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 = 3.6239511 3.6239511 3.6239511 Created orthogonal box = (0.0000000 -69.330267 0.0000000) to (40.027848 69.330267 6.2768674) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9057481 5.3039548 6.2768674 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -69.330267 0.0000000) to (40.027848 69.330267 6.2768674) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9057481 5.3039548 6.2768674 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -69.330267 0.0000000) to (40.027848 69.330267 6.2768674) create_atoms CPU = 0.003 seconds 1465 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 = 12 40 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2928 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_427873955970_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 = 12 40 2 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) = 6.202 | 6.202 | 6.202 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11802.342 0 -11802.342 47720.372 588 0 -12401.542 0 -12401.542 -3848.3639 Loop time of 209.796 on 1 procs for 588 steps with 2928 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 = -11802.3418313205 -12401.5295991286 -12401.5416439166 Force two-norm initial, final = 909.46699 0.37914350 Force max component initial, final = 207.26196 0.12099449 Final line search alpha, max atom move = 0.80478427 0.097374462 Iterations, force evaluations = 588 1065 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 209.07 | 209.07 | 209.07 | 0.0 | 99.65 Neigh | 0.43797 | 0.43797 | 0.43797 | 0.0 | 0.21 Comm | 0.14543 | 0.14543 | 0.14543 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1473 | | | 0.07 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11118.0 ave 11118 max 11118 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: 356458.0 ave 356458 max 356458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 356458 Ave neighs/atom = 121.74112 Neighbor list builds = 20 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 = 12 40 2 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 : 588 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.199 | 6.199 | 6.199 Mbytes Step Temp E_pair E_mol TotEng Press Volume 588 0 -12401.542 0 -12401.542 -3848.3639 34838.389 606 0 -12406.941 0 -12406.941 -15.589933 34750.161 Loop time of 4.96458 on 1 procs for 18 steps with 2928 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 = -12401.5416439166 -12406.9371644825 -12406.9410559729 Force two-norm initial, final = 606.50714 1.5747783 Force max component initial, final = 390.75222 0.58630607 Final line search alpha, max atom move = 8.1746973e-05 4.7928747e-05 Iterations, force evaluations = 18 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9296 | 4.9296 | 4.9296 | 0.0 | 99.30 Neigh | 0.020903 | 0.020903 | 0.020903 | 0.0 | 0.42 Comm | 0.0022948 | 0.0022948 | 0.0022948 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01179 | | | 0.24 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11060.0 ave 11060 max 11060 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: 357628.0 ave 357628 max 357628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 357628 Ave neighs/atom = 122.14071 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 = 12 40 2 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) = 6.336 | 6.336 | 6.336 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12406.941 0 -12406.941 -15.589933 Loop time of 2.128e-06 on 1 procs for 0 steps with 2928 atoms 235.0% 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 | | 2.128e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11010.0 ave 11010 max 11010 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: 357404.0 ave 357404 max 357404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 357404 Ave neighs/atom = 122.06421 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 = 12 40 2 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) = 6.336 | 6.336 | 6.336 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 -12406.941 -12406.941 39.801958 137.24396 6.3614944 -15.589933 -15.589933 -26.879434 -6.9817917 -12.908573 2.2326055 8037.5851 Loop time of 1.977e-06 on 1 procs for 0 steps with 2928 atoms 252.9% 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 | | 1.977e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11010.0 ave 11010 max 11010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 178702.0 ave 178702 max 178702 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 357404.0 ave 357404 max 357404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 357404 Ave neighs/atom = 122.06421 Neighbor list builds = 0 Dangerous builds = 0 2928 -12406.9410559729 eV 2.23260548145642 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:03:35