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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -63.179465 0.0000000) to (31.589732 63.179465 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6965091 5.6965091 4.0446508 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -63.179465 0.0000000) to (31.589732 63.179465 4.0446508) create_atoms CPU = 0.002 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6965091 5.6965091 4.0446508 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -63.179465 0.0000000) to (31.589732 63.179465 4.0446508) create_atoms CPU = 0.002 seconds 490 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_099716416216_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.576 | 4.576 | 4.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3172.3148 0 -3172.3148 20988.682 76 0 -3280.3506 0 -3280.3506 3505.1321 Loop time of 11.6738 on 1 procs for 76 steps with 978 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 = -3172.31482482283 -3280.34786998351 -3280.3505838118 Force two-norm initial, final = 143.06397 0.12621829 Force max component initial, final = 29.798325 0.022488005 Final line search alpha, max atom move = 1.0000000 0.022488005 Iterations, force evaluations = 76 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.626 | 11.626 | 11.626 | 0.0 | 99.59 Neigh | 0.011595 | 0.011595 | 0.011595 | 0.0 | 0.10 Comm | 0.018319 | 0.018319 | 0.018319 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01793 | | | 0.15 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5490.00 ave 5490 max 5490 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: 74964.0 ave 74964 max 74964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74964 Ave neighs/atom = 76.650307 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.585 | 4.585 | 4.585 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -3280.3506 0 -3280.3506 3505.1321 16144.809 82 0 -3280.5068 0 -3280.5068 -189.3315 16219.428 Loop time of 0.750329 on 1 procs for 6 steps with 978 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 = -3280.35058381181 -3280.50557393109 -3280.5068030726 Force two-norm initial, final = 68.759883 3.6759760 Force max component initial, final = 60.833351 3.0083571 Final line search alpha, max atom move = 0.00022609594 0.00068017734 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74463 | 0.74463 | 0.74463 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011387 | 0.0011387 | 0.0011387 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004561 | | | 0.61 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5865.00 ave 5865 max 5865 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: 75052.0 ave 75052 max 75052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75052 Ave neighs/atom = 76.740286 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.724 | 4.724 | 4.724 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3280.5068 0 -3280.5068 -189.3315 Loop time of 8.84e-06 on 1 procs for 0 steps with 978 atoms 158.4% 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 | | 8.84e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5865.00 ave 5865 max 5865 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: 74832.0 ave 74832 max 74832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74832 Ave neighs/atom = 76.515337 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.724 | 4.724 | 4.724 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 -3280.5068 -3280.5068 31.593755 127.05301 4.0406324 -189.3315 -189.3315 -193.15779 -77.962452 -296.87425 2.5590426 173.36125 Loop time of 6.716e-06 on 1 procs for 0 steps with 978 atoms 312.7% 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 | | 6.716e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5865.00 ave 5865 max 5865 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37416.0 ave 37416 max 37416 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74832.0 ave 74832 max 74832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74832 Ave neighs/atom = 76.515337 Neighbor list builds = 0 Dangerous builds = 0 978 -3280.5068030726 eV 2.55904264711665 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13