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 -77.994259 0) to (45.030006 77.994259 6.7376777) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0488068 6.2084982 6.7376777 Created 1608 atoms using lattice units in orthogonal box = (0 -77.994259 0) to (45.030006 77.994259 6.7376777) create_atoms CPU = 0.002 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0488068 6.2084982 6.7376777 Created 1610 atoms using lattice units in orthogonal box = (0 -77.994259 0) to (45.030006 77.994259 6.7376777) create_atoms CPU = 0.001 seconds 1610 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 36 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 2 atoms, new total = 3216 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 36 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) = 15.64 | 15.64 | 15.64 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9828.5765 0 -9828.5765 118110.74 108 0 -12470.345 0 -12470.345 6645.885 Loop time of 3.24228 on 1 procs for 108 steps with 3216 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 = -9828.57653405501 -12470.3339205228 -12470.3448650569 Force two-norm initial, final = 2052.03 0.45317395 Force max component initial, final = 444.56275 0.10046536 Final line search alpha, max atom move = 1 0.10046536 Iterations, force evaluations = 108 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2089 | 3.2089 | 3.2089 | 0.0 | 98.97 Neigh | 0.0141 | 0.0141 | 0.0141 | 0.0 | 0.43 Comm | 0.010251 | 0.010251 | 0.010251 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009038 | | | 0.28 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13505 ave 13505 max 13505 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 320612 ave 320612 max 320612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320612 Ave neighs/atom = 99.692786 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 : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.64 | 15.64 | 15.64 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -12470.345 0 -12470.345 6645.885 47326.553 113 0 -12470.964 0 -12470.964 -13.155491 47484.019 Loop time of 0.134026 on 1 procs for 5 steps with 3216 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 = -12470.3448650569 -12470.9604862574 -12470.9642687259 Force two-norm initial, final = 373.87429 4.1268123 Force max component initial, final = 314.292 3.5421429 Final line search alpha, max atom move = 2.6155498e-05 9.2646511e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13199 | 0.13199 | 0.13199 | 0.0 | 98.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038774 | 0.00038774 | 0.00038774 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001652 | | | 1.23 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13833 ave 13833 max 13833 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 320320 ave 320320 max 320320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320320 Ave neighs/atom = 99.60199 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 36 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) = 14.53 | 14.53 | 14.53 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12470.964 0 -12470.964 -13.155491 Loop time of 6.72e-07 on 1 procs for 0 steps with 3216 atoms 297.6% 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 | | 6.72e-07 | | |100.00 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13906 ave 13906 max 13906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 320130 ave 320130 max 320130 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 = 320130 Ave neighs/atom = 99.54291 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) = 14.53 | 14.53 | 14.53 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 -12470.964 -12470.964 45.049718 156.62927 6.7294948 -13.155491 -13.155491 -119.56912 12.795076 67.30757 2.5113721 1311.8325 Loop time of 3.5e-07 on 1 procs for 0 steps with 3216 atoms 857.1% 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 | | 3.5e-07 | | |100.00 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13906 ave 13906 max 13906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 320130 ave 320130 max 320130 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 640260 ave 640260 max 640260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 640260 Ave neighs/atom = 199.08582 Neighbor list builds = 0 Dangerous builds = 0 3216 -12470.9642687259 eV 2.51137212781336 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03