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 = 3.5196184 3.5196184 3.5196184 Created orthogonal box = (0.0000000 -37.579241 0.0000000) to (21.696385 37.579241 6.0961579) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7095750 5.2742794 6.0961579 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.579241 0.0000000) to (21.696385 37.579241 6.0961579) create_atoms CPU = 0.003 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7095750 5.2742794 6.0961579 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.579241 0.0000000) to (21.696385 37.579241 6.0961579) create_atoms CPU = 0.003 seconds 458 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 6 20 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 7.565005302429199 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 914 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_110256178378_005#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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 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) = 5.000 | 5.000 | 5.000 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3723.2582 0 -3723.2582 91186.388 106 0 -4046.5685 0 -4046.5685 15376.905 Loop time of 3.25112 on 1 procs for 106 steps with 914 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 = -3723.25817179958 -4046.56471373625 -4046.56847411205 Force two-norm initial, final = 465.27402 0.23539822 Force max component initial, final = 120.42056 0.046532484 Final line search alpha, max atom move = 1.0000000 0.046532484 Iterations, force evaluations = 106 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0928 | 3.0928 | 3.0928 | 0.0 | 95.13 Neigh | 0.10918 | 0.10918 | 0.10918 | 0.0 | 3.36 Comm | 0.025978 | 0.025978 | 0.025978 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02321 | | | 0.71 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5292.00 ave 5292 max 5292 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: 158360.0 ave 158360 max 158360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158360 Ave neighs/atom = 173.26039 Neighbor list builds = 5 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.000 | 5.000 | 5.000 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -4046.5685 0 -4046.5685 15376.905 9940.8055 115 0 -4047.1903 0 -4047.1903 -19.481499 10028.625 Loop time of 0.195206 on 1 procs for 9 steps with 914 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 = -4046.56847411205 -4047.19026239374 -4047.19034972061 Force two-norm initial, final = 180.93188 0.65021546 Force max component initial, final = 154.60107 0.36716020 Final line search alpha, max atom move = 0.00048989823 0.00017987113 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18879 | 0.18879 | 0.18879 | 0.0 | 96.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013632 | 0.0013632 | 0.0013632 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005049 | | | 2.59 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5288.00 ave 5288 max 5288 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: 158376.0 ave 158376 max 158376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158376 Ave neighs/atom = 173.27790 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 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) = 5.138 | 5.138 | 5.138 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4047.1903 0 -4047.1903 -19.481499 Loop time of 6.304e-06 on 1 procs for 0 steps with 914 atoms 190.4% 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 | | 6.304e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5284.00 ave 5284 max 5284 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: 157988.0 ave 157988 max 157988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157988 Ave neighs/atom = 172.85339 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 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) = 5.138 | 5.138 | 5.138 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 -4047.1903 -4047.1903 21.716243 75.733086 6.0977699 -19.481499 -19.481499 -58.711326 -32.231028 32.497858 2.2673451 581.40506 Loop time of 7.407e-06 on 1 procs for 0 steps with 914 atoms 229.5% 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 | | 7.407e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5284.00 ave 5284 max 5284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78994.0 ave 78994 max 78994 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 157988.0 ave 157988 max 157988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157988 Ave neighs/atom = 172.85339 Neighbor list builds = 0 Dangerous builds = 0 914 -4047.19056763519 eV 2.26734506134625 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03