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 -45.364806 0) to (22.682403 45.364806 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3370361 5.3370361 3.8900001 Created 272 atoms using lattice units in orthogonal box = (0 -45.364806 0) to (22.682403 45.364806 3.8900001) create_atoms CPU = 0.000 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3370361 5.3370361 3.8900001 Created 274 atoms using lattice units in orthogonal box = (0 -45.364806 0) to (22.682403 45.364806 3.8900001) create_atoms CPU = 0.000 seconds 274 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 1 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 6 atoms, new total = 540 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 21 1 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) = 7.141 | 7.141 | 7.141 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1715.5738 0 -1715.5738 111239.71 101 0 -2089.6996 0 -2089.6996 -3007.123 Loop time of 0.556534 on 1 procs for 101 steps with 540 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1715.57377332573 -2089.69801418426 -2089.69957594368 Force two-norm initial, final = 716.00224 0.16295514 Force max component initial, final = 244.66666 0.039014933 Final line search alpha, max atom move = 1 0.039014933 Iterations, force evaluations = 101 188 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54781 | 0.54781 | 0.54781 | 0.0 | 98.43 Neigh | 0.0024565 | 0.0024565 | 0.0024565 | 0.0 | 0.44 Comm | 0.0044296 | 0.0044296 | 0.0044296 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001837 | | | 0.33 Nlocal: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5779 ave 5779 max 5779 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53532 ave 53532 max 53532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53532 Ave neighs/atom = 99.133333 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 : 101 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.141 | 7.141 | 7.141 Mbytes Step Temp E_pair E_mol TotEng Press Volume 101 0 -2089.6996 0 -2089.6996 -3007.123 8005.4866 104 0 -2089.7193 0 -2089.7193 -36.135983 7993.1216 Loop time of 0.0203689 on 1 procs for 3 steps with 540 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 = -2089.69957594369 -2089.71881947131 -2089.71931131217 Force two-norm initial, final = 27.596758 0.36155006 Force max component initial, final = 22.454584 0.18334022 Final line search alpha, max atom move = 0.00065787031 0.00012061409 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.019799 | 0.019799 | 0.019799 | 0.0 | 97.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013937 | 0.00013937 | 0.00013937 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004306 | | | 2.11 Nlocal: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5803 ave 5803 max 5803 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53596 ave 53596 max 53596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53596 Ave neighs/atom = 99.251852 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 21 1 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) = 6.772 | 6.772 | 6.772 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2089.7193 0 -2089.7193 -36.135983 Loop time of 9.22e-07 on 1 procs for 0 steps with 540 atoms 108.5% 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 | | 9.22e-07 | | |100.00 Nlocal: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5815 ave 5815 max 5815 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53600 ave 53600 max 53600 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 = 53600 Ave neighs/atom = 99.259259 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) = 6.772 | 6.772 | 6.772 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 -2089.7193 -2089.7193 22.637695 90.726288 3.8918051 -36.135983 -36.135983 -36.677086 -35.076083 -36.654779 2.5150836 311.13917 Loop time of 4.8e-07 on 1 procs for 0 steps with 540 atoms 208.3% 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 | | 4.8e-07 | | |100.00 Nlocal: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5815 ave 5815 max 5815 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53600 ave 53600 max 53600 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107200 ave 107200 max 107200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107200 Ave neighs/atom = 198.51852 Neighbor list builds = 0 Dangerous builds = 0 540 -2089.71931131217 eV 2.51508363659662 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00