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 -37.629541 0.0000000) to (26.605612 37.629541 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1344163 5.9409501 4.9836877 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.629541 0.0000000) to (26.605612 37.629541 4.9836877) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1344163 5.9409501 4.9836877 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.629541 0.0000000) to (26.605612 37.629541 4.9836877) create_atoms CPU = 0.001 seconds 458 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 17 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 16 atoms, new total = 900 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 17 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) = 7.696 | 7.696 | 7.696 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3949.8222 0 -3949.8222 9664.1218 50 0 -3975.8519 0 -3975.8519 -10959.726 Loop time of 1.41145 on 1 procs for 50 steps with 900 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 = -3949.82216026033 -3975.84807997107 -3975.85188187509 Force two-norm initial, final = 63.049345 0.21484048 Force max component initial, final = 24.015207 0.048672227 Final line search alpha, max atom move = 1.0000000 0.048672227 Iterations, force evaluations = 50 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3959 | 1.3959 | 1.3959 | 0.0 | 98.90 Neigh | 0.0052906 | 0.0052906 | 0.0052906 | 0.0 | 0.37 Comm | 0.0060602 | 0.0060602 | 0.0060602 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004237 | | | 0.30 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7434.00 ave 7434 max 7434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112420.0 ave 112420 max 112420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112420 Ave neighs/atom = 124.91111 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.696 | 7.696 | 7.696 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -3975.8519 0 -3975.8519 -10959.726 9978.9075 55 0 -3975.98 0 -3975.98 -4122.7472 9940.9247 Loop time of 0.125886 on 1 procs for 5 steps with 900 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 = -3975.85188187509 -3975.97987357961 -3975.979993156 Force two-norm initial, final = 75.324926 0.27333744 Force max component initial, final = 67.803304 0.052099103 Final line search alpha, max atom move = 0.00043706013 2.2770440e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12367 | 0.12367 | 0.12367 | 0.0 | 98.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042624 | 0.00042624 | 0.00042624 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001791 | | | 1.42 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7461.00 ave 7461 max 7461 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112580.0 ave 112580 max 112580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112580 Ave neighs/atom = 125.08889 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 17 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) = 7.327 | 7.327 | 7.327 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3975.98 0 -3975.98 -4122.7472 Loop time of 1.771e-06 on 1 procs for 0 steps with 900 atoms 225.9% 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 | | 1.771e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7461.00 ave 7461 max 7461 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112976.0 ave 112976 max 112976 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 = 112976 Ave neighs/atom = 125.52889 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) = 7.327 | 7.327 | 7.327 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 -3975.98 -3975.98 26.50653 75.259083 4.9832764 -4122.7472 -4122.7472 4.8335658 -12370.664 -2.4114051 2.2933532 644.53587 Loop time of 2.166e-06 on 1 procs for 0 steps with 900 atoms 184.7% 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 | | 2.166e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7461.00 ave 7461 max 7461 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112976.0 ave 112976 max 112976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225952.0 ave 225952 max 225952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225952 Ave neighs/atom = 251.05778 Neighbor list builds = 0 Dangerous builds = 0 900 -3975.979993156 eV 2.29335323558238 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01