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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -43.252122 0.0000000) to (15.291934 43.252122 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0973115 6.0072392 5.0973115 Created 288 atoms using lattice units in orthogonal box = (0.0000000 -43.252122 0.0000000) to (15.291934 43.252122 5.0973115) create_atoms CPU = 0.001 seconds 288 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0973115 6.0072392 5.0973115 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -43.252122 0.0000000) to (15.291934 43.252122 5.0973115) create_atoms CPU = 0.001 seconds 292 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 29 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 572 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_492310898779_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.503 | 4.503 | 4.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2400.6906 0 -2400.6906 6304.6117 48 0 -2419.8124 0 -2419.8124 -7073.7156 Loop time of 1.82264 on 1 procs for 48 steps with 572 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 = -2400.69059877849 -2419.81041619321 -2419.81244421606 Force two-norm initial, final = 28.967577 0.12744246 Force max component initial, final = 6.4724565 0.018838158 Final line search alpha, max atom move = 1.0000000 0.018838158 Iterations, force evaluations = 48 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8133 | 1.8133 | 1.8133 | 0.0 | 99.49 Neigh | 0.0031392 | 0.0031392 | 0.0031392 | 0.0 | 0.17 Comm | 0.0031271 | 0.0031271 | 0.0031271 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003118 | | | 0.17 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3350.00 ave 3350 max 3350 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: 44032.0 ave 44032 max 44032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44032 Ave neighs/atom = 76.979021 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.502 | 4.502 | 4.502 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -2419.8124 0 -2419.8124 -7073.7156 6742.8114 58 0 -2420.0065 0 -2420.0065 122.4263 6712.264 Loop time of 0.236944 on 1 procs for 10 steps with 572 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 = -2419.81244421606 -2420.0064345877 -2420.00648151465 Force two-norm initial, final = 58.283728 0.96930891 Force max component initial, final = 51.946283 0.55879832 Final line search alpha, max atom move = 0.0021676834 0.0012112979 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23508 | 0.23508 | 0.23508 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033008 | 0.00033008 | 0.00033008 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001537 | | | 0.65 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3300.00 ave 3300 max 3300 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: 44032.0 ave 44032 max 44032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44032 Ave neighs/atom = 76.979021 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.640 | 4.640 | 4.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2420.0065 0 -2420.0065 122.4263 Loop time of 1.562e-06 on 1 procs for 0 steps with 572 atoms 128.0% 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 | | 1.562e-06 | | |100.00 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3276.00 ave 3276 max 3276 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: 44088.0 ave 44088 max 44088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44088 Ave neighs/atom = 77.076923 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.640 | 4.640 | 4.640 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 -2420.0065 -2420.0065 15.152459 86.667167 5.1112994 122.4263 122.4263 101.40822 132.1229 133.74778 2.3372472 418.24101 Loop time of 1.373e-06 on 1 procs for 0 steps with 572 atoms 145.7% 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 | | 1.373e-06 | | |100.00 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3276.00 ave 3276 max 3276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22044.0 ave 22044 max 22044 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44088.0 ave 44088 max 44088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44088 Ave neighs/atom = 77.076923 Neighbor list builds = 0 Dangerous builds = 0 572 -2420.00648151465 eV 2.33724721357938 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02