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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -40.848971 0.0000000) to (28.884584 40.848971 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0972796 6.4076817 5.7200000 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.848971 0.0000000) to (28.884584 40.848971 5.7200000) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0972796 6.4076817 5.7200000 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.848971 0.0000000) to (28.884584 40.848971 5.7200000) create_atoms CPU = 0.001 seconds 410 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 = 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 812 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_058537087384_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 24 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) = 4.543 | 4.543 | 4.543 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2498.7612 0 -2498.7612 34024.294 69 0 -2717.5967 0 -2717.5967 1877.1272 Loop time of 4.62392 on 1 procs for 69 steps with 812 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2498.76118693354 -2717.59414041785 -2717.59670149208 Force two-norm initial, final = 319.93929 0.12154396 Force max component initial, final = 94.676114 0.021966476 Final line search alpha, max atom move = 1.0000000 0.021966476 Iterations, force evaluations = 69 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6024 | 4.6024 | 4.6024 | 0.0 | 99.53 Neigh | 0.010068 | 0.010068 | 0.010068 | 0.0 | 0.22 Comm | 0.0058125 | 0.0058125 | 0.0058125 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005662 | | | 0.12 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4103.00 ave 4103 max 4103 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: 65740.0 ave 65740 max 65740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65740 Ave neighs/atom = 80.960591 Neighbor list builds = 2 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 = 9 24 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 : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.544 | 4.544 | 4.544 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -2717.5967 0 -2717.5967 1877.1272 13498.12 74 0 -2717.6569 0 -2717.6569 3.0040408 13530.601 Loop time of 0.290653 on 1 procs for 5 steps with 812 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2717.59670149208 -2717.65692186639 -2717.65693881463 Force two-norm initial, final = 34.658426 0.19471840 Force max component initial, final = 31.983049 0.068768241 Final line search alpha, max atom move = 0.0018802169 0.00012929921 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28906 | 0.28906 | 0.28906 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027984 | 0.00027984 | 0.00027984 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00131 | | | 0.45 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4137.00 ave 4137 max 4137 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: 65804.0 ave 65804 max 65804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65804 Ave neighs/atom = 81.039409 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 = 9 24 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) = 4.682 | 4.682 | 4.682 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2717.6569 0 -2717.6569 3.0040408 Loop time of 1.909e-06 on 1 procs for 0 steps with 812 atoms 104.8% 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 | | 1.909e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4137.00 ave 4137 max 4137 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: 66172.0 ave 66172 max 66172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66172 Ave neighs/atom = 81.492611 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 = 9 24 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) = 4.682 | 4.682 | 4.682 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 -2717.6569 -2717.6569 28.893197 82.007231 5.710437 3.0040408 3.0040408 -3.4874729 4.3702702 8.1293251 2.5693698 576.74157 Loop time of 1.462e-06 on 1 procs for 0 steps with 812 atoms 205.2% 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 | | 1.462e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4137.00 ave 4137 max 4137 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33086.0 ave 33086 max 33086 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 66172.0 ave 66172 max 66172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66172 Ave neighs/atom = 81.492611 Neighbor list builds = 0 Dangerous builds = 0 812 -2717.65693881463 eV 2.56936980922011 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05