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 -41.096542 0.0000000) to (14.529822 41.096542 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9828678 6.0436091 4.9836877 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -41.096542 0.0000000) to (14.529822 41.096542 4.9836877) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9828678 6.0436091 4.9836877 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.096542 0.0000000) to (14.529822 41.096542 4.9836877) create_atoms CPU = 0.001 seconds 274 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 = 4 19 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 6 atoms, new total = 540 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 = 4 19 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) = 7.206 | 7.206 | 7.206 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2167.8294 0 -2167.8294 102892.19 49 0 -2389.5245 0 -2389.5245 -5508.4334 Loop time of 0.932836 on 1 procs for 49 steps with 540 atoms 97.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2167.82937296347 -2389.52214309484 -2389.5245234431 Force two-norm initial, final = 588.05328 0.16329665 Force max component initial, final = 196.06599 0.030049415 Final line search alpha, max atom move = 1.0000000 0.030049415 Iterations, force evaluations = 49 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9188 | 0.9188 | 0.9188 | 0.0 | 98.49 Neigh | 0.0040185 | 0.0040185 | 0.0040185 | 0.0 | 0.43 Comm | 0.0058708 | 0.0058708 | 0.0058708 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004151 | | | 0.45 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6411.00 ave 6411 max 6411 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68308.0 ave 68308 max 68308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68308 Ave neighs/atom = 126.49630 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 : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.206 | 7.206 | 7.206 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -2389.5245 0 -2389.5245 -5508.4334 5951.7733 53 0 -2389.5902 0 -2389.5902 -215.0599 5934.2972 Loop time of 0.0608856 on 1 procs for 4 steps with 540 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 = -2389.5245234431 -2389.58959326128 -2389.59024354674 Force two-norm initial, final = 43.479144 1.6953241 Force max component initial, final = 40.757243 1.5800334 Final line search alpha, max atom move = 0.00034987859 0.00055281988 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.059381 | 0.059381 | 0.059381 | 0.0 | 97.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030608 | 0.00030608 | 0.00030608 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001199 | | | 1.97 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6441.00 ave 6441 max 6441 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67650.0 ave 67650 max 67650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67650 Ave neighs/atom = 125.27778 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 = 4 19 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) = 6.837 | 6.837 | 6.837 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2389.5902 0 -2389.5902 -215.0599 Loop time of 2.288e-06 on 1 procs for 0 steps with 540 atoms 174.8% 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 | | 2.288e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6441.00 ave 6441 max 6441 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67750.0 ave 67750 max 67750 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 = 67750 Ave neighs/atom = 125.46296 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) = 6.837 | 6.837 | 6.837 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 -2389.5902 -2389.5902 14.534685 81.938046 4.982853 -215.0599 -215.0599 -118.34092 -425.26307 -101.57572 2.3482415 277.38002 Loop time of 2.236e-06 on 1 procs for 0 steps with 540 atoms 178.9% 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 | | 2.236e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6441.00 ave 6441 max 6441 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67750.0 ave 67750 max 67750 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 135500.0 ave 135500 max 135500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135500 Ave neighs/atom = 250.92593 Neighbor list builds = 0 Dangerous builds = 0 540 -2389.59024354674 eV 2.34824152963159 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01