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 -63.822343 0.0000000) to (22.564606 63.822343 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0539187 5.4482488 4.9836877 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -63.822343 0.0000000) to (22.564606 63.822343 4.9836877) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0539187 5.4482488 4.9836877 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.822343 0.0000000) to (22.564606 63.822343 4.9836877) create_atoms CPU = 0.002 seconds 658 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 = 6 29 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 = 1312 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 = 6 29 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) = 7.919 | 7.919 | 7.919 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5340.5871 0 -5340.5871 95131.133 74 0 -5814.9701 0 -5814.9701 3520.2779 Loop time of 3.70538 on 1 procs for 74 steps with 1312 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5340.58713851503 -5814.96505576418 -5814.9700556344 Force two-norm initial, final = 881.24665 0.23740135 Force max component initial, final = 246.15096 0.039281893 Final line search alpha, max atom move = 1.0000000 0.039281893 Iterations, force evaluations = 74 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6541 | 3.6541 | 3.6541 | 0.0 | 98.62 Neigh | 0.018243 | 0.018243 | 0.018243 | 0.0 | 0.49 Comm | 0.0197 | 0.0197 | 0.0197 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01335 | | | 0.36 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10685.0 ave 10685 max 10685 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165362.0 ave 165362 max 165362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165362 Ave neighs/atom = 126.03811 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 : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.919 | 7.919 | 7.919 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -5814.9701 0 -5814.9701 3520.2779 14354.277 77 0 -5815.0209 0 -5815.0209 -58.623449 14382.002 Loop time of 0.302551 on 1 procs for 3 steps with 1312 atoms 48.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5814.9700556344 -5815.02071817317 -5815.02086805715 Force two-norm initial, final = 62.337712 0.96590608 Force max component initial, final = 49.582053 0.65502779 Final line search alpha, max atom move = 0.00043586272 0.00028550220 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29997 | 0.29997 | 0.29997 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050132 | 0.00050132 | 0.00050132 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002077 | | | 0.69 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10631.0 ave 10631 max 10631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165634.0 ave 165634 max 165634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165634 Ave neighs/atom = 126.24543 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 = 6 29 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) = 7.551 | 7.551 | 7.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5815.0209 0 -5815.0209 -58.623449 Loop time of 2.312e-06 on 1 procs for 0 steps with 1312 atoms 173.0% 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 | | 2.312e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10631.0 ave 10631 max 10631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165274.0 ave 165274 max 165274 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 = 165274 Ave neighs/atom = 125.97104 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) = 7.551 | 7.551 | 7.551 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 -5815.0209 -5815.0209 22.595492 127.77928 4.9812357 -58.623449 -58.623449 -73.070957 -40.245772 -62.553617 2.3237673 490.94627 Loop time of 2.458e-06 on 1 procs for 0 steps with 1312 atoms 244.1% 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 | | 2.458e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10631.0 ave 10631 max 10631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165274.0 ave 165274 max 165274 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 330548.0 ave 330548 max 330548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330548 Ave neighs/atom = 251.94207 Neighbor list builds = 0 Dangerous builds = 0 1312 -5815.02086805715 eV 2.32376734940977 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04