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 -53.214748 0.0000000) to (37.626017 53.214748 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9409501 5.1344163 4.9836877 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.214748 0.0000000) to (37.626017 53.214748 4.9836877) create_atoms CPU = 0.002 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9409501 5.1344163 4.9836877 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.214748 0.0000000) to (37.626017 53.214748 4.9836877) create_atoms CPU = 0.002 seconds 916 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 = 9 24 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 24 atoms, new total = 1808 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 = 9 24 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) = 8.442 | 8.442 | 8.442 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7972.6687 0 -7972.6687 3983.7757 46 0 -8006.5773 0 -8006.5773 -10042.738 Loop time of 2.78352 on 1 procs for 46 steps with 1808 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 = -7972.66872680188 -8006.56975778984 -8006.57734676259 Force two-norm initial, final = 48.607799 0.28371657 Force max component initial, final = 11.903422 0.030587004 Final line search alpha, max atom move = 1.0000000 0.030587004 Iterations, force evaluations = 46 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7622 | 2.7622 | 2.7622 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012024 | 0.012024 | 0.012024 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009253 | | | 0.33 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12899.0 ave 12899 max 12899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 223592.0 ave 223592 max 223592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223592 Ave neighs/atom = 123.66814 Neighbor list builds = 0 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.443 | 8.443 | 8.443 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -8006.5773 0 -8006.5773 -10042.738 19957.267 49 0 -8006.7822 0 -8006.7822 -2884.6123 19879.367 Loop time of 0.156566 on 1 procs for 3 steps with 1808 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 = -8006.57734676259 -8006.77829180751 -8006.78218623068 Force two-norm initial, final = 145.60424 3.5595284 Force max component initial, final = 116.75826 3.3760450 Final line search alpha, max atom move = 5.3942344e-05 0.00018211178 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15413 | 0.15413 | 0.15413 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045461 | 0.00045461 | 0.00045461 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001981 | | | 1.27 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12944.0 ave 12944 max 12944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 226584.0 ave 226584 max 226584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226584 Ave neighs/atom = 125.32301 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 = 9 24 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) = 8.074 | 8.074 | 8.074 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8006.7822 0 -8006.7822 -2884.6123 Loop time of 2.082e-06 on 1 procs for 0 steps with 1808 atoms 192.1% 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 | | 2.082e-06 | | |100.00 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12944.0 ave 12944 max 12944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 226984.0 ave 226984 max 226984 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 = 226984 Ave neighs/atom = 125.54425 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) = 8.074 | 8.074 | 8.074 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 -8006.7822 -8006.7822 37.568669 106.4295 4.9718124 -2884.6123 -2884.6123 271.67746 -8838.354 -87.160261 2.3215244 557.11612 Loop time of 2.323e-06 on 1 procs for 0 steps with 1808 atoms 258.3% 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 | | 2.323e-06 | | |100.00 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12944.0 ave 12944 max 12944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 226984.0 ave 226984 max 226984 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 453968.0 ave 453968 max 453968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 453968 Ave neighs/atom = 251.08850 Neighbor list builds = 0 Dangerous builds = 0 1808 -8006.78218623068 eV 2.3215244420382 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03