LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -47.642576 0) to (6.7376777 47.642576 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7376777 6.3523435 5.5012908 Created 120 atoms using lattice units in orthogonal box = (0 -47.642576 0) to (6.7376777 47.642576 5.5012908) create_atoms CPU = 0.000 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7376777 6.3523435 5.5012908 Created 122 atoms using lattice units in orthogonal box = (0 -47.642576 0) to (6.7376777 47.642576 5.5012908) create_atoms CPU = 0.000 seconds 122 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 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 2 atoms, new total = 240 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:187) 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 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) = 7.091 | 7.091 | 7.091 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -891.69675 0 -891.69675 74689.616 57 0 -930.31488 0 -930.31488 6152.7634 Loop time of 0.151149 on 1 procs for 57 steps with 240 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 = -891.696752156673 -930.314024741842 -930.314878440895 Force two-norm initial, final = 135.33211 0.094881101 Force max component initial, final = 41.868292 0.018841288 Final line search alpha, max atom move = 1 0.018841288 Iterations, force evaluations = 57 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14891 | 0.14891 | 0.14891 | 0.0 | 98.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016522 | 0.0016522 | 0.0016522 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005834 | | | 0.39 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4212 ave 4212 max 4212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23956 ave 23956 max 23956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23956 Ave neighs/atom = 99.816667 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.091 | 7.091 | 7.091 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -930.31488 0 -930.31488 6152.7634 3531.8323 61 0 -930.33948 0 -930.33948 37.240628 3542.6624 Loop time of 0.0109918 on 1 procs for 4 steps with 240 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 = -930.314878440895 -930.33947311584 -930.339479484638 Force two-norm initial, final = 23.923239 0.17318835 Force max component initial, final = 15.985409 0.10142262 Final line search alpha, max atom move = 0.0068702323 0.00069679699 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010555 | 0.010555 | 0.010555 | 0.0 | 96.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011078 | 0.00011078 | 0.00011078 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003258 | | | 2.96 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4059 ave 4059 max 4059 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23924 ave 23924 max 23924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23924 Ave neighs/atom = 99.683333 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 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) = 6.721 | 6.721 | 6.721 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -930.33948 0 -930.33948 37.240628 Loop time of 6.42e-07 on 1 procs for 0 steps with 240 atoms 155.8% 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 | | 6.42e-07 | | |100.00 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4069 ave 4069 max 4069 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23916 ave 23916 max 23916 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23916 Ave neighs/atom = 99.65 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.721 | 6.721 | 6.721 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 -930.33948 -930.33948 6.747407 95.468668 5.4996113 37.240628 37.240628 45.934829 32.95102 32.836034 2.6226333 145.81889 Loop time of 4.81e-07 on 1 procs for 0 steps with 240 atoms 415.8% 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 | | 4.81e-07 | | |100.00 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4069 ave 4069 max 4069 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23916 ave 23916 max 23916 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47832 ave 47832 max 47832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47832 Ave neighs/atom = 199.3 Neighbor list builds = 0 Dangerous builds = 0 240 -930.339479484638 eV 2.62263332836146 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00