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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -55.164285 0.0000000) to (39.007040 55.164285 5.1666087) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1590064 5.3228696 5.1666087 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -55.164285 0.0000000) to (39.007040 55.164285 5.1666087) create_atoms CPU = 0.006 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1590064 5.3228696 5.1666087 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -55.164285 0.0000000) to (39.007040 55.164285 5.1666087) create_atoms CPU = 0.006 seconds 916 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 9 26 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1816 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_673777079812_004#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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 6.390 | 6.390 | 6.390 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5419.5587 0 -5419.5587 33414.932 195 0 -5924.6998 0 -5924.6998 -6363.1893 Loop time of 14.0652 on 1 procs for 195 steps with 1816 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 = -5419.55866095434 -5924.69408251297 -5924.6998472649 Force two-norm initial, final = 607.10434 0.29572505 Force max component initial, final = 147.56633 0.018328083 Final line search alpha, max atom move = 1.0000000 0.018328083 Iterations, force evaluations = 195 348 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.627 | 13.627 | 13.627 | 0.0 | 96.89 Neigh | 0.26859 | 0.26859 | 0.26859 | 0.0 | 1.91 Comm | 0.09483 | 0.09483 | 0.09483 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07462 | | | 0.53 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11157.0 ave 11157 max 11157 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: 406240.0 ave 406240 max 406240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 406240 Ave neighs/atom = 223.70044 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 195 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.391 | 6.391 | 6.391 Mbytes Step Temp E_pair E_mol TotEng Press Volume 195 0 -5924.6998 0 -5924.6998 -6363.1893 22234.971 200 0 -5925.0462 0 -5925.0462 202.87428 22115.883 Loop time of 0.292551 on 1 procs for 5 steps with 1816 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5924.69984726493 -5925.04383792969 -5925.04618695209 Force two-norm initial, final = 165.05683 6.5588719 Force max component initial, final = 120.57693 6.3291189 Final line search alpha, max atom move = 0.00011196771 0.00070865692 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28376 | 0.28376 | 0.28376 | 0.0 | 96.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018387 | 0.0018387 | 0.0018387 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006955 | | | 2.38 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11259.0 ave 11259 max 11259 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: 406904.0 ave 406904 max 406904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 406904 Ave neighs/atom = 224.06608 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 6.529 | 6.529 | 6.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5925.0462 0 -5925.0462 202.87428 Loop time of 6.645e-06 on 1 procs for 0 steps with 1816 atoms 165.5% 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 | | 6.645e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11311.0 ave 11311 max 11311 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: 407504.0 ave 407504 max 407504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407504 Ave neighs/atom = 224.39648 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 6.529 | 6.529 | 6.529 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 -5925.0462 -5925.0462 38.897013 110.45108 5.1477572 202.87428 202.87428 116.01735 459.01969 33.585817 2.4235624 856.60172 Loop time of 6.555e-06 on 1 procs for 0 steps with 1816 atoms 274.6% 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 | | 6.555e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11311.0 ave 11311 max 11311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203752.0 ave 203752 max 203752 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 407504.0 ave 407504 max 407504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407504 Ave neighs/atom = 224.39648 Neighbor list builds = 0 Dangerous builds = 0 1816 -5925.04618695209 eV 2.42356240801026 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15