Prescribed and Interactive Ocean Biology in modelE
(by Natassa Romanou, Watson Gregg and Gavin Schmidt)
=========================================

This document describes the steps and methodology for
running (non)interactive chlorophyll and interactive carbon
cycle etc.

step 1: Check out the model from CVS as usual
cvs checkout modelE 

step 2: Choose which ocean model to use if any at all

step 3: Choose whether you want to do 
        i) chlorophyll-radiation feedbacks
       ii) real or prescribed chlorophyll and ocean biology
      iii) CO2 gas exchange with the atmosphere
       iv) prognostic alkalinity

Then in the decks directory use the appropriate rundeck.
=========================================

Description of CPPs to be used in the rundecks

#define CHECK_OCEAN_HYCOM           ! HYCOM ocean: needed for CMPE002 only
#define HYCOM_RESOLUTION_2deg       ! HYCOM ocean: use 2deg resolution for HYCOM ocean

#define CHECK_OCEAN                 ! RUSSELL ocean: needed to compile aux/file CMPE002

#define TRACERS_OCEAN               ! RUSSELL ocean: ocean tracers activated
#define TRACERS_OCEAN_INDEP         ! RUSSELL ocean: independently defined ocn tracers

#define OBIO_ON_GARYocean           ! RUSSELL ocean: prognostic ocean biology
#define CHL_from_SeaWIFs            ! RUSSELL ocean: read in SeaWIFs

#define TRACERS_OceanBiology        ! ANY ocean: Watson Gregg's ocean bio-geo-chem model

#define OBIO_RAD_coupling           ! ANY ocean: radiation -- ocean biology coupling
#define pCO2_ONLINE                 ! ANY ocean: pCO2_seawater computed online

#define TRACERS_ON                  ! ANY ocean: ATMOS tracers: include tracers code

#define TRACERS_GASEXCH_ocean       ! ANY ocean: special tracers to be passed to ocean
#define TRACERS_GASEXCH_ocean_CO2   ! ANY ocean: special tracers to be passed to ocean

#define CHL_from_OBIO               ! ANY ocean: interactive CHL

#define TRACERS_GASEXCH_CFC_Natassa ! ANY ocean: CFC-11 or CFC-12

#ifdef TRACERS_Alkalinity           ! ANY ocean: prognostic alkalinity

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Rundecks to be used for each case: 

E1ar_prescrocn.R   ! for prescribed ocean + seawifs

E1arobio_h.R       ! hycom ocean + obio 
    .... (more to come)

E1arobio_g.R       ! russell ocean + obio  
E1arseawifs.R      ! russell ocean + seawifs
E1arseawifs_2deg.R ! russell ocean + seawifs
E1arobiogasx.R     ! russell ocean + obio + gas exchange
E1arobio_alk.R     ! russell ocean + obio + alkalinity

=========================================
Important:

when using Russell ocean model **even without interctive gas exchange*
you need to compile the following routines that refer to TRACERS_OCEAN

TRACER_COM  TRACERS_DRV              ! configurable tracer code
TRACERS                             ! generic tracer code