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 -67.376777 0) to (27.506454 67.376777 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.601549 5.8393207 6.3523435 Created 1197 atoms using lattice units in orthogonal box = (0 -67.376777 0) to (27.506454 67.376777 9.5285152) create_atoms CPU = 0.001 seconds 1197 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.601549 5.8393207 6.3523435 Created 1205 atoms using lattice units in orthogonal box = (0 -67.376777 0) to (27.506454 67.376777 9.5285152) create_atoms CPU = 0.001 seconds 1205 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 31 3 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 = 2400 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 = 7 31 3 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) = 8.675 | 8.675 | 8.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7034.4672 0 -7034.4672 144652.24 56 0 -9310.8662 0 -9310.8662 4879.7919 Loop time of 1.14973 on 1 procs for 56 steps with 2400 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 = -7034.46718055585 -9310.85831874352 -9310.8662311495 Force two-norm initial, final = 1878.2718 0.32327557 Force max component initial, final = 249.06643 0.064722422 Final line search alpha, max atom move = 1 0.064722422 Iterations, force evaluations = 56 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1314 | 1.1314 | 1.1314 | 0.0 | 98.40 Neigh | 0.011051 | 0.011051 | 0.011051 | 0.0 | 0.96 Comm | 0.0036741 | 0.0036741 | 0.0036741 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003623 | | | 0.32 Nlocal: 2400 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10593 ave 10593 max 10593 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 239087 ave 239087 max 239087 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239087 Ave neighs/atom = 99.619583 Neighbor list builds = 2 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.675 | 8.675 | 8.675 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -9310.8662 0 -9310.8662 4879.7919 35318.323 62 0 -9311.3708 0 -9311.3708 2.3653727 35402.144 Loop time of 0.100594 on 1 procs for 6 steps with 2400 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 = -9310.86623114952 -9311.36915656911 -9311.37083264769 Force two-norm initial, final = 235.65831 0.95897709 Force max component initial, final = 223.09196 0.66473536 Final line search alpha, max atom move = 5.1476314e-05 3.4218126e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.099035 | 0.099035 | 0.099035 | 0.0 | 98.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028224 | 0.00028224 | 0.00028224 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001276 | | | 1.27 Nlocal: 2400 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10554 ave 10554 max 10554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 238992 ave 238992 max 238992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238992 Ave neighs/atom = 99.58 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 = 7 31 3 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) = 8.306 | 8.306 | 8.306 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9311.3708 0 -9311.3708 2.3653727 Loop time of 5.61e-07 on 1 procs for 0 steps with 2400 atoms 178.3% 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 | | 5.61e-07 | | |100.00 Nlocal: 2400 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10575 ave 10575 max 10575 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 238752 ave 238752 max 238752 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 = 238752 Ave neighs/atom = 99.48 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) = 8.306 | 8.306 | 8.306 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 -9311.3708 -9311.3708 27.49456 135.42866 9.5076287 2.3653727 2.3653727 30.070576 -0.6289721 -22.345485 2.5919603 989.57455 Loop time of 5.11e-07 on 1 procs for 0 steps with 2400 atoms 195.7% 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 | | 5.11e-07 | | |100.00 Nlocal: 2400 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10575 ave 10575 max 10575 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 238752 ave 238752 max 238752 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 477504 ave 477504 max 477504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 477504 Ave neighs/atom = 198.96 Neighbor list builds = 0 Dangerous builds = 0 2400 -9311.37083264769 eV 2.59196027931608 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01