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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -35.900618 0.0000000) to (31.087798 35.900618 6.0968189) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5798613 5.5226304 6.0968189 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -35.900618 0.0000000) to (31.087798 35.900618 6.0968189) create_atoms CPU = 0.001 seconds 627 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5798613 5.5226304 6.0968189 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -35.900618 0.0000000) to (31.087798 35.900618 6.0968189) create_atoms CPU = 0.001 seconds 628 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 = 8 17 2 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 21 atoms, new total = 1234 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_103383163946_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 = 8 17 2 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) = 5.493 | 5.493 | 5.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5416.3219 0 -5416.3219 14147.106 62 0 -5457.3543 0 -5457.3543 -6558.437 Loop time of 1.46539 on 1 procs for 62 steps with 1234 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 = -5416.32187743749 -5457.34910080771 -5457.35428318555 Force two-norm initial, final = 67.113529 0.22065148 Force max component initial, final = 11.138866 0.035365061 Final line search alpha, max atom move = 0.49726673 0.017585869 Iterations, force evaluations = 62 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4305 | 1.4305 | 1.4305 | 0.0 | 97.62 Neigh | 0.016817 | 0.016817 | 0.016817 | 0.0 | 1.15 Comm | 0.0097545 | 0.0097545 | 0.0097545 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008338 | | | 0.57 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8174.00 ave 8174 max 8174 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: 275560.0 ave 275560 max 275560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275560 Ave neighs/atom = 223.30632 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 = 8 17 2 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.493 | 5.493 | 5.493 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -5457.3543 0 -5457.3543 -6558.437 13608.968 65 0 -5457.4275 0 -5457.4275 -2098.6061 13574.465 Loop time of 0.0809542 on 1 procs for 3 steps with 1234 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 = -5457.35428318549 -5457.42658901731 -5457.42745558429 Force two-norm initial, final = 70.085009 0.23220295 Force max component initial, final = 63.905237 0.031200231 Final line search alpha, max atom move = 0.00018047682 5.6309186e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.078867 | 0.078867 | 0.078867 | 0.0 | 97.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038693 | 0.00038693 | 0.00038693 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0017 | | | 2.10 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8170.00 ave 8170 max 8170 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: 275684.0 ave 275684 max 275684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275684 Ave neighs/atom = 223.40681 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 = 8 17 2 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) = 5.631 | 5.631 | 5.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5457.4275 0 -5457.4275 -2098.6061 Loop time of 2.249e-06 on 1 procs for 0 steps with 1234 atoms 177.9% 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 | | 2.249e-06 | | |100.00 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8178.00 ave 8178 max 8178 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: 275786.0 ave 275786 max 275786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275786 Ave neighs/atom = 223.48947 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 = 8 17 2 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) = 5.631 | 5.631 | 5.631 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 -5457.4275 -5457.4275 31.073548 71.801235 6.0841506 -2098.6061 -2098.6061 -2.5067674 -6294.549 1.237587 2.1911769 843.85534 Loop time of 2.249e-06 on 1 procs for 0 steps with 1234 atoms 222.3% 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 | | 2.249e-06 | | |100.00 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8178.00 ave 8178 max 8178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 137893.0 ave 137893 max 137893 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 275786.0 ave 275786 max 275786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275786 Ave neighs/atom = 223.48947 Neighbor list builds = 0 Dangerous builds = 0 1234 -5423.82401114669 eV 2.19117690860233 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01