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 -47.163744 0) to (38.509036 47.163744 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5012908 5.4543106 6.3523435 Created 1176 atoms using lattice units in orthogonal box = (0 -47.163744 0) to (38.509036 47.163744 9.5285152) create_atoms CPU = 0.001 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5012908 5.4543106 6.3523435 Created 1184 atoms using lattice units in orthogonal box = (0 -47.163744 0) to (38.509036 47.163744 9.5285152) create_atoms CPU = 0.001 seconds 1184 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 = 9 22 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 24 atoms, new total = 2336 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 = 9 22 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) = 8.586 | 8.586 | 8.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7849.6634 0 -7849.6634 99315.576 86 0 -9037.4119 0 -9037.4119 -806.44564 Loop time of 2.00303 on 1 procs for 86 steps with 2336 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7849.66341854918 -9037.40466068605 -9037.41191917757 Force two-norm initial, final = 1191.4968 0.32895346 Force max component initial, final = 181.7516 0.034710902 Final line search alpha, max atom move = 1 0.034710902 Iterations, force evaluations = 86 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9809 | 1.9809 | 1.9809 | 0.0 | 98.90 Neigh | 0.011014 | 0.011014 | 0.011014 | 0.0 | 0.55 Comm | 0.00562 | 0.00562 | 0.00562 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005487 | | | 0.27 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9462 ave 9462 max 9462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231528 ave 231528 max 231528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231528 Ave neighs/atom = 99.113014 Neighbor list builds = 2 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 : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.586 | 8.586 | 8.586 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -9037.4119 0 -9037.4119 -806.44564 34611.957 90 0 -9037.5646 0 -9037.5646 54.383334 34595.357 Loop time of 0.0841921 on 1 procs for 4 steps with 2336 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9037.41191917755 -9037.55971999666 -9037.56460307157 Force two-norm initial, final = 88.760462 5.0736959 Force max component initial, final = 65.593201 4.6663114 Final line search alpha, max atom move = 2.7610388e-05 0.00012883867 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.083019 | 0.083019 | 0.083019 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021573 | 0.00021573 | 0.00021573 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009569 | | | 1.14 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9154 ave 9154 max 9154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231840 ave 231840 max 231840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231840 Ave neighs/atom = 99.246575 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 = 9 22 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) = 8.215 | 8.215 | 8.215 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9037.5646 0 -9037.5646 54.383334 Loop time of 5.31e-07 on 1 procs for 0 steps with 2336 atoms 376.6% 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 | | 5.31e-07 | | |100.00 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9169 ave 9169 max 9169 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231728 ave 231728 max 231728 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 = 231728 Ave neighs/atom = 99.19863 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) = 8.215 | 8.215 | 8.215 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 -9037.5646 -9037.5646 38.463203 94.589809 9.5088506 54.383334 54.383334 -82.689716 30.179993 215.65972 2.5116241 1597.2225 Loop time of 5.31e-07 on 1 procs for 0 steps with 2336 atoms 565.0% 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 | | 5.31e-07 | | |100.00 Nlocal: 2336 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9169 ave 9169 max 9169 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231728 ave 231728 max 231728 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 463456 ave 463456 max 463456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463456 Ave neighs/atom = 198.39726 Neighbor list builds = 0 Dangerous builds = 0 2336 -9037.56460307157 eV 2.51162408871894 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02