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 -53.675960 0.0000000) to (26.837980 53.675960 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6272379 4.6272379 3.5239994 Created 464 atoms using lattice units in orthogonal box = (0.0000000 -53.675960 0.0000000) to (26.837980 53.675960 3.5239994) create_atoms CPU = 0.001 seconds 464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6272379 4.6272379 3.5239994 Created 466 atoms using lattice units in orthogonal box = (0.0000000 -53.675960 0.0000000) to (26.837980 53.675960 3.5239994) create_atoms CPU = 0.001 seconds 466 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 25 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 4 atoms, new total = 926 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 25 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) = 7.716 | 7.716 | 7.716 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3303.8572 0 -3303.8572 152801.91 75 0 -4095.0279 0 -4095.0279 6663.889 Loop time of 2.36196 on 1 procs for 75 steps with 926 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3303.8571858396 -4095.02385843028 -4095.02785027694 Force two-norm initial, final = 1308.2738 0.25485833 Force max component initial, final = 305.74270 0.052320064 Final line search alpha, max atom move = 1.0000000 0.052320064 Iterations, force evaluations = 75 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3137 | 2.3137 | 2.3137 | 0.0 | 97.96 Neigh | 0.023856 | 0.023856 | 0.023856 | 0.0 | 1.01 Comm | 0.015391 | 0.015391 | 0.015391 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008969 | | | 0.38 Nlocal: 926.000 ave 926 max 926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9838.00 ave 9838 max 9838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116118.0 ave 116118 max 116118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116118 Ave neighs/atom = 125.39741 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 : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.716 | 7.716 | 7.716 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -4095.0279 0 -4095.0279 6663.889 10153.025 81 0 -4095.212 0 -4095.212 -196.24278 10190.723 Loop time of 0.162342 on 1 procs for 6 steps with 926 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 = -4095.02785027694 -4095.21167701346 -4095.21203580303 Force two-norm initial, final = 88.080874 2.3687655 Force max component initial, final = 81.462746 1.7846077 Final line search alpha, max atom move = 0.00040503411 0.00072282699 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15845 | 0.15845 | 0.15845 | 0.0 | 97.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00070055 | 0.00070055 | 0.00070055 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003196 | | | 1.97 Nlocal: 926.000 ave 926 max 926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9850.00 ave 9850 max 9850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115568.0 ave 115568 max 115568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115568 Ave neighs/atom = 124.80346 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 25 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) = 7.347 | 7.347 | 7.347 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4095.212 0 -4095.212 -196.24278 Loop time of 2.041e-06 on 1 procs for 0 steps with 926 atoms 147.0% 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 | | 2.041e-06 | | |100.00 Nlocal: 926.000 ave 926 max 926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9850.00 ave 9850 max 9850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115318.0 ave 115318 max 115318 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 = 115318 Ave neighs/atom = 124.53348 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) = 7.347 | 7.347 | 7.347 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 -4095.212 -4095.212 26.819753 107.88358 3.5220448 -196.24278 -196.24278 -84.229112 -224.08039 -280.41882 2.2152547 391.23994 Loop time of 2.44e-06 on 1 procs for 0 steps with 926 atoms 163.9% 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 | | 2.44e-06 | | |100.00 Nlocal: 926.000 ave 926 max 926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9850.00 ave 9850 max 9850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115318.0 ave 115318 max 115318 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 230636.0 ave 230636 max 230636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230636 Ave neighs/atom = 249.06695 Neighbor list builds = 0 Dangerous builds = 0 926 -4095.21203580303 eV 2.21525474893817 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02