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 -43.491523 0) to (8.6983046 43.491523 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2189827 5.2189827 3.8900001 Created 100 atoms using lattice units in orthogonal box = (0 -43.491523 0) to (8.6983046 43.491523 3.8900001) create_atoms CPU = 0.000 seconds 100 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2189827 5.2189827 3.8900001 Created 102 atoms using lattice units in orthogonal box = (0 -43.491523 0) to (8.6983046 43.491523 3.8900001) create_atoms CPU = 0.000 seconds 102 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 = 2 20 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 4 atoms, new total = 198 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 = 2 20 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) = 7.019 | 7.019 | 7.019 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -733.14571 0 -733.14571 48707.597 32 0 -765.6962 0 -765.6962 -5678.7169 Loop time of 0.0654796 on 1 procs for 32 steps with 198 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 = -733.145709532223 -765.695699077271 -765.696202326534 Force two-norm initial, final = 148.70023 0.078913815 Force max component initial, final = 71.537528 0.022425252 Final line search alpha, max atom move = 1 0.022425252 Iterations, force evaluations = 32 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.064423 | 0.064423 | 0.064423 | 0.0 | 98.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079654 | 0.00079654 | 0.00079654 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002599 | | | 0.40 Nlocal: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3729 ave 3729 max 3729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19582 ave 19582 max 19582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19582 Ave neighs/atom = 98.89899 Neighbor list builds = 0 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.019 | 7.019 | 7.019 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -765.6962 0 -765.6962 -5678.7169 2943.1936 36 0 -765.71507 0 -765.71507 42.954291 2934.3932 Loop time of 0.00795998 on 1 procs for 4 steps with 198 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 = -765.696202326535 -765.714850750213 -765.715072755795 Force two-norm initial, final = 18.351827 0.18691006 Force max component initial, final = 12.08262 0.099869786 Final line search alpha, max atom move = 0.0016020845 0.00015999983 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.007607 | 0.007607 | 0.007607 | 0.0 | 95.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.1662e-05 | 9.1662e-05 | 9.1662e-05 | 0.0 | 1.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002614 | | | 3.28 Nlocal: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3735 ave 3735 max 3735 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19636 ave 19636 max 19636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19636 Ave neighs/atom = 99.171717 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 = 2 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) = 6.65 | 6.65 | 6.65 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -765.71507 0 -765.71507 42.954291 Loop time of 6.61e-07 on 1 procs for 0 steps with 198 atoms 151.3% 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 | | 6.61e-07 | | |100.00 Nlocal: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3735 ave 3735 max 3735 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19634 ave 19634 max 19634 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 = 19634 Ave neighs/atom = 99.161616 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) = 6.65 | 6.65 | 6.65 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 -765.71507 -765.71507 8.6891316 87.034371 3.8801734 42.954291 42.954291 42.739139 31.732652 54.391082 2.5136069 139.41226 Loop time of 4.41e-07 on 1 procs for 0 steps with 198 atoms 226.8% 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 | | 4.41e-07 | | |100.00 Nlocal: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3735 ave 3735 max 3735 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19634 ave 19634 max 19634 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39268 ave 39268 max 39268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39268 Ave neighs/atom = 198.32323 Neighbor list builds = 0 Dangerous builds = 0 198 -765.715072755795 eV 2.51360687321265 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00