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 -38.121406 0.0000000) to (12.705961 38.121406 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8869079 4.8869079 3.5239994 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -38.121406 0.0000000) to (12.705961 38.121406 3.5239994) create_atoms CPU = 0.002 seconds 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8869079 4.8869079 3.5239994 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -38.121406 0.0000000) to (12.705961 38.121406 3.5239994) create_atoms CPU = 0.001 seconds 158 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 = 3 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 6 atoms, new total = 310 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 = 3 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) = 7.074 | 7.074 | 7.074 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1347.0497 0 -1347.0497 39569.468 40 0 -1370.1302 0 -1370.1302 -416.89592 Loop time of 0.80269 on 1 procs for 40 steps with 310 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1347.04965648638 -1370.12909846045 -1370.13015480361 Force two-norm initial, final = 63.061807 0.10151298 Force max component initial, final = 28.378822 0.025119519 Final line search alpha, max atom move = 1.0000000 0.025119519 Iterations, force evaluations = 40 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78515 | 0.78515 | 0.78515 | 0.0 | 97.81 Neigh | 0.0047214 | 0.0047214 | 0.0047214 | 0.0 | 0.59 Comm | 0.0079775 | 0.0079775 | 0.0079775 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004843 | | | 0.60 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5258.00 ave 5258 max 5258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39110.0 ave 39110 max 39110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39110 Ave neighs/atom = 126.16129 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.074 | 7.074 | 7.074 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -1370.1302 0 -1370.1302 -416.89592 3413.8326 42 0 -1370.1334 0 -1370.1334 499.24513 3412.0942 Loop time of 0.0644661 on 1 procs for 2 steps with 310 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1370.13015480361 -1370.13250839067 -1370.13336908987 Force two-norm initial, final = 5.7010304 0.10825555 Force max component initial, final = 5.6982877 0.026823838 Final line search alpha, max atom move = 0.00039006233 1.0462969e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.062392 | 0.062392 | 0.062392 | 0.0 | 96.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055922 | 0.00055922 | 0.00055922 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001515 | | | 2.35 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5234.00 ave 5234 max 5234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38866.0 ave 38866 max 38866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38866 Ave neighs/atom = 125.37419 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 = 3 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) = 6.705 | 6.705 | 6.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1370.1334 0 -1370.1334 499.24513 Loop time of 6.164e-06 on 1 procs for 0 steps with 310 atoms 162.2% 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 | | 6.164e-06 | | |100.00 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5234.00 ave 5234 max 5234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38894.0 ave 38894 max 38894 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 = 38894 Ave neighs/atom = 125.46452 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) = 6.705 | 6.705 | 6.705 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 -1370.1334 -1370.1334 12.691459 76.242811 3.5262295 499.24513 499.24513 3.6408308 1494.1526 -0.05805518 2.247304 148.04693 Loop time of 6.675e-06 on 1 procs for 0 steps with 310 atoms 254.7% 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 | | 6.675e-06 | | |100.00 Nlocal: 310.000 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5234.00 ave 5234 max 5234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38894.0 ave 38894 max 38894 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77788.0 ave 77788 max 77788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77788 Ave neighs/atom = 250.92903 Neighbor list builds = 0 Dangerous builds = 0 310 -1370.13336908987 eV 2.24730395347447 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01