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 -61.040984 0.0000000) to (24.918439 61.040984 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9804253 5.2899132 5.7546669 Created 1207 atoms using lattice units in orthogonal box = (0.0000000 -61.040984 0.0000000) to (24.918439 61.040984 8.6320004) create_atoms CPU = 0.002 seconds 1207 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9804253 5.2899132 5.7546669 Created 1207 atoms using lattice units in orthogonal box = (0.0000000 -61.040984 0.0000000) to (24.918439 61.040984 8.6320004) create_atoms CPU = 0.002 seconds 1207 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 = 6 28 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 30 atoms, new total = 2384 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 = 6 28 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) = 9.176 | 9.176 | 9.176 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10521.271 0 -10521.271 3977.6949 24 0 -10559.119 0 -10559.119 -7025.4335 Loop time of 1.8616 on 1 procs for 24 steps with 2384 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10521.2711611972 -10559.1108859354 -10559.1190293094 Force two-norm initial, final = 44.057500 0.29647976 Force max component initial, final = 6.9376847 0.031512828 Final line search alpha, max atom move = 1.0000000 0.031512828 Iterations, force evaluations = 24 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8296 | 1.8296 | 1.8296 | 0.0 | 98.28 Neigh | 0.017721 | 0.017721 | 0.017721 | 0.0 | 0.95 Comm | 0.0073397 | 0.0073397 | 0.0073397 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006902 | | | 0.37 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12066.0 ave 12066 max 12066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 298298.0 ave 298298 max 298298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298298 Ave neighs/atom = 125.12500 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 : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.177 | 9.177 | 9.177 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -10559.119 0 -10559.119 -7025.4335 26259.34 27 0 -10559.271 0 -10559.271 -1854.1948 26185.204 Loop time of 0.246804 on 1 procs for 3 steps with 2384 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 = -10559.1190293094 -10559.2697520678 -10559.2709166168 Force two-norm initial, final = 144.24079 0.30932127 Force max component initial, final = 118.96906 0.033103031 Final line search alpha, max atom move = 0.00012189750 4.0351767e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24377 | 0.24377 | 0.24377 | 0.0 | 98.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052387 | 0.00052387 | 0.00052387 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002509 | | | 1.02 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12042.0 ave 12042 max 12042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 298132.0 ave 298132 max 298132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298132 Ave neighs/atom = 125.05537 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 = 6 28 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) = 8.808 | 8.808 | 8.808 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10559.271 0 -10559.271 -1854.1948 Loop time of 2.016e-06 on 1 procs for 0 steps with 2384 atoms 148.8% 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 | | 2.016e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12054.0 ave 12054 max 12054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 298332.0 ave 298332 max 298332 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 = 298332 Ave neighs/atom = 125.13926 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) = 8.808 | 8.808 | 8.808 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 -10559.271 -10559.271 24.896396 122.08197 8.6152513 -1854.1948 -1854.1948 -1.7800466 -5559.3479 -1.456385 2.3377226 712.63852 Loop time of 1.945e-06 on 1 procs for 0 steps with 2384 atoms 308.5% 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 | | 1.945e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12054.0 ave 12054 max 12054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 298332.0 ave 298332 max 298332 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 596664.0 ave 596664 max 596664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 596664 Ave neighs/atom = 250.27852 Neighbor list builds = 0 Dangerous builds = 0 2384 -10559.2709166168 eV 2.33772260005424 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02