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 = 4.0499989 4.0499989 4.0499989 Created orthogonal box = (0.0000000 -81.202225 0.0000000) to (46.882126 81.202225 7.0148038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2975991 6.4638587 7.0148038 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -81.202225 0.0000000) to (46.882126 81.202225 7.0148038) create_atoms CPU = 0.016 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2975991 6.4638587 7.0148038 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -81.202225 0.0000000) to (46.882126 81.202225 7.0148038) create_atoms CPU = 0.014 seconds 1610 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 = 14 47 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 = 3218 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_315820974149_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 = 14 47 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) = 5.843 | 5.843 | 5.843 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10283.559 0 -10283.559 27033.341 171 0 -10785.966 0 -10785.966 4473.7415 Loop time of 65.9726 on 1 procs for 171 steps with 3218 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 = -10283.5589048668 -10785.9561667836 -10785.9659857728 Force two-norm initial, final = 470.30735 0.40628575 Force max component initial, final = 103.70710 0.086107281 Final line search alpha, max atom move = 1.0000000 0.086107281 Iterations, force evaluations = 171 330 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 65.622 | 65.622 | 65.622 | 0.0 | 99.47 Neigh | 0.16855 | 0.16855 | 0.16855 | 0.0 | 0.26 Comm | 0.080545 | 0.080545 | 0.080545 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1016 | | | 0.15 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10375.0 ave 10375 max 10375 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: 260072.0 ave 260072 max 260072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260072 Ave neighs/atom = 80.817899 Neighbor list builds = 4 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 = 14 47 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 : 171 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.842 | 5.842 | 5.842 Mbytes Step Temp E_pair E_mol TotEng Press Volume 171 0 -10785.966 0 -10785.966 4473.7415 53409.776 178 0 -10786.861 0 -10786.861 18.589832 53713.923 Loop time of 1.85176 on 1 procs for 7 steps with 3218 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10785.9659857728 -10786.852715463 -10786.8612576623 Force two-norm initial, final = 305.62416 1.8321993 Force max component initial, final = 279.60336 1.6008533 Final line search alpha, max atom move = 5.8096270e-05 9.3003604e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7973 | 1.7973 | 1.7973 | 0.0 | 97.06 Neigh | 0.041988 | 0.041988 | 0.041988 | 0.0 | 2.27 Comm | 0.0027726 | 0.0027726 | 0.0027726 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00971 | | | 0.52 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10352.0 ave 10352 max 10352 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: 253068.0 ave 253068 max 253068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253068 Ave neighs/atom = 78.641392 Neighbor list builds = 1 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 = 14 47 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) = 5.980 | 5.980 | 5.980 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10786.861 0 -10786.861 18.589832 Loop time of 6.234e-06 on 1 procs for 0 steps with 3218 atoms 224.6% 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 | | 6.234e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10352.0 ave 10352 max 10352 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: 253060.0 ave 253060 max 253060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253060 Ave neighs/atom = 78.638906 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 = 14 47 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) = 5.980 | 5.980 | 5.980 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 -10786.861 -10786.861 46.888175 163.48411 7.0072564 18.589832 18.589832 -10.432464 18.503156 47.698804 2.5272422 1257.6246 Loop time of 7.177e-06 on 1 procs for 0 steps with 3218 atoms 264.7% 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 | | 7.177e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10352.0 ave 10352 max 10352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126530.0 ave 126530 max 126530 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 253060.0 ave 253060 max 253060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253060 Ave neighs/atom = 78.638906 Neighbor list builds = 0 Dangerous builds = 0 3218 -10786.8612576623 eV 2.52724223466175 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:09