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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -50.345331 0.0000000) to (29.066890 50.345331 4.9367658) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4718293 4.5181707 4.9367658 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -50.345331 0.0000000) to (29.066890 50.345331 4.9367658) create_atoms CPU = 0.002 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4718293 4.5181707 4.9367658 Created 626 atoms using lattice units in orthogonal box = (0.0000000 -50.345331 0.0000000) to (29.066890 50.345331 4.9367658) create_atoms CPU = 0.002 seconds 626 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 34 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1248 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.650 | 4.650 | 4.650 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4767.6952 0 -4767.6952 137814.46 50 0 -5334.7958 0 -5334.7958 5143.4685 Loop time of 7.21354 on 1 procs for 50 steps with 1248 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4767.69519150282 -5334.79134088474 -5334.79578663451 Force two-norm initial, final = 1436.4692 0.20288739 Force max component initial, final = 256.47644 0.026648033 Final line search alpha, max atom move = 1.0000000 0.026648033 Iterations, force evaluations = 50 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.1906 | 7.1906 | 7.1906 | 0.0 | 99.68 Neigh | 0.0077662 | 0.0077662 | 0.0077662 | 0.0 | 0.11 Comm | 0.0077057 | 0.0077057 | 0.0077057 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007494 | | | 0.10 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5710.00 ave 5710 max 5710 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: 82244.0 ave 82244 max 82244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82244 Ave neighs/atom = 65.900641 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.650 | 4.650 | 4.650 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -5334.7958 0 -5334.7958 5143.4685 14448.75 52 0 -5334.8745 0 -5334.8745 -312.6622 14496.09 Loop time of 0.308842 on 1 procs for 2 steps with 1248 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 = -5334.79578663449 -5334.86971695002 -5334.87454591084 Force two-norm initial, final = 82.169929 7.4735807 Force max component initial, final = 54.324044 7.4153583 Final line search alpha, max atom move = 7.8387539e-05 0.00058127169 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30778 | 0.30778 | 0.30778 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019238 | 0.00019238 | 0.00019238 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008707 | | | 0.28 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5710.00 ave 5710 max 5710 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: 82016.0 ave 82016 max 82016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82016 Ave neighs/atom = 65.717949 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.788 | 4.788 | 4.788 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5334.8745 0 -5334.8745 -312.6622 Loop time of 2.323e-06 on 1 procs for 0 steps with 1248 atoms 172.2% 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 | | 2.323e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5710.00 ave 5710 max 5710 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: 81872.0 ave 81872 max 81872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81872 Ave neighs/atom = 65.602564 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.788 | 4.788 | 4.788 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 -5334.8745 -5334.8745 29.082702 100.82581 4.9436122 -312.6622 -312.6622 -820.02632 -19.288446 -98.671829 2.3054873 736.48823 Loop time of 2.227e-06 on 1 procs for 0 steps with 1248 atoms 224.5% 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 | | 2.227e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5710.00 ave 5710 max 5710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40936.0 ave 40936 max 40936 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81872.0 ave 81872 max 81872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81872 Ave neighs/atom = 65.602564 Neighbor list builds = 0 Dangerous builds = 0 1248 -5334.87454591084 eV 2.30548726162313 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08