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 = 3.6149590 3.6149590 3.6149590 Created orthogonal box = (0.0000000 -38.934300 0.0000000) to (19.467150 38.934300 3.6149590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6989672 4.6989672 3.6149590 Created 232 atoms using lattice units in orthogonal box = (0.0000000 -38.934300 0.0000000) to (19.467150 38.934300 3.6149590) create_atoms CPU = 0.002 seconds 232 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6989672 4.6989672 3.6149590 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -38.934300 0.0000000) to (19.467150 38.934300 3.6149590) create_atoms CPU = 0.001 seconds 234 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 6 21 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 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 466 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_759493141826_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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 4.496 | 4.496 | 4.496 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1569.0403 0 -1569.0403 47732.548 36 0 -1641.1999 0 -1641.1999 19897.905 Loop time of 0.64629 on 1 procs for 36 steps with 466 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 = -1569.04030836018 -1641.19834205683 -1641.19985659948 Force two-norm initial, final = 141.17062 0.14622276 Force max component initial, final = 46.818735 0.032385615 Final line search alpha, max atom move = 1.0000000 0.032385615 Iterations, force evaluations = 36 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63296 | 0.63296 | 0.63296 | 0.0 | 97.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0080017 | 0.0080017 | 0.0080017 | 0.0 | 1.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005332 | | | 0.82 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5013.00 ave 5013 max 5013 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: 81652.0 ave 81652 max 81652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81652 Ave neighs/atom = 175.21888 Neighbor list builds = 0 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.496 | 4.496 | 4.496 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -1641.1999 0 -1641.1999 19897.905 5479.8429 54 0 -1642.0001 0 -1642.0001 148.87593 5554.8776 Loop time of 0.197319 on 1 procs for 18 steps with 466 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1641.19985659948 -1641.99942891576 -1642.0001483567 Force two-norm initial, final = 127.71951 1.0608906 Force max component initial, final = 107.73393 0.60857160 Final line search alpha, max atom move = 0.00078059651 0.00047504886 Iterations, force evaluations = 18 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17851 | 0.17851 | 0.17851 | 0.0 | 90.47 Neigh | 0.0096244 | 0.0096244 | 0.0096244 | 0.0 | 4.88 Comm | 0.002313 | 0.002313 | 0.002313 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006869 | | | 3.48 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5013.00 ave 5013 max 5013 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: 79724.0 ave 79724 max 79724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79724 Ave neighs/atom = 171.08155 Neighbor list builds = 1 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 4.634 | 4.634 | 4.634 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1642.0001 0 -1642.0001 148.87593 Loop time of 6.375e-06 on 1 procs for 0 steps with 466 atoms 203.9% 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 | | 6.375e-06 | | |100.00 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5013.00 ave 5013 max 5013 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: 79592.0 ave 79592 max 79592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79592 Ave neighs/atom = 170.79828 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 4.634 | 4.634 | 4.634 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 -1642.0001 -1642.0001 19.461492 79.206538 3.6036061 148.87593 148.87593 95.36155 176.28903 174.97721 2.2945645 291.7622 Loop time of 9.822e-06 on 1 procs for 0 steps with 466 atoms 193.4% 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 | | 9.822e-06 | | |100.00 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5013.00 ave 5013 max 5013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39796.0 ave 39796 max 39796 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 79592.0 ave 79592 max 79592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79592 Ave neighs/atom = 170.79828 Neighbor list builds = 0 Dangerous builds = 0 466 -1642.0001483567 eV 2.2945645441464 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01