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 -41.896583 0) to (20.948291 41.896583 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0564841 5.0564841 3.8900001 Created 231 atoms using lattice units in orthogonal box = (0 -41.896583 0) to (20.948291 41.896583 3.8900001) create_atoms CPU = 0.000 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0564841 5.0564841 3.8900001 Created 233 atoms using lattice units in orthogonal box = (0 -41.896583 0) to (20.948291 41.896583 3.8900001) create_atoms CPU = 0.000 seconds 233 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 19 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 = 464 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 19 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) = 7.104 | 7.104 | 7.104 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1436.8934 0 -1436.8934 191615.98 99 0 -1793.2138 0 -1793.2138 14642.293 Loop time of 0.485877 on 1 procs for 99 steps with 464 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 = -1436.89336169024 -1793.21239602596 -1793.21384822715 Force two-norm initial, final = 601.16272 0.18263189 Force max component initial, final = 163.54312 0.064171487 Final line search alpha, max atom move = 1 0.064171487 Iterations, force evaluations = 99 191 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47958 | 0.47958 | 0.47958 | 0.0 | 98.70 Neigh | 0.0011337 | 0.0011337 | 0.0011337 | 0.0 | 0.23 Comm | 0.0036653 | 0.0036653 | 0.0036653 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001501 | | | 0.31 Nlocal: 464 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5251 ave 5251 max 5251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45995 ave 45995 max 45995 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45995 Ave neighs/atom = 99.127155 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 : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.104 | 7.104 | 7.104 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -1793.2138 0 -1793.2138 14642.293 6828.2091 110 0 -1793.6334 0 -1793.6334 366.54365 6876.3349 Loop time of 0.0332121 on 1 procs for 11 steps with 464 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 = -1793.21384822715 -1793.63295062281 -1793.63335267761 Force two-norm initial, final = 115.88656 3.0128512 Force max component initial, final = 95.742989 2.2082213 Final line search alpha, max atom move = 0.00047437862 0.001047533 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.032184 | 0.032184 | 0.032184 | 0.0 | 96.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024023 | 0.00024023 | 0.00024023 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007877 | | | 2.37 Nlocal: 464 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5239 ave 5239 max 5239 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46081 ave 46081 max 46081 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46081 Ave neighs/atom = 99.3125 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 20 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) = 6.736 | 6.736 | 6.736 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1793.6334 0 -1793.6334 366.54365 Loop time of 5.51e-07 on 1 procs for 0 steps with 464 atoms 181.5% 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 | | 5.51e-07 | | |100.00 Nlocal: 464 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5217 ave 5217 max 5217 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45996 ave 45996 max 45996 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 = 45996 Ave neighs/atom = 99.12931 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) = 6.736 | 6.736 | 6.736 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 -1793.6334 -1793.6334 20.905381 84.639902 3.8861877 366.54365 366.54365 433.68772 519.71169 146.23153 2.507707 315.01933 Loop time of 4.81e-07 on 1 procs for 0 steps with 464 atoms 207.9% 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 | | 4.81e-07 | | |100.00 Nlocal: 464 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5217 ave 5217 max 5217 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45996 ave 45996 max 45996 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91992 ave 91992 max 91992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91992 Ave neighs/atom = 198.25862 Neighbor list builds = 0 Dangerous builds = 0 464 -1793.63335267761 eV 2.50770698109921 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00