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 -50.336303 0.0000000) to (35.590649 50.336303 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5828469 4.4411275 4.9836877 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -50.336303 0.0000000) to (35.590649 50.336303 4.9836877) create_atoms CPU = 0.002 seconds 822 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5828469 4.4411275 4.9836877 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -50.336303 0.0000000) to (35.590649 50.336303 4.9836877) create_atoms CPU = 0.001 seconds 822 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 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 20 atoms, new total = 1624 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 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) = 8.384 | 8.384 | 8.384 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7112.32 0 -7112.32 25593.523 36 0 -7186.4276 0 -7186.4276 -1255.2908 Loop time of 2.17988 on 1 procs for 36 steps with 1624 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 = -7112.31997815789 -7186.42143881429 -7186.42759290937 Force two-norm initial, final = 119.86063 0.27710047 Force max component initial, final = 26.444555 0.023702342 Final line search alpha, max atom move = 0.90166445 0.021371559 Iterations, force evaluations = 36 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1487 | 2.1487 | 2.1487 | 0.0 | 98.57 Neigh | 0.012627 | 0.012627 | 0.012627 | 0.0 | 0.58 Comm | 0.010836 | 0.010836 | 0.010836 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007681 | | | 0.35 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11942.0 ave 11942 max 11942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203322.0 ave 203322 max 203322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203322 Ave neighs/atom = 125.19828 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.384 | 8.384 | 8.384 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -7186.4276 0 -7186.4276 -1255.2908 17856.57 37 0 -7186.4301 0 -7186.4301 -1002.115 17854.153 Loop time of 0.0872101 on 1 procs for 1 steps with 1624 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 = -7186.42759290937 -7186.42759290937 -7186.43012662498 Force two-norm initial, final = 12.292831 1.6057124 Force max component initial, final = 10.474681 1.3598000 Final line search alpha, max atom move = 9.5468304e-05 0.00012981780 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.085984 | 0.085984 | 0.085984 | 0.0 | 98.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026426 | 0.00026426 | 0.00026426 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000962 | | | 1.10 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11942.0 ave 11942 max 11942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203240.0 ave 203240 max 203240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203240 Ave neighs/atom = 125.14778 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 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) = 8.014 | 8.014 | 8.014 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7186.4301 0 -7186.4301 -1002.115 Loop time of 2.183e-06 on 1 procs for 0 steps with 1624 atoms 183.2% 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 | | 2.183e-06 | | |100.00 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11942.0 ave 11942 max 11942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203234.0 ave 203234 max 203234 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 = 203234 Ave neighs/atom = 125.14409 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) = 8.014 | 8.014 | 8.014 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 -7186.4301 -7186.4301 35.598298 100.67261 4.9819425 -1002.115 -1002.115 122.05047 -3200.7602 72.364822 2.3576312 453.44882 Loop time of 2.326e-06 on 1 procs for 0 steps with 1624 atoms 258.0% 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 | | 2.326e-06 | | |100.00 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11942.0 ave 11942 max 11942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203234.0 ave 203234 max 203234 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 406468.0 ave 406468 max 406468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 406468 Ave neighs/atom = 250.28818 Neighbor list builds = 0 Dangerous builds = 0 1624 -7186.43012662498 eV 2.35763123905727 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02