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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -42.840613 0.0000000) to (52.464388 42.840613 8.8681001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9959300 5.5076134 5.9120667 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -42.840613 0.0000000) to (52.464388 42.840613 8.8681001) create_atoms CPU = 0.003 seconds 1690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9959300 5.5076134 5.9120667 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -42.840613 0.0000000) to (52.464388 42.840613 8.8681001) create_atoms CPU = 0.002 seconds 1690 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 68 atoms, new total = 3312 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_390178379548_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.654 | 5.654 | 5.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11640.163 0 -11640.163 -2989.9412 42 0 -11674.324 0 -11674.324 -12909.221 Loop time of 3.62734 on 1 procs for 42 steps with 3312 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 = -11640.1632282925 -11674.3125446824 -11674.323839061 Force two-norm initial, final = 43.370556 0.26126395 Force max component initial, final = 8.9109415 0.062555765 Final line search alpha, max atom move = 0.97119826 0.060754050 Iterations, force evaluations = 42 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.587 | 3.587 | 3.587 | 0.0 | 98.89 Neigh | 0.020993 | 0.020993 | 0.020993 | 0.0 | 0.58 Comm | 0.0071162 | 0.0071162 | 0.0071162 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01218 | | | 0.34 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7888.00 ave 7888 max 7888 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: 255042.0 ave 255042 max 255042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255042 Ave neighs/atom = 77.005435 Neighbor list builds = 1 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.655 | 5.655 | 5.655 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -11674.324 0 -11674.324 -12909.221 39864 48 0 -11675.307 0 -11675.307 -3409.9905 39592.991 Loop time of 0.483503 on 1 procs for 6 steps with 3312 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 = -11674.3238390611 -11675.3053077822 -11675.3073323925 Force two-norm initial, final = 386.00078 0.36093695 Force max component initial, final = 314.09556 0.073360100 Final line search alpha, max atom move = 6.4462082e-05 4.7289448e-06 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47843 | 0.47843 | 0.47843 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060674 | 0.00060674 | 0.00060674 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004464 | | | 0.92 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7955.00 ave 7955 max 7955 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: 255152.0 ave 255152 max 255152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255152 Ave neighs/atom = 77.038647 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.793 | 5.793 | 5.793 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11675.307 0 -11675.307 -3409.9905 Loop time of 2.517e-06 on 1 procs for 0 steps with 3312 atoms 158.9% 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 | | 2.517e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7978.00 ave 7978 max 7978 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: 255230.0 ave 255230 max 255230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255230 Ave neighs/atom = 77.062198 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.793 | 5.793 | 5.793 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 -11675.307 -11675.307 52.357884 85.681227 8.8257283 -3409.9905 -3409.9905 -2.1957868 -10226.269 -1.5062123 2.3709072 1620.5374 Loop time of 2.41e-06 on 1 procs for 0 steps with 3312 atoms 249.0% 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 | | 2.41e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7978.00 ave 7978 max 7978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 127615.0 ave 127615 max 127615 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 255230.0 ave 255230 max 255230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255230 Ave neighs/atom = 77.062198 Neighbor list builds = 0 Dangerous builds = 0 3312 -11675.3073323925 eV 2.37090716914624 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04