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 -40.491195 0.0000000) to (28.629106 40.491195 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0728408 5.5210460 4.9836877 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.491195 0.0000000) to (28.629106 40.491195 4.9836877) create_atoms CPU = 0.001 seconds 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0728408 5.5210460 4.9836877 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.491195 0.0000000) to (28.629106 40.491195 4.9836877) create_atoms CPU = 0.001 seconds 532 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 = 7 19 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 16 atoms, new total = 1048 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 = 7 19 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) = 7.766 | 7.766 | 7.766 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4599.9321 0 -4599.9321 13966.182 52 0 -4638.5497 0 -4638.5497 -7697.0845 Loop time of 1.83027 on 1 procs for 52 steps with 1048 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 = -4599.9321279981 -4638.54539034172 -4638.54968992323 Force two-norm initial, final = 67.655382 0.23062863 Force max component initial, final = 15.140467 0.030914808 Final line search alpha, max atom move = 1.0000000 0.030914808 Iterations, force evaluations = 52 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.809 | 1.809 | 1.809 | 0.0 | 98.84 Neigh | 0.0063862 | 0.0063862 | 0.0063862 | 0.0 | 0.35 Comm | 0.0085821 | 0.0085821 | 0.0085821 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006267 | | | 0.34 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8739.00 ave 8739 max 8739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 132792.0 ave 132792 max 132792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132792 Ave neighs/atom = 126.70992 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 : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.766 | 7.766 | 7.766 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -4638.5497 0 -4638.5497 -7697.0845 11554.448 56 0 -4638.6331 0 -4638.6331 -4135.5075 11531.886 Loop time of 0.128781 on 1 procs for 4 steps with 1048 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 = -4638.54968992323 -4638.63302408488 -4638.63309873064 Force two-norm initial, final = 60.894344 0.27278848 Force max component initial, final = 60.872975 0.043224154 Final line search alpha, max atom move = 0.00052090827 2.2515820e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12654 | 0.12654 | 0.12654 | 0.0 | 98.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042581 | 0.00042581 | 0.00042581 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001817 | | | 1.41 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8749.00 ave 8749 max 8749 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 132680.0 ave 132680 max 132680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132680 Ave neighs/atom = 126.60305 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 = 7 19 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) = 7.397 | 7.397 | 7.397 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4638.6331 0 -4638.6331 -4135.5075 Loop time of 1.934e-06 on 1 procs for 0 steps with 1048 atoms 155.1% 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 | | 1.934e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8749.00 ave 8749 max 8749 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 132768.0 ave 132768 max 132768 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 = 132768 Ave neighs/atom = 126.68702 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) = 7.397 | 7.397 | 7.397 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 -4638.6331 -4638.6331 28.650723 80.982389 4.9702037 -4135.5075 -4135.5075 -3.7554999 -12397.116 -5.6513964 2.3319155 608.01638 Loop time of 2.297e-06 on 1 procs for 0 steps with 1048 atoms 304.7% 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 | | 2.297e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8749.00 ave 8749 max 8749 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 132768.0 ave 132768 max 132768 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 265536.0 ave 265536 max 265536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 265536 Ave neighs/atom = 253.37405 Neighbor list builds = 0 Dangerous builds = 0 1048 -4638.63309873064 eV 2.33191548119539 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02