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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -40.256446 0.0000000) to (20.128223 40.256446 3.1435003) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4183904 4.4183904 3.1435003 Created 164 atoms using lattice units in orthogonal box = (0.0000000 -40.256446 0.0000000) to (20.128223 40.256446 3.1435003) create_atoms CPU = 0.001 seconds 164 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4183904 4.4183904 3.1435003 Created 165 atoms using lattice units in orthogonal box = (0.0000000 -40.256446 0.0000000) to (20.128223 40.256446 3.1435003) create_atoms CPU = 0.000 seconds 165 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 17 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 325 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_534363225491_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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1844.5928 0 -1844.5928 135226.48 120 0 -2166.5938 0 -2166.5938 -16207.401 Loop time of 1.77289 on 1 procs for 120 steps with 325 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1844.59278439478 -2166.59184420252 -2166.59377604638 Force two-norm initial, final = 861.47273 0.24888923 Force max component initial, final = 418.80973 0.068967996 Final line search alpha, max atom move = 0.55621814 0.038361250 Iterations, force evaluations = 120 216 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7252 | 1.7252 | 1.7252 | 0.0 | 97.31 Neigh | 0.018047 | 0.018047 | 0.018047 | 0.0 | 1.02 Comm | 0.018756 | 0.018756 | 0.018756 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01092 | | | 0.62 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5296.00 ave 5296 max 5296 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: 88872.0 ave 88872 max 88872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88872 Ave neighs/atom = 273.45231 Neighbor list builds = 2 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 120 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press Volume 120 0 -2166.5938 0 -2166.5938 -16207.401 5094.2982 193 0 -2173.9599 0 -2173.9599 -479.86562 5057.0278 Loop time of 0.690927 on 1 procs for 73 steps with 325 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2166.59377604637 -2173.95824119494 -2173.95985378266 Force two-norm initial, final = 186.75011 5.0667776 Force max component initial, final = 175.97973 2.7037957 Final line search alpha, max atom move = 0.00020261101 0.00054781880 Iterations, force evaluations = 73 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63676 | 0.63676 | 0.63676 | 0.0 | 92.16 Neigh | 0.018835 | 0.018835 | 0.018835 | 0.0 | 2.73 Comm | 0.0071549 | 0.0071549 | 0.0071549 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02818 | | | 4.08 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5939.00 ave 5939 max 5939 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: 89894.0 ave 89894 max 89894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89894 Ave neighs/atom = 276.59692 Neighbor list builds = 2 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.623 | 4.623 | 4.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2173.9599 0 -2173.9599 -479.86562 Loop time of 3.035e-06 on 1 procs for 0 steps with 325 atoms 131.8% 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 | | 3.035e-06 | | |100.00 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5939.00 ave 5939 max 5939 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: 89854.0 ave 89854 max 89854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89854 Ave neighs/atom = 276.47385 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.623 | 4.623 | 4.623 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 -2173.9599 -2173.9599 20.707877 82.452201 2.9618122 -479.86562 -479.86562 -812.6366 180.15008 -807.11034 2.5904773 188.50782 Loop time of 3.286e-06 on 1 procs for 0 steps with 325 atoms 152.2% 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 | | 3.286e-06 | | |100.00 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5939.00 ave 5939 max 5939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 44927.0 ave 44927 max 44927 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 89854.0 ave 89854 max 89854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89854 Ave neighs/atom = 276.47385 Neighbor list builds = 0 Dangerous builds = 0 325 -2173.95985378266 eV 2.5904772558211 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02