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 = 2.8510002 2.8510002 2.8510002 Created orthogonal box = (0.0000000 -40.720427 0.0000000) to (28.793690 40.720427 4.0319231) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5166573 3.5929789 4.0319231 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.720427 0.0000000) to (28.793690 40.720427 4.0319231) create_atoms CPU = 0.003 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5166573 3.5929789 4.0319231 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.720427 0.0000000) to (28.793690 40.720427 4.0319231) create_atoms CPU = 0.002 seconds 410 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 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, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 812 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_492310898779_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2961.3991 0 -2961.3991 134470.34 54 0 -3466.0811 0 -3466.0811 -820.81615 Loop time of 5.12117 on 1 procs for 54 steps with 812 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 = -2961.3991216969 -3466.077828896 -3466.08109867096 Force two-norm initial, final = 1408.9762 0.16093670 Force max component initial, final = 483.84128 0.018989627 Final line search alpha, max atom move = 1.0000000 0.018989627 Iterations, force evaluations = 54 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0829 | 5.0829 | 5.0829 | 0.0 | 99.25 Neigh | 0.01874 | 0.01874 | 0.01874 | 0.0 | 0.37 Comm | 0.0092011 | 0.0092011 | 0.0092011 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01033 | | | 0.20 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3791.00 ave 3791 max 3791 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: 52288.0 ave 52288 max 52288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52288 Ave neighs/atom = 64.394089 Neighbor list builds = 2 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -3466.0811 0 -3466.0811 -820.81615 9454.7899 57 0 -3466.1172 0 -3466.1172 311.16565 9448.2991 Loop time of 0.291023 on 1 procs for 3 steps with 812 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 = -3466.08109867096 -3466.11396312075 -3466.11718424014 Force two-norm initial, final = 22.488036 3.3990356 Force max component initial, final = 13.568319 2.8055787 Final line search alpha, max atom move = 0.00016556848 0.00046451539 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28892 | 0.28892 | 0.28892 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044857 | 0.00044857 | 0.00044857 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001658 | | | 0.57 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3821.00 ave 3821 max 3821 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: 52292.0 ave 52292 max 52292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52292 Ave neighs/atom = 64.399015 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.671 | 4.671 | 4.671 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3466.1172 0 -3466.1172 311.16565 Loop time of 6.876e-06 on 1 procs for 0 steps with 812 atoms 174.5% 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 | | 6.876e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3821.00 ave 3821 max 3821 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: 52276.0 ave 52276 max 52276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52276 Ave neighs/atom = 64.379310 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.671 | 4.671 | 4.671 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 -3466.1172 -3466.1172 28.749924 81.63409 4.0257368 311.16565 311.16565 233.7155 476.87923 222.90223 2.2948041 454.48782 Loop time of 6.886e-06 on 1 procs for 0 steps with 812 atoms 261.4% 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 | | 6.886e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3821.00 ave 3821 max 3821 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26138.0 ave 26138 max 26138 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52276.0 ave 52276 max 52276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52276 Ave neighs/atom = 64.379310 Neighbor list builds = 0 Dangerous builds = 0 812 -3466.11718424014 eV 2.29480408742808 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05