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_NiRh__SM_306597220004_000 # For Simulator : LAMMPS 30 Jul 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239998 3.5239998 3.5239998 Created orthogonal box = (0.0000000 -50.332784 0.0000000) to (35.590653 50.332784 4.9836883) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5828475 4.4411280 4.9836883 Created 813 atoms using lattice units in orthogonal box = (0.0000000 -50.332784 0.0000000) to (35.590653 50.332784 4.9836883) create_atoms CPU = 0.002 seconds 813 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5828475 4.4411280 4.9836883 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -50.332784 0.0000000) to (35.590653 50.332784 4.9836883) create_atoms CPU = 0.001 seconds 821 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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, bins = 9 23 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 = 1632 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_306597220004_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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, bins = 9 23 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) = 8.356 | 8.356 | 8.356 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5861.4914 0 -5861.4914 166932.41 56 0 -7222.5151 0 -7222.5151 8050.1627 Loop time of 3.57338 on 1 procs for 56 steps with 1632 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 = -5861.49141947818 -7222.50945474601 -7222.51507794914 Force two-norm initial, final = 1613.3584 0.25603703 Force max component initial, final = 244.30550 0.032477106 Final line search alpha, max atom move = 1.0000000 0.032477106 Iterations, force evaluations = 56 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5316 | 3.5316 | 3.5316 | 0.0 | 98.83 Neigh | 0.0097792 | 0.0097792 | 0.0097792 | 0.0 | 0.27 Comm | 0.018925 | 0.018925 | 0.018925 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01308 | | | 0.37 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11247.0 ave 11247 max 11247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203559.0 ave 203559 max 203559 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203559 Ave neighs/atom = 124.72978 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.356 | 8.356 | 8.356 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -7222.5151 0 -7222.5151 8050.1627 17855.326 61 0 -7222.7952 0 -7222.7952 -4.4579852 17933.109 Loop time of 0.255269 on 1 procs for 5 steps with 1632 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 = -7222.51507794914 -7222.78955071579 -7222.79522737127 Force two-norm initial, final = 162.88570 0.95788755 Force max component initial, final = 128.55238 0.68624978 Final line search alpha, max atom move = 3.6648035e-05 2.5149706e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.251 | 0.251 | 0.251 | 0.0 | 98.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076352 | 0.00076352 | 0.00076352 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003503 | | | 1.37 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11256.0 ave 11256 max 11256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203434.0 ave 203434 max 203434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203434 Ave neighs/atom = 124.65319 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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, bins = 9 23 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) = 7.988 | 7.988 | 7.988 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7222.7952 0 -7222.7952 -4.4579852 Loop time of 2.389e-06 on 1 procs for 0 steps with 1632 atoms 167.4% 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 | | 2.389e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11256.0 ave 11256 max 11256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203302.0 ave 203302 max 203302 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 = 203302 Ave neighs/atom = 124.57230 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) = 7.988 | 7.988 | 7.988 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 -7222.7952 -7222.7952 35.581449 101.10167 4.9850971 -4.4579852 -4.4579852 49.802151 -1.8479746 -61.328132 2.3607372 756.22183 Loop time of 2.868e-06 on 1 procs for 0 steps with 1632 atoms 278.9% 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 | | 2.868e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11256.0 ave 11256 max 11256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203302.0 ave 203302 max 203302 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 406604.0 ave 406604 max 406604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 406604 Ave neighs/atom = 249.14461 Neighbor list builds = 0 Dangerous builds = 0 1632 -7222.79522737127 eV 2.36073715064216 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04