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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -69.369808 0.0000000) to (34.684904 69.369808 4.0320382) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6245791 5.6245791 4.0320382 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -69.369808 0.0000000) to (34.684904 69.369808 4.0320382) create_atoms CPU = 0.004 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6245791 5.6245791 4.0320382 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -69.369808 0.0000000) to (34.684904 69.369808 4.0320382) create_atoms CPU = 0.003 seconds 594 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 32 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1186 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.466 | 5.466 | 5.466 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3889.4238 0 -3889.4238 11856.266 77 0 -3976.6846 0 -3976.6846 4856.3395 Loop time of 3.7104 on 1 procs for 77 steps with 1186 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 = -3889.42376834461 -3976.68202307721 -3976.68457843145 Force two-norm initial, final = 50.527151 0.15206648 Force max component initial, final = 7.5721081 0.041881232 Final line search alpha, max atom move = 1.0000000 0.041881232 Iterations, force evaluations = 77 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5939 | 3.5939 | 3.5939 | 0.0 | 96.86 Neigh | 0.057287 | 0.057287 | 0.057287 | 0.0 | 1.54 Comm | 0.035895 | 0.035895 | 0.035895 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0233 | | | 0.63 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9803.00 ave 9803 max 9803 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: 206468.0 ave 206468 max 206468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206468 Ave neighs/atom = 174.08769 Neighbor list builds = 2 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.465 | 5.465 | 5.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -3976.6846 0 -3976.6846 4856.3395 19402.855 85 0 -3977.0645 0 -3977.0645 -7.2858998 19512.186 Loop time of 0.279169 on 1 procs for 8 steps with 1186 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 = -3976.68457843146 -3977.06405120915 -3977.06448356553 Force two-norm initial, final = 120.22780 0.39487531 Force max component initial, final = 107.05887 0.26112830 Final line search alpha, max atom move = 0.00045795728 0.00011958560 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24084 | 0.24084 | 0.24084 | 0.0 | 86.27 Neigh | 0.028828 | 0.028828 | 0.028828 | 0.0 | 10.33 Comm | 0.0027639 | 0.0027639 | 0.0027639 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006733 | | | 2.41 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9818.00 ave 9818 max 9818 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: 206548.0 ave 206548 max 206548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206548 Ave neighs/atom = 174.15514 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.604 | 5.604 | 5.604 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3977.0645 0 -3977.0645 -7.2858998 Loop time of 6.716e-06 on 1 procs for 0 steps with 1186 atoms 178.7% 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 | | 6.716e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9818.00 ave 9818 max 9818 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: 206556.0 ave 206556 max 206556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206556 Ave neighs/atom = 174.16189 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.604 | 5.604 | 5.604 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 -3977.0645 -3977.0645 34.594236 139.74849 4.0360362 -7.2858998 -7.2858998 6.7625407 -7.157322 -21.462918 2.5740216 412.80322 Loop time of 7.127e-06 on 1 procs for 0 steps with 1186 atoms 266.6% 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 | | 7.127e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9818.00 ave 9818 max 9818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103278.0 ave 103278 max 103278 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206556.0 ave 206556 max 206556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206556 Ave neighs/atom = 174.16189 Neighbor list builds = 0 Dangerous builds = 0 1186 -3977.06448356553 eV 2.57402159595162 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04