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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -40.854508 0.0000000) to (20.425809 40.854508 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.2681295 3.2681295 2.8886457 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -40.854508 0.0000000) to (20.425809 40.854508 2.8886457) create_atoms CPU = 0.002 seconds 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.2681295 3.2681295 2.8886457 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -40.854508 0.0000000) to (20.425809 40.854508 2.8886457) create_atoms CPU = 0.001 seconds 202 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 31 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 8 atoms, new total = 396 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.813 | 4.813 | 4.813 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1628.16 0 -1628.16 5773.1394 44 0 -1647.1381 0 -1647.1381 -11597.13 Loop time of 7.0318 on 1 procs for 44 steps with 396 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 = -1628.15995341685 -1647.13667879376 -1647.13808707935 Force two-norm initial, final = 32.718797 0.14279118 Force max component initial, final = 8.7074785 0.022646671 Final line search alpha, max atom move = 1.0000000 0.022646671 Iterations, force evaluations = 44 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0188 | 7.0188 | 7.0188 | 0.0 | 99.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0066979 | 0.0066979 | 0.0066979 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00632 | | | 0.09 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2711.00 ave 2711 max 2711 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: 22592.0 ave 22592 max 22592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22592 Ave neighs/atom = 57.050505 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.816 | 4.816 | 4.816 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -1647.1381 0 -1647.1381 -11597.13 4821.071 49 0 -1647.2785 0 -1647.2785 655.60451 4786.8736 Loop time of 0.61588 on 1 procs for 5 steps with 396 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 = -1647.13808707935 -1647.27775375841 -1647.27848697395 Force two-norm initial, final = 56.122132 1.9869761 Force max component initial, final = 44.556098 1.7387524 Final line search alpha, max atom move = 0.00045228663 0.00078641447 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61364 | 0.61364 | 0.61364 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048484 | 0.00048484 | 0.00048484 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00175 | | | 0.28 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3054.00 ave 3054 max 3054 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: 22760.0 ave 22760 max 22760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22760 Ave neighs/atom = 57.474747 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.954 | 4.954 | 4.954 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1647.2785 0 -1647.2785 655.60451 Loop time of 6.064e-06 on 1 procs for 0 steps with 396 atoms 181.4% 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 | | 6.064e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3054.00 ave 3054 max 3054 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: 22768.0 ave 22768 max 22768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22768 Ave neighs/atom = 57.494949 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.954 | 4.954 | 4.954 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 -1647.2785 -1647.2785 20.333117 81.709015 2.8812306 655.60451 655.60451 280.6665 1105.6769 580.47014 2.3833477 145.37459 Loop time of 6.344e-06 on 1 procs for 0 steps with 396 atoms 252.2% 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 | | 6.344e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3054.00 ave 3054 max 3054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11384.0 ave 11384 max 11384 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22768.0 ave 22768 max 22768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22768 Ave neighs/atom = 57.494949 Neighbor list builds = 0 Dangerous builds = 0 396 -1647.27848697395 eV 2.3833476983554 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08