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 -62.249764 0.0000000) to (35.937883 62.249764 6.1037460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5289051 5.5862010 6.1037460 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -62.249764 0.0000000) to (35.937883 62.249764 6.1037460) create_atoms CPU = 0.008 seconds 1251 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5289051 5.5862010 6.1037460 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -62.249764 0.0000000) to (35.937883 62.249764 6.1037460) create_atoms CPU = 0.007 seconds 1251 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 = 9 28 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 22 atoms, new total = 2480 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 = 9 28 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) = 15.48 | 15.48 | 15.48 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10927.106 0 -10927.106 9075.6089 24 0 -10976.088 0 -10976.088 -3901.2097 Loop time of 4.26497 on 1 procs for 24 steps with 2480 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 = -10927.1062320741 -10976.076734449 -10976.0876073872 Force two-norm initial, final = 103.29784 0.33531118 Force max component initial, final = 18.081125 0.040190948 Final line search alpha, max atom move = 0.88621957 0.035618004 Iterations, force evaluations = 24 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.239 | 4.239 | 4.239 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0146 | 0.0146 | 0.0146 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01137 | | | 0.27 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14380.0 ave 14380 max 14380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 307155.0 ave 307155 max 307155 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 307155 Ave neighs/atom = 123.85282 Neighbor list builds = 0 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 : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.48 | 15.48 | 15.48 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -10976.088 0 -10976.088 -3901.2097 27309.682 26 0 -10976.131 0 -10976.131 -1177.2389 27269.265 Loop time of 0.481378 on 1 procs for 2 steps with 2480 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10976.0876073872 -10976.1311988505 -10976.1314147785 Force two-norm initial, final = 80.866617 0.34050099 Force max component initial, final = 66.305178 0.061508832 Final line search alpha, max atom move = 0.00029937914 1.8414461e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47517 | 0.47517 | 0.47517 | 0.0 | 98.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016148 | 0.0016148 | 0.0016148 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004597 | | | 0.95 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14368.0 ave 14368 max 14368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 308805.0 ave 308805 max 308805 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 308805 Ave neighs/atom = 124.51815 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 = 9 28 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) = 14.36 | 14.36 | 14.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10976.131 0 -10976.131 -1177.2389 Loop time of 6.585e-06 on 1 procs for 0 steps with 2480 atoms 167.0% 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 | | 6.585e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14368.0 ave 14368 max 14368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 308895.0 ave 308895 max 308895 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 = 308895 Ave neighs/atom = 124.55444 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) = 14.36 | 14.36 | 14.36 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 -10976.131 -10976.131 35.918639 124.49953 6.0979781 -1177.2389 -1177.2389 -3.6119504 -3527.6413 -0.46339285 2.2481029 989.94928 Loop time of 6.775e-06 on 1 procs for 0 steps with 2480 atoms 280.4% 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 | | 6.775e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14368.0 ave 14368 max 14368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 308895.0 ave 308895 max 308895 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 617790.0 ave 617790 max 617790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 617790 Ave neighs/atom = 249.10887 Neighbor list builds = 0 Dangerous builds = 0 2480 -10976.1314147785 eV 2.24810285421741 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05