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 -63.20502 0) to (12.901671 63.20502 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8643957 5.7459109 6.3523435 Created 528 atoms using lattice units in orthogonal box = (0 -63.20502 0) to (12.901671 63.20502 9.5285152) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8643957 5.7459109 6.3523435 Created 530 atoms using lattice units in orthogonal box = (0 -63.20502 0) to (12.901671 63.20502 9.5285152) create_atoms CPU = 0.000 seconds 530 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 = 3 29 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 6 atoms, new total = 1052 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 = 3 29 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) = 7.912 | 7.912 | 7.912 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2867.6164 0 -2867.6164 126445.27 131 0 -4077.0702 0 -4077.0702 591.08081 Loop time of 1.38651 on 1 procs for 131 steps with 1052 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 = -2867.61643613439 -4077.06613880562 -4077.07016542419 Force two-norm initial, final = 1506.9643 0.29793543 Force max component initial, final = 470.55878 0.083846919 Final line search alpha, max atom move = 1 0.083846919 Iterations, force evaluations = 131 242 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3683 | 1.3683 | 1.3683 | 0.0 | 98.69 Neigh | 0.0081925 | 0.0081925 | 0.0081925 | 0.0 | 0.59 Comm | 0.0061978 | 0.0061978 | 0.0061978 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003824 | | | 0.28 Nlocal: 1052 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7102 ave 7102 max 7102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104610 ave 104610 max 104610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104610 Ave neighs/atom = 99.439163 Neighbor list builds = 3 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 : 131 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.914 | 7.914 | 7.914 Mbytes Step Temp E_pair E_mol TotEng Press Volume 131 0 -4077.0702 0 -4077.0702 591.08081 15540.062 135 0 -4077.1074 0 -4077.1074 -80.150278 15544.97 Loop time of 0.0452815 on 1 procs for 4 steps with 1052 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 = -4077.07016542419 -4077.10733172567 -4077.10740641923 Force two-norm initial, final = 28.948023 1.6068479 Force max component initial, final = 26.94069 1.1370838 Final line search alpha, max atom move = 0.00052795578 0.00060032996 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.044356 | 0.044356 | 0.044356 | 0.0 | 97.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019887 | 0.00019887 | 0.00019887 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007268 | | | 1.61 Nlocal: 1052 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7510 ave 7510 max 7510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104652 ave 104652 max 104652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104652 Ave neighs/atom = 99.479087 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 = 3 29 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) = 7.546 | 7.546 | 7.546 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4077.1074 0 -4077.1074 -80.150278 Loop time of 7.01e-07 on 1 procs for 0 steps with 1052 atoms 142.7% 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 | | 7.01e-07 | | |100.00 Nlocal: 1052 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7486 ave 7486 max 7486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104638 ave 104638 max 104638 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 = 104638 Ave neighs/atom = 99.465779 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) = 7.546 | 7.546 | 7.546 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 -4077.1074 -4077.1074 12.880572 126.68446 9.5264564 -80.150278 -80.150278 -110.84056 -117.45046 -12.159813 2.5033622 487.48811 Loop time of 6.21e-07 on 1 procs for 0 steps with 1052 atoms 322.1% 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 | | 6.21e-07 | | |100.00 Nlocal: 1052 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7486 ave 7486 max 7486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104638 ave 104638 max 104638 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 209276 ave 209276 max 209276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209276 Ave neighs/atom = 198.93156 Neighbor list builds = 0 Dangerous builds = 0 1052 -4077.10740641923 eV 2.50336218787454 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01