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 = 3.6150127 3.6150127 3.6150127 Created orthogonal box = (0.0000000 -43.680364 0.0000000) to (53.497302 43.680364 8.8549365) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1298783 5.3852504 5.9032910 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -43.680364 0.0000000) to (53.497302 43.680364 8.8549365) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1298783 5.3852504 5.9032910 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -43.680364 0.0000000) to (53.497302 43.680364 8.8549365) create_atoms CPU = 0.002 seconds 1757 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 ghost atom cutoff = 7 binsize = 3.5, bins = 16 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3504 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_028979335952_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.493 | 6.493 | 6.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10687.444 0 -10687.444 82072.527 95 0 -12344.444 0 -12344.444 5958.2894 Loop time of 32.5038 on 1 procs for 95 steps with 3504 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10687.4443960001 -12344.4327306195 -12344.4443069158 Force two-norm initial, final = 1244.1805 0.38278189 Force max component initial, final = 160.70890 0.10027641 Final line search alpha, max atom move = 1.0000000 0.10027641 Iterations, force evaluations = 95 178 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 32.422 | 32.422 | 32.422 | 0.0 | 99.75 Neigh | 0.029802 | 0.029802 | 0.029802 | 0.0 | 0.09 Comm | 0.020854 | 0.020854 | 0.020854 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03163 | | | 0.10 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9508.00 ave 9508 max 9508 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: 462796.0 ave 462796 max 462796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462796 Ave neighs/atom = 132.07648 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.497 | 6.497 | 6.497 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -12344.444 0 -12344.444 5958.2894 41384.106 106 0 -12346.394 0 -12346.394 0.82473102 41553.446 Loop time of 2.36489 on 1 procs for 11 steps with 3504 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 = -12344.4443069158 -12346.3939538908 -12346.3940186095 Force two-norm initial, final = 400.03098 0.94873077 Force max component initial, final = 390.17332 0.35642638 Final line search alpha, max atom move = 0.00096096843 0.00034251450 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3272 | 2.3272 | 2.3272 | 0.0 | 98.41 Neigh | 0.028939 | 0.028939 | 0.028939 | 0.0 | 1.22 Comm | 0.0013999 | 0.0013999 | 0.0013999 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007365 | | | 0.31 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9741.00 ave 9741 max 9741 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: 461602.0 ave 461602 max 461602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461602 Ave neighs/atom = 131.73573 Neighbor list builds = 1 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 ghost atom cutoff = 7 binsize = 3.5, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.635 | 6.635 | 6.635 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12346.394 0 -12346.394 0.82473102 Loop time of 2.136e-06 on 1 procs for 0 steps with 3504 atoms 187.3% 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 | | 2.136e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9741.00 ave 9741 max 9741 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: 461618.0 ave 461618 max 461618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461618 Ave neighs/atom = 131.74030 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 ghost atom cutoff = 7 binsize = 3.5, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.635 | 6.635 | 6.635 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 -12346.394 -12346.394 53.225055 88.238878 8.8477113 0.82473102 0.82473102 13.672798 -12.496436 1.2978314 2.3342718 1582.2466 Loop time of 2.218e-06 on 1 procs for 0 steps with 3504 atoms 225.4% 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 | | 2.218e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9741.00 ave 9741 max 9741 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230809.0 ave 230809 max 230809 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 461618.0 ave 461618 max 461618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461618 Ave neighs/atom = 131.74030 Neighbor list builds = 0 Dangerous builds = 0 3504 -12346.3940186095 eV 2.33427179870483 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:35