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Holzapfel material model and test #151

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Holzapfel material model and test #151

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Commits on Dec 15, 2022

  1. first commit

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Commits on Dec 16, 2022

  1. Add initial code.

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Commits on Dec 17, 2022

  1. Add functions to run a simulation.

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  2. Move tinyxml to ThirdParty.

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Commits on Jan 14, 2023

  1. Create README.md

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Commits on Jan 15, 2023

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Commits on Jan 18, 2023

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Commits on Jan 19, 2023

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Commits on Jan 20, 2023

  1. Update README.md

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Commits on Jan 24, 2023

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Commits on Feb 2, 2023

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Commits on Feb 3, 2023

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Commits on Feb 4, 2023

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Commits on Feb 14, 2023

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Commits on Feb 16, 2023

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Commits on Feb 17, 2023

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Commits on Feb 23, 2023

  1. Remove Fortran references in CMake files.

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  2. Merge pull request #5 from ktbolt/fix_find_blas_error_4 

    Remove Fortran references in CMake files.
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  3. Merge pull request #6 from ktbolt/update-README 

    Update readme
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  4. Fix spelling.

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  5. Fix spelling.

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Commits on Feb 24, 2023

  1. Remove zlib files.

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  2. Merge pull request #8 from ktbolt/Remove_CMake_zlib_references_7 

    Remove zlib files.
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  3. Fix CMake to include vtk files. (#9) 

    Co-authored-by: Dave Parker <[email protected]>
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Commits on Mar 11, 2023

  1. Add build testing (Mac OS, Ubuntu) (#12)

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Commits on Mar 13, 2023

  1. Fix setting cell type. (#16)

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Commits on Mar 14, 2023

  1. Add a vtkObject::GlobalWarningDisplayOff() call to disable VTK warnin… 

    …gs for 2-sided polygons used for 2D BC faces. (#18)
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Commits on Mar 15, 2023

  1. Add integration testing (#19)

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Commits on Mar 30, 2023

  1. Niederer benchmark test for CI (#24) 

    Co-authored-by: Matteo Salvador <[email protected]>
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  2. Add badges (#28)

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Commits on Apr 3, 2023

  1. Diffusion test case for CI (#29)

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Commits on Apr 5, 2023

  1. enforce C90 for externals (#32)

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Commits on Apr 6, 2023

  1. Change the write_disabled flag to write_enabled. (#34)

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Commits on Apr 17, 2023

  1. Disable Array and Vector index checking. (#37)

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Commits on Apr 19, 2023

  1. Add histor file 11 (#41) 

    * Add class to write to histor.dat file.

* Add some checks.
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Commits on May 12, 2023

  1. Fix Mac build (#52) 

    * remove qt5 version from path

* fix typo
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  2. Add remeshing 1 (#50) 

    * Add remeshing code.

* Add some vtk funcs, document.

* Add some documentation.

* Add release mesh objects, fix indexing bugs, etc.

* Fix some bugs.

* Fix some remeshing bugs.

* Fix a few bugs.

* Fixes for 0-size arrays.

---------

Co-authored-by: Matteo Salvador <[email protected]>
    @ktbolt @MatteoSalvador
    ktbolt and MatteoSalvador authored May 12, 2023
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Commits on May 15, 2023

  1. 1d face exception 51 (#53) 

    * Fix setting properties for 1-noded face elements.

* Add missing PNT element types, add support for 0-size Array3.

---------

Co-authored-by: Matteo Salvador <[email protected]>
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Commits on May 16, 2023

  1. Code coverage (#47) 

    * add coverage to cmake

* generate coverage report

* fix make bug

* upload artifact

* disable long test cases

* fix line breaks

* upload coverage artifact

* re-add tests

* simplify test execution

* exclude externals

* add coverage comment

* fix coverage report

* Trigger Build

* remove barecheck
    @mrp089
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Commits on May 18, 2023

  1. Multiple add project statements 58 (#61) 

    * Fix reading in fiber node IDs and a counting problem.

* Remove some debugging statements.
    @ktbolt
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  2. New CEP features: ECGs, non-gaussian quadrature rules, ttp XML interf… 

    …ace (#56)

* Niederer benchmark test for CI

* Add ECGLeadsParameters class

* Integrate ECGs in EquationParameters

* Import ECG leads in Cep

* ECG leads input/output

* WIP: pseudo ECG computation

* Pseudo ECG computation

* Change relevant ttp parameters from xml file

* New non-gaussian quadrature rules for TRI3 faces and TET4 3D meshes (P1 Finite Elements only)

* Add G_to ttp parameter to xml interface

* Minor

* std::pow -> pow in CEP

* Update Niederer benchmark (ECGs + optimal quadrature)

* Add pandas
    @MatteoSalvador
    MatteoSalvador authored May 18, 2023
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Commits on May 19, 2023

  1. Add writing VTK files with element connectivity for all element types… 

    …. Also remove writing element and node IDs to VTK files. (#64)
    @ktbolt
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  2. Add a check for cep_mod.ecgleads.num_leads zero to avoid bcast() exce… 

    …ption. (#65)
    @ktbolt
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  3. Solid viscosity bug 35 (#55) 

    * Convert new ustruct code.

* Add solid viscosity parameter, fix indexing problem.

---------

Co-authored-by: Matteo Salvador <[email protected]>
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    ktbolt and MatteoSalvador authored May 19, 2023
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  4. include svFSILS coverage (#66) 

    Co-authored-by: Matteo Salvador <[email protected]>
    @mrp089 @MatteoSalvador
    mrp089 and MatteoSalvador authored May 19, 2023
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  5. Run all tests in parallel (#63) 

    Co-authored-by: Dave Parker <[email protected]>
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Commits on May 23, 2023

  1. Fix setting VTK higher-order cell types when writing results VTK file… 

    …s. (#67)

Co-authored-by: Martin R. Pfaller <[email protected]>
    @ktbolt @mrp089
    ktbolt and mrp089 authored May 23, 2023
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Commits on Jun 1, 2023

  1. Add fluids integration test case (#60)

    @zinanhu0810
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Commits on Jun 28, 2023

  1. Update README with coding standards. (#72) 

    * Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md
    @ktbolt
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Commits on Jul 6, 2023

  1. Add new shell implementation 69 (#75) 

    * Add shells and material models.

* Add follower forces function.

* Add processing Lee-Sacks parameters.

* Add Lee-Sacks material model, xml parameters for it, fix some shell processing bugs.

* Add debugging messages, remove left-over debugging code in fft, causing a crash.

* Fix indexing bugs, set ATOL to be a bit smaller than Fortran.

* Post processing for shells.

* Add thowing an exception if trying to run in parallel with tri3 shells.

* Add shell contact.

* Add some debug, check for not Contact parameter.

* Add missing include DbgMsg.
    @ktbolt
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Commits on Aug 8, 2023

  1. Fix indexing bug. (#80)

    @ktbolt
    ktbolt authored Aug 8, 2023
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Commits on Aug 9, 2023

  1. Fix Compilation Errors with Trilino: change input arguments in trilin… 

    …os_doassem_ and added a header file within shell.cpp (#81)

Co-authored-by: Weiguang Yang <[email protected]>
    @wgyang
    wgyang and Weiguang Yang authored Aug 9, 2023
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Commits on Sep 5, 2023

  1. Actions macos build fail (#91)

    @ktbolt
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  2. Improve fluid perf 79 (#87) 

    * Replace Array objects with array.

* Replace more Array.

* Replace Array objects with arrays.

* Disable using raw data for arrays in fsils_spar_mul_sv.

* Enable using raw data in fsils_spar_mul_sv.

* Replace the Array3.slice() calls with Array3.rslice().

* Replace slice with rslice.

* Fix problem with using rcol().

* Clean up prototype code.

* Clean up prototype code.

* Remove using raw pointers, doesn't seem to matter much.
    @ktbolt
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Commits on Sep 11, 2023

  1. Add ALE test case (#93) 

    * adding ale pipe test

* adapting test to svFSI+ format

* modify test file

* changing reference to orginal svFSI output

* removing non-lfs files

* adding test as lfs compatible

* adding files for 1 timestep check

* modifying test ale for 1 timestep

* modifying test ale for 1 timestep

* make FSI mesh much coarser

* remove fine mesh results

* give more meaningful error message

* run 5 steps

* add int32 coarse meash

* also test pressure and velocity

---------

Co-authored-by: Erica <[email protected]>
Co-authored-by: Erica Leigh Schwarz <[email protected]>
    @mrp089 @schwarz-e
    3 people authored Sep 11, 2023
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Commits on Sep 13, 2023

  1. CG and BICG implementation for all equations (#98) 

    * CG for vectors

* BICG for vectors

* Add new tests for 3D CEP: (CG, BICG, GMRES), (epi, endo, myo), (AP, BO, TTP)

* Remove ECGs + typo

* Relative errors for ECGs + error message
    @MatteoSalvador
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Commits on Sep 14, 2023

  1. Test different LS with the same reference solution (diffusion_line_so… 

    …urce) (#101)
    @MatteoSalvador
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  2. Add test cases for CEP (1Dcable_TTP, 2Dsquare_BO, 2Dspiral_BO, purkin… 

    …je) (#102)
    @MatteoSalvador
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Commits on Sep 20, 2023

  1. Doxygen (#100) 

    * rough first doxygen

* add workflow file

* update paths

* convert existing comments to Doxygen

* fix build

* manually build Doxygen

* change path

* print paths

* echo

* add svFSILS

* add checkout to actions

* include markdown files in Doxygen
    @mrp089
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Commits on Sep 21, 2023

  1. Fix deployment if statement (#104)

    @mrp089
    mrp089 authored Sep 21, 2023
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  2. fix links in readme (#108)

    @mrp089
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Commits on Sep 22, 2023

  1. Add printing valid material model types in the error message. (#106) 

    Co-authored-by: Matteo Salvador <[email protected]>
    @ktbolt @MatteoSalvador
    ktbolt and MatteoSalvador authored Sep 22, 2023
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Commits on Oct 3, 2023

  1. Fluid and ustruct test cases (#115) 

    Co-authored-by: Elena Martinez <[email protected]>
    @elenasmartinez
    elenasmartinez and Elena Martinez authored Oct 3, 2023
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Commits on Oct 4, 2023

  1. ustruct tests (P1P1-VMS block compression, tensile adventitia HGO, LV… 

    … guccione active) (#113)
    @MatteoSalvador
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Commits on Oct 9, 2023

  1. Add a CMM test case (#117) 

    * Add a CMM test case. Results are consistent with svFSI output. Prestress examples will be added.

* Use a linear solver setting without Trilinos for the cmm inflation test case.

* Remove .inp files in the cmm test case. Reduce the number of time steps for the inflation procedure.

* Add prestress examples for the cmm test case.

---------

Co-authored-by: Martin R. Pfaller <[email protected]>
    @wgyang @mrp089
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Commits on Oct 24, 2023

  1. Copyright workflow and licensing (#122)

    @MatteoSalvador
    MatteoSalvador authored Oct 24, 2023
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Commits on Oct 31, 2023

  1. Bueno-Orovio parameters (#130) 

    * Expose tau_fi and tau_si from BO in the XML interface

* Tests
    @MatteoSalvador
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Commits on Nov 6, 2023

  1. Fix bug in set_bc_rbnl (#134)

    @kharold23
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Commits on Nov 7, 2023

  1. 0 indexed meshes(#114) (#120) 

    * adding darcy equation

* darcy equation can be built but generates a trivially zero solution

* commenting files to find mesh indexing error

* correcting gN, gE, and IEN after reading meshes

* removing IEN resetting in vtk_xml.cpp since this functionality is moved into load_msh.cpp

* adding general parameters for unsteady darcy problem

* added final version of the hash map for gN, gE, and IEN setting for face meshes

* adding binary mask permutation for non-tet elements (#114)

* adding boundary node counter-clockwise ordering to element matching (#114)

* completed 2D darcy general model formulation for (#71)

* adding scientific notation and 16 precision to global node matching (#114)

* Revert "Merge branch 'Tissue-perfusion-model-#71' into 0-indexed-meshes(#114)"

This reverts commit 7cbf43a0b21cdb5706b5292f8c5f62cd8b0d4070, reversing
changes made to 7a97ef62e0b7b2e1d380230b081f62e508dce471.

* encapsulating hash map generation (#114)

* remove commented lines performing un-encapsulated hash map generation

* adding error checking for duplicate nodes during hash map generation (#114)

---------

Co-authored-by: Dave Parker <[email protected]>
    @zasexton @ktbolt
    zasexton and ktbolt authored Nov 7, 2023
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  2. Correct array dimensions for EquationProps. (#135)

    @ktbolt
    ktbolt authored Nov 7, 2023
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  3. Update ParMETIS third party software (#132) 

    * Add gklib and copy over new code.

* Set int and real widths to 32, setting to 64 does not work.

* Add some READMEs.
    @ktbolt
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Commits on Nov 10, 2023

  1. Add a better error message is Int32 data is not found for GlobalNodeI… 

    …D. (#138)
    @ktbolt
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Commits on Nov 15, 2023

  1. Re-organize tests (#141) 

    * modify python

* move cep

* move cmm

* move fluid

* move fsi

* move heats

* mvoe stokes

* move struct

* move ustruct

* move cep

* move cep

* fix move

* fix name

* fix cmm

* fix run_with_reference call

* fix relative paths
    @mrp089
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Commits on Nov 16, 2023

  1. Fix indexing bug. (#139) 

    * Fix indexing bug.

* Fix indexing problem (again).

* Modify the calls to all_fun::integ() functions to pass in an array's 0-based index range.

---------

Co-authored-by: Matteo Salvador <[email protected]>
    @ktbolt @MatteoSalvador
    ktbolt and MatteoSalvador authored Nov 16, 2023
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  2. Disable debugging messages in distribute and part_mesh functions. (#144) 

    Co-authored-by: Matteo Salvador <[email protected]>
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    ktbolt and MatteoSalvador authored Nov 16, 2023
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Commits on Nov 22, 2023

  1. fix error in test error (#147)

    @mrp089
    mrp089 authored Nov 22, 2023
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Commits on Nov 30, 2023

  1. Add processing the Holzapfel material model. 

    Copy commits to process Holzapfel material model from Dave, originally in SimVascular/svFSIplus#131
    @aabrown100-git
    aabrown100-git committed Nov 30, 2023
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  2. Add LV_Holzapfel_passive test case

    @aabrown100-git
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Commits on Dec 4, 2023

  1. Iliac artery test case (#152) 

    Co-authored-by: Elena Martinez <[email protected]>
    @elenasmartinez
    elenasmartinez and Elena Martinez authored Dec 4, 2023
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Commits on Dec 11, 2023

  1. adding support for higher-order elements (#154) 

    * adding support for higher-order elements qudratic tet, hex, tri, quad, and biquadtratic quad

* Fixing support for VTK_QUADRATIC_HEXAHEDRON and adding support for VTK_TRIQUADRATIC_HEXAHEDRON #114
    @zasexton
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  2. Simplify paths and unify fields in tests (#157) 

    * Simplify paths, unify fields

* Fix cmm
    @mrp089
    mrp089 authored Dec 11, 2023
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Commits on Dec 12, 2023

  1. Fix Robin boundary condition 148 (#155) 

    * Update set_bc_rbnl() with svFSI bugs fixes, fix test for Robin BC.

* Fix some more c++/fortran implementation differences.

* Remove some debugging statements.

* Update set_bc_rbnl() with svFSI bugs fixes, fix test for Robin BC.

* Add Robin test

* Fix typo

---------

Co-authored-by: Martin R. Pfaller <[email protected]>
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    ktbolt and mrp089 authored Dec 12, 2023
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Commits on Dec 13, 2023

  1. Merge branch 'SimVascular:main' into Holzapfel_material_model

    @aabrown100-git
    aabrown100-git authored Dec 13, 2023
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  2. Update new test format

    @aabrown100-git
    aabrown100-git committed Dec 13, 2023
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