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 -42.874827 0.0000000) to (21.435651 42.874827 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0553935 4.0553935 3.5239994 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -42.874827 0.0000000) to (21.435651 42.874827 3.5239994) create_atoms CPU = 0.002 seconds 298 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0553935 4.0553935 3.5239994 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -42.874827 0.0000000) to (21.435651 42.874827 3.5239994) create_atoms CPU = 0.001 seconds 298 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 = 5 20 1 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 8 atoms, new total = 588 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 = 5 20 1 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) = 7.184 | 7.184 | 7.184 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2580.7965 0 -2580.7965 16160.881 18 0 -2599.5494 0 -2599.5494 -2178.1627 Loop time of 0.726701 on 1 procs for 18 steps with 588 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 = -2580.79652366729 -2599.54687205295 -2599.54939591954 Force two-norm initial, final = 46.139662 0.14637256 Force max component initial, final = 13.980119 0.022187701 Final line search alpha, max atom move = 1.0000000 0.022187701 Iterations, force evaluations = 18 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7184 | 0.7184 | 0.7184 | 0.0 | 98.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0049584 | 0.0049584 | 0.0049584 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003347 | | | 0.46 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7152.00 ave 7152 max 7152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 72940.0 ave 72940 max 72940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72940 Ave neighs/atom = 124.04762 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 : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.184 | 7.184 | 7.184 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -2599.5494 0 -2599.5494 -2178.1627 6477.4622 20 0 -2599.5533 0 -2599.5533 -713.99999 6472.2915 Loop time of 0.120249 on 1 procs for 2 steps with 588 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 = -2599.54939591954 -2599.55266190619 -2599.55325606477 Force two-norm initial, final = 9.9943413 0.14758820 Force max component initial, final = 9.0051189 0.020824475 Final line search alpha, max atom move = 0.00052242298 1.0879184e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11752 | 0.11752 | 0.11752 | 0.0 | 97.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076199 | 0.00076199 | 0.00076199 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001967 | | | 1.64 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7152.00 ave 7152 max 7152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73768.0 ave 73768 max 73768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73768 Ave neighs/atom = 125.45578 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 = 5 20 1 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) = 6.815 | 6.815 | 6.815 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2599.5533 0 -2599.5533 -713.99999 Loop time of 6.575e-06 on 1 procs for 0 steps with 588 atoms 152.1% 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 | | 6.575e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7152.00 ave 7152 max 7152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73828.0 ave 73828 max 73828 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 = 73828 Ave neighs/atom = 125.55782 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) = 6.815 | 6.815 | 6.815 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 -2599.5533 -2599.5533 21.416197 85.749654 3.5243849 -713.99999 -713.99999 -1.7465671 -2135.9651 -4.2883528 2.3100135 193.33735 Loop time of 6.585e-06 on 1 procs for 0 steps with 588 atoms 334.1% 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 | | 6.585e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7152.00 ave 7152 max 7152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73828.0 ave 73828 max 73828 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 147656.0 ave 147656 max 147656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147656 Ave neighs/atom = 251.11565 Neighbor list builds = 0 Dangerous builds = 0 588 -2599.55325606477 eV 2.31001345553031 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01