LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -44.010327 0) to (5.5012908 44.010327 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5012908 5.5012908 3.8900001 Created 64 atoms using lattice units in orthogonal box = (0 -44.010327 0) to (5.5012908 44.010327 3.8900001) create_atoms CPU = 0.000 seconds 64 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5012908 5.5012908 3.8900001 Created 66 atoms using lattice units in orthogonal box = (0 -44.010327 0) to (5.5012908 44.010327 3.8900001) create_atoms CPU = 0.000 seconds 66 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 = 2 20 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 2 atoms, new total = 128 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:187) 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 = 2 20 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) = 7.001 | 7.001 | 7.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -497.92 0 -497.92 -0.037709282 1 0 -497.92 0 -497.92 -0.037709282 Loop time of 0.00217133 on 1 procs for 1 steps with 128 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -497.920000612521 -497.920000612521 -497.920000612526 Force two-norm initial, final = 7.8047855e-08 2.4277533e-08 Force max component initial, final = 3.3489463e-08 1.0515661e-08 Final line search alpha, max atom move = 1 1.0515661e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0021071 | 0.0021071 | 0.0021071 | 0.0 | 97.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 3.6808e-05 | 3.6808e-05 | 3.6808e-05 | 0.0 | 1.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.738e-05 | | | 1.26 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3498 ave 3498 max 3498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12800 ave 12800 max 12800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12800 Ave neighs/atom = 100 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.001 | 7.001 | 7.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -497.92 0 -497.92 -0.037709282 1883.6439 2 0 -497.92 0 -497.92 6.1145874e-09 1883.6439 Loop time of 0.00213653 on 1 procs for 1 steps with 128 atoms 96.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -497.920000612526 -497.920000612526 -497.920000612499 Force two-norm initial, final = 7.6788783e-05 8.569223e-08 Force max component initial, final = 4.441783e-05 6.5045456e-08 Final line search alpha, max atom move = 1 6.5045456e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0020125 | 0.0020125 | 0.0020125 | 0.0 | 94.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 3.6348e-05 | 3.6348e-05 | 3.6348e-05 | 0.0 | 1.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 8.767e-05 | | | 4.10 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3498 ave 3498 max 3498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12800 ave 12800 max 12800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12800 Ave neighs/atom = 100 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 = 2 20 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) = 6.632 | 6.632 | 6.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -497.92 0 -497.92 6.1145874e-09 Loop time of 8.92e-07 on 1 procs for 0 steps with 128 atoms 224.2% 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 | | 8.92e-07 | | |100.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3498 ave 3498 max 3498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12800 ave 12800 max 12800 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12800 Ave neighs/atom = 100 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.632 | 6.632 | 6.632 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 -497.92 -497.92 5.5012908 88.020653 3.89 6.1145874e-09 6.1145874e-09 3.9807876e-05 -5.5325904e-05 1.5536372e-05 2.7506454 9.4908978e-17 Loop time of 6.01e-07 on 1 procs for 0 steps with 128 atoms 332.8% 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 | | 6.01e-07 | | |100.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3498 ave 3498 max 3498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12800 ave 12800 max 12800 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25600 ave 25600 max 25600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25600 Ave neighs/atom = 200 Neighbor list builds = 0 Dangerous builds = 0 128 -497.920000612499 eV 2.75064540370214 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00