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 -67.418078 0.0000000) to (38.923846 67.418078 6.1037460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7428625 5.1576672 6.1037460 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -67.418078 0.0000000) to (38.923846 67.418078 6.1037460) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7428625 5.1576672 6.1037460 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.418078 0.0000000) to (38.923846 67.418078 6.1037460) create_atoms CPU = 0.002 seconds 1466 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 31 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 4 atoms, new total = 2926 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 31 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) = 15.63 | 15.63 | 15.63 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11593.283 0 -11593.283 102497.01 104 0 -12953.845 0 -12953.845 5312.5557 Loop time of 11.0314 on 1 procs for 104 steps with 2926 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 = -11593.2833855356 -12953.8339577979 -12953.8453455901 Force two-norm initial, final = 1624.1263 0.39832712 Force max component initial, final = 400.02315 0.10193476 Final line search alpha, max atom move = 0.57457994 0.058569666 Iterations, force evaluations = 104 186 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.865 | 10.865 | 10.865 | 0.0 | 98.49 Neigh | 0.079159 | 0.079159 | 0.079159 | 0.0 | 0.72 Comm | 0.050006 | 0.050006 | 0.050006 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03715 | | | 0.34 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16358.0 ave 16358 max 16358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 366800.0 ave 366800 max 366800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366800 Ave neighs/atom = 125.35885 Neighbor list builds = 4 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 : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.63 | 15.63 | 15.63 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -12953.845 0 -12953.845 5312.5557 32034.545 107 0 -12954.058 0 -12954.058 5.9144639 32126.275 Loop time of 0.310995 on 1 procs for 3 steps with 2926 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 = -12953.8453455901 -12954.0483828348 -12954.0580064329 Force two-norm initial, final = 197.75878 2.2663672 Force max component initial, final = 164.69046 1.8479014 Final line search alpha, max atom move = 3.7618967e-05 6.9516143e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30657 | 0.30657 | 0.30657 | 0.0 | 98.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076981 | 0.00076981 | 0.00076981 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003653 | | | 1.17 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16370.0 ave 16370 max 16370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 366984.0 ave 366984 max 366984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366984 Ave neighs/atom = 125.42174 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 31 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) = 14.51 | 14.51 | 14.51 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12954.058 0 -12954.058 5.9144639 Loop time of 2.17e-06 on 1 procs for 0 steps with 2926 atoms 184.3% 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 | | 2.17e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16346.0 ave 16346 max 16346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 366424.0 ave 366424 max 366424 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 = 366424 Ave neighs/atom = 125.23035 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) = 14.51 | 14.51 | 14.51 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 -12954.058 -12954.058 38.925301 135.14717 6.106909 5.9144639 5.9144639 -60.249104 -14.212358 92.204854 2.250435 975.3123 Loop time of 2.38e-06 on 1 procs for 0 steps with 2926 atoms 336.1% 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 | | 2.38e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16346.0 ave 16346 max 16346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 366424.0 ave 366424 max 366424 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 732848.0 ave 732848 max 732848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 732848 Ave neighs/atom = 250.46070 Neighbor list builds = 0 Dangerous builds = 0 2926 -12954.0580064329 eV 2.25043495470407 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11