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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -43.560732 0.0000000) to (14.519070 43.560732 3.5213917) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2703147 4.2703147 3.5213917 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -43.560732 0.0000000) to (14.519070 43.560732 3.5213917) create_atoms CPU = 0.002 seconds 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2703147 4.2703147 3.5213917 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -43.560732 0.0000000) to (14.519070 43.560732 3.5213917) create_atoms CPU = 0.001 seconds 206 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 27 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 404 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_008996216289_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.463 | 4.463 | 4.463 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1774.6306 0 -1774.6306 9192.0979 62 0 -1788.2567 0 -1788.2567 -5688.1566 Loop time of 5.93145 on 1 procs for 62 steps with 404 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 = -1774.63056608475 -1788.25538772829 -1788.25669790579 Force two-norm initial, final = 37.570706 0.12234532 Force max component initial, final = 10.160049 0.023518401 Final line search alpha, max atom move = 1.0000000 0.023518401 Iterations, force evaluations = 62 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9052 | 5.9052 | 5.9052 | 0.0 | 99.56 Neigh | 0.0064747 | 0.0064747 | 0.0064747 | 0.0 | 0.11 Comm | 0.011226 | 0.011226 | 0.011226 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008529 | | | 0.14 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3971.00 ave 3971 max 3971 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: 35348.0 ave 35348 max 35348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35348 Ave neighs/atom = 87.495050 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.464 | 4.464 | 4.464 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -1788.2567 0 -1788.2567 -5688.1566 4454.2881 65 0 -1788.279 0 -1788.279 -1017.4128 4442.9356 Loop time of 0.343195 on 1 procs for 3 steps with 404 atoms 92.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1788.25669790579 -1788.27760813371 -1788.27904334816 Force two-norm initial, final = 20.846009 0.14189273 Force max component initial, final = 17.814838 0.035159195 Final line search alpha, max atom move = 0.00033351522 1.1726126e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34066 | 0.34066 | 0.34066 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057831 | 0.00057831 | 0.00057831 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001954 | | | 0.57 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026.00 ave 4026 max 4026 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: 35320.0 ave 35320 max 35320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35320 Ave neighs/atom = 87.425743 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.602 | 4.602 | 4.602 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1788.279 0 -1788.279 -1017.4128 Loop time of 8.83e-06 on 1 procs for 0 steps with 404 atoms 158.6% 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 | | 8.83e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026.00 ave 4026 max 4026 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: 35368.0 ave 35368 max 35368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35368 Ave neighs/atom = 87.544554 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.602 | 4.602 | 4.602 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 -1788.279 -1788.279 14.517372 87.121464 3.5128278 -1017.4128 -1017.4128 -2.5391792 -3051.1105 1.4113455 2.3076497 175.82364 Loop time of 1.0464e-05 on 1 procs for 0 steps with 404 atoms 210.2% 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 | | 1.046e-05 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026.00 ave 4026 max 4026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17684.0 ave 17684 max 17684 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35368.0 ave 35368 max 35368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35368 Ave neighs/atom = 87.544554 Neighbor list builds = 0 Dangerous builds = 0 404 -1788.27904334816 eV 2.30764969083528 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06