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 -37.626017 0.0000000) to (26.605612 37.626017 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1344163 5.9409501 4.9836877 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.626017 0.0000000) to (26.605612 37.626017 4.9836877) create_atoms CPU = 0.002 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1344163 5.9409501 4.9836877 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.626017 0.0000000) to (26.605612 37.626017 4.9836877) create_atoms CPU = 0.001 seconds 458 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 = 6 17 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 4 atoms, new total = 910 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 = 6 17 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) = 7.695 | 7.695 | 7.695 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3312.7704 0 -3312.7704 170341.95 71 0 -4020.7584 0 -4020.7584 8741.0455 Loop time of 2.40285 on 1 procs for 71 steps with 910 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3312.77040136087 -4020.75466291944 -4020.75835826979 Force two-norm initial, final = 1160.0126 0.22191910 Force max component initial, final = 283.41942 0.052181740 Final line search alpha, max atom move = 1.0000000 0.052181740 Iterations, force evaluations = 71 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3697 | 2.3697 | 2.3697 | 0.0 | 98.62 Neigh | 0.012845 | 0.012845 | 0.012845 | 0.0 | 0.53 Comm | 0.012065 | 0.012065 | 0.012065 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008202 | | | 0.34 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7550.00 ave 7550 max 7550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114374.0 ave 114374 max 114374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114374 Ave neighs/atom = 125.68571 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 : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.695 | 7.695 | 7.695 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4020.7584 0 -4020.7584 8741.0455 9977.9729 76 0 -4020.9712 0 -4020.9712 142.66365 10024.447 Loop time of 0.117677 on 1 procs for 5 steps with 910 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 = -4020.75835826979 -4020.97056719989 -4020.9712402997 Force two-norm initial, final = 107.68352 2.2164427 Force max component initial, final = 94.727605 2.1596966 Final line search alpha, max atom move = 0.00022903276 0.00049464128 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11542 | 0.11542 | 0.11542 | 0.0 | 98.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042689 | 0.00042689 | 0.00042689 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001826 | | | 1.55 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7550.00 ave 7550 max 7550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114376.0 ave 114376 max 114376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114376 Ave neighs/atom = 125.68791 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 = 6 17 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) = 7.327 | 7.327 | 7.327 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4020.9712 0 -4020.9712 142.66365 Loop time of 2.061e-06 on 1 procs for 0 steps with 910 atoms 145.6% 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 | | 2.061e-06 | | |100.00 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7532.00 ave 7532 max 7532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113900.0 ave 113900 max 113900 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 = 113900 Ave neighs/atom = 125.16484 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) = 7.327 | 7.327 | 7.327 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 -4020.9712 -4020.9712 26.631283 75.555978 4.9819516 142.66365 142.66365 31.996254 346.57183 49.422854 2.2911966 637.42062 Loop time of 2.441e-06 on 1 procs for 0 steps with 910 atoms 204.8% 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 | | 2.441e-06 | | |100.00 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7532.00 ave 7532 max 7532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113900.0 ave 113900 max 113900 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227800.0 ave 227800 max 227800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227800 Ave neighs/atom = 250.32967 Neighbor list builds = 0 Dangerous builds = 0 910 -4020.9712402997 eV 2.29119656784924 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02