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 = 3.5192945 3.5192945 3.5192945 Created orthogonal box = (0.0000000 -62.166653 0.0000000) to (35.889902 62.166653 6.0955968) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5215234 5.5787428 6.0955968 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -62.166653 0.0000000) to (35.889902 62.166653 6.0955968) create_atoms CPU = 0.008 seconds 1249 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5215234 5.5787428 6.0955968 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -62.166653 0.0000000) to (35.889902 62.166653 6.0955968) create_atoms CPU = 0.008 seconds 1249 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 21 atoms, new total = 2477 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.539 | 6.539 | 6.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10950.133 0 -10950.133 6384.3844 30 0 -10984.266 0 -10984.266 -5812.2864 Loop time of 2.5099 on 1 procs for 30 steps with 2477 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 = -10950.1328549416 -10984.2563639573 -10984.2662737283 Force two-norm initial, final = 74.127586 0.37355294 Force max component initial, final = 13.204505 0.073591565 Final line search alpha, max atom move = 1.0000000 0.073591565 Iterations, force evaluations = 30 53 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4802 | 2.4802 | 2.4802 | 0.0 | 98.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015402 | 0.015402 | 0.015402 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01426 | | | 0.57 Nlocal: 2477.00 ave 2477 max 2477 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12100.0 ave 12100 max 12100 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: 431890.0 ave 431890 max 431890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 431890 Ave neighs/atom = 174.36011 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.539 | 6.539 | 6.539 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -10984.266 0 -10984.266 -5812.2864 27200.444 32 0 -10984.34 0 -10984.34 -2250.1762 27145.634 Loop time of 0.189105 on 1 procs for 2 steps with 2477 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 = -10984.2662737282 -10984.3391557529 -10984.3401654239 Force two-norm initial, final = 102.94490 1.4196017 Force max component initial, final = 80.893980 1.2301616 Final line search alpha, max atom move = 9.4574768e-05 0.00011634225 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18473 | 0.18473 | 0.18473 | 0.0 | 97.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011234 | 0.0011234 | 0.0011234 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003254 | | | 1.72 Nlocal: 2477.00 ave 2477 max 2477 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12037.0 ave 12037 max 12037 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: 431806.0 ave 431806 max 431806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 431806 Ave neighs/atom = 174.32620 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.677 | 6.677 | 6.677 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10984.34 0 -10984.34 -2250.1762 Loop time of 6.254e-06 on 1 procs for 0 steps with 2477 atoms 191.9% 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 | | 6.254e-06 | | |100.00 Nlocal: 2477.00 ave 2477 max 2477 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12049.0 ave 12049 max 12049 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: 431894.0 ave 431894 max 431894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 431894 Ave neighs/atom = 174.36173 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.677 | 6.677 | 6.677 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 -10984.34 -10984.34 35.858892 124.33331 6.0885746 -2250.1762 -2250.1762 72.543271 -6787.9923 -35.079546 2.1781069 947.85912 Loop time of 6.826e-06 on 1 procs for 0 steps with 2477 atoms 278.3% 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 | | 6.826e-06 | | |100.00 Nlocal: 2477.00 ave 2477 max 2477 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12049.0 ave 12049 max 12049 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 215947.0 ave 215947 max 215947 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 431894.0 ave 431894 max 431894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 431894 Ave neighs/atom = 174.36173 Neighbor list builds = 0 Dangerous builds = 0 2477 -10984.3401654239 eV 2.17810685694255 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03