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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -49.974880 0.0000000) to (35.335103 49.974880 4.9479041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5427612 4.4092396 4.9479041 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -49.974880 0.0000000) to (35.335103 49.974880 4.9479041) create_atoms CPU = 0.001 seconds 821 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5427612 4.4092396 4.9479041 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -49.974880 0.0000000) to (35.335103 49.974880 4.9479041) create_atoms CPU = 0.001 seconds 821 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 27 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1626 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_677715648236_000#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.558 | 5.558 | 5.558 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6523.9589 0 -6523.9589 69758.941 35 0 -6672.3364 0 -6672.3364 782.00781 Loop time of 0.89463 on 1 procs for 35 steps with 1626 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 = -6523.9589464627 -6672.32975340917 -6672.33636586028 Force two-norm initial, final = 214.31311 0.38109111 Force max component initial, final = 43.067657 0.13517559 Final line search alpha, max atom move = 1.0000000 0.13517559 Iterations, force evaluations = 35 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.88452 | 0.88452 | 0.88452 | 0.0 | 98.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0052012 | 0.0052012 | 0.0052012 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004913 | | | 0.55 Nlocal: 1626.00 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9742.00 ave 9742 max 9742 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: 284602.0 ave 284602 max 284602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 284602 Ave neighs/atom = 175.03198 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.558 | 5.558 | 5.558 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -6672.3364 0 -6672.3364 782.00781 17474.686 37 0 -6672.3654 0 -6672.3654 -1337.5337 17505.722 Loop time of 0.056232 on 1 procs for 2 steps with 1626 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 = -6672.33636586028 -6672.36316697319 -6672.36542498454 Force two-norm initial, final = 40.292645 0.98028195 Force max component initial, final = 38.477748 0.88832547 Final line search alpha, max atom move = 9.1288545e-05 8.1093940e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.054818 | 0.054818 | 0.054818 | 0.0 | 97.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028836 | 0.00028836 | 0.00028836 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001125 | | | 2.00 Nlocal: 1626.00 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9766.00 ave 9766 max 9766 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: 284450.0 ave 284450 max 284450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 284450 Ave neighs/atom = 174.93850 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.696 | 5.696 | 5.696 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6672.3654 0 -6672.3654 -1337.5337 Loop time of 1.811e-06 on 1 procs for 0 steps with 1626 atoms 165.7% 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 | | 1.811e-06 | | |100.00 Nlocal: 1626.00 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9766.00 ave 9766 max 9766 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: 284354.0 ave 284354 max 284354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 284354 Ave neighs/atom = 174.87946 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.696 | 5.696 | 5.696 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 -6672.3654 -6672.3654 35.384732 99.949761 4.9497398 -1337.5337 -1337.5337 7.1608584 -3938.4294 -81.33239 2.306752 524.24697 Loop time of 1.73e-06 on 1 procs for 0 steps with 1626 atoms 231.2% 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 | | 1.73e-06 | | |100.00 Nlocal: 1626.00 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9766.00 ave 9766 max 9766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 142177.0 ave 142177 max 142177 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 284354.0 ave 284354 max 284354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 284354 Ave neighs/atom = 174.87946 Neighbor list builds = 0 Dangerous builds = 0 1626 -6672.36542498454 eV 2.3067519810593 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01