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 -70.659492 0.0000000) to (40.793242 70.659492 6.1037460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4796893 5.6243557 6.1037460 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.659492 0.0000000) to (40.793242 70.659492 6.1037460) create_atoms CPU = 0.010 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4796893 5.6243557 6.1037460 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.659492 0.0000000) to (40.793242 70.659492 6.1037460) create_atoms CPU = 0.010 seconds 1610 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 = 10 32 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 28 atoms, new total = 3192 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 = 10 32 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) = 16.13 | 16.13 | 16.13 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14084.826 0 -14084.826 4192.5836 27 0 -14132.879 0 -14132.879 -6766.3548 Loop time of 6.32754 on 1 procs for 27 steps with 3192 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14084.8257466735 -14132.8691803662 -14132.8794792867 Force two-norm initial, final = 84.527386 0.33318347 Force max component initial, final = 19.816080 0.046173942 Final line search alpha, max atom move = 0.89713112 0.041424081 Iterations, force evaluations = 27 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2395 | 6.2395 | 6.2395 | 0.0 | 98.61 Neigh | 0.051237 | 0.051237 | 0.051237 | 0.0 | 0.81 Comm | 0.020492 | 0.020492 | 0.020492 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01634 | | | 0.26 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17400.0 ave 17400 max 17400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 397068.0 ave 397068 max 397068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 397068 Ave neighs/atom = 124.39474 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 16.13 | 16.13 | 16.13 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -14132.879 0 -14132.879 -6766.3548 35187.238 29 0 -14133.006 0 -14133.006 -2616.2512 35107.7 Loop time of 0.631887 on 1 procs for 2 steps with 3192 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14132.8794792867 -14133.0004952757 -14133.0055580907 Force two-norm initial, final = 156.26985 1.7981443 Force max component initial, final = 121.20517 1.3877571 Final line search alpha, max atom move = 3.8755717e-05 5.3783523e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62476 | 0.62476 | 0.62476 | 0.0 | 98.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017272 | 0.0017272 | 0.0017272 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005404 | | | 0.86 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17428.0 ave 17428 max 17428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 397286.0 ave 397286 max 397286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 397286 Ave neighs/atom = 124.46303 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 = 10 32 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) = 15.02 | 15.02 | 15.02 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14133.006 0 -14133.006 -2616.2512 Loop time of 7.167e-06 on 1 procs for 0 steps with 3192 atoms 195.3% 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 | | 7.167e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17428.0 ave 17428 max 17428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 397500.0 ave 397500 max 397500 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 = 397500 Ave neighs/atom = 124.53008 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) = 15.02 | 15.02 | 15.02 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 -14133.006 -14133.006 40.752602 141.31898 6.0960221 -2616.2512 -2616.2512 63.268649 -7862.4091 -49.613175 2.2537665 1037.9935 Loop time of 6.866e-06 on 1 procs for 0 steps with 3192 atoms 320.4% 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 | | 6.866e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17428.0 ave 17428 max 17428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 397500.0 ave 397500 max 397500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 795000.0 ave 795000 max 795000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 795000 Ave neighs/atom = 249.06015 Neighbor list builds = 0 Dangerous builds = 0 3192 -14133.0055580907 eV 2.25376649189912 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08