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 -51.016873 0) to (36.074377 51.016873 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7115119 6.5254139 5.5012908 Created 682 atoms using lattice units in orthogonal box = (0 -51.016873 0) to (36.074377 51.016873 5.5012908) create_atoms CPU = 0.001 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7115119 6.5254139 5.5012908 Created 690 atoms using lattice units in orthogonal box = (0 -51.016873 0) to (36.074377 51.016873 5.5012908) create_atoms CPU = 0.001 seconds 690 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 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 2 atoms, new total = 1370 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 = 9 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) = 7.846 | 7.846 | 7.846 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5056.9063 0 -5056.9063 71842.764 103 0 -5310.3173 0 -5310.3173 -2296.8475 Loop time of 1.44186 on 1 procs for 103 steps with 1370 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 = -5056.90631466242 -5310.31297439604 -5310.31732494945 Force two-norm initial, final = 371.0975 0.2359045 Force max component initial, final = 53.473571 0.059318164 Final line search alpha, max atom move = 1 0.059318164 Iterations, force evaluations = 103 200 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4254 | 1.4254 | 1.4254 | 0.0 | 98.86 Neigh | 0.0057632 | 0.0057632 | 0.0057632 | 0.0 | 0.40 Comm | 0.0063615 | 0.0063615 | 0.0063615 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004295 | | | 0.30 Nlocal: 1370 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8759 ave 8759 max 8759 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136318 ave 136318 max 136318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136318 Ave neighs/atom = 99.50219 Neighbor list builds = 2 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 : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.846 | 7.846 | 7.846 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -5310.3173 0 -5310.3173 -2296.8475 20249.172 106 0 -5310.3542 0 -5310.3542 -2.7499093 20225.811 Loop time of 0.0501002 on 1 procs for 3 steps with 1370 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5310.31732494944 -5310.35416176599 -5310.3541709351 Force two-norm initial, final = 57.196546 0.37564604 Force max component initial, final = 47.656413 0.24305826 Final line search alpha, max atom move = 0.0041860465 0.0010174532 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049181 | 0.049181 | 0.049181 | 0.0 | 98.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020374 | 0.00020374 | 0.00020374 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007153 | | | 1.43 Nlocal: 1370 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8293 ave 8293 max 8293 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136312 ave 136312 max 136312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136312 Ave neighs/atom = 99.49781 Neighbor list builds = 0 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 = 9 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) = 7.473 | 7.473 | 7.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5310.3542 0 -5310.3542 -2.7499093 Loop time of 5.41e-07 on 1 procs for 0 steps with 1370 atoms 184.8% 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 | | 5.41e-07 | | |100.00 Nlocal: 1370 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8303 ave 8303 max 8303 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136348 ave 136348 max 136348 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 = 136348 Ave neighs/atom = 99.524088 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) = 7.473 | 7.473 | 7.473 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 -5310.3542 -5310.3542 36.098558 101.89065 5.498975 -2.7499093 -2.7499093 5.2854745 5.7104181 -19.245621 2.5929264 1144.364 Loop time of 4.71e-07 on 1 procs for 0 steps with 1370 atoms 212.3% 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 | | 4.71e-07 | | |100.00 Nlocal: 1370 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8303 ave 8303 max 8303 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136348 ave 136348 max 136348 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 272696 ave 272696 max 272696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272696 Ave neighs/atom = 199.04818 Neighbor list builds = 0 Dangerous builds = 0 1370 -5310.3541709351 eV 2.59292636808788 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01