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 -71.728057 0) to (35.864028 71.728057 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4850867 5.4850867 3.8900001 Created 679 atoms using lattice units in orthogonal box = (0 -71.728057 0) to (35.864028 71.728057 3.8900001) create_atoms CPU = 0.000 seconds 679 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4850867 5.4850867 3.8900001 Created 681 atoms using lattice units in orthogonal box = (0 -71.728057 0) to (35.864028 71.728057 3.8900001) create_atoms CPU = 0.000 seconds 681 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 = 9 33 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 0 atoms, new total = 1360 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 = 9 33 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) = 7.848 | 7.848 | 7.848 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4678.3767 0 -4678.3767 111843.23 108 0 -5279.9972 0 -5279.9972 3891.181 Loop time of 1.3927 on 1 procs for 108 steps with 1360 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4678.37672314486 -5279.99267403921 -5279.99723088862 Force two-norm initial, final = 769.16961 0.2953741 Force max component initial, final = 154.46436 0.098530128 Final line search alpha, max atom move = 1 0.098530128 Iterations, force evaluations = 108 194 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3715 | 1.3715 | 1.3715 | 0.0 | 98.48 Neigh | 0.0087304 | 0.0087304 | 0.0087304 | 0.0 | 0.63 Comm | 0.0080309 | 0.0080309 | 0.0080309 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004471 | | | 0.32 Nlocal: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11224 ave 11224 max 11224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135519 ave 135519 max 135519 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135519 Ave neighs/atom = 99.646324 Neighbor list builds = 3 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 : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.848 | 7.848 | 7.848 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -5279.9972 0 -5279.9972 3891.181 20013.716 111 0 -5280.0749 0 -5280.0749 -98.595931 20053.635 Loop time of 0.0364184 on 1 procs for 3 steps with 1360 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 = -5279.99723088862 -5280.07462796601 -5280.0749498306 Force two-norm initial, final = 90.613366 3.4594413 Force max component initial, final = 70.609637 3.168293 Final line search alpha, max atom move = 0.00020873249 0.00066132571 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035592 | 0.035592 | 0.035592 | 0.0 | 97.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019136 | 0.00019136 | 0.00019136 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006347 | | | 1.74 Nlocal: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11224 ave 11224 max 11224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135549 ave 135549 max 135549 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135549 Ave neighs/atom = 99.668382 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 = 9 33 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) = 7.479 | 7.479 | 7.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5280.0749 0 -5280.0749 -98.595931 Loop time of 6.51e-07 on 1 procs for 0 steps with 1360 atoms 307.2% 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 | | 6.51e-07 | | |100.00 Nlocal: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11224 ave 11224 max 11224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135491 ave 135491 max 135491 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 = 135491 Ave neighs/atom = 99.625735 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) = 7.479 | 7.479 | 7.479 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 -5280.0749 -5280.0749 35.84005 143.70826 3.8935233 -98.595931 -98.595931 -252.96017 -95.125471 52.297845 2.5077521 182.93969 Loop time of 9.41e-07 on 1 procs for 0 steps with 1360 atoms 318.8% 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 | | 9.41e-07 | | |100.00 Nlocal: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11224 ave 11224 max 11224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135491 ave 135491 max 135491 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 270982 ave 270982 max 270982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270982 Ave neighs/atom = 199.25147 Neighbor list builds = 0 Dangerous builds = 0 1360 -5280.0749498306 eV 2.50775207336025 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01