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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -80.842115 0.0000000) to (46.674217 80.842115 6.9836950) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2696709 6.4351932 6.9836950 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -80.842115 0.0000000) to (46.674217 80.842115 6.9836950) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2696709 6.4351932 6.9836950 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -80.842115 0.0000000) to (46.674217 80.842115 6.9836950) create_atoms CPU = 0.004 seconds 1610 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 11 38 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.052 | 7.052 | 7.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10622.081 0 -10622.081 5318.9054 64 0 -10783.314 0 -10783.314 3588.1212 Loop time of 3.24031 on 1 procs for 64 steps with 3216 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10622.081274635 -10783.3048470999 -10783.3144346414 Force two-norm initial, final = 59.059813 0.24097741 Force max component initial, final = 8.0204598 0.035420703 Final line search alpha, max atom move = 0.91417456 0.032380706 Iterations, force evaluations = 64 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0824 | 3.0824 | 3.0824 | 0.0 | 95.13 Neigh | 0.11672 | 0.11672 | 0.11672 | 0.0 | 3.60 Comm | 0.020541 | 0.020541 | 0.020541 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02067 | | | 0.64 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13031.0 ave 13031 max 13031 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: 560464.0 ave 560464 max 560464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560464 Ave neighs/atom = 174.27363 Neighbor list builds = 3 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.052 | 7.052 | 7.052 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -10783.314 0 -10783.314 3588.1212 52702.348 71 0 -10783.956 0 -10783.956 40.604578 52922.59 Loop time of 0.282331 on 1 procs for 7 steps with 3216 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 = -10783.3144346413 -10783.9560833004 -10783.9563549922 Force two-norm initial, final = 246.52787 3.1661553 Force max component initial, final = 225.77177 3.0458133 Final line search alpha, max atom move = 0.00026253965 0.00079964676 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24401 | 0.24401 | 0.24401 | 0.0 | 86.43 Neigh | 0.031881 | 0.031881 | 0.031881 | 0.0 | 11.29 Comm | 0.0012591 | 0.0012591 | 0.0012591 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005178 | | | 1.83 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13037.0 ave 13037 max 13037 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: 560352.0 ave 560352 max 560352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560352 Ave neighs/atom = 174.23881 Neighbor list builds = 1 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.190 | 7.190 | 7.190 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10783.956 0 -10783.956 40.604578 Loop time of 2.024e-06 on 1 procs for 0 steps with 3216 atoms 148.2% 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 | | 2.024e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13023.0 ave 13023 max 13023 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: 560268.0 ave 560268 max 560268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560268 Ave neighs/atom = 174.21269 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.190 | 7.190 | 7.190 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 -10783.956 -10783.956 46.682633 162.65801 6.9696392 40.604578 40.604578 7.0023983 92.764185 22.047151 2.5753359 1376.0342 Loop time of 2.362e-06 on 1 procs for 0 steps with 3216 atoms 254.0% 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 | | 2.362e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13023.0 ave 13023 max 13023 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 280134.0 ave 280134 max 280134 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 560268.0 ave 560268 max 560268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560268 Ave neighs/atom = 174.21269 Neighbor list builds = 0 Dangerous builds = 0 3216 -10783.9563549922 eV 2.57533589868572 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04