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 -44.856714 0.0000000) to (10.571998 44.856714 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8733323 4.9836877 4.9836877 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -44.856714 0.0000000) to (10.571998 44.856714 4.9836877) create_atoms CPU = 0.001 seconds 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8733323 4.9836877 4.9836877 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -44.856714 0.0000000) to (10.571998 44.856714 4.9836877) create_atoms CPU = 0.000 seconds 218 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 21 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 4 atoms, new total = 432 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 21 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) = 7.180 | 7.180 | 7.180 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1860.594 0 -1860.594 74962.656 42 0 -1911.6038 0 -1911.6038 7908.8768 Loop time of 0.604957 on 1 procs for 42 steps with 432 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 = -1860.59403425416 -1911.60219630981 -1911.60378946929 Force two-norm initial, final = 139.62446 0.13549076 Force max component initial, final = 40.478367 0.032440835 Final line search alpha, max atom move = 1.0000000 0.032440835 Iterations, force evaluations = 42 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59904 | 0.59904 | 0.59904 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0038264 | 0.0038264 | 0.0038264 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002093 | | | 0.35 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6121.00 ave 6121 max 6121 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54090.0 ave 54090 max 54090 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54090 Ave neighs/atom = 125.20833 Neighbor list builds = 0 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.181 | 7.181 | 7.181 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -1911.6038 0 -1911.6038 7908.8768 4726.7796 45 0 -1911.6295 0 -1911.6295 2577.1746 4740.223 Loop time of 0.0541523 on 1 procs for 3 steps with 432 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 = -1911.60378946929 -1911.62951814178 -1911.62952845535 Force two-norm initial, final = 25.487958 0.15246345 Force max component initial, final = 19.588618 0.049531403 Final line search alpha, max atom move = 0.0038544686 0.00019091724 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.052554 | 0.052554 | 0.052554 | 0.0 | 97.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031005 | 0.00031005 | 0.00031005 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001289 | | | 2.38 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6247.00 ave 6247 max 6247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54404.0 ave 54404 max 54404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54404 Ave neighs/atom = 125.93519 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 21 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) = 6.813 | 6.813 | 6.813 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1911.6295 0 -1911.6295 2577.1746 Loop time of 1.844e-06 on 1 procs for 0 steps with 432 atoms 162.7% 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 | | 1.844e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6247.00 ave 6247 max 6247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54288.0 ave 54288 max 54288 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 = 54288 Ave neighs/atom = 125.66667 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) = 6.813 | 6.813 | 6.813 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 -1911.6295 -1911.6295 10.589 89.713427 4.9898372 2577.1746 2577.1746 -16.76834 7737.0464 11.245667 2.3304604 169.50748 Loop time of 2.34e-06 on 1 procs for 0 steps with 432 atoms 170.9% 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 | | 2.34e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6247.00 ave 6247 max 6247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54288.0 ave 54288 max 54288 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108576.0 ave 108576 max 108576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108576 Ave neighs/atom = 251.33333 Neighbor list builds = 0 Dangerous builds = 0 432 -1911.62952845535 eV 2.33046041003404 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00