--- manual/s_software/text/sarch.tex	2006/04/04 18:33:52	1.22
+++ manual/s_software/text/sarch.tex	2006/04/05 01:12:02	1.24
@@ -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 1.24 2006/04/05 01:12:02 jmc Exp $
 
 This chapter focuses on describing the {\bf WRAPPER} environment
 within which both the core numerics and the pluggable packages
@@ -165,6 +165,7 @@
 scientific computing community.
 
 \subsection{Machine model parallelism}
+\label{sect:domain_decomposition}
 \begin{rawhtml}
 <!-- CMIREDIR:domain_decomp: -->
 \end{rawhtml}
@@ -1481,7 +1482,6 @@
 {\footnotesize
 \begin{verbatim}
 C
-C
 C Invocation from WRAPPER level...
 C  :
 C  :
@@ -1545,22 +1545,25 @@
 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 +1588,10 @@
 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 +1599,8 @@
 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 +1627,15 @@
 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 +1678,22 @@
 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 +1711,9 @@
 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 +1723,31 @@
 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 +1806,10 @@
 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 +1820,10 @@
 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 +1841,7 @@
 C    |
 C    |-COMM_STATS     :: Summarise inter-proc and inter-thread communication
 C                     :: events.
-C 
+C
 \end{verbatim}
 }
 
