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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -67.345551 0.0000000) to (38.879940 67.345551 6.0968610) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7363846 5.1518494 6.0968610 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.345551 0.0000000) to (38.879940 67.345551 6.0968610) create_atoms CPU = 0.008 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7363846 5.1518494 6.0968610 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.345551 0.0000000) to (38.879940 67.345551 6.0968610) create_atoms CPU = 0.007 seconds 1466 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 10 33 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2904 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 11.30 | 11.30 | 11.30 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12840.993 0 -12840.993 2545.5746 43 0 -12880.207 0 -12880.207 -8412.6509 Loop time of 6.20253 on 1 procs for 43 steps with 2904 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12840.9934594812 -12880.196062725 -12880.2071073799 Force two-norm initial, final = 52.850122 0.33335343 Force max component initial, final = 8.9703489 0.044541435 Final line search alpha, max atom move = 0.91877048 0.040923356 Iterations, force evaluations = 43 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0547 | 6.0547 | 6.0547 | 0.0 | 97.62 Neigh | 0.088053 | 0.088053 | 0.088053 | 0.0 | 1.42 Comm | 0.032675 | 0.032675 | 0.032675 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02712 | | | 0.44 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14258.0 ave 14258 max 14258 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: 647312.0 ave 647312 max 647312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 647312 Ave neighs/atom = 222.90358 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.30 | 11.30 | 11.30 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -12880.207 0 -12880.207 -8412.6509 31927.932 46 0 -12880.363 0 -12880.363 -3750.7883 31843.722 Loop time of 0.408851 on 1 procs for 3 steps with 2904 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 = -12880.2071073799 -12880.3621601909 -12880.3634681979 Force two-norm initial, final = 158.40145 0.34874520 Force max component initial, final = 130.74260 0.050455848 Final line search alpha, max atom move = 0.00010267775 5.1806928e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40063 | 0.40063 | 0.40063 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020707 | 0.0020707 | 0.0020707 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006153 | | | 1.51 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14242.0 ave 14242 max 14242 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: 647368.0 ave 647368 max 647368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 647368 Ave neighs/atom = 222.92287 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 10.81 | 10.81 | 10.81 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12880.363 0 -12880.363 -3750.7883 Loop time of 6.364e-06 on 1 procs for 0 steps with 2904 atoms 204.3% 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 | | 6.364e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14258.0 ave 14258 max 14258 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: 647488.0 ave 647488 max 647488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 647488 Ave neighs/atom = 222.96419 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 10.81 | 10.81 | 10.81 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 -12880.363 -12880.363 38.808455 134.6911 6.0919814 -3750.7883 -3750.7883 -1.4539716 -11248.374 -2.5365902 2.2289847 856.72673 Loop time of 6.936e-06 on 1 procs for 0 steps with 2904 atoms 288.4% 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 | | 6.936e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14258.0 ave 14258 max 14258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 323744.0 ave 323744 max 323744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 647488.0 ave 647488 max 647488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 647488 Ave neighs/atom = 222.96419 Neighbor list builds = 0 Dangerous builds = 0 2904 -12801.1963573707 eV 2.2289847412975 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08