LAMMPS (30 Jul 2021) 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 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created orthogonal box = (0.0000000 -55.046630 0.0000000) to (27.523315 55.046630 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9632208 4.9632208 3.5239994 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -55.046630 0.0000000) to (27.523315 55.046630 3.5239994) create_atoms CPU = 0.001 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9632208 4.9632208 3.5239994 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.046630 0.0000000) to (27.523315 55.046630 3.5239994) create_atoms CPU = 0.001 seconds 490 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 = 7 25 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 = 978 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:189) 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 = 7 25 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) = 7.735 | 7.735 | 7.735 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3915.5277 0 -3915.5277 147965.35 80 0 -4332.4716 0 -4332.4716 8898.9042 Loop time of 2.74781 on 1 procs for 80 steps with 978 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3915.52767352627 -4332.46804000927 -4332.47160342943 Force two-norm initial, final = 710.37046 0.21444223 Force max component initial, final = 138.21113 0.050396391 Final line search alpha, max atom move = 1.0000000 0.050396391 Iterations, force evaluations = 80 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7102 | 2.7102 | 2.7102 | 0.0 | 98.63 Neigh | 0.012275 | 0.012275 | 0.012275 | 0.0 | 0.45 Comm | 0.016232 | 0.016232 | 0.016232 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009062 | | | 0.33 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10230.0 ave 10230 max 10230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124908.0 ave 124908 max 124908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124908 Ave neighs/atom = 127.71779 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.735 | 7.735 | 7.735 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -4332.4716 0 -4332.4716 8898.9042 10678.182 86 0 -4332.7489 0 -4332.7489 -87.673403 10729.505 Loop time of 0.185219 on 1 procs for 6 steps with 978 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4332.47160342942 -4332.74863903204 -4332.74887590179 Force two-norm initial, final = 123.58407 1.8243480 Force max component initial, final = 110.36491 1.7273338 Final line search alpha, max atom move = 0.00033012370 0.00057023384 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18089 | 0.18089 | 0.18089 | 0.0 | 97.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007671 | 0.0007671 | 0.0007671 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003562 | | | 1.92 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10242.0 ave 10242 max 10242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124174.0 ave 124174 max 124174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124174 Ave neighs/atom = 126.96728 Neighbor list builds = 0 Dangerous builds = 0 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 = 7 25 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) = 7.366 | 7.366 | 7.366 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4332.7489 0 -4332.7489 -87.673403 Loop time of 2.044e-06 on 1 procs for 0 steps with 978 atoms 146.8% 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 | | 2.044e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10224.0 ave 10224 max 10224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 123494.0 ave 123494 max 123494 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123494 Ave neighs/atom = 126.27198 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.366 | 7.366 | 7.366 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 -4332.7489 -4332.7489 27.497482 110.61106 3.527672 -87.673403 -87.673403 53.702168 -58.520539 -258.20184 2.2503249 147.33175 Loop time of 2.265e-06 on 1 procs for 0 steps with 978 atoms 264.9% 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 | | 2.265e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10224.0 ave 10224 max 10224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 123494.0 ave 123494 max 123494 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 246988.0 ave 246988 max 246988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 246988 Ave neighs/atom = 252.54397 Neighbor list builds = 0 Dangerous builds = 0 978 -4332.74887590179 eV 2.25032490980365 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03