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Here is a paper reviewing charge transport in molecular junctions: J. Chem. Phys. 148, 030901 (2018), http://dx.doi.org/10.1063/1.5003306 A typical way to treat such a problem is to couple the Non-equilibrium Green's function (NEGF) formalism with density-functional-theory (DFT), short NEGF-DFT. You need to solve $$ (E-H-\Sigma^{R,B}(E))\cdot G^R(E) = I, $$ ...


14

The specific questions: Only $l = 0$ overlaps are (currently) considered, in the spirit of atoms being represented by (only) a spherical charge distribution (point charges). The overlap/attenuation function for the bond capacities is very (!) preliminary. It should be designed to reflect the actual physics, and this is work in progress. However, any ...


10

This is a very general answer, but let me point you in the right direction at least. If you are looking at a molecular system such as C6H6, you will likely want to use a non-periodic code such as Gaussian. This page describes many different methods of charge analysis and you can use this information to calculate charge transfer complexes and local charges on ...


8

Complementing the answer by @Tristan, in this question you will find the several methods used to determine the atomic charges. Also, you can use Gaussian to calculate/export the wavefunction and them use Multiwfn package to estimate the system charges using several approaches: Population analysis. Hirshfeld, Hirshfeld-I, VDD, Mulliken, Löwdin, Modified ...


8

Here's another approach for strongly correlated systems: Al-Hassanieh et al. Phys. Rev. B 73 195304 2006. In this case, they use time-dependent DMRG. They treat the wire as a chain of sites occupied by spinless Fermions and the junction as an impurity in the wire. They can't observe a steady state current because their system has hard boundaries (the wires ...


7

The Bader Charge Analysis can do just this. If you can get your charge density into a CHGCAR format, you can use this program with any code. It will divide the charge density into volumes by looking at the zero flux surfaces between atoms. This is just one example of a atom in molecule analysis though, but one that is particularly robust for planewave ...


6

There are couple of options: Bader analysis Charge density difference (plot in vesta is easy). Take CHGCAR(A+B) and subtract CHGCAR(A) and CHGCAR(B). It can be easily done in vesta >edit> volumetric data Mulken population analysis (use chgmol programme)


5

It would help to know what you need the potentials for, since this will affect the techniques that are necessary to evaluate the potential. Point charges are trivial, as the potential generated by each charge is just -Z/r; the trick is mostly how to make the evaluation efficient, this is achieved with methods like fast multipoles or particle mesh Ewald. (...


3

A straightforward way to model the interaction of charged species with a surface is to use a cluster model instead of simulating the surface as a slab with periodic boundary conditions (1). Cluster models are not perfect, they can be affected by border effects that require large clusters, to be representative of the bulk system, by coverage effects, as a ...


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