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 -47.323893 0) to (23.661947 47.323893 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4765845 4.4765845 3.8900001 Created 296 atoms using lattice units in orthogonal box = (0 -47.323893 0) to (23.661947 47.323893 3.8900001) create_atoms CPU = 0.000 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4765845 4.4765845 3.8900001 Created 298 atoms using lattice units in orthogonal box = (0 -47.323893 0) to (23.661947 47.323893 3.8900001) create_atoms CPU = 0.000 seconds 298 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 22 1 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 = 588 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 22 1 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) = 7.165 | 7.165 | 7.165 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1793.4794 0 -1793.4794 119414.35 66 0 -2275.9664 0 -2275.9664 -2545.3315 Loop time of 0.388127 on 1 procs for 66 steps with 588 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1793.47941154883 -2275.96419007699 -2275.96636684498 Force two-norm initial, final = 849.96212 0.15253048 Force max component initial, final = 293.33718 0.039757183 Final line search alpha, max atom move = 0.73813674 0.029346238 Iterations, force evaluations = 66 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38259 | 0.38259 | 0.38259 | 0.0 | 98.57 Neigh | 0.0013383 | 0.0013383 | 0.0013383 | 0.0 | 0.34 Comm | 0.0029528 | 0.0029528 | 0.0029528 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001248 | | | 0.32 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6726 ave 6726 max 6726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58400 ave 58400 max 58400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58400 Ave neighs/atom = 99.319728 Neighbor list builds = 1 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 : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.165 | 7.165 | 7.165 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -2275.9664 0 -2275.9664 -2545.3315 8711.853 68 0 -2275.9778 0 -2275.9778 -5.441508 8700.6229 Loop time of 0.0158286 on 1 procs for 2 steps with 588 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2275.96636684498 -2275.97588251643 -2275.97784701797 Force two-norm initial, final = 24.340803 0.31977539 Force max component initial, final = 16.674785 0.24530553 Final line search alpha, max atom move = 0.00034944315 8.5720336e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.015378 | 0.015378 | 0.015378 | 0.0 | 97.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011944 | 0.00011944 | 0.00011944 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003317 | | | 2.10 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6702 ave 6702 max 6702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58408 ave 58408 max 58408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58408 Ave neighs/atom = 99.333333 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 22 1 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) = 6.796 | 6.796 | 6.796 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2275.9778 0 -2275.9778 -5.441508 Loop time of 6.01e-07 on 1 procs for 0 steps with 588 atoms 166.4% 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 | | 6.01e-07 | | |100.00 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6720 ave 6720 max 6720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58414 ave 58414 max 58414 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 = 58414 Ave neighs/atom = 99.343537 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) = 6.796 | 6.796 | 6.796 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 -2275.9778 -2275.9778 23.633037 94.598512 3.891764 -5.441508 -5.441508 18.183953 -45.148278 10.639801 2.5580346 241.91256 Loop time of 4.41e-07 on 1 procs for 0 steps with 588 atoms 453.5% 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 | | 4.41e-07 | | |100.00 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6720 ave 6720 max 6720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58414 ave 58414 max 58414 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 116828 ave 116828 max 116828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116828 Ave neighs/atom = 198.68707 Neighbor list builds = 0 Dangerous builds = 0 588 -2275.97784701797 eV 2.55803462643363 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00