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 -35.937883 0.0000000) to (31.123120 35.937883 6.1037460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5862010 5.5289051 6.1037460 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -35.937883 0.0000000) to (31.123120 35.937883 6.1037460) create_atoms CPU = 0.002 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5862010 5.5289051 6.1037460 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -35.937883 0.0000000) to (31.123120 35.937883 6.1037460) create_atoms CPU = 0.001 seconds 629 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 17 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 = 1251 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 17 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) = 7.845 | 7.845 | 7.845 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3415.8583 0 -3415.8583 288734.97 94 0 -5521.8183 0 -5521.8183 17882.566 Loop time of 4.0792 on 1 procs for 94 steps with 1251 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 = -3415.85828454714 -5521.81291937744 -5521.81826372531 Force two-norm initial, final = 2191.4497 0.28771879 Force max component initial, final = 462.34658 0.10166964 Final line search alpha, max atom move = 0.83216879 0.084606303 Iterations, force evaluations = 94 166 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.021 | 4.021 | 4.021 | 0.0 | 98.57 Neigh | 0.026672 | 0.026672 | 0.026672 | 0.0 | 0.65 Comm | 0.018234 | 0.018234 | 0.018234 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01329 | | | 0.33 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8541.00 ave 8541 max 8541 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160848.0 ave 160848 max 160848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160848 Ave neighs/atom = 128.57554 Neighbor list builds = 3 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 : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.847 | 7.847 | 7.847 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -5521.8183 0 -5521.8183 17882.566 13654.068 104 0 -5523.145 0 -5523.145 68.57029 13785.003 Loop time of 0.34883 on 1 procs for 10 steps with 1251 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 = -5521.81826372532 -5523.14169874186 -5523.14497027546 Force two-norm initial, final = 307.25918 1.5742794 Force max component initial, final = 274.33036 1.3057881 Final line search alpha, max atom move = 0.00011749244 0.00015342023 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34309 | 0.34309 | 0.34309 | 0.0 | 98.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010627 | 0.0010627 | 0.0010627 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004674 | | | 1.34 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8537.00 ave 8537 max 8537 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160707.0 ave 160707 max 160707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160707 Ave neighs/atom = 128.46283 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 = 8 17 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) = 7.479 | 7.479 | 7.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5523.145 0 -5523.145 68.57029 Loop time of 4.054e-06 on 1 procs for 0 steps with 1251 atoms 172.7% 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 | | 4.054e-06 | | |100.00 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8529.00 ave 8529 max 8529 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 157057.0 ave 157057 max 157057 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 = 157057 Ave neighs/atom = 125.54516 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) = 7.479 | 7.479 | 7.479 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 -5523.145 -5523.145 31.160106 72.55667 6.0972022 68.57029 68.57029 -1.5525767 55.65956 151.60389 2.2225693 823.82433 Loop time of 4.488e-06 on 1 procs for 0 steps with 1251 atoms 200.5% 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 | | 4.488e-06 | | |100.00 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8529.00 ave 8529 max 8529 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 157057.0 ave 157057 max 157057 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 314114.0 ave 314114 max 314114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314114 Ave neighs/atom = 251.09033 Neighbor list builds = 0 Dangerous builds = 0 1251 -5523.14497027546 eV 2.22256925439167 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04