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 -63.435513 0.0000000) to (44.853190 63.435513 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0911739 5.8733323 4.9836877 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -63.435513 0.0000000) to (44.853190 63.435513 4.9836877) create_atoms CPU = 0.004 seconds 1299 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0911739 5.8733323 4.9836877 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -63.435513 0.0000000) to (44.853190 63.435513 4.9836877) create_atoms CPU = 0.003 seconds 1299 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 = 11 29 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 18 atoms, new total = 2580 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 = 11 29 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 -11329.567 0 -11329.567 19580.499 75 0 -11427.303 0 -11427.303 -3169.2556 Loop time of 6.66209 on 1 procs for 75 steps with 2580 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11329.5668941421 -11427.2921823204 -11427.3033228887 Force two-norm initial, final = 172.69560 0.39617556 Force max component initial, final = 46.675554 0.076213871 Final line search alpha, max atom move = 1.0000000 0.076213871 Iterations, force evaluations = 75 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.592 | 6.592 | 6.592 | 0.0 | 98.95 Neigh | 0.017174 | 0.017174 | 0.017174 | 0.0 | 0.26 Comm | 0.030138 | 0.030138 | 0.030138 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02279 | | | 0.34 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15897.0 ave 15897 max 15897 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 322954.0 ave 322954 max 322954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322954 Ave neighs/atom = 125.17597 Neighbor list builds = 1 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 : 75 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 75 0 -11427.303 0 -11427.303 -3169.2556 28360.025 76 0 -11427.315 0 -11427.315 -1854.2811 28339.851 Loop time of 0.134525 on 1 procs for 1 steps with 2580 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 = -11427.3033228887 -11427.3033228887 -11427.3146065528 Force two-norm initial, final = 39.895623 8.9480655 Force max component initial, final = 37.921738 8.4768532 Final line search alpha, max atom move = 2.6370099e-05 0.00022353546 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13283 | 0.13283 | 0.13283 | 0.0 | 98.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037896 | 0.00037896 | 0.00037896 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001317 | | | 0.98 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15861.0 ave 15861 max 15861 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 322610.0 ave 322610 max 322610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322610 Ave neighs/atom = 125.04264 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 = 11 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) = 14.35 | 14.35 | 14.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11427.315 0 -11427.315 -1854.2811 Loop time of 1.904e-06 on 1 procs for 0 steps with 2580 atoms 157.6% 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 | | 1.904e-06 | | |100.00 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15861.0 ave 15861 max 15861 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 322666.0 ave 322666 max 322666 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 = 322666 Ave neighs/atom = 125.06434 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) = 14.35 | 14.35 | 14.35 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 -11427.315 -11427.315 44.845333 126.87103 4.9810152 -1854.2811 -1854.2811 479.14987 -5881.6489 -160.34427 2.3380352 1241.8243 Loop time of 2.178e-06 on 1 procs for 0 steps with 2580 atoms 229.6% 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 | | 2.178e-06 | | |100.00 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15861.0 ave 15861 max 15861 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 322666.0 ave 322666 max 322666 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 645332.0 ave 645332 max 645332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 645332 Ave neighs/atom = 250.12868 Neighbor list builds = 0 Dangerous builds = 0 2580 -11427.3146065528 eV 2.3380351905377 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07