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 -46.027101 0) to (56.371456 46.027101 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4424522 5.9177702 6.3523435 Created 1665 atoms using lattice units in orthogonal box = (0 -46.027101 0) to (56.371456 46.027101 9.5285152) create_atoms CPU = 0.001 seconds 1665 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4424522 5.9177702 6.3523435 Created 1689 atoms using lattice units in orthogonal box = (0 -46.027101 0) to (56.371456 46.027101 9.5285152) create_atoms CPU = 0.001 seconds 1689 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 = 13 21 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 = 3354 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 = 13 21 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) = 9.199 | 9.199 | 9.199 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10246.64 0 -10246.64 152852.23 150 0 -12985.126 0 -12985.126 6276.7884 Loop time of 4.70451 on 1 procs for 150 steps with 3354 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 = -10246.6401237968 -12985.11364822 -12985.1260360551 Force two-norm initial, final = 1864.7751 0.46559226 Force max component initial, final = 254.08834 0.13286967 Final line search alpha, max atom move = 0.48480207 0.064415489 Iterations, force evaluations = 150 264 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6153 | 4.6153 | 4.6153 | 0.0 | 98.10 Neigh | 0.062023 | 0.062023 | 0.062023 | 0.0 | 1.32 Comm | 0.013203 | 0.013203 | 0.013203 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01399 | | | 0.30 Nlocal: 3354 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11582 ave 11582 max 11582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 332989 ave 332989 max 332989 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332989 Ave neighs/atom = 99.281157 Neighbor list builds = 8 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 : 150 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.199 | 9.199 | 9.199 Mbytes Step Temp E_pair E_mol TotEng Press Volume 150 0 -12985.126 0 -12985.126 6276.7884 49445.652 156 0 -12985.932 0 -12985.932 0.1851364 49597.603 Loop time of 0.157522 on 1 procs for 6 steps with 3354 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 = -12985.1260360551 -12985.9211118842 -12985.9316902391 Force two-norm initial, final = 388.42115 0.79967186 Force max component initial, final = 345.86592 0.18772367 Final line search alpha, max atom move = 1.9011388e-05 3.5688875e-06 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1554 | 0.1554 | 0.1554 | 0.0 | 98.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035169 | 0.00035169 | 0.00035169 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001768 | | | 1.12 Nlocal: 3354 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11582 ave 11582 max 11582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 332993 ave 332993 max 332993 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332993 Ave neighs/atom = 99.282349 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 = 13 21 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) = 8.83 | 8.83 | 8.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12985.932 0 -12985.932 0.1851364 Loop time of 3.41e-07 on 1 procs for 0 steps with 3354 atoms 293.3% 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 | | 3.41e-07 | | |100.00 Nlocal: 3354 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11570 ave 11570 max 11570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 332674 ave 332674 max 332674 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 = 332674 Ave neighs/atom = 99.187239 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) = 8.83 | 8.83 | 8.83 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 -12985.932 -12985.932 56.379563 92.526591 9.5076333 0.1851364 0.1851364 6.065005 -0.89987065 -4.6097251 2.5133534 2151.1136 Loop time of 8.31e-07 on 1 procs for 0 steps with 3354 atoms 240.7% 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 | | 8.31e-07 | | |100.00 Nlocal: 3354 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11570 ave 11570 max 11570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 332674 ave 332674 max 332674 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 665348 ave 665348 max 665348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 665348 Ave neighs/atom = 198.37448 Neighbor list builds = 0 Dangerous builds = 0 3354 -12985.9316902391 eV 2.513353392822 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05