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 -37.954635 0.0000000) to (18.977318 37.954635 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5807318 4.5807318 3.5239994 Created 231 atoms using lattice units in orthogonal box = (0.0000000 -37.954635 0.0000000) to (18.977318 37.954635 3.5239994) create_atoms CPU = 0.001 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5807318 4.5807318 3.5239994 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -37.954635 0.0000000) to (18.977318 37.954635 3.5239994) create_atoms CPU = 0.000 seconds 233 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 18 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 = 464 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 18 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) = 7.128 | 7.128 | 7.128 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1304.4632 0 -1304.4632 261950.01 50 0 -2048.4386 0 -2048.4386 15025.173 Loop time of 0.790837 on 1 procs for 50 steps with 464 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 = -1304.46315103724 -2048.4367814483 -2048.43864058733 Force two-norm initial, final = 1308.4992 0.13957932 Force max component initial, final = 322.92920 0.041866465 Final line search alpha, max atom move = 1.0000000 0.041866465 Iterations, force evaluations = 50 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77534 | 0.77534 | 0.77534 | 0.0 | 98.04 Neigh | 0.0063956 | 0.0063956 | 0.0063956 | 0.0 | 0.81 Comm | 0.0060501 | 0.0060501 | 0.0060501 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00305 | | | 0.39 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6184.00 ave 6184 max 6184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60299.0 ave 60299 max 60299 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60299 Ave neighs/atom = 129.95474 Neighbor list builds = 2 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.128 | 7.128 | 7.128 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -2048.4386 0 -2048.4386 15025.173 5076.5125 61 0 -2048.8168 0 -2048.8168 177.50331 5117.2687 Loop time of 0.136079 on 1 procs for 11 steps with 464 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 = -2048.43864058733 -2048.81669015906 -2048.8168448418 Force two-norm initial, final = 93.548202 1.1325115 Force max component initial, final = 83.156278 0.82357455 Final line search alpha, max atom move = 0.00087439331 0.00072012807 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13218 | 0.13218 | 0.13218 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007119 | 0.0007119 | 0.0007119 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003182 | | | 2.34 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6142.00 ave 6142 max 6142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59009.0 ave 59009 max 59009 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59009 Ave neighs/atom = 127.17457 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 18 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) = 6.759 | 6.759 | 6.759 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2048.8168 0 -2048.8168 177.50331 Loop time of 2.383e-06 on 1 procs for 0 steps with 464 atoms 209.8% 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 | | 2.383e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6142.00 ave 6142 max 6142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57816.0 ave 57816 max 57816 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 = 57816 Ave neighs/atom = 124.60345 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) = 6.759 | 6.759 | 6.759 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 -2048.8168 -2048.8168 18.964907 76.656408 3.5199705 177.50331 177.50331 257.68608 122.93873 151.88511 2.2281755 290.67855 Loop time of 2.52e-06 on 1 procs for 0 steps with 464 atoms 238.1% 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 | | 2.52e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6142.00 ave 6142 max 6142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57816.0 ave 57816 max 57816 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 115632.0 ave 115632 max 115632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115632 Ave neighs/atom = 249.20690 Neighbor list builds = 0 Dangerous builds = 0 464 -2048.8168448418 eV 2.22817550698113 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01