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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -59.800251 0.0000000) to (48.826700 59.800251 9.8982079) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0197302 5.7342706 6.5988053 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -59.800251 0.0000000) to (48.826700 59.800251 9.8982079) create_atoms CPU = 0.002 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0197302 5.7342706 6.5988053 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -59.800251 0.0000000) to (48.826700 59.800251 9.8982079) create_atoms CPU = 0.002 seconds 1756 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 24 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3502 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 12.21 | 12.21 | 12.21 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12823.242 0 -12823.242 34536.315 73 0 -13642.44 0 -13642.44 4745.8671 Loop time of 6.20268 on 1 procs for 73 steps with 3502 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 = -12823.2416507078 -13642.4277078715 -13642.4397562857 Force two-norm initial, final = 753.16823 0.30456584 Force max component initial, final = 104.42326 0.082946925 Final line search alpha, max atom move = 1.0000000 0.082946925 Iterations, force evaluations = 73 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9996 | 5.9996 | 5.9996 | 0.0 | 96.73 Neigh | 0.15749 | 0.15749 | 0.15749 | 0.0 | 2.54 Comm | 0.019565 | 0.019565 | 0.019565 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02605 | | | 0.42 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13776.0 ave 13776 max 13776 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: 862994.0 ave 862994 max 862994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 862994 Ave neighs/atom = 246.42890 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.21 | 12.21 | 12.21 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -13642.44 0 -13642.44 4745.8671 57802.544 82 0 -13643.594 0 -13643.594 9.9432929 58132.571 Loop time of 0.578403 on 1 procs for 9 steps with 3502 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13642.4397562858 -13643.5939275204 -13643.5940345374 Force two-norm initial, final = 350.68709 1.4160901 Force max component initial, final = 323.59794 1.2469101 Final line search alpha, max atom move = 0.00027975068 0.00034882395 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56897 | 0.56897 | 0.56897 | 0.0 | 98.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013067 | 0.0013067 | 0.0013067 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008128 | | | 1.41 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13771.0 ave 13771 max 13771 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: 863370.0 ave 863370 max 863370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 863370 Ave neighs/atom = 246.53626 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 11.72 | 11.72 | 11.72 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13643.594 0 -13643.594 9.9432929 Loop time of 1.786e-06 on 1 procs for 0 steps with 3502 atoms 168.0% 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 | | 1.786e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13723.0 ave 13723 max 13723 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: 861976.0 ave 861976 max 861976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 861976 Ave neighs/atom = 246.13821 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 11.72 | 11.72 | 11.72 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 -13643.594 -13643.594 48.776184 120.54408 9.8870291 9.9432929 9.9432929 -10.158177 5.6611055 34.32695 2.5511386 2226.2136 Loop time of 2.197e-06 on 1 procs for 0 steps with 3502 atoms 273.1% 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 | | 2.197e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13723.0 ave 13723 max 13723 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 430988.0 ave 430988 max 430988 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 861976.0 ave 861976 max 861976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 861976 Ave neighs/atom = 246.13821 Neighbor list builds = 0 Dangerous builds = 0 3502 -13643.5940345373 eV 2.55113856700398 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07