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 -59.441418 0.0000000) to (21.015715 59.441418 5.1737114) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7315586 6.3043928 5.1737114 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -59.441418 0.0000000) to (21.015715 59.441418 5.1737114) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7315586 6.3043928 5.1737114 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -59.441418 0.0000000) to (21.015715 59.441418 5.1737114) create_atoms CPU = 0.001 seconds 530 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 = 6 33 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 = 1058 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 = 6 33 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) = 5.039 | 5.039 | 5.039 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4090.1541 0 -4090.1541 41996.917 760 0 -4305.4724 0 -4305.4724 -62780.932 Loop time of 11.6671 on 1 procs for 760 steps with 1058 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4090.15406785637 -4305.46892280605 -4305.47239003108 Force two-norm initial, final = 326.36714 0.17723300 Force max component initial, final = 82.847783 0.020852022 Final line search alpha, max atom move = 1.0000000 0.020852022 Iterations, force evaluations = 760 1419 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.328 | 11.328 | 11.328 | 0.0 | 97.10 Neigh | 0.14836 | 0.14836 | 0.14836 | 0.0 | 1.27 Comm | 0.10793 | 0.10793 | 0.10793 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0823 | | | 0.71 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6611.00 ave 6611 max 6611 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: 143224.0 ave 143224 max 143224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143224 Ave neighs/atom = 135.37240 Neighbor list builds = 15 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 = 6 33 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 : 760 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.036 | 5.036 | 5.036 Mbytes Step Temp E_pair E_mol TotEng Press Volume 760 0 -4305.4724 0 -4305.4724 -62780.932 12926.041 806 0 -4329.5393 0 -4329.5393 -26.119382 12361.785 Loop time of 0.406777 on 1 procs for 46 steps with 1058 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 = -4305.47239003109 -4329.53501361124 -4329.53933387996 Force two-norm initial, final = 1007.6686 2.1682791 Force max component initial, final = 910.28032 0.76106795 Final line search alpha, max atom move = 0.00011072185 8.4266852e-05 Iterations, force evaluations = 46 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38878 | 0.38878 | 0.38878 | 0.0 | 95.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028272 | 0.0028272 | 0.0028272 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01517 | | | 3.73 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6625.00 ave 6625 max 6625 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: 143188.0 ave 143188 max 143188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143188 Ave neighs/atom = 135.33837 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 = 6 33 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) = 5.177 | 5.177 | 5.177 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4329.5393 0 -4329.5393 -26.119382 Loop time of 2.418e-06 on 1 procs for 0 steps with 1058 atoms 165.4% 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 | | 2.418e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6926.00 ave 6926 max 6926 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: 147164.0 ave 147164 max 147164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147164 Ave neighs/atom = 139.09641 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 = 6 33 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) = 5.177 | 5.177 | 5.177 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 -4329.5393 -4329.5393 21.001426 119.19476 4.9382747 -26.119382 -26.119382 -98.572828 4.2558006 15.958882 2.3482221 3796.3078 Loop time of 2.571e-06 on 1 procs for 0 steps with 1058 atoms 233.4% 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 | | 2.571e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6926.00 ave 6926 max 6926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73582.0 ave 73582 max 73582 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 147164.0 ave 147164 max 147164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147164 Ave neighs/atom = 139.09641 Neighbor list builds = 0 Dangerous builds = 0 1058 -4329.53933387996 eV 2.34822207486354 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12