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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -56.762032 0.0000000) to (28.379256 56.762032 3.5200135) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8026434 4.8026434 3.5200135 Created 521 atoms using lattice units in orthogonal box = (0.0000000 -56.762032 0.0000000) to (28.379256 56.762032 3.5200135) create_atoms CPU = 0.001 seconds 521 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8026434 4.8026434 3.5200135 Created 521 atoms using lattice units in orthogonal box = (0.0000000 -56.762032 0.0000000) to (28.379256 56.762032 3.5200135) create_atoms CPU = 0.001 seconds 521 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 27 1 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1036 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.451 | 5.451 | 5.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4571.9958 0 -4571.9958 5290.6575 54 0 -4592.5839 0 -4592.5839 2297.7164 Loop time of 1.07287 on 1 procs for 54 steps with 1036 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 = -4571.99579243463 -4592.57947785809 -4592.58394908848 Force two-norm initial, final = 18.468654 0.22462053 Force max component initial, final = 4.6625801 0.039843525 Final line search alpha, max atom move = 1.0000000 0.039843525 Iterations, force evaluations = 54 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0413 | 1.0413 | 1.0413 | 0.0 | 97.06 Neigh | 0.015198 | 0.015198 | 0.015198 | 0.0 | 1.42 Comm | 0.0098702 | 0.0098702 | 0.0098702 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006476 | | | 0.60 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10346.0 ave 10346 max 10346 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: 232058.0 ave 232058 max 232058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232058 Ave neighs/atom = 223.99421 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.452 | 5.452 | 5.452 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -4592.5839 0 -4592.5839 2297.7164 11340.528 57 0 -4592.6072 0 -4592.6072 1678.4253 11344.405 Loop time of 0.0689658 on 1 procs for 3 steps with 1036 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 = -4592.58394908848 -4592.60719256329 -4592.60719785191 Force two-norm initial, final = 19.584340 0.26960527 Force max component initial, final = 15.244878 0.099551537 Final line search alpha, max atom move = 0.0031620617 0.00031478810 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.066755 | 0.066755 | 0.066755 | 0.0 | 96.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004473 | 0.0004473 | 0.0004473 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001764 | | | 2.56 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10370.0 ave 10370 max 10370 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: 231646.0 ave 231646 max 231646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231646 Ave neighs/atom = 223.59653 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.590 | 5.590 | 5.590 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4592.6072 0 -4592.6072 1678.4253 Loop time of 1.921e-06 on 1 procs for 0 steps with 1036 atoms 156.2% 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 | | 1.921e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10370.0 ave 10370 max 10370 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: 231618.0 ave 231618 max 231618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231618 Ave neighs/atom = 223.56950 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.590 | 5.590 | 5.590 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 -4592.6072 -4592.6072 28.336863 113.52406 3.5264849 1678.4253 1678.4253 -14.038715 5061.3414 -12.026765 2.2173593 419.99889 Loop time of 2.006e-06 on 1 procs for 0 steps with 1036 atoms 199.4% 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 | | 2.006e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10370.0 ave 10370 max 10370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115809.0 ave 115809 max 115809 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 231618.0 ave 231618 max 231618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231618 Ave neighs/atom = 223.56950 Neighbor list builds = 0 Dangerous builds = 0 1036 -4564.36438563686 eV 2.21735932801862 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01