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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -34.002154 0.0000000) to (11.334051 34.002154 3.1435003) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3592506 4.3592506 3.1435003 Created 78 atoms using lattice units in orthogonal box = (0.0000000 -34.002154 0.0000000) to (11.334051 34.002154 3.1435003) create_atoms CPU = 0.001 seconds 78 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3592506 4.3592506 3.1435003 Created 79 atoms using lattice units in orthogonal box = (0.0000000 -34.002154 0.0000000) to (11.334051 34.002154 3.1435003) create_atoms CPU = 0.000 seconds 79 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 3 14 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 155 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_534363225491_004#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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 3 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.429 | 4.429 | 4.429 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -870.27996 0 -870.27996 164474.95 94 0 -1028.6732 0 -1028.6732 1658.0473 Loop time of 0.372903 on 1 procs for 94 steps with 155 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 = -870.279962666558 -1028.67244181723 -1028.6732171722 Force two-norm initial, final = 498.14498 0.15605065 Force max component initial, final = 234.81346 0.032521773 Final line search alpha, max atom move = 0.99357549 0.032312836 Iterations, force evaluations = 94 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35975 | 0.35975 | 0.35975 | 0.0 | 96.47 Neigh | 0.0052523 | 0.0052523 | 0.0052523 | 0.0 | 1.41 Comm | 0.0052511 | 0.0052511 | 0.0052511 | 0.0 | 1.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002653 | | | 0.71 Nlocal: 155.000 ave 155 max 155 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3695.00 ave 3695 max 3695 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: 42434.0 ave 42434 max 42434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42434 Ave neighs/atom = 273.76774 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 3 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -1028.6732 0 -1028.6732 1658.0473 2422.8979 493 0 -1040.5501 0 -1040.5501 981.84159 2410.3338 Loop time of 1.09008 on 1 procs for 399 steps with 155 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 = -1028.6732171722 -1040.54929205526 -1040.5501453328 Force two-norm initial, final = 88.248276 3.4583571 Force max component initial, final = 68.195880 2.7250098 Final line search alpha, max atom move = 0.00079465092 0.0021654315 Iterations, force evaluations = 399 462 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99991 | 0.99991 | 0.99991 | 0.0 | 91.73 Neigh | 0.010662 | 0.010662 | 0.010662 | 0.0 | 0.98 Comm | 0.016477 | 0.016477 | 0.016477 | 0.0 | 1.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06302 | | | 5.78 Nlocal: 155.000 ave 155 max 155 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4133.00 ave 4133 max 4133 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: 42576.0 ave 42576 max 42576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42576 Ave neighs/atom = 274.68387 Neighbor list builds = 4 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.571 | 4.571 | 4.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1040.5501 0 -1040.5501 981.84159 Loop time of 2.091e-06 on 1 procs for 0 steps with 155 atoms 143.5% 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 | | 2.091e-06 | | |100.00 Nlocal: 155.000 ave 155 max 155 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4157.00 ave 4157 max 4157 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: 42492.0 ave 42492 max 42492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42492 Ave neighs/atom = 274.14194 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.571 | 4.571 | 4.571 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 -1040.5501 -1040.5501 11.720126 72.112222 2.8519114 981.84159 981.84159 1873.0455 808.21328 264.26594 2.6260418 517.09786 Loop time of 3.31e-06 on 1 procs for 0 steps with 155 atoms 211.5% 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 | | 3.31e-06 | | |100.00 Nlocal: 155.000 ave 155 max 155 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4157.00 ave 4157 max 4157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21246.0 ave 21246 max 21246 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42492.0 ave 42492 max 42492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42492 Ave neighs/atom = 274.14194 Neighbor list builds = 0 Dangerous builds = 0 155 -1040.5501453328 eV 2.62604182686277 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01