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 = 3.5200010 3.5200010 3.5200010 Created orthogonal box = (0.0000000 -41.649213 0.0000000) to (51.009661 41.649213 8.6222063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8296755 5.3548989 5.7481376 Created 1665 atoms using lattice units in orthogonal box = (0.0000000 -41.649213 0.0000000) to (51.009661 41.649213 8.6222063) create_atoms CPU = 0.003 seconds 1665 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8296755 5.3548989 5.7481376 Created 1689 atoms using lattice units in orthogonal box = (0.0000000 -41.649213 0.0000000) to (51.009661 41.649213 8.6222063) create_atoms CPU = 0.003 seconds 1689 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3354 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.984 | 6.984 | 6.984 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13917.974 0 -13917.974 86809.491 111 0 -14863.643 0 -14863.643 9506.4418 Loop time of 5.64425 on 1 procs for 111 steps with 3354 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 = -13917.9735873157 -14863.6321100805 -14863.6429048621 Force two-norm initial, final = 728.92586 0.40191171 Force max component initial, final = 70.269459 0.070637372 Final line search alpha, max atom move = 0.55827752 0.039435257 Iterations, force evaluations = 111 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3622 | 5.3622 | 5.3622 | 0.0 | 95.00 Neigh | 0.22501 | 0.22501 | 0.22501 | 0.0 | 3.99 Comm | 0.022909 | 0.022909 | 0.022909 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03409 | | | 0.60 Nlocal: 3354.00 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10759.0 ave 10759 max 10759 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: 581548.0 ave 581548 max 581548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581548 Ave neighs/atom = 173.38939 Neighbor list builds = 6 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 111 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.984 | 6.984 | 6.984 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -14863.643 0 -14863.643 9506.4418 36635.966 119 0 -14865.051 0 -14865.051 -8.0916641 36829.197 Loop time of 0.316696 on 1 procs for 8 steps with 3354 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 = -14863.6429048621 -14865.0513950294 -14865.0514160093 Force two-norm initial, final = 465.76211 0.84869915 Force max component initial, final = 436.09604 0.24043133 Final line search alpha, max atom move = 0.00082294780 0.00019786243 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30915 | 0.30915 | 0.30915 | 0.0 | 97.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000987 | 0.000987 | 0.000987 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006562 | | | 2.07 Nlocal: 3354.00 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10759.0 ave 10759 max 10759 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: 581616.0 ave 581616 max 581616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581616 Ave neighs/atom = 173.40966 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.123 | 7.123 | 7.123 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14865.051 0 -14865.051 -8.0916641 Loop time of 2.116e-06 on 1 procs for 0 steps with 3354 atoms 141.8% 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 | | 2.116e-06 | | |100.00 Nlocal: 3354.00 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10759.0 ave 10759 max 10759 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: 581048.0 ave 581048 max 581048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581048 Ave neighs/atom = 173.24031 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.123 | 7.123 | 7.123 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 -14865.051 -14865.051 51.021675 83.858994 8.6077151 -8.0916641 -8.0916641 -6.3153328 -10.529846 -7.4298136 2.3104776 1528.5808 Loop time of 2.493e-06 on 1 procs for 0 steps with 3354 atoms 280.8% 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 | | 2.493e-06 | | |100.00 Nlocal: 3354.00 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10759.0 ave 10759 max 10759 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 290524.0 ave 290524 max 290524 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 581048.0 ave 581048 max 581048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581048 Ave neighs/atom = 173.24031 Neighbor list builds = 0 Dangerous builds = 0 3354 -14742.7906816929 eV 2.31047764605201 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06