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 -57.693880 0.0000000) to (40.793242 57.693880 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0885436 5.5968256 4.9836877 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -57.693880 0.0000000) to (40.793242 57.693880 4.9836877) create_atoms CPU = 0.003 seconds 1079 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0885436 5.5968256 4.9836877 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -57.693880 0.0000000) to (40.793242 57.693880 4.9836877) create_atoms CPU = 0.003 seconds 1079 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 = 10 26 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 15 atoms, new total = 2143 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 = 10 26 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) = 8.567 | 8.567 | 8.567 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9310.6561 0 -9310.6561 52805.025 51 0 -9492.0225 0 -9492.0225 3971.9176 Loop time of 3.57783 on 1 procs for 51 steps with 2143 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 = -9310.65606944221 -9492.01535846694 -9492.02249925844 Force two-norm initial, final = 252.63131 0.29415615 Force max component initial, final = 31.189652 0.027989526 Final line search alpha, max atom move = 1.0000000 0.027989526 Iterations, force evaluations = 51 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.522 | 3.522 | 3.522 | 0.0 | 98.44 Neigh | 0.026885 | 0.026885 | 0.026885 | 0.0 | 0.75 Comm | 0.01668 | 0.01668 | 0.01668 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01228 | | | 0.34 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13801.0 ave 13801 max 13801 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271468.0 ave 271468 max 271468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271468 Ave neighs/atom = 126.67662 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 : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.567 | 8.567 | 8.567 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -9492.0225 0 -9492.0225 3971.9176 23458.422 54 0 -9492.1222 0 -9492.1222 888.43422 23497.424 Loop time of 0.239149 on 1 procs for 3 steps with 2143 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 = -9492.02249925842 -9492.12044623216 -9492.12221551988 Force two-norm initial, final = 101.54542 0.31129381 Force max component initial, final = 101.02895 0.042457917 Final line search alpha, max atom move = 7.2447407e-05 3.0759660e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23573 | 0.23573 | 0.23573 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064667 | 0.00064667 | 0.00064667 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00277 | | | 1.16 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13801.0 ave 13801 max 13801 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271369.0 ave 271369 max 271369 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271369 Ave neighs/atom = 126.63042 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 = 10 26 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) = 8.198 | 8.198 | 8.198 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9492.1222 0 -9492.1222 888.43422 Loop time of 1.815e-06 on 1 procs for 0 steps with 2143 atoms 220.4% 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 | | 1.815e-06 | | |100.00 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13801.0 ave 13801 max 13801 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271121.0 ave 271121 max 271121 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 = 271121 Ave neighs/atom = 126.51470 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) = 8.198 | 8.198 | 8.198 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 -9492.1222 -9492.1222 40.87537 115.38776 4.9819437 888.43422 888.43422 -2.0354996 2670.2322 -2.8939883 2.3045041 1014.9129 Loop time of 1.73e-06 on 1 procs for 0 steps with 2143 atoms 231.2% 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 | | 1.73e-06 | | |100.00 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13801.0 ave 13801 max 13801 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271121.0 ave 271121 max 271121 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 542242.0 ave 542242 max 542242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 542242 Ave neighs/atom = 253.02940 Neighbor list builds = 0 Dangerous builds = 0 2143 -9492.12221551988 eV 2.30450414225831 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04