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 -56.822783 0.0000000) to (28.411391 56.822783 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8080816 4.8080816 3.5239994 Created 519 atoms using lattice units in orthogonal box = (0.0000000 -56.822783 0.0000000) to (28.411391 56.822783 3.5239994) create_atoms CPU = 0.001 seconds 519 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8080816 4.8080816 3.5239994 Created 521 atoms using lattice units in orthogonal box = (0.0000000 -56.822783 0.0000000) to (28.411391 56.822783 3.5239994) create_atoms CPU = 0.001 seconds 521 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 = 7 26 1 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 0 atoms, new total = 1040 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 = 7 26 1 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) = 7.757 | 7.757 | 7.757 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4213.3165 0 -4213.3165 113413.69 84 0 -4601.589 0 -4601.589 8839.0553 Loop time of 3.24077 on 1 procs for 84 steps with 1040 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 = -4213.31653515866 -4601.58535085974 -4601.58898340263 Force two-norm initial, final = 751.74466 0.24516474 Force max component initial, final = 177.19280 0.052375557 Final line search alpha, max atom move = 1.0000000 0.052375557 Iterations, force evaluations = 84 156 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1967 | 3.1967 | 3.1967 | 0.0 | 98.64 Neigh | 0.013691 | 0.013691 | 0.013691 | 0.0 | 0.42 Comm | 0.019336 | 0.019336 | 0.019336 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01107 | | | 0.34 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11116.0 ave 11116 max 11116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130966.0 ave 130966 max 130966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130966 Ave neighs/atom = 125.92885 Neighbor list builds = 2 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 : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -4601.589 0 -4601.589 8839.0553 11378.39 90 0 -4601.8827 0 -4601.8827 -260.72893 11434.062 Loop time of 0.163161 on 1 procs for 6 steps with 1040 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 = -4601.58898340263 -4601.8820755181 -4601.88270802409 Force two-norm initial, final = 127.61678 3.8860161 Force max component initial, final = 114.54948 3.6026977 Final line search alpha, max atom move = 0.00030091422 0.0010841030 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15908 | 0.15908 | 0.15908 | 0.0 | 97.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075893 | 0.00075893 | 0.00075893 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003323 | | | 2.04 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11686.0 ave 11686 max 11686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130162.0 ave 130162 max 130162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130162 Ave neighs/atom = 125.15577 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 = 7 26 1 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) = 7.400 | 7.400 | 7.400 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4601.8827 0 -4601.8827 -260.72893 Loop time of 1.923e-06 on 1 procs for 0 steps with 1040 atoms 156.0% 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 | | 1.923e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11686.0 ave 11686 max 11686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129773.0 ave 129773 max 129773 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 = 129773 Ave neighs/atom = 124.78173 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) = 7.400 | 7.400 | 7.400 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 -4601.8827 -4601.8827 28.391372 114.23302 3.5255146 -260.72893 -260.72893 -113.47107 -163.67739 -505.03832 2.2398807 383.54081 Loop time of 2.239e-06 on 1 procs for 0 steps with 1040 atoms 223.3% 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 | | 2.239e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11686.0 ave 11686 max 11686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129773.0 ave 129773 max 129773 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 259546.0 ave 259546 max 259546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259546 Ave neighs/atom = 249.56346 Neighbor list builds = 0 Dangerous builds = 0 1040 -4601.88270802409 eV 2.23988069280365 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03