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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -41.390325 0.0000000) to (6.3360136 41.390325 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3360136 5.1733334 5.9736509 Created 198 atoms using lattice units in orthogonal box = (0.0000000 -41.390325 0.0000000) to (6.3360136 41.390325 8.9604763) create_atoms CPU = 0.001 seconds 198 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3360136 5.1733334 5.9736509 Created 198 atoms using lattice units in orthogonal box = (0.0000000 -41.390325 0.0000000) to (6.3360136 41.390325 8.9604763) create_atoms CPU = 0.000 seconds 198 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 23 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 17 atoms, new total = 379 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_634187028437_000#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.518 | 4.518 | 4.518 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1455.0829 0 -1455.0829 6450.3252 549 0 -1492.5531 0 -1492.5531 -81946.787 Loop time of 3.70816 on 1 procs for 549 steps with 379 atoms 89.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1455.08294962952 -1492.55189430884 -1492.55305628822 Force two-norm initial, final = 35.196912 0.089843454 Force max component initial, final = 6.3440744 0.018735922 Final line search alpha, max atom move = 1.0000000 0.018735922 Iterations, force evaluations = 549 1084 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6018 | 3.6018 | 3.6018 | 0.0 | 97.13 Neigh | 0.043311 | 0.043311 | 0.043311 | 0.0 | 1.17 Comm | 0.040646 | 0.040646 | 0.040646 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02236 | | | 0.60 Nlocal: 379.000 ave 379 max 379 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3495.00 ave 3495 max 3495 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: 50516.0 ave 50516 max 50516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50516 Ave neighs/atom = 133.28760 Neighbor list builds = 10 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 549 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.518 | 4.518 | 4.518 Mbytes Step Temp E_pair E_mol TotEng Press Volume 549 0 -1492.5531 0 -1492.5531 -81946.787 4699.7638 603 0 -1500.0343 0 -1500.0343 -16417.031 4474.3398 Loop time of 0.189363 on 1 procs for 54 steps with 379 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 = -1492.55305628822 -1500.03307503292 -1500.03433338533 Force two-norm initial, final = 337.89724 3.0904000 Force max component initial, final = 300.20111 1.8051629 Final line search alpha, max atom move = 0.00034652149 0.00062552772 Iterations, force evaluations = 54 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17954 | 0.17954 | 0.17954 | 0.0 | 94.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016392 | 0.0016392 | 0.0016392 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00818 | | | 4.32 Nlocal: 379.000 ave 379 max 379 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3479.00 ave 3479 max 3479 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: 50346.0 ave 50346 max 50346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50346 Ave neighs/atom = 132.83905 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.656 | 4.656 | 4.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1500.0343 0 -1500.0343 -16417.031 Loop time of 1.949e-06 on 1 procs for 0 steps with 379 atoms 153.9% 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 | | 1.949e-06 | | |100.00 Nlocal: 379.000 ave 379 max 379 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3592.00 ave 3592 max 3592 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: 53808.0 ave 53808 max 53808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53808 Ave neighs/atom = 141.97361 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.656 | 4.656 | 4.656 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 -1500.0343 -1500.0343 6.3276414 82.780651 8.5419744 -16417.031 -16417.031 645.54058 -50410.564 513.93094 2.2699382 1030.0787 Loop time of 1.912e-06 on 1 procs for 0 steps with 379 atoms 156.9% 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 | | 1.912e-06 | | |100.00 Nlocal: 379.000 ave 379 max 379 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3592.00 ave 3592 max 3592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26904.0 ave 26904 max 26904 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53808.0 ave 53808 max 53808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53808 Ave neighs/atom = 141.97361 Neighbor list builds = 0 Dangerous builds = 0 379 -1446.43553792221 eV 2.26993817970794 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04