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 -62.246240 0.0000000) to (35.937883 62.246240 6.1037460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5289051 5.5862010 6.1037460 Created 1247 atoms using lattice units in orthogonal box = (0.0000000 -62.246240 0.0000000) to (35.937883 62.246240 6.1037460) create_atoms CPU = 0.002 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5289051 5.5862010 6.1037460 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -62.246240 0.0000000) to (35.937883 62.246240 6.1037460) create_atoms CPU = 0.002 seconds 1251 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 = 9 28 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 8 atoms, new total = 2490 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 = 9 28 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) = 15.47 | 15.47 | 15.47 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10618.718 0 -10618.718 67738.059 72 0 -11020.147 0 -11020.147 3343.5528 Loop time of 11.7235 on 1 procs for 72 steps with 2490 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10618.7175849289 -11020.1363563858 -11020.1467329207 Force two-norm initial, final = 588.16538 0.39098016 Force max component initial, final = 109.63312 0.092104405 Final line search alpha, max atom move = 1.0000000 0.092104405 Iterations, force evaluations = 72 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.542 | 11.542 | 11.542 | 0.0 | 98.45 Neigh | 0.099537 | 0.099537 | 0.099537 | 0.0 | 0.85 Comm | 0.046409 | 0.046409 | 0.046409 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03567 | | | 0.30 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14486.0 ave 14486 max 14486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 311415.0 ave 311415 max 311415 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 311415 Ave neighs/atom = 125.06627 Neighbor list builds = 3 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 : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.47 | 15.47 | 15.47 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -11020.147 0 -11020.147 3343.5528 27308.136 75 0 -11020.278 0 -11020.278 74.33808 27356.421 Loop time of 0.478259 on 1 procs for 3 steps with 2490 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 = -11020.1467329207 -11020.2758093229 -11020.2781965681 Force two-norm initial, final = 128.14467 4.0029769 Force max component initial, final = 115.86931 3.5940588 Final line search alpha, max atom move = 6.7826702e-05 0.00024377315 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47159 | 0.47159 | 0.47159 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011823 | 0.0011823 | 0.0011823 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005486 | | | 1.15 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14506.0 ave 14506 max 14506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 310913.0 ave 310913 max 310913 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 310913 Ave neighs/atom = 124.86466 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 = 9 29 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) = 14.36 | 14.36 | 14.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11020.278 0 -11020.278 74.33808 Loop time of 4.047e-06 on 1 procs for 0 steps with 2490 atoms 148.3% 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 | | 4.047e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14506.0 ave 14506 max 14506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 310635.0 ave 310635 max 310635 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 = 310635 Ave neighs/atom = 124.75301 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) = 14.36 | 14.36 | 14.36 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 -11020.278 -11020.278 35.953558 124.74415 6.099542 74.33808 74.33808 -64.612452 210.91784 76.708853 2.2357255 978.93922 Loop time of 4.604e-06 on 1 procs for 0 steps with 2490 atoms 217.2% 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 | | 4.604e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14506.0 ave 14506 max 14506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 310635.0 ave 310635 max 310635 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 621270.0 ave 621270 max 621270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621270 Ave neighs/atom = 249.50602 Neighbor list builds = 0 Dangerous builds = 0 2490 -11020.2781965681 eV 2.23572545492324 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13