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 = 4.0248454 4.0248454 4.0248454 Created orthogonal box = (0.0000000 -80.697899 0.0000000) to (46.590954 80.697899 6.9712367) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2584863 6.4237133 6.9712367 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -80.697899 0.0000000) to (46.590954 80.697899 6.9712367) create_atoms CPU = 0.010 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2584863 6.4237133 6.9712367 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -80.697899 0.0000000) to (46.590954 80.697899 6.9712367) create_atoms CPU = 0.009 seconds 1610 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 12 39 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3214 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_149316865608_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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.663 | 6.663 | 6.663 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8217.6836 0 -8217.6836 12998.631 187 0 -8486.0778 0 -8486.0778 3089.9021 Loop time of 19.8827 on 1 procs for 187 steps with 3214 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 = -8217.68356792666 -8486.07039253727 -8486.07780030652 Force two-norm initial, final = 297.22503 0.22126230 Force max component initial, final = 58.849004 0.050044669 Final line search alpha, max atom move = 0.62890328 0.031473256 Iterations, force evaluations = 187 349 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.318 | 19.318 | 19.318 | 0.0 | 97.16 Neigh | 0.33215 | 0.33215 | 0.33215 | 0.0 | 1.67 Comm | 0.1176 | 0.1176 | 0.1176 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1146 | | | 0.58 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12829.0 ave 12829 max 12829 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: 450200.0 ave 450200 max 450200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450200 Ave neighs/atom = 140.07467 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 187 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.663 | 6.663 | 6.663 Mbytes Step Temp E_pair E_mol TotEng Press Volume 187 0 -8486.0778 0 -8486.0778 3089.9021 52420.801 194 0 -8486.6495 0 -8486.6495 67.897181 52617.633 Loop time of 0.591625 on 1 procs for 7 steps with 3214 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 = -8486.07780030654 -8486.64895852267 -8486.64950050005 Force two-norm initial, final = 215.32882 4.5370174 Force max component initial, final = 200.65176 4.1628977 Final line search alpha, max atom move = 0.00024092109 0.0010029298 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50574 | 0.50574 | 0.50574 | 0.0 | 85.48 Neigh | 0.070998 | 0.070998 | 0.070998 | 0.0 | 12.00 Comm | 0.0037207 | 0.0037207 | 0.0037207 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01117 | | | 1.89 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12810.0 ave 12810 max 12810 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: 449920.0 ave 449920 max 449920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449920 Ave neighs/atom = 139.98755 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.801 | 6.801 | 6.801 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8486.6495 0 -8486.6495 67.897181 Loop time of 6.885e-06 on 1 procs for 0 steps with 3214 atoms 188.8% 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 | | 6.885e-06 | | |100.00 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12804.0 ave 12804 max 12804 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: 449904.0 ave 449904 max 449904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449904 Ave neighs/atom = 139.98258 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.801 | 6.801 | 6.801 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 -8486.6495 -8486.6495 46.578649 162.37517 6.9570447 67.897181 67.897181 37.483547 127.52701 38.680984 2.5514752 1339.9312 Loop time of 6.856e-06 on 1 procs for 0 steps with 3214 atoms 320.9% 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 | | 6.856e-06 | | |100.00 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12804.0 ave 12804 max 12804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 224952.0 ave 224952 max 224952 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 449904.0 ave 449904 max 449904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449904 Ave neighs/atom = 139.98258 Neighbor list builds = 0 Dangerous builds = 0 3214 -8387.86957888011 eV 2.55147519410594 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21