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 -44.853190 0.0000000) to (31.715995 44.853190 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8733323 6.0911739 4.9836877 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -44.853190 0.0000000) to (31.715995 44.853190 4.9836877) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8733323 6.0911739 4.9836877 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -44.853190 0.0000000) to (31.715995 44.853190 4.9836877) create_atoms CPU = 0.002 seconds 650 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 = 8 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 6 atoms, new total = 1292 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 = 8 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) = 7.864 | 7.864 | 7.864 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5170.7742 0 -5170.7742 100618.58 48 0 -5723.7898 0 -5723.7898 -820.108 Loop time of 2.05954 on 1 procs for 48 steps with 1292 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5170.77424880823 -5723.78567753201 -5723.78983326636 Force two-norm initial, final = 976.70606 0.20919359 Force max component initial, final = 303.14598 0.027285830 Final line search alpha, max atom move = 1.0000000 0.027285830 Iterations, force evaluations = 48 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0251 | 2.0251 | 2.0251 | 0.0 | 98.33 Neigh | 0.017471 | 0.017471 | 0.017471 | 0.0 | 0.85 Comm | 0.0097242 | 0.0097242 | 0.0097242 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007272 | | | 0.35 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10190.0 ave 10190 max 10190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163466.0 ave 163466 max 163466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163466 Ave neighs/atom = 126.52167 Neighbor list builds = 2 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 : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.864 | 7.864 | 7.864 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -5723.7898 0 -5723.7898 -820.108 14179.225 49 0 -5723.7939 0 -5723.7939 276.61923 14170.789 Loop time of 0.0707923 on 1 procs for 1 steps with 1292 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 = -5723.78983326636 -5723.78983326636 -5723.79386269112 Force two-norm initial, final = 17.147780 6.2858931 Force max component initial, final = 15.426247 5.8847683 Final line search alpha, max atom move = 6.4824581e-05 0.00038147764 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.069694 | 0.069694 | 0.069694 | 0.0 | 98.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023547 | 0.00023547 | 0.00023547 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008624 | | | 1.22 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10190.0 ave 10190 max 10190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163196.0 ave 163196 max 163196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163196 Ave neighs/atom = 126.31269 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 = 8 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) = 7.495 | 7.495 | 7.495 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5723.7939 0 -5723.7939 276.61923 Loop time of 2.036e-06 on 1 procs for 0 steps with 1292 atoms 196.5% 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 | | 2.036e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10190.0 ave 10190 max 10190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163288.0 ave 163288 max 163288 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 = 163288 Ave neighs/atom = 126.38390 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) = 7.495 | 7.495 | 7.495 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 -5723.7939 -5723.7939 31.716915 89.668564 4.9826786 276.61923 276.61923 665.36247 -73.126601 237.62182 2.3105851 449.88043 Loop time of 2.731e-06 on 1 procs for 0 steps with 1292 atoms 329.5% 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 | | 2.731e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10190.0 ave 10190 max 10190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163288.0 ave 163288 max 163288 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 326576.0 ave 326576 max 326576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 326576 Ave neighs/atom = 252.76780 Neighbor list builds = 0 Dangerous builds = 0 1292 -5723.79386269112 eV 2.310585108623 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02