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 = 3.6583664 3.6583664 3.6583664 Created orthogonal box = (0.0000000 -43.286375 0.0000000) to (53.014766 43.286375 8.9611309) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0588303 5.5653910 5.9740873 Created 1665 atoms using lattice units in orthogonal box = (0.0000000 -43.286375 0.0000000) to (53.014766 43.286375 8.9611309) create_atoms CPU = 0.003 seconds 1665 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0588303 5.5653910 5.9740873 Created 1689 atoms using lattice units in orthogonal box = (0.0000000 -43.286375 0.0000000) to (53.014766 43.286375 8.9611309) create_atoms CPU = 0.003 seconds 1689 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 = 15 24 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3352 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_807997826449_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 3 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) = 6.538 | 6.538 | 6.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12771.113 0 -12771.113 57903.367 1108 0 -13593.171 0 -13593.171 -68932.51 Loop time of 48.1767 on 1 procs for 1108 steps with 3352 atoms 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12771.113002382 -13593.1580000964 -13593.1707844315 Force two-norm initial, final = 594.14526 0.34743354 Force max component initial, final = 53.607251 0.051965203 Final line search alpha, max atom move = 0.69599673 0.036167611 Iterations, force evaluations = 1108 2126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 46.662 | 46.662 | 46.662 | 0.0 | 96.86 Neigh | 0.95808 | 0.95808 | 0.95808 | 0.0 | 1.99 Comm | 0.23556 | 0.23556 | 0.23556 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3214 | | | 0.67 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9825.00 ave 9825 max 9825 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: 461938.0 ave 461938 max 461938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461938 Ave neighs/atom = 137.80967 Neighbor list builds = 30 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 = 15 24 3 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 : 1108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.537 | 6.537 | 6.537 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1108 0 -13593.171 0 -13593.171 -68932.51 41128.311 1173 0 -13722.032 0 -13722.032 316.11447 39309.75 Loop time of 1.59584 on 1 procs for 65 steps with 3352 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 = -13593.1707844315 -13722.0276560732 -13722.0318096035 Force two-norm initial, final = 3840.9677 18.504055 Force max component initial, final = 2934.0846 16.855617 Final line search alpha, max atom move = 9.9230445e-05 0.0016725904 Iterations, force evaluations = 65 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4331 | 1.4331 | 1.4331 | 0.0 | 89.80 Neigh | 0.12064 | 0.12064 | 0.12064 | 0.0 | 7.56 Comm | 0.0060147 | 0.0060147 | 0.0060147 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03608 | | | 2.26 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9709.00 ave 9709 max 9709 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: 478846.0 ave 478846 max 478846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478846 Ave neighs/atom = 142.85382 Neighbor list builds = 4 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 = 15 23 3 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) = 6.673 | 6.673 | 6.673 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13722.032 0 -13722.032 316.11447 Loop time of 2.094e-06 on 1 procs for 0 steps with 3352 atoms 191.0% 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 | | 2.094e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9611.00 ave 9611 max 9611 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: 478506.0 ave 478506 max 478506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478506 Ave neighs/atom = 142.75239 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 = 15 23 3 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) = 6.673 | 6.673 | 6.673 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 -13722.032 -13722.032 51.278947 82.140834 9.3325877 316.11447 316.11447 35.535995 651.82741 260.97999 2.2608655 6259.4855 Loop time of 4.328e-06 on 1 procs for 0 steps with 3352 atoms 254.2% 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 | | 4.328e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9611.00 ave 9611 max 9611 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 239253.0 ave 239253 max 239253 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 478506.0 ave 478506 max 478506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478506 Ave neighs/atom = 142.75239 Neighbor list builds = 0 Dangerous builds = 0 3352 -13722.0318096034 eV 2.2608655426744 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:50