LAMMPS (30 Jul 2021) 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 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created orthogonal box = (0.0000000 -45.132736 0.0000000) to (31.911172 45.132736 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4482488 6.0539187 4.9836877 Created 659 atoms using lattice units in orthogonal box = (0.0000000 -45.132736 0.0000000) to (31.911172 45.132736 4.9836877) create_atoms CPU = 0.002 seconds 659 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4482488 6.0539187 4.9836877 Created 659 atoms using lattice units in orthogonal box = (0.0000000 -45.132736 0.0000000) to (31.911172 45.132736 4.9836877) create_atoms CPU = 0.001 seconds 659 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 = 8 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 11 atoms, new total = 1307 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:189) 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 = 8 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) = 7.872 | 7.872 | 7.872 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5736.3277 0 -5736.3277 19288.505 57 0 -5784.5912 0 -5784.5912 434.75682 Loop time of 2.39789 on 1 procs for 57 steps with 1307 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5736.327706309 -5784.58577601811 -5784.59121155052 Force two-norm initial, final = 71.488996 0.27102155 Force max component initial, final = 14.267043 0.089270748 Final line search alpha, max atom move = 1.0000000 0.089270748 Iterations, force evaluations = 57 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3647 | 2.3647 | 2.3647 | 0.0 | 98.62 Neigh | 0.015298 | 0.015298 | 0.015298 | 0.0 | 0.64 Comm | 0.010603 | 0.010603 | 0.010603 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007271 | | | 0.30 Nlocal: 1307.00 ave 1307 max 1307 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10250.0 ave 10250 max 10250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164399.0 ave 164399 max 164399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164399 Ave neighs/atom = 125.78347 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.872 | 7.872 | 7.872 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -5784.5912 0 -5784.5912 434.75682 14355.398 58 0 -5784.5958 0 -5784.5958 1508.9023 14347.024 Loop time of 0.0674339 on 1 procs for 1 steps with 1307 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5784.59121155053 -5784.59121155053 -5784.59575972297 Force two-norm initial, final = 16.142039 6.6276290 Force max component initial, final = 16.127805 6.6162557 Final line search alpha, max atom move = 6.2004720e-05 0.00041023908 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.066484 | 0.066484 | 0.066484 | 0.0 | 98.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021466 | 0.00021466 | 0.00021466 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007353 | | | 1.09 Nlocal: 1307.00 ave 1307 max 1307 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10242.0 ave 10242 max 10242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164275.0 ave 164275 max 164275 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164275 Ave neighs/atom = 125.68860 Neighbor list builds = 0 Dangerous builds = 0 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 = 8 21 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) = 7.504 | 7.504 | 7.504 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5784.5958 0 -5784.5958 1508.9023 Loop time of 2.157e-06 on 1 procs for 0 steps with 1307 atoms 139.1% 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 | | 2.157e-06 | | |100.00 Nlocal: 1307.00 ave 1307 max 1307 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10242.0 ave 10242 max 10242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164309.0 ave 164309 max 164309 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164309 Ave neighs/atom = 125.71461 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.504 | 7.504 | 7.504 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 -5784.5958 -5784.5958 31.893247 90.265472 4.9835799 1508.9023 1508.9023 -30.873252 3818.7385 738.84175 2.2814467 603.99213 Loop time of 2.366e-06 on 1 procs for 0 steps with 1307 atoms 211.3% 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 | | 2.366e-06 | | |100.00 Nlocal: 1307.00 ave 1307 max 1307 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10242.0 ave 10242 max 10242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164309.0 ave 164309 max 164309 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 328618.0 ave 328618 max 328618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328618 Ave neighs/atom = 251.42923 Neighbor list builds = 0 Dangerous builds = 0 1307 -5784.59575972297 eV 2.28144665227124 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02