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 -51.606683 0) to (18.245718 51.606683 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6348064 5.8643957 5.5012908 Created 352 atoms using lattice units in orthogonal box = (0 -51.606683 0) to (18.245718 51.606683 5.5012908) create_atoms CPU = 0.000 seconds 352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6348064 5.8643957 5.5012908 Created 360 atoms using lattice units in orthogonal box = (0 -51.606683 0) to (18.245718 51.606683 5.5012908) create_atoms CPU = 0.000 seconds 360 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 = 5 24 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 8 atoms, new total = 704 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 = 5 24 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) = 7.247 | 7.247 | 7.247 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2727.1874 0 -2727.1874 7853.7223 12 0 -2733.7647 0 -2733.7647 3094.0109 Loop time of 0.0837072 on 1 procs for 12 steps with 704 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 = -2727.18736188972 -2733.76239343741 -2733.76470083557 Force two-norm initial, final = 24.451269 0.10999922 Force max component initial, final = 4.3186681 0.0094078232 Final line search alpha, max atom move = 1 0.0094078232 Iterations, force evaluations = 12 23 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.082827 | 0.082827 | 0.082827 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054893 | 0.00054893 | 0.00054893 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000331 | | | 0.40 Nlocal: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6219 ave 6219 max 6219 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70480 ave 70480 max 70480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70480 Ave neighs/atom = 100.11364 Neighbor list builds = 0 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 : 12 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 12 0 -2733.7647 0 -2733.7647 3094.0109 10360.041 17 0 -2733.8682 0 -2733.8682 415.84082 10373.419 Loop time of 0.0253498 on 1 procs for 5 steps with 704 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 = -2733.76470083558 -2733.8660563413 -2733.86823262777 Force two-norm initial, final = 49.261525 6.0283619 Force max component initial, final = 48.301863 5.7696969 Final line search alpha, max atom move = 0.00012914717 0.00074514 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.024699 | 0.024699 | 0.024699 | 0.0 | 97.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014597 | 0.00014597 | 0.00014597 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000505 | | | 1.99 Nlocal: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6219 ave 6219 max 6219 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70224 ave 70224 max 70224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70224 Ave neighs/atom = 99.75 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 = 5 24 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) = 6.878 | 6.878 | 6.878 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2733.8682 0 -2733.8682 415.84082 Loop time of 8.32e-07 on 1 procs for 0 steps with 704 atoms 120.2% 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 | | 8.32e-07 | | |100.00 Nlocal: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6219 ave 6219 max 6219 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70224 ave 70224 max 70224 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 = 70224 Ave neighs/atom = 99.75 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) = 6.878 | 6.878 | 6.878 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 -2733.8682 -2733.8682 18.229479 103.63896 5.490661 415.84082 415.84082 244.54541 894.80527 108.17178 2.6051089 259.73413 Loop time of 4.51e-07 on 1 procs for 0 steps with 704 atoms 443.5% 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 | | 4.51e-07 | | |100.00 Nlocal: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6219 ave 6219 max 6219 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70224 ave 70224 max 70224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 140448 ave 140448 max 140448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140448 Ave neighs/atom = 199.5 Neighbor list builds = 0 Dangerous builds = 0 704 -2733.86823262777 eV 2.60510885318145 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00