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 = 4.0320000 4.0320000 4.0320000 Created orthogonal box = (0.0000000 -53.490524 0.0000000) to (32.756123 53.490524 9.8763426) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9556587 6.0784687 6.5842284 Created 1047 atoms using lattice units in orthogonal box = (0.0000000 -53.490524 0.0000000) to (32.756123 53.490524 9.8763426) create_atoms CPU = 0.002 seconds 1047 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9556587 6.0784687 6.5842284 Created 1071 atoms using lattice units in orthogonal box = (0.0000000 -53.490524 0.0000000) to (32.756123 53.490524 9.8763426) create_atoms CPU = 0.001 seconds 1071 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 8 25 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2110 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_519613893196_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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 6.029 | 6.029 | 6.029 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7048.1341 0 -7048.1341 4737.9537 47 0 -7082.9084 0 -7082.9084 1304.8628 Loop time of 1.81725 on 1 procs for 47 steps with 2110 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7048.13413321746 -7082.90238860291 -7082.90842143279 Force two-norm initial, final = 32.332590 0.16428338 Force max component initial, final = 4.1650382 0.019639217 Final line search alpha, max atom move = 1.0000000 0.019639217 Iterations, force evaluations = 47 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7727 | 1.7727 | 1.7727 | 0.0 | 97.55 Neigh | 0.02375 | 0.02375 | 0.02375 | 0.0 | 1.31 Comm | 0.0089562 | 0.0089562 | 0.0089562 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01185 | | | 0.65 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8359.00 ave 8359 max 8359 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: 369964.0 ave 369964 max 369964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369964 Ave neighs/atom = 175.33839 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.029 | 6.029 | 6.029 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -7082.9084 0 -7082.9084 1304.8628 34609.513 51 0 -7083.0044 0 -7083.0044 -5.1940465 34664.851 Loop time of 0.13912 on 1 procs for 4 steps with 2110 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 = -7082.9084214328 -7083.00259424835 -7083.00438155156 Force two-norm initial, final = 66.154435 1.2314900 Force max component initial, final = 64.296986 0.97502152 Final line search alpha, max atom move = 6.9748984e-05 6.8006761e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13551 | 0.13551 | 0.13551 | 0.0 | 97.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051396 | 0.00051396 | 0.00051396 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003092 | | | 2.22 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8344.00 ave 8344 max 8344 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: 369850.0 ave 369850 max 369850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369850 Ave neighs/atom = 175.28436 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 8 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 6.167 | 6.167 | 6.167 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7083.0044 0 -7083.0044 -5.1940465 Loop time of 2.631e-06 on 1 procs for 0 steps with 2110 atoms 190.0% 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 | | 2.631e-06 | | |100.00 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8344.00 ave 8344 max 8344 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: 369810.0 ave 369810 max 369810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369810 Ave neighs/atom = 175.26540 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 8 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 6.167 | 6.167 | 6.167 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 -7083.0044 -7083.0044 32.735137 107.32738 9.8665352 -5.1940465 -5.1940465 -45.035697 -3.9837799 33.437337 2.6795366 908.80522 Loop time of 2.424e-06 on 1 procs for 0 steps with 2110 atoms 288.8% 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 | | 2.424e-06 | | |100.00 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8344.00 ave 8344 max 8344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 184905.0 ave 184905 max 184905 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 369810.0 ave 369810 max 369810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369810 Ave neighs/atom = 175.26540 Neighbor list builds = 0 Dangerous builds = 0 2110 -7083.00438155156 eV 2.67953662486733 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02