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 -46.751135 0.0000000) to (16.529022 46.751135 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0105536 5.3126290 4.9836877 Created 350 atoms using lattice units in orthogonal box = (0.0000000 -46.751135 0.0000000) to (16.529022 46.751135 4.9836877) create_atoms CPU = 0.001 seconds 350 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0105536 5.3126290 4.9836877 Created 358 atoms using lattice units in orthogonal box = (0.0000000 -46.751135 0.0000000) to (16.529022 46.751135 4.9836877) create_atoms CPU = 0.001 seconds 358 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 = 4 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 4 atoms, new total = 704 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 = 4 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) = 7.284 | 7.284 | 7.284 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3105.459 0 -3105.459 11046.006 36 0 -3121.0696 0 -3121.0696 3547.1772 Loop time of 1.01275 on 1 procs for 36 steps with 704 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3105.45899231486 -3121.0674997836 -3121.06963343951 Force two-norm initial, final = 27.788559 0.11394593 Force max component initial, final = 4.2162339 0.0099119693 Final line search alpha, max atom move = 1.0000000 0.0099119693 Iterations, force evaluations = 36 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0025 | 1.0025 | 1.0025 | 0.0 | 98.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0059762 | 0.0059762 | 0.0059762 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004222 | | | 0.42 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7547.00 ave 7547 max 7547 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88038.0 ave 88038 max 88038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88038 Ave neighs/atom = 125.05398 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.287 | 7.287 | 7.287 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -3121.0696 0 -3121.0696 3547.1772 7702.2949 41 0 -3121.1552 0 -3121.1552 -4.5953886 7716.9984 Loop time of 0.1128 on 1 procs for 5 steps with 704 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 = -3121.06963343951 -3121.15511597743 -3121.15515732184 Force two-norm initial, final = 45.752560 0.20453941 Force max component initial, final = 45.543158 0.073080681 Final line search alpha, max atom move = 0.00094241323 6.8872200e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10999 | 0.10999 | 0.10999 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051049 | 0.00051049 | 0.00051049 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002303 | | | 2.04 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7528.00 ave 7528 max 7528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87632.0 ave 87632 max 87632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87632 Ave neighs/atom = 124.47727 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 = 4 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) = 6.918 | 6.918 | 6.918 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3121.1552 0 -3121.1552 -4.5953886 Loop time of 2.652e-06 on 1 procs for 0 steps with 704 atoms 150.8% 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 | | 2.652e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7528.00 ave 7528 max 7528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87632.0 ave 87632 max 87632 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 = 87632 Ave neighs/atom = 124.47727 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) = 6.918 | 6.918 | 6.918 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 -3121.1552 -3121.1552 16.517278 93.864525 4.9774675 -4.5953886 -4.5953886 8.2168257 -6.8491707 -15.153821 2.3591395 211.55808 Loop time of 2.646e-06 on 1 procs for 0 steps with 704 atoms 264.6% 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 | | 2.646e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7528.00 ave 7528 max 7528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87632.0 ave 87632 max 87632 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 175264.0 ave 175264 max 175264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175264 Ave neighs/atom = 248.95455 Neighbor list builds = 0 Dangerous builds = 0 704 -3121.15515732184 eV 2.35913951491248 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01