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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -41.069653 0.0000000) to (20.533066 41.069653 3.5213917) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8313096 4.8313096 3.5213917 Created 273 atoms using lattice units in orthogonal box = (0.0000000 -41.069653 0.0000000) to (20.533066 41.069653 3.5213917) create_atoms CPU = 0.001 seconds 273 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8313096 4.8313096 3.5213917 Created 273 atoms using lattice units in orthogonal box = (0.0000000 -41.069653 0.0000000) to (20.533066 41.069653 3.5213917) create_atoms CPU = 0.000 seconds 273 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 27 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 536 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2354.0211 0 -2354.0211 5969.9116 69 0 -2374.0972 0 -2374.0972 -14670.803 Loop time of 2.35898 on 1 procs for 69 steps with 536 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2354.02106021089 -2374.09499650757 -2374.09718762288 Force two-norm initial, final = 40.689637 0.17067597 Force max component initial, final = 12.044831 0.051106643 Final line search alpha, max atom move = 1.0000000 0.051106643 Iterations, force evaluations = 69 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.344 | 2.344 | 2.344 | 0.0 | 99.37 Neigh | 0.0066534 | 0.0066534 | 0.0066534 | 0.0 | 0.28 Comm | 0.0045085 | 0.0045085 | 0.0045085 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003798 | | | 0.16 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3896.00 ave 3896 max 3896 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: 45766.0 ave 45766 max 45766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45766 Ave neighs/atom = 85.384328 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.485 | 4.485 | 4.485 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -2374.0972 0 -2374.0972 -14670.803 5939.08 74 0 -2374.2554 0 -2374.2554 -3215.0277 5901.5952 Loop time of 0.146591 on 1 procs for 5 steps with 536 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 = -2374.09718762288 -2374.25373877157 -2374.25540223187 Force two-norm initial, final = 69.288301 0.22392062 Force max component initial, final = 51.454022 0.043512869 Final line search alpha, max atom move = 0.00024394029 1.0614542e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14525 | 0.14525 | 0.14525 | 0.0 | 99.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025545 | 0.00025545 | 0.00025545 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001085 | | | 0.74 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4379.00 ave 4379 max 4379 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: 45792.0 ave 45792 max 45792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45792 Ave neighs/atom = 85.432836 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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 -2374.2554 0 -2374.2554 -3215.0277 Loop time of 1.674e-06 on 1 procs for 0 steps with 536 atoms 119.5% 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 | | 1.674e-06 | | |100.00 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4379.00 ave 4379 max 4379 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: 45798.0 ave 45798 max 45798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45798 Ave neighs/atom = 85.444030 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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 -2374.2554 -2374.2554 20.492127 82.139306 3.5061568 -3215.0277 -3215.0277 -4.9854458 -9642.4109 2.3133635 2.2611283 298.66285 Loop time of 1.651e-06 on 1 procs for 0 steps with 536 atoms 181.7% 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 | | 1.651e-06 | | |100.00 Nlocal: 536.000 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4379.00 ave 4379 max 4379 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22899.0 ave 22899 max 22899 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 45798.0 ave 45798 max 45798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45798 Ave neighs/atom = 85.444030 Neighbor list builds = 0 Dangerous builds = 0 536 -2374.25540223187 eV 2.26112830098542 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02