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 = 3.4921275 3.4921275 3.4921275 Created orthogonal box = (0.0000000 -46.328307 0.0000000) to (28.370178 46.328307 8.5539306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1582142 5.2645804 5.7026204 Created 1052 atoms using lattice units in orthogonal box = (0.0000000 -46.328307 0.0000000) to (28.370178 46.328307 8.5539306) create_atoms CPU = 0.002 seconds 1052 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1582142 5.2645804 5.7026204 Created 1076 atoms using lattice units in orthogonal box = (0.0000000 -46.328307 0.0000000) to (28.370178 46.328307 8.5539306) create_atoms CPU = 0.002 seconds 1076 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 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 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 2112 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_270337113239_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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 6.432 | 6.432 | 6.432 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7001.3165 0 -7001.3165 2486.9788 12 0 -7006.6572 0 -7006.6572 1749.0067 Loop time of 0.451293 on 1 procs for 12 steps with 2112 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 = -7001.31650997121 -7006.65192679098 -7006.65720689469 Force two-norm initial, final = 11.945994 0.12238604 Force max component initial, final = 1.2350753 0.010025635 Final line search alpha, max atom move = 1.0000000 0.010025635 Iterations, force evaluations = 12 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44671 | 0.44671 | 0.44671 | 0.0 | 98.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020029 | 0.0020029 | 0.0020029 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00258 | | | 0.57 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8820.00 ave 8820 max 8820 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: 422784.0 ave 422784 max 422784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 422784 Ave neighs/atom = 200.18182 Neighbor list builds = 0 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.432 | 6.432 | 6.432 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -7006.6572 0 -7006.6572 1749.0067 22485.586 17 0 -7006.7848 0 -7006.7848 159.03855 22517.323 Loop time of 0.12866 on 1 procs for 5 steps with 2112 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 = -7006.65720689485 -7006.78333966797 -7006.78476353573 Force two-norm initial, final = 62.400665 5.5562076 Force max component initial, final = 61.747088 5.4329787 Final line search alpha, max atom move = 0.00014196917 0.00077131549 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12551 | 0.12551 | 0.12551 | 0.0 | 97.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048975 | 0.00048975 | 0.00048975 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002663 | | | 2.07 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8820.00 ave 8820 max 8820 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: 421454.0 ave 421454 max 421454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 421454 Ave neighs/atom = 199.55208 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 6.570 | 6.570 | 6.570 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7006.7848 0 -7006.7848 159.03855 Loop time of 2.574e-06 on 1 procs for 0 steps with 2112 atoms 194.3% 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 | | 2.574e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8820.00 ave 8820 max 8820 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: 421326.0 ave 421326 max 421326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 421326 Ave neighs/atom = 199.49148 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 6.570 | 6.570 | 6.570 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 -7006.7848 -7006.7848 28.32293 93.031861 8.5456847 159.03855 159.03855 7.5989424 388.13865 81.37807 2.3225819 600.06218 Loop time of 9.426e-06 on 1 procs for 0 steps with 2112 atoms 159.1% 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 | | 9.426e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8820.00 ave 8820 max 8820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210663.0 ave 210663 max 210663 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 421326.0 ave 421326 max 421326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 421326 Ave neighs/atom = 199.49148 Neighbor list builds = 0 Dangerous builds = 0 2112 -6917.60845251942 eV 2.32258189388675 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01