Encapsulate Newton iteration in Integrator class (#442) by Eleven7825 · Pull Request #450 · SimVascular/svMultiPhysics

Eleven7825 · 2025-10-13T02:36:25Z

Current situation

This PR addresses #442 - Encapsulate the Newton iteration in main.cpp.

As discussed in the issue, this is the first step toward implementing a partitioned Fluid-Structure
Interaction (FSI) by creating an Integrator class to handle the Newton iteration loop. This
refactoring prepares the codebase for future work where separate integrators will be used for fluid
and structure domains.

Release Notes

Refactoring: Encapsulated Newton iteration logic into a new Integrator class
Architecture: New Integrator class manages solution variables (Ag, Yg, Dg) and handles
complete Newton iteration workflow
Backward Compatibility: No changes to physics or numerics - pure refactoring with identical
behavior
Build System: Added integrator.h and integrator.cpp to CMakeLists.txt

Documentation

Added comprehensive class documentation in integrator.h header file
Documented all public and private methods with parameter descriptions
Added inline comments explaining the Newton iteration workflow
Maintained existing code comments from original main.cpp implementation
Updated file headers with proper copyright notices

Testing

Build: Compiles successfully without errors or warnings
Manual Testing: Validated with fluid/pipe_RCR_3d test case
- 2 timesteps completed successfully
- Newton iterations converge correctly (residuals: ~10^-13)
- Output matches expected convergence behavior
Integration: All existing functionality preserved

Code Coverage: The new Integrator class executes the same code paths as the original
implementation, maintaining existing test coverage. The refactoring does not introduce new physics
or algorithms requiring additional test cases.

Code of Conduct & Contributing Guidelines

I agree to follow the Code of
Conduct and Contributing
Guidelines.

- Add CMake-generated files (CMakeCache.txt, CMakeFiles/, Makefile, etc.) - Add build directories (*-build/, *-prefix/) - Add compiled outputs (Code/bin/, Code/lib/) - Add generated headers - Add vim swap files (*.swp, *.swo, *~) Related to SimVascular#442

- Create integrator.h and integrator.cpp with Integrator class - Encapsulates solution variables (Ag, Yg, Dg) - Handles Newton iteration loop - Manages linear system assembly and solve - Applies boundary conditions - Update CMakeLists.txt to include new source files This is the first step toward implementing partitioned FSI as described in SimVascular#442

- Replace Newton iteration loop with Integrator::step() call - Remove local Ag, Yg, Dg arrays (now managed by Integrator) - Simplify iterate_solution() function - Add integrator.h include Addresses SimVascular#442: Encapsulate Newton iteration in main.cpp

The iEqOld variable is needed for output::output_result() calls after the Newton iteration completes. This variable tracks which equation was solved in the last iteration.

codecov · 2025-10-13T17:08:03Z

Codecov Report

❌ Patch coverage is 82.35294% with 120 lines in your changes missing coverage. Please review.
✅ Project coverage is 68.02%. Comparing base (6801130) to head (21ade6b).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
Code/Source/solver/ris.cpp	26.31%	28 Missing ⚠️
Code/Source/solver/initialize.cpp	61.66%	23 Missing ⚠️
Code/Source/solver/post.cpp	52.94%	16 Missing ⚠️
Code/Source/solver/read_msh.cpp	0.00%	13 Missing ⚠️
Code/Source/solver/Integrator.cpp	94.73%	11 Missing ⚠️
Code/Source/solver/set_bc.cpp	91.30%	8 Missing ⚠️
Code/Source/solver/main.cpp	81.25%	6 Missing ⚠️
Code/Source/solver/txt.cpp	71.42%	6 Missing ⚠️
Code/Source/solver/output.cpp	44.44%	5 Missing ⚠️
Code/Source/solver/Simulation.cpp	83.33%	1 Missing ⚠️
... and 3 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #450      +/-   ##
==========================================
+ Coverage   67.89%   68.02%   +0.12%     
==========================================
  Files         168      170       +2     
  Lines       32898    33093     +195     
  Branches     5782     5780       -2     
==========================================
+ Hits        22336    22510     +174     
- Misses      10425    10446      +21     
  Partials      137      137

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mrp089

Thanks for taking a crack at this, @Eleven7825! I've added some comments.

ktbolt · 2025-10-15T01:20:23Z

@Eleven7825 This is a big change and needs to be discussed with the solver team.

mrp089 · 2025-10-15T20:00:12Z

Sounds good! Who do we talk to and when?

Eleven7825 · 2025-10-15T20:06:41Z

Maybe we could bring this up this Friday during the refactory meeting?

ktbolt · 2025-10-15T20:45:14Z

@mrp089 The initial refactoring effort will be the design and implementation of some sort of solver class to encapsulate solver data and support G&R. We can start this discussion in the first svMultiPhysics c++ OO refactor planning meeting.

mrp089 · 2025-10-20T20:43:48Z

@dcodoni suggested removing com_mod from all function calls in Integrator (which will require changes in other functions/classes, too). This will require following the function calls with that have com_mod as an argument all the way down and figuring out which parts of com_mod are actually needed. It might be necessary to create a few structs in Integrator that encapsulate a few items to avoid having functions with a ton of arguments.

- Rename integrator.h to Integrator.h - Rename integrator.cpp to Integrator.cpp - Update all #include statements in main.cpp and Integrator.cpp - Update CMakeLists.txt reference Addresses PR SimVascular#450 review feedback on file naming convention.

@brief

- Use JavaDoc-style /** */ comments throughout Integrator.h - Add @brief, @param, and @return tags following svZeroDSolver conventions - Document all public methods and private members - Improve descriptions for solution variables (Ag, Yg, Dg) and helper methods Addresses PR SimVascular#450 review feedback on Doxygen documentation format.

- Add istr_ as private member variable in Integrator class - Update step() method to set istr_ instead of using local variable - Replace all istr references with istr_ throughout the code - Simplify debug write statements in apply_boundary_conditions() This change enables individual helper functions to access istr_ for their own debug outputs, preparing for the next step of moving write statements into individual functions. Addresses PR SimVascular#450 review feedback on variable management.

- Move all .write() debug statements from step() to their respective helper functions - initiator_step() now handles its own debug output (Ag, Yg, Dg, Yn) - allocate_linear_system() now handles Val output - set_body_forces() now handles Val output - assemble_equations() now handles R and Val output - apply_boundary_conditions() now handles Val, R, Yg, Dg output - solve_linear_system() now handles Val and R output - corrector_and_check_convergence() now handles Yn output This makes step() cleaner and more focused on orchestration, while each helper function manages its own debug logging. All functions now use the istr_ class member variable for consistent debug naming. Addresses PR SimVascular#450 review feedback on code organization.

…oop' - Rename inner_count_ to newton_count_ throughout Integrator class - Update comments to use 'Newton iteration' instead of 'inner loop' - Update debug messages to show 'Newton Iteration' instead of 'Inner Loop' This makes the terminology more precise and consistent with standard computational mechanics nomenclature, clarifying that we're referring to the Newton iteration within each time step (as opposed to the outer time loop). Addresses PR SimVascular#450 review feedback on terminology consistency.

- Move debug print statements from step() into individual helper functions - Each function now handles its own debug output: * initiator_step() * allocate_linear_system() * set_body_forces() * assemble_equations() * apply_boundary_conditions() * update_residual_arrays() * solve_linear_system() * corrector_and_check_convergence() - Makes step() method cleaner and more focused on orchestration - Each helper function is now self-contained with its own debug logging This addresses PR SimVascular#450 review feedback on code organization.

Eleven7825 · 2025-10-24T20:02:00Z

Hi Martin, I have moved the debug messages into respective functions, and the code is ready for review. As for your last comment, I think we should address it in another issue and PR.

Moved all pic namespace functions (picp, pici, picc, pic_eth) into the Integrator class as member functions: - picp -> predictor() (public method, called from main.cpp) - pici -> pici() (private method) - picc -> picc() (private method) - pic_eth -> pic_eth() (private method) Updated all call sites to use the new member functions. Removed pic.h and pic.cpp files and updated CMakeLists.txt. Related to GitHub issue SimVascular#459.

Move time integration variables An (acceleration), Dn (displacement), and Yn (velocity) from the global ComMod structure into the Integrator class. These variables are now passed as function parameters throughout the codebase instead of accessing them through ComMod. Changes include: - Add An_, Dn_, Yn_ members to Integrator with public getters - Initialize from Ao, Do, Yo in Integrator::initialize_arrays() - Update 19 files to pass these variables as Array<double>& parameters - Remove An, Dn, Yn declarations from ComMod.h

This commit completes the extraction of time-level variables from the global ComMod structure to the Integrator class. Ao, Do, Yo (old acceleration, displacement, velocity at time level n) join An, Dn, Yn as Integrator members. Key changes: - ComMod.h: Removed Ao, Do, Yo member variables - Integrator.h/cpp: Added Ao_, Do_, Yo_ members with move constructor and getters - Simulation.h/cpp: Added initialize_integrator() to transfer ownership - initialize.cpp: Made Ao, Do, Yo local variables, moved to Integrator - Updated 25+ files with function signatures to pass Ao/Do/Yo parameters - Fixed default parameter placement (declarations only, not definitions) All time integration state is now encapsulated in the Integrator class, improving modularity and preparing for future multi-physics enhancements.

mrp089

Great job, @shiyi! I definitely appreciate the missing lines in ComMod.h!

I had mostly minor comments. Two major things I noticed:

Does the remeshing still work as intended? I'm not sure if this is covered by a test.
It seems in initialize.cpp there are a few things that are not adapted yet to the n's, potentially set_bc::set_bc_dir and txt_ns::txt.
We should look at the coverage report carefully for this one and make sure all the changed lines are covered by a test.

…nd integration functions Following the extraction of Ao/Do/Yo from ComMod to Integrator class, this commit completes the parameter threading work by updating all functions that perform face integration or boundary condition operations to accept and pass Do/Dn parameters. Changes include: Boundary Condition Functions: - bc_ini(): Add Do parameter, update 3 integ() calls for parabolic profiles and flux normalization - set_bc_cmm(), set_bc_cmm_l(): Add Do parameter for CMM boundary conditions - set_bc_neu(), set_bc_neu_l(): Add Do parameter for Neumann boundary conditions - set_bc_dir_w(), set_bc_dir_wl(): Add Do parameter for Dirichlet wall conditions - set_bc_trac_l(): Add Do parameter for traction boundary conditions - set_bc_rbnl(): Add Do parameter for Robin boundary conditions - set_bc_cpl(): Update to pass Do to bc_ini() for coupled BC area recalculation FSI and Mesh Functions: - fsi_ls_upd(): Add both Dn and Do parameters for level set updates - fsi_ls_ini(): Add Do parameter for FSI initialization - b_assem_neu_bc(), b_neu_folw_p(): Add Do parameter for Neumann BC assembly RIS (Reduced Immersed Surface) Functions: - ris_meanq(): Add Do parameter, update 2 integ() calls for pressure/flow computation - ris0d_status(): Add Do parameter, update 3 integ() calls for 0D coupling - ris_resbc(), setbc_ris(), ris0d_bc(): Add Do parameter for RIS boundary conditions CMM (Coupled Momentum Method): - cmm_b(): Add Do parameter, update nn::gnnb() call with full parameters Integration Functions: - All face-based integ() calls updated to pass Do parameter via pointer - Updated calls to use proper signatures with pFlag, cfg, Dn, and Do parameters - Enhanced error reporting in nn::gnnb() to include face name, mesh name, and element Main Integration Loop: - Integrator::iterate(): Updated all set_bc calls to pass Do_ parameter - main.cpp: Updated ris_meanq() and ris0d_status() calls to pass Do

This commit fixes systematic issues with displacement parameter passing throughout the solver: 1. Corrected parameter confusion in set_bc.cpp where An/Ao were incorrectly used instead of Dn/Do 2. Replaced nullptr with proper Dn/Do parameters in 14 integ() calls across ris.cpp, txt.cpp, baf_ini.cpp, and set_bc.cpp 3. Fixed critical bug in txt.cpp:520 where missing pFlag parameter caused &Do to be misinterpreted as boolean 4. Enhanced error messages in all_fun.cpp to identify exact failure locations These fixes resolve 12 test failures in moving mesh simulations (genBC and RIS tests).

I participated in the refactoring, so my review should be replaced by someone else's

mrp089 · 2026-04-01T22:21:25Z

This is ready from our side. @ktbolt, @aabrown100-git, please give it a review. Thank you!

Copilot

Pull request overview

Refactors the solver time-stepping workflow to encapsulate the Newton iteration loop into a new Integrator class and to centralize solution variable handling via SolutionStates, as groundwork for future partitioned FSI (separate integrators per domain).

Changes:

Introduced SolutionStates to carry old/current solution arrays and threaded it through BC, post-processing, IO, and mesh utilities.
Added Integrator class to own the Newton loop and generalized-alpha working arrays (Ag/Yg/Dg), and updated main.cpp to delegate predictor + Newton step.
Removed Ao/An/Yo/Yn/Do/Dn from ComMod and updated build + related call sites accordingly.

Reviewed changes

Copilot reviewed 43 out of 44 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
Code/Source/solver/vtk_xml.h	Updates VTU writer API to accept `SolutionStates`.
Code/Source/solver/vtk_xml.cpp	Uses `SolutionStates` for VTU output and routes post-processing calls accordingly.
Code/Source/solver/Vector.h	Adds `<cstring>` include (likely for mem ops used in Vector implementation).
Code/Source/solver/uris.h	Updates URIS APIs to accept `SolutionStates`.
Code/Source/solver/uris.cpp	Switches URIS computations to read state from `SolutionStates` and passes it into integrations.
Code/Source/solver/txt.h	Updates TXT output APIs to accept `SolutionStates`.
Code/Source/solver/txt.cpp	Switches TXT output and integral writers to use `SolutionStates`.
Code/Source/solver/SolutionStates.h	Adds new `Solution` / `SolutionStates` containers for old/current solution arrays.
Code/Source/solver/Simulation.h	Adds integrator ownership/accessors and `initialize_integrator()`.
Code/Source/solver/Simulation.cpp	Implements integrator initialization and guarded accessor.
Code/Source/solver/set_bc.h	Threads `SolutionStates` through BC APIs; changes `set_bc_dir` signature.
Code/Source/solver/set_bc.cpp	Updates BC implementations to use `SolutionStates` and updated integration/normal APIs.
Code/Source/solver/ris.h	Updates RIS APIs to accept `SolutionStates`.
Code/Source/solver/ris.cpp	Switches RIS logic to use `SolutionStates` (including updater/status paths).
Code/Source/solver/remesh.cpp	Removes clearing of `ComMod` solution arrays now managed elsewhere.
Code/Source/solver/read_msh.h	Threads `SolutionStates` into mesh quality checks (mvMsh displacement access).
Code/Source/solver/read_msh.cpp	Uses `SolutionStates` displacement when computing mesh properties.
Code/Source/solver/post.h	Updates post-processing APIs to accept `SolutionStates`.
Code/Source/solver/post.cpp	Switches post-processing to read from `SolutionStates`; updates bin2vtk path to use temp states.
Code/Source/solver/pic.h	Removes legacy PIC header (predictor/initiator/corrector moved into `Integrator`).
Code/Source/solver/output.h	Threads `SolutionStates` into restart/results writing.
Code/Source/solver/output.cpp	Uses `SolutionStates` arrays for restart/results output.
Code/Source/solver/nn.h	Updates `gnnb()` signature to accept `SolutionStates` for configuration-based geometry.
Code/Source/solver/nn.cpp	Uses `SolutionStates` displacement in `gnnb()` (mvMsh and timestep configs).
Code/Source/solver/mesh.h	Threads `SolutionStates` into mesh construction.
Code/Source/solver/mesh.cpp	Uses `SolutionStates` displacement instead of `ComMod.Do`.
Code/Source/solver/main.cpp	Replaces inline Newton loop with `Integrator` calls; routes outputs/BC/RIS/URIS via `SolutionStates`.
Code/Source/solver/Integrator.h	Adds new `Integrator` interface encapsulating Newton iteration + generalized-alpha state.
Code/Source/solver/Integrator.cpp	Implements predictor/initiator/corrector and Newton loop formerly in `main.cpp`/PIC routines.
Code/Source/solver/initialize.h	Updates init APIs to fill `SolutionStates` rather than `ComMod` solution arrays.
Code/Source/solver/initialize.cpp	Builds initial `SolutionStates`, applies BCs, initializes integrator, updates restart/init paths.
Code/Source/solver/eq_assem.h	Threads `SolutionStates` into assembly helpers and global assembly.
Code/Source/solver/eq_assem.cpp	Passes `SolutionStates` into mesh construction and BC-related normal computations.
Code/Source/solver/ComMod.h	Removes `Ao/An/Yo/Yn/Do/Dn` members from `ComMod`.
Code/Source/solver/cmm.h	Threads `SolutionStates` into CMM boundary routine signature.
Code/Source/solver/cmm.cpp	Passes `SolutionStates` into `nn::gnnb()` for consistent geometry configuration.
Code/Source/solver/CMakeLists.txt	Adds `Integrator.` and removes `pic.` from build.
Code/Source/solver/cep_ion.h	Updates CEP integration API to accept `SolutionStates`.
Code/Source/solver/cep_ion.cpp	Uses `SolutionStates` (and updated post API) for CEP state integration.
Code/Source/solver/baf_ini.h	Threads `SolutionStates` into face/bc initialization and FSILS init APIs.
Code/Source/solver/baf_ini.cpp	Updates BAF init to pass `SolutionStates` into face/bc init and coupling init calls.
Code/Source/solver/all_fun.h	Threads `SolutionStates` through integration overloads (mvMsh displacement access).
Code/Source/solver/all_fun.cpp	Uses `SolutionStates` displacement in volume/face integrals and normal computations.
.gitignore	Expands ignored build artifacts and generated outputs/headers.

Comments suppressed due to low confidence (2)

Code/Source/solver/Integrator.cpp:365

res_ is a persistent member but is never reset in update_residual_arrays(). Only entries touched by lsPtr are overwritten, so stale values from previous equations/iterations can leak into ls_solve() for indices not set this call. Clear res_ (or at least the active indices) at the start of this function, alongside incL_ = 0.
Code/Source/solver/Integrator.cpp:464
Inside the #ifdef debug_picp block, coef is logged before it is declared/initialized (dmsg << "coef: " << coef; comes before double coef = ...). If debug_picp is enabled this won’t compile (or may print an indeterminate value if an outer coef exists). Move the debug print after the coef definition or log eq.gam only.

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Eleven7825

Reply to @zasexton and @aabrown100-git review

…r to accept SolutionStates

zasexton

I have completed review of the PR for the integrator encapsulation. I believe it should be fine to pull in. If we believe it is necessary we can add additional issues for cleanup of ownership and dataflow but there is nothing precluding this code. It removes some members from com_mod so it is definitely in the right direction.

aabrown100-git

Looks good, I approve!

zasexton · 2026-04-13T20:22:14Z

@ktbolt we believe this PR is in a sufficient position for now to merge.

ktbolt · 2026-04-13T21:08:26Z

@zasexton Looks good to me too.

@Eleven7825 Thank you for all of your hard work on this !

Eleven7825 added 4 commits October 13, 2025 01:57

Fix: Add missing iEqOld variable for output calls

7eec430

The iEqOld variable is needed for output::output_result() calls after the Newton iteration completes. This variable tracks which equation was solved in the last iteration.

mrp089 requested changes Oct 14, 2025

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mrp089 added 2 commits October 17, 2025 11:34

Merge branch 'main' into feature/issue-442-integrator-class

d095026

change license header

1d7c5cf

ktbolt self-requested a review October 18, 2025 02:02

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Comment thread Code/Source/solver/CMakeLists.txt Outdated

Eleven7825 added 5 commits October 23, 2025 03:31

Eleven7825 marked this pull request as ready for review October 23, 2025 18:58

Eleven7825 added 4 commits November 6, 2025 17:14

Merge remote changes with Ao, Do, Yo extraction work

bbb88d6

mrp089 requested changes Nov 7, 2025

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Eleven7825 added 2 commits November 12, 2025 23:50

mrp089 added 4 commits April 1, 2026 17:53

move Solution and SolutionStates objects to new file

6b15c85

small fixes in Integrator

c0442e0

make solution components private and exclusively use getter functions

0d3a664

small fixes

c740b98

mrp089 requested review from aabrown100-git and ktbolt April 1, 2026 22:20

mrp089 mentioned this pull request Apr 1, 2026

Refactor pic namespace to TimeIntegration class #459

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Eleven7825 requested a review from zasexton April 9, 2026 03:38

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Comment thread Code/Source/solver/Integrator.cpp

Add intermediate variables to solutions, renaming local name variables

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Comment thread Code/Source/solver/Integrator.h Outdated

Eleven7825 commented Apr 10, 2026

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Comment thread Code/Source/solver/baf_ini.cpp

Comment thread Code/Source/solver/Integrator.cpp

shiyi and others added 2 commits April 10, 2026 20:59

Move Ag/Yg/Dg into SolutionStates::intermediate and refactor initiato…

d2861dd

…r to accept SolutionStates

Merge branch 'main' into feature/issue-442-integrator-class

21ade6b

mrp089 requested a review from aabrown100-git April 10, 2026 21:22

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Comment thread Code/Source/solver/baf_ini.cpp

zasexton approved these changes Apr 13, 2026

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aabrown100-git approved these changes Apr 13, 2026

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mrp089 merged commit 97ef512 into SimVascular:main Apr 13, 2026
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mrp089 mentioned this pull request Apr 13, 2026

Encapusulate the newton iteration in main.ccp #442

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Eleven7825 mentioned this pull request Apr 14, 2026

Top-level abstraction for partitioned FSI with growth and remodeling (svFSGe) #528

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Eleven7825 commented Oct 13, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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