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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -48.532785 0.0000000) to (29.720140 48.532785 8.9609594) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4036618 5.5150893 5.9739729 Created 1049 atoms using lattice units in orthogonal box = (0.0000000 -48.532785 0.0000000) to (29.720140 48.532785 8.9609594) create_atoms CPU = 0.002 seconds 1049 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4036618 5.5150893 5.9739729 Created 1073 atoms using lattice units in orthogonal box = (0.0000000 -48.532785 0.0000000) to (29.720140 48.532785 8.9609594) create_atoms CPU = 0.001 seconds 1073 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 ghost atom cutoff = 8 binsize = 4, bins = 8 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 2112 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_942420706858_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.004 | 6.004 | 6.004 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8270.5639 0 -8270.5639 56592.724 485 0 -8579.7659 0 -8579.7659 -87916.411 Loop time of 17.5262 on 1 procs for 485 steps with 2112 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 = -8270.56394139374 -8579.75807821556 -8579.76594750916 Force two-norm initial, final = 308.00479 0.26037382 Force max component initial, final = 25.660874 0.014165701 Final line search alpha, max atom move = 1.0000000 0.014165701 Iterations, force evaluations = 485 926 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.006 | 17.006 | 17.006 | 0.0 | 97.03 Neigh | 0.34396 | 0.34396 | 0.34396 | 0.0 | 1.96 Comm | 0.07919 | 0.07919 | 0.07919 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09709 | | | 0.55 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8491.00 ave 8491 max 8491 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: 364210.0 ave 364210 max 364210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 364210 Ave neighs/atom = 172.44792 Neighbor list builds = 14 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 ghost atom cutoff = 8 binsize = 4, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 485 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.005 | 6.005 | 6.005 Mbytes Step Temp E_pair E_mol TotEng Press Volume 485 0 -8579.7659 0 -8579.7659 -87916.411 25850.597 550 0 -8706.6343 0 -8706.6343 -9.002226 24557.878 Loop time of 1.25216 on 1 procs for 65 steps with 2112 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 = -8579.76594750915 -8706.63326143743 -8706.63431930611 Force two-norm initial, final = 3287.8793 3.4022028 Force max component initial, final = 2413.5149 1.1849454 Final line search alpha, max atom move = 0.00020979266 0.00024859285 Iterations, force evaluations = 65 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1204 | 1.1204 | 1.1204 | 0.0 | 89.48 Neigh | 0.0944 | 0.0944 | 0.0944 | 0.0 | 7.54 Comm | 0.005698 | 0.005698 | 0.005698 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03163 | | | 2.53 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8753.00 ave 8753 max 8753 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: 358854.0 ave 358854 max 358854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 358854 Ave neighs/atom = 169.91193 Neighbor list builds = 4 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 ghost atom cutoff = 8 binsize = 4, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.159 | 6.159 | 6.159 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8706.6343 0 -8706.6343 -9.002226 Loop time of 2.527e-06 on 1 procs for 0 steps with 2112 atoms 158.3% 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 | | 2.527e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8781.00 ave 8781 max 8781 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: 360300.0 ave 360300 max 360300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 360300 Ave neighs/atom = 170.59659 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 ghost atom cutoff = 8 binsize = 4, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.159 | 6.159 | 6.159 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 -8706.6343 -8706.6343 28.382655 101.75253 8.5034001 -9.002226 -9.002226 -6.6355708 -81.039707 60.6686 2.4061284 2162.7829 Loop time of 2.996e-06 on 1 procs for 0 steps with 2112 atoms 267.0% 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 | | 2.996e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8781.00 ave 8781 max 8781 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 180150.0 ave 180150 max 180150 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 360300.0 ave 360300 max 360300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 360300 Ave neighs/atom = 170.59659 Neighbor list builds = 0 Dangerous builds = 0 2112 -8706.6343193061 eV 2.4061284163996 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19