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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -43.811498 0.0000000) to (14.602483 43.811498 4.0500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6163395 5.6163395 4.0500000 Created 157 atoms using lattice units in orthogonal box = (0.0000000 -43.811498 0.0000000) to (14.602483 43.811498 4.0500000) create_atoms CPU = 0.002 seconds 157 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6163395 5.6163395 4.0500000 Created 157 atoms using lattice units in orthogonal box = (0.0000000 -43.811498 0.0000000) to (14.602483 43.811498 4.0500000) create_atoms CPU = 0.001 seconds 157 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 = 5 26 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 308 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_971738391444_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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 26 2 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) = 4.427 | 4.427 | 4.427 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1023.1647 0 -1023.1647 -1135.6775 41 0 -1028.1084 0 -1028.1084 -6849.8386 Loop time of 2.80469 on 1 procs for 41 steps with 308 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 = -1023.16466364554 -1028.10764038746 -1028.10837810537 Force two-norm initial, final = 6.2370009 0.076366092 Force max component initial, final = 1.6737079 0.010911822 Final line search alpha, max atom move = 1.0000000 0.010911822 Iterations, force evaluations = 41 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7956 | 2.7956 | 2.7956 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0046802 | 0.0046802 | 0.0046802 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00446 | | | 0.16 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2484.00 ave 2484 max 2484 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: 23864.0 ave 23864 max 23864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23864 Ave neighs/atom = 77.480519 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 26 2 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.426 | 4.426 | 4.426 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -1028.1084 0 -1028.1084 -6849.8386 5182.0288 45 0 -1028.1613 0 -1028.1613 -2186.5341 5149.8707 Loop time of 0.221141 on 1 procs for 4 steps with 308 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1028.10837810537 -1028.16043516582 -1028.16125074985 Force two-norm initial, final = 24.012086 0.73984704 Force max component initial, final = 17.973996 0.68202881 Final line search alpha, max atom move = 0.00037806111 0.00025784857 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21968 | 0.21968 | 0.21968 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034332 | 0.00034332 | 0.00034332 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001121 | | | 0.51 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2432.00 ave 2432 max 2432 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: 24232.0 ave 24232 max 24232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24232 Ave neighs/atom = 78.675325 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 = 5 26 2 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) = 4.565 | 4.565 | 4.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1028.1613 0 -1028.1613 -2186.5341 Loop time of 6.304e-06 on 1 procs for 0 steps with 308 atoms 174.5% 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 | | 6.304e-06 | | |100.00 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2492.00 ave 2492 max 2492 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: 25124.0 ave 25124 max 25124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25124 Ave neighs/atom = 81.571429 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 = 5 26 2 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) = 4.565 | 4.565 | 4.565 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 -1028.1613 -1028.1613 14.550926 87.622996 4.0391279 -2186.5341 -2186.5341 -84.628044 -6686.5906 211.61641 2.349849 174.49923 Loop time of 6.405e-06 on 1 procs for 0 steps with 308 atoms 218.6% 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 | | 6.405e-06 | | |100.00 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12562.0 ave 12562 max 12562 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25124.0 ave 25124 max 25124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25124 Ave neighs/atom = 81.571429 Neighbor list builds = 0 Dangerous builds = 0 308 -1028.16125074985 eV 2.3498490371267 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03