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 -38.607003 0.0000000) to (7.8799022 38.607003 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7279413 5.1471306 5.7546669 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -38.607003 0.0000000) to (7.8799022 38.607003 8.6320004) create_atoms CPU = 0.001 seconds 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7279413 5.1471306 5.7546669 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -38.607003 0.0000000) to (7.8799022 38.607003 8.6320004) create_atoms CPU = 0.000 seconds 242 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 = 2 18 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 = 476 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 = 2 18 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) = 7.315 | 7.315 | 7.315 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2080.9705 0 -2080.9705 21676.223 82 0 -2103.2289 0 -2103.2289 -3088.0441 Loop time of 1.36077 on 1 procs for 82 steps with 476 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2080.97053547752 -2103.22682690197 -2103.22891424566 Force two-norm initial, final = 64.556297 0.17337013 Force max component initial, final = 20.232057 0.048128322 Final line search alpha, max atom move = 1.0000000 0.048128322 Iterations, force evaluations = 82 161 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3491 | 1.3491 | 1.3491 | 0.0 | 99.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0071581 | 0.0071581 | 0.0071581 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00448 | | | 0.33 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5460.00 ave 5460 max 5460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59052.0 ave 59052 max 59052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59052 Ave neighs/atom = 124.05882 Neighbor list builds = 0 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 : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.315 | 7.315 | 7.315 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -2103.2289 0 -2103.2289 -3088.0441 5252.0441 84 0 -2103.2496 0 -2103.2496 1347.269 5239.3306 Loop time of 0.0334604 on 1 procs for 2 steps with 476 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2103.22891424566 -2103.24834641173 -2103.24959036637 Force two-norm initial, final = 23.965966 0.30635875 Force max component initial, final = 18.420330 0.17978823 Final line search alpha, max atom move = 0.00021297968 3.8291240e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.032803 | 0.032803 | 0.032803 | 0.0 | 98.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014005 | 0.00014005 | 0.00014005 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005174 | | | 1.55 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5110.00 ave 5110 max 5110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59424.0 ave 59424 max 59424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59424 Ave neighs/atom = 124.84034 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 = 2 18 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) = 6.944 | 6.944 | 6.944 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2103.2496 0 -2103.2496 1347.269 Loop time of 1.849e-06 on 1 procs for 0 steps with 476 atoms 162.2% 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 | | 1.849e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5123.00 ave 5123 max 5123 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59490.0 ave 59490 max 59490 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 = 59490 Ave neighs/atom = 124.97899 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) = 6.944 | 6.944 | 6.944 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 -2103.2496 -2103.2496 7.8713443 77.214006 8.6204673 1347.269 1347.269 54.919161 4031.8238 -44.936118 2.2213267 272.00671 Loop time of 2.073e-06 on 1 procs for 0 steps with 476 atoms 193.0% 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 | | 2.073e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5123.00 ave 5123 max 5123 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59490.0 ave 59490 max 59490 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118980.0 ave 118980 max 118980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118980 Ave neighs/atom = 249.95798 Neighbor list builds = 0 Dangerous builds = 0 476 -2103.24959036637 eV 2.22132674456639 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01