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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -30.088545 0.0000000) to (36.850792 30.088545 7.0271702) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6901007 4.3765157 4.6847802 Created 657 atoms using lattice units in orthogonal box = (0.0000000 -30.088545 0.0000000) to (36.850792 30.088545 7.0271702) create_atoms CPU = 0.002 seconds 657 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6901007 4.3765157 4.6847802 Created 663 atoms using lattice units in orthogonal box = (0.0000000 -30.088545 0.0000000) to (36.850792 30.088545 7.0271702) create_atoms CPU = 0.001 seconds 663 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 12 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1320 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 12 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.697 | 6.697 | 6.697 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5069.6707 0 -5069.6707 54851.058 142 0 -5408.1119 0 -5408.1119 9215.98 Loop time of 5.15307 on 1 procs for 142 steps with 1320 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5069.67074582025 -5408.10687004583 -5408.11189709971 Force two-norm initial, final = 342.75717 0.31848408 Force max component initial, final = 68.603361 0.056237537 Final line search alpha, max atom move = 1.0000000 0.056237537 Iterations, force evaluations = 142 269 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9954 | 4.9954 | 4.9954 | 0.0 | 96.94 Neigh | 0.11045 | 0.11045 | 0.11045 | 0.0 | 2.14 Comm | 0.027241 | 0.027241 | 0.027241 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01998 | | | 0.39 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9565.00 ave 9565 max 9565 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: 509134.0 ave 509134 max 509134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509134 Ave neighs/atom = 385.70758 Neighbor list builds = 4 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 12 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.696 | 6.696 | 6.696 Mbytes Step Temp E_pair E_mol TotEng Press Volume 142 0 -5408.1119 0 -5408.1119 9215.98 15583.266 148 0 -5408.6181 0 -5408.6181 -20.345584 15668.049 Loop time of 0.159787 on 1 procs for 6 steps with 1320 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 = -5408.1118970997 -5408.61755386326 -5408.6180630526 Force two-norm initial, final = 189.21382 1.1080126 Force max component initial, final = 142.27674 0.92629421 Final line search alpha, max atom move = 0.00015404718 0.00014269301 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15638 | 0.15638 | 0.15638 | 0.0 | 97.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064973 | 0.00064973 | 0.00064973 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00276 | | | 1.73 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9522.00 ave 9522 max 9522 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: 509570.0 ave 509570 max 509570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509570 Ave neighs/atom = 386.03788 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 12 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.834 | 6.834 | 6.834 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5408.6181 0 -5408.6181 -20.345584 Loop time of 2.22e-06 on 1 procs for 0 steps with 1320 atoms 180.2% 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 | | 2.22e-06 | | |100.00 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9553.00 ave 9553 max 9553 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: 504958.0 ave 504958 max 504958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 504958 Ave neighs/atom = 382.54394 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 12 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.834 | 6.834 | 6.834 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 -5408.6181 -5408.6181 36.959215 60.454106 7.0123949 -20.345584 -20.345584 -94.999279 16.800709 17.161817 2.3237051 2100.808 Loop time of 2.585e-06 on 1 procs for 0 steps with 1320 atoms 232.1% 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 | | 2.585e-06 | | |100.00 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9553.00 ave 9553 max 9553 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 252479.0 ave 252479 max 252479 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 504958.0 ave 504958 max 504958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 504958 Ave neighs/atom = 382.54394 Neighbor list builds = 0 Dangerous builds = 0 1320 -5408.6180630526 eV 2.32370512577356 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05