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 Lattice spacing in x,y,z = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -59.268285 0.0000000) to (41.909006 59.268285 5.1200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2550755 5.7499082 5.1200000 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.268285 0.0000000) to (41.909006 59.268285 5.1200000) create_atoms CPU = 0.008 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2550755 5.7499082 5.1200000 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.268285 0.0000000) to (41.909006 59.268285 5.1200000) create_atoms CPU = 0.008 seconds 1080 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 40 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 kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2152 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/MO_390178379548_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.214 | 5.214 | 5.214 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7171.6407 0 -7171.6407 52591.869 75 0 -7603.9624 0 -7603.9624 8254.9048 Loop time of 12.0074 on 1 procs for 75 steps with 2152 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 = -7171.6406510677 -7603.95660473377 -7603.96239854404 Force two-norm initial, final = 360.91338 0.19939924 Force max component initial, final = 45.266350 0.012015808 Final line search alpha, max atom move = 1.0000000 0.012015808 Iterations, force evaluations = 75 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.92 | 11.92 | 11.92 | 0.0 | 99.28 Neigh | 0.026897 | 0.026897 | 0.026897 | 0.0 | 0.22 Comm | 0.02819 | 0.02819 | 0.02819 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03184 | | | 0.27 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7779.00 ave 7779 max 7779 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 166528.0 ave 166528 max 166528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166528 Ave neighs/atom = 77.382900 Neighbor list builds = 1 Dangerous builds = 0 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.215 | 5.215 | 5.215 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -7603.9624 0 -7603.9624 8254.9048 25434.879 80 0 -7604.4108 0 -7604.4108 -74.170449 25581.459 Loop time of 0.567818 on 1 procs for 5 steps with 2152 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 = -7603.96239854405 -7604.410487346 -7604.41081566572 Force two-norm initial, final = 233.46078 2.6515151 Force max component initial, final = 163.91455 1.9105388 Final line search alpha, max atom move = 0.00018718877 0.00035763141 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5617 | 0.5617 | 0.5617 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001159 | 0.001159 | 0.001159 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004954 | | | 0.87 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7779.00 ave 7779 max 7779 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 166336.0 ave 166336 max 166336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166336 Ave neighs/atom = 77.293680 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 15 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/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 attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.354 | 5.354 | 5.354 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7604.4108 0 -7604.4108 -74.170449 Loop time of 7.327e-06 on 1 procs for 0 steps with 2152 atoms 163.8% 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 | | 7.327e-06 | | |100.00 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7773.00 ave 7773 max 7773 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 166224.0 ave 166224 max 166224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166224 Ave neighs/atom = 77.241636 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 15 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/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 attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.354 | 5.354 | 5.354 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 -7604.4108 -7604.4108 42.00232 118.97393 5.119178 -74.170449 -74.170449 -119.9242 10.910364 -113.49751 2.4078009 1113.764 Loop time of 7.156e-06 on 1 procs for 0 steps with 2152 atoms 279.5% 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 | | 7.156e-06 | | |100.00 Nlocal: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7773.00 ave 7773 max 7773 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 83112.0 ave 83112 max 83112 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 166224.0 ave 166224 max 166224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166224 Ave neighs/atom = 77.241636 Neighbor list builds = 0 Dangerous builds = 0 2152 -7604.41081566572 eV 2.40780087492093 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13