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 -39.403035 0.0000000) to (19.301740 39.403035 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1471306 4.7279413 5.7546669 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -39.403035 0.0000000) to (19.301740 39.403035 8.6320004) create_atoms CPU = 0.001 seconds 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1471306 4.7279413 5.7546669 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -39.403035 0.0000000) to (19.301740 39.403035 8.6320004) create_atoms CPU = 0.001 seconds 612 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 18 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 48 atoms, new total = 1176 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 18 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) = 7.932 | 7.932 | 7.932 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5165.7051 0 -5165.7051 -2626.0517 51 0 -5192.569 0 -5192.569 -21729.369 Loop time of 1.95152 on 1 procs for 51 steps with 1176 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 = -5165.70507862103 -5192.56515461 -5192.56901928418 Force two-norm initial, final = 23.498895 0.17793004 Force max component initial, final = 3.1668771 0.012424091 Final line search alpha, max atom move = 1.0000000 0.012424091 Iterations, force evaluations = 51 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9404 | 1.9404 | 1.9404 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058465 | 0.0058465 | 0.0058465 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005253 | | | 0.27 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7323.00 ave 7323 max 7323 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144336.0 ave 144336 max 144336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 144336 Ave neighs/atom = 122.73469 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 : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.932 | 7.932 | 7.932 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -5192.569 0 -5192.569 -21729.369 13130.086 57 0 -5193.2111 0 -5193.2111 -6387.7061 13017.256 Loop time of 0.182599 on 1 procs for 6 steps with 1176 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 = -5192.56901928419 -5193.20993337792 -5193.21108524326 Force two-norm initial, final = 207.77238 0.41506496 Force max component initial, final = 154.45136 0.058842628 Final line search alpha, max atom move = 0.00019736700 1.1613593e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17995 | 0.17995 | 0.17995 | 0.0 | 98.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045816 | 0.00045816 | 0.00045816 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002189 | | | 1.20 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7312.00 ave 7312 max 7312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145596.0 ave 145596 max 145596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 145596 Ave neighs/atom = 123.80612 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 18 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) = 7.563 | 7.563 | 7.563 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5193.2111 0 -5193.2111 -6387.7061 Loop time of 2.014e-06 on 1 procs for 0 steps with 1176 atoms 149.0% 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 | | 2.014e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7346.00 ave 7346 max 7346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145944.0 ave 145944 max 145944 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 = 145944 Ave neighs/atom = 124.10204 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) = 7.563 | 7.563 | 7.563 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 -5193.2111 -5193.2111 19.202967 78.80607 8.6018414 -6387.7061 -6387.7061 1.9000809 -19162.345 -2.6732038 2.2802642 795.41843 Loop time of 2.28e-06 on 1 procs for 0 steps with 1176 atoms 175.4% 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 | | 2.28e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7346.00 ave 7346 max 7346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145944.0 ave 145944 max 145944 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 291888.0 ave 291888 max 291888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291888 Ave neighs/atom = 248.20408 Neighbor list builds = 0 Dangerous builds = 0 1176 -5193.21108524326 eV 2.28026424440288 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02