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 -51.488941 0.0000000) to (36.408179 51.488941 5.7209934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7422554 6.9923253 5.7209934 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -51.488941 0.0000000) to (36.408179 51.488941 5.7209934) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7422554 6.9923253 5.7209934 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.488941 0.0000000) to (36.408179 51.488941 5.7209934) create_atoms CPU = 0.001 seconds 650 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 = 12 33 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 0 atoms, new total = 1298 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 = 12 33 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) = 4.643 | 4.643 | 4.643 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4265.4235 0 -4265.4235 11985.396 68 0 -4353.2493 0 -4353.2493 2955.317 Loop time of 4.91546 on 1 procs for 68 steps with 1298 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4265.42348260851 -4353.24591104946 -4353.24929569867 Force two-norm initial, final = 112.37086 0.13997726 Force max component initial, final = 33.739724 0.016489865 Final line search alpha, max atom move = 1.0000000 0.016489865 Iterations, force evaluations = 68 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8978 | 4.8978 | 4.8978 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0084487 | 0.0084487 | 0.0084487 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009213 | | | 0.19 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5065.00 ave 5065 max 5065 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: 70876.0 ave 70876 max 70876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70876 Ave neighs/atom = 54.604006 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 = 12 33 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 : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -4353.2493 0 -4353.2493 2955.317 21449.361 74 0 -4353.4032 0 -4353.4032 0.57321198 21534.816 Loop time of 0.374506 on 1 procs for 6 steps with 1298 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4353.24929569868 -4353.40318295751 -4353.40321486587 Force two-norm initial, final = 76.770121 0.16838476 Force max component initial, final = 67.717410 0.054602390 Final line search alpha, max atom move = 0.0010398820 5.6780044e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37192 | 0.37192 | 0.37192 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034918 | 0.00034918 | 0.00034918 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002233 | | | 0.60 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4534.00 ave 4534 max 4534 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: 70696.0 ave 70696 max 70696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70696 Ave neighs/atom = 54.465331 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 = 12 34 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) = 4.777 | 4.777 | 4.777 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4353.4032 0 -4353.4032 0.57321198 Loop time of 2.318e-06 on 1 procs for 0 steps with 1298 atoms 172.6% 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 | | 2.318e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4534.00 ave 4534 max 4534 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: 70572.0 ave 70572 max 70572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70572 Ave neighs/atom = 54.369800 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 = 12 34 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) = 4.777 | 4.777 | 4.777 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 -4353.4032 -4353.4032 36.402148 103.48167 5.7167699 0.57321198 0.57321198 4.0617099 -0.095701843 -2.2463721 2.6044771 604.02433 Loop time of 2.383e-06 on 1 procs for 0 steps with 1298 atoms 209.8% 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 | | 2.383e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4534.00 ave 4534 max 4534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35286.0 ave 35286 max 35286 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70572.0 ave 70572 max 70572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70572 Ave neighs/atom = 54.369800 Neighbor list builds = 0 Dangerous builds = 0 1298 -4353.40321486587 eV 2.60447714851613 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05