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 = 3.5162328 3.5162328 3.5162328 Created orthogonal box = (0.0000000 -45.980710 0.0000000) to (21.675515 45.980710 4.9727041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5632662 5.6467539 4.9727041 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -45.980710 0.0000000) to (21.675515 45.980710 4.9727041) create_atoms CPU = 0.001 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5632662 5.6467539 4.9727041 Created 462 atoms using lattice units in orthogonal box = (0.0000000 -45.980710 0.0000000) to (21.675515 45.980710 4.9727041) create_atoms CPU = 0.001 seconds 462 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 5 21 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 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 912 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_047308317761_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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 5 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.425 | 5.425 | 5.425 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4319.5232 0 -4319.5232 58102.545 18 0 -4428.3295 0 -4428.3295 10163.619 Loop time of 0.480111 on 1 procs for 18 steps with 912 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 = -4319.52322936916 -4428.32558058542 -4428.32948294756 Force two-norm initial, final = 225.45077 0.17757058 Force max component initial, final = 38.513815 0.018099340 Final line search alpha, max atom move = 1.0000000 0.018099340 Iterations, force evaluations = 18 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47598 | 0.47598 | 0.47598 | 0.0 | 99.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023708 | 0.0023708 | 0.0023708 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001757 | | | 0.37 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8052.00 ave 8052 max 8052 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: 228264.0 ave 228264 max 228264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228264 Ave neighs/atom = 250.28947 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 5 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.424 | 5.424 | 5.424 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -4428.3295 0 -4428.3295 10163.619 9912.1463 24 0 -4428.632 0 -4428.632 105.74279 9967.0282 Loop time of 0.110543 on 1 procs for 6 steps with 912 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 = -4428.32948294755 -4428.63183936937 -4428.63195135876 Force two-norm initial, final = 125.56271 1.4893671 Force max component initial, final = 109.48313 1.0432998 Final line search alpha, max atom move = 0.00051695004 0.00053933390 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10797 | 0.10797 | 0.10797 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049563 | 0.00049563 | 0.00049563 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00208 | | | 1.88 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7910.00 ave 7910 max 7910 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: 229400.0 ave 229400 max 229400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229400 Ave neighs/atom = 251.53509 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 5 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.562 | 5.562 | 5.562 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4428.632 0 -4428.632 105.74279 Loop time of 2.027e-06 on 1 procs for 0 steps with 912 atoms 148.0% 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 | | 2.027e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7912.00 ave 7912 max 7912 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: 228832.0 ave 228832 max 228832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228832 Ave neighs/atom = 250.91228 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 5 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.562 | 5.562 | 5.562 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 -4428.632 -4428.632 21.70412 92.420778 4.9688272 105.74279 105.74279 -12.185664 161.83676 167.57726 2.25487 360.77762 Loop time of 2.253e-06 on 1 procs for 0 steps with 912 atoms 221.9% 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 | | 2.253e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7912.00 ave 7912 max 7912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114416.0 ave 114416 max 114416 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 228832.0 ave 228832 max 228832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228832 Ave neighs/atom = 250.91228 Neighbor list builds = 0 Dangerous builds = 0 912 -4428.63195135876 eV 2.25487002080665 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01