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 = 3.5937292 3.5937292 3.5937292 Created orthogonal box = (0.0000000 -71.152208 0.0000000) to (43.571651 71.152208 8.8028028) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0388984 5.0823006 5.8685352 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -71.152208 0.0000000) to (43.571651 71.152208 8.8028028) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0388984 5.0823006 5.8685352 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.152208 0.0000000) to (43.571651 71.152208 8.8028028) create_atoms CPU = 0.003 seconds 2358 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 = 13 41 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 4710 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 13 41 3 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) = 11.41 | 11.41 | 11.41 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -17206.131 0 -17206.131 134291.24 89 0 -20065.978 0 -20065.978 6960.0729 Loop time of 40.7964 on 1 procs for 89 steps with 4710 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 = -17206.1308128634 -20065.9584236508 -20065.9776636604 Force two-norm initial, final = 1716.7642 0.49449482 Force max component initial, final = 325.83112 0.059303043 Final line search alpha, max atom move = 0.77707163 0.046082712 Iterations, force evaluations = 89 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 40.685 | 40.685 | 40.685 | 0.0 | 99.73 Neigh | 0.039563 | 0.039563 | 0.039563 | 0.0 | 0.10 Comm | 0.030093 | 0.030093 | 0.030093 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0417 | | | 0.10 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12898.0 ave 12898 max 12898 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: 627300.0 ave 627300 max 627300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 627300 Ave neighs/atom = 133.18471 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 = 13 41 3 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 : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.41 | 11.41 | 11.41 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -20065.978 0 -20065.978 6960.0729 54581.235 93 0 -20066.633 0 -20066.633 459.5807 54797.251 Loop time of 1.5858 on 1 procs for 4 steps with 4710 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 = -20065.9776636604 -20066.6156867492 -20066.632679763 Force two-norm initial, final = 426.79823 32.694056 Force max component initial, final = 331.50808 29.840084 Final line search alpha, max atom move = 2.5523910e-05 0.00076163560 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5805 | 1.5805 | 1.5805 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007134 | 0.0007134 | 0.0007134 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004558 | | | 0.29 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12931.0 ave 12931 max 12931 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: 626340.0 ave 626340 max 626340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 626340 Ave neighs/atom = 132.98089 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 = 13 41 3 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) = 10.92 | 10.92 | 10.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20066.633 0 -20066.633 459.5807 Loop time of 2.166e-06 on 1 procs for 0 steps with 4710 atoms 184.7% 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 | | 2.166e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12931.0 ave 12931 max 12931 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: 626088.0 ave 626088 max 626088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 626088 Ave neighs/atom = 132.92739 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 = 13 41 3 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) = 10.92 | 10.92 | 10.92 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 -20066.633 -20066.633 43.588797 142.76596 8.8056053 459.5807 459.5807 138.56004 875.302 364.88005 2.3278686 1812.5876 Loop time of 2.53e-06 on 1 procs for 0 steps with 4710 atoms 316.2% 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 | | 2.53e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12931.0 ave 12931 max 12931 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 313044.0 ave 313044 max 313044 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 626088.0 ave 626088 max 626088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 626088 Ave neighs/atom = 132.92739 Neighbor list builds = 0 Dangerous builds = 0 4710 -20066.632679763 eV 2.32786864784665 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:44