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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -65.014663 0.0000000) to (32.507331 65.014663 4.0320382) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5010151 4.5010151 4.0320382 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -65.014663 0.0000000) to (32.507331 65.014663 4.0320382) create_atoms CPU = 0.002 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5010151 4.5010151 4.0320382 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -65.014663 0.0000000) to (32.507331 65.014663 4.0320382) create_atoms CPU = 0.001 seconds 522 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 30 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1040 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.041 | 5.041 | 5.041 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3399.3653 0 -3399.3653 8264.2241 72 0 -3486.3335 0 -3486.3335 3515.6308 Loop time of 2.83622 on 1 procs for 72 steps with 1040 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 = -3399.36530892112 -3486.33025903474 -3486.33351635991 Force two-norm initial, final = 37.250083 0.15301491 Force max component initial, final = 6.6845554 0.038275947 Final line search alpha, max atom move = 1.0000000 0.038275947 Iterations, force evaluations = 72 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7707 | 2.7707 | 2.7707 | 0.0 | 97.69 Neigh | 0.023155 | 0.023155 | 0.023155 | 0.0 | 0.82 Comm | 0.024205 | 0.024205 | 0.024205 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0182 | | | 0.64 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8000.00 ave 8000 max 8000 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: 180804.0 ave 180804 max 180804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180804 Ave neighs/atom = 173.85000 Neighbor list builds = 1 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.041 | 5.041 | 5.041 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -3486.3335 0 -3486.3335 3515.6308 17043.048 75 0 -3486.412 0 -3486.412 -3.1779149 17114.316 Loop time of 0.12945 on 1 procs for 3 steps with 1040 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 = -3486.33351635992 -3486.41162154573 -3486.41199668838 Force two-norm initial, final = 64.851125 0.17822516 Force max component initial, final = 39.437270 0.086747529 Final line search alpha, max atom move = 0.00057699192 5.0052623e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12539 | 0.12539 | 0.12539 | 0.0 | 96.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096758 | 0.00096758 | 0.00096758 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003096 | | | 2.39 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8025.00 ave 8025 max 8025 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: 181028.0 ave 181028 max 181028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181028 Ave neighs/atom = 174.06538 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.180 | 5.180 | 5.180 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3486.412 0 -3486.412 -3.1779149 Loop time of 6.384e-06 on 1 procs for 0 steps with 1040 atoms 203.6% 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 | | 6.384e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8025.00 ave 8025 max 8025 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: 180816.0 ave 180816 max 180816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180816 Ave neighs/atom = 173.86154 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.180 | 5.180 | 5.180 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 -3486.412 -3486.412 32.539217 130.25285 4.03799 -3.1779149 -3.1779149 0.055057701 -1.4558448 -8.1329577 2.5180547 344.01472 Loop time of 6.816e-06 on 1 procs for 0 steps with 1040 atoms 264.1% 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 | | 6.816e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8025.00 ave 8025 max 8025 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90408.0 ave 90408 max 90408 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180816.0 ave 180816 max 180816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180816 Ave neighs/atom = 173.86154 Neighbor list builds = 0 Dangerous builds = 0 1040 -3486.41199668838 eV 2.5180547106666 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03