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 -39.869502 0.0000000) to (17.264001 39.869502 6.1037460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7546669 4.9836877 6.1037460 Created 384 atoms using lattice units in orthogonal box = (0.0000000 -39.869502 0.0000000) to (17.264001 39.869502 6.1037460) create_atoms CPU = 0.001 seconds 384 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7546669 4.9836877 6.1037460 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -39.869502 0.0000000) to (17.264001 39.869502 6.1037460) create_atoms CPU = 0.001 seconds 396 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 18 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 = 776 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 18 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) = 7.703 | 7.703 | 7.703 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2521.6517 0 -2521.6517 346927.55 83 0 -3426.0127 0 -3426.0127 30052.183 Loop time of 4.28844 on 1 procs for 83 steps with 776 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2521.65166272131 -3426.00948579437 -3426.01265833427 Force two-norm initial, final = 1049.2927 0.22244774 Force max component initial, final = 254.78708 0.035940673 Final line search alpha, max atom move = 1.0000000 0.035940673 Iterations, force evaluations = 83 155 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2411 | 4.2411 | 4.2411 | 0.0 | 98.90 Neigh | 0.012496 | 0.012496 | 0.012496 | 0.0 | 0.29 Comm | 0.021033 | 0.021033 | 0.021033 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01384 | | | 0.32 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6987.00 ave 6987 max 6987 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102260.0 ave 102260 max 102260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102260 Ave neighs/atom = 131.77835 Neighbor list builds = 1 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.703 | 7.703 | 7.703 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -3426.0127 0 -3426.0127 30052.183 8402.5035 98 0 -3427.8735 0 -3427.8735 -79.059308 8536.8819 Loop time of 0.581789 on 1 procs for 15 steps with 776 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3426.01265833427 -3427.87345944316 -3427.87350023241 Force two-norm initial, final = 299.13666 1.0247166 Force max component initial, final = 256.61973 0.47808576 Final line search alpha, max atom move = 0.0014604775 0.00069823347 Iterations, force evaluations = 15 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55741 | 0.55741 | 0.55741 | 0.0 | 95.81 Neigh | 0.011885 | 0.011885 | 0.011885 | 0.0 | 2.04 Comm | 0.0024302 | 0.0024302 | 0.0024302 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01007 | | | 1.73 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6962.00 ave 6962 max 6962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98076.0 ave 98076 max 98076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98076 Ave neighs/atom = 126.38660 Neighbor list builds = 1 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 19 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) = 6.953 | 6.953 | 6.953 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3427.8735 0 -3427.8735 -79.059308 Loop time of 3.754e-06 on 1 procs for 0 steps with 776 atoms 186.5% 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 | | 3.754e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6962.00 ave 6962 max 6962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98056.0 ave 98056 max 98056 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 = 98056 Ave neighs/atom = 126.36082 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) = 6.953 | 6.953 | 6.953 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 -3427.8735 -3427.8735 17.256998 80.840474 6.1193485 -79.059308 -79.059308 -71.359741 -90.965128 -74.853055 2.3027635 434.74455 Loop time of 4.566e-06 on 1 procs for 0 steps with 776 atoms 175.2% 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 | | 4.566e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6962.00 ave 6962 max 6962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98056.0 ave 98056 max 98056 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 196112.0 ave 196112 max 196112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196112 Ave neighs/atom = 252.72165 Neighbor list builds = 0 Dangerous builds = 0 776 -3427.87350023241 eV 2.30276345004913 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05