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 -37.460627 0.0000000) to (37.460627 37.460627 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9726497 4.9726497 3.5239994 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -37.460627 0.0000000) to (37.460627 37.460627 3.5239994) create_atoms CPU = 0.001 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9726497 4.9726497 3.5239994 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -37.460627 0.0000000) to (37.460627 37.460627 3.5239994) create_atoms CPU = 0.001 seconds 454 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 = 9 17 1 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 0 atoms, new total = 906 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 = 9 17 1 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) = 7.673 | 7.673 | 7.673 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3482.6866 0 -3482.6866 193790.34 97 0 -4011.2858 0 -4011.2858 10123.881 Loop time of 2.86779 on 1 procs for 97 steps with 906 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 = -3482.68662498546 -4011.28253613608 -4011.28580130024 Force two-norm initial, final = 832.97593 0.20464243 Force max component initial, final = 179.30327 0.026272222 Final line search alpha, max atom move = 1.0000000 0.026272222 Iterations, force evaluations = 97 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8255 | 2.8255 | 2.8255 | 0.0 | 98.52 Neigh | 0.01621 | 0.01621 | 0.01621 | 0.0 | 0.57 Comm | 0.016411 | 0.016411 | 0.016411 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009707 | | | 0.34 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9000.00 ave 9000 max 9000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117636.0 ave 117636 max 117636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117636 Ave neighs/atom = 129.84106 Neighbor list builds = 3 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 : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.673 | 7.673 | 7.673 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -4011.2858 0 -4011.2858 10123.881 9890.4469 103 0 -4011.618 0 -4011.618 184.95594 9943.1092 Loop time of 0.136491 on 1 procs for 6 steps with 906 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 = -4011.28580130024 -4011.61733992597 -4011.61804891985 Force two-norm initial, final = 130.47221 2.3700015 Force max component initial, final = 115.68618 2.0611641 Final line search alpha, max atom move = 0.00027257153 0.00056181464 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13373 | 0.13373 | 0.13373 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054836 | 0.00054836 | 0.00054836 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002213 | | | 1.62 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8994.00 ave 8994 max 8994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117146.0 ave 117146 max 117146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117146 Ave neighs/atom = 129.30022 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 = 9 17 1 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) = 7.305 | 7.305 | 7.305 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4011.618 0 -4011.618 184.95594 Loop time of 1.942e-06 on 1 procs for 0 steps with 906 atoms 206.0% 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 | | 1.942e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8982.00 ave 8982 max 8982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115942.0 ave 115942 max 115942 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 = 115942 Ave neighs/atom = 127.97130 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) = 7.305 | 7.305 | 7.305 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 -4011.618 -4011.618 37.415797 75.305055 3.5289303 184.95594 184.95594 179.37536 333.82573 41.666723 2.2494871 135.39977 Loop time of 2.076e-06 on 1 procs for 0 steps with 906 atoms 240.8% 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 | | 2.076e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8982.00 ave 8982 max 8982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115942.0 ave 115942 max 115942 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 231884.0 ave 231884 max 231884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231884 Ave neighs/atom = 255.94260 Neighbor list builds = 0 Dangerous builds = 0 906 -4011.61804891985 eV 2.24948713932603 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03