59 steps with 576 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 = -1848.35558668785 -2230.36996422369 -2230.37205169016 Force two-norm initial, final = 604.11885 0.16236121 Force max component initial, final = 144.58143 0.025820072 Final line search alpha, max atom move = 1 0.025820072 Iterations, force evaluations = 59 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33798 | 0.33798 | 0.33798 | 0.0 | 98.66 Neigh | 0.0013655 | 0.0013655 | 0.0013655 | 0.0 | 0.40 Comm | 0.0021659 | 0.0021659 | 0.0021659 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001042 | | | 0.30 Nlocal: 576 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5474 ave 5474 max 5474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57304 ave 57304 max 57304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57304 Ave neighs/atom = 99.486111 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.183 | 7.183 | 7.183 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -2230.3721 0 -2230.3721 10785.851 8476.3975 65 0 -2230.5907 0 -2230.5907 24.293762 8522.063 Loop time of 0.0274029 on 1 procs for 6 steps with 576 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 = -2230.37205169016 -2230.59057209401 -2230.59074173012 Force two-norm initial, final = 103.88455 0.81429236 Force max component initial, final = 78.950552 0.72218831 Final line search alpha, max atom move = 0.00034164438 0.00024673158 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.026668 | 0.026668 | 0.026668 | 0.0 | 97.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001659 | 0.0001659 | 0.0001659 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005692 | | | 2.08 Nlocal: 576 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5483 ave 5483 max 5483 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57332 ave 57332 max 57332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57332 Ave neighs/atom = 99.534722 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 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) = 6.815 | 6.815 | 6.815 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2230.5907 0 -2230.5907 24.293762 Loop time of 6.41e-07 on 1 procs for 0 steps with 576 atoms 156.0% 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 | | 6.41e-07 | | |100.00 Nlocal: 576 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5483 ave 5483 max 5483 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57324 ave 57324 max 57324 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 = 57324 Ave neighs/atom = 99.520833 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) = 6.815 | 6.815 | 6.815 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 -2230.5907 -2230.5907 16.540212 93.780824 5.4940122 24.293762 24.293762 136.07279 -54.860929 -8.330575 2.5728301 424.8768 Loop time of 4.41e-07 on 1 procs for 0 steps with 576 atoms 226.8% 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 | | 4.41e-07 | | |100.00 Nlocal: 576 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5483 ave 5483 max 5483 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57324 ave 57324 max 57324 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114648 ave 114648 max 114648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114648 Ave neighs/atom = 199.04167 Neighbor list builds = 0 Dangerous builds = 0 576 -2230.59074173013 eV 2.57283006505404 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00