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 -65.360452 0.0000000) to (23.108409 65.360452 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9114536 6.0800420 4.9836877 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -65.360452 0.0000000) to (23.108409 65.360452 4.9836877) create_atoms CPU = 0.003 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9114536 6.0800420 4.9836877 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -65.360452 0.0000000) to (23.108409 65.360452 4.9836877) create_atoms CPU = 0.002 seconds 690 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 = 6 30 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 = 1372 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 = 6 30 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) = 7.956 | 7.956 | 7.956 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5648.4626 0 -5648.4626 71140.878 63 0 -6080.9482 0 -6080.9482 -1320.7325 Loop time of 3.24066 on 1 procs for 63 steps with 1372 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5648.46256324842 -6080.94223317178 -6080.94818632378 Force two-norm initial, final = 873.53265 0.27201253 Force max component initial, final = 292.54422 0.071179434 Final line search alpha, max atom move = 1.0000000 0.071179434 Iterations, force evaluations = 63 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2027 | 3.2027 | 3.2027 | 0.0 | 98.83 Neigh | 0.00968 | 0.00968 | 0.00968 | 0.0 | 0.30 Comm | 0.01696 | 0.01696 | 0.01696 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01131 | | | 0.35 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11693.0 ave 11693 max 11693 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 172824.0 ave 172824 max 172824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172824 Ave neighs/atom = 125.96501 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.961 | 7.961 | 7.961 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -6080.9482 0 -6080.9482 -1320.7325 15054.485 65 0 -6080.9584 0 -6080.9584 -4.6226304 15043.732 Loop time of 0.128115 on 1 procs for 2 steps with 1372 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 = -6080.94818632378 -6080.95708820609 -6080.95839226835 Force two-norm initial, final = 27.188504 0.35130877 Force max component initial, final = 25.940301 0.19277385 Final line search alpha, max atom move = 0.00017169623 3.3098542e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12579 | 0.12579 | 0.12579 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046713 | 0.00046713 | 0.00046713 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001859 | | | 1.45 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11696.0 ave 11696 max 11696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171972.0 ave 171972 max 171972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171972 Ave neighs/atom = 125.34402 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 = 6 30 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) = 7.592 | 7.592 | 7.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6080.9584 0 -6080.9584 -4.6226304 Loop time of 2.332e-06 on 1 procs for 0 steps with 1372 atoms 171.5% 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 | | 2.332e-06 | | |100.00 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11696.0 ave 11696 max 11696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 172036.0 ave 172036 max 172036 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 = 172036 Ave neighs/atom = 125.39067 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) = 7.592 | 7.592 | 7.592 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 -6080.9584 -6080.9584 23.110356 130.61623 4.9836991 -4.6226304 -4.6226304 -20.532388 -3.5365815 10.201079 2.31881 354.98144 Loop time of 2.487e-06 on 1 procs for 0 steps with 1372 atoms 281.5% 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 | | 2.487e-06 | | |100.00 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11696.0 ave 11696 max 11696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 172036.0 ave 172036 max 172036 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 344072.0 ave 344072 max 344072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 344072 Ave neighs/atom = 250.78134 Neighbor list builds = 0 Dangerous builds = 0 1372 -6080.95839226835 eV 2.31881003767789 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03