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 = 3.5200001 3.5200001 3.5200001 Created orthogonal box = (0.0000000 -70.575782 0.0000000) to (40.746947 70.575782 6.0968190) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4734704 5.6179727 6.0968190 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -70.575782 0.0000000) to (40.746947 70.575782 6.0968190) create_atoms CPU = 0.011 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4734704 5.6179727 6.0968190 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.575782 0.0000000) to (40.746947 70.575782 6.0968190) create_atoms CPU = 0.011 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 12 42 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 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3214 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_776437554506_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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 12 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 6.647 | 6.647 | 6.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14018.546 0 -14018.546 14847.163 142 0 -14263.615 0 -14263.615 5668.0325 Loop time of 10.2 on 1 procs for 142 steps with 3214 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 = -14018.5459997983 -14263.6021330117 -14263.6152978214 Force two-norm initial, final = 156.84575 0.42701922 Force max component initial, final = 29.922184 0.062107722 Final line search alpha, max atom move = 0.86615947 0.053795191 Iterations, force evaluations = 142 265 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.7341 | 9.7341 | 9.7341 | 0.0 | 95.43 Neigh | 0.29485 | 0.29485 | 0.29485 | 0.0 | 2.89 Comm | 0.086926 | 0.086926 | 0.086926 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08417 | | | 0.83 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12448.0 ave 12448 max 12448 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: 427164.0 ave 427164 max 427164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 427164 Ave neighs/atom = 132.90728 Neighbor list builds = 5 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 12 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 142 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.649 | 6.649 | 6.649 Mbytes Step Temp E_pair E_mol TotEng Press Volume 142 0 -14263.615 0 -14263.615 5668.0325 35065.825 146 0 -14264.039 0 -14264.039 392.23107 35169.32 Loop time of 0.225868 on 1 procs for 4 steps with 3214 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 = -14263.6152978213 -14264.0270312213 -14264.0386311244 Force two-norm initial, final = 260.09129 16.225164 Force max component initial, final = 235.80745 13.401197 Final line search alpha, max atom move = 4.3278108e-05 0.00057997847 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2177 | 0.2177 | 0.2177 | 0.0 | 96.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017213 | 0.0017213 | 0.0017213 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006445 | | | 2.85 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12452.0 ave 12452 max 12452 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: 427176.0 ave 427176 max 427176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 427176 Ave neighs/atom = 132.91101 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 12 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 6.787 | 6.787 | 6.787 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14264.039 0 -14264.039 392.23107 Loop time of 6.114e-06 on 1 procs for 0 steps with 3214 atoms 179.9% 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 | | 6.114e-06 | | |100.00 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12452.0 ave 12452 max 12452 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: 427044.0 ave 427044 max 427044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 427044 Ave neighs/atom = 132.86994 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 12 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 6.787 | 6.787 | 6.787 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 -14264.039 -14264.039 40.762788 141.62713 6.0919121 392.23107 392.23107 198.97341 612.563 365.1568 2.2236034 1000.864 Loop time of 6.435e-06 on 1 procs for 0 steps with 3214 atoms 310.8% 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: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12452.0 ave 12452 max 12452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 213522.0 ave 213522 max 213522 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 427044.0 ave 427044 max 427044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 427044 Ave neighs/atom = 132.86994 Neighbor list builds = 0 Dangerous builds = 0 3214 -14264.0386311244 eV 2.22360338847047 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11