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 -36.963541 0.0000000) to (45.266592 36.963541 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7612026 5.3760025 5.7546669 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -36.963541 0.0000000) to (45.266592 36.963541 8.6320004) create_atoms CPU = 0.002 seconds 1323 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7612026 5.3760025 5.7546669 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -36.963541 0.0000000) to (45.266592 36.963541 8.6320004) create_atoms CPU = 0.002 seconds 1323 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 17 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 54 atoms, new total = 2592 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 17 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) = 9.137 | 9.137 | 9.137 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11408.591 0 -11408.591 -4468.2464 29 0 -11449.245 0 -11449.245 -20432.8 Loop time of 2.21665 on 1 procs for 29 steps with 2592 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 = -11408.5912059607 -11449.2340680508 -11449.2445608506 Force two-norm initial, final = 28.595826 0.34301938 Force max component initial, final = 4.0454210 0.043555209 Final line search alpha, max atom move = 1.0000000 0.043555209 Iterations, force evaluations = 29 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1853 | 2.1853 | 2.1853 | 0.0 | 98.59 Neigh | 0.015748 | 0.015748 | 0.015748 | 0.0 | 0.71 Comm | 0.0078081 | 0.0078081 | 0.0078081 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0078 | | | 0.35 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11186.0 ave 11186 max 11186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 322640.0 ave 322640 max 322640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322640 Ave neighs/atom = 124.47531 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.137 | 9.137 | 9.137 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -11449.245 0 -11449.245 -20432.8 28886.36 34 0 -11450.347 0 -11450.347 -6924.4792 28667.965 Loop time of 0.314612 on 1 procs for 5 steps with 2592 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 = -11449.2445608506 -11450.3392116549 -11450.3471244867 Force two-norm initial, final = 406.85475 7.9482672 Force max component initial, final = 314.57540 7.6788519 Final line search alpha, max atom move = 3.1630175e-05 0.00024288343 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31094 | 0.31094 | 0.31094 | 0.0 | 98.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055727 | 0.00055727 | 0.00055727 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003114 | | | 0.99 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11186.0 ave 11186 max 11186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 322965.0 ave 322965 max 322965 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322965 Ave neighs/atom = 124.60069 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 17 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) = 8.768 | 8.768 | 8.768 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11450.347 0 -11450.347 -6924.4792 Loop time of 1.977e-06 on 1 procs for 0 steps with 2592 atoms 202.3% 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 | | 1.977e-06 | | |100.00 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11192.0 ave 11192 max 11192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 324412.0 ave 324412 max 324412 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 = 324412 Ave neighs/atom = 125.15895 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) = 8.768 | 8.768 | 8.768 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 -11450.347 -11450.347 45.12603 73.927083 8.5934225 -6924.4792 -6924.4792 427.81807 -21089.816 -111.44001 2.2892237 1298.1227 Loop time of 4.405e-06 on 1 procs for 0 steps with 2592 atoms 227.0% 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 | | 4.405e-06 | | |100.00 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11192.0 ave 11192 max 11192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 324412.0 ave 324412 max 324412 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 648824.0 ave 648824 max 648824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 648824 Ave neighs/atom = 250.31790 Neighbor list builds = 0 Dangerous builds = 0 2592 -11450.3471244867 eV 2.28922372336493 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03