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 -54.737153 0) to (12.901671 54.737153 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8643957 6.6348064 5.5012908 Created 264 atoms using lattice units in orthogonal box = (0 -54.737153 0) to (12.901671 54.737153 5.5012908) create_atoms CPU = 0.000 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8643957 6.6348064 5.5012908 Created 266 atoms using lattice units in orthogonal box = (0 -54.737153 0) to (12.901671 54.737153 5.5012908) create_atoms CPU = 0.000 seconds 266 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 = 3 25 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 = 528 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 = 3 25 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) = 7.189 | 7.189 | 7.189 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1206.1805 0 -1206.1805 193434.7 111 0 -2046.6618 0 -2046.6618 7304.5583 Loop time of 0.598711 on 1 procs for 111 steps with 528 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1206.18047028052 -2046.66010638304 -2046.66184839227 Force two-norm initial, final = 1235.6632 0.15474514 Force max component initial, final = 336.49 0.034811082 Final line search alpha, max atom move = 1 0.034811082 Iterations, force evaluations = 111 211 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59005 | 0.59005 | 0.59005 | 0.0 | 98.55 Neigh | 0.0025523 | 0.0025523 | 0.0025523 | 0.0 | 0.43 Comm | 0.0042375 | 0.0042375 | 0.0042375 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001867 | | | 0.31 Nlocal: 528 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5651 ave 5651 max 5651 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52530 ave 52530 max 52530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52530 Ave neighs/atom = 99.488636 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 : 111 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.189 | 7.189 | 7.189 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -2046.6618 0 -2046.6618 7304.5583 7770.0311 116 0 -2046.7757 0 -2046.7757 -9.5098759 7798.2999 Loop time of 0.0226031 on 1 procs for 5 steps with 528 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2046.66184839227 -2046.77419710807 -2046.77569547103 Force two-norm initial, final = 66.908321 0.68371196 Force max component initial, final = 56.900582 0.51757789 Final line search alpha, max atom move = 0.0001006864 5.2113054e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021979 | 0.021979 | 0.021979 | 0.0 | 97.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014348 | 0.00014348 | 0.00014348 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004807 | | | 2.13 Nlocal: 528 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5308 ave 5308 max 5308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52610 ave 52610 max 52610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52610 Ave neighs/atom = 99.640152 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 = 3 25 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) = 6.818 | 6.818 | 6.818 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2046.7757 0 -2046.7757 -9.5098759 Loop time of 6.21e-07 on 1 procs for 0 steps with 528 atoms 322.1% 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 | | 6.21e-07 | | |100.00 Nlocal: 528 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5356 ave 5356 max 5356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52580 ave 52580 max 52580 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 = 52580 Ave neighs/atom = 99.583333 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) = 6.818 | 6.818 | 6.818 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 -2046.7757 -2046.7757 12.902236 109.9406 5.4976472 -9.5098759 -9.5098759 -106.34208 0.72900132 77.083455 2.5616315 309.56833 Loop time of 4.61e-07 on 1 procs for 0 steps with 528 atoms 216.9% 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 | | 4.61e-07 | | |100.00 Nlocal: 528 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5356 ave 5356 max 5356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52580 ave 52580 max 52580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105160 ave 105160 max 105160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105160 Ave neighs/atom = 199.16667 Neighbor list builds = 0 Dangerous builds = 0 528 -2046.77569547103 eV 2.56163152756917 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00