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 -45.129212 0.0000000) to (31.911172 45.129212 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4482488 6.0539187 4.9836877 Created 655 atoms using lattice units in orthogonal box = (0.0000000 -45.129212 0.0000000) to (31.911172 45.129212 4.9836877) create_atoms CPU = 0.002 seconds 655 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4482488 6.0539187 4.9836877 Created 659 atoms using lattice units in orthogonal box = (0.0000000 -45.129212 0.0000000) to (31.911172 45.129212 4.9836877) create_atoms CPU = 0.002 seconds 659 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 = 8 21 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 10 atoms, new total = 1304 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 = 8 21 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) = 7.866 | 7.866 | 7.866 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4918.2759 0 -4918.2759 129639.5 128 0 -5772.371 0 -5772.371 -4075.1501 Loop time of 6.41227 on 1 procs for 128 steps with 1304 atoms 96.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4918.27585928258 -5772.36640277969 -5772.3709943646 Force two-norm initial, final = 1285.8425 0.21585448 Force max component initial, final = 314.32602 0.043427137 Final line search alpha, max atom move = 1.0000000 0.043427137 Iterations, force evaluations = 128 247 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3443 | 6.3443 | 6.3443 | 0.0 | 98.94 Neigh | 0.01646 | 0.01646 | 0.01646 | 0.0 | 0.26 Comm | 0.03025 | 0.03025 | 0.03025 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02126 | | | 0.33 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9622.00 ave 9622 max 9622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164661.0 ave 164661 max 164661 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164661 Ave neighs/atom = 126.27377 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 : 128 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.866 | 7.866 | 7.866 Mbytes Step Temp E_pair E_mol TotEng Press Volume 128 0 -5772.371 0 -5772.371 -4075.1501 14354.277 130 0 -5772.4236 0 -5772.4236 -71.733445 14322.798 Loop time of 0.103025 on 1 procs for 2 steps with 1304 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 = -5772.3709943646 -5772.419106652 -5772.42357851162 Force two-norm initial, final = 66.585222 2.2963454 Force max component initial, final = 46.839514 1.8953080 Final line search alpha, max atom move = 8.6843969e-05 0.00016459607 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10122 | 0.10122 | 0.10122 | 0.0 | 98.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033412 | 0.00033412 | 0.00033412 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001467 | | | 1.42 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9640.00 ave 9640 max 9640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163386.0 ave 163386 max 163386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163386 Ave neighs/atom = 125.29601 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 = 8 21 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) = 7.493 | 7.493 | 7.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5772.4236 0 -5772.4236 -71.733445 Loop time of 2.526e-06 on 1 procs for 0 steps with 1304 atoms 158.4% 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 | | 2.526e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9640.00 ave 9640 max 9640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163681.0 ave 163681 max 163681 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 = 163681 Ave neighs/atom = 125.52224 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) = 7.493 | 7.493 | 7.493 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 -5772.4236 -5772.4236 31.868776 90.164686 4.9845505 -71.733445 -71.733445 -211.73124 99.155067 -102.62417 2.3077735 584.64853 Loop time of 2.347e-06 on 1 procs for 0 steps with 1304 atoms 298.3% 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 | | 2.347e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9640.00 ave 9640 max 9640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163681.0 ave 163681 max 163681 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 327362.0 ave 327362 max 327362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327362 Ave neighs/atom = 251.04448 Neighbor list builds = 0 Dangerous builds = 0 1304 -5772.42357851162 eV 2.30777345657921 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07