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 = 3.6150017 3.6150017 3.6150017 Created orthogonal box = (0.0000000 -42.773277 0.0000000) to (52.386351 42.773277 8.8549095) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9870116 5.4994213 5.9032730 Created 1661 atoms using lattice units in orthogonal box = (0.0000000 -42.773277 0.0000000) to (52.386351 42.773277 8.8549095) create_atoms CPU = 0.003 seconds 1661 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9870116 5.4994213 5.9032730 Created 1685 atoms using lattice units in orthogonal box = (0.0000000 -42.773277 0.0000000) to (52.386351 42.773277 8.8549095) create_atoms CPU = 0.002 seconds 1685 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 13 21 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3346 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_592013496703_005#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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 7.470 | 7.470 | 7.470 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11460.313 0 -11460.313 24711.889 133 0 -11801.355 0 -11801.355 464.60002 Loop time of 7.82177 on 1 procs for 133 steps with 3346 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 = -11460.3127737805 -11801.3439381525 -11801.3550104387 Force two-norm initial, final = 251.76015 0.32527643 Force max component initial, final = 43.443276 0.080476687 Final line search alpha, max atom move = 1.0000000 0.080476687 Iterations, force evaluations = 133 225 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.4787 | 7.4787 | 7.4787 | 0.0 | 95.61 Neigh | 0.27338 | 0.27338 | 0.27338 | 0.0 | 3.50 Comm | 0.029664 | 0.029664 | 0.029664 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03997 | | | 0.51 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12052.0 ave 12052 max 12052 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: 685334.0 ave 685334 max 685334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 685334 Ave neighs/atom = 204.82188 Neighbor list builds = 7 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 133 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.470 | 7.470 | 7.470 Mbytes Step Temp E_pair E_mol TotEng Press Volume 133 0 -11801.355 0 -11801.355 464.60002 39683.027 137 0 -11801.52 0 -11801.52 9.5968584 39695.303 Loop time of 0.239812 on 1 procs for 4 steps with 3346 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 = -11801.3550104387 -11801.5201720138 -11801.5203976239 Force two-norm initial, final = 100.62947 1.4103516 Force max component initial, final = 91.497319 1.1842216 Final line search alpha, max atom move = 0.00017491451 0.00020713754 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23492 | 0.23492 | 0.23492 | 0.0 | 97.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067752 | 0.00067752 | 0.00067752 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004212 | | | 1.76 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12047.0 ave 12047 max 12047 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: 684638.0 ave 684638 max 684638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 684638 Ave neighs/atom = 204.61387 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 7.608 | 7.608 | 7.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11801.52 0 -11801.52 9.5968584 Loop time of 2.734e-06 on 1 procs for 0 steps with 3346 atoms 146.3% 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 | | 2.734e-06 | | |100.00 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12065.0 ave 12065 max 12065 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: 686372.0 ave 686372 max 686372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 686372 Ave neighs/atom = 205.13210 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 7.608 | 7.608 | 7.608 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 -11801.52 -11801.52 52.314493 85.788316 8.8448192 9.5968584 9.5968584 47.731829 6.1697621 -25.111017 2.3366665 1827.9238 Loop time of 2.551e-06 on 1 procs for 0 steps with 3346 atoms 235.2% 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 | | 2.551e-06 | | |100.00 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12065.0 ave 12065 max 12065 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 343186.0 ave 343186 max 343186 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 686372.0 ave 686372 max 686372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 686372 Ave neighs/atom = 205.13210 Neighbor list builds = 0 Dangerous builds = 0 3346 -11801.5203976239 eV 2.33666646213251 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08