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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -53.115253 0.0000000) to (37.558156 53.115253 5.7275650) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9875638 6.7938114 5.7275650 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -53.115253 0.0000000) to (37.558156 53.115253 5.7275650) create_atoms CPU = 0.006 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9875638 6.7938114 5.7275650 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -53.115253 0.0000000) to (37.558156 53.115253 5.7275650) create_atoms CPU = 0.005 seconds 690 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 28 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1372 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.071 | 5.071 | 5.071 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4487.5767 0 -4487.5767 13709.948 53 0 -4603.6773 0 -4603.6773 3347.9062 Loop time of 1.55623 on 1 procs for 53 steps with 1372 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 = -4487.57666600171 -4603.67333509077 -4603.67727803314 Force two-norm initial, final = 115.71517 0.14461241 Force max component initial, final = 21.294075 0.040089334 Final line search alpha, max atom move = 1.0000000 0.040089334 Iterations, force evaluations = 53 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4746 | 1.4746 | 1.4746 | 0.0 | 94.75 Neigh | 0.049574 | 0.049574 | 0.049574 | 0.0 | 3.19 Comm | 0.016305 | 0.016305 | 0.016305 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01577 | | | 1.01 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6937.00 ave 6937 max 6937 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: 179020.0 ave 179020 max 179020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179020 Ave neighs/atom = 130.48105 Neighbor list builds = 2 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.071 | 5.071 | 5.071 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -4603.6773 0 -4603.6773 3347.9062 22851.964 60 0 -4603.9465 0 -4603.9465 -3.6763805 22950.871 Loop time of 0.152208 on 1 procs for 7 steps with 1372 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 = -4603.67727803313 -4603.94426105211 -4603.94654780675 Force two-norm initial, final = 98.437595 0.26471631 Force max component initial, final = 91.235502 0.10251870 Final line search alpha, max atom move = 0.00019496389 1.9987444e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14566 | 0.14566 | 0.14566 | 0.0 | 95.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00129 | 0.00129 | 0.00129 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005263 | | | 3.46 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6930.00 ave 6930 max 6930 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: 179556.0 ave 179556 max 179556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179556 Ave neighs/atom = 130.87172 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.208 | 5.208 | 5.208 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4603.9465 0 -4603.9465 -3.6763805 Loop time of 6.335e-06 on 1 procs for 0 steps with 1372 atoms 221.0% 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 | | 6.335e-06 | | |100.00 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6930.00 ave 6930 max 6930 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: 179108.0 ave 179108 max 179108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179108 Ave neighs/atom = 130.54519 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.208 | 5.208 | 5.208 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 -4603.9465 -4603.9465 37.507337 106.93357 5.7222767 -3.6763805 -3.6763805 0.40671035 -4.2857357 -7.150116 2.6414644 1001.4416 Loop time of 7.497e-06 on 1 procs for 0 steps with 1372 atoms 280.1% 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 | | 7.497e-06 | | |100.00 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6930.00 ave 6930 max 6930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89554.0 ave 89554 max 89554 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179108.0 ave 179108 max 179108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179108 Ave neighs/atom = 130.54519 Neighbor list builds = 0 Dangerous builds = 0 1372 -4603.94654780675 eV 2.64146444870388 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02