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 = 3.4921275 3.4921275 3.4921275 Created orthogonal box = (0.0000000 -54.994080 0.0000000) to (33.676858 54.994080 8.5539306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4317514 5.3220077 5.7026204 Created 1484 atoms using lattice units in orthogonal box = (0.0000000 -54.994080 0.0000000) to (33.676858 54.994080 8.5539306) create_atoms CPU = 0.003 seconds 1484 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4317514 5.3220077 5.7026204 Created 1490 atoms using lattice units in orthogonal box = (0.0000000 -54.994080 0.0000000) to (33.676858 54.994080 8.5539306) create_atoms CPU = 0.002 seconds 1490 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 9 28 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 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2974 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_270337113239_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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 7.366 | 7.366 | 7.366 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9670.8861 0 -9670.8861 22900.594 100 0 -9858.1951 0 -9858.1951 2094.9641 Loop time of 4.72238 on 1 procs for 100 steps with 2974 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9670.88607256541 -9858.18567468344 -9858.19514322765 Force two-norm initial, final = 191.44060 0.26318938 Force max component initial, final = 57.039082 0.069352344 Final line search alpha, max atom move = 1.0000000 0.069352344 Iterations, force evaluations = 100 168 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5336 | 4.5336 | 4.5336 | 0.0 | 96.00 Neigh | 0.13653 | 0.13653 | 0.13653 | 0.0 | 2.89 Comm | 0.022777 | 0.022777 | 0.022777 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02945 | | | 0.62 Nlocal: 2974.00 ave 2974 max 2974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11352.0 ave 11352 max 11352 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: 593106.0 ave 593106 max 593106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 593106 Ave neighs/atom = 199.43040 Neighbor list builds = 4 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.369 | 7.369 | 7.369 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -9858.1951 0 -9858.1951 2094.9641 31684.235 103 0 -9858.2724 0 -9858.2724 -107.14371 31750.653 Loop time of 0.144854 on 1 procs for 3 steps with 2974 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 = -9858.19514322767 -9858.27162491424 -9858.27236899884 Force two-norm initial, final = 80.129651 4.5339982 Force max component initial, final = 60.231552 4.2756599 Final line search alpha, max atom move = 0.00021046045 0.00089985730 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14137 | 0.14137 | 0.14137 | 0.0 | 97.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050566 | 0.00050566 | 0.00050566 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002982 | | | 2.06 Nlocal: 2974.00 ave 2974 max 2974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11629.0 ave 11629 max 11629 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: 593096.0 ave 593096 max 593096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 593096 Ave neighs/atom = 199.42703 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 7.507 | 7.507 | 7.507 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9858.2724 0 -9858.2724 -107.14371 Loop time of 2.375e-06 on 1 procs for 0 steps with 2974 atoms 210.5% 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 | | 2.375e-06 | | |100.00 Nlocal: 2974.00 ave 2974 max 2974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11633.0 ave 11633 max 11633 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: 592834.0 ave 592834 max 592834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 592834 Ave neighs/atom = 199.33894 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 7.507 | 7.507 | 7.507 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 -9858.2724 -9858.2724 33.733967 110.12637 8.5466111 -107.14371 -107.14371 -56.860903 -48.999845 -215.57037 2.2180088 919.52281 Loop time of 2.701e-06 on 1 procs for 0 steps with 2974 atoms 259.2% 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 | | 2.701e-06 | | |100.00 Nlocal: 2974.00 ave 2974 max 2974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11633.0 ave 11633 max 11633 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296417.0 ave 296417 max 296417 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 592834.0 ave 592834 max 592834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 592834 Ave neighs/atom = 199.33894 Neighbor list builds = 0 Dangerous builds = 0 2974 -9732.69928710371 eV 2.21800876911986 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05