Representation of Molecular Systems in Quantarhei
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Here we describe how molecular systems are represented in |Qrhei|_. 
We distinguish three different components of molecular open quantum systems. 

Molecules
---------

At the center of everything are **Molecules** as the basic building blocks. 
They are characterized by the spatial structure (often in a limited 
representation which comprises e.g. just their *positions* and
*transition dipole moments*) and energy level structure. 
Most often we represent molecules as two-level systems.

Molecular Environment
---------------------

Unless the molecules are in gas phase, they are naturally embedded is
some kind of an environment. Actually, even in gaas phases the molecules
interact with electromagnetic field, and we can therefore still consider
them embedded in an environment, and therefore open.





.. |Qrhei| replace:: **Quantarhei**
.. _Qrhei: http://github.com/tmancal74/quantarhei