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_NiPd__SM_559286646876_000 # For Simulator : LAMMPS 29 Sep 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created orthogonal box = (0.0000000 -41.100066 0.0000000) to (20.548271 41.100066 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8348873 4.8348873 3.5239994 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.100066 0.0000000) to (20.548271 41.100066 3.5239994) create_atoms CPU = 0.003 seconds 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8348873 4.8348873 3.5239994 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.100066 0.0000000) to (20.548271 41.100066 3.5239994) create_atoms CPU = 0.001 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 = 5 19 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 8 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:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 5 19 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) = 7.172 | 7.172 | 7.172 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2358.2512 0 -2358.2512 26196.534 41 0 -2386.7045 0 -2386.7045 -2034.7201 Loop time of 1.36915 on 1 procs for 41 steps with 540 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2358.25120647132 -2386.70217710663 -2386.70446053547 Force two-norm initial, final = 42.838760 0.16288017 Force max component initial, final = 15.973874 0.028946583 Final line search alpha, max atom move = 1.0000000 0.028946583 Iterations, force evaluations = 41 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3437 | 1.3437 | 1.3437 | 0.0 | 98.14 Neigh | 0.0084811 | 0.0084811 | 0.0084811 | 0.0 | 0.62 Comm | 0.010397 | 0.010397 | 0.010397 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006594 | | | 0.48 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7428.00 ave 7428 max 7428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67710.0 ave 67710 max 67710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67710 Ave neighs/atom = 125.38889 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.172 | 7.172 | 7.172 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -2386.7045 0 -2386.7045 -2034.7201 5952.2837 43 0 -2386.7124 0 -2386.7124 -112.75518 5946.0197 Loop time of 0.112034 on 1 procs for 2 steps with 540 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2386.70446053547 -2386.71134528922 -2386.71242500676 Force two-norm initial, final = 14.344101 0.16828069 Force max component initial, final = 13.446650 0.028545212 Final line search alpha, max atom move = 0.00034382276 9.8144936e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10926 | 0.10926 | 0.10926 | 0.0 | 97.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074101 | 0.00074101 | 0.00074101 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002038 | | | 1.82 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7429.00 ave 7429 max 7429 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67462.0 ave 67462 max 67462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67462 Ave neighs/atom = 124.92963 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 5 19 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) = 6.803 | 6.803 | 6.803 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2386.7124 0 -2386.7124 -112.75518 Loop time of 6.245e-06 on 1 procs for 0 steps with 540 atoms 160.1% 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 | | 6.245e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7429.00 ave 7429 max 7429 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67508.0 ave 67508 max 67508 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 = 67508 Ave neighs/atom = 125.01481 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) = 6.803 | 6.803 | 6.803 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 -2386.7124 -2386.7124 20.522401 82.200132 3.5247283 -112.75518 -112.75518 3.3164134 -342.23455 0.65259992 2.2619023 261.34547 Loop time of 6.715e-06 on 1 procs for 0 steps with 540 atoms 327.6% 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 | | 6.715e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7429.00 ave 7429 max 7429 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67508.0 ave 67508 max 67508 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 135016.0 ave 135016 max 135016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135016 Ave neighs/atom = 250.02963 Neighbor list builds = 0 Dangerous builds = 0 540 -2386.71242500676 eV 2.26190225796948 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02