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Array kernel #13528

Merged
merged 69 commits into from
Jul 10, 2019
Merged

Array kernel #13528

merged 69 commits into from
Jul 10, 2019

Commits on Jul 7, 2019

  1. a compilable stage with variable, coupleable, assembly and systems ex… 

    …tended to array variable idaholab#6881
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  2. add array variable action and array initial condition and a simple test 

    idaholab#6881
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    YaqiWang committed Jul 7, 2019
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  3. add function array IC idaholab#6881

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  4. useful changes

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  5. some cleanup

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  6. change vector to set? may not be a good idea

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  7. use auto in several places to reduce the code size

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  8. finally compiling and not breaking tests

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  9. add array kernel

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  10. add arry data type to data IO

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  11. add mapped grad test and change from Eigen::Array to Eigen::Matrix to… 

    … simplify the array kernel
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  12. add support for parameters to read in eigen array

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  13. make array variable return its base name but not the name of its firs… 

    …t component
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  14. add a new function in moose variable and use it in nodal bc

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  15. some minor fixes for array kernel

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  16. add array diffusion kernel, array dirichlet bc and array material

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  17. the simplest array kernel test

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  18. clang formatting

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  19. use pragma once

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  20. ignore a warning in Eigen

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  21. fix tensor mechanics module due to variable interface change

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  22. fix chemical reactions module due to interface change in addVariableA… 

    …ction
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  23. better variable name checking detected by level set module

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  24. add doc stubs

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  25. add some class description

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  26. allow 2D eigen matrix as an input parameter

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  27. small bug fixes noticed by a coming test

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  28. add a material for evaluating constant property in type of Eigen matrix

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  29. add array reaction kernel

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  30. a test with component coupling of an array variable

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  31. create an aux kernel to extract a component of an array variable

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  32. more pattened fixes in Assembly for array

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  33. some small style improvements in array kernels

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  34. add array integrated bcs

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  35. shuff codes in DGKernelBase and DGKernels for preparing ArrayDGKernel

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  36. add array DG kernel

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  37. some simplification on assembling the off-diag jacobian in ArrayKernel

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  38. some simplification in assembling jacobian for integrated bc and add … 

    …array penalty dirichlet bc
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  39. a DG test for array kernels

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  40. add array dg diffusion

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  41. add one more test to test the coupling from a standard variable to an… 

    … array variable
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  42. add capability to allow couple array variables in a standard kernel

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  43. documentations of array kernel and SQA requirements

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  44. final clang formatting after resolving conflict

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  45. add few neighbor coupleable functions that will be useful for array i… 

    …nterface kernels or constraints
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  46. add a missing function implementation and some cleanups

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  47. address Alex's comments

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  48. change back to vector, using set to store points could be a really ba… 

    …d idea, codes are added to ensure the entries in the vectors are unique
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  49. rename RealArrayValue to RealEigenVector

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  50. rename RealArray to RealEigenMatrix

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  51. add array kernel in the coming newsletter

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  52. add a moose error to prevent users from using vector types in an arra… 

    …y variable
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  53. Update error message for vector kernel

    @permcody @YaqiWang
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  54. no need to call zero because within resize it has been called

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  55. protect component param from being set to zero accidentally

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  56. allow feproblem to add array aux variables

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  57. fix a bug causing diagonal save in not working properly for integrate… 

    …d BCs
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  58. another apparent bug in diagonal save in

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  59. remove checking _has_dof_values because these functions are providing… 

    … them
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  60. enable save-in for array kernels and integrated bcs and add a test

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  61. fix a bug in GenericConstntMaterial idaholab#13601

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  62. an micro optimization important for cases with array variables and PJ… 

    …FNK solve type
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  63. another micro optimization to avoid double loop particularly for case… 

    …s with large number of components
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  64. add two rules in build.mk

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  65. provide two virtual functions that can be called just in qp loop

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  66. let's not prepare jacobian when not doing jacobian evaluation

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  67. small clang formatting

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  68. make hide/show work for array variables

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  69. minor improves

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