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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -42.535842 0.0000000) to (52.091243 42.535842 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950507 5.2437109 5.7481360 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.535842 0.0000000) to (52.091243 42.535842 8.6222040) create_atoms CPU = 0.002 seconds 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950507 5.2437109 5.7481360 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.535842 0.0000000) to (52.091243 42.535842 8.6222040) create_atoms CPU = 0.002 seconds 1756 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 3456 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.902 | 7.902 | 7.902 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15252.571 0 -15252.571 873.71971 61 0 -15322.988 0 -15322.988 -15141.341 Loop time of 3.69751 on 1 procs for 61 steps with 3456 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15252.570691444 -15322.9725447641 -15322.9877048525 Force two-norm initial, final = 58.185841 0.40486084 Force max component initial, final = 10.717492 0.025603607 Final line search alpha, max atom move = 1.0000000 0.025603607 Iterations, force evaluations = 61 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5782 | 3.5782 | 3.5782 | 0.0 | 96.77 Neigh | 0.086815 | 0.086815 | 0.086815 | 0.0 | 2.35 Comm | 0.013944 | 0.013944 | 0.013944 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01857 | | | 0.50 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12598.0 ave 12598 max 12598 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: 773374.0 ave 773374 max 773374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 773374 Ave neighs/atom = 223.77720 Neighbor list builds = 2 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.903 | 7.903 | 7.903 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -15322.988 0 -15322.988 -15141.341 38209.209 66 0 -15324.108 0 -15324.108 -3350.1479 37950.974 Loop time of 0.266038 on 1 procs for 5 steps with 3456 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 = -15322.9877048525 -15324.1049942602 -15324.1075465168 Force two-norm initial, final = 459.62556 0.57209767 Force max component initial, final = 348.68786 0.054054850 Final line search alpha, max atom move = 7.8044657e-05 4.2186922e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26128 | 0.26128 | 0.26128 | 0.0 | 98.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069923 | 0.00069923 | 0.00069923 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004061 | | | 1.53 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12564.0 ave 12564 max 12564 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: 773200.0 ave 773200 max 773200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 773200 Ave neighs/atom = 223.72685 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.041 | 8.041 | 8.041 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15324.108 0 -15324.108 -3350.1479 Loop time of 1.969e-06 on 1 procs for 0 steps with 3456 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 | | 1.969e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12610.0 ave 12610 max 12610 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: 774330.0 ave 774330 max 774330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774330 Ave neighs/atom = 224.05382 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.041 | 8.041 | 8.041 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 -15324.108 -15324.108 51.877293 85.071684 8.5992503 -3350.1479 -3350.1479 0.63909407 -10049.545 -1.5379296 2.2165133 1570.2863 Loop time of 2.401e-06 on 1 procs for 0 steps with 3456 atoms 208.2% 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 | | 2.401e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12610.0 ave 12610 max 12610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 387165.0 ave 387165 max 387165 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 774330.0 ave 774330 max 774330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774330 Ave neighs/atom = 224.05382 Neighbor list builds = 0 Dangerous builds = 0 3456 -15229.9961170384 eV 2.21651329067201 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04