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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -69.720000 0.0000000) to (42.694606 69.720000 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9374715 4.9800000 5.7504087 Created 2350 atoms using lattice units in orthogonal box = (0.0000000 -69.720000 0.0000000) to (42.694606 69.720000 8.6256130) create_atoms CPU = 0.004 seconds 2350 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9374715 4.9800000 5.7504087 Created 2356 atoms using lattice units in orthogonal box = (0.0000000 -69.720000 0.0000000) to (42.694606 69.720000 8.6256130) create_atoms CPU = 0.003 seconds 2356 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 43 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 4692 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_500937681860_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 10.57 | 10.57 | 10.57 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19505.269 0 -19505.269 55244.147 113 0 -20807.516 0 -20807.516 4560.5186 Loop time of 43.3632 on 1 procs for 113 steps with 4692 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -19505.2693466925 -20807.4961626309 -20807.5156180004 Force two-norm initial, final = 1080.9637 0.58428321 Force max component initial, final = 144.11616 0.14160438 Final line search alpha, max atom move = 1.0000000 0.14160438 Iterations, force evaluations = 113 217 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 43.217 | 43.217 | 43.217 | 0.0 | 99.66 Neigh | 0.06711 | 0.06711 | 0.06711 | 0.0 | 0.15 Comm | 0.030795 | 0.030795 | 0.030795 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0478 | | | 0.11 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11968.0 ave 11968 max 11968 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: 408202.0 ave 408202 max 408202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 408202 Ave neighs/atom = 86.999574 Neighbor list builds = 2 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.57 | 10.57 | 10.57 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -20807.516 0 -20807.516 4560.5186 51351.172 118 0 -20808.086 0 -20808.086 -34.73652 51477.287 Loop time of 1.58197 on 1 procs for 5 steps with 4692 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20807.5156180002 -20808.0846214483 -20808.0859537904 Force two-norm initial, final = 333.41545 5.0297647 Force max component initial, final = 319.69132 4.0235278 Final line search alpha, max atom move = 5.7338118e-05 0.00023070151 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5758 | 1.5758 | 1.5758 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076638 | 0.00076638 | 0.00076638 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005386 | | | 0.34 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12013.0 ave 12013 max 12013 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: 407478.0 ave 407478 max 407478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407478 Ave neighs/atom = 86.845269 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 44 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 10.08 | 10.08 | 10.08 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20808.086 0 -20808.086 -34.73652 Loop time of 2.11e-06 on 1 procs for 0 steps with 4692 atoms 189.6% 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 | | 2.11e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12013.0 ave 12013 max 12013 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: 407156.0 ave 407156 max 407156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407156 Ave neighs/atom = 86.776641 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 44 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 10.08 | 10.08 | 10.08 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 -20808.086 -20808.086 42.672575 139.97427 8.61824 -34.73652 -34.73652 -125.16346 -53.038837 73.992736 2.1928958 1708.8918 Loop time of 4.414e-06 on 1 procs for 0 steps with 4692 atoms 271.9% 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 | | 4.414e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12013.0 ave 12013 max 12013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203578.0 ave 203578 max 203578 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 407156.0 ave 407156 max 407156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407156 Ave neighs/atom = 86.776641 Neighbor list builds = 0 Dangerous builds = 0 4692 -20808.0859537904 eV 2.19289580948222 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:46