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 -70.450897 0) to (24.908154 70.450897 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6826754 6.014101 5.5012908 Created 656 atoms using lattice units in orthogonal box = (0 -70.450897 0) to (24.908154 70.450897 5.5012908) create_atoms CPU = 0.001 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6826754 6.014101 5.5012908 Created 658 atoms using lattice units in orthogonal box = (0 -70.450897 0) to (24.908154 70.450897 5.5012908) create_atoms CPU = 0.001 seconds 658 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 = 6 32 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 2 atoms, new total = 1312 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 = 6 32 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) = 7.884 | 7.884 | 7.884 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4434.8569 0 -4434.8569 96435.665 126 0 -5093.5202 0 -5093.5202 3097.5097 Loop time of 1.66674 on 1 procs for 126 steps with 1312 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4434.85686587117 -5093.51529928712 -5093.5201783065 Force two-norm initial, final = 934.47579 0.23275697 Force max component initial, final = 247.50094 0.037930707 Final line search alpha, max atom move = 1 0.037930707 Iterations, force evaluations = 126 239 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6468 | 1.6468 | 1.6468 | 0.0 | 98.80 Neigh | 0.0063238 | 0.0063238 | 0.0063238 | 0.0 | 0.38 Comm | 0.0085109 | 0.0085109 | 0.0085109 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005158 | | | 0.31 Nlocal: 1312 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9446 ave 9446 max 9446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130742 ave 130742 max 130742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130742 Ave neighs/atom = 99.650915 Neighbor list builds = 2 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 : 126 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.884 | 7.884 | 7.884 Mbytes Step Temp E_pair E_mol TotEng Press Volume 126 0 -5093.5202 0 -5093.5202 3097.5097 19307.35 129 0 -5093.5807 0 -5093.5807 200.47301 19335.358 Loop time of 0.0420087 on 1 procs for 3 steps with 1312 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5093.52017830649 -5093.58015597194 -5093.58073742578 Force two-norm initial, final = 72.306096 4.5701026 Force max component initial, final = 56.91716 3.6723718 Final line search alpha, max atom move = 0.0002056559 0.00075524492 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041179 | 0.041179 | 0.041179 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018481 | 0.00018481 | 0.00018481 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006449 | | | 1.54 Nlocal: 1312 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9129 ave 9129 max 9129 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130908 ave 130908 max 130908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130908 Ave neighs/atom = 99.777439 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 = 6 32 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) = 7.514 | 7.514 | 7.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5093.5807 0 -5093.5807 200.47301 Loop time of 7.02e-07 on 1 procs for 0 steps with 1312 atoms 142.5% 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 | | 7.02e-07 | | |100.00 Nlocal: 1312 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9329 ave 9329 max 9329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130852 ave 130852 max 130852 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 = 130852 Ave neighs/atom = 99.734756 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) = 7.514 | 7.514 | 7.514 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 -5093.5807 -5093.5807 24.946623 141.03163 5.4957117 200.47301 200.47301 205.3081 304.58238 91.528542 2.5789109 607.31768 Loop time of 6.71e-07 on 1 procs for 0 steps with 1312 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 | | 6.71e-07 | | |100.00 Nlocal: 1312 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9329 ave 9329 max 9329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130852 ave 130852 max 130852 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 261704 ave 261704 max 261704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261704 Ave neighs/atom = 199.46951 Neighbor list builds = 0 Dangerous builds = 0 1312 -5093.58073742578 eV 2.57891088571689 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01