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 = 3.6583648 3.6583648 3.6583648 Created orthogonal box = (0.0000000 -69.988640 0.0000000) to (40.407960 69.988640 6.3364737) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9618302 5.3543222 6.3364737 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.988640 0.0000000) to (40.407960 69.988640 6.3364737) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9618302 5.3543222 6.3364737 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.988640 0.0000000) to (40.407960 69.988640 6.3364737) create_atoms CPU = 0.003 seconds 1466 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2930 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_769582363439_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.592 | 6.592 | 6.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10889.344 0 -10889.344 65168.607 784 0 -11894.026 0 -11894.026 -62911.788 Loop time of 33.4547 on 1 procs for 784 steps with 2930 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10889.3438891041 -11894.0166954442 -11894.0255030045 Force two-norm initial, final = 1520.0782 0.24523270 Force max component initial, final = 470.66740 0.061002422 Final line search alpha, max atom move = 1.0000000 0.061002422 Iterations, force evaluations = 784 1536 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 32.578 | 32.578 | 32.578 | 0.0 | 97.38 Neigh | 0.41827 | 0.41827 | 0.41827 | 0.0 | 1.25 Comm | 0.23057 | 0.23057 | 0.23057 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2278 | | | 0.68 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11573.0 ave 11573 max 11573 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: 397846.0 ave 397846 max 397846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 397846 Ave neighs/atom = 135.78362 Neighbor list builds = 16 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 784 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.591 | 6.591 | 6.591 Mbytes Step Temp E_pair E_mol TotEng Press Volume 784 0 -11894.026 0 -11894.026 -62911.788 35840.339 813 0 -11930.435 0 -11930.435 -166.51054 34347.619 Loop time of 0.837128 on 1 procs for 29 steps with 2930 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 = -11894.0255030046 -11930.4306248572 -11930.435062063 Force two-norm initial, final = 2510.5315 11.352775 Force max component initial, final = 1681.3400 9.2180685 Final line search alpha, max atom move = 4.2382277e-05 0.00039068273 Iterations, force evaluations = 29 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72636 | 0.72636 | 0.72636 | 0.0 | 86.77 Neigh | 0.084223 | 0.084223 | 0.084223 | 0.0 | 10.06 Comm | 0.0043495 | 0.0043495 | 0.0043495 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0222 | | | 2.65 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11731.0 ave 11731 max 11731 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: 413768.0 ave 413768 max 413768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413768 Ave neighs/atom = 141.21775 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.728 | 6.728 | 6.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11930.435 0 -11930.435 -166.51054 Loop time of 2.226e-06 on 1 procs for 0 steps with 2930 atoms 179.7% 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 | | 2.226e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11695.0 ave 11695 max 11695 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: 413336.0 ave 413336 max 413336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413336 Ave neighs/atom = 141.07031 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.728 | 6.728 | 6.728 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 -11930.435 -11930.435 39.551921 136.78253 6.3488989 -166.51054 -166.51054 114.98017 -420.17165 -194.34015 2.2228166 8735.269 Loop time of 2.607e-06 on 1 procs for 0 steps with 2930 atoms 345.2% 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 | | 2.607e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11695.0 ave 11695 max 11695 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 206668.0 ave 206668 max 206668 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 413336.0 ave 413336 max 413336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413336 Ave neighs/atom = 141.07031 Neighbor list builds = 0 Dangerous builds = 0 2930 -11930.435062063 eV 2.22281656920039 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:34