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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -35.599251 0.0000000) to (5.4500000 35.599251 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4500000 4.4499063 5.1383093 Created 96 atoms using lattice units in orthogonal box = (0.0000000 -35.599251 0.0000000) to (5.4500000 35.599251 7.7074639) create_atoms CPU = 0.001 seconds 96 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4500000 4.4499063 5.1383093 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -35.599251 0.0000000) to (5.4500000 35.599251 7.7074639) create_atoms CPU = 0.000 seconds 102 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 2 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 198 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 2 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.389 | 4.389 | 4.389 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1189.0191 0 -1189.0191 195742.37 13 0 -4038.1723 0 -4038.1723 111940.39 Loop time of 0.578129 on 1 procs for 13 steps with 198 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 = -1189.01910539449 -4038.17084895393 -4038.17233403393 Force two-norm initial, final = 35.988277 292.08443 Force max component initial, final = 7.6588040 76.144811 Final line search alpha, max atom move = 4.1915795e-08 3.1916703e-06 Iterations, force evaluations = 13 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57558 | 0.57558 | 0.57558 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014739 | 0.0014739 | 0.0014739 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001073 | | | 0.19 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1518.00 ave 1518 max 1518 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: 11844.0 ave 11844 max 11844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11844 Ave neighs/atom = 59.818182 Neighbor list builds = 0 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 2 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 13 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.389 | 4.389 | 4.389 Mbytes Step Temp E_pair E_mol TotEng Press Volume 13 0 -4038.1723 0 -4038.1723 111940.39 2990.7413 14 0 -4038.173 0 -4038.173 110221.59 2990.7573 Loop time of 0.0166416 on 1 procs for 1 steps with 198 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 = -4038.17233403393 -4038.17233403393 -4038.17297084042 Force two-norm initial, final = 466.06543 764.86741 Force max component initial, final = 229.42617 228.13306 Final line search alpha, max atom move = 4.3587006e-06 0.00099436373 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.016443 | 0.016443 | 0.016443 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 3.7842e-05 | 3.7842e-05 | 3.7842e-05 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001605 | | | 0.96 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1528.00 ave 1528 max 1528 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: 11868.0 ave 11868 max 11868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11868 Ave neighs/atom = 59.939394 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 2 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4038.173 0 -4038.173 110221.59 Loop time of 1.723e-06 on 1 procs for 0 steps with 198 atoms 174.1% 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 | | 1.723e-06 | | |100.00 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1528.00 ave 1528 max 1528 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: 11868.0 ave 11868 max 11868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11868 Ave neighs/atom = 59.939394 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 2 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.527 | 4.527 | 4.527 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 -4038.173 -4038.173 5.4500106 71.198614 7.7074777 110221.59 110221.59 122213.24 99800.643 108650.88 0.0056894123 200.17313 Loop time of 1.565e-06 on 1 procs for 0 steps with 198 atoms 191.7% 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 | | 1.565e-06 | | |100.00 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1528.00 ave 1528 max 1528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5934.00 ave 5934 max 5934 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11868.0 ave 11868 max 11868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11868 Ave neighs/atom = 59.939394 Neighbor list builds = 0 Dangerous builds = 0 198 -4038.17297084042 eV 0.00568941232416146 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00