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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -72.306142 0.0000000) to (41.745971 72.306142 6.2462993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6076677 5.7557128 6.2462993 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -72.306142 0.0000000) to (41.745971 72.306142 6.2462993) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6076677 5.7557128 6.2462993 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.306142 0.0000000) to (41.745971 72.306142 6.2462993) create_atoms CPU = 0.004 seconds 1610 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 25 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3214 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 16.92 | 16.92 | 16.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12908.931 0 -12908.931 32305.845 108 0 -13454.012 0 -13454.012 3921.8177 Loop time of 30.0219 on 1 procs for 108 steps with 3214 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12908.9313546995 -13454.0000917147 -13454.012053997 Force two-norm initial, final = 529.48277 0.51779427 Force max component initial, final = 121.70165 0.11354318 Final line search alpha, max atom move = 1.0000000 0.11354318 Iterations, force evaluations = 108 196 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.119 | 29.119 | 29.119 | 0.0 | 96.99 Neigh | 0.73966 | 0.73966 | 0.73966 | 0.0 | 2.46 Comm | 0.09791 | 0.09791 | 0.09791 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06574 | | | 0.22 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24292.0 ave 24292 max 24292 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: 1.99028e+06 ave 1.99028e+06 max 1.99028e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1990284 Ave neighs/atom = 619.25451 Neighbor list builds = 4 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 16.92 | 16.92 | 16.92 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -13454.012 0 -13454.012 3921.8177 37708.785 111 0 -13454.214 0 -13454.214 46.363077 37793.54 Loop time of 0.423893 on 1 procs for 3 steps with 3214 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 = -13454.012053997 -13454.2088754406 -13454.2140362719 Force two-norm initial, final = 194.45159 5.2881070 Force max component initial, final = 175.16654 3.7554895 Final line search alpha, max atom move = 4.6738532e-05 0.00017552607 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41895 | 0.41895 | 0.41895 | 0.0 | 98.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094895 | 0.00094895 | 0.00094895 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003989 | | | 0.94 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24260.0 ave 24260 max 24260 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: 1.99158e+06 ave 1.99158e+06 max 1.99158e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1991584 Ave neighs/atom = 619.65899 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 16.43 | 16.43 | 16.43 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13454.214 0 -13454.214 46.363077 Loop time of 3.675e-06 on 1 procs for 0 steps with 3214 atoms 163.3% 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 | | 3.675e-06 | | |100.00 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24255.0 ave 24255 max 24255 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: 1.98641e+06 ave 1.98641e+06 max 1.98641e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1986412 Ave neighs/atom = 618.04978 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 16.43 | 16.43 | 16.43 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 -13454.214 -13454.214 41.764477 144.9198 6.2442864 46.363077 46.363077 -120.0437 99.978271 159.15466 2.2465006 1138.6276 Loop time of 3.775e-06 on 1 procs for 0 steps with 3214 atoms 238.4% 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 | | 3.775e-06 | | |100.00 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24255.0 ave 24255 max 24255 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 993206.0 ave 993206 max 993206 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.98641e+06 ave 1.98641e+06 max 1.98641e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1986412 Ave neighs/atom = 618.04978 Neighbor list builds = 0 Dangerous builds = 0 3214 -13454.2140362719 eV 2.24650064246602 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:32