RPYMobility.hpp File Reference

Per-molecule translation-only RPY mobility / resistance assembly. More...

#include <vector>
#include "math/DynamicRectMatrix.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"

Go to the source code of this file.

Classes
class	OpenMD::RPYMobility

Namespaces
namespace	OpenMD
	This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.

Detailed Description

Per-molecule translation-only RPY mobility / resistance assembly.

Builds, for one molecule of N spherical beads, the 3N x 3N grand translational mobility M (tt blocks only), inverts it to the grand resistance R = M^{-1}, and Cholesky-factors R for fluctuation-dissipation consistent random forces. The dipolar (td) rows enter only through the effective ambient velocity

v_inf_eff_i = v_inf_i + sum_{j!=i} mu_td_ij : E ,

so the hydrodynamic drag in the no-projection (J = 1) inertial scheme is

f_hydro = R ( v_inf_eff - v ),

and the random force is sqrt(2 kT / dt) * S * Z, S S^T = R, Z ~ N(0,1).

This is the orientation-less (unstructured spherical atom) case: no rotational degrees of freedom, hence no tr/rt/rr/rd blocks. Rotational hydrodynamic coupling, which would feed the translational resistance through the full 6N inversion, is therefore neglected here by construction.

Definition in file RPYMobility.hpp.