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 -40.426066 0) to (9.5285152 40.426066 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3523435 6.7376777 5.5012908 Created 143 atoms using lattice units in orthogonal box = (0 -40.426066 0) to (9.5285152 40.426066 5.5012908) create_atoms CPU = 0.000 seconds 143 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3523435 6.7376777 5.5012908 Created 151 atoms using lattice units in orthogonal box = (0 -40.426066 0) to (9.5285152 40.426066 5.5012908) create_atoms CPU = 0.000 seconds 151 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 = 3 19 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 6 atoms, new total = 288 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 = 3 19 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) = 7.063 | 7.063 | 7.063 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1118.0732 0 -1118.0732 4035.2141 32 0 -1120.0736 0 -1120.0736 -438.30919 Loop time of 0.0907703 on 1 procs for 32 steps with 288 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 = -1118.07323413683 -1120.07290398093 -1120.07363802421 Force two-norm initial, final = 9.1018573 0.069557751 Force max component initial, final = 5.2419715 0.010438988 Final line search alpha, max atom move = 1 0.010438988 Iterations, force evaluations = 32 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.089596 | 0.089596 | 0.089596 | 0.0 | 98.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083595 | 0.00083595 | 0.00083595 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003378 | | | 0.37 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3860 ave 3860 max 3860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28752 ave 28752 max 28752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28752 Ave neighs/atom = 99.833333 Neighbor list builds = 0 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.063 | 7.063 | 7.063 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -1120.0736 0 -1120.0736 -438.30919 4238.1988 33 0 -1120.0738 0 -1120.0738 39.799097 4237.1675 Loop time of 0.00448409 on 1 procs for 1 steps with 288 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 = -1120.07363802421 -1120.07363802421 -1120.07379773384 Force two-norm initial, final = 2.1323421 0.56680307 Force max component initial, final = 1.4649389 0.53956277 Final line search alpha, max atom move = 0.00068262234 0.0003683176 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0043493 | 0.0043493 | 0.0043493 | 0.0 | 97.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 3.7169e-05 | 3.7169e-05 | 3.7169e-05 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.757e-05 | | | 2.18 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3616 ave 3616 max 3616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28832 ave 28832 max 28832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28832 Ave neighs/atom = 100.11111 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 = 3 19 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) = 6.692 | 6.692 | 6.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1120.0738 0 -1120.0738 39.799097 Loop time of 5.61e-07 on 1 procs for 0 steps with 288 atoms 0.0% 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 | | 5.61e-07 | | |100.00 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3616 ave 3616 max 3616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28832 ave 28832 max 28832 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 = 28832 Ave neighs/atom = 100.11111 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) = 6.692 | 6.692 | 6.692 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 -1120.0738 -1120.0738 9.5275387 80.848869 5.5007381 39.799097 39.799097 -46.563348 204.01362 -38.052985 2.7452263 120.89081 Loop time of 4.81e-07 on 1 procs for 0 steps with 288 atoms 207.9% 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 | | 4.81e-07 | | |100.00 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3616 ave 3616 max 3616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28832 ave 28832 max 28832 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57664 ave 57664 max 57664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57664 Ave neighs/atom = 200.22222 Neighbor list builds = 0 Dangerous builds = 0 288 -1120.07379773384 eV 2.7452262570669 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00