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 -49.590591 0.0000000) to (11.687784 49.590591 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3126290 6.0105536 4.9836877 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -49.590591 0.0000000) to (11.687784 49.590591 4.9836877) create_atoms CPU = 0.001 seconds 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3126290 6.0105536 4.9836877 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -49.590591 0.0000000) to (11.687784 49.590591 4.9836877) create_atoms CPU = 0.001 seconds 266 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 = 3 23 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 = 524 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 = 3 23 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 -2305.5098 0 -2305.5098 10888.864 66 0 -2319.1519 0 -2319.1519 -5881.7593 Loop time of 1.15577 on 1 procs for 66 steps with 524 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2305.50977915775 -2319.14998533976 -2319.15192561923 Force two-norm initial, final = 47.965339 0.15755473 Force max component initial, final = 18.528166 0.031353453 Final line search alpha, max atom move = 1.0000000 0.031353453 Iterations, force evaluations = 66 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1417 | 1.1417 | 1.1417 | 0.0 | 98.78 Neigh | 0.0032515 | 0.0032515 | 0.0032515 | 0.0 | 0.28 Comm | 0.0068898 | 0.0068898 | 0.0068898 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003943 | | | 0.34 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6921.00 ave 6921 max 6921 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65534.0 ave 65534 max 65534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65534 Ave neighs/atom = 125.06489 Neighbor list builds = 1 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 : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.245 | 7.245 | 7.245 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -2319.1519 0 -2319.1519 -5881.7593 5777.1317 68 0 -2319.1657 0 -2319.1657 -2552.2533 5766.6292 Loop time of 0.036903 on 1 procs for 2 steps with 524 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 = -2319.15192561923 -2319.16472444919 -2319.16573638653 Force two-norm initial, final = 19.958250 1.2609064 Force max component initial, final = 17.180222 1.1084318 Final line search alpha, max atom move = 0.00029325619 0.00032505450 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.036049 | 0.036049 | 0.036049 | 0.0 | 97.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019238 | 0.00019238 | 0.00019238 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006621 | | | 1.79 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6921.00 ave 6921 max 6921 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65440.0 ave 65440 max 65440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65440 Ave neighs/atom = 124.88550 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 = 3 23 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) = 6.876 | 6.876 | 6.876 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2319.1657 0 -2319.1657 -2552.2533 Loop time of 1.847e-06 on 1 procs for 0 steps with 524 atoms 162.4% 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 | | 1.847e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6921.00 ave 6921 max 6921 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65472.0 ave 65472 max 65472 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 = 65472 Ave neighs/atom = 124.94656 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) = 6.876 | 6.876 | 6.876 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 -2319.1657 -2319.1657 11.670621 99.181182 4.9819431 -2552.2533 -2552.2533 160.44817 -8125.0624 307.85433 2.3043075 252.88717 Loop time of 2.113e-06 on 1 procs for 0 steps with 524 atoms 142.0% 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 | | 2.113e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6921.00 ave 6921 max 6921 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65472.0 ave 65472 max 65472 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 130944.0 ave 130944 max 130944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130944 Ave neighs/atom = 249.89313 Neighbor list builds = 0 Dangerous builds = 0 524 -2319.16573638653 eV 2.30430748423344 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01