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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -57.624883 0.0000000) to (40.746946 57.624883 4.9780317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0816337 5.5904738 4.9780317 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -57.624883 0.0000000) to (40.746946 57.624883 4.9780317) create_atoms CPU = 0.008 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0816337 5.5904738 4.9780317 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -57.624883 0.0000000) to (40.746946 57.624883 4.9780317) create_atoms CPU = 0.008 seconds 1080 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 28 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2144 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 6.485 | 6.485 | 6.485 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8986.8691 0 -8986.8691 41625.049 72 0 -9519.3185 0 -9519.3185 4303.3478 Loop time of 6.83477 on 1 procs for 72 steps with 2144 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 = -8986.86909386085 -9519.31163714332 -9519.31847555196 Force two-norm initial, final = 481.32464 0.27784816 Force max component initial, final = 65.323040 0.029873100 Final line search alpha, max atom move = 1.0000000 0.029873100 Iterations, force evaluations = 72 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6323 | 6.6323 | 6.6323 | 0.0 | 97.04 Neigh | 0.12946 | 0.12946 | 0.12946 | 0.0 | 1.89 Comm | 0.041718 | 0.041718 | 0.041718 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03128 | | | 0.46 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13465.0 ave 13465 max 13465 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: 480496.0 ave 480496 max 480496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 480496 Ave neighs/atom = 224.11194 Neighbor list builds = 2 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 6.485 | 6.485 | 6.485 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -9519.3185 0 -9519.3185 4303.3478 23377.215 74 0 -9519.4046 0 -9519.4046 80.749032 23432.665 Loop time of 0.203518 on 1 procs for 2 steps with 2144 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 = -9519.31847555183 -9519.40090484184 -9519.40464823499 Force two-norm initial, final = 111.77699 2.9765061 Force max component initial, final = 77.214121 2.8416121 Final line search alpha, max atom move = 7.5593300e-05 0.00021480683 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19895 | 0.19895 | 0.19895 | 0.0 | 97.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012151 | 0.0012151 | 0.0012151 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003356 | | | 1.65 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13453.0 ave 13453 max 13453 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: 481024.0 ave 481024 max 481024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 481024 Ave neighs/atom = 224.35821 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 6.623 | 6.623 | 6.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9519.4046 0 -9519.4046 80.749032 Loop time of 6.435e-06 on 1 procs for 0 steps with 2144 atoms 186.5% 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 | | 6.435e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13453.0 ave 13453 max 13453 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: 480816.0 ave 480816 max 480816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 480816 Ave neighs/atom = 224.26119 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 6.623 | 6.623 | 6.623 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 -9519.4046 -9519.4046 40.796138 115.36848 4.9786944 80.749032 80.749032 -9.0581334 194.49147 56.813753 2.3120843 837.57467 Loop time of 6.635e-06 on 1 procs for 0 steps with 2144 atoms 271.3% 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 | | 6.635e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13453.0 ave 13453 max 13453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 240408.0 ave 240408 max 240408 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 480816.0 ave 480816 max 480816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 480816 Ave neighs/atom = 224.26119 Neighbor list builds = 0 Dangerous builds = 0 2144 -9519.40464823499 eV 2.31208426633763 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08