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 -38.900001 0) to (19.45 38.900001 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4460001 5.4460001 3.8900001 Created 199 atoms using lattice units in orthogonal box = (0 -38.900001 0) to (19.45 38.900001 3.8900001) create_atoms CPU = 0.000 seconds 199 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4460001 5.4460001 3.8900001 Created 201 atoms using lattice units in orthogonal box = (0 -38.900001 0) to (19.45 38.900001 3.8900001) create_atoms CPU = 0.000 seconds 201 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 = 5 18 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 0 atoms, new total = 400 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 = 5 18 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) = 7.07 | 7.07 | 7.07 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1238.379 0 -1238.379 207963.46 56 0 -1548.1723 0 -1548.1723 10443.526 Loop time of 0.231338 on 1 procs for 56 steps with 400 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 = -1238.3790138192 -1548.17084483005 -1548.17234159828 Force two-norm initial, final = 537.07445 0.16176366 Force max component initial, final = 111.55701 0.053434737 Final line search alpha, max atom move = 1 0.053434737 Iterations, force evaluations = 56 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22783 | 0.22783 | 0.22783 | 0.0 | 98.48 Neigh | 0.00089909 | 0.00089909 | 0.00089909 | 0.0 | 0.39 Comm | 0.0018267 | 0.0018267 | 0.0018267 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007798 | | | 0.34 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4775 ave 4775 max 4775 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39687 ave 39687 max 39687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39687 Ave neighs/atom = 99.2175 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.07 | 7.07 | 7.07 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -1548.1723 0 -1548.1723 10443.526 5886.3872 62 0 -1548.3353 0 -1548.3353 -238.81976 5917.1062 Loop time of 0.0178961 on 1 procs for 6 steps with 400 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 = -1548.17234159828 -1548.33468691812 -1548.33529005951 Force two-norm initial, final = 71.924064 2.3370212 Force max component initial, final = 57.742251 2.3078821 Final line search alpha, max atom move = 0.0002972021 0.00068590742 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.017344 | 0.017344 | 0.017344 | 0.0 | 96.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013696 | 0.00013696 | 0.00013696 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004155 | | | 2.32 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4757 ave 4757 max 4757 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39787 ave 39787 max 39787 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39787 Ave neighs/atom = 99.4675 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 = 5 18 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) = 6.701 | 6.701 | 6.701 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1548.3353 0 -1548.3353 -238.81976 Loop time of 6.41e-07 on 1 procs for 0 steps with 400 atoms 156.0% 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 | | 6.41e-07 | | |100.00 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4757 ave 4757 max 4757 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39730 ave 39730 max 39730 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 = 39730 Ave neighs/atom = 99.325 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) = 6.701 | 6.701 | 6.701 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 -1548.3353 -1548.3353 19.418653 78.176467 3.8977522 -238.81976 -238.81976 -623.89874 -23.070059 -69.490478 2.5086307 181.45449 Loop time of 4.21e-07 on 1 procs for 0 steps with 400 atoms 237.5% 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 | | 4.21e-07 | | |100.00 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4757 ave 4757 max 4757 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39730 ave 39730 max 39730 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 79460 ave 79460 max 79460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79460 Ave neighs/atom = 198.65 Neighbor list builds = 0 Dangerous builds = 0 400 -1548.33529005951 eV 2.50863074133908 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00