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 -49.205041 0) to (12.30126 49.205041 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9205041 4.9205041 3.8900001 Created 160 atoms using lattice units in orthogonal box = (0 -49.205041 0) to (12.30126 49.205041 3.8900001) create_atoms CPU = 0.000 seconds 160 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9205041 4.9205041 3.8900001 Created 162 atoms using lattice units in orthogonal box = (0 -49.205041 0) to (12.30126 49.205041 3.8900001) create_atoms CPU = 0.000 seconds 162 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 = 3 23 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 2 atoms, new total = 320 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 = 3 23 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) = 7.071 | 7.071 | 7.071 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1166.6144 0 -1166.6144 88982.257 20 0 -1238.5019 0 -1238.5019 11430.415 Loop time of 0.0659404 on 1 procs for 20 steps with 320 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1166.61444569934 -1238.50088980976 -1238.50192860005 Force two-norm initial, final = 211.28651 0.13510647 Force max component initial, final = 69.242843 0.032315458 Final line search alpha, max atom move = 1 0.032315458 Iterations, force evaluations = 20 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.064893 | 0.064893 | 0.064893 | 0.0 | 98.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074306 | 0.00074306 | 0.00074306 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003042 | | | 0.46 Nlocal: 320 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5236 ave 5236 max 5236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32008 ave 32008 max 32008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32008 Ave neighs/atom = 100.025 Neighbor list builds = 0 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 : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.071 | 7.071 | 7.071 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -1238.5019 0 -1238.5019 11430.415 4709.1097 31 0 -1238.7367 0 -1238.7367 162.64223 4735.3842 Loop time of 0.0238078 on 1 procs for 11 steps with 320 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1238.50192860005 -1238.73602834002 -1238.73672447473 Force two-norm initial, final = 64.345082 1.0362634 Force max component initial, final = 55.77557 0.75638453 Final line search alpha, max atom move = 0.00087125087 0.00065900067 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022025 | 0.022025 | 0.022025 | 0.0 | 92.51 Neigh | 0.0007656 | 0.0007656 | 0.0007656 | 0.0 | 3.22 Comm | 0.00027662 | 0.00027662 | 0.00027662 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007408 | | | 3.11 Nlocal: 320 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5236 ave 5236 max 5236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31752 ave 31752 max 31752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31752 Ave neighs/atom = 99.225 Neighbor list builds = 1 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 = 3 23 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) = 6.702 | 6.702 | 6.702 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1238.7367 0 -1238.7367 162.64223 Loop time of 4.51e-07 on 1 procs for 0 steps with 320 atoms 221.7% 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 | | 4.51e-07 | | |100.00 Nlocal: 320 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5236 ave 5236 max 5236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31752 ave 31752 max 31752 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 = 31752 Ave neighs/atom = 99.225 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) = 6.702 | 6.702 | 6.702 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 -1238.7367 -1238.7367 12.270799 99.44823 3.8804788 162.64223 162.64223 255.28248 89.449497 143.19471 2.5389141 203.70411 Loop time of 4.51e-07 on 1 procs for 0 steps with 320 atoms 443.5% 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 | | 4.51e-07 | | |100.00 Nlocal: 320 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5236 ave 5236 max 5236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31752 ave 31752 max 31752 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63504 ave 63504 max 63504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63504 Ave neighs/atom = 198.45 Neighbor list builds = 0 Dangerous builds = 0 320 -1238.73672447473 eV 2.53891414589457 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00