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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -42.681416 0.0000000) to (34.846356 42.681416 8.6222370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9780508 4.9355390 5.7481580 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -42.681416 0.0000000) to (34.846356 42.681416 8.6222370) create_atoms CPU = 0.002 seconds 1184 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9780508 4.9355390 5.7481580 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -42.681416 0.0000000) to (34.846356 42.681416 8.6222370) create_atoms CPU = 0.001 seconds 1184 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 2320 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.913 | 6.913 | 6.913 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10235.855 0 -10235.855 -988.52638 50 0 -10269.164 0 -10269.164 -12723.195 Loop time of 2.12199 on 1 procs for 50 steps with 2320 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 = -10235.8547221219 -10269.1556535504 -10269.1644379053 Force two-norm initial, final = 23.931202 0.29967002 Force max component initial, final = 4.2297446 0.016404838 Final line search alpha, max atom move = 1.0000000 0.016404838 Iterations, force evaluations = 50 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0766 | 2.0766 | 2.0766 | 0.0 | 97.86 Neigh | 0.028196 | 0.028196 | 0.028196 | 0.0 | 1.33 Comm | 0.0078958 | 0.0078958 | 0.0078958 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009286 | | | 0.44 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9763.00 ave 9763 max 9763 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: 518640.0 ave 518640 max 518640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518640 Ave neighs/atom = 223.55172 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.913 | 6.913 | 6.913 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -10269.164 0 -10269.164 -12723.195 25647.565 54 0 -10269.561 0 -10269.561 -4090.8618 25520.468 Loop time of 0.153973 on 1 procs for 4 steps with 2320 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 = -10269.1644379053 -10269.5603976506 -10269.5610264138 Force two-norm initial, final = 225.13761 0.37577480 Force max component initial, final = 160.27622 0.059628075 Final line search alpha, max atom move = 0.00021781513 1.2987897e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15105 | 0.15105 | 0.15105 | 0.0 | 98.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047755 | 0.00047755 | 0.00047755 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002449 | | | 1.59 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9727.00 ave 9727 max 9727 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: 518880.0 ave 518880 max 518880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518880 Ave neighs/atom = 223.65517 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.051 | 7.051 | 7.051 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10269.561 0 -10269.561 -4090.8618 Loop time of 1.869e-06 on 1 procs for 0 steps with 2320 atoms 107.0% 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 | | 1.869e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9739.00 ave 9739 max 9739 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: 519088.0 ave 519088 max 519088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 519088 Ave neighs/atom = 223.74483 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.051 | 7.051 | 7.051 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 -10269.561 -10269.561 34.7504 85.362831 8.6032 -4090.8618 -4090.8618 -1.7285858 -12267.122 -3.7351889 2.2230132 1350.0759 Loop time of 2.362e-06 on 1 procs for 0 steps with 2320 atoms 169.3% 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 | | 2.362e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9739.00 ave 9739 max 9739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 259544.0 ave 259544 max 259544 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 519088.0 ave 519088 max 519088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 519088 Ave neighs/atom = 223.74483 Neighbor list builds = 0 Dangerous builds = 0 2320 -10206.3145743492 eV 2.22301316244956 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02