Fix masked variables from parent scope

[sbryngelson]

User description

For a long time, we have had the issue of masked variables from the parent scope. I'm not sure if this has caused bugs or not, but it certainly isn't good practice. This PR fixes the issue.

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PR Type

Bug fix, Documentation

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Description

• Fixed variable masking issues across multiple modules by renaming parameters and local variables to avoid conflicts with parent scope
• Renamed parameters like pb to pb_in, mv to mv_in, and added _local or _in suffixes to prevent variable shadowing
• Updated function signatures and parameter names in critical modules including RHS computation, boundary conditions, IBM, bubble dynamics, and MPI communication
• Fixed parameter masking in time stepping, data output, and finite difference computation routines
• Updated documentation formatting and fixed typos in agent rules file

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Diagram Walkthrough

flowchart LR
  A["Global Variables"] --> B["Function Parameters"]
  B --> C["Parameter Renaming"]
  C --> D["pb → pb_in"]
  C --> E["mv → mv_in"] 
  C --> F["local vars → *_local"]
  D --> G["Fixed Masking"]
  E --> G
  F --> G

Loading

File Walkthrough

	Relevant files
Bug fix	15 files m_patches.fpp Fix variable masking in patch geometry subroutines              src/pre_process/m_patches.fpp • Renamed parameter ib to ib_flag in multiple subroutines to avoid variable name conflicts • Renamed variable ca to ca_in in airfoil-related subroutines to prevent masking • Renamed local variables like x_centroid, y_centroid, eta, smooth_coeff to include _local suffix • Renamed non_axis_sym to non_axis_sym_in to avoid scope conflicts +96/-96  m_boundary_common.fpp Resolve parameter name conflicts in boundary condition routines src/common/m_boundary_common.fpp • Renamed parameters pb and mv to pb_in and mv_in in multiple boundary condition subroutines • Updated all references to use the new parameter names throughout the file • Renamed old_grid parameter to old_grid_in in boundary condition file writing function +102/-102 m_ibm.fpp Fix variable masking in immersed boundary method functions src/simulation/m_ibm.fpp • Renamed pb and mv parameters to pb_in and mv_in in IBM correction subroutines • Renamed function parameters like ghost_points, levelset, levelset_norm with _in suffix • Updated variable names like num_gps to num_gps_out for output parameters +70/-70  m_rhs.fpp Resolve variable name masking in RHS computation module    src/simulation/m_rhs.fpp • Renamed pb and mv parameters to pb_in and mv_in in RHS computation functions • Renamed flux_src_n parameter to flux_src_n_in to avoid conflicts • Fixed incorrect variable reference in additional physics RHS computation +35/-34  m_helper.fpp Fix variable name conflicts in helper utility functions    src/common/m_helper.fpp • Renamed local variables m, n to local_m, local_n in matrix printing function • Renamed function parameters like weight, R0 to local_weight, local_R0 • Renamed variables in mathematical functions to avoid conflicts with global scope • Updated parameter names in transformation and polynomial functions +69/-69  m_mpi_common.fpp Resolve variable masking in MPI communication routines      src/common/m_mpi_common.fpp • Renamed ierr to local_ierr in MPI communication functions • Renamed pb and mv parameters to pb_in and mv_in in MPI buffer operations • Updated all references to use the new parameter names consistently +18/-18  m_start_up.fpp Fix parameter name masking in startup data reading functions src/pre_process/m_start_up.fpp • Renamed function parameters q_cons_vf and ib_markers to include _in suffix • Updated parameter names in both serial and parallel IC data file reading functions • Maintained consistency in parameter naming across abstract interface definitions +13/-13  m_bubbles_EE.fpp Fix variable masking in bubble computation subroutines      src/simulation/m_bubbles_EE.fpp • Renamed parameter divu to divu_in in subroutine s_compute_bubbles_EE_rhs to avoid variable masking • Added divu_in parameter to s_compute_bubble_EE_source subroutine signature • Renamed local variables pb and mv to pb_local and mv_local to prevent scope masking • Updated all references to use the new parameter and variable names +23/-22  m_hyperelastic.fpp Rename btensor parameter to prevent variable masking          src/simulation/m_hyperelastic.fpp • Renamed parameter btensor to btensor_in in both s_neoHookean_cauchy_solver and s_Mooney_Rivlin_cauchy_solver • Updated all references to use the new parameter name btensor_in • Maintains same functionality while avoiding variable name conflicts +14/-14  m_bubbles_EL.fpp Fix omegaN variable masking in bubble frequency calculation src/simulation/m_bubbles_EL.fpp • Renamed local variable omegaN to omegaN_local to avoid masking from parent scope • Updated all references to use the new variable name +5/-5      m_bubbles.fpp Rename parameters in bubble wall property subroutine          src/simulation/m_bubbles.fpp • Renamed parameter pb to pb_in in s_bwproperty subroutine • Renamed output parameters to include _out suffix: chi_vw_out, k_mw_out, rho_mw_out • Updated all references to use the new parameter names +10/-10  m_data_output.fpp Fix parameter masking in center of mass output subroutine src/simulation/m_data_output.fpp • Removed empty line at beginning of file • Renamed parameter c_mass to c_mass_in in s_write_com_files subroutine • Updated all references to use the new parameter name +14/-15  m_time_steppers.fpp Fix parameter masking in time stepping subroutines              src/simulation/m_time_steppers.fpp • Added divu parameter to s_compute_bubble_EE_source function call • Renamed parameters in s_apply_bodyforces from q_prim_vf and rhs_vf to q_prim_vf_in and rhs_vf_in • Updated all references to use the new parameter names +6/-6      m_data_input.f90 Rename start_idx parameter to prevent variable masking      src/post_process/m_data_input.f90 • Renamed parameter start_idx to local_start_idx in s_allocate_field_arrays subroutine • Updated all references to use the new parameter name +6/-6      m_finite_differences.fpp Fix buffer size parameter masking in finite differences    src/common/m_finite_differences.fpp • Renamed parameter buff_size to local_buff_size in s_compute_finite_difference_coefficients • Updated array dimension declaration to use the new parameter name +3/-3
Documentation	1 files mfc-agent-rules.mdc Update documentation formatting and fix typos in agent rules .cursor/rules/mfc-agent-rules.mdc • Fixed YAML front matter formatting by changing dashes to proper YAML format • Fixed typo: "respository" to "repository" • Reorganized sections and improved GPU programming guidelines documentation • Enhanced error handling documentation with clearer examples +37/-38

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[Copilot]

Pull Request Overview

This PR fixes instances of variable masking from parent scope throughout the MFC codebase. Variable masking occurs when local variables or parameters in subroutines have the same name as variables from the module or parent scope, which can lead to confusion and potential bugs. The changes rename these variables with more descriptive names (often adding suffixes like _in, _out, _local) to avoid masking.

• Renames procedure parameters to avoid masking module-level variables
• Updates local variable names to prevent conflicts with parent scope
• Ensures consistent naming patterns while maintaining functionality

Reviewed Changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/simulation/m_time_steppers.fpp	Renames parameters in bubble computation and body forces routines
src/simulation/m_rhs.fpp	Updates parameter names in RHS computation and physics routines
src/simulation/m_ibm.fpp	Renames variables in IBM state correction and ghost point routines
src/simulation/m_hyperelastic.fpp	Updates tensor parameter names in stress computation
src/simulation/m_data_output.fpp	Renames center of mass parameter and removes blank line
src/simulation/m_bubbles_EL.fpp	Updates local variable name in bubble frequency computation
src/simulation/m_bubbles_EE.fpp	Renames parameters in bubble source computation
src/simulation/m_bubbles.fpp	Updates bubble property computation parameter names
src/pre_process/m_start_up.fpp	Renames parameters in data file reading routines
src/pre_process/m_patches.fpp	Updates variable names in patch geometry routines
src/post_process/m_data_input.f90	Renames array allocation parameter
src/common/m_mpi_common.fpp	Updates MPI communication parameter names
src/common/m_helper.fpp	Renames various utility function parameters
src/common/m_finite_differences.fpp	Updates finite difference parameter name
src/common/m_boundary_common.fpp	Renames boundary condition parameter names
.cursor/rules/mfc-agent-rules.mdc	Minor formatting and documentation updates

Comments suppressed due to low confidence (2)

src/simulation/m_bubbles_EL.fpp:296

• [nitpick] The variable name 'omegaN_local' follows an inconsistent naming pattern. Consider using 'omega_n_local' to align with Fortran naming conventions.

        real(wp) :: omegaN_local, PeG, PeT, rhol, pcrit, qv, gamma, pi_inf, dynP

[qodo-merge-pro]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 4 🔵🔵🔵🔵⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Variable Masking The variable ca is renamed to ca_in to avoid masking, but this creates potential inconsistency if other parts of the codebase still reference the original variable name. Need to verify all references are updated consistently across the entire codebase. ca_in = patch_ib(patch_id)%c pa = patch_ib(patch_id)%p Parameter Renaming Parameters pb and mv are renamed to pb_in and mv_in throughout multiple subroutines. This is a widespread change that could introduce bugs if any calls to these subroutines weren't updated to match the new parameter names. real(wp), optional, dimension(idwbuff(1)%beg:, idwbuff(2)%beg:, idwbuff(3)%beg:, 1:, 1:), intent(inout) :: pb_in, mv_in type(integer_field), dimension(1:num_dims, -1:1), intent(in) :: bc_type Variable Shadowing The variable ierr is renamed to local_ierr to avoid masking. However, need to ensure this doesn't conflict with existing error handling patterns and that all MPI error checking still functions correctly. integer :: i, local_ierr integer, allocatable :: recounts(:), displs(:)

[qodo-merge-pro]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
General	Add consistent local variable naming The variable radius is not renamed with a _local suffix like other local variables in this scope. This inconsistency could lead to confusion about variable scope and potential conflicts with module-level variables. src/pre_process/m_patches.fpp [1420-1421] -real(wp) :: radius, x_centroid_local, y_centroid_local, z_centroid_local, eta_local, smooth_coeff_local +real(wp) :: radius_local, x_centroid_local, y_centroid_local, z_centroid_local, eta_local, smooth_coeff_local logical :: non_axis_sym_in Suggestion importance[1-10]: 6 __ Why: The suggestion correctly identifies that radius was not renamed to radius_local for consistency with other local variables in the same scope, which improves code clarity and maintainability.	Low
	Rename radius to radius_local consistently The variable radius should be renamed to radius_local to maintain consistency with the local variable naming pattern and avoid potential conflicts with module-level variables. src/pre_process/m_patches.fpp [1431-1479] -radius = patch_icpp(patch_id)%radius +radius_local = patch_icpp(patch_id)%radius ... r = sqrt((x_cc(i) - x_centroid_local)**2 + (cart_y - y_centroid_local)**2 + (cart_z - z_centroid_local)**2) + eps ... -r - as(2)*Ps(2) - as(3)*Ps(3) - as(4)*Ps(4) - as(5)*Ps(5) - as(6)*Ps(6) - as(7)*Ps(7) <= radius +r - as(2)*Ps(2) - as(3)*Ps(3) - as(4)*Ps(4) - as(5)*Ps(5) - as(6)*Ps(6) - as(7)*Ps(7) <= radius_local Suggestion importance[1-10]: 6 __ Why: This suggestion correctly points out the usages of the radius variable that should be renamed to radius_local for consistency, following on from the variable declaration.	Low
Update

[codecov]

Codecov Report

Attention: Patch coverage is 25.31328% with 298 lines in your changes missing coverage. Please review.

Project coverage is 44.08%. Comparing base (658f188) to head (71a9bf0).
Report is 9 commits behind head on master.

Files with missing lines	Patch %	Lines
src/common/m_boundary_common.fpp	16.45%	65 Missing and 1 partial ⚠️
src/pre_process/m_patches.fpp	28.57%	43 Missing and 12 partials ⚠️
src/common/m_helper.fpp	20.00%	40 Missing ⚠️
src/simulation/m_ibm.fpp	38.18%	33 Missing and 1 partial ⚠️
src/simulation/m_rhs.fpp	24.13%	22 Missing ⚠️
src/simulation/m_data_output.fpp	18.18%	18 Missing ⚠️
src/simulation/m_hyperelastic.fpp	0.00%	18 Missing ⚠️
src/common/m_mpi_common.fpp	7.14%	12 Missing and 1 partial ⚠️
src/simulation/m_bubbles_EE.fpp	35.29%	11 Missing ⚠️
src/pre_process/m_start_up.fpp	0.00%	6 Missing ⚠️
... and 7 more

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #959   +/-   ##
=======================================
  Coverage   44.08%   44.08%           
=======================================
  Files          69       69           
  Lines       19573    19573           
  Branches     2428     2428           
=======================================
  Hits         8628     8628           
  Misses       9444     9444           
  Partials     1501     1501           

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