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 -56.826307 0.0000000) to (28.411391 56.826307 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8080816 4.8080816 3.5239994 Created 521 atoms using lattice units in orthogonal box = (0.0000000 -56.826307 0.0000000) to (28.411391 56.826307 3.5239994) create_atoms CPU = 0.003 seconds 521 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8080816 4.8080816 3.5239994 Created 521 atoms using lattice units in orthogonal box = (0.0000000 -56.826307 0.0000000) to (28.411391 56.826307 3.5239994) create_atoms CPU = 0.002 seconds 521 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 = 7 26 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 10 atoms, new total = 1032 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 = 7 26 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) = 7.757 | 7.757 | 7.757 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4546.5851 0 -4546.5851 7193.9897 28 0 -4566.3255 0 -4566.3255 -5258.4673 Loop time of 2.56116 on 1 procs for 28 steps with 1032 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 = -4546.58507334324 -4566.32149326451 -4566.32546022481 Force two-norm initial, final = 72.322601 0.23818236 Force max component initial, final = 25.389028 0.071689853 Final line search alpha, max atom move = 1.0000000 0.071689853 Iterations, force evaluations = 28 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5219 | 2.5219 | 2.5219 | 0.0 | 98.47 Neigh | 0.016354 | 0.016354 | 0.016354 | 0.0 | 0.64 Comm | 0.014388 | 0.014388 | 0.014388 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0085 | | | 0.33 Nlocal: 1032.00 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10566.0 ave 10566 max 10566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 128568.0 ave 128568 max 128568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128568 Ave neighs/atom = 124.58140 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 : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.758 | 7.758 | 7.758 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -4566.3255 0 -4566.3255 -5258.4673 11379.096 30 0 -4566.3604 0 -4566.3604 -1326.8319 11354.773 Loop time of 0.166532 on 1 procs for 2 steps with 1032 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 = -4566.32546022481 -4566.35999231233 -4566.36038794731 Force two-norm initial, final = 46.361462 1.0560583 Force max component initial, final = 34.262326 0.86508247 Final line search alpha, max atom move = 0.00024794961 0.00021449686 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16317 | 0.16317 | 0.16317 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089372 | 0.00089372 | 0.00089372 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002466 | | | 1.48 Nlocal: 1032.00 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10572.0 ave 10572 max 10572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 128519.0 ave 128519 max 128519 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128519 Ave neighs/atom = 124.53391 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 = 7 26 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) = 7.389 | 7.389 | 7.389 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4566.3604 0 -4566.3604 -1326.8319 Loop time of 6.325e-06 on 1 procs for 0 steps with 1032 atoms 173.9% 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 | | 6.325e-06 | | |100.00 Nlocal: 1032.00 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10590.0 ave 10590 max 10590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 128599.0 ave 128599 max 128599 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 = 128599 Ave neighs/atom = 124.61143 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) = 7.389 | 7.389 | 7.389 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 -4566.3604 -4566.3604 28.380469 113.65261 3.5202982 -1326.8319 -1326.8319 121.93166 -4024.3289 -78.098616 2.2419276 381.38995 Loop time of 6.745e-06 on 1 procs for 0 steps with 1032 atoms 266.9% 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 | | 6.745e-06 | | |100.00 Nlocal: 1032.00 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10590.0 ave 10590 max 10590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 128599.0 ave 128599 max 128599 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 257198.0 ave 257198 max 257198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257198 Ave neighs/atom = 249.22287 Neighbor list builds = 0 Dangerous builds = 0 1032 -4566.36038794731 eV 2.24192756757444 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03