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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -31.980817 0.0000000) to (15.665936 31.980817 7.0060194) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1775828 3.8373549 4.6706796 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -31.980817 0.0000000) to (15.665936 31.980817 7.0060194) create_atoms CPU = 0.001 seconds 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1775828 3.8373549 4.6706796 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -31.980817 0.0000000) to (15.665936 31.980817 7.0060194) create_atoms CPU = 0.000 seconds 306 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 24 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 24 atoms, new total = 588 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.845 | 4.845 | 4.845 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2482.7892 0 -2482.7892 -6923.288 66 0 -2499.9757 0 -2499.9757 -24403.207 Loop time of 4.60904 on 1 procs for 66 steps with 588 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 = -2482.78915178972 -2499.97386823742 -2499.97568253763 Force two-norm initial, final = 17.977287 0.15570801 Force max component initial, final = 4.0612077 0.018094555 Final line search alpha, max atom move = 1.0000000 0.018094555 Iterations, force evaluations = 66 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6027 | 4.6027 | 4.6027 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028462 | 0.0028462 | 0.0028462 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003524 | | | 0.08 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2518.00 ave 2518 max 2518 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: 33336.0 ave 33336 max 33336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33336 Ave neighs/atom = 56.693878 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.844 | 4.844 | 4.844 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -2499.9757 0 -2499.9757 -24403.207 7020.1636 75 0 -2500.6783 0 -2500.6783 -3190.4123 6930.8134 Loop time of 0.41444 on 1 procs for 9 steps with 588 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 = -2499.97568253763 -2500.67747519473 -2500.67826490249 Force two-norm initial, final = 151.89721 0.63525963 Force max component initial, final = 114.13877 0.098337435 Final line search alpha, max atom move = 0.00023721520 2.3327134e-05 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4131 | 0.4131 | 0.4131 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021529 | 0.00021529 | 0.00021529 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001126 | | | 0.27 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2298.00 ave 2298 max 2298 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: 33696.0 ave 33696 max 33696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33696 Ave neighs/atom = 57.306122 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2500.6783 0 -2500.6783 -3190.4123 Loop time of 1.68e-06 on 1 procs for 0 steps with 588 atoms 178.6% 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 | | 1.68e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2329.00 ave 2329 max 2329 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: 33744.0 ave 33744 max 33744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33744 Ave neighs/atom = 57.387755 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.982 | 4.982 | 4.982 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 -2500.6783 -2500.6783 15.539548 63.961635 6.973106 -3190.4123 -3190.4123 7.9266312 -9556.5379 -22.625592 2.3972161 477.88313 Loop time of 1.529e-06 on 1 procs for 0 steps with 588 atoms 261.6% 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 | | 1.529e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2329.00 ave 2329 max 2329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16872.0 ave 16872 max 16872 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33744.0 ave 33744 max 33744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33744 Ave neighs/atom = 57.387755 Neighbor list builds = 0 Dangerous builds = 0 588 -2500.67826490249 eV 2.39721606749095 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05