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 = 3.5200004 3.5200004 3.5200004 Created orthogonal box = (0.0000000 -65.286281 0.0000000) to (23.082186 65.286281 4.9780323) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9047453 6.0731424 4.9780323 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -65.286281 0.0000000) to (23.082186 65.286281 4.9780323) create_atoms CPU = 0.010 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9047453 6.0731424 4.9780323 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -65.286281 0.0000000) to (23.082186 65.286281 4.9780323) create_atoms CPU = 0.009 seconds 690 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 7 35 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1378 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.534 | 5.534 | 5.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6052.2768 0 -6052.2768 13243.451 72 0 -6121.8792 0 -6121.8792 8429.3604 Loop time of 3.78077 on 1 procs for 72 steps with 1378 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 = -6052.27677170291 -6121.87419380595 -6121.87920843866 Force two-norm initial, final = 57.531554 0.24796503 Force max component initial, final = 12.411933 0.048696434 Final line search alpha, max atom move = 1.0000000 0.048696434 Iterations, force evaluations = 72 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7283 | 3.7283 | 3.7283 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.029934 | 0.029934 | 0.029934 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02258 | | | 0.60 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9432.00 ave 9432 max 9432 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: 242448.0 ave 242448 max 242448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 242448 Ave neighs/atom = 175.94194 Neighbor list builds = 0 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.535 | 5.535 | 5.535 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -6121.8792 0 -6121.8792 8429.3604 15003.292 78 0 -6122.2781 0 -6122.2781 72.121074 15073.165 Loop time of 0.222099 on 1 procs for 6 steps with 1378 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 = -6121.87920843866 -6122.27786738414 -6122.27805317306 Force two-norm initial, final = 169.22766 1.3466052 Force max component initial, final = 159.56666 1.1373911 Final line search alpha, max atom move = 0.00044720012 0.00050864142 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21478 | 0.21478 | 0.21478 | 0.0 | 96.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017604 | 0.0017604 | 0.0017604 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005558 | | | 2.50 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9526.00 ave 9526 max 9526 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: 241192.0 ave 241192 max 241192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241192 Ave neighs/atom = 175.03048 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.673 | 5.673 | 5.673 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6122.2781 0 -6122.2781 72.121074 Loop time of 6.284e-06 on 1 procs for 0 steps with 1378 atoms 191.0% 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 | | 6.284e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9534.00 ave 9534 max 9534 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: 240964.0 ave 240964 max 240964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240964 Ave neighs/atom = 174.86502 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.673 | 5.673 | 5.673 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 -6122.2781 -6122.2781 23.069347 131.23232 4.9788422 72.121074 72.121074 61.146425 121.50792 33.70888 2.3007602 380.52962 Loop time of 6.997e-06 on 1 procs for 0 steps with 1378 atoms 271.5% 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 | | 6.997e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9534.00 ave 9534 max 9534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120482.0 ave 120482 max 120482 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 240964.0 ave 240964 max 240964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240964 Ave neighs/atom = 174.86502 Neighbor list builds = 0 Dangerous builds = 0 1378 -6122.27805317306 eV 2.30076016604167 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04