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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -43.414633 0.0000000) to (15.349391 43.414633 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6550387 4.5699614 4.9800000 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -43.414633 0.0000000) to (15.349391 43.414633 4.9800000) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6550387 4.5699614 4.9800000 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.414633 0.0000000) to (15.349391 43.414633 4.9800000) create_atoms CPU = 0.001 seconds 306 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 604 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_663355627503_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.532 | 4.532 | 4.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2565.1036 0 -2565.1036 38093.084 69 0 -2676.4263 0 -2676.4263 -3077.0978 Loop time of 5.37988 on 1 procs for 69 steps with 604 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 = -2565.10362940127 -2676.42385260723 -2676.42633566007 Force two-norm initial, final = 247.54012 0.16922577 Force max component initial, final = 82.063689 0.023808774 Final line search alpha, max atom move = 1.0000000 0.023808774 Iterations, force evaluations = 69 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3607 | 5.3607 | 5.3607 | 0.0 | 99.64 Neigh | 0.0053826 | 0.0053826 | 0.0053826 | 0.0 | 0.10 Comm | 0.0076555 | 0.0076555 | 0.0076555 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006154 | | | 0.11 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4479.00 ave 4479 max 4479 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: 80680.0 ave 80680 max 80680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80680 Ave neighs/atom = 133.57616 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.535 | 4.535 | 4.535 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -2676.4263 0 -2676.4263 -3077.0978 6637.2261 71 0 -2676.4421 0 -2676.4421 -0.80329597 6626.071 Loop time of 0.198534 on 1 procs for 2 steps with 604 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 = -2676.42633566007 -2676.4403395837 -2676.44207323587 Force two-norm initial, final = 24.010163 0.44216913 Force max component initial, final = 18.969517 0.33126390 Final line search alpha, max atom move = 0.00019703764 6.5271459e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19753 | 0.19753 | 0.19753 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019725 | 0.00019725 | 0.00019725 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008024 | | | 0.40 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4700.00 ave 4700 max 4700 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: 80560.0 ave 80560 max 80560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80560 Ave neighs/atom = 133.37748 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.673 | 4.673 | 4.673 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2676.4421 0 -2676.4421 -0.80329597 Loop time of 2.306e-06 on 1 procs for 0 steps with 604 atoms 173.5% 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 | | 2.306e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4700.00 ave 4700 max 4700 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: 80592.0 ave 80592 max 80592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80592 Ave neighs/atom = 133.43046 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.673 | 4.673 | 4.673 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 -2676.4421 -2676.4421 15.330239 86.770855 4.9811918 -0.80329597 -0.80329597 51.506707 -80.045354 26.12876 2.3331559 276.93589 Loop time of 2.419e-06 on 1 procs for 0 steps with 604 atoms 372.1% 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 | | 2.419e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4700.00 ave 4700 max 4700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40296.0 ave 40296 max 40296 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80592.0 ave 80592 max 80592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80592 Ave neighs/atom = 133.43046 Neighbor list builds = 0 Dangerous builds = 0 604 -2676.44207323587 eV 2.3331558892895 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05