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 -45.679777 0.0000000) to (26.371197 45.679777 6.1037460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6509707 5.4376491 6.1037460 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -45.679777 0.0000000) to (26.371197 45.679777 6.1037460) create_atoms CPU = 0.004 seconds 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6509707 5.4376491 6.1037460 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -45.679777 0.0000000) to (26.371197 45.679777 6.1037460) create_atoms CPU = 0.003 seconds 676 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 21 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 20 atoms, new total = 1332 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 21 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) = 7.894 | 7.894 | 7.894 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5848.2526 0 -5848.2526 12461.573 56 0 -5888.6794 0 -5888.6794 -6198.176 Loop time of 5.6876 on 1 procs for 56 steps with 1332 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5848.25259525577 -5888.67479854167 -5888.67940057544 Force two-norm initial, final = 96.146745 0.21675419 Force max component initial, final = 19.929147 0.029527177 Final line search alpha, max atom move = 1.0000000 0.029527177 Iterations, force evaluations = 56 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6489 | 5.6489 | 5.6489 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.021362 | 0.021362 | 0.021362 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01733 | | | 0.30 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8316.00 ave 8316 max 8316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164908.0 ave 164908 max 164908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164908 Ave neighs/atom = 123.80480 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.895 | 7.895 | 7.895 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -5888.6794 0 -5888.6794 -6198.176 14705.516 58 0 -5888.717 0 -5888.717 -2795.7689 14678.058 Loop time of 0.208291 on 1 procs for 2 steps with 1332 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5888.67940057544 -5888.71546361322 -5888.7169870816 Force two-norm initial, final = 54.040946 2.7198456 Force max component initial, final = 47.301129 2.7065178 Final line search alpha, max atom move = 9.9553546e-05 0.00026944345 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20532 | 0.20532 | 0.20532 | 0.0 | 98.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079589 | 0.00079589 | 0.00079589 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002171 | | | 1.04 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8432.00 ave 8432 max 8432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 166216.0 ave 166216 max 166216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166216 Ave neighs/atom = 124.78679 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 21 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) = 7.526 | 7.526 | 7.526 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5888.717 0 -5888.717 -2795.7689 Loop time of 6.415e-06 on 1 procs for 0 steps with 1332 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 | | 6.415e-06 | | |100.00 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8450.00 ave 8450 max 8450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 166284.0 ave 166284 max 166284 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 = 166284 Ave neighs/atom = 124.83784 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) = 7.526 | 7.526 | 7.526 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 -5888.717 -5888.717 26.35627 91.359553 6.0957994 -2795.7689 -2795.7689 295.26147 -8667.757 -14.811331 2.3024676 701.50685 Loop time of 7.748e-06 on 1 procs for 0 steps with 1332 atoms 0.0% 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 | | 7.748e-06 | | |100.00 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8450.00 ave 8450 max 8450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 166284.0 ave 166284 max 166284 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 332568.0 ave 332568 max 332568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332568 Ave neighs/atom = 249.67568 Neighbor list builds = 0 Dangerous builds = 0 1332 -5888.7169870816 eV 2.30246763453816 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06