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 -41.700052 0.0000000) to (51.067608 41.700052 8.6320013) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8362981 5.3609821 5.7546675 Created 1684 atoms using lattice units in orthogonal box = (0.0000000 -41.700052 0.0000000) to (51.067608 41.700052 8.6320013) create_atoms CPU = 0.002 seconds 1684 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8362981 5.3609821 5.7546675 Created 1684 atoms using lattice units in orthogonal box = (0.0000000 -41.700052 0.0000000) to (51.067608 41.700052 8.6320013) create_atoms CPU = 0.002 seconds 1684 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 = 12 19 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 56 atoms, new total = 3312 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 = 12 19 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) = 16.15 | 16.15 | 16.15 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14542.869 0 -14542.869 4325.9902 63 0 -14645.961 0 -14645.961 -16191.915 Loop time of 6.21711 on 1 procs for 63 steps with 3312 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 = -14542.8692469982 -14645.9480216852 -14645.9609738272 Force two-norm initial, final = 74.442310 0.35004584 Force max component initial, final = 7.7552170 0.022673271 Final line search alpha, max atom move = 1.0000000 0.022673271 Iterations, force evaluations = 63 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1435 | 6.1435 | 6.1435 | 0.0 | 98.82 Neigh | 0.037997 | 0.037997 | 0.037997 | 0.0 | 0.61 Comm | 0.017272 | 0.017272 | 0.017272 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0183 | | | 0.29 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13198.0 ave 13198 max 13198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 410480.0 ave 410480 max 410480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 410480 Ave neighs/atom = 123.93720 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 16.15 | 16.15 | 16.15 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -14645.961 0 -14645.961 -16191.915 36764.071 68 0 -14646.884 0 -14646.884 -5275.293 36541.515 Loop time of 0.443379 on 1 procs for 5 steps with 3312 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 = -14645.9609738272 -14646.882733551 -14646.8836040575 Force two-norm initial, final = 422.33134 0.42188469 Force max component initial, final = 324.81062 0.045990560 Final line search alpha, max atom move = 0.00011724997 5.3923917e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43867 | 0.43867 | 0.43867 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00070055 | 0.00070055 | 0.00070055 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00401 | | | 0.90 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12858.0 ave 12858 max 12858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 410679.0 ave 410679 max 410679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 410679 Ave neighs/atom = 123.99728 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 = 12 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) = 15.02 | 15.02 | 15.02 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14646.884 0 -14646.884 -5275.293 Loop time of 2.111e-06 on 1 procs for 0 steps with 3312 atoms 189.5% 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 | | 2.111e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12860.0 ave 12860 max 12860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 411095.0 ave 411095 max 411095 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 = 411095 Ave neighs/atom = 124.12289 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) = 15.02 | 15.02 | 15.02 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 -14646.884 -14646.884 50.94412 83.400103 8.6005435 -5275.293 -5275.293 -2.0115974 -15822.689 -1.1785938 2.3437189 1584.0954 Loop time of 2.221e-06 on 1 procs for 0 steps with 3312 atoms 270.1% 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 | | 2.221e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12860.0 ave 12860 max 12860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 411095.0 ave 411095 max 411095 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 822190.0 ave 822190 max 822190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 822190 Ave neighs/atom = 248.24577 Neighbor list builds = 0 Dangerous builds = 0 3312 -14646.8836040575 eV 2.34371888365924 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07