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Advection diffusion - DO NOT MERGE#788

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uschille wants to merge 107 commits intohemelb-codes:mainhemelb-codes/hemelb:mainfrom uschille:advection-diffusionuschille/hemelb:advection-diffusionCopy head branch name to clipboard

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Commits

Commits on Oct 2, 2020

• Attempted to change path initialisation for property extraction.

  uschille

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  3b0febb

• Remove PathManager::SaveConfiguration which was defunct anyway.

  uschille

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  9c08f93

• Introduce a map that allows different data sources for property output.

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  5c5c8b6

• In hemelb::extraction::LocalPropertyOutput, rather store the dataSourceMap than a single dataSource. This is still not fully general, as the size and position will always be determine from the firs…

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  8d7cdc4

Commits on Aug 22, 2021

• Add stubs for advectionDiffusionModel.

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  ac0cef7

• Add advectionDiffusionModel to SimulationMaster.h.

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  c7a37b9

• Add constructors and initialization for advectionDiffusionData, advectionDiffusionDataManager, advectionDiffusionModel.

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  a37bb13

• Moved local variable propertyCache inside the colloid section

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  377fb61

• Add property extractor instances for advection diffusion.

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  4bdc3d6

• Introduce a map that allows different data sources for property output.

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  273e783

• Removed the second PropertyActor which will not be needed thanks to

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  4ea4b39

• Added conduits for new property outputs from individual property caches.

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  5c50795

• Add separate advectionDiffusionLatticeType.

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  8349bbd

• Add inlet/outlet conditions for advection diffusion.

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  9f93093

• Add advection diffusion inlet/outlet conditions to header file.

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  eb8c35c

• Change of behavior of the GeometryReader and LatticeData!

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  d69f011

Commits on Oct 8, 2021

• Modified OutputGeneration.py to recognize two parts

  

  Mehrdad Yousefi

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  eb23e52

• Append part number and second seed point in profile

  

  Mehrdad Yousefi

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  16b6a44

• Add second seed point functionallity

  

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  f40b7c9

• Multi parts embedded in profile file

  

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  b90bea3

• Remove second seed point from model generation

  

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  276e773

• Add correct test dataset

  

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  fc67a01

• Correct multi part functionality

  

  Mehrdad Yousefi

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  ad71217

• Assign different id to each part

  

  Mehrdad Yousefi

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  a93cf37

• Add stent intersection in geometry generator

  

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  18140d4

• Add stent functionality in xml writer

  

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  6eb3588

• Add stent recognization to geometry library

  

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  6add036

• Add stent intersection to neighbouring data manager and decomposition

  

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  f4766d4

• Revert "Add stent intersection to neighbouring data manager and decomposition"

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  42680c8

• Revert "Add stent recognization to geometry library"

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  476c757

• Revert "Add stent intersection in geometry generator"

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  Mehrdad Yousefi

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  5b66e71

• Add new stent recognization to geometry generator just based on negative IDs

  

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  da2eab1

• Add wall ID to gmy extraction

  

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  b73a4fc

• Add vessel wall and stent wall recognization based on negative IDs

  

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  5dd04d1

• Add advection diffusion lattice classes

  

  Mehrdad Yousefi

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  793446e

• Fixed typo for advection diffusion class

  

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  c0a8389

• Add advection diffusion lattices to header file

  

  Mehrdad Yousefi

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  c1d00b2

• Add advection diffusion lattices to CMakeLists.txt of lb library

  

  Mehrdad Yousefi

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  dced2fa

• Fixed typo in advection diffusion lattice header file

  

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  f96593a

• Create Advection Diffusion LBGK Kernel

  

  Mehrdad Yousefi

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  a208de7

• Correct advection diffusion kernel class

  

  Mehrdad Yousefi

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  ad1f543

• Fixed typo in advection diffusion base kernel

  

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  d472729

• Fixed typo in advection diffusion base kernel

  

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  3cf3930

• Revert "Fixed typo in advection diffusion base kernel"

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  Mehrdad Yousefi

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  274c308

• Revert "Fixed typo in advection diffusion base kernel"

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  6e87e99

• Revert "Correct advection diffusion kernel class"

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  a0b3275

• Revert "Create Advection Diffusion LBGK Kernel"

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  Mehrdad Yousefi

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  aeed2cc

• Create advection diffusion kernel class

  

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  23b6480

• Create advection diffusion collision operator

  

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  c61b5c1

• Add advection diffusion collision operator to Collisions header file

  

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  9180962

• Revert "Add advection diffusion collision operator to Collisions header file"

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  d2db2f2

• Revert "Create advection diffusion collision operator"

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  39fc23d

• Revert "Create advection diffusion kernel class"

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  Mehrdad Yousefi

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  214d09a

• Consistent advection diffusion lattice definition

  

  Mehrdad Yousefi

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  a18bc6e

• Create Advection Diffusion kernel and collision operator based on macroscopic property cache

  

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  e19f4a4

• Add stent boundary value to lattice boltzmann library

  

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  30e43cf

• Create Advection Diffusion MRT kernel

  

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  58c72f7

• Add Advection Diffusion MRT kernel to hydrovars friend classes list

  

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  8f675ce

• Add Advection Diffusion streamers and boundary conditions according to Yoshida and Nagauka article

  

  Mehrdad Yousefi

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  9f9cd6e

• Fixed typo in advection diffusion BFL and GZS BCs

  

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  b3afddc

• Add build parameters for advection diffusion BCs

  

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  26cb67c

• Add stent ID reader to GeometryReader functionality

  

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  5746b4a

• Change the BCs logics to get fix six collision types

  

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  ef869aa

• Refactor lattice types and remain second instance independent

  

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  11f4507

• Fixed incorrectly removed D315 class

  

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  401bc45

• Add D3Q7 to lattice header file

  

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  c3dcb34

• Fixed typo for lattice header file

  

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  e08c035

• Remove GZS BCs for ADE

  

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  46fb9d6

• Add stents header file to simulation config and remove lattice data header file from boundary comms

  

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  7305e04

• Add stent IO to configuration library

  

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  5f560d8

• Create ADE Class

  

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  5edd321

• Add stent ID to make a difference between iolet and stent IDs

  

  Mehrdad Yousefi

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  9018c29

• Correct stent ID assignment

  

  Mehrdad Yousefi

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  0d2f2f8

• Change unit of BC and initial condition for stents

  

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  8dbf89c

• Connect first/second instances together and complete ADE simulation workflow

  

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  d1bca2e

• Remove backup file

  

  Mehrdad Yousefi

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  5f948fc

• Remove backup file

  

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  c130fba

• Update test case

  

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  10196eb

• Add coupled lattice data

  

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  765ccf3

• Revert "Add coupled lattice data"

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  Mehrdad Yousefi

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  2fc30b1

• Add Outflow BC

  

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  f89176e

• Add Dirichlet BC for Inlet

  

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  4f56b9d

• Correct linear equilibrium function

  

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  35211b6

• Correct XML writer

  

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  1633995

• Correct XML writer

  

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  6acecba

• Update test case

  

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  8e4cecb

• Add Zero Diffusion BC at Outlet

  

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  1c82698

• Correct relaxation time reffering to hydrovars class which doesn't have effect on simulation results!

  

  Mehrdad Yousefi

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  c67f867

• Add Vessel Wall Absorption (Robin) Boundary Condition

  

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  47110aa

• Add Hollow Parabolic Velocity Profile

  

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  f5bc9ad

• Correct Hollow Parabolic Distance

  

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  6f7faae

• Create Hollow File Velocity Boundary Condition

  

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  e64ab46

• Add SSE3 functionality for ADE

  

  Mehrdad Yousefi

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  1a57e62

• Correct SSE3 functionality

  

  Mehrdad Yousefi

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  74eab1d

• Correct a typo

  

  Mehrdad Yousefi

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  0bd8550

• Add vessel and stent walls selector functionallity to extraction library

  

  Mehrdad Yousefi

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  7f289aa

• Change the lattice type to D3Q19

  

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  7400752

• Add flux calculation from eq. and neq. parts of distribution

  

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  828865b

• Change lattice type to D3Q15

  

  Mehrdad Yousefi

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  1b4b000

• Force to link zlib libraries and avoid undefined references

  

  myousefi2016

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  5bdde3e

• Correct flux calculation from eq. and neq. part of distribution functions

  

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  64498d8

• Correct VTK libraries link to setuptool

  

  Mehrdad Yousefi

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  67e0bcb

• Add Coating Concentration and Flux Boundary Conditions

  

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  c635028

• Tune parameters

  

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  3e6b192

• Enable ADE from config file

  

  Mehrdad Yousefi

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  aa09584

• Add iolet geometry selector

  

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  34ecbbf

• Correct iolet type conversion

  

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  74af04f