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 -43.163526 0.0000000) to (6.1037460 43.163526 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1037460 5.7546669 4.9836877 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -43.163526 0.0000000) to (6.1037460 43.163526 4.9836877) create_atoms CPU = 0.001 seconds 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1037460 5.7546669 4.9836877 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -43.163526 0.0000000) to (6.1037460 43.163526 4.9836877) create_atoms CPU = 0.001 seconds 122 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 = 2 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 4 atoms, new total = 240 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 = 2 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) = 7.100 | 7.100 | 7.100 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1051.1041 0 -1051.1041 23778.088 43 0 -1062.1956 0 -1062.1956 6501.403 Loop time of 0.401373 on 1 procs for 43 steps with 240 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 = -1051.10405654112 -1062.1947614476 -1062.19563381556 Force two-norm initial, final = 27.241826 0.10257387 Force max component initial, final = 8.7372689 0.019253134 Final line search alpha, max atom move = 1.0000000 0.019253134 Iterations, force evaluations = 43 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39604 | 0.39604 | 0.39604 | 0.0 | 98.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0035852 | 0.0035852 | 0.0035852 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001743 | | | 0.43 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4548.00 ave 4548 max 4548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30086.0 ave 30086 max 30086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30086 Ave neighs/atom = 125.35833 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 : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.103 | 7.103 | 7.103 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -1062.1956 0 -1062.1956 6501.403 2625.9967 46 0 -1062.2096 0 -1062.2096 1536.4398 2633.0136 Loop time of 0.0266601 on 1 procs for 3 steps with 240 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 = -1062.19563381556 -1062.20952724691 -1062.20956688333 Force two-norm initial, final = 14.217390 0.10615573 Force max component initial, final = 11.790364 0.021443351 Final line search alpha, max atom move = 0.0021803441 4.6753884e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.025735 | 0.025735 | 0.025735 | 0.0 | 96.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021275 | 0.00021275 | 0.00021275 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007125 | | | 2.67 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4926.00 ave 4926 max 4926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30364.0 ave 30364 max 30364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30364 Ave neighs/atom = 126.51667 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 = 2 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) = 6.735 | 6.735 | 6.735 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1062.2096 0 -1062.2096 1536.4398 Loop time of 2.191e-06 on 1 procs for 0 steps with 240 atoms 182.6% 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 | | 2.191e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4926.00 ave 4926 max 4926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30320.0 ave 30320 max 30320 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 = 30320 Ave neighs/atom = 126.33333 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) = 6.735 | 6.735 | 6.735 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 -1062.2096 -1062.2096 6.1144159 86.327052 4.9882845 1536.4398 1536.4398 -10.001772 4613.366 5.9549899 2.3704146 120.29969 Loop time of 1.749e-06 on 1 procs for 0 steps with 240 atoms 171.5% 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 | | 1.749e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4926.00 ave 4926 max 4926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30320.0 ave 30320 max 30320 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 60640.0 ave 60640 max 60640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60640 Ave neighs/atom = 252.66667 Neighbor list builds = 0 Dangerous builds = 0 240 -1062.20956688333 eV 2.37041456576508 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00