LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -51.606683 0) to (31.60251 51.606683 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7459109 5.8643957 6.3523435 Created 1044 atoms using lattice units in orthogonal box = (0 -51.606683 0) to (31.60251 51.606683 9.5285152) create_atoms CPU = 0.001 seconds 1044 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7459109 5.8643957 6.3523435 Created 1068 atoms using lattice units in orthogonal box = (0 -51.606683 0) to (31.60251 51.606683 9.5285152) create_atoms CPU = 0.001 seconds 1068 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 24 3 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 0 atoms, new total = 2112 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:187) 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 24 3 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) = 8.529 | 8.529 | 8.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6968.2466 0 -6968.2466 107027.87 91 0 -8201.2761 0 -8201.2761 3095.0774 Loop time of 1.51651 on 1 procs for 91 steps with 2112 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6968.24660893971 -8201.27039011995 -8201.27614673495 Force two-norm initial, final = 1008.7306 0.25605122 Force max component initial, final = 291.75629 0.04034726 Final line search alpha, max atom move = 1 0.04034726 Iterations, force evaluations = 91 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4877 | 1.4877 | 1.4877 | 0.0 | 98.10 Neigh | 0.018849 | 0.018849 | 0.018849 | 0.0 | 1.24 Comm | 0.0048483 | 0.0048483 | 0.0048483 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005085 | | | 0.34 Nlocal: 2112 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9028 ave 9028 max 9028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210705 ave 210705 max 210705 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210705 Ave neighs/atom = 99.765625 Neighbor list builds = 4 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.529 | 8.529 | 8.529 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -8201.2761 0 -8201.2761 3095.0774 31080.124 97 0 -8201.5651 0 -8201.5651 13.512138 31126.58 Loop time of 0.0966761 on 1 procs for 6 steps with 2112 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8201.27614673495 -8201.56464032911 -8201.56512529046 Force two-norm initial, final = 144.18731 0.77258043 Force max component initial, final = 140.98545 0.53422503 Final line search alpha, max atom move = 0.00010428726 5.5712865e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.095189 | 0.095189 | 0.095189 | 0.0 | 98.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026619 | 0.00026619 | 0.00026619 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001221 | | | 1.26 Nlocal: 2112 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8807 ave 8807 max 8807 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210631 ave 210631 max 210631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210631 Ave neighs/atom = 99.730587 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 24 3 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) = 8.158 | 8.158 | 8.158 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8201.5651 0 -8201.5651 13.512138 Loop time of 4.71e-07 on 1 procs for 0 steps with 2112 atoms 212.3% 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 | | 4.71e-07 | | |100.00 Nlocal: 2112 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8807 ave 8807 max 8807 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210576 ave 210576 max 210576 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210576 Ave neighs/atom = 99.704545 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.158 | 8.158 | 8.158 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 -8201.5651 -8201.5651 31.538623 103.67338 9.5196591 13.512138 13.512138 9.3392317 3.724609 27.472574 2.6047673 749.18401 Loop time of 4.6e-07 on 1 procs for 0 steps with 2112 atoms 434.8% 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 | | 4.6e-07 | | |100.00 Nlocal: 2112 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8807 ave 8807 max 8807 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210576 ave 210576 max 210576 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 421152 ave 421152 max 421152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 421152 Ave neighs/atom = 199.40909 Neighbor list builds = 0 Dangerous builds = 0 2112 -8201.56512529046 eV 2.60476732698506 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01