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 = 3.4986963 3.4986963 3.4986963 Created orthogonal box = (0.0000000 -44.808673 0.0000000) to (31.682043 44.808673 4.9479038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4091293 6.0104503 4.9479038 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -44.808673 0.0000000) to (31.682043 44.808673 4.9479038) create_atoms CPU = 0.005 seconds 660 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4091293 6.0104503 4.9479038 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -44.808673 0.0000000) to (31.682043 44.808673 4.9479038) create_atoms CPU = 0.005 seconds 660 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 24 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1304 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.468 | 5.468 | 5.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5317.5565 0 -5317.5565 8514.3366 40 0 -5351.2293 0 -5351.2293 -5086.9242 Loop time of 1.85781 on 1 procs for 40 steps with 1304 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 = -5317.55652972992 -5351.22515280265 -5351.22926974317 Force two-norm initial, final = 38.767068 0.25041267 Force max component initial, final = 10.074810 0.045779309 Final line search alpha, max atom move = 0.98577714 0.045128197 Iterations, force evaluations = 40 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8332 | 1.8332 | 1.8332 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012982 | 0.012982 | 0.012982 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01161 | | | 0.62 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7696.00 ave 7696 max 7696 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: 227416.0 ave 227416 max 227416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227416 Ave neighs/atom = 174.39877 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.469 | 5.469 | 5.469 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -5351.2293 0 -5351.2293 -5086.9242 14048.388 45 0 -5351.4104 0 -5351.4104 -707.09598 13997.287 Loop time of 0.178329 on 1 procs for 5 steps with 1304 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 = -5351.22926974316 -5351.4056668115 -5351.41040343554 Force two-norm initial, final = 82.826219 1.7834016 Force max component initial, final = 81.442257 1.3142363 Final line search alpha, max atom move = 0.00011834711 0.00015553607 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17338 | 0.17338 | 0.17338 | 0.0 | 97.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011081 | 0.0011081 | 0.0011081 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003844 | | | 2.16 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7720.00 ave 7720 max 7720 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: 226840.0 ave 226840 max 226840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226840 Ave neighs/atom = 173.95706 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.607 | 5.607 | 5.607 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5351.4104 0 -5351.4104 -707.09598 Loop time of 6.906e-06 on 1 procs for 0 steps with 1304 atoms 173.8% 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 | | 6.906e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7736.00 ave 7736 max 7736 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: 227088.0 ave 227088 max 227088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227088 Ave neighs/atom = 174.14724 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.607 | 5.607 | 5.607 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 -5351.4104 -5351.4104 31.537826 89.617347 4.9524492 -707.09598 -707.09598 -149.74713 -1841.1823 -130.35854 2.2603606 631.33009 Loop time of 6.746e-06 on 1 procs for 0 steps with 1304 atoms 222.4% 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 | | 6.746e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7736.00 ave 7736 max 7736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113544.0 ave 113544 max 113544 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227088.0 ave 227088 max 227088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227088 Ave neighs/atom = 174.14724 Neighbor list builds = 0 Dangerous builds = 0 1304 -5351.41040343554 eV 2.26036059522375 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02