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 = 3.6150017 3.6150017 3.6150017 Created orthogonal box = (0.0000000 -36.865928 0.0000000) to (18.432964 36.865928 3.6150017) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2537609 4.2537609 3.6150017 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -36.865928 0.0000000) to (18.432964 36.865928 3.6150017) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2537609 4.2537609 3.6150017 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -36.865928 0.0000000) to (18.432964 36.865928 3.6150017) create_atoms CPU = 0.001 seconds 210 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 = 5 18 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 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_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 = 5 18 1 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) = 4.491 | 4.491 | 4.491 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1412.9864 0 -1412.9864 15085.285 44 0 -1451.2382 0 -1451.2382 -4627.3711 Loop time of 0.883069 on 1 procs for 44 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 = -1412.98638187026 -1451.23723760199 -1451.23819186808 Force two-norm initial, final = 88.211626 0.079106529 Force max component initial, final = 30.914855 0.011921147 Final line search alpha, max atom move = 1.0000000 0.011921147 Iterations, force evaluations = 44 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8553 | 0.8553 | 0.8553 | 0.0 | 96.86 Neigh | 0.011298 | 0.011298 | 0.011298 | 0.0 | 1.28 Comm | 0.0099711 | 0.0099711 | 0.0099711 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006497 | | | 0.74 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4900.00 ave 4900 max 4900 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: 85536.0 ave 85536 max 85536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85536 Ave neighs/atom = 207.61165 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 18 1 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 : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.491 | 4.491 | 4.491 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -1451.2382 0 -1451.2382 -4627.3711 4913.1367 47 0 -1451.264 0 -1451.264 -3.6388694 4896.6248 Loop time of 0.0637003 on 1 procs for 3 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 = -1451.23819186807 -1451.26285155395 -1451.26401030043 Force two-norm initial, final = 24.702621 0.30519467 Force max component initial, final = 16.120032 0.24658948 Final line search alpha, max atom move = 0.00062110673 0.00015315839 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.061302 | 0.061302 | 0.061302 | 0.0 | 96.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006019 | 0.0006019 | 0.0006019 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001796 | | | 2.82 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4872.00 ave 4872 max 4872 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: 83212.0 ave 83212 max 83212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83212 Ave neighs/atom = 201.97087 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 = 5 18 1 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) = 4.629 | 4.629 | 4.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1451.264 0 -1451.264 -3.6388694 Loop time of 6.355e-06 on 1 procs for 0 steps with 412 atoms 173.1% 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 | | 6.355e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4882.00 ave 4882 max 4882 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: 83464.0 ave 83464 max 83464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83464 Ave neighs/atom = 202.58252 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 = 5 18 1 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) = 4.629 | 4.629 | 4.629 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 -1451.264 -1451.264 18.390755 73.663829 3.6144562 -3.6388694 -3.6388694 25.518679 -80.609681 44.174394 2.3438707 202.43975 Loop time of 6.826e-06 on 1 procs for 0 steps with 412 atoms 263.7% 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: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4882.00 ave 4882 max 4882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41732.0 ave 41732 max 41732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 83464.0 ave 83464 max 83464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83464 Ave neighs/atom = 202.58252 Neighbor list builds = 0 Dangerous builds = 0 412 -1451.26401030043 eV 2.34387069212948 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01