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SVN, MercuryDPM basics, etc.

Documentation; Sydney demo programs for teaching - Convert MercurySimpleDemos to tutorials.

MercurySimpleDemos:

•  CubicCell.cpp
•  FreeCooling2DPeriodicDemo.cpp
•  FreeCooling3Demo.cpp
•  FreeCoolingDemo.cpp
•  FreeCoolingTryplePeriodic.cpp
•  HeaterBoundaryTest.cpp
•  HourGlass2DDemo.cpp
•  HourGlass2DDemoMPI.cpp
•  HourGlass3DDemo.cpp
•  MinimalExampleDrum.cpp
•  ParticleInclusion.cpp
•  REV_IsotropicCompression.cpp
•  REV_PurShear.cpp
•  REV_SimpleShear.cpp
•  HourGlassSelfTest.cpp Warning: This file cannot be moved
  
  

Could I move these self tests to SelfTests directory?

A// Yes

•  FreeFallSelfTest.cpp

•  InsertionBoundarySelfTestMPI.cpp
•  MasterChuteUnitTestMPI.cpp

•  ParticleCreationSelfTest.cpp
•  FreeFallInteractionSelfTest.cpp : Warning: interaction file will take up a lot of disk space! 
  
  

Could I move these unit tests to UnitTests directory?

A// Yes

•  PeriodicBoundaryUnitTestMPI.cpp
•  PeriodicChuteUnitTestMPI.cpp
•  PeriodicWallsUnitTest.cpp
•  ParallelUnitTest.cpp
•  HGridUnitTest.cpp
  
  

Which demo tests does Anthony Thornton want for teaching?

R//

•  Job MDPM 301: Update Hour Glass Demo. The description of this job is: This code is written in a weird way with respect to what N.
  To update the structure, some changes need to be done. Maybe I could rewrite this code using the tutorial format.
  
•  Job MDPM 282: Write a tutorial on how to create your own code
•  Documentation: Write your own code. Updated.
•  Job 306: Add a review doc of what files can be turned on
•  Job 304: Hourglass does not seem able to write multiple data files.
•  Job 293: Document quarterian

•  Resurrect old Driver code directories (SerializedDriver, Leidenfrost, GranularJet, Avalanching, CartesianShearCell, Segregation), see r4549
•  Thomas Weinhart Contraction directory cannot be resurrected, make a new Contraction driver.
•  Anthony Thornton look at Chute directory, Codes are extremely old (#include "scr/Chute.h")
•  

  Send Juan paper on Chargedbonded.

•  Merge completed features from my Branches (MercuryLab, ResurrectOldDriverCodes/) into Trunk, see r4522, r4549
•  Julius Mbaziira Check whether *SelfTestMPI.cpp/*UnitTestMPI.cpp is executed if MPI=ON
  No, they are never executed. They need to be renamed *MPI2Test.cpp
•  Fixed "Mathjax not displayed" issue in documentation, see r4554
•  Add Test rules to coding style
•  Clean up Doxygen section in coding style, add /ref
•  Update license
•  Discuss: HertzMindlin tied together, or shear modulus updated from Hertz.

1. Change settings of MercuryDPM website [done]
2. Make mercurydpm forward-only email adresses work (info, personal, etc)
3. Backup script for web pages

•  Finish off oomph-lib testing branch, so we have an oomphlib branch we can commit to
  

•  Documentation Mindlin
•  Enhance Mindlin
•  Implement a collisionselftest for mindlin
  
•  Walls doc
  

Doxygen infinite loop script (now works in background): DoxyLoop.sh

1. Coupling;
2. look at open jobs at JIRA (started)

•  Tutorial on 2D and 3D parameter studies (JIRA MDPM - 307)
  •  Code
  •  Documentation
  •  Validation
    

•  Make the structure of the coupled codes consistent
  •  Clean up my branches to be merged with Mitchel's
  •  CoupledProblem class and how to inherit
•  Volume coupling
  •  Match the current velocity
  •  (Augmented) Lagrange multiplier
  •  Merge implicit and explicit branches into the main coupling branch
•  Surface coupling
  •  Smooth particle-finite element contacts
  •  Triangulated walls with prescribed velocity from Oomph-lib
  •  Coarse-Grained coupling force
•  Marnix \mu(I) rheology
•  Works on a CG converter tool (e.g. stat2vtu.py). In Tools

• Clean up melting, add test cases (PS: My branch should not be merged back till the work is published).

•  Coding style and format
•  Error checks
•  Test Cases:
  
  •  ....
•  Update ThermalParticleVtkWriter: to avoid dynamic_cast!

• JIRA jobs:
• I noticed some jobs are repeated: Do not delete, just link them (e.g. latex pb in documentations).
• Test failing on cluster and Windows 10 [MDPM-311] : I ran fullTest on Win10 and cluster, all passed.
• Add Doxygen section to the "Coding style of the kernel" on the website [MDPM-95]: The section already on the website, do we need to add it in the documentation?
• make separate VTKWriter class for Wall/Interaction VTK writer [MDPM-240]: There is also done, right? -> a unit test is needed.
• Adhesive particle contacts increases simulation time [MDPM-323]: which adhesive species? -> we need to contact Nikzad Falahati, Anthony knows him.
• ..

Check the StressStrainControlBoundary:

•  Check the comment of each function implemented in this boundary and modify the documentation.
•  Add a detailed version of the tutorial of one deformation mode. (New page on Isotropic compression.)
•  Update the detailed pdf and it to the additional document.
•  Maybe add more videos and tutorials on different deformation modes:
  •  PureShear,
  •  SimpleShear, (Volume conserving, no stress control activated)
  •  SimpleShear, (Changing volume, activate the stress control)
•  How to deal with the input data folder? Reference it? Or make them separate folders but then need to check all the other folders also.

Please don't copy input data, instead refer to the source directory using getMercurySourceDir in CMakeDefinitions.

Include the path in the cpp file and read the input data from there, so avoid copying.

Here is the issue of MPI without c++ binding issue. I think it is general in all the new version of openmpi, not only on mac.

can someone test this with newest openmpi on either windows or linux?

Added the logo with slogan to the NewDocumentation branch.