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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -74.682360 0.0000000) to (37.339155 74.682360 4.0500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7106943 5.7106943 4.0500000 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.682360 0.0000000) to (37.339155 74.682360 4.0500000) create_atoms CPU = 0.003 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7106943 5.7106943 4.0500000 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.682360 0.0000000) to (37.339155 74.682360 4.0500000) create_atoms CPU = 0.002 seconds 682 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1356 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_971738391444_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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.069 | 5.069 | 5.069 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4511.6941 0 -4511.6941 2522.7723 75 0 -4539.0138 0 -4539.0138 -1527.2301 Loop time of 19.0566 on 1 procs for 75 steps with 1356 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 = -4511.69408583532 -4539.00972490956 -4539.0137650835 Force two-norm initial, final = 16.691493 0.18567743 Force max component initial, final = 3.5146513 0.012159892 Final line search alpha, max atom move = 1.0000000 0.012159892 Iterations, force evaluations = 75 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.995 | 18.995 | 18.995 | 0.0 | 99.67 Neigh | 0.018426 | 0.018426 | 0.018426 | 0.0 | 0.10 Comm | 0.022411 | 0.022411 | 0.022411 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02115 | | | 0.11 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7826.00 ave 7826 max 7826 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: 107288.0 ave 107288 max 107288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107288 Ave neighs/atom = 79.120944 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.072 | 5.072 | 5.072 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -4539.0138 0 -4539.0138 -1527.2301 22587.467 77 0 -4539.0237 0 -4539.0237 -599.83102 22560.186 Loop time of 0.77451 on 1 procs for 2 steps with 1356 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4539.01376508348 -4539.0231900411 -4539.02368279092 Force two-norm initial, final = 21.116835 0.18671540 Force max component initial, final = 17.682743 0.020081097 Final line search alpha, max atom move = 0.00041617282 8.3572067e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77111 | 0.77111 | 0.77111 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083066 | 0.00083066 | 0.00083066 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002567 | | | 0.33 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7830.00 ave 7830 max 7830 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: 107208.0 ave 107208 max 107208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107208 Ave neighs/atom = 79.061947 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.210 | 5.210 | 5.210 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4539.0237 0 -4539.0237 -599.83102 Loop time of 6.305e-06 on 1 procs for 0 steps with 1356 atoms 174.5% 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 | | 6.305e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7830.00 ave 7830 max 7830 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: 107336.0 ave 107336 max 107336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107336 Ave neighs/atom = 79.156342 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.210 | 5.210 | 5.210 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 -4539.0237 -4539.0237 37.303534 149.36472 4.048971 -599.83102 -599.83102 -0.15302453 -1797.9143 -1.4257545 2.422054 161.41418 Loop time of 7.036e-06 on 1 procs for 0 steps with 1356 atoms 284.3% 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 | | 7.036e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7830.00 ave 7830 max 7830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53668.0 ave 53668 max 53668 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107336.0 ave 107336 max 107336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107336 Ave neighs/atom = 79.156342 Neighbor list builds = 0 Dangerous builds = 0 1356 -4539.02368279092 eV 2.42205402760493 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20