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 -58.737713 0) to (41.533835 58.737713 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.557974 5.667674 5.5012908 Created 912 atoms using lattice units in orthogonal box = (0 -58.737713 0) to (41.533835 58.737713 5.5012908) create_atoms CPU = 0.001 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.557974 5.667674 5.5012908 Created 916 atoms using lattice units in orthogonal box = (0 -58.737713 0) to (41.533835 58.737713 5.5012908) create_atoms CPU = 0.001 seconds 916 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 = 10 27 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 4 atoms, new total = 1824 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 = 10 27 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) = 8.004 | 8.004 | 8.004 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4676.4811 0 -4676.4811 178767.61 81 0 -7075.1527 0 -7075.1527 4781.5344 Loop time of 1.44447 on 1 procs for 81 steps with 1824 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4676.48105926491 -7075.14632603753 -7075.15271015608 Force two-norm initial, final = 2012.4705 0.30038677 Force max component initial, final = 282.0496 0.036160666 Final line search alpha, max atom move = 1 0.036160666 Iterations, force evaluations = 81 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.43 | 1.43 | 1.43 | 0.0 | 99.00 Neigh | 0.0039179 | 0.0039179 | 0.0039179 | 0.0 | 0.27 Comm | 0.0061367 | 0.0061367 | 0.0061367 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004411 | | | 0.31 Nlocal: 1824 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10919 ave 10919 max 10919 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 181820 ave 181820 max 181820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181820 Ave neighs/atom = 99.682018 Neighbor list builds = 1 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 : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.005 | 8.005 | 8.005 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -7075.1527 0 -7075.1527 4781.5344 26841.926 86 0 -7075.3519 0 -7075.3519 -5.6394903 26905.616 Loop time of 0.0764183 on 1 procs for 5 steps with 1824 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7075.15271015608 -7075.35181184862 -7075.35188645928 Force two-norm initial, final = 150.7476 0.443664 Force max component initial, final = 127.85338 0.17069749 Final line search alpha, max atom move = 0.00034453908 5.8811958e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.074984 | 0.074984 | 0.074984 | 0.0 | 98.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029464 | 0.00029464 | 0.00029464 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00114 | | | 1.49 Nlocal: 1824 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10944 ave 10944 max 10944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 181720 ave 181720 max 181720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181720 Ave neighs/atom = 99.627193 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 = 10 27 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) = 7.636 | 7.636 | 7.636 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7075.3519 0 -7075.3519 -5.6394903 Loop time of 5.41e-07 on 1 procs for 0 steps with 1824 atoms 184.8% 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 | | 5.41e-07 | | |100.00 Nlocal: 1824 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10944 ave 10944 max 10944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 181604 ave 181604 max 181604 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 = 181604 Ave neighs/atom = 99.563596 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) = 7.636 | 7.636 | 7.636 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 -7075.3519 -7075.3519 41.520628 117.90779 5.4958709 -5.6394903 -5.6394903 -2.1152337 -10.202111 -4.6011265 2.5695926 860.79495 Loop time of 5.11e-07 on 1 procs for 0 steps with 1824 atoms 391.4% 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 | | 5.11e-07 | | |100.00 Nlocal: 1824 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10944 ave 10944 max 10944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 181604 ave 181604 max 181604 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 363208 ave 363208 max 363208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363208 Ave neighs/atom = 199.12719 Neighbor list builds = 0 Dangerous builds = 0 1824 -7075.35188645928 eV 2.56959264508761 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01