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 -35.937883 0.0000000) to (17.968942 35.937883 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1466788 4.1466788 3.5239994 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -35.937883 0.0000000) to (17.968942 35.937883 3.5239994) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1466788 4.1466788 3.5239994 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -35.937883 0.0000000) to (17.968942 35.937883 3.5239994) create_atoms CPU = 0.000 seconds 210 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 17 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 6 atoms, new total = 412 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 = 5 17 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) = 7.113 | 7.113 | 7.113 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1702.3039 0 -1702.3039 87600.183 41 0 -1819.5771 0 -1819.5771 -4455.1634 Loop time of 0.702277 on 1 procs for 41 steps with 412 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1702.30390504926 -1819.5753583472 -1819.57709611857 Force two-norm initial, final = 380.23082 0.12055315 Force max component initial, final = 130.60121 0.017606375 Final line search alpha, max atom move = 1.0000000 0.017606375 Iterations, force evaluations = 41 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.69105 | 0.69105 | 0.69105 | 0.0 | 98.40 Neigh | 0.0029947 | 0.0029947 | 0.0029947 | 0.0 | 0.43 Comm | 0.0055546 | 0.0055546 | 0.0055546 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002675 | | | 0.38 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6219.00 ave 6219 max 6219 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52052.0 ave 52052 max 52052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52052 Ave neighs/atom = 126.33981 Neighbor list builds = 1 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.113 | 7.113 | 7.113 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -1819.5771 0 -1819.5771 -4455.1634 4551.3561 44 0 -1819.5958 0 -1819.5958 -11.845108 4540.1836 Loop time of 0.0543604 on 1 procs for 3 steps with 412 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 = -1819.57709611857 -1819.59572467502 -1819.59579293667 Force two-norm initial, final = 22.341685 0.25545783 Force max component initial, final = 15.803219 0.20512474 Final line search alpha, max atom move = 0.00074733890 0.00015329770 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.052707 | 0.052707 | 0.052707 | 0.0 | 96.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032589 | 0.00032589 | 0.00032589 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001328 | | | 2.44 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6180.00 ave 6180 max 6180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51584.0 ave 51584 max 51584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51584 Ave neighs/atom = 125.20388 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 = 5 17 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) = 6.744 | 6.744 | 6.744 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1819.5958 0 -1819.5958 -11.845108 Loop time of 1.709e-06 on 1 procs for 0 steps with 412 atoms 117.0% 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 | | 1.709e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6180.00 ave 6180 max 6180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51644.0 ave 51644 max 51644 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 = 51644 Ave neighs/atom = 125.34951 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) = 6.744 | 6.744 | 6.744 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 -1819.5958 -1819.5958 17.954951 71.743156 3.5245908 -11.845108 -11.845108 -72.32971 18.242637 18.55175 2.3014641 190.46807 Loop time of 3.795e-06 on 1 procs for 0 steps with 412 atoms 210.8% 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 | | 3.795e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6180.00 ave 6180 max 6180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51644.0 ave 51644 max 51644 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103288.0 ave 103288 max 103288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103288 Ave neighs/atom = 250.69903 Neighbor list builds = 0 Dangerous builds = 0 412 -1819.59579293667 eV 2.30146412559859 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00