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_PunDarlingKecskes_2015_CuTa__SM_399364650444_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -53.497117 0.0000000) to (43.680213 53.497117 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3852317 5.1298605 5.9032705 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -53.497117 0.0000000) to (43.680213 53.497117 8.8549058) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3852317 5.1298605 5.9032705 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -53.497117 0.0000000) to (43.680213 53.497117 8.8549058) create_atoms CPU = 0.002 seconds 1758 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 = 8.150959 ghost atom cutoff = 8.150959 binsize = 4.0754795, bins = 11 27 3 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 4 atoms, new total = 3504 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_399364650444_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 = 8.150959 ghost atom cutoff = 8.150959 binsize = 4.0754795, bins = 11 27 3 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) = 9.268 | 9.268 | 9.268 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10306.211 0 -10306.211 141523.89 83 0 -12359.225 0 -12359.225 6095.8574 Loop time of 6.07467 on 1 procs for 83 steps with 3504 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 = -10306.2113190746 -12359.2138982889 -12359.2247485067 Force two-norm initial, final = 2791.8180 0.37817353 Force max component initial, final = 394.82209 0.075902320 Final line search alpha, max atom move = 1.0000000 0.075902320 Iterations, force evaluations = 83 156 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9934 | 5.9934 | 5.9934 | 0.0 | 98.66 Neigh | 0.032179 | 0.032179 | 0.032179 | 0.0 | 0.53 Comm | 0.021884 | 0.021884 | 0.021884 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02724 | | | 0.45 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12151.0 ave 12151 max 12151 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 344862.0 ave 344862 max 344862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 344862 Ave neighs/atom = 98.419521 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.268 | 9.268 | 9.268 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -12359.225 0 -12359.225 6095.8574 41383.676 89 0 -12359.896 0 -12359.896 -300.86176 41573.549 Loop time of 0.295548 on 1 procs for 6 steps with 3504 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12359.2247485067 -12359.8918596414 -12359.895922484 Force two-norm initial, final = 304.00364 15.608810 Force max component initial, final = 266.98893 13.459503 Final line search alpha, max atom move = 5.8084166e-05 0.00078178400 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29073 | 0.29073 | 0.29073 | 0.0 | 98.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071356 | 0.00071356 | 0.00071356 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004101 | | | 1.39 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12152.0 ave 12152 max 12152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 347004.0 ave 347004 max 347004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 347004 Ave neighs/atom = 99.030822 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 = 8.150959 ghost atom cutoff = 8.150959 binsize = 4.0754795, bins = 11 27 3 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) = 8.899 | 8.899 | 8.899 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12359.896 0 -12359.896 -300.86176 Loop time of 1.814e-06 on 1 procs for 0 steps with 3504 atoms 165.4% 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 | | 1.814e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12152.0 ave 12152 max 12152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 346548.0 ave 346548 max 346548 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 = 346548 Ave neighs/atom = 98.900685 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) = 8.899 | 8.899 | 8.899 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 -12359.896 -12359.896 43.650959 107.57103 8.8537652 -300.86176 -300.86176 -518.35982 -95.77108 -288.45438 2.3006284 1586.7764 Loop time of 2.11e-06 on 1 procs for 0 steps with 3504 atoms 331.8% 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 | | 2.11e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12152.0 ave 12152 max 12152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 346548.0 ave 346548 max 346548 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 693096.0 ave 693096 max 693096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 693096 Ave neighs/atom = 197.80137 Neighbor list builds = 0 Dangerous builds = 0 3504 -12359.895922484 eV 2.30062838130219 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07