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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -36.766457 0.0000000) to (8.6659370 36.766457 4.0851619) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8144095 4.0851619 4.0851619 Created 108 atoms using lattice units in orthogonal box = (0.0000000 -36.766457 0.0000000) to (8.6659370 36.766457 4.0851619) create_atoms CPU = 0.001 seconds 108 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8144095 4.0851619 4.0851619 Created 110 atoms using lattice units in orthogonal box = (0.0000000 -36.766457 0.0000000) to (8.6659370 36.766457 4.0851619) create_atoms CPU = 0.000 seconds 110 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 28 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 218 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.397 | 4.397 | 4.397 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -727.00612 0 -727.00612 190272.84 46 0 -904.63915 0 -904.63915 26359.288 Loop time of 2.0112 on 1 procs for 46 steps with 218 atoms 94.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -727.006124877252 -904.63837317252 -904.639154835401 Force two-norm initial, final = 405.51707 0.098988961 Force max component initial, final = 123.47803 0.021377649 Final line search alpha, max atom move = 1.0000000 0.021377649 Iterations, force evaluations = 46 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9991 | 1.9991 | 1.9991 | 0.0 | 99.40 Neigh | 0.0077469 | 0.0077469 | 0.0077469 | 0.0 | 0.39 Comm | 0.0022641 | 0.0022641 | 0.0022641 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002118 | | | 0.11 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1711.00 ave 1711 max 1711 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: 12540.0 ave 12540 max 12540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12540 Ave neighs/atom = 57.522936 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.397 | 4.397 | 4.397 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -904.63915 0 -904.63915 26359.288 2603.1943 71 0 -905.27107 0 -905.27107 294.87612 2642.6109 Loop time of 0.490099 on 1 procs for 25 steps with 218 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 = -904.639154835402 -905.270841608742 -905.271066450285 Force two-norm initial, final = 83.009738 0.96960160 Force max component initial, final = 73.245742 0.78144656 Final line search alpha, max atom move = 0.0010526845 0.00082261670 Iterations, force evaluations = 25 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47964 | 0.47964 | 0.47964 | 0.0 | 97.87 Neigh | 0.0075853 | 0.0075853 | 0.0075853 | 0.0 | 1.55 Comm | 0.00052878 | 0.00052878 | 0.00052878 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002341 | | | 0.48 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1711.00 ave 1711 max 1711 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: 12492.0 ave 12492 max 12492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12492 Ave neighs/atom = 57.302752 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.535 | 4.535 | 4.535 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -905.27107 0 -905.27107 294.87612 Loop time of 1.948e-06 on 1 procs for 0 steps with 218 atoms 154.0% 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 | | 1.948e-06 | | |100.00 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1711.00 ave 1711 max 1711 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: 12484.0 ave 12484 max 12484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12484 Ave neighs/atom = 57.266055 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.535 | 4.535 | 4.535 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 -905.27107 -905.27107 8.6552093 74.909469 4.0758569 294.87612 294.87612 200.46053 482.64895 201.51889 2.340487 185.22272 Loop time of 1.87e-06 on 1 procs for 0 steps with 218 atoms 160.4% 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 | | 1.87e-06 | | |100.00 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1711.00 ave 1711 max 1711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6242.00 ave 6242 max 6242 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 12484.0 ave 12484 max 12484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12484 Ave neighs/atom = 57.266055 Neighbor list builds = 0 Dangerous builds = 0 218 -905.271066450286 eV 2.34048697718608 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02