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 -48.450506 0.0000000) to (13.185598 48.450506 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6509707 5.3829980 5.7546669 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -48.450506 0.0000000) to (13.185598 48.450506 8.6320004) create_atoms CPU = 0.001 seconds 507 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6509707 5.3829980 5.7546669 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -48.450506 0.0000000) to (13.185598 48.450506 8.6320004) create_atoms CPU = 0.001 seconds 507 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 = 3 22 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 22 atoms, new total = 992 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 = 3 22 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) = 7.910 | 7.910 | 7.910 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4379.1275 0 -4379.1275 -6738.1191 20 0 -4387.5897 0 -4387.5897 -19473.198 Loop time of 0.593873 on 1 procs for 20 steps with 992 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 = -4379.1275059314 -4387.58634410372 -4387.58973353827 Force two-norm initial, final = 5.4854438 0.18282331 Force max component initial, final = 1.0148428 0.015451765 Final line search alpha, max atom move = 1.0000000 0.015451765 Iterations, force evaluations = 20 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59012 | 0.59012 | 0.59012 | 0.0 | 99.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021286 | 0.0021286 | 0.0021286 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00162 | | | 0.27 Nlocal: 992.000 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7408.00 ave 7408 max 7408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 121848.0 ave 121848 max 121848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121848 Ave neighs/atom = 122.83065 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 : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.910 | 7.910 | 7.910 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -4387.5897 0 -4387.5897 -19473.198 11029.088 25 0 -4387.9405 0 -4387.9405 -7137.4084 10953.405 Loop time of 0.140541 on 1 procs for 5 steps with 992 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 = -4387.58973353827 -4387.94022969097 -4387.94045312248 Force two-norm initial, final = 142.61520 0.22715516 Force max component initial, final = 106.84435 0.028171919 Final line search alpha, max atom move = 0.00048835381 1.3757864e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1383 | 0.1383 | 0.1383 | 0.0 | 98.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043294 | 0.00043294 | 0.00043294 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00181 | | | 1.29 Nlocal: 992.000 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7408.00 ave 7408 max 7408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 123308.0 ave 123308 max 123308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123308 Ave neighs/atom = 124.30242 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 = 3 22 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) = 7.541 | 7.541 | 7.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4387.9405 0 -4387.9405 -7137.4084 Loop time of 1.836e-06 on 1 procs for 0 steps with 992 atoms 163.4% 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 | | 1.836e-06 | | |100.00 Nlocal: 992.000 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7408.00 ave 7408 max 7408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 123632.0 ave 123632 max 123632 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 = 123632 Ave neighs/atom = 124.62903 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) = 7.541 | 7.541 | 7.541 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 -4387.9405 -4387.9405 13.146372 96.901012 8.5983463 -7137.4084 -7137.4084 -4.1085039 -21407.72 -0.39628929 2.2900811 381.76277 Loop time of 8.262e-06 on 1 procs for 0 steps with 992 atoms 145.2% 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 | | 8.262e-06 | | |100.00 Nlocal: 992.000 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7408.00 ave 7408 max 7408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 123632.0 ave 123632 max 123632 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 247264.0 ave 247264 max 247264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 247264 Ave neighs/atom = 249.25806 Neighbor list builds = 0 Dangerous builds = 0 992 -4387.94045312248 eV 2.29008105120542 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01