[DOLFWAVE 09.27]

First Steps towards a Boussinesq FEniCS Application. Updates, Changes and TODOS. Warning: there is no such thing as a STABLE version.

1 NUMERICAL IMPLEMENTATION
2 FORMS
3 DOLFIN & C++
4 DEMOS & SANDBOX & MESHES
5 SCONS & HG & OTHER TOOLS
6 BUGS
7 DOCUMENTATION
8 CODE DOWNLOAD and GALLERY

1 NUMERICAL IMPLEMENTATION

INPROGRESS [#A] Implement moving Bottom for several models
```
see mvbottom demo
```
TODO [#C] Redesign Runge-Kutta and Predictor Corrector Classes.
```
assemble, boundary conditions, solve etc
```
- TODO [#A] 4th-order explicit runge-kutta initialization.

TODO [#C] Generalize MultiStep Corrector with different subspaces for phi and eta

Currently MultiStep Corrector scheme assumes eta and phi in the same subspace V0->P1. <2009-04-18 Sat>

2 FORMS

TODO [#A] NEW FORMULATIONS Implement 4th-order LPT forms with CDG P2. [Started 2009-06-03 Wed]
- DONE Added file LPTcgdI.ufl 2009-07-07 Tue

3 DOLFIN & C++

INPROGRESS Integration of LPTcgdI.ufl in the code Started 2009-07-08 Wed
INPROGRESS [#A] Update the LinearFormsInit functions, for several sponge layers.
```
 Decide about the interface
```
INPROGRESS Starting LPTtI model implementation 2009-06-03 Wed

TODO [#C] Update to DOLFIN >0.9.2 versions

 Problems with ufc ufl versions ffc compatibility...

INPROGRESS [#A] Implement a generic DOLFWAVESolver::solve for all problems
```
DOLFWAVESolver::solve(mesh,model,h,h0,level,src,flux,sponge....)
```
INPROGRESS [#A] Read the Dolfwave Options/Parameters from a file. 2009-06-17 Wed
```
 Dolfwave dw("parameters_file.txt); //(Usage Example) 
```
TODO [#C] Overload plot function with runway argument for timedependent solutions
```
Ask for the feature to viper  and Xd3d authors. 
```
TODO [#C] Redesign the Pointers notation and function calls.
INPROGRESS Redesign the Classes.
- TODO [#B] Decide what should be private.
- TODO [#A] LinearSolver options and Algebra BackEnd.
- TODO [#A] Use lu.factorized or gmres
```
The solution depends  on the class redesign
```
TODO Xd3dPlotRaw("mesh name", "file.raw") with default values

TODO [#B] Converge to a standard notation. For instance:

'FistSecondThird' for public class members 
'firstsecondthird' for private class members
'first_second_third' for function arguments

TODO [#A] Insert 'const' identifiers at proper function places and arguments. 2009-07-06 Mon
DONE Replace SUCCESS and FAILURE MACROS by inline destructor and AbortDolfwave. 2009-07-06 Mon
DONE Move TimerStart and Stop to private. 2009-07-06 Mon
DONE replace all dolfwave_macros by private inline members. 2009-07-06 Mon
- DONE Updated Assert and NotImplemented Functions 2009-07-08 Wed
DONE FunFunctions renamed to MatrixSparsityPlot 2009-07-06 Mon

4 DEMOS & SANDBOX & MESHES

TODO harbour 2009-03-02 Mon Zhao

Wave generation by Dirichlet boundary conditions
Using Zhao Teng and Cheng form Zhao.ufl
Sponge Layer Plot
Viper preview
Saving Raw file format

INPROGRESS mvbottom LPT

Wave generation by moving mottom
Using LPT2z0.ufl 
Xd3d preview

INPROGRESS Pillar LPT

Periodic wave through pilar 
LPT modified 2nd order system (LPT2z0.ufl)
Viper preview

INPROGRESS square and ficsquare Zhao

Standard Gaussian wave Benchmark 
Using Zhao.ufl 
Viper preview in square
File initial conditions in ficsquare
Xd3d preview in ficsquare

5 SCONS & HG & OTHER TOOLS

TODO [#C] Create a clean hg repository for code update.
```
Hopefully  someone will ask for it :D
```
DONE Update SConstruct, now release is made with 'hg archive -t "tgz"' 2009-07-08 Wed
```
scons release=1 
```
DONE Updated postprocessor/profile 2009-07-08 Wed
TODO Update the other tools
DONE Some cleaning on SConstruct

6 BUGS

7 DOCUMENTATION

INPROGRESS [#A] See for 'Doxygen'
TODO [#A] comments on *.ufl, *.cpp, and *.h files
INPROGRESS [#A] introduce python scripts for dispersion relations. "dir doc/dispersion" 2009-05-19 Tue
```
 'foo'.py are python classes or modules
```

8 CODE DOWNLOAD and GALLERY

DOWNLOAD 09.27-changing-all-the-time...

Gallery

RELEASE 09.27

Added dolfwave_macros.h 2009-07-02 Thu
Several fixed in included headers 2009-07-02 Thu
Moving dolfin::dolfwave functions to DolfwaveClass Started 2009-07-02 Thu
FunctionSpaces and SubSpaces are DolfwaveClass members. 2009-07-02 Thu
Linear and Bilinear forms moved to DolfwaveClass members 2009-07-02 Thu
Vector Moved to DolfwaveClass member. 2009-07-02 Thu
M, Mf and lu factorized solver are members of DolfwaveClass. 2009-07-03 Fri
Runge-Kutta and Predictor controled by members of DolfwaveClass. 2009-07-02 Thu
Added Time as a DolfwaveClass member. 2009-07-03 Fri
Decide about PcEpsilon 2009-07-03 Fri
Added SUCCESSDOLFWAVE and FAILUREDOLFWAVE exit macros 2009-07-02 Thu
DolfwaveClass in several classes 2009-07-03 Fri
Demos updated to the new DolfwaveClass members<2009-07-03 Fri
Added .hgingnore for scons hg configuration 2009-07-02 Thu
+ignoring emacs temp files *.bin *.os *.so *.eps *.ps
Velocities Field Calculation (With GradP0) 2009-07-33 Sun
Implement plot function for point profiles: dw.PointPlot(X,Y,function,"filename") 2009-07-33 Fri
rectangle demo renamed baddemorect and removed from demos 2009-07-03 Fri
```
RELEASE 09.26
```
Correction of ZhaoPotentialTrans.ufl for physical potential calculation 2009-06-27 Sat
+ Using week form with P1 elements and O(mu⁴) approximation
+ For a stronger solution involving the div grad it requires P2 and DG methods
+ Using direct week for with P1 elements is problematic (?No coercivity?!)
+ Updated Boundary conditions (Neumann for the original Dirichlet) 2009-06-29 Mon
Generalize the sponge layer terms in Zhao.ufl. 2009-06-19 Fri
Removed all the wrong 4th order forms 2009-06-26 Fri
Added ASSERT macro, to abort the code is something fails. 2009-06-30 Tue
Removed calls of the 4th order ufl forms 2009-06-26 Fri
for Zhao.ufl 2009-06-19 Fri
Horizontal grad plot for velocities. 2009-06-29 Mon
Plot now plots surface elevation and (equations/transformed) potential, when show=true 2009-06-28 Sun
PhyPhiPlot now needs and switch function for Neumann Boundary condition identification. 2009-06-29 Mon
Updated to the 4 sponge layers interface 2009-06-20 Sat
Updated to multistep pred.corr constructor 2009-06-21 Sun
Updated to the 4 sponge layers interface 2009-06-19&20 Sat
Plot initial conditions on ficsquare demo 2009-06-28 Sun
Rectangle updated to 4 sponge layers. 2009-06-21 Sun
Several Constant function(0.0) named zero 2009-06-21 Sun
Removed 4th order sandboxes 2009-06-26 Fri
HorVel time profile extract components and speed. 2009-06-30 Tue
Use dolfwave for time profile postprocessing. 2009-06-30 Tue
mv profile dir to postprocessor dir. 2009-06-29 Mon
Change name of PhysicalPotential dir to postprocessor. 2009-06-29 Mon
Added tool for post-processing calculation. 2009-06-28 Sun
DONE Change zhao to phyphiplotzhao 2009-06-30 Tue
+Just for Zhao 2004 problem.
+Physical potential calculation
+Horizontal velocities.
Updated SConstruct 2009-06-26 Fri
+"scons enableCommit=1" will ask for a comment.
Set enableCommit=1 by default in SConstruct 2009-06-27 Sat
Revert commit option to default 0 2009-06-29 Mon
+Use scons commit to commit and build
Updated SConstruct for exporting path's 2009-06-22 Mon
Added run_and_log tool. A script for logfile.txt and stdERROR.txt output. 2009-06-22 Mon
+dolf_run_log.sh "dolfwave_program"
Added DirichletBC dir with a python script for Dirichlet boundary conditions data calculator. 2009-06-22 Mon
+python datacalculator.py
Mv DirichletBC to dirichletbc. 2009-06-29 Mon
Solved Open files assert don't work. 2009-06-30 Tue
+ Using ASSERT MACRO
Some TO be removed code deleted from dolfwave.* 2009-06-30 Tue
```
RELEASE 09.25 Changelog
```
If MultiStep error is NAN or INF then abort and send error to stderr. 2009-06-16 Tue
Remove default value (in PredictorCorrector.h) from pc constructor for multi-step error. 2009-06-19 Fri
+We have to pass explicitely the PcEpsilon value.
Load eta and phi from files (P1xP1 case only) 2009-06-17 Wed
+ For safety purposes (long runs, electrical shutdowns...etc
Some TO BE REMOVED MARKS in DolfaweClassPlot.cpp and DolfwaveClass.h 2009-06-17 Wed
Removed booleans from DolfwaveClass ShowEta,SaveEta,etc. 2009-06-17 Wed
Add real_harbour.avoir2D to harbour mesh 2009-06-19 Fri
DONE rectangle :Zhao:
+ An Ugly Low level implementation
+ Period wave in a rectangle
+ Using GMRES
+ Using Zhao.ufl
+ Xd3d xyz preview
CLOSED 2009-06-17 Wed
Insert comments in Several Plot function arguments to reduce code. 2009-06-17 Wed
Initialize the Dolfwave options explicitely 2009-06-17 Wed
real scale mesh of the harbour geometry () 2009-06-15 Mon
Move workdir to sandbox 2009-06-16 Tue
Added parameters dir to sandbox. 2009-06-17 Wed
Added file_init_cond dir to demo. 2009-06-17 Wed
+Example of howto read initial conditions from last outputed eta and phi raw files
+ Mv file_init_cond dir to ficsquare 2009-06-18 Thu
include sandbox in release 2009-06-16 Tue
DONE Add commit to ARGUMENTS for hg commit update. 2009-06-17 Wed
+scons enableCommit=1
Update ./SConstruct for including */*~ and */*/*~ in cleanAll=1 2009-06-17 Wed
Add enableSandbox to ARGUMENTS for sandbox demos compilation. 2009-06-17 Wed
Update ficsquare SConstruct to demo.bin. 2009-06-19 Fri
Clean the "nan's" at the MultiStep error. 2009-06-14 Sun
+ with the ufl format and with the V0 spacefunction for phi it seems solved.
+ Added abort() if a nan or inf occurs.
Added datacalculator.py in DirichletBC dir. 2009-06-19 Fri
+Calculate appropriate DirichletBC
+Dispersion properties are considered
+For Zhao.ufl form only
Update the time step if ficsquare 2009-06-19 Fri
+It is important in when boundary conditions are time-dependent.
```
RELEASE 09.23-24 Changelog
```
More work and bug correction on ufl files 2009-06-08 Mon
comment some "to be removed" code 2009-06-03 Wed
Removed FormNameList[] from dolfwave.h/cpp using strings instead 2009-06-03 Wed
decrease the number of iterations and augment the step size in several demos 2009-06-03 Wed
rectangle demo working 2009-06-09 Tue
src/SConstruct changed. Working with (UBUNTU JAUNTY) 2009-06-09 Tue
Gravity acceleration as a constant in forms: Scale issues 2009-06-09 Tue
Corrected on LinearFormsInit: Passed as a Function( ) in ufl form files. 2009-06-08 Mon
DONE Corrected on demos: g should be passed explicitly as Constant function with the appropriate scale in *.cpp 2009-06-08 Mon
```
RELEASE 09.22 Changelog
```
Work on dispersion scripts several py classes and modules added to doc/dispersion/
remove boussdispclass.py and dispchar.py -standing for copy paste- 2009-05-20 Wed
SConstruct for plotting via scons 2009-05-20 Wed
```
RELEASE 09.19-21 Changelog
```
Created Xd3dXyzPlot for previewing with xd3d. 2009-05-05 Tue
Started Work on Dispersion Properties 2009-05-19 Tue
ABORTED LPT4cd.ufl useless 2009-05-19 Tue
NOTUSED LPT4z0.ufl not interesting since the dispersion relation is very BAD 2009-04-22 Wed
NOTUSED LPT2cd.ufl for LPT transformed 2nd-order with Potential evaluated at the bottom. not interesting since it is a particular case of LPT2z0 2009-05-19 Tue
Some tools added in tools dir. animation and profile 2009-05-08 Fri
```
RELEASE 09.18 Changelog
```
Updating SConstruct for generation of doxy documentation 'scons doxy=1' 2009-04-26 Sun
Exclude the ffc header files from doxygen documentation . 2009-04-26 Sun
Matrix plot function, for pattern plot :MatrixPlot(Matrix,"file.pbm") :FunFunctions: 2009-04-30 Thu
```
RELEASE 09.17 Changelog
```
For P1 and P2 interpolation. See square demo. InitialCondition(P2)(*V,eta_phi,eta_init,phi_init,eta,phi) 2009-04-24 Fri
NOTUSED LPT4z0.ufl not interesting since the dispersion relation is very BAD. 2009-04-22 Wed
LPT4cd P2xP2 with Zero Neumann boundary conditions Requires an much smaller timestep 0.001->0.0001 2009-04-24 Fri
Updated Init Functions for New 4th order forms. 2009-04-22 Wed
Remove the gap and step from the plot functions. 2009-04-21 Tue
Zhao Model with new interface in square demo 2009-04-24 Fri
Updates to SConstruct files, clean for workdir 2009-04-25 Sat
Created tools for auxiliar scripts and c++ codes 2009-04-20 Mon
DONE created "profile" program for time profile in individual points 2009-04-20 Mon
scripts for animation generation 2009-04-20 Mon
```
RELEASE 09.16 Changelog
```
Created 'GradP2.ufl' and 'GradP0.ufl' for (horizontal) grad calculation. 2009-04-18 Sat
DOLFIN::RAWFile.cpp updated to cell based values plot. 2009-04-18 Sat :DOLFIN:
Added Prof.ufl for standard projection. (sponge layer plot) 2009-04-19 Sun
Migrate to DOLFIN 0.9.2 ->FFC UFL forms. 2009-04-18 Sat
Maintaining the form files but DOLFWAVE is compiled with the new (ufl)header files
Remove macros from dolfwave.h. 2009-04-19 Sun
Depth plot function (using symmetric depth). 2009-04-18 Sat
SpongePlot function 2009-04-19 Sun
Using the new interface in harbour demo. 2009-04-18 Sat
demo/harbour&pillar/Sconstruct updated. dolfin_plot_data.xml removed from release. 2009-04-19 Sun
Update version numbers to YY.WEAK .Release will be done at monday, or in other day :D 2009-04-09 Thu
scons release update local and ptmat page 2009-04-15 Wed
Found Bug on Multicorrector steps with phi_old definined with the bad "(V1)" space (See Numerical Implementation Section) 2009-04-18 Sat
```
RELEASE 09.04 Changelog
```
'Options' Changed to 'DolfwaveOptions' 2009-04-14 Tue
'DolfwaveOptions' changed to 'Dolfwave' 2009-04-15 Wed
Moving bottom For LPT2z0.form 2009-04-08 Wed
Copied solve functions for cases with no Dirichlet boundary conditions 2009-04-15 Wed
Implented solve functions for Runge Kutta Predictor and Corrector steps 2009-04-09 Thu
Using generic Linear and Bilinear Forms in Predictor-Corrector and Runge-Kutta 2009-03-27 Fri
Added plotting functions in DolfwaveOptions 2009-04-14 Tue
Added Namespace dolfin::dolfwave 2009-04-13 Mon
Added FormInit functions 2009-04-13 Mon
Added Functions Init, for initialization of solutions functions. 2009-04-14 Tue
Added Function Space and SubSpace Init functions. 2009-04-13 Mon
Added DolfwaveOptions.cpp&h for parameters class. 2009-04-14 Tue
DolfwaveOptions.* changed to DolfwaveClass.* 2009-04-15 Wed
'Options' Changed to 'DolfwaveOptions' 2009-04-14 Tue
'DolfwaveOptions' changed to 'Dolfwave' 2009-04-15 Wed
DONE Several updates to the Plot system. 2009-04-15 Wed
Created workdir for tests (not included in release)
Updated harbour mesh (Note: Xd3d post-process reads medit "*.msh" files) 2009-04-02 Thu
harbour output as raw files for Xd3d 2009-04-02 Thu
Removed system("clear") and cstdlib include.
mvbottom :LPT:
Using new interface: simplified code 2009-04-15 Wed
Pillar :LPT:
Using new interface: simplified code 2009-04-13 Mon 2009-04-15 Wed
Release option updated for not inclusion of older releases 2009-03-27 Fri
Update version numbers to YY.MM 2009-04-09 Thu
Updated Sconstruct for release_archive exclusion 2009-04-15 Wed
LPT2z0 bug in the Linear form 2009-04-08 Wed
```
 RELEASE 09.03 Changelog
```
Consider *.h form headers in src/form dir. 2009-03-31 Tue
Added LPT2z0.form for LPT transformed 2nd-order equation z=0 expansion. 2009-03-26 Thu
Sconstruct version update 2009-03-27 Fri
Updated meshes directory and mesh paths 2009-03-27 Fri
Updated dolfwave.h includes 2009-03-27 Fri
Updated Zhao forms for Source Functions 2009-03-09 Mon
Equal sbfctn_update for PredCorr and RungeKutta subfunction update 2009-03-09 Mon
Symetric projection for depth post-processing. 2009-03-09 Mon
Migrate to DOLFIN 0.9.1 2009-03-09 Mon
Class DEPTH removed from demo. 2009-03-06 Fri 12:50
Harbour 2009-03-02 Mon :Zhao:
Working with 0.9.1 2009-03-10 Tue
Depth plot via symmetric projection. 2009-03-10 Tue
Rectangle 2009-03-13 Fri :Zhao:
Square Gaussian wave For Standard benchmark 2009-03-06 Fri 12:47 :Zhao:
Create tgz file for release 2009-03-17 Tue
Remove *.os from release 2009-03-10 Tue
Set "enableDemo=yes" option to scons 2009-03-04 Fri
Set "cleanall" option for scons to remove demo output dirs also 2009-03-04 Wed
Demo executables changed to "demo.bin" 2009-03-04 Wed
Demo output files to "output" dir. 2009-03-02 Mon
Euler solved 2009-03-06 Fri
Doc dir created 2009-03-18 Wed

This document was made using emacs Org-mode

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Author: Nuno David Lopes <ndl@ptmat.fc.ul.pt>

Date: 2009/07/08 12:18:16 PM

[DOLFWAVE 09.27]

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