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 -56.822783 0.0000000) to (28.411391 56.822783 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9338850 3.9338850 3.5239994 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -56.822783 0.0000000) to (28.411391 56.822783 3.5239994) create_atoms CPU = 0.001 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9338850 3.9338850 3.5239994 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -56.822783 0.0000000) to (28.411391 56.822783 3.5239994) create_atoms CPU = 0.001 seconds 522 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 = 7 26 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 6 atoms, new total = 1036 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 = 7 26 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) = 7.772 | 7.772 | 7.772 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3666.2524 0 -3666.2524 136934.26 64 0 -4586.1925 0 -4586.1925 -225.55884 Loop time of 2.44056 on 1 procs for 64 steps with 1036 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3666.25237982622 -4586.1890968612 -4586.19253031377 Force two-norm initial, final = 1467.4088 0.21347268 Force max component initial, final = 470.35225 0.042712605 Final line search alpha, max atom move = 1.0000000 0.042712605 Iterations, force evaluations = 64 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4062 | 2.4062 | 2.4062 | 0.0 | 98.59 Neigh | 0.0075296 | 0.0075296 | 0.0075296 | 0.0 | 0.31 Comm | 0.017569 | 0.017569 | 0.017569 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009258 | | | 0.38 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11602.0 ave 11602 max 11602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131888.0 ave 131888 max 131888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131888 Ave neighs/atom = 127.30502 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.774 | 7.774 | 7.774 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -4586.1925 0 -4586.1925 -225.55884 11378.39 66 0 -4586.199 0 -4586.199 -2.6211846 11376.826 Loop time of 0.107898 on 1 procs for 2 steps with 1036 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 = -4586.19253031379 -4586.19785861022 -4586.19898752228 Force two-norm initial, final = 10.251982 0.25657593 Force max component initial, final = 8.6839640 0.10883843 Final line search alpha, max atom move = 0.00010311554 1.1222933e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10543 | 0.10543 | 0.10543 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047796 | 0.00047796 | 0.00047796 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001988 | | | 1.84 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11639.0 ave 11639 max 11639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130506.0 ave 130506 max 130506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130506 Ave neighs/atom = 125.97104 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 = 7 26 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) = 7.405 | 7.405 | 7.405 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4586.199 0 -4586.199 -2.6211846 Loop time of 2.389e-06 on 1 procs for 0 steps with 1036 atoms 167.4% 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 | | 2.389e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11639.0 ave 11639 max 11639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130528.0 ave 130528 max 130528 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 = 130528 Ave neighs/atom = 125.99228 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) = 7.405 | 7.405 | 7.405 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 -4586.199 -4586.199 28.410807 113.53571 3.5269968 -2.6211846 -2.6211846 -15.327191 4.1006659 3.3629711 2.3100757 196.99784 Loop time of 2.342e-06 on 1 procs for 0 steps with 1036 atoms 256.2% 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 | | 2.342e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11639.0 ave 11639 max 11639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130528.0 ave 130528 max 130528 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 261056.0 ave 261056 max 261056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261056 Ave neighs/atom = 251.98456 Neighbor list builds = 0 Dangerous builds = 0 1036 -4586.19898752228 eV 2.31007574484719 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03