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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -33.883114 0.0000000) to (41.498170 33.883114 7.0144710) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7426480 4.3564004 4.6763140 Created 837 atoms using lattice units in orthogonal box = (0.0000000 -33.883114 0.0000000) to (41.498170 33.883114 7.0144710) create_atoms CPU = 0.001 seconds 837 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7426480 4.3564004 4.6763140 Created 843 atoms using lattice units in orthogonal box = (0.0000000 -33.883114 0.0000000) to (41.498170 33.883114 7.0144710) create_atoms CPU = 0.001 seconds 843 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 21 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1678 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_179420363944_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.125 | 5.125 | 5.125 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5752.4213 0 -5752.4213 133225 98 0 -7155.8729 0 -7155.8729 7762.5503 Loop time of 21.3512 on 1 procs for 98 steps with 1678 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5752.42127501629 -7155.86593516881 -7155.87290808264 Force two-norm initial, final = 1417.5819 0.28172711 Force max component initial, final = 225.67172 0.051138098 Final line search alpha, max atom move = 0.60147829 0.030758456 Iterations, force evaluations = 98 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.272 | 21.272 | 21.272 | 0.0 | 99.63 Neigh | 0.049307 | 0.049307 | 0.049307 | 0.0 | 0.23 Comm | 0.012614 | 0.012614 | 0.012614 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01676 | | | 0.08 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5764.00 ave 5764 max 5764 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: 182366.0 ave 182366 max 182366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182366 Ave neighs/atom = 108.68057 Neighbor list builds = 4 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.122 | 5.122 | 5.122 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -7155.8729 0 -7155.8729 7762.5503 19725.916 105 0 -7156.4447 0 -7156.4447 -3.991295 19814.188 Loop time of 1.27452 on 1 procs for 7 steps with 1678 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7155.87290808265 -7156.44461611292 -7156.44471854088 Force two-norm initial, final = 208.58190 0.49515781 Force max component initial, final = 196.05406 0.099899929 Final line search alpha, max atom move = 0.00039214239 3.9174997e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2712 | 1.2712 | 1.2712 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004574 | 0.0004574 | 0.0004574 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002903 | | | 0.23 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5754.00 ave 5754 max 5754 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: 182470.0 ave 182470 max 182470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182470 Ave neighs/atom = 108.74255 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.260 | 5.260 | 5.260 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7156.4447 0 -7156.4447 -3.991295 Loop time of 2.256e-06 on 1 procs for 0 steps with 1678 atoms 177.3% 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 | | 2.256e-06 | | |100.00 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5754.00 ave 5754 max 5754 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: 182128.0 ave 182128 max 182128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182128 Ave neighs/atom = 108.53874 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.260 | 5.260 | 5.260 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 -7156.4447 -7156.4447 41.507966 68.172756 7.0021913 -3.991295 -3.991295 -8.0798215 -3.3233819 -0.5706817 2.2830005 1690.7817 Loop time of 2.595e-06 on 1 procs for 0 steps with 1678 atoms 231.2% 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 | | 2.595e-06 | | |100.00 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5754.00 ave 5754 max 5754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 91064.0 ave 91064 max 91064 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 182128.0 ave 182128 max 182128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182128 Ave neighs/atom = 108.53874 Neighbor list builds = 0 Dangerous builds = 0 1678 -7156.44471854088 eV 2.28300051328796 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23