# Example: Subtropical North Atlantic and Labrador Sea Areas
# ==========================================================
# - forward/adjoint run
# - optimization cost function
# - with KPP & shortwave heating
# - gmredi turned off (until merge to c48)
# - The input data is real*8
# - 4 timesteps

####################
# Experiment no. 1 #
####################
# Use air-sea fluxes as controls (standard case):
# perform gradient checks for first four elements of the
# heat flux part of the control vector (grdchkvarindex = 3).

# Compile code in bin/:
 cd bin
 cp ../verification/natl_box_adjoint/code/.genmakerc .
 cp ../verification/natl_box_adjoint/code/*.h .
# Configure and compile the code:
 ../tools/genmake -makefile
 make depend
# Generate the adjoint code:
 cd ../adjoint
 make adtaf
 make adchange
# Go back and compile the code:
 cd ../bin
 make
# To run:
 cd ../exe
 cp ../verification/natl_box_adjoint/input/* .
 mitgcmuv >&! output.txt
# To verify the results of the gradient check, type:
 grep ph-grd output.txt
# A reference output is in:
 grep ph-grd ../verification/natl_box_adjoint/results/output.txt


####################
# Experiment no. 2 #
####################
# Use bulk formulae and atmospheric state controls
# (only differences to experiment 1 are in
# ECCO_CPPOPTIONS.h and in data.grdchk):
# perform gradient checks for first four elements of the
# air temperture part of the control vector (grdchkvarindex = 7).

# Compile code in bin/:
 cd ../bin
 rm -rf *.o *.f *.p rii_files
 rm -rf *.F *.h *.c Makefile*
 cp ../verification/natl_box_adjoint/code_bulk/.genmakerc .
 cp ../verification/natl_box_adjoint/code_bulk/*.h .
# Configure and compile the code:
 ../tools/genmake -makefile
 make depend
# Generate the adjoint code:
 cd ../adjoint
 make adtaf
 make adchange
# Go back and compile the code:
 cd ../bin
 make
# To run:
 cd ../exe
 cp ../verification/natl_box_adjoint/input_bulk/* .
 cp ../verification/natl_box_adjoint/input/PH_*.data .
 ./mitgcmuv >&! output.txt
# To verify the results of the gradient check, type:
 grep ph-grd output.txt
# A reference output is in:
 grep ph-grd ../verification/natl_box_adjoint/results_bulk/output.txt


####################
# Experiment no. 3 #
####################
# Same as exp. 2, but with ALLOW_SEAICE defined.

# Compile code in bin/:
 cd ../bin
 rm -rf *.o *.f *.p rii_files
 rm -rf *.F *.h *.c Makefile*
 cp ../verification/natl_box_adjoint/code_seaice/*.h .
 cp ../verification/natl_box_adjoint/code_seaice/.genmakerc .
 cp ../verification/natl_box_adjoint/code_seaice/SEAICE_OPTIONS.h.FLUXES SEAICE_OPTIONS.h
# Configure and compile the code:
 ../tools/genmake -makefile
 make depend
# Generate the adjoint code:
 cd ../adjoint
 mv makefile makefile.old
 cp ../verification/natl_box_adjoint/code_seaice/makefile .
 make adtaf
 make adchange
 rm -f makefile
 mv makefile.old makefile
# Go back and compile the code:
 cd ../bin
 make
# To run:
 cd ../exe
 cp ../verification/natl_box_adjoint/input_bulk/* .
 cp ../verification/natl_box_adjoint/input/PH_*.data .
 ./mitgcmuv >&! output.txt
# To verify the results of the gradient check, type:
 grep ph-grd output.txt
# A reference output is in:
grep ph-grd ../verification/natl_box_adjoint/results_bulk/output.txt


####################
# Experiment no. 4 #
####################
# Uses same executable as exp. 3, but with useseaice = .true.

# To run:
 cd ../exe
 cp ../verification/natl_box_adjoint/input_bulk/* .
 cp ../verification/natl_box_adjoint/input_seaice/data.seaice.cgrid data.seaice
 cp ../verification/natl_box_adjoint/input_seaice/data.pkg .
 cp ../verification/natl_box_adjoint/input/PH_*.data .
 ./mitgcmuv >&! output.txt
# To verify the results of the gradient check, type:
 grep ph-grd output.txt
# A reference output is in:
 grep ph-grd ../verification/natl_box_adjoint/results_bulk/output.txt


####################
# Experiment no. 5 #
####################
# Same as exp. 4, but using sea-ice bulk formulae.
# This experiment tests pkg/seaice bulk formulae over open water.
# No sea-ice is formed anywhere in the domain.
# There is a worrisome 3-4% discrepancy between ajoint
# model and finite difference gradients.

# Compile code in bin/:
 cd ../bin
 rm -rf *.o *.f *.p rii_files
 rm -rf *.F *.h *.c Makefile*
 cp ../verification/natl_box_adjoint/code_seaice/*.h .
 cp ../verification/natl_box_adjoint/code_seaice/.genmakerc .
# Configure and compile the code:
 ../tools/genmake -makefile
 make depend
# Generate the adjoint code:
 cd ../adjoint
 mv makefile makefile.old
 cp ../verification/natl_box_adjoint/code_seaice/makefile .
 make adtaf
 make adchange
 rm -f makefile
 mv makefile.old makefile
# Go back and compile the code:
 cd ../bin
 make
# To run:
 cd ../exe
 cp ../verification/natl_box_adjoint/input_bulk/* .
 cp ../verification/natl_box_adjoint/input_seaice/data.seaice.cgrid data.seaice
 cp ../verification/natl_box_adjoint/input_seaice/data.pkg .
 cp ../verification/natl_box_adjoint/input/PH_*.data .
 ./mitgcmuv >&! output.txt
# To verify the results of the gradient check, type:
 grep ph-grd output.txt
# A reference output is in:
 grep ph-grd ../verification/natl_box_adjoint/results_bulk/output.exp5


####################
# Experiment no. 6 #
####################
# Same as experiment 5, but in the Labrador Sea rather than in
# the North Atlantic subduction region.  This experiment does
# include sea-ice, but cost function data files are bogus:
# labsea_TP_fields   : filled with -9999
# labsea_TP_mean     : hour 100 ssh (cm) of lab_sea experiment
# labsea_ERS_fields  : filled with -9999
# labsea_SST_fields  : 14 * Levitus annual mean SST
# labsea_Lev.ptmp    : 14 * Levitus annual mean temperature
# labsea_Lev.salt    : 14 * Levitus annual mean salinity
# labsea_ssh.err     : filled with -9999
# labsea_geoid.err   : constant 0.2 with -9999 landmask
# labsea_totflux.err : 100 with -9999 landmask
# labsea_pme.err     : 4e-8 with -9999 landmask
# labsea_ustress.err : 3 with -9999 landmask
# labsea_vstress.err : 3 with -9999 landmask
# The gradient check does not work.  The finite difference
# gradient has a strong dependence on grdchk_eps.

# To run:
 cd ../exe
 cp ../verification/natl_box_adjoint/input_seaice/* .
 ./mitgcmuv >&! output.txt
# To verify the results of the gradient check, type:
 grep ph-grd output.txt
# A reference output is in:
 grep ph-grd ../verification/natl_box_adjoint/results_seaice/output.txt