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 -69.775152 0.0000000) to (42.726222 69.775152 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9411277 4.9836877 5.7546669 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -69.775152 0.0000000) to (42.726222 69.775152 8.6320004) create_atoms CPU = 0.003 seconds 2357 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9411277 4.9836877 5.7546669 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -69.775152 0.0000000) to (42.726222 69.775152 8.6320004) create_atoms CPU = 0.003 seconds 2357 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 = 10 32 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 47 atoms, new total = 4667 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 = 10 32 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) = 17.04 | 17.04 | 17.04 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20606.192 0 -20606.192 2365.418 22 0 -20659.769 0 -20659.769 -6659.583 Loop time of 2.89788 on 1 procs for 22 steps with 4667 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 = -20606.1921070317 -20659.751320653 -20659.7693818311 Force two-norm initial, final = 121.40295 0.49113326 Force max component initial, final = 25.142360 0.14616979 Final line search alpha, max atom move = 1.0000000 0.14616979 Iterations, force evaluations = 22 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8816 | 2.8816 | 2.8816 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0073666 | 0.0073666 | 0.0073666 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008906 | | | 0.31 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18214.0 ave 18214 max 18214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 576820.0 ave 576820 max 576820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576820 Ave neighs/atom = 123.59546 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 17.04 | 17.04 | 17.04 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -20659.769 0 -20659.769 -6659.583 51467.934 25 0 -20660.051 0 -20660.051 -1393.4594 51320.596 Loop time of 0.471118 on 1 procs for 3 steps with 4667 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 = -20659.7693818311 -20660.0510423768 -20660.0512119799 Force two-norm initial, final = 277.61794 0.55251812 Force max component initial, final = 199.97463 0.18676583 Final line search alpha, max atom move = 0.00029651298 5.5378494e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46616 | 0.46616 | 0.46616 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078922 | 0.00078922 | 0.00078922 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004173 | | | 0.89 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18265.0 ave 18265 max 18265 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 579492.0 ave 579492 max 579492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579492 Ave neighs/atom = 124.16799 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 = 10 32 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) = 15.93 | 15.93 | 15.93 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20660.051 0 -20660.051 -1393.4594 Loop time of 2.325e-06 on 1 procs for 0 steps with 4667 atoms 172.0% 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 | | 2.325e-06 | | |100.00 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18265.0 ave 18265 max 18265 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 579957.0 ave 579957 max 579957 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 = 579957 Ave neighs/atom = 124.26762 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) = 15.93 | 15.93 | 15.93 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 -20660.051 -20660.051 42.662971 139.5503 8.6200505 -1393.4594 -1393.4594 -3.5813133 -4170.9744 -5.8225664 2.2148546 1693.1752 Loop time of 2.562e-06 on 1 procs for 0 steps with 4667 atoms 273.2% 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 | | 2.562e-06 | | |100.00 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18265.0 ave 18265 max 18265 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 579957.0 ave 579957 max 579957 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.15991e+06 ave 1.15991e+06 max 1.15991e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1159914 Ave neighs/atom = 248.53525 Neighbor list builds = 0 Dangerous builds = 0 4667 -20660.0512119799 eV 2.21485456550613 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04