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 -43.446782 0.0000000) to (15.360757 43.446782 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6592263 4.5733455 4.9836877 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -43.446782 0.0000000) to (15.360757 43.446782 4.9836877) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6592263 4.5733455 4.9836877 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.446782 0.0000000) to (15.360757 43.446782 4.9836877) create_atoms CPU = 0.001 seconds 306 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 = 4 20 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 0 atoms, new total = 610 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 = 4 20 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) = 7.239 | 7.239 | 7.239 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1719.5787 0 -1719.5787 296573.49 97 0 -2697.7563 0 -2697.7563 14358.356 Loop time of 2.32282 on 1 procs for 97 steps with 610 atoms 96.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1719.5786551894 -2697.75397973486 -2697.75625264305 Force two-norm initial, final = 1413.1381 0.17195513 Force max component initial, final = 483.32375 0.033867415 Final line search alpha, max atom move = 1.0000000 0.033867415 Iterations, force evaluations = 97 177 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2864 | 2.2864 | 2.2864 | 0.0 | 98.43 Neigh | 0.01367 | 0.01367 | 0.01367 | 0.0 | 0.59 Comm | 0.013899 | 0.013899 | 0.013899 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008842 | | | 0.38 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78284.0 ave 78284 max 78284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78284 Ave neighs/atom = 128.33443 Neighbor list builds = 3 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 : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.239 | 7.239 | 7.239 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -2697.7563 0 -2697.7563 14358.356 6651.982 105 0 -2698.0916 0 -2698.0916 -270.25282 6704.6133 Loop time of 0.126042 on 1 procs for 8 steps with 610 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 = -2697.75625264304 -2698.08955746266 -2698.09164036489 Force two-norm initial, final = 108.61285 2.0012193 Force max component initial, final = 86.981704 1.2513866 Final line search alpha, max atom move = 0.00023249793 0.00029094478 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1229 | 0.1229 | 0.1229 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056663 | 0.00056663 | 0.00056663 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002571 | | | 2.04 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6903.00 ave 6903 max 6903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77854.0 ave 77854 max 77854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77854 Ave neighs/atom = 127.62951 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 = 4 20 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) = 6.870 | 6.870 | 6.870 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2698.0916 0 -2698.0916 -270.25282 Loop time of 2.229e-06 on 1 procs for 0 steps with 610 atoms 179.5% 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 | | 2.229e-06 | | |100.00 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6885.00 ave 6885 max 6885 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77000.0 ave 77000 max 77000 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 = 77000 Ave neighs/atom = 126.22951 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) = 6.870 | 6.870 | 6.870 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 -2698.0916 -2698.0916 15.359304 87.568401 4.9848807 -270.25282 -270.25282 -299.0109 -220.14187 -291.60567 2.3237867 442.27581 Loop time of 2.487e-06 on 1 procs for 0 steps with 610 atoms 281.5% 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 | | 2.487e-06 | | |100.00 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6885.00 ave 6885 max 6885 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77000.0 ave 77000 max 77000 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 154000.0 ave 154000 max 154000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154000 Ave neighs/atom = 252.45902 Neighbor list builds = 0 Dangerous builds = 0 610 -2698.09164036489 eV 2.32378674397743 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02