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 = 4.0499989 4.0499989 4.0499989 Created orthogonal box = (0.0000000 -41.306097 0.0000000) to (35.768622 41.306097 7.0148038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4200090 6.3541610 7.0148038 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.306097 0.0000000) to (35.768622 41.306097 7.0148038) create_atoms CPU = 0.004 seconds 629 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4200090 6.3541610 7.0148038 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.306097 0.0000000) to (35.768622 41.306097 7.0148038) create_atoms CPU = 0.004 seconds 629 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 24 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1232 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_315820974149_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.642 | 4.642 | 4.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4071.4943 0 -4071.4943 8788.8927 82 0 -4118.9194 0 -4118.9194 -2017.2913 Loop time of 11.3451 on 1 procs for 82 steps with 1232 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 = -4071.49432505016 -4118.91579986942 -4118.91936893214 Force two-norm initial, final = 62.987089 0.24329019 Force max component initial, final = 14.416931 0.077015849 Final line search alpha, max atom move = 1.0000000 0.077015849 Iterations, force evaluations = 82 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.291 | 11.291 | 11.291 | 0.0 | 99.52 Neigh | 0.015419 | 0.015419 | 0.015419 | 0.0 | 0.14 Comm | 0.016989 | 0.016989 | 0.016989 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0219 | | | 0.19 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4747.00 ave 4747 max 4747 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: 96426.0 ave 96426 max 96426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96426 Ave neighs/atom = 78.267857 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.642 | 4.642 | 4.642 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -4118.9194 0 -4118.9194 -2017.2913 20728.214 85 0 -4118.9638 0 -4118.9638 -124.88935 20676.17 Loop time of 0.436009 on 1 procs for 3 steps with 1232 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4118.91936893214 -4118.96297497232 -4118.96383226518 Force two-norm initial, final = 43.291672 0.26464974 Force max component initial, final = 38.506912 0.084601952 Final line search alpha, max atom move = 0.00024515858 2.0740895e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43293 | 0.43293 | 0.43293 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058415 | 0.00058415 | 0.00058415 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002491 | | | 0.57 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4756.00 ave 4756 max 4756 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: 96304.0 ave 96304 max 96304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96304 Ave neighs/atom = 78.168831 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.780 | 4.780 | 4.780 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4118.9638 0 -4118.9638 -124.88935 Loop time of 6.736e-06 on 1 procs for 0 steps with 1232 atoms 178.1% 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 | | 6.736e-06 | | |100.00 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4756.00 ave 4756 max 4756 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: 96428.0 ave 96428 max 96428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96428 Ave neighs/atom = 78.269481 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.780 | 4.780 | 4.780 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 -4118.9638 -4118.9638 35.753102 82.612193 7.0002284 -124.88935 -124.88935 -2.3391566 -373.17426 0.8453549 2.501918 1080.2543 Loop time of 6.956e-06 on 1 procs for 0 steps with 1232 atoms 330.6% 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 | | 6.956e-06 | | |100.00 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4756.00 ave 4756 max 4756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48214.0 ave 48214 max 48214 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 96428.0 ave 96428 max 96428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96428 Ave neighs/atom = 78.269481 Neighbor list builds = 0 Dangerous builds = 0 1232 -4118.96383226518 eV 2.50191797704763 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12