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 -39.670372 0) to (34.35555 39.670372 6.7376777) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1663808 6.1031342 6.7376777 Created 622 atoms using lattice units in orthogonal box = (0 -39.670372 0) to (34.35555 39.670372 6.7376777) create_atoms CPU = 0.001 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1663808 6.1031342 6.7376777 Created 629 atoms using lattice units in orthogonal box = (0 -39.670372 0) to (34.35555 39.670372 6.7376777) create_atoms CPU = 0.000 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 = 8 18 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 1 atoms, new total = 1250 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 = 8 18 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) = 7.802 | 7.802 | 7.802 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3504.3288 0 -3504.3288 231197.96 184 0 -4830.9107 0 -4830.9107 15823.705 Loop time of 2.37256 on 1 procs for 184 steps with 1250 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 = -3504.32877761615 -4830.90593600812 -4830.91070548558 Force two-norm initial, final = 1234.0895 0.29110091 Force max component initial, final = 262.79926 0.11537158 Final line search alpha, max atom move = 0.51711743 0.059660657 Iterations, force evaluations = 184 347 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.335 | 2.335 | 2.335 | 0.0 | 98.42 Neigh | 0.021254 | 0.021254 | 0.021254 | 0.0 | 0.90 Comm | 0.0097189 | 0.0097189 | 0.0097189 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006548 | | | 0.28 Nlocal: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7250 ave 7250 max 7250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124187 ave 124187 max 124187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124187 Ave neighs/atom = 99.3496 Neighbor list builds = 7 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 : 184 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.802 | 7.802 | 7.802 Mbytes Step Temp E_pair E_mol TotEng Press Volume 184 0 -4830.9107 0 -4830.9107 15823.705 18365.528 192 0 -4831.9038 0 -4831.9038 391.77456 18504.402 Loop time of 0.0682091 on 1 procs for 8 steps with 1250 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 = -4830.91070548558 -4831.90122249854 -4831.90381287128 Force two-norm initial, final = 329.42358 8.2617764 Force max component initial, final = 258.23879 6.6359001 Final line search alpha, max atom move = 0.00016550593 0.0010982808 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.066947 | 0.066947 | 0.066947 | 0.0 | 98.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002469 | 0.0002469 | 0.0002469 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001015 | | | 1.49 Nlocal: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7252 ave 7252 max 7252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124181 ave 124181 max 124181 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124181 Ave neighs/atom = 99.3448 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 = 8 18 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) = 7.433 | 7.433 | 7.433 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4831.9038 0 -4831.9038 391.77456 Loop time of 6.41e-07 on 1 procs for 0 steps with 1250 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 | | 6.41e-07 | | |100.00 Nlocal: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7209 ave 7209 max 7209 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 123947 ave 123947 max 123947 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 = 123947 Ave neighs/atom = 99.1576 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) = 7.433 | 7.433 | 7.433 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 -4831.9038 -4831.9038 34.394858 79.920145 6.731708 391.77456 391.77456 282.83418 578.7555 313.73401 2.5262504 1087.9816 Loop time of 4.61e-07 on 1 procs for 0 steps with 1250 atoms 433.8% 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 | | 4.61e-07 | | |100.00 Nlocal: 1250 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7209 ave 7209 max 7209 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 123947 ave 123947 max 123947 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 247894 ave 247894 max 247894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 247894 Ave neighs/atom = 198.3152 Neighbor list builds = 0 Dangerous builds = 0 1250 -4831.90381287128 eV 2.52625039918315 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02