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PhysiMeSS addon and sample project #167

Merged
merged 55 commits into from
Jul 27, 2023
Merged

PhysiMeSS addon and sample project #167

merged 55 commits into from
Jul 27, 2023

Commits on Jul 27, 2023

  1. Added PhysiMeSS addon

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  2. Added PhysiMeSS sample project

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  3. Added small test in github actions

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    vincent-noel committed Jul 27, 2023
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  4. Fix path for windows test

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    vincent-noel committed Jul 27, 2023
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  5. Added a version number to PhysiMeSS addon

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  6. Added readme in the PhysiMeSS addon folder

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    vincent-noel committed Jul 27, 2023
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  7. Fibre initialisation default values

    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  8. fibre initialisation default values

    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  9. Delete config/Fibre_Initialisation directory

    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  10. Update README.md 

    fibre initialisation description
    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  11. physimess changes: uodate to readme and new fibre initialisation file

    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  12. physimess changes: fibre degradation files update and changes to ReadMe

    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  13. physimess change: change to some print statements

    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  14. physimess changes: updates to ReadMe detailing examples

    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  15. physimess changes: updates to ReadMe

    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  16. physimess changes: print statements for listing agent voxels

    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  17. physimess changes: config directory with voxel/neighbour checking exa… 

    …mple
    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  18. physimess changes: updates to crosslink finding function and simple e… 

    …xample directory to go with
    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  19. Implementation of physimess_neighbors

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    vincent-noel committed Jul 27, 2023
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  20. Now using original add potentials, and only use physimess neighbors w… 

    …hen fibers are involved
    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  21. Now storing the list of voxels for each agent

    @vincent-noel
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  22. Using the voxel size from the container in register_fibre_voxels

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  23. Added custom cellcount function to the PhysiMESS sample project

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  24. Added a mechanism to clean PhysiMESS data structure if a fibre is del… 

    …eted
    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  25. Added a mechanism to initialize PhysiMESS datastructure for new cells… 

    … created from division
    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  26. Improved make reset for PhysiMESS

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  27. Added omp critical pragmas when modifying the agent grid

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  28. phsyimess changes: update to make reset and correction in Fibre_Cross… 

    …link mymodel files to pick up correct csv file
    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  29. Added draft of paint by cell pressure, and increased degradation rate… 

    … due to cell pressure
    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  30. physimess changes: fibre degradation updates

    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  31. physimess changes: updates to initialisation .xmls including fibre ra… 

    …dius now normalised
    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  32. physimess updates: some changes to names of parameters and additional… 

    … parameters
    @CicelyKrystyna @vincent-noel
    CicelyKrystyna authored and vincent-noel committed Jul 27, 2023
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  33. Fix makefile after 1.12.0

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    vincent-noel committed Jul 27, 2023
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  34. New version using Cell derived classes

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  35. Fix add potentials

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  36. add_potentials_* are now class member functions

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  37. Cleanup

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  38. Degrade fibre is now within a virtual function, called in the add_pot… 

    …ential_from_fibre, and that can be overloaded in derived PhysiMESS_Cell classes
    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  39. Cleanup

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    vincent-noel committed Jul 27, 2023
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  40. Default degradation function doesn't use cell pressure

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  41. Added example of custom fibre degradation implementation

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  42. Cleanup

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  43. Added parameter to choose if cell degradation depends on pressure

    @vincent-noel
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  44. Added a parameter to control the minimal movement to declare a cell s… 

    …tuck
    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  45. Renaming PhysiMESS -> PhysiMeSS

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  46. Commented all outputs

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  47. Assigning fibre orientation for randomly assigned fibres

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  48. Calling check_out_of_bounds after assign_fibre_orientation

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    vincent-noel committed Jul 27, 2023
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  49. Simplifying create_cell_types call by introducing a function to get a… 

    …ll fibre cell defs
    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  50. Fix building of Fibre cell definitions vector

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  51. Disabling spring adhesion of Fibre degradation example

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  52. Activating degradation by default in the fibre_degradation example

    @vincent-noel
    vincent-noel committed Jul 27, 2023
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  53. rename fibre_degradation_depends_on_pressure with fibre_custom_degrad… 

    …ation
    @vincent-noel
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  54. Moved a bit the attractant in fibre_degradation so it won't be pushed… 

    … around
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  55. Made add_potential functions virtual so they can be overloaded

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    vincent-noel committed Jul 27, 2023
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