--- manual/manual_todo.txt	2006/04/06 19:54:06	1.9
+++ manual/manual_todo.txt	2006/04/06 20:03:45	1.10
@@ -207,13 +207,190 @@
           o Gas giant?
 
 
-Master list of packages
+>>>> from JM
+
+
+manual, section.2 :
+
+In general: 
+- add more refences/links to S/R & variable name
+- would be nice to have an active link to the fortran-file 
+  for all the S/R & eq.Number in the "calling-tree" boxes
+- search for CALC_MOM_RHS and replace it by the appropriate S/R
+  (mom_flux_form, mom_vecinv, dynamics)
+- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
+was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
+in section.2, \vec{\bf v} is used instead and 3.D velocity vector is 
+simply written \vec{v}.
+I would suggest to keep the notation as they are (since they are consistent 
+inside each section) but may be to move the "notation.tex" piece
+at the beginning of section.2 and to mention clearly the changes between 
+the 2 sections.
+
+in content: Horizontal Dissipation: 2 times in vector-invariant section
+
+2.1 time-stepping (part2/time_stepping.tex)
+
+- this is not clear to me:
+
+>> In all the above configurations it is also possible to substitute the
+>> Adams-Bashforth with an alternative time-stepping scheme for terms
+>> evaluated explicitly in time
+
+
+2.2 rigid-lid:
+
+- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
+  to stay closer to the code.
+- mention section 2.5 implicit-Time-stepping (for vertical viscosity)
+
+2.3 linear free-surface: 
+- add ref(+link) to S/R names:
+- add ref(+link) to Crank-Nickelson section 2.9.1
+
+2.4 Adams-Bashforth
+- add stability diagrams (I have some figures that I can put)
+- add link for var. forcing_In_AB
+- add S/R link for S/R ADAMS_BASHFORTH2
+
+2.5 Implicit time-stepping 
+- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
+	SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
+- update: also used for vertical advection
+
+2.6 Synchronous time-stepping:
+- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,  
+                   MOMENTUM_CORRECTION_STEP.
+
+2.7 Stagger baroclinic time-stepping
+- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
+
+2.8 NH
+- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
+
+2.9 Variants on Free-Surface
+- Delta.t mis-written (eq.2.73)
+- Eq.Num missing (has been fixed since)
+- u* is stored in gU (and not in gUnm1)
+- Phi_nh in NH_VARS.h
+- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, 
+  INI_CG2D, INI_CG3D
+
+2.9.1 Crank-Nickelson
+- link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
+ 
+2.9.2 NLFS
+- eq.Nb are wrong in html
+- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) 
+
+2.10.1 Notation
+- Area definition is not really used like this
+
+>> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
+
+  Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to 
+  the model variables) are used (e.g., see section 2.10.5)
+
+2.10.5 Horizontal grid:
+- fig.2.8 : should use Aw,As consistently in this figure description,
+  in the figure itself, as it is in the text.
+- curvilinear: 
+  to add: mention the angle of the grid direction relative to 
+  Eastward, Northward direction.
+  + mention horizGridFile= in file "data" (PARM04)
+- add cylindrical grid description
+   need to do a better job of relating model variables to this diagram
+
+
+2.11 Continuity & Horizontal Pressure gradient terms
+ - mention that d.Phi/dr|s =g if using z coordinate 
+ - eq. 2.90 not clear regarding \delta_k(P-E)
+ better to add the free surface eq: d.eta/dt = w_s + P-E
+
+2.12 Hydrostatic balance
+ - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
+   is hard to find
+ - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
+    and in section 1.3.4: remove the 1.3.4.3.2 subsection: 
+                       Quasi-nonhydrostatic Atmosphere
+
+2.13.2 Coriolis terms
+ - note: the discretization used when useEnergyConservingCoriolis=T  
+   has no hFac and no Area and is still different from the form 
+   described here (with Area & hFac);
+
+2.13.5 Lateral dissipation
+ - add description of how to use cosFactor & cosPower
+ - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 
+    o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
+      in code need to explain why cos()3/2 turns out to be
+      scaling (not cos()2)
+
+2.13.6 Vertical dissipation 
+ - mention the implicit vertical viscosity option and ref to section 2.5
+ - add the parameter correspondence: Av <-> viscAr (and might change also
+   the notation to Ar)
+
+2.14 Vector invariant momentum equations
+ - indicate that the NH pieces (vertical momentum eq) are not yet coded
+   and that the NH code uses the flux form.
+
+2.14.6 Horizontal dissipation -> Horizontal Divergence
+
+2.14.7 Horizontal dissipation
+ - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ  
+   and A_D4,A_z4 <-> viscA4D,viscA4Z 
+
+2.16 & 2.17 & 2.18 : 
+ - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
+
+2.20.2 mercator, non-dimensional Equations:
+- does not use std notation
+- would be better as an appendix of section 2.20:
+(e.g changing the tile to:
+ Appendix: non-dimensional Equations on Spherical-Polar grid.)
+
+JM
+
+>>>> From Ed
+
+Here are the remaining bits for Chap 4 :
+
+ - The grammar/flow could still use some work.  Boo was an English
+   major and has experience editing/proofing technical papers.  I
+   could print out a copy and ask her to read it and suggest
+   improvements.
+
+ - missing references (if you point me towards URLs, I'll add them
+   to the bibliography):
+     \ref{ref hoe and hill, ecmwf}
+     \ref{magicgarden}
+     \ref{IBMLAPI}
+     \ref{Memorychannel}
+     \ref{hoe-hill:99}
+
+ - There are a few empty sub-sections at the end of Chap 4 that
+   should either be commented out or fleshed out.
+
+and thats about it for Chap 4.
+
+
+Add more to quick links on front page
+
+Chapter 6
+
+   the master package diagram does not appear in the document
+
+   pkg/ptracers doesn't seem to have any documentation (see packages list below)
+
+
+Master list of packages (add this to beginning of chap 6)
 
 admtlm/               - autodiff (chapter 5)
-aim/                  - 6.4.1 (content needs fixing - JM to do)
+aim/                  - retired
 aim_compon_interf/    - 6.6 (no content yet)
 aim_ocn_coupler/      - 6.6 (no content yet)
-aim_v23/              - retired
+aim_v23/              - 6.4.1 (content needs fixing - JM to do)
 atm_common/           - 6.6 (no content yet)
 autodiff/             - autodiff (chapter 5)
 bulk_force/           - 6.3.3
@@ -280,37 +457,8 @@
 
 Figure 6.8 is missing
 
-
->>>> From Ed
-
-Here are the remaining bits for Chap 4 :
-
- - The grammar/flow could still use some work.  Boo was an English
-   major and has experience editing/proofing technical papers.  I
-   could print out a copy and ask her to read it and suggest
-   improvements.
-
- - missing references (if you point me towards URLs, I'll add them
-   to the bibliography):
-     \ref{ref hoe and hill, ecmwf}
-     \ref{magicgarden}
-     \ref{IBMLAPI}
-     \ref{Memorychannel}
-     \ref{hoe-hill:99}
-
- - There are a few empty sub-sections at the end of Chap 4 that
-   should either be commented out or fleshed out.
-
-and thats about it for Chap 4.
-
-
-Add more to quick links on front page
-
-Chapter 6
-
-   the master package diagram does not appear in the document
-
-   pkg/ptracers doesn't seem to have any documentation (see packages list below)
+6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 
+ Figure 6.8 is missing
 
 
 >>>> From Andrea
@@ -422,152 +570,6 @@
      offline - duplicate inputs, what is it, tidy up cfc v.
                other offline. JM thinks these need tidying up.
 
->>>> from JM
-
-
-
-manual, section.2 :
-
-In general: 
-- add more refences/links to S/R & variable name
-- would be nice to have an active link to the fortran-file 
-  for all the S/R & eq.Number in the "calling-tree" boxes
-- search for CALC_MOM_RHS and replace it by the appropriate S/R
-  (mom_flux_form, mom_vecinv, dynamics)
-- Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
-was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
-in section.2, \vec{\bf v} is used instead and 3.D velocity vector is 
-simply written \vec{v}.
-I would suggest to keep the notation as they are (since they are consistent 
-inside each section) but may be to move the "notation.tex" piece
-at the beginning of section.2 and to mention clearly the changes between 
-the 2 sections.
-
-in content: Horizontal Dissipation: 2 times in vector-invariant section
-
-2.1 time-stepping (part2/time_stepping.tex)
-
-- this is not clear to me:
-
->> In all the above configurations it is also possible to substitute the
->> Adams-Bashforth with an alternative time-stepping scheme for terms
->> evaluated explicitly in time
-
-
-2.2 rigid-lid:
-
-- At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
-  to stay closer to the code.
-- mention section 2.5 implicit-Time-stepping (for vertical viscosity)
-
-2.3 linear free-surface: 
-- add ref(+link) to S/R names:
-- add ref(+link) to Crank-Nickelson section 2.9.1
-
-2.4 Adams-Bashforth
-- add stability diagrams (I have some figures that I can put)
-- add link for var. forcing_In_AB
-- add S/R link for S/R ADAMS_BASHFORTH2
-
-2.5 Implicit time-stepping 
-- add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
-	SOLVE_TRIDIAGONAL, SOLVE_PENTADIAGONAL
-- update: also used for vertical advection
-
-2.6 Synchronous time-stepping:
-- add link for S/R THERMODYNAMICS, DYNAMCIS, SOLVE_FOR_PRESSURE,  
-                   MOMENTUM_CORRECTION_STEP.
-
-2.7 Stagger baroclinic time-stepping
-- mention AB(T,S) instead of AB(Gt,Gs) (in development) at the end
-
-2.8 NH
-- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
-
-2.9 Variants on Free-Surface
-- Delta.t mis-written (eq.2.73)
-- Eq.Num missing (has been fixed since)
-- u* is stored in gU (and not in gUnm1)
-- Phi_nh in NH_VARS.h
-- add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D, 
-  INI_CG2D, INI_CG3D
-
-2.9.1 Crank-Nickelson
-- link for variable: implicSurfPress, implicDiv2DFlow, useRealFreshWater
- 
-2.9.2 NLFS
-- eq.Nb are wrong in html
-- 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi) 
-
-2.10.1 Notation
-- Area definition is not really used like this
-
->> Ao : Area of the face orthogonal to "o" direction (o=u,v,w)
-
-  Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to 
-  the model variables) are used (e.g., see section 2.10.5)
-
-2.10.5 Horizontal grid:
-- fig.2.8 : should use Aw,As consistently in this figure description,
-  in the figure itself, as it is in the text.
-- curvilinear: 
-  to add: mention the angle of the grid direction relative to 
-  Eastward, Northward direction.
-  + mention horizGridFile= in file "data" (PARM04)
-- add cylindrical grid description
-   need to do a better job of relating model variables to this diagram
-
-
-2.11 Continuity & Horizontal Pressure gradient terms
- - mention that d.Phi/dr|s =g if using z coordinate 
- - eq. 2.90 not clear regarding \delta_k(P-E)
- better to add the free surface eq: d.eta/dt = w_s + P-E
-
-2.12 Hydrostatic balance
- - add ref to Atmosphere Appendix section (1.4) since Adcroft 2002
-   is hard to find
- - add ref to section 1.3.4 (Hydrostatic, Quasi-Hydrostatic & Non-H)
-    and in section 1.3.4: remove the 1.3.4.3.2 subsection: 
-                       Quasi-nonhydrostatic Atmosphere
-
-2.13.2 Coriolis terms
- - note: the discretization used when useEnergyConservingCoriolis=T  
-   has no hFac and no Area and is still different from the form 
-   described here (with Area & hFac);
-
-2.13.5 Lateral dissipation
- - add description of how to use cosFactor & cosPower
- - add the parameter correspondence: Ah <-> viscAh ; A4 <-> viscA4 
-    o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
-      in code need to explain why cos()3/2 turns out to be
-      scaling (not cos()2)
-
-2.13.6 Vertical dissipation 
- - mention the implicit vertical viscosity option and ref to section 2.5
- - add the parameter correspondence: Av <-> viscAr (and might change also
-   the notation to Ar)
-
-2.14 Vector invariant momentum equations
- - indicate that the NH pieces (vertical momentum eq) are not yet coded
-   and that the NH code uses the flux form.
-
-2.14.6 Horizontal dissipation -> Horizontal Divergence
-
-2.14.7 Horizontal dissipation
- - add the parameter correspondence: A_D,A_z <-> viscAhD,viscAhZ  
-   and A_D4,A_z4 <-> viscA4D,viscA4Z 
-
-2.16 & 2.17 & 2.18 : 
- - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
-
-2.20.2 mercator, non-dimensional Equations:
-- does not use std notation
-- would be better as an appendix of section 2.20:
-(e.g changing the tile to:
- Appendix: non-dimensional Equations on Spherical-Polar grid.)
-
-JM
-
 
 9. Model uses
    Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...