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 -43.491523 0) to (21.306408 43.491523 9.5285152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6817088 5.2189827 6.3523435 Created 600 atoms using lattice units in orthogonal box = (0 -43.491523 0) to (21.306408 43.491523 9.5285152) create_atoms CPU = 0.000 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6817088 5.2189827 6.3523435 Created 612 atoms using lattice units in orthogonal box = (0 -43.491523 0) to (21.306408 43.491523 9.5285152) create_atoms CPU = 0.000 seconds 612 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 = 5 20 3 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 24 atoms, new total = 1188 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 = 5 20 3 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) = 7.82 | 7.82 | 7.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4513.631 0 -4513.631 33305.164 39 0 -4594.212 0 -4594.212 -5664.9991 Loop time of 0.449103 on 1 procs for 39 steps with 1188 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4513.63100867115 -4594.20814653041 -4594.21202908969 Force two-norm initial, final = 130.01867 0.23327998 Force max component initial, final = 27.772364 0.031762866 Final line search alpha, max atom move = 1 0.031762866 Iterations, force evaluations = 39 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4433 | 0.4433 | 0.4433 | 0.0 | 98.71 Neigh | 0.0029105 | 0.0029105 | 0.0029105 | 0.0 | 0.65 Comm | 0.0016563 | 0.0016563 | 0.0016563 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001234 | | | 0.27 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6249 ave 6249 max 6249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117696 ave 117696 max 117696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117696 Ave neighs/atom = 99.070707 Neighbor list builds = 1 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 : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.82 | 7.82 | 7.82 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -4594.212 0 -4594.212 -5664.9991 17659.162 43 0 -4594.3222 0 -4594.3222 23.319676 17606.672 Loop time of 0.0495575 on 1 procs for 4 steps with 1188 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4594.2120290897 -4594.32208652446 -4594.32224383941 Force two-norm initial, final = 109.84688 0.51677553 Force max component initial, final = 71.94009 0.32008674 Final line search alpha, max atom move = 0.00063953978 0.0002047082 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.048724 | 0.048724 | 0.048724 | 0.0 | 98.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016812 | 0.00016812 | 0.00016812 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006651 | | | 1.34 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6241 ave 6241 max 6241 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117768 ave 117768 max 117768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117768 Ave neighs/atom = 99.131313 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 = 5 20 3 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) = 7.451 | 7.451 | 7.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4594.3222 0 -4594.3222 23.319676 Loop time of 5.51e-07 on 1 procs for 0 steps with 1188 atoms 181.5% 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 | | 5.51e-07 | | |100.00 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6241 ave 6241 max 6241 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117768 ave 117768 max 117768 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 = 117768 Ave neighs/atom = 99.131313 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) = 7.451 | 7.451 | 7.451 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 -4594.3222 -4594.3222 21.263113 87.023066 9.5151587 23.319676 23.319676 26.773291 14.09923 29.086507 2.512505 838.68786 Loop time of 5.11e-07 on 1 procs for 0 steps with 1188 atoms 195.7% 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 | | 5.11e-07 | | |100.00 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6241 ave 6241 max 6241 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117768 ave 117768 max 117768 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235536 ave 235536 max 235536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235536 Ave neighs/atom = 198.26263 Neighbor list builds = 0 Dangerous builds = 0 1188 -4594.32224383941 eV 2.51250501213319 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00