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 -50.332779 0.0000000) to (35.590649 50.332779 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5828469 4.4411275 4.9836877 Created 814 atoms using lattice units in orthogonal box = (0.0000000 -50.332779 0.0000000) to (35.590649 50.332779 4.9836877) create_atoms CPU = 0.002 seconds 814 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5828469 4.4411275 4.9836877 Created 822 atoms using lattice units in orthogonal box = (0.0000000 -50.332779 0.0000000) to (35.590649 50.332779 4.9836877) create_atoms CPU = 0.001 seconds 822 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 23 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 4 atoms, new total = 1632 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 = 8 23 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) = 8.362 | 8.362 | 8.362 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6119.2716 0 -6119.2716 154670.98 65 0 -7222.4852 0 -7222.4852 7872.6872 Loop time of 4.12233 on 1 procs for 65 steps with 1632 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 = -6119.27158661569 -7222.47888429439 -7222.48520702181 Force two-norm initial, final = 1384.6259 0.28356968 Force max component initial, final = 200.24011 0.035382743 Final line search alpha, max atom move = 1.0000000 0.035382743 Iterations, force evaluations = 65 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0779 | 4.0779 | 4.0779 | 0.0 | 98.92 Neigh | 0.010263 | 0.010263 | 0.010263 | 0.0 | 0.25 Comm | 0.019791 | 0.019791 | 0.019791 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01433 | | | 0.35 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11345.0 ave 11345 max 11345 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 206274.0 ave 206274 max 206274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206274 Ave neighs/atom = 126.39338 Neighbor list builds = 1 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.375 | 8.375 | 8.375 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -7222.4852 0 -7222.4852 7872.6872 17855.32 71 0 -7222.8525 0 -7222.8525 -150.92926 17932.922 Loop time of 0.264837 on 1 procs for 6 steps with 1632 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 = -7222.48520702181 -7222.85003836333 -7222.85245668954 Force two-norm initial, final = 168.53071 3.0290311 Force max component initial, final = 143.82192 2.1919884 Final line search alpha, max atom move = 0.00013684660 0.00029996616 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25989 | 0.25989 | 0.25989 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008004 | 0.0008004 | 0.0008004 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004144 | | | 1.56 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11991.0 ave 11991 max 11991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 205083.0 ave 205083 max 205083 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205083 Ave neighs/atom = 125.66360 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 23 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) = 8.007 | 8.007 | 8.007 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7222.8525 0 -7222.8525 -150.92926 Loop time of 2.11e-06 on 1 procs for 0 steps with 1632 atoms 189.6% 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 | | 2.11e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11991.0 ave 11991 max 11991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 204390.0 ave 204390 max 204390 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 = 204390 Ave neighs/atom = 125.23897 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) = 8.007 | 8.007 | 8.007 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 -7222.8525 -7222.8525 35.549762 101.21991 4.9836602 -150.92926 -150.92926 -195.61328 -125.63337 -131.54112 2.3539091 954.09497 Loop time of 3.165e-06 on 1 procs for 0 steps with 1632 atoms 221.2% 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 | | 3.165e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11991.0 ave 11991 max 11991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 204390.0 ave 204390 max 204390 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 408780.0 ave 408780 max 408780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 408780 Ave neighs/atom = 250.47794 Neighbor list builds = 0 Dangerous builds = 0 1632 -7222.85245668954 eV 2.35390911018354 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04