# Build executable for ECCO-Darwin version 3
# with circa-2011 MITgcm code, equivalent to
# /nobackup/hbrix/MITgcm_110502/build_darwin_p6/mitgcmuv

cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co -D "2011-05-12 10:30:47" MITgcm_code
cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co -D "2011-05-12 10:30:47" MITgcm_contrib/darwin/pkg/darwin
cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co MITgcm_contrib/ecco_darwin/v3_cs510_Brix
cd MITgcm/pkg
ln -sf ../../MITgcm_contrib/darwin/pkg/darwin .
cd ..
mkdir build
cd build
module purge
module load comp-intel/2016.2.181 mpi-sgi/mpt.2.14r19 hdf4/4.2.12 hdf5/1.8.18_mpt netcdf/4.4.1.1_mpt
../tools/genmake2 -of \
    ../../MITgcm_contrib/ecco_darwin/v3_cs510_Brix/code/linux_amd64_ifort+mpi_ice_nas \
    -mo ../../MITgcm_contrib/ecco_darwin/v3_cs510_Brix/code
make depend
make -j 16

==============
# Instructions for running Version 3 (cg1) to 2009-2013.

cd ..
mkdir run
cd run
ln -sf ../build/mitgcmuv .
cp ../../MITgcm_contrib/ecco_darwin/v3_cs510_Brix/input/* .
ln -sf ~dmenemen/CMS/run_template_cg1/darwin* .
ln -sf ~dmenemen/CMS/run_template_cg1/DIFFKR_2_20_1_lat6070_cube81 .
ln -sf /nobackup/hzhang1/cs510/run_template/GEBCO_510x6x510_ver06_dig.bin .
ln -sf /nobackup/hzhang1/forcing/jra25/jra25_dlw* .
ln -sf /nobackup/hzhang1/cs510/ICBC_2009_iter26/jra25_xx_* .
ln -sf /nobackup/hbrix/ICBC/pco2a_blended_* .
ln -sf pco2a_blended_2012 pco2a_blended_2013
ln -sf pco2a_blended_2012 pco2a_blended_2014
ln -sf /nobackup/hzhang1/cs510/ICBC_2009_iter26/pickup.0000000001.data_xx pickup.0000000001.data
ln -sf /nobackup/hzhang1/cs510/ICBC_2009/pickup*.0000000001.??ta .
ln -sf /nobackup/dmenemen/forcing/runoff/runoff-360x180x12.bin .
ln -sf /nobackup/hzhang1/cs510/run_template/tile00* .

# modify run_darwin_450 as needed
qsub run_darwin_450

##############################################################

From ftp://ecco.jpl.nasa.gov/ECCO2/Darwin/CarbFlux_v2
Global Attributes:
 description              = 'ECCO2-Darwin CS510 run ag4 monthly average'
 MITgcmUV_version         = 'checkpoint62w'
 IntegrationPeriod        = '2009-01-01 -- 2010-12-31'
 InitialConditionsPhysics = 'ECCO2-CS510 ver. 2 (adjoint), Jan09-Apr10,
                             iter. 22.'
 InitialConditionsBGC     = 'Linear combination of the initial conditions of
                             five sensitivity experiments for all
                             biogeochemical tracers (Greens functions run
                             ag4)'
 SurfaceForcingPhysics    = 'ECCO2-CS510 ver. 2 (adjoint), Jan09-Apr10,
                             iter. 22. JRA-25 after Apr10.'
 SurfaceForcingBGC        = 'Time and space variable atmospheric pCO2 blended
                             from daily 2009 GEOS-Chem results provided by
                             Kevin Bowman (JPL) on 3/3/2011 and global
                             atmospheric monthly means from NOAA
                             ESRL. Iron/dust climatological values from
                             Mahowald (2006).'
 ModelParametersPhysics   = 'ECCO2-CS510 ver. 2 (adjoint), Jan09-Apr10,
                             iter. 22.'
 ModelParametersBGC       = '5 phytoplankton species, set-up from Stephanie
                             Dutkiewicz (MIT);  PIC phytoplankton production
                             relative to organic carbon (R_PICPOC) = 0.133.'
 author                   = 'Holger Brix -- UCLA/JPL'
 date                     = '10-Feb-2012'
 contact                  = 'hbrix@ucla.edu'

From pfe:/home5/hbrix/README_gf
runs={'a4v' 'a5v' 'a6v' 'a7v' 'a9v'}; gfrun='ag4';
fact1 = 0.16033; 
fact2 = 0.56404; 
fact3 = -0.077899; 
fact4 = 0.10418;
fact5 = 0.24935;
piston velocity factor in dic_surfforcing.F from 0.337 to 0.34822
R_PICPOC in darwin_generate_phyto.F from 0.04 to 0.133.
optimization based on:
    'a4v'    'a6v'    'a7v'    'a9v'    'a10v'    'a13v'
Globflux_err = 0.01
a5v -0.57061
a4v 0.16033 +/- 0.010098
a6v -0.077899 +/- 0.035022
a7v 0.10418 +/- 0.0089553
a9v 0.24935 +/- 0.0076539
a10v -0.41537 +/- 0.047835
 -> piston factor = 0.34822
a13v 1.55 +/- 0.064771
 -> R_PICPOC = 0.133
global-mean flux: -2.5471

From pfe:/home5/hbrix/README_runs
darwin_ag4:
Starting beginning of 2009 from a weighted comination of the ptracers and dic
pickup files from darwin runs 'a4v' 'a5v' 'a6v' 'a7v' 'a9v' with fact1 =
0.16033; fact2 = 0.56404; fact3 = -0.077899; fact4 = 0.10418; fact5 = 0.24935;
Base run is a5v. Factors are from Green's function analysis of these four runs
for 2009/10 using LDEO surface pCO2, Takahashi pCO2 climatology (variability,
not absolute values and the global mean CO2 flux for 2010. pickup and
pickup_seaice file are from 2009 adjoint integration. More info about
parameters in README_gf.  01FEB12

There is instructions how to set-up the run in
/home5/hbrix/README_preprun_darwin