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 -66.494212 0.0000000) to (33.245344 66.494212 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8560615 4.8560615 3.5239994 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -66.494212 0.0000000) to (33.245344 66.494212 3.5239994) create_atoms CPU = 0.003 seconds 714 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8560615 4.8560615 3.5239994 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -66.494212 0.0000000) to (33.245344 66.494212 3.5239994) create_atoms CPU = 0.002 seconds 714 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 = 8 30 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 12 atoms, new total = 1416 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 = 8 30 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) = 7.943 | 7.943 | 7.943 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6238.9813 0 -6238.9813 8496.4396 45 0 -6269.5808 0 -6269.5808 -3350.4006 Loop time of 4.10417 on 1 procs for 45 steps with 1416 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 = -6238.98129071752 -6269.57569109219 -6269.58082604549 Force two-norm initial, final = 40.133393 0.26630612 Force max component initial, final = 12.821710 0.070274290 Final line search alpha, max atom move = 1.0000000 0.070274290 Iterations, force evaluations = 45 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0441 | 4.0441 | 4.0441 | 0.0 | 98.54 Neigh | 0.02125 | 0.02125 | 0.02125 | 0.0 | 0.52 Comm | 0.024532 | 0.024532 | 0.024532 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01433 | | | 0.35 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14551.0 ave 14551 max 14551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 176666.0 ave 176666 max 176666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176666 Ave neighs/atom = 124.76412 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 : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.946 | 7.946 | 7.946 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -6269.5808 0 -6269.5808 -3350.4006 15580.468 47 0 -6269.6005 0 -6269.6005 -913.55093 15559.894 Loop time of 0.281785 on 1 procs for 2 steps with 1416 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 = -6269.58082604549 -6269.60041398535 -6269.60049610242 Force two-norm initial, final = 40.867883 0.27653272 Force max component initial, final = 32.809068 0.064805207 Final line search alpha, max atom move = 0.00090074631 5.8373051e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27632 | 0.27632 | 0.27632 | 0.0 | 98.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014968 | 0.0014968 | 0.0014968 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003972 | | | 1.41 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14551.0 ave 14551 max 14551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 176574.0 ave 176574 max 176574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176574 Ave neighs/atom = 124.69915 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 = 8 30 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) = 7.578 | 7.578 | 7.578 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6269.6005 0 -6269.6005 -913.55093 Loop time of 6.264e-06 on 1 procs for 0 steps with 1416 atoms 191.6% 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 | | 6.264e-06 | | |100.00 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14551.0 ave 14551 max 14551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 176632.0 ave 176632 max 176632 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 = 176632 Ave neighs/atom = 124.74011 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) = 7.578 | 7.578 | 7.578 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 -6269.6005 -6269.6005 33.217505 132.98842 3.5222955 -913.55093 -913.55093 -0.21032312 -2734.2866 -6.1558231 2.2322741 409.64185 Loop time of 6.886e-06 on 1 procs for 0 steps with 1416 atoms 290.4% 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 | | 6.886e-06 | | |100.00 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14551.0 ave 14551 max 14551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 176632.0 ave 176632 max 176632 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 353264.0 ave 353264 max 353264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 353264 Ave neighs/atom = 249.48023 Neighbor list builds = 0 Dangerous builds = 0 1416 -6269.60049610242 eV 2.2322740698401 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05