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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -47.856942 0.0000000) to (16.919984 47.856942 5.1015671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1527214 5.4382888 5.1015671 Created 351 atoms using lattice units in orthogonal box = (0.0000000 -47.856942 0.0000000) to (16.919984 47.856942 5.1015671) create_atoms CPU = 0.001 seconds 351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1527214 5.4382888 5.1015671 Created 359 atoms using lattice units in orthogonal box = (0.0000000 -47.856942 0.0000000) to (16.919984 47.856942 5.1015671) create_atoms CPU = 0.001 seconds 359 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 16 1 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 704 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_151002396060_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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.256 | 6.256 | 6.256 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2475.7749 0 -2475.7749 4445.7791 19 0 -2482.8817 0 -2482.8817 2079.747 Loop time of 0.755501 on 1 procs for 19 steps with 704 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 = -2475.7748691946 -2482.87981066727 -2482.88166320816 Force two-norm initial, final = 17.250114 0.15899765 Force max component initial, final = 7.5243303 0.011702507 Final line search alpha, max atom move = 1.0000000 0.011702507 Iterations, force evaluations = 19 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74824 | 0.74824 | 0.74824 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002256 | | | 0.30 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11831.0 ave 11831 max 11831 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: 441796.0 ave 441796 max 441796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 441796 Ave neighs/atom = 627.55114 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.256 | 6.256 | 6.256 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -2482.8817 0 -2482.8817 2079.747 8261.8725 25 0 -2483.011 0 -2483.011 9.8578587 8273.8837 Loop time of 0.194506 on 1 procs for 6 steps with 704 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 = -2482.88166320817 -2483.01094260949 -2483.01095141713 Force two-norm initial, final = 46.720631 0.40653324 Force max component initial, final = 41.969031 0.30963727 Final line search alpha, max atom move = 0.0087023051 0.0026945580 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18983 | 0.18983 | 0.18983 | 0.0 | 97.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092329 | 0.00092329 | 0.00092329 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003756 | | | 1.93 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11834.0 ave 11834 max 11834 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: 440866.0 ave 440866 max 440866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440866 Ave neighs/atom = 626.23011 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.394 | 6.394 | 6.394 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2483.011 0 -2483.011 9.8578587 Loop time of 2.134e-06 on 1 procs for 0 steps with 704 atoms 140.6% 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 | | 2.134e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11846.0 ave 11846 max 11846 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: 440512.0 ave 440512 max 440512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440512 Ave neighs/atom = 625.72727 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.394 | 6.394 | 6.394 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 -2483.011 -2483.011 16.914636 96.178215 5.085926 9.8578587 9.8578587 59.94002 -0.95544107 -29.411003 2.4377475 145.98722 Loop time of 2.255e-06 on 1 procs for 0 steps with 704 atoms 266.1% 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 | | 2.255e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11846.0 ave 11846 max 11846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 220256.0 ave 220256 max 220256 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 440512.0 ave 440512 max 440512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440512 Ave neighs/atom = 625.72727 Neighbor list builds = 0 Dangerous builds = 0 704 -2483.01095141713 eV 2.43774751522891 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01