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 4.3377434 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 upper Displacing atoms ... Lattice spacing in x,y,z = 5.5210460 4.3377434 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) = 7.828 | 7.828 | 7.828 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4611.3179 0 -4611.3179 25287.452 27 0 -4657.0243 0 -4657.0243 -218.07277 Loop time of 0.937165 on 1 procs for 27 steps with 1052 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 = -4611.31791365254 -4657.02001349222 -4657.02429997597 Force two-norm initial, final = 93.253799 0.24936477 Force max component initial, final = 29.653115 0.039733583 Final line search alpha, max atom move = 1.0000000 0.039733583 Iterations, force evaluations = 27 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92095 | 0.92095 | 0.92095 | 0.0 | 98.27 Neigh | 0.0066394 | 0.0066394 | 0.0066394 | 0.0 | 0.71 Comm | 0.005561 | 0.005561 | 0.005561 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004017 | | | 0.43 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9271.00 ave 9271 max 9271 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131820.0 ave 131820 max 131820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131820 Ave neighs/atom = 125.30418 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.828 | 7.828 | 7.828 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -4657.0243 0 -4657.0243 -218.07277 11554.153 28 0 -4657.0272 0 -4657.0272 -1025.1914 11559.194 Loop time of 0.056737 on 1 procs for 1 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 = -4657.02429997597 -4657.02429997597 -4657.02723587242 Force two-norm initial, final = 11.578248 2.7182670 Force max component initial, final = 11.472308 2.6781352 Final line search alpha, max atom move = 8.7166420e-05 0.00023344346 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055762 | 0.055762 | 0.055762 | 0.0 | 98.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021636 | 0.00021636 | 0.00021636 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007581 | | | 1.34 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9271.00 ave 9271 max 9271 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131880.0 ave 131880 max 131880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131880 Ave neighs/atom = 125.36122 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) = 7.459 | 7.459 | 7.459 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4657.0272 0 -4657.0272 -1025.1914 Loop time of 2.682e-06 on 1 procs for 0 steps with 1052 atoms 111.9% 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 | | 2.682e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9253.00 ave 9253 max 9253 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 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131858 Ave neighs/atom = 125.34030 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) = 7.459 | 7.459 | 7.459 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 -4657.0272 -4657.0272 20.254039 114.52347 4.9833499 -1025.1914 -1025.1914 -54.435279 -2649.9578 -371.18112 2.338943 265.3512 Loop time of 2.564e-06 on 1 procs for 0 steps with 1052 atoms 195.0% 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 | | 2.564e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9253.00 ave 9253 max 9253 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 FullNghs: 263716.0 ave 263716 max 263716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263716 Ave neighs/atom = 250.68061 Neighbor list builds = 0 Dangerous builds = 0 1052 -4657.02723587242 eV 2.33894295664219 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01