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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -37.949585 0.0000000) to (13.416193 37.949585 4.0451344) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8786157 4.3121278 4.0451344 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -37.949585 0.0000000) to (13.416193 37.949585 4.0451344) create_atoms CPU = 0.001 seconds 178 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8786157 4.3121278 4.0451344 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -37.949585 0.0000000) to (13.416193 37.949585 4.0451344) create_atoms CPU = 0.000 seconds 178 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 351 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.466 | 4.466 | 4.466 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1467.7105 0 -1467.7105 28632.638 128 0 -1534.8846 0 -1534.8846 1511.8055 Loop time of 0.64976 on 1 procs for 128 steps with 351 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 = -1467.71053393443 -1534.88309792365 -1534.88456706621 Force two-norm initial, final = 102.07001 0.18859679 Force max component initial, final = 37.702968 0.060268762 Final line search alpha, max atom move = 1.0000000 0.060268762 Iterations, force evaluations = 128 219 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62488 | 0.62488 | 0.62488 | 0.0 | 96.17 Neigh | 0.014131 | 0.014131 | 0.014131 | 0.0 | 2.17 Comm | 0.0065377 | 0.0065377 | 0.0065377 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004214 | | | 0.65 Nlocal: 351.000 ave 351 max 351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4164.00 ave 4164 max 4164 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: 56562.0 ave 56562 max 56562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56562 Ave neighs/atom = 161.14530 Neighbor list builds = 4 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 128 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.467 | 4.467 | 4.467 Mbytes Step Temp E_pair E_mol TotEng Press Volume 128 0 -1534.8846 0 -1534.8846 1511.8055 4119.0711 137 0 -1535.1473 0 -1535.1473 5300.7068 4107.3984 Loop time of 0.0324774 on 1 procs for 9 steps with 351 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 = -1534.88456706621 -1535.14655204211 -1535.14730091996 Force two-norm initial, final = 52.785046 0.81225190 Force max component initial, final = 44.544622 0.21373049 Final line search alpha, max atom move = 0.00048195895 0.00010300932 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.030858 | 0.030858 | 0.030858 | 0.0 | 95.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031683 | 0.00031683 | 0.00031683 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001303 | | | 4.01 Nlocal: 351.000 ave 351 max 351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4284.00 ave 4284 max 4284 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: 56064.0 ave 56064 max 56064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56064 Ave neighs/atom = 159.72650 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.605 | 4.605 | 4.605 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1535.1473 0 -1535.1473 5300.7068 Loop time of 1.553e-06 on 1 procs for 0 steps with 351 atoms 128.8% 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 | | 1.553e-06 | | |100.00 Nlocal: 351.000 ave 351 max 351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4284.00 ave 4284 max 4284 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: 56196.0 ave 56196 max 56196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56196 Ave neighs/atom = 160.10256 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.605 | 4.605 | 4.605 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 -1535.1473 -1535.1473 13.302637 75.89917 4.068104 5300.7068 5300.7068 82.664392 15863.313 -43.85693 2.3238893 1983.0128 Loop time of 1.64e-06 on 1 procs for 0 steps with 351 atoms 122.0% 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 | | 1.64e-06 | | |100.00 Nlocal: 351.000 ave 351 max 351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4284.00 ave 4284 max 4284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28098.0 ave 28098 max 28098 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56196.0 ave 56196 max 56196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56196 Ave neighs/atom = 160.10256 Neighbor list builds = 0 Dangerous builds = 0 351 -1535.14730091996 eV 2.32388932771578 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00