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 -50.739885 0.0000000) to (25.368369 50.739885 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5125434 3.5125434 3.1465590 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -50.739885 0.0000000) to (25.368369 50.739885 3.1465590) create_atoms CPU = 0.002 seconds 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5125434 3.5125434 3.1465590 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -50.739885 0.0000000) to (25.368369 50.739885 3.1465590) create_atoms CPU = 0.001 seconds 261 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 = 9 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 516 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 = 9 35 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) = 4.458 | 4.458 | 4.458 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3484.0815 0 -3484.0815 1102.9584 20 0 -3499.4282 0 -3499.4282 -12111.677 Loop time of 0.965315 on 1 procs for 20 steps with 516 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 = -3484.08149517324 -3499.42537275081 -3499.42819747423 Force two-norm initial, final = 18.116584 0.15239693 Force max component initial, final = 5.8622120 0.024522801 Final line search alpha, max atom move = 1.0000000 0.024522801 Iterations, force evaluations = 20 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96007 | 0.96007 | 0.96007 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024975 | 0.0024975 | 0.0024975 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002743 | | | 0.28 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3247.00 ave 3247 max 3247 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: 29556.0 ave 29556 max 29556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29556 Ave neighs/atom = 57.279070 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 35 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 : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -3499.4282 0 -3499.4282 -12111.677 8100.4268 24 0 -3499.5742 0 -3499.5742 -986.59907 8065.8933 Loop time of 0.253377 on 1 procs for 4 steps with 516 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3499.42819747423 -3499.57392317167 -3499.57422017045 Force two-norm initial, final = 94.264400 0.18633976 Force max component initial, final = 74.322578 0.032331191 Final line search alpha, max atom move = 0.00040557896 1.3112851e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25056 | 0.25056 | 0.25056 | 0.0 | 98.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055543 | 0.00055543 | 0.00055543 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002263 | | | 0.89 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3267.00 ave 3267 max 3267 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: 29764.0 ave 29764 max 29764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29764 Ave neighs/atom = 57.682171 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 = 9 35 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) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3499.5742 0 -3499.5742 -986.59907 Loop time of 8.911e-06 on 1 procs for 0 steps with 516 atoms 190.8% 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 | | 8.911e-06 | | |100.00 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3275.00 ave 3275 max 3275 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: 29768.0 ave 29768 max 29768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29768 Ave neighs/atom = 57.689922 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 = 9 35 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) = 4.597 | 4.597 | 4.597 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 -3499.5742 -3499.5742 25.327713 101.47977 3.138174 -986.59907 -986.59907 -6.1186587 -2950.963 -2.7155807 2.4319638 152.89204 Loop time of 1.0785e-05 on 1 procs for 0 steps with 516 atoms 231.8% 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 | | 1.079e-05 | | |100.00 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3275.00 ave 3275 max 3275 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14884.0 ave 14884 max 14884 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29768.0 ave 29768 max 29768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29768 Ave neighs/atom = 57.689922 Neighbor list builds = 0 Dangerous builds = 0 516 -3499.57422017045 eV 2.4319638235988 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01