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 -43.450306 0.0000000) to (15.360757 43.450306 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6592263 4.5733455 4.9836877 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.450306 0.0000000) to (15.360757 43.450306 4.9836877) create_atoms CPU = 0.001 seconds 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6592263 4.5733455 4.9836877 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.450306 0.0000000) to (15.360757 43.450306 4.9836877) create_atoms CPU = 0.001 seconds 306 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 = 4 20 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 8 atoms, new total = 604 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 = 4 20 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) = 7.248 | 7.248 | 7.248 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2651.3594 0 -2651.3594 17704.32 19 0 -2671.1183 0 -2671.1183 -2654.0127 Loop time of 0.378025 on 1 procs for 19 steps with 604 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2651.35944739603 -2671.11658912092 -2671.11834551075 Force two-norm initial, final = 52.536834 0.13710024 Force max component initial, final = 16.134040 0.023829219 Final line search alpha, max atom move = 1.0000000 0.023829219 Iterations, force evaluations = 19 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37459 | 0.37459 | 0.37459 | 0.0 | 99.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021492 | 0.0021492 | 0.0021492 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001286 | | | 0.34 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6650.00 ave 6650 max 6650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74996.0 ave 74996 max 74996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74996 Ave neighs/atom = 124.16556 Neighbor list builds = 0 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 : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.248 | 7.248 | 7.248 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -2671.1183 0 -2671.1183 -2654.0127 6652.5215 20 0 -2671.121 0 -2671.121 -1344.1032 6647.8106 Loop time of 0.0312691 on 1 procs for 1 steps with 604 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 = -2671.11834551075 -2671.11834551075 -2671.12100912455 Force two-norm initial, final = 9.0686617 1.6927662 Force max component initial, final = 8.8070910 1.6354048 Final line search alpha, max atom move = 0.00011354487 0.00018569183 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.030687 | 0.030687 | 0.030687 | 0.0 | 98.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013977 | 0.00013977 | 0.00013977 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000442 | | | 1.41 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6542.00 ave 6542 max 6542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75636.0 ave 75636 max 75636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75636 Ave neighs/atom = 125.22517 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 = 4 20 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) = 6.879 | 6.879 | 6.879 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2671.121 0 -2671.121 -1344.1032 Loop time of 1.868e-06 on 1 procs for 0 steps with 604 atoms 160.6% 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 | | 1.868e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6542.00 ave 6542 max 6542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75648.0 ave 75648 max 75648 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 = 75648 Ave neighs/atom = 125.24503 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) = 6.879 | 6.879 | 6.879 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 -2671.121 -2671.121 15.358616 86.900613 4.9808528 -1344.1032 -1344.1032 394.09094 -4326.3924 -100.00811 2.3497221 227.78546 Loop time of 2.208e-06 on 1 procs for 0 steps with 604 atoms 181.2% 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 | | 2.208e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6542.00 ave 6542 max 6542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75648.0 ave 75648 max 75648 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 151296.0 ave 151296 max 151296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151296 Ave neighs/atom = 250.49007 Neighbor list builds = 0 Dangerous builds = 0 604 -2671.12100912455 eV 2.34972209472486 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00