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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -41.519769 0.0000000) to (35.953649 41.519769 7.0510907) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4532191 6.3870305 7.0510907 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.519769 0.0000000) to (35.953649 41.519769 7.0510907) create_atoms CPU = 0.001 seconds 629 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4532191 6.3870305 7.0510907 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -41.519769 0.0000000) to (35.953649 41.519769 7.0510907) create_atoms CPU = 0.001 seconds 630 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 27 atoms, new total = 1232 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4117.3202 0 -4117.3202 100.65396 28 0 -4129.9734 0 -4129.9734 -6037.8 Loop time of 1.65882 on 1 procs for 28 steps with 1232 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 = -4117.32018384337 -4129.96958141971 -4129.97337804261 Force two-norm initial, final = 16.085584 0.14299074 Force max component initial, final = 3.6917682 0.026322546 Final line search alpha, max atom move = 1.0000000 0.026322546 Iterations, force evaluations = 28 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6541 | 1.6541 | 1.6541 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017327 | 0.0017327 | 0.0017327 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002966 | | | 0.18 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3783.00 ave 3783 max 3783 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: 65880.0 ave 65880 max 65880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65880 Ave neighs/atom = 53.474026 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -4129.9734 0 -4129.9734 -6037.8 21051.556 32 0 -4130.1768 0 -4130.1768 -865.49049 20941.921 Loop time of 0.194117 on 1 procs for 4 steps with 1232 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 = -4129.97337804262 -4130.17293487679 -4130.17678562333 Force two-norm initial, final = 108.34161 0.42423616 Force max component initial, final = 82.085432 0.26071890 Final line search alpha, max atom move = 0.00017427640 4.5437152e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1929 | 0.1929 | 0.1929 | 0.0 | 99.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017668 | 0.00017668 | 0.00017668 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001043 | | | 0.54 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3793.00 ave 3793 max 3793 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: 66020.0 ave 66020 max 66020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66020 Ave neighs/atom = 53.587662 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.738 | 4.738 | 4.738 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4130.1768 0 -4130.1768 -865.49049 Loop time of 1.617e-06 on 1 procs for 0 steps with 1232 atoms 185.5% 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 | | 1.617e-06 | | |100.00 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3803.00 ave 3803 max 3803 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: 66068.0 ave 66068 max 66068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66068 Ave neighs/atom = 53.626623 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.738 | 4.738 | 4.738 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 -4130.1768 -4130.1768 35.899813 83.039538 7.0248881 -865.49049 -865.49049 -19.916617 -2559.1856 -17.369231 2.5479859 1048.6478 Loop time of 1.729e-06 on 1 procs for 0 steps with 1232 atoms 231.3% 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 | | 1.729e-06 | | |100.00 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3803.00 ave 3803 max 3803 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33034.0 ave 33034 max 33034 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 66068.0 ave 66068 max 66068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66068 Ave neighs/atom = 53.626623 Neighbor list builds = 0 Dangerous builds = 0 1232 -4130.17678562333 eV 2.54798593554876 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02