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 -40.798665 0) to (49.967956 40.798665 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.359558 5.9343512 6.3523435 Created 1318 atoms using lattice units in orthogonal box = (0 -40.798665 0) to (49.967956 40.798665 9.5285152) create_atoms CPU = 0.001 seconds 1318 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.359558 5.9343512 6.3523435 Created 1324 atoms using lattice units in orthogonal box = (0 -40.798665 0) to (49.967956 40.798665 9.5285152) create_atoms CPU = 0.001 seconds 1324 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 = 12 19 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 14 atoms, new total = 2628 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 = 12 19 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) = 8.65 | 8.65 | 8.65 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6243.0751 0 -6243.0751 201956.95 84 0 -10166.901 0 -10166.901 2667.3444 Loop time of 2.11348 on 1 procs for 84 steps with 2628 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 = -6243.07505313973 -10166.8939927191 -10166.9012209247 Force two-norm initial, final = 2557.6549 0.3090081 Force max component initial, final = 303.94063 0.071848751 Final line search alpha, max atom move = 1 0.071848751 Iterations, force evaluations = 84 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0846 | 2.0846 | 2.0846 | 0.0 | 98.63 Neigh | 0.017816 | 0.017816 | 0.017816 | 0.0 | 0.84 Comm | 0.0054604 | 0.0054604 | 0.0054604 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005637 | | | 0.27 Nlocal: 2628 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9702 ave 9702 max 9702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 260963 ave 260963 max 260963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260963 Ave neighs/atom = 99.300989 Neighbor list builds = 3 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 : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.65 | 8.65 | 8.65 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -10166.901 0 -10166.901 2667.3444 38850.155 89 0 -10167.28 0 -10167.28 -0.99121334 38898.957 Loop time of 0.11092 on 1 procs for 5 steps with 2628 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 = -10166.9012209247 -10167.2738422545 -10167.2797728552 Force two-norm initial, final = 179.44021 1.0959657 Force max component initial, final = 161.42914 0.82668684 Final line search alpha, max atom move = 2.4084259e-05 1.9910139e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10943 | 0.10943 | 0.10943 | 0.0 | 98.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026374 | 0.00026374 | 0.00026374 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001224 | | | 1.10 Nlocal: 2628 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9643 ave 9643 max 9643 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 260796 ave 260796 max 260796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260796 Ave neighs/atom = 99.237443 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 = 12 19 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) = 8.279 | 8.279 | 8.279 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10167.28 0 -10167.28 -0.99121334 Loop time of 5.51e-07 on 1 procs for 0 steps with 2628 atoms 181.5% 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 | | 5.51e-07 | | |100.00 Nlocal: 2628 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9614 ave 9614 max 9614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 260593 ave 260593 max 260593 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 = 260593 Ave neighs/atom = 99.160198 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) = 8.279 | 8.279 | 8.279 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 -10167.28 -10167.28 49.992516 81.91012 9.4993829 -0.99121334 -0.99121334 -34.066447 15.631847 15.460961 2.525978 1671.8519 Loop time of 5.62e-07 on 1 procs for 0 steps with 2628 atoms 355.9% 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 | | 5.62e-07 | | |100.00 Nlocal: 2628 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9614 ave 9614 max 9614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 260593 ave 260593 max 260593 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 521186 ave 521186 max 521186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 521186 Ave neighs/atom = 198.3204 Neighbor list builds = 0 Dangerous builds = 0 2628 -10167.2797728552 eV 2.52597804343208 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02