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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -73.281155 0.0000000) to (51.814723 73.281155 5.7571914) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 7.0365673 6.7849152 5.7571914 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -73.281155 0.0000000) to (51.814723 73.281155 5.7571914) create_atoms CPU = 0.011 seconds 1299 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 7.0365673 6.7849152 5.7571914 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -73.281155 0.0000000) to (51.814723 73.281155 5.7571914) create_atoms CPU = 0.010 seconds 1299 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 49 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 11 atoms, new total = 2587 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 49 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.308 | 5.308 | 5.308 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8665.1809 0 -8665.1809 3180.3756 29 0 -8695.7742 0 -8695.7742 1333.6974 Loop time of 9.5996 on 1 procs for 29 steps with 2587 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 = -8665.18086417216 -8695.76730237347 -8695.77424464611 Force two-norm initial, final = 29.669267 0.23013183 Force max component initial, final = 5.4887159 0.023146877 Final line search alpha, max atom move = 1.0000000 0.023146877 Iterations, force evaluations = 29 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.5442 | 9.5442 | 9.5442 | 0.0 | 99.42 Neigh | 0.027919 | 0.027919 | 0.027919 | 0.0 | 0.29 Comm | 0.012681 | 0.012681 | 0.012681 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01484 | | | 0.15 Nlocal: 2587.00 ave 2587 max 2587 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8656.00 ave 8656 max 8656 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: 139314.0 ave 139314 max 139314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139314 Ave neighs/atom = 53.851566 Neighbor list builds = 1 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 49 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.308 | 5.308 | 5.308 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -8695.7742 0 -8695.7742 1333.6974 43720.604 30 0 -8695.7769 0 -8695.7769 932.80854 43738.694 Loop time of 0.574952 on 1 procs for 1 steps with 2587 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 = -8695.7742446461 -8695.7742446461 -8695.77691064874 Force two-norm initial, final = 17.830261 0.72361866 Force max component initial, final = 14.060682 0.57933277 Final line search alpha, max atom move = 7.1120307e-05 4.1202325e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5719 | 0.5719 | 0.5719 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060115 | 0.00060115 | 0.00060115 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002448 | | | 0.43 Nlocal: 2587.00 ave 2587 max 2587 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8656.00 ave 8656 max 8656 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: 139356.0 ave 139356 max 139356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139356 Ave neighs/atom = 53.867801 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 49 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.446 | 5.446 | 5.446 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8695.7769 0 -8695.7769 932.80854 Loop time of 9.211e-06 on 1 procs for 0 steps with 2587 atoms 152.0% 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 | | 9.211e-06 | | |100.00 Nlocal: 2587.00 ave 2587 max 2587 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8656.00 ave 8656 max 8656 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: 139356.0 ave 139356 max 139356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139356 Ave neighs/atom = 53.867801 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 49 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.446 | 5.446 | 5.446 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 -8695.7769 -8695.7769 51.824114 146.56231 5.7585299 932.80854 932.80854 -13.45314 2790.6525 21.226266 2.5418985 1600.2981 Loop time of 7.458e-06 on 1 procs for 0 steps with 2587 atoms 254.8% 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 | | 7.458e-06 | | |100.00 Nlocal: 2587.00 ave 2587 max 2587 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8656.00 ave 8656 max 8656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69678.0 ave 69678 max 69678 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139356.0 ave 139356 max 139356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139356 Ave neighs/atom = 53.867801 Neighbor list builds = 0 Dangerous builds = 0 2587 -8695.77691064874 eV 2.54189848716193 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11