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 -64.979338 0.0000000) to (32.489669 64.979338 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9690082 4.9690082 3.5239994 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -64.979338 0.0000000) to (32.489669 64.979338 3.5239994) create_atoms CPU = 0.001 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9690082 4.9690082 3.5239994 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -64.979338 0.0000000) to (32.489669 64.979338 3.5239994) create_atoms CPU = 0.001 seconds 682 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 = 8 30 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 = 1362 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 = 8 30 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) = 7.903 | 7.903 | 7.903 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5589.6188 0 -5589.6188 119526.64 83 0 -6036.7094 0 -6036.7094 6646.0119 Loop time of 3.8774 on 1 procs for 83 steps with 1362 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5589.61883021768 -6036.7044441823 -6036.70936370532 Force two-norm initial, final = 705.93448 0.27131570 Force max component initial, final = 129.11656 0.056942794 Final line search alpha, max atom move = 1.0000000 0.056942794 Iterations, force evaluations = 83 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8221 | 3.8221 | 3.8221 | 0.0 | 98.57 Neigh | 0.016113 | 0.016113 | 0.016113 | 0.0 | 0.42 Comm | 0.025239 | 0.025239 | 0.025239 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01397 | | | 0.36 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12990.0 ave 12990 max 12990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173036.0 ave 173036 max 173036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173036 Ave neighs/atom = 127.04552 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.903 | 7.903 | 7.903 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -6036.7094 0 -6036.7094 6646.0119 14879.433 87 0 -6036.9267 0 -6036.9267 330.99028 14929.635 Loop time of 0.169904 on 1 procs for 4 steps with 1362 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 = -6036.70936370532 -6036.92135632509 -6036.92665406384 Force two-norm initial, final = 129.06085 5.9081093 Force max component initial, final = 115.19168 4.9277706 Final line search alpha, max atom move = 7.9615880e-05 0.00039232879 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16647 | 0.16647 | 0.16647 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064715 | 0.00064715 | 0.00064715 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002782 | | | 1.64 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13008.0 ave 13008 max 13008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 172252.0 ave 172252 max 172252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172252 Ave neighs/atom = 126.46990 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 = 8 30 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) = 7.535 | 7.535 | 7.535 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6036.9267 0 -6036.9267 330.99028 Loop time of 2.288e-06 on 1 procs for 0 steps with 1362 atoms 174.8% 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 | | 2.288e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12990.0 ave 12990 max 12990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171670.0 ave 171670 max 171670 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 = 171670 Ave neighs/atom = 126.04258 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) = 7.535 | 7.535 | 7.535 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 -6036.9267 -6036.9267 32.464164 130.39392 3.5268551 330.99028 330.99028 316.08374 530.5957 146.29141 2.2526629 144.76218 Loop time of 2.588e-06 on 1 procs for 0 steps with 1362 atoms 270.5% 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 | | 2.588e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12990.0 ave 12990 max 12990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171670.0 ave 171670 max 171670 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 343340.0 ave 343340 max 343340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 343340 Ave neighs/atom = 252.08517 Neighbor list builds = 0 Dangerous builds = 0 1362 -6036.92665406384 eV 2.25266289910609 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04