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 -40.793242 0.0000000) to (28.845178 40.793242 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5968256 6.0885436 4.9836877 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -40.793242 0.0000000) to (28.845178 40.793242 4.9836877) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5968256 6.0885436 4.9836877 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -40.793242 0.0000000) to (28.845178 40.793242 4.9836877) create_atoms CPU = 0.001 seconds 538 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 = 7 19 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 = 1070 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 = 7 19 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) = 7.762 | 7.762 | 7.762 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4160.9089 0 -4160.9089 126001.7 67 0 -4739.4982 0 -4739.4982 1323.3005 Loop time of 2.74023 on 1 procs for 67 steps with 1070 atoms 97.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4160.90885610359 -4739.4939862265 -4739.4982173339 Force two-norm initial, final = 1013.4578 0.22907013 Force max component initial, final = 311.94935 0.057733866 Final line search alpha, max atom move = 1.0000000 0.057733866 Iterations, force evaluations = 67 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7112 | 2.7112 | 2.7112 | 0.0 | 98.94 Neigh | 0.0075117 | 0.0075117 | 0.0075117 | 0.0 | 0.27 Comm | 0.011831 | 0.011831 | 0.011831 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009688 | | | 0.35 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8404.00 ave 8404 max 8404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136936.0 ave 136936 max 136936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136936 Ave neighs/atom = 127.97757 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.762 | 7.762 | 7.762 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -4739.4982 0 -4739.4982 1323.3005 11728.495 71 0 -4739.6283 0 -4739.6283 -94.336916 11737.328 Loop time of 0.123198 on 1 procs for 4 steps with 1070 atoms 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4739.4982173339 -4739.62788120671 -4739.62831271847 Force two-norm initial, final = 67.915185 1.2542657 Force max component initial, final = 59.043689 0.87318322 Final line search alpha, max atom move = 0.00035682600 0.00031157448 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12109 | 0.12109 | 0.12109 | 0.0 | 98.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041516 | 0.00041516 | 0.00041516 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001697 | | | 1.38 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8398.00 ave 8398 max 8398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135956.0 ave 135956 max 135956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135956 Ave neighs/atom = 127.06168 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 = 7 19 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) = 7.394 | 7.394 | 7.394 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4739.6283 0 -4739.6283 -94.336916 Loop time of 2.301e-06 on 1 procs for 0 steps with 1070 atoms 217.3% 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 | | 2.301e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8380.00 ave 8380 max 8380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135724.0 ave 135724 max 135724 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 = 135724 Ave neighs/atom = 126.84486 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) = 7.394 | 7.394 | 7.394 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 -4739.6283 -4739.6283 28.773664 81.829651 4.9849796 -94.336916 -94.336916 -118.89633 -82.644149 -81.470275 2.3057673 500.57707 Loop time of 2.258e-06 on 1 procs for 0 steps with 1070 atoms 221.4% 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 | | 2.258e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8380.00 ave 8380 max 8380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135724.0 ave 135724 max 135724 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 271448.0 ave 271448 max 271448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271448 Ave neighs/atom = 253.68972 Neighbor list builds = 0 Dangerous builds = 0 1070 -4739.62831271847 eV 2.30576729570334 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03