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 = 3.5226425 3.5226425 3.5226425 Created orthogonal box = (0.0000000 -41.080718 0.0000000) to (20.540359 41.080718 3.5226425) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8330256 4.8330256 3.5226425 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -41.080718 0.0000000) to (20.540359 41.080718 3.5226425) create_atoms CPU = 0.002 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8330256 4.8330256 3.5226425 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.080718 0.0000000) to (20.540359 41.080718 3.5226425) create_atoms CPU = 0.001 seconds 274 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 14 1 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 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_381861218831_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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 5.770 | 5.770 | 5.770 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2067.5678 0 -2067.5678 73458.824 61 0 -2289.6154 0 -2289.6154 9342.6861 Loop time of 5.58396 on 1 procs for 61 steps with 544 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 = -2067.56779854302 -2289.61383869693 -2289.61538045481 Force two-norm initial, final = 407.35779 0.18390937 Force max component initial, final = 114.40505 0.031204625 Final line search alpha, max atom move = 1.0000000 0.031204625 Iterations, force evaluations = 61 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5046 | 5.5046 | 5.5046 | 0.0 | 98.58 Neigh | 0.03856 | 0.03856 | 0.03856 | 0.0 | 0.69 Comm | 0.028451 | 0.028451 | 0.028451 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01235 | | | 0.22 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10922.0 ave 10922 max 10922 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: 338728.0 ave 338728 max 338728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338728 Ave neighs/atom = 622.66176 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.776 | 5.776 | 5.776 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -2289.6154 0 -2289.6154 9342.6861 5944.9009 69 0 -2289.8402 0 -2289.8402 -9.4750122 5974.5821 Loop time of 0.543362 on 1 procs for 8 steps with 544 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2289.61538045481 -2289.8387948912 -2289.84018653119 Force two-norm initial, final = 74.475029 0.61193470 Force max component initial, final = 56.227821 0.28855350 Final line search alpha, max atom move = 0.00012127572 3.4994535e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53361 | 0.53361 | 0.53361 | 0.0 | 98.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026646 | 0.0026646 | 0.0026646 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007092 | | | 1.31 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11400.0 ave 11400 max 11400 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: 338792.0 ave 338792 max 338792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338792 Ave neighs/atom = 622.77941 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 5.914 | 5.914 | 5.914 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2289.8402 0 -2289.8402 -9.4750122 Loop time of 6.445e-06 on 1 procs for 0 steps with 544 atoms 186.2% 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 | | 6.445e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11456.0 ave 11456 max 11456 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: 338272.0 ave 338272 max 338272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338272 Ave neighs/atom = 621.82353 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 5.914 | 5.914 | 5.914 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 -2289.8402 -2289.8402 20.461493 82.323508 3.5468787 -9.4750122 -9.4750122 64.654001 -77.53272 -15.546317 2.2236387 228.34201 Loop time of 7.016e-06 on 1 procs for 0 steps with 544 atoms 228.1% 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 | | 7.016e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11456.0 ave 11456 max 11456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 169136.0 ave 169136 max 169136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 338272.0 ave 338272 max 338272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338272 Ave neighs/atom = 621.82353 Neighbor list builds = 0 Dangerous builds = 0 544 -2289.84018653119 eV 2.22363871952482 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06