# [DOLFWAVE 09.27]

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

## Table of Contents

- 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 dolfwavemacros 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 dolfwavemacros.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 runandlog tool. A script for logfile.txt and stdERROR.txt output. 2009-06-22 Mon
- +dolfrunlog.sh "dolfwaveprogram"
- 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 realharbour.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,etaphi,etainit,phiinit,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. dolfinplotdata.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 phiold 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 releasearchive 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