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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -69.988641 0.0000000) to (40.407961 69.988641 6.3364738) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9618302 5.3543222 6.3364738 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.988641 0.0000000) to (40.407961 69.988641 6.3364738) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9618302 5.3543222 6.3364738 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.988641 0.0000000) to (40.407961 69.988641 6.3364738) create_atoms CPU = 0.003 seconds 1466 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 37 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2928 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_267721408934_005#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.600 | 6.600 | 6.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11186.09 0 -11186.09 45991.222 766 0 -11882.939 0 -11882.939 -63253.6 Loop time of 33.8649 on 1 procs for 766 steps with 2928 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 = -11186.0902634658 -11882.9273375457 -11882.9385706772 Force two-norm initial, final = 937.53499 0.38133765 Force max component initial, final = 307.26742 0.099380079 Final line search alpha, max atom move = 0.87889772 0.087344925 Iterations, force evaluations = 766 1510 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.039 | 33.039 | 33.039 | 0.0 | 97.56 Neigh | 0.39172 | 0.39172 | 0.39172 | 0.0 | 1.16 Comm | 0.22199 | 0.22199 | 0.22199 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2118 | | | 0.63 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12229.0 ave 12229 max 12229 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: 456448.0 ave 456448 max 456448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 456448 Ave neighs/atom = 155.89071 Neighbor list builds = 13 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 766 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.602 | 6.602 | 6.602 Mbytes Step Temp E_pair E_mol TotEng Press Volume 766 0 -11882.939 0 -11882.939 -63253.6 35840.341 797 0 -11921.165 0 -11921.165 -348.39786 34326.018 Loop time of 0.907408 on 1 procs for 31 steps with 2928 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 = -11882.9385706772 -11921.1579602452 -11921.1650007108 Force two-norm initial, final = 2531.8736 14.554072 Force max component initial, final = 1735.0491 10.200573 Final line search alpha, max atom move = 4.6625546e-05 0.00047560729 Iterations, force evaluations = 31 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78905 | 0.78905 | 0.78905 | 0.0 | 86.96 Neigh | 0.089929 | 0.089929 | 0.089929 | 0.0 | 9.91 Comm | 0.0049381 | 0.0049381 | 0.0049381 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02349 | | | 2.59 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12391.0 ave 12391 max 12391 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: 470578.0 ave 470578 max 470578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 470578 Ave neighs/atom = 160.71653 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.740 | 6.740 | 6.740 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11921.165 0 -11921.165 -348.39786 Loop time of 2.758e-06 on 1 procs for 0 steps with 2928 atoms 145.0% 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 | | 2.758e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12330.0 ave 12330 max 12330 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: 471330.0 ave 471330 max 471330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 471330 Ave neighs/atom = 160.97336 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.740 | 6.740 | 6.740 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 -11921.165 -11921.165 39.558537 136.50264 6.3568528 -348.39786 -348.39786 -203.73277 -464.29606 -377.16476 2.1945175 9903.839 Loop time of 2.527e-06 on 1 procs for 0 steps with 2928 atoms 277.0% 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 | | 2.527e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12330.0 ave 12330 max 12330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 235665.0 ave 235665 max 235665 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 471330.0 ave 471330 max 471330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 471330 Ave neighs/atom = 160.97336 Neighbor list builds = 0 Dangerous builds = 0 2928 -11921.1650007108 eV 2.19451754228344 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:35