.. _doc.MUSTANG.bioturb:

Bioturbation within sediment 
+++++++++++++++++++++++++++++

* Bioturbation is the result of all activities of the meio and macro-fauna living in the water-sediment interface or in the upper layers of the sediment. 
* Bioturbation processes include :
     * "surface biodiffusion" 
         | resulting of benthic organisms living in the first centimeters of the sediment. 
	     | Their movement causes the mechanical homogenization of the substrate and randomly in three dimensions;
	     
     * "bioirrigation"
         generated by agencies that construct galleries or burrows in the sediment. 
	     These biodiffuseurs gallery provide irrigation sediment creating water currents to respiratory and food purposes.
	     
     * "bioadvection" 
         induced by organisms that ingest sediment particles in depth (anoxic zone) and discharge their fecal pellets on the sediment surface. 
	     This transport facing up induces a direct link between two non-adjacent geochemical and different strata. 
	     The bioadvection may also be downwardly directed
	     
* **But in a first step, bioturbation is considered here only as an apparent biodiffusion mixing coefficient Db**.
         The coefficient Db at each point and in each sediment layer is evaluated based on an average profile 
	     with a maximum bioturbation intensity (Db1 in m^2.s^-1) near the interface to a specified depth (zdbm, m), 
	     then a decrease in depth according to a slope coefficient (xdb2 without unit) to a maximum depth of bioturbation (zdb0 in m), 
	     beyond which the bioturbation is considered null (Figure)
	 
.. image:: FIG/SEDIM/fig_bioturb_Db.jpg

.. note::
   These processes are available in MUSTANG but they mus be tested and developped by researchers.
   
* For dissolved substances, bioturbation processes are resolved simultaneously with the diffusion process in the sediment (diffusion routine)
* For particulate substances, 
    * either bioturbation processes are not involved 
    * or (to be checked) resolved simultaneously with the consolidation process, but explicitly in time with fractionnary time step; and if consolidation is not taking account, bioturbation for particulate variables are resolved alone in the consolidation routine.
      
* Parameters for bioturbation are given in paraMUSTANG.txt (:ref:`doc.paraMUSTANG`)
     | **l_bioturb**       :  boolean set to .true. si taking into account bioturbation diffusion in sediment
     | **xbioturbmax**     : max diffusion coefficient by bioturbation Db (in surface)
     | **xbioturbk**       : coef (slope) for bioturbation coefficient between max Db at sediment surface and 0 at bottom
     | **dbiotu0**         : max depth beneath the sediment surface below which there is no bioturbation
     | **dbiotum**         : sediment thickness wherein the diffusion-bioturbation coefficient Db is constant (max)
     | **frmud_db_min**    : mud fraction limit (min) below which there is no Bioturbation
     | **frmud_db_max**    : mud fraction limit (max) above which the bioturbation coefficient Db is maximum (muddy sediment)