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 = 2.8147787 2.8147787 2.8147787 Created orthogonal box = (0.0000000 -53.109139 0.0000000) to (26.554569 53.109139 2.8147787) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8787573 3.8787573 2.8147787 Created 356 atoms using lattice units in orthogonal box = (0.0000000 -53.109139 0.0000000) to (26.554569 53.109139 2.8147787) create_atoms CPU = 0.001 seconds 356 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8787573 3.8787573 2.8147787 Created 357 atoms using lattice units in orthogonal box = (0.0000000 -53.109139 0.0000000) to (26.554569 53.109139 2.8147787) create_atoms CPU = 0.000 seconds 357 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 8 29 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 713 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.950 | 4.950 | 4.950 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2712.09 0 -2712.09 80697.568 63 0 -2929.7769 0 -2929.7769 9698.6688 Loop time of 1.18737 on 1 procs for 63 steps with 713 atoms 95.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2712.08997139067 -2929.77412771593 -2929.77688751212 Force two-norm initial, final = 451.60655 0.24390057 Force max component initial, final = 149.81807 0.083188028 Final line search alpha, max atom move = 1.0000000 0.083188028 Iterations, force evaluations = 63 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1645 | 1.1645 | 1.1645 | 0.0 | 98.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014606 | 0.014606 | 0.014606 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008245 | | | 0.69 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7553.00 ave 7553 max 7553 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: 119462.0 ave 119462 max 119462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119462 Ave neighs/atom = 167.54839 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.950 | 4.950 | 4.950 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -2929.7769 0 -2929.7769 9698.6688 7939.3104 72 0 -2930.1116 0 -2930.1116 27.583863 7981.1738 Loop time of 0.16771 on 1 procs for 9 steps with 713 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2929.77688751212 -2930.11137166822 -2930.1116060807 Force two-norm initial, final = 103.35411 0.91522542 Force max component initial, final = 97.744797 0.26153949 Final line search alpha, max atom move = 0.00028819119 7.5373376e-05 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15987 | 0.15987 | 0.15987 | 0.0 | 95.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014393 | 0.0014393 | 0.0014393 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006398 | | | 3.82 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7559.00 ave 7559 max 7559 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: 118588.0 ave 118588 max 118588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118588 Ave neighs/atom = 166.32258 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.088 | 5.088 | 5.088 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2930.1116 0 -2930.1116 27.583863 Loop time of 3.697e-06 on 1 procs for 0 steps with 713 atoms 162.3% 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 | | 3.697e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7559.00 ave 7559 max 7559 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: 118472.0 ave 118472 max 118472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118472 Ave neighs/atom = 166.15989 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.088 | 5.088 | 5.088 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 -2930.1116 -2930.1116 26.554559 107.01055 2.8086724 27.583863 27.583863 -1.6324655 31.995347 52.388707 2.3018768 440.92454 Loop time of 3.774e-06 on 1 procs for 0 steps with 713 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 | | 3.774e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7559.00 ave 7559 max 7559 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59236.0 ave 59236 max 59236 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118472.0 ave 118472 max 118472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118472 Ave neighs/atom = 166.15989 Neighbor list builds = 0 Dangerous builds = 0 713 -2930.1116060807 eV 2.30187675050906 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02