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 -63.825867 0.0000000) to (22.564606 63.825867 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0539187 5.4482488 4.9836877 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.825867 0.0000000) to (22.564606 63.825867 4.9836877) create_atoms CPU = 0.002 seconds 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0539187 5.4482488 4.9836877 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.825867 0.0000000) to (22.564606 63.825867 4.9836877) create_atoms CPU = 0.001 seconds 658 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 29 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 12 atoms, new total = 1304 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 29 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) = 7.925 | 7.925 | 7.925 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5744.6149 0 -5744.6149 9495.3483 36 0 -5779.1662 0 -5779.1662 -7608.2607 Loop time of 1.48066 on 1 procs for 36 steps with 1304 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5744.61494280082 -5779.1611281805 -5779.16620118407 Force two-norm initial, final = 74.851433 0.24309134 Force max component initial, final = 24.662136 0.019979588 Final line search alpha, max atom move = 1.0000000 0.019979588 Iterations, force evaluations = 36 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4604 | 1.4604 | 1.4604 | 0.0 | 98.63 Neigh | 0.0073302 | 0.0073302 | 0.0073302 | 0.0 | 0.50 Comm | 0.0076693 | 0.0076693 | 0.0076693 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00528 | | | 0.36 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10657.0 ave 10657 max 10657 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163602.0 ave 163602 max 163602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163602 Ave neighs/atom = 125.46166 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.925 | 7.925 | 7.925 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -5779.1662 0 -5779.1662 -7608.2607 14355.069 39 0 -5779.2506 0 -5779.2506 -3131.5921 14320.074 Loop time of 0.11365 on 1 procs for 3 steps with 1304 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 = -5779.16620118407 -5779.24828978363 -5779.25061029727 Force two-norm initial, final = 74.547355 0.27540013 Force max component initial, final = 71.212897 0.071869719 Final line search alpha, max atom move = 0.00013309927 9.5658073e-06 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11169 | 0.11169 | 0.11169 | 0.0 | 98.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039632 | 0.00039632 | 0.00039632 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001561 | | | 1.37 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10612.0 ave 10612 max 10612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163718.0 ave 163718 max 163718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163718 Ave neighs/atom = 125.55061 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 29 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) = 7.556 | 7.556 | 7.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5779.2506 0 -5779.2506 -3131.5921 Loop time of 2.202e-06 on 1 procs for 0 steps with 1304 atoms 181.7% 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 | | 2.202e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10612.0 ave 10612 max 10612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163830.0 ave 163830 max 163830 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 = 163830 Ave neighs/atom = 125.63650 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) = 7.556 | 7.556 | 7.556 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 -5779.2506 -5779.2506 22.562022 127.65173 4.9721076 -3131.5921 -3131.5921 -6.0038767 -9380.75 -8.0223342 2.3235164 435.71482 Loop time of 2.178e-06 on 1 procs for 0 steps with 1304 atoms 229.6% 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 | | 2.178e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10612.0 ave 10612 max 10612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163830.0 ave 163830 max 163830 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 327660.0 ave 327660 max 327660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327660 Ave neighs/atom = 251.27301 Neighbor list builds = 0 Dangerous builds = 0 1304 -5779.25061029727 eV 2.32351638717031 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01