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--- manual/s_software/text/sarch.tex 2006/04/04 18:33:52 1.22
+++ manual/s_software/text/sarch.tex 2006/04/04 19:14:14 1.23
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_software/text/sarch.tex,v 1.22 2006/04/04 18:33:52 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_software/text/sarch.tex,v 1.23 2006/04/04 19:14:14 edhill Exp $
This chapter focuses on describing the {\bf WRAPPER} environment
within which both the core numerics and the pluggable packages
@@ -1481,7 +1481,6 @@
{\footnotesize
\begin{verbatim}
C
-C
C Invocation from WRAPPER level...
C :
C :
@@ -1545,22 +1544,25 @@
C | | |-OPTIM_READPARMS :: Optimisation support package. see pkg/ctrl
C | | |-GRDCHK_READPARMS :: Gradient check package. see pkg/grdchk
C | | |-ECCO_READPARMS :: ECCO Support Package. see pkg/ecco
+C | | |-PTRACERS_READPARMS :: multiple tracer package, see pkg/ptracers
+C | | |-GCHEM_READPARMS :: tracer interface package, see pkg/gchem
C | |
C | |-PACKAGES_CHECK
C | | |
C | | |-KPP_CHECK :: KPP Package. pkg/kpp
-C | | |-OBCS_CHECK :: Open bndy Package. pkg/obcs
+C | | |-OBCS_CHECK :: Open bndy Pacakge. pkg/obcs
C | | |-GMREDI_CHECK :: GM Package. pkg/gmredi
C | |
C | |-PACKAGES_INIT_FIXED
C | | |-OBCS_INIT_FIXED :: Open bndy Package. see pkg/obcs
C | | |-FLT_INIT :: Floats Package. see pkg/flt
+C | | |-GCHEM_INIT_FIXED :: tracer interface pachage, see pkg/gchem
C | |
C | |-ZONAL_FILT_INIT :: FFT filter Package. see pkg/zonal_filt
C | |
-C | |-INI_CG2D :: 2d con. grad solver initialisation.
+C | |-INI_CG2D :: 2d con. grad solver initialization.
C | |
-C | |-INI_CG3D :: 3d con. grad solver initialisation.
+C | |-INI_CG3D :: 3d con. grad solver initialization.
C | |
C | |-CONFIG_SUMMARY :: Provide synopsis of kernel setup.
C | :: Includes annotated table of kernel
@@ -1585,10 +1587,10 @@
C | | |-INI_CORI :: Set coriolis term. zero, f-plane, beta-plane,
C | | | :: sphere options are coded.
C | | |
-C | | |-INI_CG2D :: 2d con. grad solver initialisation.
-C | | |-INI_CG3D :: 3d con. grad solver initialisation.
-C | | |-INI_MIXING :: Initialise diapycnal diffusivity.
-C | | |-INI_DYNVARS :: Initialise to zero all DYNVARS.h arrays (dynamical
+C | | |-INI_CG2D :: 2d con. grad solver initialization.
+C | | |-INI_CG3D :: 3d con. grad solver initialization.
+C | | |-INI_MIXING :: Initialize diapycnal diffusivity.
+C | | |-INI_DYNVARS :: Initialize to zero all DYNVARS.h arrays (dynamical
C | | | :: fields).
C | | |
C | | |-INI_FIELDS :: Control initializing model fields to non-zero
@@ -1596,8 +1598,8 @@
C | | | |-INI_THETA :: Set model initial temperature field.
C | | | |-INI_SALT :: Set model initial salinity field.
C | | | |-INI_PSURF :: Set model initial free-surface height/pressure.
-C | | |
-C | | |-INI_TR1 :: Set initial tracer 1 distribution.
+C | | | |-INI_PRESSURE :: Compute model initial hydrostatic pressure
+C | | | |-READ_CHECKPOINT :: Read the checkpoint
C | | |
C | | |-THE_CORRECTION_STEP :: Step forward to next time step.
C | | | | :: Here applied to move restart conditions
@@ -1624,13 +1626,15 @@
C | | | |-CONVECT :: Mix static instability.
C | | | |-TIMEAVE_CUMULATE :: Update convection statistics.
C | | |
-C | | |-PACKAGES_INIT_VARIABLES :: Does initialisation of time evolving
+C | | |-PACKAGES_INIT_VARIABLES :: Does initialization of time evolving
C | | | | :: package data.
C | | | |
C | | | |-GMREDI_INIT :: GM package. ( see pkg/gmredi )
C | | | |-KPP_INIT :: KPP package. ( see pkg/kpp )
C | | | |-KPP_OPEN_DIAGS
C | | | |-OBCS_INIT_VARIABLES :: Open bndy. package. ( see pkg/obcs )
+C | | | |-PTRACERS_INIT :: multi. tracer package,(see pkg/ptracers)
+C | | | |-GCHEM_INIT :: tracer interface pkg (see pkh/gchem)
C | | | |-AIM_INIT :: Interm. atmos package. ( see pkg/aim )
C | | | |-CTRL_MAP_INI :: Control vector package.( see pkg/ctrl )
C | | | |-COST_INIT :: Cost function package. ( see pkg/cost )
@@ -1673,18 +1677,22 @@
C/\ | | | | :: for forcing datasets.
C/\ | | | |
C/\ | | | |-EXCH :: Sync forcing. in overlap regions.
+C/\ | | |-SEAICE_MODEL :: Compute sea-ice terms. ( pkg/seaice )
+C/\ | | |-FREEZE :: Limit surface temperature.
+C/\ | | |-GCHEM_FIELD_LOAD :: load tracer forcing fields (pkg/gchem)
C/\ | | |
C/\ | | |-THERMODYNAMICS :: theta, salt + tracer equations driver.
C/\ | | | |
C/\ | | | |-INTEGRATE_FOR_W :: Integrate for vertical velocity.
C/\ | | | |-OBCS_APPLY_W :: Open bndy. package ( see pkg/obcs ).
-C/\ | | | |-FIND_RHO :: Calculates [rho(S,T,z)-Rhonil] of a slice
+C/\ | | | |-FIND_RHO :: Calculates [rho(S,T,z)-RhoConst] of a slice
C/\ | | | |-GRAD_SIGMA :: Calculate isoneutral gradients
C/\ | | | |-CALC_IVDC :: Set Implicit Vertical Diffusivity for Convection
C/\ | | | |
C/\ | | | |-OBCS_CALC :: Open bndy. package ( see pkg/obcs ).
C/\ | | | |-EXTERNAL_FORCING_SURF:: Accumulates appropriately dimensioned
-C/\ | | | | :: forcing terms.
+C/\ | | | | | :: forcing terms.
+C/\ | | | | |-PTRACERS_FORCING_SURF :: Tracer package ( see pkg/ptracers ).
C/\ | | | |
C/\ | | | |-GMREDI_CALC_TENSOR :: GM package ( see pkg/gmredi ).
C/\ | | | |-GMREDI_CALC_TENSOR_DUMMY :: GM package ( see pkg/gmredi ).
@@ -1702,7 +1710,9 @@
C/\ | | | |-CALC_GT :: Calculate the temperature tendency terms
C/\ | | | | |
C/\ | | | | |-GAD_CALC_RHS :: Generalised advection package
-C/\ | | | | | :: ( see pkg/gad )
+C/\ | | | | | | :: ( see pkg/gad )
+C/\ | | | | | |-KPP_TRANSPORT_T :: KPP non-local transport ( see pkg/kpp ).
+C/\ | | | | |
C/\ | | | | |-EXTERNAL_FORCING_T :: Problem specific forcing for temperature.
C/\ | | | | |-ADAMS_BASHFORTH2 :: Extrapolate tendencies forward in time.
C/\ | | | | |-FREESURF_RESCALE_G :: Re-scale Gt for free-surface height.
@@ -1712,24 +1722,31 @@
C/\ | | | |-CALC_GS :: Calculate the salinity tendency terms
C/\ | | | | |
C/\ | | | | |-GAD_CALC_RHS :: Generalised advection package
-C/\ | | | | | :: ( see pkg/gad )
+C/\ | | | | | | :: ( see pkg/gad )
+C/\ | | | | | |-KPP_TRANSPORT_S :: KPP non-local transport ( see pkg/kpp ).
+C/\ | | | | |
C/\ | | | | |-EXTERNAL_FORCING_S :: Problem specific forcing for salt.
C/\ | | | | |-ADAMS_BASHFORTH2 :: Extrapolate tendencies forward in time.
C/\ | | | | |-FREESURF_RESCALE_G :: Re-scale Gs for free-surface height.
C/\ | | | |
C/\ | | | |-TIMESTEP_TRACER :: Step tracer field forward in time
C/\ | | | |
-C/\ | | | |-CALC_GTR1 :: Calculate other tracer(s) tendency terms
+C/\ | | | |-TIMESTEP_TRACER :: Step tracer field forward in time
+C/\ | | | |
+C/\ | | | |-PTRACERS_INTEGRATE :: Integrate other tracer(s) (see pkg/ptracers).
C/\ | | | | |
C/\ | | | | |-GAD_CALC_RHS :: Generalised advection package
-C/\ | | | | | :: ( see pkg/gad )
-C/\ | | | | |-EXTERNAL_FORCING_TR:: Problem specific forcing for tracer.
+C/\ | | | | | | :: ( see pkg/gad )
+C/\ | | | | | |-KPP_TRANSPORT_PTR:: KPP non-local transport ( see pkg/kpp ).
+C/\ | | | | |
+C/\ | | | | |-PTRACERS_FORCING :: Problem specific forcing for tracer.
+C/\ | | | | |-GCHEM_FORCING_INT :: tracer forcing for gchem pkg (if all
+C/\ | | | | | tendancy terms calcualted together)
C/\ | | | | |-ADAMS_BASHFORTH2 :: Extrapolate tendencies forward in time.
C/\ | | | | |-FREESURF_RESCALE_G :: Re-scale Gs for free-surface height.
+C/\ | | | | |-TIMESTEP_TRACER :: Step tracer field forward in time
C/\ | | | |
-C/\ | | | |-TIMESTEP_TRACER :: Step tracer field forward in time
C/\ | | | |-OBCS_APPLY_TS :: Open bndy. package (see pkg/obcs ).
-C/\ | | | |-FREEZE :: Limit range of temperature.
C/\ | | | |
C/\ | | | |-IMPLDIFF :: Solve vertical implicit diffusion equation.
C/\ | | | |-OBCS_APPLY_TS :: Open bndy. package (see pkg/obcs ).
@@ -1788,6 +1805,10 @@
C/\ | | |-DO_FIELDS_BLOCKING_EXCHANGES :: Sync up overlap regions.
C/\ | | | |-EXCH
C/\ | | |
+C/\ | | |-GCHEM_FORCING_SEP :: tracer forcing for gchem pkg (if
+C/\ | | | tracer dependent tendencies calculated
+C/\ | | | separatly)
+C/\ | | |
C/\ | | |-FLT_MAIN :: Float package ( pkg/flt ).
C/\ | | |
C/\ | | |-MONITOR :: Monitor package ( pkg/monitor ).
@@ -1798,6 +1819,10 @@
C/\ | | | |-AIM_WRITE_DIAGS :: Intermed. atmos diags. see pkg/aim
C/\ | | | |-GMREDI_DIAGS :: GM diags. see pkg/gmredi
C/\ | | | |-KPP_DO_DIAGS :: KPP diags. see pkg/kpp
+C/\ | | | |-SBO_CALC :: SBO diags. see pkg/sbo
+C/\ | | | |-SBO_DIAGS :: SBO diags. see pkg/sbo
+C/\ | | | |-SEAICE_DO_DIAGS :: SEAICE diags. see pkg/seaice
+C/\ | | | |-GCHEM_DIAGS :: gchem diags. see pkg/gchem
C/\ | | |
C/\ | | |-WRITE_CHECKPOINT :: Do I/O for restart files.
C/\ | |
@@ -1815,7 +1840,7 @@
C |
C |-COMM_STATS :: Summarise inter-proc and inter-thread communication
C :: events.
-C
+C
\end{verbatim}
}
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