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 -57.261737 0.0000000) to (20.243835 57.261737 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5210460 6.0728408 4.9836877 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.261737 0.0000000) to (20.243835 57.261737 4.9836877) create_atoms CPU = 0.002 seconds 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5210460 6.0728408 4.9836877 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.261737 0.0000000) to (20.243835 57.261737 4.9836877) create_atoms CPU = 0.001 seconds 530 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 = 5 26 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 8 atoms, new total = 1052 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 = 5 26 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) = 7.837 | 7.837 | 7.837 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4630.1162 0 -4630.1162 15049.421 41 0 -4661.1178 0 -4661.1178 -2457.4656 Loop time of 1.29047 on 1 procs for 41 steps with 1052 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 = -4630.11622076298 -4661.11325184572 -4661.11777510656 Force two-norm initial, final = 79.156640 0.22510985 Force max component initial, final = 28.454263 0.035730628 Final line search alpha, max atom move = 0.96059518 0.034322670 Iterations, force evaluations = 41 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2731 | 1.2731 | 1.2731 | 0.0 | 98.65 Neigh | 0.0064505 | 0.0064505 | 0.0064505 | 0.0 | 0.50 Comm | 0.0066045 | 0.0066045 | 0.0066045 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004325 | | | 0.34 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9802.00 ave 9802 max 9802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131858.0 ave 131858 max 131858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131858 Ave neighs/atom = 125.34030 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.837 | 7.837 | 7.837 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -4661.1178 0 -4661.1178 -2457.4656 11554.153 43 0 -4661.1389 0 -4661.1389 -136.87879 11539.577 Loop time of 0.0729463 on 1 procs for 2 steps with 1052 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 = -4661.11777510654 -4661.13668326054 -4661.13890177889 Force two-norm initial, final = 33.285280 1.9684147 Force max component initial, final = 31.003123 1.5716498 Final line search alpha, max atom move = 0.00015069598 0.00023684131 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071675 | 0.071675 | 0.071675 | 0.0 | 98.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027677 | 0.00027677 | 0.00027677 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009943 | | | 1.36 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9812.00 ave 9812 max 9812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 132030.0 ave 132030 max 132030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132030 Ave neighs/atom = 125.50380 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 = 5 26 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) = 7.468 | 7.468 | 7.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4661.1389 0 -4661.1389 -136.87879 Loop time of 1.891e-06 on 1 procs for 0 steps with 1052 atoms 158.6% 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 | | 1.891e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9830.00 ave 9830 max 9830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 132092.0 ave 132092 max 132092 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 = 132092 Ave neighs/atom = 125.56274 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) = 7.468 | 7.468 | 7.468 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 -4661.1389 -4661.1389 20.217155 114.52347 4.9839689 -136.87879 -136.87879 -217.92322 -31.359404 -161.35375 2.3029263 357.64554 Loop time of 1.915e-06 on 1 procs for 0 steps with 1052 atoms 208.9% 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 | | 1.915e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9830.00 ave 9830 max 9830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 132092.0 ave 132092 max 132092 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 264184.0 ave 264184 max 264184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264184 Ave neighs/atom = 251.12548 Neighbor list builds = 0 Dangerous builds = 0 1052 -4661.13890177889 eV 2.30292629650689 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01