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 = 3.5618363 3.5618363 3.5618363 Created orthogonal box = (0.0000000 -38.030005 0.0000000) to (26.891275 38.030005 5.0371973) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1895442 6.0047377 5.0371973 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.030005 0.0000000) to (26.891275 38.030005 5.0371973) create_atoms CPU = 0.004 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1895442 6.0047377 5.0371973 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.030005 0.0000000) to (26.891275 38.030005 5.0371973) create_atoms CPU = 0.003 seconds 458 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 18 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 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_322509103239_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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.396 | 5.396 | 5.396 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3382.6316 0 -3382.6316 43553.361 70 0 -3564.8205 0 -3564.8205 6576.4823 Loop time of 3.07052 on 1 procs for 70 steps with 912 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 = -3382.63155548732 -3564.8173279778 -3564.82046363961 Force two-norm initial, final = 293.16960 0.24398341 Force max component initial, final = 93.705830 0.028419462 Final line search alpha, max atom move = 1.0000000 0.028419462 Iterations, force evaluations = 70 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.995 | 2.995 | 2.995 | 0.0 | 97.54 Neigh | 0.030614 | 0.030614 | 0.030614 | 0.0 | 1.00 Comm | 0.026054 | 0.026054 | 0.026054 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01884 | | | 0.61 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7251.00 ave 7251 max 7251 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: 203616.0 ave 203616 max 203616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203616 Ave neighs/atom = 223.26316 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.396 | 5.396 | 5.396 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -3564.8205 0 -3564.8205 6576.4823 10302.835 77 0 -3565.177 0 -3565.177 -91.914068 10341.412 Loop time of 0.204616 on 1 procs for 7 steps with 912 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 = -3564.82046363961 -3565.17575946767 -3565.17701573877 Force two-norm initial, final = 120.19003 2.1926855 Force max component initial, final = 119.93144 1.5779976 Final line search alpha, max atom move = 0.00020819729 0.00032853484 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19747 | 0.19747 | 0.19747 | 0.0 | 96.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015077 | 0.0015077 | 0.0015077 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005643 | | | 2.76 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7233.00 ave 7233 max 7233 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: 203620.0 ave 203620 max 203620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203620 Ave neighs/atom = 223.26754 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.533 | 5.533 | 5.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3565.177 0 -3565.177 -91.914068 Loop time of 6.946e-06 on 1 procs for 0 steps with 912 atoms 201.6% 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 | | 6.946e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7193.00 ave 7193 max 7193 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: 203300.0 ave 203300 max 203300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203300 Ave neighs/atom = 222.91667 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.533 | 5.533 | 5.533 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 -3565.177 -3565.177 26.824041 76.505352 5.039226 -91.914068 -91.914068 -243.86511 134.88919 -166.76629 2.2922933 637.80719 Loop time of 9.522e-06 on 1 procs for 0 steps with 912 atoms 231.0% 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 | | 9.522e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7193.00 ave 7193 max 7193 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101650.0 ave 101650 max 101650 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203300.0 ave 203300 max 203300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203300 Ave neighs/atom = 222.91667 Neighbor list builds = 0 Dangerous builds = 0 912 -3565.17701573877 eV 2.29229331929316 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03