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 (4.9836877 43.163526 6.1037460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9836877 5.7546669 6.1037460 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -43.163526 0.0000000) to (4.9836877 43.163526 6.1037460) create_atoms CPU = 0.004 seconds 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9836877 5.7546669 6.1037460 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -43.163526 0.0000000) to (4.9836877 43.163526 6.1037460) create_atoms CPU = 0.002 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) = 7.178 | 7.178 | 7.178 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1065.5993 0 -1065.5993 -151.65359 1 0 -1065.5998 0 -1065.5998 -152.61543 Loop time of 0.0441821 on 1 procs for 1 steps with 240 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 = -1065.59930052962 -1065.59930052962 -1065.59975583832 Force two-norm initial, final = 0.11195711 0.038193314 Force max component initial, final = 0.035197569 0.012740114 Final line search alpha, max atom move = 1.0000000 0.012740114 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.043259 | 0.043259 | 0.043259 | 0.0 | 97.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051781 | 0.00051781 | 0.00051781 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004056 | | | 0.92 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5268.00 ave 5268 max 5268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29760.0 ave 29760 max 29760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29760 Ave neighs/atom = 124.00000 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 : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.178 | 7.178 | 7.178 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -1065.5998 0 -1065.5998 -152.61543 2625.9967 2 0 -1065.5998 0 -1065.5998 -73.276635 2625.8857 Loop time of 0.0463316 on 1 procs for 1 steps with 240 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1065.59975583832 -1065.59975583832 -1065.59975917116 Force two-norm initial, final = 0.21702738 0.042138703 Force max component initial, final = 0.16684707 0.016820781 Final line search alpha, max atom move = 0.0059935126 0.00010081556 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.044447 | 0.044447 | 0.044447 | 0.0 | 95.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049649 | 0.00049649 | 0.00049649 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001388 | | | 3.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5268.00 ave 5268 max 5268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29760.0 ave 29760 max 29760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29760 Ave neighs/atom = 124.00000 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) = 6.810 | 6.810 | 6.810 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1065.5998 0 -1065.5998 -73.276635 Loop time of 1.2469e-05 on 1 procs for 0 steps with 240 atoms 88.2% 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 | | 1.247e-05 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5268.00 ave 5268 max 5268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29760.0 ave 29760 max 29760 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 = 29760 Ave neighs/atom = 124.00000 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) = 6.810 | 6.810 | 6.810 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 -1065.5998 -1065.5998 4.9835706 86.327052 6.1036313 -73.276635 -73.276635 -3.7106401 -226.38222 10.262957 2.4915141 0.00029692183 Loop time of 1.3592e-05 on 1 procs for 0 steps with 240 atoms 183.9% 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 | | 1.359e-05 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5268.00 ave 5268 max 5268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29760.0 ave 29760 max 29760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59520.0 ave 59520 max 59520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59520 Ave neighs/atom = 248.00000 Neighbor list builds = 0 Dangerous builds = 0 240 -1065.59975917116 eV 2.49151414039739 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00