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 -72.148753 0) to (25.508436 72.148753 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5254139 6.7115119 5.5012908 Created 688 atoms using lattice units in orthogonal box = (0 -72.148753 0) to (25.508436 72.148753 5.5012908) create_atoms CPU = 0.001 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5254139 6.7115119 5.5012908 Created 690 atoms using lattice units in orthogonal box = (0 -72.148753 0) to (25.508436 72.148753 5.5012908) create_atoms CPU = 0.001 seconds 690 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 33 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 2 atoms, new total = 1376 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 33 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) = 7.906 | 7.906 | 7.906 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4716.7838 0 -4716.7838 88834.887 104 0 -5341.9479 0 -5341.9479 2962.0407 Loop time of 1.4284 on 1 procs for 104 steps with 1376 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 = -4716.78382134642 -5341.94330609974 -5341.94785437963 Force two-norm initial, final = 915.94961 0.2372861 Force max component initial, final = 289.6453 0.048883011 Final line search alpha, max atom move = 1 0.048883011 Iterations, force evaluations = 104 199 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4132 | 1.4132 | 1.4132 | 0.0 | 98.94 Neigh | 0.0032585 | 0.0032585 | 0.0032585 | 0.0 | 0.23 Comm | 0.0073257 | 0.0073257 | 0.0073257 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004596 | | | 0.32 Nlocal: 1376 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9769 ave 9769 max 9769 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 137250 ave 137250 max 137250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137250 Ave neighs/atom = 99.74564 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 : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.906 | 7.906 | 7.906 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -5341.9479 0 -5341.9479 2962.0407 20249.172 107 0 -5342.0164 0 -5342.0164 -88.375368 20280.232 Loop time of 0.0359406 on 1 procs for 3 steps with 1376 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 = -5341.94785437962 -5342.01554102426 -5342.01637044299 Force two-norm initial, final = 75.17608 3.4012303 Force max component initial, final = 68.220538 3.1402625 Final line search alpha, max atom move = 0.00010463677 0.00032858692 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035209 | 0.035209 | 0.035209 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016394 | 0.00016394 | 0.00016394 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005672 | | | 1.58 Nlocal: 1376 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9769 ave 9769 max 9769 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 137174 ave 137174 max 137174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137174 Ave neighs/atom = 99.690407 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 33 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) = 7.537 | 7.537 | 7.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5342.0164 0 -5342.0164 -88.375368 Loop time of 6.41e-07 on 1 procs for 0 steps with 1376 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: 1376 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9769 ave 9769 max 9769 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 137134 ave 137134 max 137134 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 = 137134 Ave neighs/atom = 99.661337 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) = 7.537 | 7.537 | 7.537 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 -5342.0164 -5342.0164 25.563539 144.23259 5.5003277 -88.375368 -88.375368 62.643712 -79.726611 -248.0432 2.5879614 617.25349 Loop time of 4.21e-07 on 1 procs for 0 steps with 1376 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: 1376 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9769 ave 9769 max 9769 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 137134 ave 137134 max 137134 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 274268 ave 274268 max 274268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274268 Ave neighs/atom = 199.32267 Neighbor list builds = 0 Dangerous builds = 0 1376 -5342.01637044299 eV 2.58796139594563 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01