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 (21.723391 37.626017 6.1037460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7166819 5.2808445 6.1037460 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.626017 0.0000000) to (21.723391 37.626017 6.1037460) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7166819 5.2808445 6.1037460 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.626017 0.0000000) to (21.723391 37.626017 6.1037460) 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 = 5 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 2 atoms, new total = 912 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 = 5 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) = 7.734 | 7.734 | 7.734 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3258.5098 0 -3258.5098 205172 119 0 -4028.6918 0 -4028.6918 10351.688 Loop time of 7.363 on 1 procs for 119 steps with 912 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 = -3258.50976555627 -4028.68832966407 -4028.69178658462 Force two-norm initial, final = 1150.5194 0.19719992 Force max component initial, final = 283.15497 0.024640901 Final line search alpha, max atom move = 1.0000000 0.024640901 Iterations, force evaluations = 119 215 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2464 | 7.2464 | 7.2464 | 0.0 | 98.42 Neigh | 0.06104 | 0.06104 | 0.06104 | 0.0 | 0.83 Comm | 0.033395 | 0.033395 | 0.033395 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02222 | | | 0.30 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7276.00 ave 7276 max 7276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115528.0 ave 115528 max 115528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115528 Ave neighs/atom = 126.67544 Neighbor list builds = 5 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 : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.734 | 7.734 | 7.734 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -4028.6918 0 -4028.6918 10351.688 9977.9729 123 0 -4028.9038 0 -4028.9038 7.836042 10034.02 Loop time of 0.249127 on 1 procs for 4 steps with 912 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 = -4028.69178658462 -4028.90083760785 -4028.90381565597 Force two-norm initial, final = 115.91519 0.98383901 Force max component initial, final = 84.645499 0.72337826 Final line search alpha, max atom move = 0.00010745478 7.7730454e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24464 | 0.24464 | 0.24464 | 0.0 | 98.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081898 | 0.00081898 | 0.00081898 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003669 | | | 1.47 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7302.00 ave 7302 max 7302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115500.0 ave 115500 max 115500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115500 Ave neighs/atom = 126.64474 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 = 5 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) = 7.365 | 7.365 | 7.365 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4028.9038 0 -4028.9038 7.836042 Loop time of 3.544e-06 on 1 procs for 0 steps with 912 atoms 141.1% 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 | | 3.544e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7286.00 ave 7286 max 7286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115068.0 ave 115068 max 115068 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 = 115068 Ave neighs/atom = 126.17105 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) = 7.365 | 7.365 | 7.365 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 -4028.9038 -4028.9038 21.766412 75.498728 6.1058829 7.836042 7.836042 -115.73377 70.828011 68.413881 2.290402 605.51264 Loop time of 3.814e-06 on 1 procs for 0 steps with 912 atoms 236.0% 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 | | 3.814e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7286.00 ave 7286 max 7286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115068.0 ave 115068 max 115068 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 230136.0 ave 230136 max 230136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230136 Ave neighs/atom = 252.34211 Neighbor list builds = 0 Dangerous builds = 0 912 -4028.90381565597 eV 2.29040201112293 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08