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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -61.087540 0.0000000) to (43.192553 61.087540 5.7209934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8198768 6.9656616 5.7209934 Created 915 atoms using lattice units in orthogonal box = (0.0000000 -61.087540 0.0000000) to (43.192553 61.087540 5.7209934) create_atoms CPU = 0.002 seconds 915 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8198768 6.9656616 5.7209934 Created 915 atoms using lattice units in orthogonal box = (0.0000000 -61.087540 0.0000000) to (43.192553 61.087540 5.7209934) create_atoms CPU = 0.002 seconds 915 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 40 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 1807 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.755 | 4.755 | 4.755 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6039.9426 0 -6039.9426 -17.602854 44 0 -6058.4982 0 -6058.4982 -4298.9256 Loop time of 3.88565 on 1 procs for 44 steps with 1807 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 = -6039.94257695391 -6058.49356781593 -6058.49819791105 Force two-norm initial, final = 18.313912 0.15060729 Force max component initial, final = 4.4367939 0.013369860 Final line search alpha, max atom move = 1.0000000 0.013369860 Iterations, force evaluations = 44 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8754 | 3.8754 | 3.8754 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0038289 | 0.0038289 | 0.0038289 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006415 | | | 0.17 Nlocal: 1807.00 ave 1807 max 1807 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5828.00 ave 5828 max 5828 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: 97270.0 ave 97270 max 97270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97270 Ave neighs/atom = 53.829552 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.137 | 5.137 | 5.137 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -6058.4982 0 -6058.4982 -4298.9256 30189.989 47 0 -6058.6387 0 -6058.6387 -1225.6919 30061.708 Loop time of 0.246321 on 1 procs for 3 steps with 1807 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 = -6058.49819791105 -6058.63648369112 -6058.63870796068 Force two-norm initial, final = 93.029599 2.1778350 Force max component initial, final = 69.433765 1.8919696 Final line search alpha, max atom move = 9.8920627e-05 0.00018715482 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24481 | 0.24481 | 0.24481 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022686 | 0.00022686 | 0.00022686 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001287 | | | 0.52 Nlocal: 1807.00 ave 1807 max 1807 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5888.00 ave 5888 max 5888 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: 98186.0 ave 98186 max 98186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98186 Ave neighs/atom = 54.336469 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.275 | 5.275 | 5.275 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6058.6387 0 -6058.6387 -1225.6919 Loop time of 1.922e-06 on 1 procs for 0 steps with 1807 atoms 156.1% 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 | | 1.922e-06 | | |100.00 Nlocal: 1807.00 ave 1807 max 1807 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5894.00 ave 5894 max 5894 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: 98194.0 ave 98194 max 98194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98194 Ave neighs/atom = 54.340897 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.275 | 5.275 | 5.275 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 -6058.6387 -6058.6387 43.109845 122.17508 5.7076136 -1225.6919 -1225.6919 100.64181 -3721.0824 -56.635108 2.6285333 848.87718 Loop time of 1.758e-06 on 1 procs for 0 steps with 1807 atoms 170.6% 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 | | 1.758e-06 | | |100.00 Nlocal: 1807.00 ave 1807 max 1807 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5894.00 ave 5894 max 5894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49097.0 ave 49097 max 49097 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 98194.0 ave 98194 max 98194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98194 Ave neighs/atom = 54.340897 Neighbor list builds = 0 Dangerous builds = 0 1807 -6058.63870796068 eV 2.62853329354798 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04