Variable Robin boundary condition and generic boundary condition class #437

aabrown100-git · 2025-09-23T07:42:30Z

Current situation

Resolves #291

Release Notes

New BoundaryCondition class to handle uniform and spatially varying BC values from a .vtp filepath provided in the input file.
New RobinBoundaryCondition class, derived from BoundaryCondition, replaces all existing code for handling Robin BCs and adds capability for defining spatially varying Robin BCs.
struct and ustruct test cases for spatially varying Robin BC.
Other additions to CmMod.h/cpp and VtkData.h/cpp necessary to implement the BoundaryCondition class.

Documentation

Should add to svMultiPhysics documentation.

Testing

Added struct and ustruct tests for spatially varying Robin BCs.

Code of Conduct & Contributing Guidelines

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

…ls with multiple processors. Other improvements to make

…ead of at every Newton iteration

…h some compilation issues now.

…ic this way

…different from struct result, so could not use result_002.vtu from the struct case

…ced custom exception classes for VTP file errors and node count mismatches. Updated point matching logic to use squared distance for efficiency. Removed redundant map clearing operations during initialization. Also, put test cases number of timesteps back to 2

…ondition classes.

…tion. Add generic flag handling in BoundaryCondition

Copilot

Pull Request Overview

This PR implements variable Robin boundary conditions and introduces a generic boundary condition class to handle spatially variable boundary condition values from VTP files. The implementation adds capability for defining Robin boundary conditions with spatially varying stiffness and damping properties.

Introduces generic BoundaryCondition class for reading spatially variable arrays from VTP files
Implements RobinBoundaryCondition class that replaces existing uniform Robin BC functionality
Adds test cases demonstrating spatially variable Robin boundary conditions for both struct and ustruct physics

Reviewed Changes

Copilot reviewed 55 out of 55 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
BoundaryCondition.h/cpp	New generic BC class for handling VTP-based spatially variable arrays
RobinBoundaryCondition.h/cpp	Robin-specific BC class extending BoundaryCondition
set_bc.h/cpp	Updates to use new RobinBoundaryCondition class in Robin BC assembly
VtkData.h/cpp	Added const correctness and copy constructors for VTP data handling
ComMod.h	Integration of RobinBoundaryCondition into bcType structure
CmMod.h/cpp	Added MPI communication methods for BC distribution
test files	New test cases for spatially variable Robin BC functionality

Comments suppressed due to low confidence (1)

Code/Source/solver/BoundaryCondition.cpp:1

Using eval() is a security risk even with a restricted namespace. Consider implementing a proper expression parser or mathematical expression library instead of eval() for safer evaluation of user-provided mathematical expressions.

/* Copyright (c) Stanford University, The Regents of the University of California, and others.

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

Code/Source/solver/set_bc.cpp

tests/cases/ustruct/spatially_variable_robin/generate_spatially_variable_robin.py

codecov · 2025-09-23T09:09:31Z

Codecov Report

❌ Patch coverage is 64.97696% with 152 lines in your changes missing coverage. Please review.
✅ Project coverage is 67.12%. Comparing base (949d1a6) to head (ee43996).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
Code/Source/solver/BoundaryCondition.cpp	84.29%	41 Missing ⚠️
Code/Source/solver/VtkData.cpp	12.82%	34 Missing ⚠️
Code/Source/solver/BoundaryCondition.h	13.15%	33 Missing ⚠️
Code/Source/solver/CmMod.cpp	25.00%	33 Missing ⚠️
Code/Source/solver/set_bc.cpp	73.91%	6 Missing ⚠️
Code/Source/solver/RobinBoundaryCondition.h	71.42%	4 Missing ⚠️
Code/Source/solver/baf_ini.cpp	66.66%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #437      +/-   ##
==========================================
+ Coverage   67.07%   67.12%   +0.04%     
==========================================
  Files         166      169       +3     
  Lines       33748    34151     +403     
  Branches     5674     5726      +52     
==========================================
+ Hits        22638    22923     +285     
- Misses      10972    11090     +118     
  Partials      138      138

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Code/Source/solver/BoundaryCondition.h

Code/Source/solver/CmMod.cpp

Code/Source/solver/VtkData.h

Code/Source/solver/BoundaryCondition.cpp

ktbolt · 2025-09-23T21:35:22Z

@aabrown100-git Great work ! And nice to clean up VtkData and add more CmMod MPI interface functions.

ktbolt · 2025-09-25T01:09:00Z

@aabrown100-git There is a lot going on in the BoundaryCondition constructors, like reading files, that can throw. I think it is a good practice to catch exceptions within constructors ?

aabrown100-git · 2025-09-25T03:24:18Z

@ktbolt Sounds good about catching exceptions within the constructors. I can put the constructor code within a try-catch block. But in the catch part, what should I do with the exceptions? Just throw it again?

…tilities/generate_boundary_condition_data/ directory, and update READMEs to reflect new location

aabrown100-git · 2025-09-25T04:39:17Z

Integration tests are currently failing to due errors when trying to build svZeroDSolver. I made an issue in svZeroDSolver and proposed a solution to try.

ktbolt · 2025-09-25T15:52:02Z

@aabrown100-git We will need to throw it again to return from the constructor.

Some software systems need to recover from an exception and continue running but in our case the solver needs to shut down when it can't read in data it needs.

aabrown100-git · 2025-09-25T16:22:18Z

@ktbolt Got it, so just what I added in this commit?

Code/Source/solver/BoundaryCondition.cpp

…uctor

…eption classes

aabrown100-git · 2025-09-26T00:44:45Z

@ktbolt Do you think okay to merge now, or would you like to see additional changes?

ktbolt · 2025-09-26T01:10:28Z

@aabrown100-git Have you tested this on a large model, maybe 1M elements ? Just curious.

aabrown100-git · 2025-09-26T01:15:52Z

@ktbolt Not yet, but I will do that soon with my cardiac mechanics model.

ktbolt

Let it be merged !

SimVascular#437) * Initial implementation and test case. Works with 1 processor, but fails with multiple processors. Other improvements to make * Put debugging statements inside debugging blocks * Add spatially_variable_robin test to pytest suite * Rename to VariableRobinBCData, initial VariableRobinBCData once, instead of at every Newton iteration * Add copyright statement * Renamed to RobinBC, partial implementation of parallelization * Refactored distribute method to use gatherv and scatterv. Dealing with some compilation issues now. * Passes test in parallel, fails with index error with 1 proc * Fixed bug, now passes test in serial * clean up debugging statements to make code more readable * Refactor vtp file reading to accept vector of array names, more generic this way * Split implementation into a BC base class and a RobinBC derived class * Update README.md and add ustruct test case. ustruct result is fairly different from struct result, so could not use result_002.vtu from the struct case * Refactor BC class to improve error handling and code clarity. Introduced custom exception classes for VTP file errors and node count mismatches. Updated point matching logic to use squared distance for efficiency. Removed redundant map clearing operations during initialization. Also, put test cases number of timesteps back to 2 * Rename BC and RobinBC classes as BoundaryCondition and RobinBoundaryCondition classes. * Clean up constructors * Remove extraneous comments and debugging statements * Reformat code * Move flag to apply in normal direction only inside RobinBoundaryCondition. Add generic flag handling in BoundaryCondition * Split up distribute method into smaller functions * Add copyrights * Implement copy-and-swap idiom, add noexcept to appropriate methods * Catch exceptions in constructors * Move generate_load.py and generate_spatially_variable_robin.py into utilities/generate_boundary_condition_data/ directory, and update READMEs to reflect new location * Initialize members with default values and use default default constructor * Remove defined_ flag, just check if arrays are allocated, add new exception classes

aabrown100-git and others added 22 commits September 18, 2025 13:37

Initial implementation and test case. Works with 1 processor, but fai…

ec16cb1

…ls with multiple processors. Other improvements to make

Put debugging statements inside debugging blocks

30982a9

Add spatially_variable_robin test to pytest suite

f51fd2f

Rename to VariableRobinBCData, initial VariableRobinBCData once, inst…

29b06b1

…ead of at every Newton iteration

Add copyright statement

c73758b

Renamed to RobinBC, partial implementation of parallelization

243a96b

Refactored distribute method to use gatherv and scatterv. Dealing wit…

b832647

…h some compilation issues now.

Passes test in parallel, fails with index error with 1 proc

a7c9aae

Fixed bug, now passes test in serial

1f4fa7d

clean up debugging statements to make code more readable

340ed6c

Refactor vtp file reading to accept vector of array names, more gener…

88bcc8a

…ic this way

Split implementation into a BC base class and a RobinBC derived class

7317db3

Update README.md and add ustruct test case. ustruct result is fairly …

36146d6

…different from struct result, so could not use result_002.vtu from the struct case

Merge branch 'SimVascular:main' into variable_Robin_BC

1ba1de0

Rename BC and RobinBC classes as BoundaryCondition and RobinBoundaryC…

634e396

…ondition classes.

Clean up constructors

80138ee

Remove extraneous comments and debugging statements

baa9734

Reformat code

0614ed9

Move flag to apply in normal direction only inside RobinBoundaryCondi…

9a1b579

…tion. Add generic flag handling in BoundaryCondition

Split up distribute method into smaller functions

1cd0112

Add copyrights

aacae9a

aabrown100-git requested review from Copilot, ktbolt, mrp089 and zasexton September 23, 2025 07:55

Copilot AI reviewed Sep 23, 2025

View reviewed changes

Code/Source/solver/set_bc.cpp Show resolved Hide resolved

tests/cases/ustruct/spatially_variable_robin/generate_spatially_variable_robin.py Outdated Show resolved Hide resolved

aabrown100-git changed the title ~~Variable Robin boundary condition and generic boundary class~~ Variable Robin boundary condition and generic boundary condition class Sep 23, 2025

Merge branch 'main' into variable_Robin_BC

3be8e84