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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -69.084382 0.0000000) to (39.885887 69.084382 6.2546061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8848030 5.2851440 6.2546061 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -69.084382 0.0000000) to (39.885887 69.084382 6.2546061) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8848030 5.2851440 6.2546061 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -69.084382 0.0000000) to (39.885887 69.084382 6.2546061) create_atoms CPU = 0.003 seconds 1465 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 = 13 43 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 0 atoms, new total = 2928 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_924736622203_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 = 13 43 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) = 5.795 | 5.795 | 5.795 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11804.647 0 -11804.647 40323.577 857 0 -12455.026 0 -12455.026 6013.7308 Loop time of 324.706 on 1 procs for 857 steps with 2928 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 = -11804.646912284 -12455.0136312611 -12455.0255735674 Force two-norm initial, final = 704.47861 0.42246660 Force max component initial, final = 175.69453 0.11172389 Final line search alpha, max atom move = 0.97979458 0.10946647 Iterations, force evaluations = 857 1571 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 323.63 | 323.63 | 323.63 | 0.0 | 99.67 Neigh | 0.60846 | 0.60846 | 0.60846 | 0.0 | 0.19 Comm | 0.21773 | 0.21773 | 0.21773 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2451 | | | 0.08 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10098.0 ave 10098 max 10098 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: 301374.0 ave 301374 max 301374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 301374 Ave neighs/atom = 102.92828 Neighbor list builds = 29 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 = 13 43 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 : 857 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.179 | 6.179 | 6.179 Mbytes Step Temp E_pair E_mol TotEng Press Volume 857 0 -12455.026 0 -12455.026 6013.7308 34469.032 865 0 -12456.42 0 -12456.42 -33.32168 34589.948 Loop time of 2.52585 on 1 procs for 8 steps with 2928 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 = -12455.0255735674 -12456.4201858235 -12456.4202247492 Force two-norm initial, final = 380.20896 1.4919746 Force max component initial, final = 354.32176 0.79572944 Final line search alpha, max atom move = 0.00080476168 0.00064037256 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5191 | 2.5191 | 2.5191 | 0.0 | 99.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089367 | 0.00089367 | 0.00089367 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005857 | | | 0.23 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10081.0 ave 10081 max 10081 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: 301816.0 ave 301816 max 301816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 301816 Ave neighs/atom = 103.07923 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 = 13 43 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) = 6.317 | 6.317 | 6.317 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12456.42 0 -12456.42 -33.32168 Loop time of 2.172e-06 on 1 procs for 0 steps with 2928 atoms 184.2% 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 | | 2.172e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10069.0 ave 10069 max 10069 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: 301832.0 ave 301832 max 301832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 301832 Ave neighs/atom = 103.08470 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 = 13 43 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) = 6.317 | 6.317 | 6.317 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 -12456.42 -12456.42 39.722312 138.29694 6.2965522 -33.32168 -33.32168 -31.485666 -36.891693 -31.587682 2.2666921 4518.7725 Loop time of 1.98e-06 on 1 procs for 0 steps with 2928 atoms 252.5% 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 | | 1.98e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10069.0 ave 10069 max 10069 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 150916.0 ave 150916 max 150916 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 301832.0 ave 301832 max 301832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 301832 Ave neighs/atom = 103.08470 Neighbor list builds = 0 Dangerous builds = 0 2928 -12456.4202247492 eV 2.26669212633653 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:05:28