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 = 3.4524642 3.4524642 3.4524642 Created orthogonal box = (0.0000000 -69.221692 0.0000000) to (39.965162 69.221692 5.9798434) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3684547 5.5101844 5.9798434 Created 1607 atoms using lattice units in orthogonal box = (0.0000000 -69.221692 0.0000000) to (39.965162 69.221692 5.9798434) create_atoms CPU = 0.010 seconds 1607 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3684547 5.5101844 5.9798434 Created 1609 atoms using lattice units in orthogonal box = (0.0000000 -69.221692 0.0000000) to (39.965162 69.221692 5.9798434) create_atoms CPU = 0.010 seconds 1609 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 11 35 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 3213 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 11 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 11.35 | 11.35 | 11.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13830.107 0 -13830.107 41507.779 94 0 -14430.209 0 -14430.209 13771.837 Loop time of 10.6585 on 1 procs for 94 steps with 3213 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 = -13830.1073103044 -14430.195038581 -14430.2087145026 Force two-norm initial, final = 655.66224 0.46056037 Force max component initial, final = 160.50030 0.17657142 Final line search alpha, max atom move = 0.96729382 0.17079644 Iterations, force evaluations = 94 153 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.203 | 10.203 | 10.203 | 0.0 | 95.72 Neigh | 0.33746 | 0.33746 | 0.33746 | 0.0 | 3.17 Comm | 0.063644 | 0.063644 | 0.063644 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05474 | | | 0.51 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15121.0 ave 15121 max 15121 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: 640362.0 ave 640362 max 640362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 640362 Ave neighs/atom = 199.30345 Neighbor list builds = 4 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 11 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.35 | 11.35 | 11.35 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -14430.209 0 -14430.209 13771.837 33085.949 99 0 -14431.137 0 -14431.137 -180.0351 33197.853 Loop time of 0.457093 on 1 procs for 5 steps with 3213 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 = -14430.2087145026 -14431.1288459196 -14431.1371525456 Force two-norm initial, final = 543.34076 9.7480594 Force max component initial, final = 471.53010 7.5499291 Final line search alpha, max atom move = 1.5848736e-05 0.00011965683 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44627 | 0.44627 | 0.44627 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024863 | 0.0024863 | 0.0024863 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008339 | | | 1.82 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15132.0 ave 15132 max 15132 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: 640566.0 ave 640566 max 640566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 640566 Ave neighs/atom = 199.36695 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 11 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 10.86 | 10.86 | 10.86 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14431.137 0 -14431.137 -180.0351 Loop time of 6.876e-06 on 1 procs for 0 steps with 3213 atoms 189.1% 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 | | 6.876e-06 | | |100.00 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15132.0 ave 15132 max 15132 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: 640290.0 ave 640290 max 640290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 640290 Ave neighs/atom = 199.28105 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 11 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 10.86 | 10.86 | 10.86 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 -14431.137 -14431.137 39.944852 139.03953 5.9773802 -180.0351 -180.0351 -277.78152 101.89664 -364.22043 2.1539654 950.22261 Loop time of 7.237e-06 on 1 procs for 0 steps with 3213 atoms 290.2% 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 | | 7.237e-06 | | |100.00 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15132.0 ave 15132 max 15132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 320145.0 ave 320145 max 320145 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 640290.0 ave 640290 max 640290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 640290 Ave neighs/atom = 199.28105 Neighbor list builds = 0 Dangerous builds = 0 3213 -14431.1371525536 eV 2.15396535541711 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12