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 -35.243518 0.0000000) to (3.5239994 35.243518 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -35.243518 0.0000000) to (3.5239994 35.243518 3.5239994) create_atoms CPU = 0.002 seconds 42 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -35.243518 0.0000000) to (3.5239994 35.243518 3.5239994) create_atoms CPU = 0.001 seconds 42 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 = 1 16 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 4 atoms, new total = 80 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 = 1 16 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) = 7.025 | 7.025 | 7.025 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -355.19975 0 -355.19975 -185.98196 1 0 -355.19991 0 -355.19991 -186.93797 Loop time of 0.0236129 on 1 procs for 1 steps with 80 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 = -355.199749393108 -355.199749393108 -355.199910216937 Force two-norm initial, final = 0.069089286 0.023657463 Force max component initial, final = 0.034527296 0.011674638 Final line search alpha, max atom move = 1.0000000 0.011674638 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022549 | 0.022549 | 0.022549 | 0.0 | 95.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006031 | 0.0006031 | 0.0006031 | 0.0 | 2.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004609 | | | 1.95 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4229.00 ave 4229 max 4229 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9920.00 ave 9920 max 9920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9920 Ave neighs/atom = 124.00000 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 : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.025 | 7.025 | 7.025 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -355.19991 0 -355.19991 -186.93797 875.34831 2 0 -355.19991 0 -355.19991 -45.26827 875.28222 Loop time of 0.020057 on 1 procs for 1 steps with 80 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -355.199910216937 -355.199910216937 -355.19991345632 Force two-norm initial, final = 0.11834674 0.023947520 Force max component initial, final = 0.081994738 0.011627299 Final line search alpha, max atom move = 0.012195905 0.00014180542 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.018492 | 0.018492 | 0.018492 | 0.0 | 92.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048814 | 0.00048814 | 0.00048814 | 0.0 | 2.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001077 | | | 5.37 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4229.00 ave 4229 max 4229 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9920.00 ave 9920 max 9920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9920 Ave neighs/atom = 124.00000 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 = 1 16 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) = 6.656 | 6.656 | 6.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -355.19991 0 -355.19991 -45.26827 Loop time of 9.341e-06 on 1 procs for 0 steps with 80 atoms 96.3% 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 | | 9.341e-06 | | |100.00 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4229.00 ave 4229 max 4229 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9920.00 ave 9920 max 9920 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 = 9920 Ave neighs/atom = 124.00000 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) = 6.656 | 6.656 | 6.656 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 -355.19991 -355.19991 3.5238664 70.487036 3.5238664 -45.26827 -45.26827 5.5054924 -146.8158 5.5054924 2.4917411 8.7953712e-05 Loop time of 9.803e-06 on 1 procs for 0 steps with 80 atoms 132.6% 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 | | 9.803e-06 | | |100.00 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4229.00 ave 4229 max 4229 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9920.00 ave 9920 max 9920 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 19840.0 ave 19840 max 19840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19840 Ave neighs/atom = 248.00000 Neighbor list builds = 0 Dangerous builds = 0 80 -355.19991345632 eV 2.49174110065234 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00