LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -63.20502 0) to (22.346349 63.20502 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0944588 4.7882591 5.5012908 Created 528 atoms using lattice units in orthogonal box = (0 -63.20502 0) to (22.346349 63.20502 5.5012908) create_atoms CPU = 0.000 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0944588 4.7882591 5.5012908 Created 530 atoms using lattice units in orthogonal box = (0 -63.20502 0) to (22.346349 63.20502 5.5012908) create_atoms CPU = 0.000 seconds 530 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 29 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 0 atoms, new total = 1058 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:187) 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 29 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) = 7.773 | 7.773 | 7.773 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3560.7417 0 -3560.7417 142602.14 78 0 -4102.5561 0 -4102.5561 9276.1885 Loop time of 0.788475 on 1 procs for 78 steps with 1058 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 = -3560.74165508537 -4102.55224616208 -4102.55606988986 Force two-norm initial, final = 631.61485 0.23860134 Force max component initial, final = 159.93268 0.038657261 Final line search alpha, max atom move = 0.49421084 0.019104838 Iterations, force evaluations = 78 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7772 | 0.7772 | 0.7772 | 0.0 | 98.57 Neigh | 0.0046508 | 0.0046508 | 0.0046508 | 0.0 | 0.59 Comm | 0.0042316 | 0.0042316 | 0.0042316 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002394 | | | 0.30 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8150 ave 8150 max 8150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105444 ave 105444 max 105444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105444 Ave neighs/atom = 99.663516 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.773 | 7.773 | 7.773 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -4102.5561 0 -4102.5561 9276.1885 15540.062 84 0 -4102.8525 0 -4102.8525 325.25792 15608.862 Loop time of 0.0452845 on 1 procs for 6 steps with 1058 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 = -4102.55606988986 -4102.8492958923 -4102.85254395367 Force two-norm initial, final = 159.96791 5.6932571 Force max component initial, final = 119.28527 4.3745124 Final line search alpha, max atom move = 0.00011499657 0.00050305391 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.044275 | 0.044275 | 0.044275 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021945 | 0.00021945 | 0.00021945 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007898 | | | 1.74 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8150 ave 8150 max 8150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105428 ave 105428 max 105428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105428 Ave neighs/atom = 99.648393 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 29 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) = 7.404 | 7.404 | 7.404 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4102.8525 0 -4102.8525 325.25792 Loop time of 5.71e-07 on 1 procs for 0 steps with 1058 atoms 175.1% 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 | | 5.71e-07 | | |100.00 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8150 ave 8150 max 8150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105308 ave 105308 max 105308 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105308 Ave neighs/atom = 99.534972 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.404 | 7.404 | 7.404 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 -4102.8525 -4102.8525 22.339486 127.10129 5.497283 325.25792 325.25792 240.41559 451.4786 283.87958 2.5852419 655.888 Loop time of 4.91e-07 on 1 procs for 0 steps with 1058 atoms 203.7% 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 | | 4.91e-07 | | |100.00 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8150 ave 8150 max 8150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105308 ave 105308 max 105308 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 210616 ave 210616 max 210616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210616 Ave neighs/atom = 199.06994 Neighbor list builds = 0 Dangerous builds = 0 1058 -4102.85254395367 eV 2.58524194944365 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00