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 -43.619835 0.0000000) to (21.809918 43.619835 4.0500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2644629 5.2644629 4.0500000 Created 231 atoms using lattice units in orthogonal box = (0.0000000 -43.619835 0.0000000) to (21.809918 43.619835 4.0500000) create_atoms CPU = 0.002 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2644629 5.2644629 4.0500000 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.619835 0.0000000) to (21.809918 43.619835 4.0500000) create_atoms CPU = 0.001 seconds 233 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 20 1 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 463 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_664470114311_005#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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 4.497 | 4.497 | 4.497 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1537.6501 0 -1537.6501 4081.9973 17 0 -1549.6579 0 -1549.6579 4436.4017 Loop time of 0.312613 on 1 procs for 17 steps with 463 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 = -1537.65008303772 -1549.65688525648 -1549.65791795983 Force two-norm initial, final = 17.754487 0.069401296 Force max component initial, final = 5.9116926 0.0080523199 Final line search alpha, max atom move = 1.0000000 0.0080523199 Iterations, force evaluations = 17 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3064 | 0.3064 | 0.3064 | 0.0 | 98.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.003575 | 0.003575 | 0.003575 | 0.0 | 1.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00264 | | | 0.84 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5083.00 ave 5083 max 5083 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: 80976.0 ave 80976 max 80976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80976 Ave neighs/atom = 174.89417 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.497 | 4.497 | 4.497 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -1549.6579 0 -1549.6579 4436.4017 7705.8946 27 0 -1549.8471 0 -1549.8471 10.886565 7748.6847 Loop time of 0.127844 on 1 procs for 10 steps with 463 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 = -1549.65791795983 -1549.84594331189 -1549.84712634551 Force two-norm initial, final = 45.862178 0.24950820 Force max component initial, final = 43.377163 0.11124156 Final line search alpha, max atom move = 0.00049684188 5.5269466e-05 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12245 | 0.12245 | 0.12245 | 0.0 | 95.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012838 | 0.0012838 | 0.0012838 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004114 | | | 3.22 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5050.00 ave 5050 max 5050 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: 80328.0 ave 80328 max 80328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80328 Ave neighs/atom = 173.49460 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 4.635 | 4.635 | 4.635 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1549.8471 0 -1549.8471 10.886565 Loop time of 6.034e-06 on 1 procs for 0 steps with 463 atoms 149.2% 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 | | 6.034e-06 | | |100.00 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5050.00 ave 5050 max 5050 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: 80158.0 ave 80158 max 80158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80158 Ave neighs/atom = 173.12743 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 4.635 | 4.635 | 4.635 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 -1549.8471 -1549.8471 21.785825 88.090481 4.0376158 10.886565 10.886565 22.975736 5.2515556 4.4324046 2.4412255 427.79387 Loop time of 6.585e-06 on 1 procs for 0 steps with 463 atoms 273.3% 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 | | 6.585e-06 | | |100.00 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5050.00 ave 5050 max 5050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40079.0 ave 40079 max 40079 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80158.0 ave 80158 max 80158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80158 Ave neighs/atom = 173.12743 Neighbor list builds = 0 Dangerous builds = 0 463 -1547.03235738795 eV 2.44122545633029 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00