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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -51.375847 0.0000000) to (36.328209 51.375847 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7587366 6.5713292 5.5400000 Created 685 atoms using lattice units in orthogonal box = (0.0000000 -51.375847 0.0000000) to (36.328209 51.375847 5.5400000) create_atoms CPU = 0.006 seconds 685 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7587366 6.5713292 5.5400000 Created 693 atoms using lattice units in orthogonal box = (0.0000000 -51.375847 0.0000000) to (36.328209 51.375847 5.5400000) create_atoms CPU = 0.005 seconds 693 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1375 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.045 | 5.045 | 5.045 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7410.7843 0 -7410.7843 65944.37 76 0 -7898.232 0 -7898.232 10501.764 Loop time of 7.09089 on 1 procs for 76 steps with 1375 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 = -7410.78427725102 -7898.22446789825 -7898.23195702897 Force two-norm initial, final = 498.43189 0.34989502 Force max component initial, final = 81.479898 0.070841467 Final line search alpha, max atom move = 0.99438410 0.070443628 Iterations, force evaluations = 76 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0336 | 7.0336 | 7.0336 | 0.0 | 99.19 Neigh | 0.017096 | 0.017096 | 0.017096 | 0.0 | 0.24 Comm | 0.018518 | 0.018518 | 0.018518 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02171 | | | 0.31 Nlocal: 1375.00 ave 1375 max 1375 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5426.00 ave 5426 max 5426 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: 106096.0 ave 106096 max 106096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106096 Ave neighs/atom = 77.160727 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.046 | 5.046 | 5.046 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -7898.232 0 -7898.232 10501.764 20679.629 82 0 -7898.8789 0 -7898.8789 245.7266 20799.757 Loop time of 0.413096 on 1 procs for 6 steps with 1375 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 = -7898.23195702897 -7898.87594076374 -7898.87887078695 Force two-norm initial, final = 264.68636 6.1121661 Force max component initial, final = 234.43178 5.0002287 Final line search alpha, max atom move = 9.6264791e-05 0.00048134597 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40801 | 0.40801 | 0.40801 | 0.0 | 98.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092894 | 0.00092894 | 0.00092894 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004154 | | | 1.01 Nlocal: 1375.00 ave 1375 max 1375 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5428.00 ave 5428 max 5428 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: 106172.0 ave 106172 max 106172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106172 Ave neighs/atom = 77.216000 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.184 | 5.184 | 5.184 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7898.8789 0 -7898.8789 245.7266 Loop time of 6.265e-06 on 1 procs for 0 steps with 1375 atoms 191.5% 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 | | 6.265e-06 | | |100.00 Nlocal: 1375.00 ave 1375 max 1375 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5422.00 ave 5422 max 5422 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: 106088.0 ave 106088 max 106088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106088 Ave neighs/atom = 77.154909 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.184 | 5.184 | 5.184 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 -7898.8789 -7898.8789 36.333867 103.2865 5.5424668 245.7266 245.7266 248.01371 387.16538 102.00069 2.5899617 966.0954 Loop time of 6.806e-06 on 1 procs for 0 steps with 1375 atoms 249.8% 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 | | 6.806e-06 | | |100.00 Nlocal: 1375.00 ave 1375 max 1375 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5422.00 ave 5422 max 5422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53044.0 ave 53044 max 53044 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106088.0 ave 106088 max 106088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106088 Ave neighs/atom = 77.154909 Neighbor list builds = 0 Dangerous builds = 0 1375 -7898.87887078695 eV 2.58996165588764 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08