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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -46.743024 0.0000000) to (26.987097 46.743024 6.2462993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7829495 5.5646457 6.2462993 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -46.743024 0.0000000) to (26.987097 46.743024 6.2462993) create_atoms CPU = 0.002 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7829495 5.5646457 6.2462993 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -46.743024 0.0000000) to (26.987097 46.743024 6.2462993) create_atoms CPU = 0.001 seconds 676 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 16 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1348 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_147603128437_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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.951 | 7.951 | 7.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4945.286 0 -4945.286 88054.627 101 0 -5630.1145 0 -5630.1145 12461.481 Loop time of 6.85996 on 1 procs for 101 steps with 1348 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 = -4945.28599996417 -5630.10971813254 -5630.11447774904 Force two-norm initial, final = 739.16066 0.30321645 Force max component initial, final = 155.28582 0.043645835 Final line search alpha, max atom move = 1.0000000 0.043645835 Iterations, force evaluations = 101 183 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6875 | 6.6875 | 6.6875 | 0.0 | 97.49 Neigh | 0.12784 | 0.12784 | 0.12784 | 0.0 | 1.86 Comm | 0.028031 | 0.028031 | 0.028031 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0166 | | | 0.24 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14501.0 ave 14501 max 14501 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: 835864.0 ave 835864 max 835864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 835864 Ave neighs/atom = 620.07715 Neighbor list builds = 3 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 101 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.948 | 7.948 | 7.948 Mbytes Step Temp E_pair E_mol TotEng Press Volume 101 0 -5630.1145 0 -5630.1145 12461.481 15758.895 108 0 -5630.7216 0 -5630.7216 -6.5010865 15872.111 Loop time of 0.376013 on 1 procs for 7 steps with 1348 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 = -5630.11447774904 -5630.72125984702 -5630.72162589906 Force two-norm initial, final = 230.07679 0.62146521 Force max component initial, final = 194.67763 0.24578868 Final line search alpha, max atom move = 0.00018922460 4.6509263e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36997 | 0.36997 | 0.36997 | 0.0 | 98.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010865 | 0.0010865 | 0.0010865 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004955 | | | 1.32 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14223.0 ave 14223 max 14223 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: 836168.0 ave 836168 max 836168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 836168 Ave neighs/atom = 620.30267 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 8.085 | 8.085 | 8.085 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5630.7216 0 -5630.7216 -6.5010865 Loop time of 2.453e-06 on 1 procs for 0 steps with 1348 atoms 163.1% 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 | | 2.453e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14053.0 ave 14053 max 14053 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: 829704.0 ave 829704 max 829704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 829704 Ave neighs/atom = 615.50742 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 8.085 | 8.085 | 8.085 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 -5630.7216 -5630.7216 26.996126 94.002592 6.2545118 -6.5010865 -6.5010865 -24.818916 -18.234433 23.550089 2.3294361 852.47526 Loop time of 2.469e-06 on 1 procs for 0 steps with 1348 atoms 364.5% 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 | | 2.469e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14053.0 ave 14053 max 14053 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 414852.0 ave 414852 max 414852 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 829704.0 ave 829704 max 829704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 829704 Ave neighs/atom = 615.50742 Neighbor list builds = 0 Dangerous builds = 0 1348 -5630.72162589906 eV 2.32943609829872 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07