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 = 3.6150127 3.6150127 3.6150127 Created orthogonal box = (0.0000000 -54.585494 0.0000000) to (38.597773 54.585494 5.1123999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0943852 5.2670214 5.1123999 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.585494 0.0000000) to (38.597773 54.585494 5.1123999) create_atoms CPU = 0.004 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0943852 5.2670214 5.1123999 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.585494 0.0000000) to (38.597773 54.585494 5.1123999) create_atoms CPU = 0.003 seconds 916 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 = 12 32 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 4 atoms, new total = 1824 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_028979335952_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 = 12 32 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) = 5.566 | 5.566 | 5.566 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6192.3757 0 -6192.3757 30455.744 68 0 -6434.6514 0 -6434.6514 3692.0933 Loop time of 29.3889 on 1 procs for 68 steps with 1824 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6192.37568949888 -6434.64571640651 -6434.65144746162 Force two-norm initial, final = 344.79809 0.27811140 Force max component initial, final = 82.579632 0.036078396 Final line search alpha, max atom move = 1.0000000 0.036078396 Iterations, force evaluations = 68 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.338 | 29.338 | 29.338 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.026819 | 0.026819 | 0.026819 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02448 | | | 0.08 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8677.00 ave 8677 max 8677 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: 242760.0 ave 242760 max 242760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 242760 Ave neighs/atom = 133.09211 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 = 12 32 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 : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.566 | 5.566 | 5.566 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -6434.6514 0 -6434.6514 3692.0933 21542.411 75 0 -6434.9745 0 -6434.9745 4.5889595 21597.598 Loop time of 2.34377 on 1 procs for 7 steps with 1824 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 = -6434.65144746162 -6434.97447090465 -6434.974486547 Force two-norm initial, final = 121.02430 0.38453769 Force max component initial, final = 119.17171 0.11781242 Final line search alpha, max atom move = 0.0011890890 0.00014008945 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3341 | 2.3341 | 2.3341 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014935 | 0.0014935 | 0.0014935 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008155 | | | 0.35 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8646.00 ave 8646 max 8646 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: 241440.0 ave 241440 max 241440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241440 Ave neighs/atom = 132.36842 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 = 12 32 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) = 5.704 | 5.704 | 5.704 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6434.9745 0 -6434.9745 4.5889595 Loop time of 4.326e-06 on 1 procs for 0 steps with 1824 atoms 161.8% 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 | | 4.326e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8627.00 ave 8627 max 8627 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: 241312.0 ave 241312 max 241312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241312 Ave neighs/atom = 132.29825 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 = 12 32 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) = 5.704 | 5.704 | 5.704 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 -6434.9745 -6434.9745 38.544273 109.81017 5.1027351 4.5889595 4.5889595 8.7275747 3.3062391 1.7330646 2.3710685 638.02671 Loop time of 4.556e-06 on 1 procs for 0 steps with 1824 atoms 197.5% 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 | | 4.556e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8627.00 ave 8627 max 8627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120656.0 ave 120656 max 120656 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 241312.0 ave 241312 max 241312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241312 Ave neighs/atom = 132.29825 Neighbor list builds = 0 Dangerous builds = 0 1824 -6434.974486547 eV 2.37106848381176 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:33