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 = 3.5181211 3.5181211 3.5181211 Created orthogonal box = (0.0000000 -35.877937 0.0000000) to (17.938968 35.877937 3.5181211) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1397619 4.1397619 3.5181211 Created 207 atoms using lattice units in orthogonal box = (0.0000000 -35.877937 0.0000000) to (17.938968 35.877937 3.5181211) create_atoms CPU = 0.002 seconds 207 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1397619 4.1397619 3.5181211 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -35.877937 0.0000000) to (17.938968 35.877937 3.5181211) create_atoms CPU = 0.001 seconds 209 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 15 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 412 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_306032198193_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 4.908 | 4.908 | 4.908 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1681.5288 0 -1681.5288 69091.687 48 0 -1796.7538 0 -1796.7538 -5536.6387 Loop time of 1.80845 on 1 procs for 48 steps with 412 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 = -1681.52879477885 -1796.75199753015 -1796.753756099 Force two-norm initial, final = 318.25719 0.12888884 Force max component initial, final = 111.72836 0.019550974 Final line search alpha, max atom move = 1.0000000 0.019550974 Iterations, force evaluations = 48 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7674 | 1.7674 | 1.7674 | 0.0 | 97.73 Neigh | 0.018719 | 0.018719 | 0.018719 | 0.0 | 1.04 Comm | 0.014344 | 0.014344 | 0.014344 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007976 | | | 0.44 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6583.00 ave 6583 max 6583 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: 133320.0 ave 133320 max 133320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133320 Ave neighs/atom = 323.59223 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.908 | 4.908 | 4.908 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -1796.7538 0 -1796.7538 -5536.6387 4528.6181 50 0 -1796.7801 0 -1796.7801 109.92256 4513.3249 Loop time of 0.0797307 on 1 procs for 2 steps with 412 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 = -1796.75375609899 -1796.77936841402 -1796.78013616457 Force two-norm initial, final = 27.174111 1.4084153 Force max component initial, final = 16.632678 1.2716350 Final line search alpha, max atom move = 0.00029298519 0.00037257022 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07766 | 0.07766 | 0.07766 | 0.0 | 97.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053696 | 0.00053696 | 0.00053696 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001534 | | | 1.92 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6555.00 ave 6555 max 6555 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: 132980.0 ave 132980 max 132980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132980 Ave neighs/atom = 322.76699 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.046 | 5.046 | 5.046 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1796.7801 0 -1796.7801 109.92256 Loop time of 6.315e-06 on 1 procs for 0 steps with 412 atoms 174.2% 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 | | 6.315e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6576.00 ave 6576 max 6576 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: 133336.0 ave 133336 max 133336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133336 Ave neighs/atom = 323.63107 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.046 | 5.046 | 5.046 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 -1796.7801 -1796.7801 17.92227 71.664559 3.5139789 109.92256 109.92256 450.99505 -195.10067 73.873282 2.2471064 186.80239 Loop time of 6.485e-06 on 1 procs for 0 steps with 412 atoms 277.6% 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 | | 6.485e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6576.00 ave 6576 max 6576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66668.0 ave 66668 max 66668 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 133336.0 ave 133336 max 133336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133336 Ave neighs/atom = 323.63107 Neighbor list builds = 0 Dangerous builds = 0 412 -1796.78013616457 eV 2.24710643624411 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02