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 -40.487671 0.0000000) to (28.629106 40.487671 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3377434 5.5210460 4.9836877 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -40.487671 0.0000000) to (28.629106 40.487671 4.9836877) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3377434 5.5210460 4.9836877 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.487671 0.0000000) to (28.629106 40.487671 4.9836877) create_atoms CPU = 0.001 seconds 532 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 19 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 12 atoms, new total = 1048 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 19 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) = 7.764 | 7.764 | 7.764 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4143.984 0 -4143.984 110785.68 52 0 -4632.8444 0 -4632.8444 -2032.2729 Loop time of 1.98506 on 1 procs for 52 steps with 1048 atoms 97.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4143.98398987482 -4632.84056929218 -4632.84435496146 Force two-norm initial, final = 895.34583 0.19717143 Force max component initial, final = 218.33921 0.025723852 Final line search alpha, max atom move = 1.0000000 0.025723852 Iterations, force evaluations = 52 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9548 | 1.9548 | 1.9548 | 0.0 | 98.48 Neigh | 0.013897 | 0.013897 | 0.013897 | 0.0 | 0.70 Comm | 0.0094535 | 0.0094535 | 0.0094535 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006902 | | | 0.35 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8780.00 ave 8780 max 8780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131108.0 ave 131108 max 131108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131108 Ave neighs/atom = 125.10305 Neighbor list builds = 2 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 : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.764 | 7.764 | 7.764 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -4632.8444 0 -4632.8444 -2032.2729 11553.442 55 0 -4632.8789 0 -4632.8789 163.25534 11539.7 Loop time of 0.106918 on 1 procs for 3 steps with 1048 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 = -4632.84435496146 -4632.87737922848 -4632.87888773807 Force two-norm initial, final = 34.660632 3.1438551 Force max component initial, final = 30.836152 3.0711377 Final line search alpha, max atom move = 0.00010207522 0.00031348706 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10497 | 0.10497 | 0.10497 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034587 | 0.00034587 | 0.00034587 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001604 | | | 1.50 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8816.00 ave 8816 max 8816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130948.0 ave 130948 max 130948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130948 Ave neighs/atom = 124.95038 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 = 7 19 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) = 7.395 | 7.395 | 7.395 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4632.8789 0 -4632.8789 163.25534 Loop time of 2.078e-06 on 1 procs for 0 steps with 1048 atoms 192.5% 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 | | 2.078e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8744.00 ave 8744 max 8744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131016.0 ave 131016 max 131016 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 = 131016 Ave neighs/atom = 125.01527 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) = 7.395 | 7.395 | 7.395 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 -4632.8789 -4632.8789 28.566715 81.060077 4.9834166 163.25534 163.25534 84.140855 -20.749625 426.37478 2.2670038 462.5709 Loop time of 2.793e-06 on 1 procs for 0 steps with 1048 atoms 250.6% 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 | | 2.793e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8744.00 ave 8744 max 8744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131016.0 ave 131016 max 131016 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 262032.0 ave 262032 max 262032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262032 Ave neighs/atom = 250.03053 Neighbor list builds = 0 Dangerous builds = 0 1048 -4632.87888773807 eV 2.26700377843162 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02