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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -52.827220 0.0000000) to (24.902990 52.827220 5.7131378) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2427348 6.4875533 5.7131378 Created 450 atoms using lattice units in orthogonal box = (0.0000000 -52.827220 0.0000000) to (24.902990 52.827220 5.7131378) create_atoms CPU = 0.001 seconds 450 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2427348 6.4875533 5.7131378 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -52.827220 0.0000000) to (24.902990 52.827220 5.7131378) create_atoms CPU = 0.001 seconds 458 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 18 1 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 906 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_279544746097_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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.855 | 5.855 | 5.855 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2558.6752 0 -2558.6752 7231.3056 109 0 -2600.8752 0 -2600.8752 -2005.9809 Loop time of 3.20305 on 1 procs for 109 steps with 906 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 = -2558.67523876709 -2600.8727123249 -2600.87523636287 Force two-norm initial, final = 40.798280 0.16014048 Force max component initial, final = 6.9297253 0.034069752 Final line search alpha, max atom move = 1.0000000 0.034069752 Iterations, force evaluations = 109 196 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1146 | 3.1146 | 3.1146 | 0.0 | 97.24 Neigh | 0.056475 | 0.056475 | 0.056475 | 0.0 | 1.76 Comm | 0.01915 | 0.01915 | 0.01915 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01278 | | | 0.40 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9876.00 ave 9876 max 9876 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: 363012.0 ave 363012 max 363012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363012 Ave neighs/atom = 400.67550 Neighbor list builds = 3 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.856 | 5.856 | 5.856 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -2600.8752 0 -2600.8752 -2005.9809 15031.902 113 0 -2600.9376 0 -2600.9376 110.49144 14989.373 Loop time of 0.108669 on 1 procs for 4 steps with 906 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 = -2600.87523636287 -2600.93656203606 -2600.93760638288 Force two-norm initial, final = 43.008180 2.7794320 Force max component initial, final = 35.092709 2.7627884 Final line search alpha, max atom move = 0.00019487550 0.00053839979 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10606 | 0.10606 | 0.10606 | 0.0 | 97.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050731 | 0.00050731 | 0.00050731 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002107 | | | 1.94 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9922.00 ave 9922 max 9922 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: 361480.0 ave 361480 max 361480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361480 Ave neighs/atom = 398.98455 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.994 | 5.994 | 5.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2600.9376 0 -2600.9376 110.49144 Loop time of 2.233e-06 on 1 procs for 0 steps with 906 atoms 134.3% 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 | | 2.233e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9924.00 ave 9924 max 9924 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: 366648.0 ave 366648 max 366648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366648 Ave neighs/atom = 404.68874 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.994 | 5.994 | 5.994 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 -2600.9376 -2600.9376 24.847776 105.44081 5.7212012 110.49144 110.49144 16.353156 294.71043 20.41075 2.5861372 746.83371 Loop time of 2.271e-06 on 1 procs for 0 steps with 906 atoms 220.2% 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 | | 2.271e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9924.00 ave 9924 max 9924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 183324.0 ave 183324 max 183324 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 366648.0 ave 366648 max 366648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366648 Ave neighs/atom = 404.68874 Neighbor list builds = 0 Dangerous builds = 0 906 -2600.93760638288 eV 2.58613721188651 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03