系综是npt，体系是金属和H2气氛，但是报错not enough space for bonds。
1.ERROR: Unrecognized pair style 'reaxff' is part of the REAXFF package which is not enabled in this LAMMPS binary. (../force.cpp:279) ERROR: Unrecognized pair style 'reaxff' is part of the REAXFF package which is not enabled in this LAMMPS binary. (../force.cpp:279) 这是由于未...
1) As Steve pointed out, there may be a problem with your time-step parameter. The fact thatreax/cruns out of space for bonds shows that your system is evolving rather too quickly (and not doing meaningful physics). I would suggest that you decrease your time-step length. 2) If you ...
interactions outside that distance are computed in reciprocal space.所以在 Equilibrate stage 的 in.f...
create_bonds.h create_box.cpp create_box.h delete_atoms.cpp delete_atoms.h delete_bonds.cpp delete_bonds.h deprecated.cpp deprecated.h dihedral.cpp dihedral.h dihedral_deprecated.cpp dihedral_deprecated.h dihedral_hybrid.cpp dihedral_hybrid.h dihedral_write.cpp dihedral_write.h dihedral_zero.cpp...
Solution method: The LAMMPS code uses parallel spatial decomposition, distributed neighbor lists, and parallel FFTs for long-range Coulombic interactions [1]. The time integration algorithm is based on the Størmer-Verlet symplectic integrator [2], which provides better stability than higher-order non...
It will not affect the simulation, only it requires more memory to store the (otherwise unused) per-atom properties. The last line, \textit{boundary p p p}, indicates that periodic boundary conditions will be used along all three directions of space (the 3 \textit{p} stand for \textit{...
For a standard DNA duplex consisting of 8 complementary base pairs we need 16 atoms, 16 ellipsoids and 14 bonds, 7 on each of the two single strands. If the strands are nicked, which we do not assume here, the number of bonds would be reduced: 16 atoms 16 ellipsoids 14 bonds We use...
The lb/fluid fix has a scalar output for the particle temperature using equipartition giving(43)T=∑i(mi+mni)vi2dofLBkB. If other constraints, such as the rigid fix, are also present then the dof removed by the other constraint will not be accounted for. However, in that case the ...
create_bonds.cpp create_bonds.h create_box.cpp create_box.h delete_atoms.cpp delete_atoms.h delete_bonds.cpp delete_bonds.h deprecated.cpp deprecated.h dihedral.cpp dihedral.h dihedral_deprecated.cpp dihedral_deprecated.h dihedral_hybrid.cpp dihedral_hybrid.h dihedral_write.cpp dihedral_...