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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -51.779479 0.0000000) to (42.274911 51.779479 8.5700212) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2119753 4.9648200 5.7133475 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -51.779479 0.0000000) to (42.274911 51.779479 8.5700212) create_atoms CPU = 0.007 seconds 1759 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2119753 4.9648200 5.7133475 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -51.779479 0.0000000) to (42.274911 51.779479 8.5700212) create_atoms CPU = 0.006 seconds 1759 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 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 kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 46 atoms, new total = 3472 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.408 | 7.408 | 7.408 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14122.643 0 -14122.643 15906.435 42 0 -14238.516 0 -14238.516 -5049.7891 Loop time of 4.51335 on 1 procs for 42 steps with 3472 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14122.6430862413 -14238.5028484863 -14238.5157279902 Force two-norm initial, final = 150.31880 0.54802321 Force max component initial, final = 24.993295 0.075666127 Final line search alpha, max atom move = 1.0000000 0.075666127 Iterations, force evaluations = 42 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3935 | 4.3935 | 4.3935 | 0.0 | 97.34 Neigh | 0.075768 | 0.075768 | 0.075768 | 0.0 | 1.68 Comm | 0.019396 | 0.019396 | 0.019396 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02469 | | | 0.55 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11407.0 ave 11407 max 11407 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: 604742.0 ave 604742 max 604742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 604742 Ave neighs/atom = 174.17684 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.408 | 7.408 | 7.408 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -14238.516 0 -14238.516 -5049.7891 37519.088 45 0 -14238.66 0 -14238.66 -1584.7698 37408.475 Loop time of 0.351956 on 1 procs for 3 steps with 3472 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14238.5157279902 -14238.6590684236 -14238.6595629154 Force two-norm initial, final = 137.51009 0.64293399 Force max component initial, final = 98.058968 0.12625852 Final line search alpha, max atom move = 0.00023295325 2.9412333e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34465 | 0.34465 | 0.34465 | 0.0 | 97.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014931 | 0.0014931 | 0.0014931 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005815 | | | 1.65 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11416.0 ave 11416 max 11416 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: 605014.0 ave 605014 max 605014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605014 Ave neighs/atom = 174.25518 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.546 | 7.546 | 7.546 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14238.66 0 -14238.66 -1584.7698 Loop time of 6.104e-06 on 1 procs for 0 steps with 3472 atoms 180.2% 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 | | 6.104e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11422.0 ave 11422 max 11422 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: 605302.0 ave 605302 max 605302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605302 Ave neighs/atom = 174.33813 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.546 | 7.546 | 7.546 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 -14238.66 -14238.66 42.205293 103.55896 8.55885 -1584.7698 -1584.7698 -1.6759254 -4747.2329 -5.4005074 2.2641441 1474.5131 Loop time of 6.535e-06 on 1 procs for 0 steps with 3472 atoms 290.7% 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 | | 6.535e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11422.0 ave 11422 max 11422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 302651.0 ave 302651 max 302651 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 605302.0 ave 605302 max 605302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605302 Ave neighs/atom = 174.33813 Neighbor list builds = 0 Dangerous builds = 0 3472 -14238.6595629154 eV 2.26414405756635 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06