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 -44.692698 0) to (31.60251 44.692698 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7882591 6.0944588 5.5012908 Created 528 atoms using lattice units in orthogonal box = (0 -44.692698 0) to (31.60251 44.692698 5.5012908) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7882591 6.0944588 5.5012908 Created 532 atoms using lattice units in orthogonal box = (0 -44.692698 0) to (31.60251 44.692698 5.5012908) create_atoms CPU = 0.000 seconds 532 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 = 8 21 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 4 atoms, new total = 1056 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 = 8 21 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) = 7.721 | 7.721 | 7.721 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2706.1137 0 -2706.1137 181649.53 104 0 -4087.6228 0 -4087.6228 10024.967 Loop time of 1.06327 on 1 procs for 104 steps with 1056 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2706.11371481751 -4087.6192494928 -4087.62277857768 Force two-norm initial, final = 1518.1534 0.21484398 Force max component initial, final = 322.55109 0.029621328 Final line search alpha, max atom move = 1 0.029621328 Iterations, force evaluations = 104 192 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0501 | 1.0501 | 1.0501 | 0.0 | 98.76 Neigh | 0.0045931 | 0.0045931 | 0.0045931 | 0.0 | 0.43 Comm | 0.0053132 | 0.0053132 | 0.0053132 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00331 | | | 0.31 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7396 ave 7396 max 7396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105168 ave 105168 max 105168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105168 Ave neighs/atom = 99.590909 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 : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.722 | 7.722 | 7.722 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -4087.6228 0 -4087.6228 10024.967 15540.062 109 0 -4087.9451 0 -4087.9451 -210.49794 15619.195 Loop time of 0.039118 on 1 procs for 5 steps with 1056 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 = -4087.62277857768 -4087.94247103643 -4087.94511330298 Force two-norm initial, final = 175.45681 4.566671 Force max component initial, final = 133.11561 3.6723186 Final line search alpha, max atom move = 6.7680213e-05 0.0002485433 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.038302 | 0.038302 | 0.038302 | 0.0 | 97.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017458 | 0.00017458 | 0.00017458 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006413 | | | 1.64 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7393 ave 7393 max 7393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105092 ave 105092 max 105092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105092 Ave neighs/atom = 99.518939 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 = 8 21 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) = 7.353 | 7.353 | 7.353 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4087.9451 0 -4087.9451 -210.49794 Loop time of 6.51e-07 on 1 procs for 0 steps with 1056 atoms 153.6% 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 | | 6.51e-07 | | |100.00 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7393 ave 7393 max 7393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104944 ave 104944 max 104944 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 = 104944 Ave neighs/atom = 99.378788 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) = 7.353 | 7.353 | 7.353 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 -4087.9451 -4087.9451 31.650012 89.745683 5.4988414 -210.49794 -210.49794 -276.13199 21.167375 -376.5292 2.5947639 899.20272 Loop time of 5.01e-07 on 1 procs for 0 steps with 1056 atoms 399.2% 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 | | 5.01e-07 | | |100.00 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7393 ave 7393 max 7393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104944 ave 104944 max 104944 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 209888 ave 209888 max 209888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209888 Ave neighs/atom = 198.75758 Neighbor list builds = 0 Dangerous builds = 0 1056 -4087.94511330298 eV 2.59476385199558 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01