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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -48.719728 0.0000000) to (59.669237 48.719728 9.8765224) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7217077 6.0065418 6.5843483 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -48.719728 0.0000000) to (59.669237 48.719728 9.8765224) create_atoms CPU = 0.007 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7217077 6.0065418 6.5843483 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -48.719728 0.0000000) to (59.669237 48.719728 9.8765224) create_atoms CPU = 0.006 seconds 1755 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 26 3 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3504 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.491 | 6.491 | 6.491 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11452.898 0 -11452.898 13893.652 102 0 -11749.517 0 -11749.517 3195.4412 Loop time of 7.09752 on 1 procs for 102 steps with 3504 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11452.8981394823 -11749.5070326651 -11749.5171213948 Force two-norm initial, final = 90.524382 0.27869804 Force max component initial, final = 8.4765738 0.043057271 Final line search alpha, max atom move = 0.76981831 0.033146276 Iterations, force evaluations = 102 161 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.599 | 6.599 | 6.599 | 0.0 | 92.98 Neigh | 0.39509 | 0.39509 | 0.39509 | 0.0 | 5.57 Comm | 0.041054 | 0.041054 | 0.041054 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06235 | | | 0.88 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9645.00 ave 9645 max 9645 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: 459984.0 ave 459984 max 459984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459984 Ave neighs/atom = 131.27397 Neighbor list builds = 6 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.494 | 6.494 | 6.494 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -11749.517 0 -11749.517 3195.4412 57423.464 108 0 -11750.033 0 -11750.033 -104.25761 57660.655 Loop time of 0.323241 on 1 procs for 6 steps with 3504 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 = -11749.5171213948 -11750.0313283968 -11750.0327444642 Force two-norm initial, final = 229.04116 7.2424464 Force max component initial, final = 204.11222 5.0918175 Final line search alpha, max atom move = 0.00010324698 0.00052571478 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31333 | 0.31333 | 0.31333 | 0.0 | 96.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001732 | 0.001732 | 0.001732 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008177 | | | 2.53 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9643.00 ave 9643 max 9643 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: 460004.0 ave 460004 max 460004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460004 Ave neighs/atom = 131.27968 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.632 | 6.632 | 6.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11750.033 0 -11750.033 -104.25761 Loop time of 6.545e-06 on 1 procs for 0 steps with 3504 atoms 198.6% 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 | | 6.545e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9605.00 ave 9605 max 9605 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: 459030.0 ave 459030 max 459030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459030 Ave neighs/atom = 131.00171 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.632 | 6.632 | 6.632 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 -11750.033 -11750.033 59.685356 97.95446 9.8625125 -104.25761 -104.25761 -141.52101 -32.51526 -138.73655 2.5852687 2147.7461 Loop time of 7.377e-06 on 1 procs for 0 steps with 3504 atoms 244.0% 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 | | 7.377e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9605.00 ave 9605 max 9605 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 229515.0 ave 229515 max 229515 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 459030.0 ave 459030 max 459030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459030 Ave neighs/atom = 131.00171 Neighbor list builds = 0 Dangerous builds = 0 3504 -11750.0327444642 eV 2.58526869318903 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08