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 = 3.5239542 3.5239542 3.5239542 Created orthogonal box = (0.0000000 -41.695988 0.0000000) to (51.066948 41.695988 8.6318896) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8362226 5.3609128 5.7545931 Created 1670 atoms using lattice units in orthogonal box = (0.0000000 -41.695988 0.0000000) to (51.066948 41.695988 8.6318896) create_atoms CPU = 0.014 seconds 1670 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8362226 5.3609128 5.7545931 Created 1694 atoms using lattice units in orthogonal box = (0.0000000 -41.695988 0.0000000) to (51.066948 41.695988 8.6318896) create_atoms CPU = 0.002 seconds 1694 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3358 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 7.387 | 7.387 | 7.387 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14469.075 0 -14469.075 26000.334 57 0 -14824.761 0 -14824.761 8621.1517 Loop time of 2.84657 on 1 procs for 57 steps with 3358 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14469.0751835298 -14824.7481980539 -14824.7611546288 Force two-norm initial, final = 217.63885 0.36399518 Force max component initial, final = 20.623733 0.055149086 Final line search alpha, max atom move = 0.51076769 0.028168372 Iterations, force evaluations = 57 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6716 | 2.6716 | 2.6716 | 0.0 | 93.85 Neigh | 0.14198 | 0.14198 | 0.14198 | 0.0 | 4.99 Comm | 0.013494 | 0.013494 | 0.013494 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01953 | | | 0.69 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10811.0 ave 10811 max 10811 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: 587708.0 ave 587708 max 587708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 587708 Ave neighs/atom = 175.01727 Neighbor list builds = 4 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.002 | 7.002 | 7.002 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -14824.761 0 -14824.761 8621.1517 36759.538 63 0 -14825.672 0 -14825.672 -139.94803 36944.273 Loop time of 0.212915 on 1 procs for 6 steps with 3358 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 = -14824.7611546288 -14825.6701668294 -14825.6722081439 Force two-norm initial, final = 392.48788 5.8693651 Force max component initial, final = 354.04717 4.1105776 Final line search alpha, max atom move = 7.5052322e-05 0.00030850840 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20828 | 0.20828 | 0.20828 | 0.0 | 97.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066056 | 0.00066056 | 0.00066056 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00397 | | | 1.86 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10811.0 ave 10811 max 10811 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: 587736.0 ave 587736 max 587736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 587736 Ave neighs/atom = 175.02561 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 7.140 | 7.140 | 7.140 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14825.672 0 -14825.672 -139.94803 Loop time of 1.968e-06 on 1 procs for 0 steps with 3358 atoms 152.4% 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 | | 1.968e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10811.0 ave 10811 max 10811 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: 587004.0 ave 587004 max 587004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 587004 Ave neighs/atom = 174.80762 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 7.140 | 7.140 | 7.140 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 -14825.672 -14825.672 51.070887 83.831478 8.6291217 -139.94803 -139.94803 -160.47461 -81.161626 -178.20784 2.2345162 1589.7931 Loop time of 2.46e-06 on 1 procs for 0 steps with 3358 atoms 243.9% 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 | | 2.46e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10811.0 ave 10811 max 10811 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 293502.0 ave 293502 max 293502 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 587004.0 ave 587004 max 587004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 587004 Ave neighs/atom = 174.80762 Neighbor list builds = 0 Dangerous builds = 0 3358 -14825.6722081439 eV 2.23451624548432 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03