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 (28.585546 40.426066 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3523435 5.240416 5.5012908 Created 432 atoms using lattice units in orthogonal box = (0 -40.426066 0) to (28.585546 40.426066 5.5012908) create_atoms CPU = 0.000 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3523435 5.240416 5.5012908 Created 440 atoms using lattice units in orthogonal box = (0 -40.426066 0) to (28.585546 40.426066 5.5012908) create_atoms CPU = 0.000 seconds 440 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 = 7 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 8 atoms, new total = 864 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 = 7 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) = 7.265 | 7.265 | 7.265 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3251.9947 0 -3251.9947 68935.889 17 0 -3344.4305 0 -3344.4305 10066.624 Loop time of 0.145816 on 1 procs for 17 steps with 864 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 = -3251.99465004735 -3344.42910723776 -3344.4304931393 Force two-norm initial, final = 155.68673 0.14558319 Force max component initial, final = 23.978541 0.019232525 Final line search alpha, max atom move = 1 0.019232525 Iterations, force evaluations = 17 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14461 | 0.14461 | 0.14461 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072696 | 0.00072696 | 0.00072696 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004779 | | | 0.33 Nlocal: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6359 ave 6359 max 6359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86544 ave 86544 max 86544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86544 Ave neighs/atom = 100.16667 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 : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.265 | 7.265 | 7.265 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -3344.4305 0 -3344.4305 10066.624 12714.596 23 0 -3344.688 0 -3344.688 -32.667938 12779.275 Loop time of 0.0404014 on 1 procs for 6 steps with 864 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 = -3344.4304931393 -3344.68512409809 -3344.68795447652 Force two-norm initial, final = 141.04261 0.60415749 Force max component initial, final = 100.61331 0.39733326 Final line search alpha, max atom move = 9.2406887e-05 3.671633e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039502 | 0.039502 | 0.039502 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019279 | 0.00019279 | 0.00019279 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007067 | | | 1.75 Nlocal: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6359 ave 6359 max 6359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85920 ave 85920 max 85920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85920 Ave neighs/atom = 99.444444 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 = 7 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) = 6.897 | 6.897 | 6.897 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3344.688 0 -3344.688 -32.667938 Loop time of 6.11e-07 on 1 procs for 0 steps with 864 atoms 163.7% 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 | | 6.11e-07 | | |100.00 Nlocal: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6359 ave 6359 max 6359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85872 ave 85872 max 85872 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 = 85872 Ave neighs/atom = 99.388889 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) = 6.897 | 6.897 | 6.897 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 -3344.688 -3344.688 28.607595 81.259038 5.4973476 -32.667938 -32.667938 -49.853301 -40.981605 -7.1689098 2.5964675 520.19337 Loop time of 1.123e-06 on 1 procs for 0 steps with 864 atoms 445.2% 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 | | 1.123e-06 | | |100.00 Nlocal: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6359 ave 6359 max 6359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85872 ave 85872 max 85872 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 171744 ave 171744 max 171744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171744 Ave neighs/atom = 198.77778 Neighbor list builds = 0 Dangerous builds = 0 864 -3344.68795447652 eV 2.59646751924592 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00