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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -41.149744 0.0000000) to (19.396692 41.149744 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0835141 5.0530909 4.4499063 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -41.149744 0.0000000) to (19.396692 41.149744 4.4499063) create_atoms CPU = 0.002 seconds 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0835141 5.0530909 4.4499063 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -41.149744 0.0000000) to (19.396692 41.149744 4.4499063) create_atoms CPU = 0.002 seconds 230 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 29 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 452 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.448 | 4.448 | 4.448 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3040.535 0 -3040.535 5123.9834 45 0 -3058.5267 0 -3058.5267 -10909.174 Loop time of 2.20492 on 1 procs for 45 steps with 452 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3040.53502400359 -3058.52387077237 -3058.52674631633 Force two-norm initial, final = 16.654028 0.15913822 Force max component initial, final = 4.4871714 0.025341876 Final line search alpha, max atom move = 1.0000000 0.025341876 Iterations, force evaluations = 45 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1896 | 2.1896 | 2.1896 | 0.0 | 99.30 Neigh | 0.0043143 | 0.0043143 | 0.0043143 | 0.0 | 0.20 Comm | 0.0052576 | 0.0052576 | 0.0052576 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005769 | | | 0.26 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2458.00 ave 2458 max 2458 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: 25928.0 ave 25928 max 25928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25928 Ave neighs/atom = 57.362832 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.448 | 4.448 | 4.448 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -3058.5267 0 -3058.5267 -10909.174 7103.5538 48 0 -3058.5849 0 -3058.5849 -3415.6641 7082.997 Loop time of 0.166122 on 1 procs for 3 steps with 452 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3058.52674631633 -3058.58457202587 -3058.58491194668 Force two-norm initial, final = 54.632085 0.17200739 Force max component initial, final = 44.103057 0.029574619 Final line search alpha, max atom move = 0.00044700801 1.3220092e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16452 | 0.16452 | 0.16452 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033427 | 0.00033427 | 0.00033427 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001266 | | | 0.76 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2467.00 ave 2467 max 2467 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: 25928.0 ave 25928 max 25928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25928 Ave neighs/atom = 57.362832 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3058.5849 0 -3058.5849 -3415.6641 Loop time of 6.746e-06 on 1 procs for 0 steps with 452 atoms 177.9% 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 | | 6.746e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2467.00 ave 2467 max 2467 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: 25928.0 ave 25928 max 25928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25928 Ave neighs/atom = 57.362832 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 7 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.586 | 4.586 | 4.586 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 -3058.5849 -3058.5849 19.359667 82.299488 4.4455147 -3415.6641 -3415.6641 -1.7581124 -10240.821 -4.4126692 2.3962043 371.24155 Loop time of 6.636e-06 on 1 procs for 0 steps with 452 atoms 271.2% 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 | | 6.636e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2467.00 ave 2467 max 2467 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12964.0 ave 12964 max 12964 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25928.0 ave 25928 max 25928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25928 Ave neighs/atom = 57.362832 Neighbor list builds = 0 Dangerous builds = 0 452 -3058.58491194668 eV 2.39620425523589 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02