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Merge remote-tracking branch 'upstream/master' into IGRMergeOne
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‎.github/copilot-instructions.md‎

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# GitHub Copilot Instructions – Pull-Request Reviews for MFC
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These instructions guide **GitHub Copilot Code Review** and **Copilot Chat** when they evaluate pull requests in this repository.
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---
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## 1 Project Context (always include)
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* **Project:** MFC (exascale many-physics solver) written in **modern Fortran 2008+**, generated with **Fypp**.
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* **Directory layout:**
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* Sources in `src/`, tests in `tests/`, examples in `examples/`.
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* Most source files are templated `.fpp`; CMake transpiles them to `.f90`.
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* **Fypp macros** are in `src/<subprogram>/include/`, where `<subprogram>` is `simulation`, `common`, `pre_process`, or `post_process`. Review these first.
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* Only `simulation` (plus its `common` dependencies) is GPU-accelerated with **OpenACC**.
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> **Copilot, when reviewing:**
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> * Treat the codebase as free-form Fortran 2008+ with `implicit none`, explicit `intent`, and standard intrinsics.
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> * Prefer `module … contains … subroutine foo()` over legacy constructs; flag uses of `COMMON`, file-level `include`, or other global state.
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---
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## 2 Incremental-Change Workflow
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Copilot, when reviewing:
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* Encourage small, buildable commits
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---
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## 3 Style & Naming Conventions (*.fpp / *.f90)
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| Element | Rule |
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|---------|------|
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| Indentation | 2 spaces; continuation lines align beneath &. |
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| Case | Lower-case keywords & intrinsics (do, end subroutine, …). |
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| Modules | m_<feature> (e.g. m_transport). |
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| Public subroutines | s_<verb>_<noun> (s_compute_flux). |
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| Public functions | f_<verb>_<noun>. |
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| Routine size | subroutine ≤ 500 lines, helper ≤ 150, function ≤ 100, file ≤ 1000. |
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| Arguments | ≤ 6; else use a derived-type params struct. |
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| Forbidden | goto (except legacy), COMMON, save globals. |
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| Variables | Every arg has explicit intent; use dimension/allocatable/pointer as appropriate. |
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| Errors | Call s_mpi_abort(<msg>), never stop or error stop. |
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Copilot, when reviewing:
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* Flag violations of any cell above.
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* Suggest refactors when size or argument limits are exceeded.
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* Ensure private helpers stay inside their defining module and avoid nested procedures.
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---
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## 4 OpenACC Guidelines (for GPU kernels)
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Wrap tight loops:
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```fortran
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!$acc parallel loop gang vector default(present) reduction(...)
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```
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* Add collapse(n) when safe.
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* Declare loop-local variables with private(...).
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* Allocate large arrays with managed or move them into a persistent !$acc enter data region at start-up.
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* Avoid stop/error stop inside device code.
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* Code must compile with Cray ftn, NVIDIA nvfortran, GNU gfortran, and Intel ifx/ifort.
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---
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## 5 Review Checklist (what Copilot should verify)
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1. Buildability: PR includes build instructions or CI passes the staged build.
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2. Tests: Focused tests are added/updated.
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3. Style compliance: All rules in §3 are satisfied.
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4. Module hygiene: No new global state; proper namespacing.
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5. Performance: GPU code follows §4; no large host/device transfers in hot loops.
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6. Documentation: Updated in-code comments and, when needed, README or docs site.
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7. Regressions: No changes to outputs of golden tests without clear justification.

‎.github/workflows/bench.yml‎

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@@ -1,6 +1,9 @@
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name: 'Benchmark'
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on: pull_request
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on:
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pull_request_review:
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types: [submitted]
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workflow_dispatch:
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jobs:
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file-changes:
@@ -20,11 +23,12 @@ jobs:
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self:
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name: Georgia Tech | Phoenix (NVHPC)
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if: github.repository == 'MFlowCode/MFC' && needs.file-changes.outputs.checkall == 'true'
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if: github.repository == 'MFlowCode/MFC' && needs.file-changes.outputs.checkall == 'true' && ${{ github.event.review.state == 'approved' }}
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needs: file-changes
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strategy:
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matrix:
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device: ['cpu', 'gpu']
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fail-fast: false
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runs-on:
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group: phoenix
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labels: gt
@@ -56,6 +60,12 @@ jobs:
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(cd pr && . ./mfc.sh load -c p -m g)
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(cd pr && ./mfc.sh bench_diff ../master/bench-${{ matrix.device }}.yaml ../pr/bench-${{ matrix.device }}.yaml)
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- name: Print Logs
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if: always()
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run: |
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cat pr/bench-${{ matrix.device }}.* 2>/dev/null || true
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cat master/bench-${{ matrix.device }}.* 2>/dev/null || true
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- name: Archive Logs
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uses: actions/upload-artifact@v4
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if: always()

‎.github/workflows/frontier/submit.sh‎

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@@ -33,10 +33,9 @@ sbatch <<EOT
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#SBATCH -A CFD154 # charge account
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#SBATCH -N 1 # Number of nodes required
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$sbatch_device_opts
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#SBATCH -t 01:59:00 # Duration of the job (Ex: 15 mins)
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#SBATCH -t 03:59:00 # Duration of the job (Ex: 15 mins)
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#SBATCH -o$job_slug.out # Combined output and error messages file
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#SBATCH -p extended # Extended partition for shorter queues
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#SBATCH -q debug # Use debug QOS - only one job per user allowed in queue!
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#SBATCH -W # Do not exit until the submitted job terminates.
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set -e

‎.github/workflows/lint-source.yml‎

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run: |
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! grep -iR -e '\.\.\.' -e '\-\-\-' -e '===' ./src/*
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- name: Looking for false integers
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run: |
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! grep -onRP '(?<![0-9.eE\-])\b[0-9]*_wp\b' src/
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- name: Looking for junk comments in examples
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run: |
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! grep -R '# ===' ./benchmarks **/*.py

‎.github/workflows/pmd.yml‎

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unzip -q pmd.zip
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PMD_HOME="pmd-bin-${PMD_VERSION}"
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SOURCE_DIR="${1:-src}"
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total_files=$(find "$SOURCE_DIR" -type f \( -name "*.f" -o -name "*.f90" -o -name "*.for" -o -name "*.fpp" -o -name "*.F" -o -name "*.F90" \) | wc -l)
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processed=0
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find "$SOURCE_DIR" -type f \( -name "*.f" -o -name "*.f90" -o -name "*.for" -o -name "*.fpp" -o -name "*.F" -o -name "*.F90" \) -print0 |
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while IFS= read -r -d $'\0' file; do
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processed=$((processed + 1))
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# Create a temporary file with same permissions as original
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TMP_FILE=$(mktemp)
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if [ $? -ne 0 ]; then
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echo -e "Failed to create temporary file for $file, skipping"
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continue
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fi
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# Copy permissions from original file
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chmod --reference="$file" "$TMP_FILE"
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# More comprehensive sed command to handle different Fortran comment styles:
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# 1. Replace lines that are entirely comments with an empty line:
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# - Lines starting with '!' (free form comments)
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# - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
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# 2. Remove end-of-line comments (anything after '!' that isn't in a string)
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# 3. Preserve strings containing '!' characters
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sed -E '
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# First handle & continuation style (modern Fortran)
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:ampersand_loop
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/&[[:space:]]*$/ {
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N
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s/&[[:space:]]*\n[[:space:]]*(&)?/ /g
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tampersand_loop
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}
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# Handle fixed-form continuation (column 6 indicator)
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:fixed_form_loop
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/^[[:space:]]{0,5}[^[:space:]!&]/ {
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N
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s/\n[[:space:]]{5}[^[:space:]]/ /g
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tfixed_form_loop
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}
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# Remove any remaining continuation markers
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s/&//g
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# Normalize spacing - replace multiple spaces with single space
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s/[[:space:]]{2,}/ /g
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# Remove spaces around mathematical operators
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s/[[:space:]]*\*[[:space:]]*/*/g
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s/[[:space:]]*\+[[:space:]]*/+/g
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s/[[:space:]]*-[[:space:]]*/-/g
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s/[[:space:]]*\/[[:space:]]*/\//g
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s/[[:space:]]*\*\*[[:space:]]*/\*\*/g
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# Remove spaces in common Fortran constructs (array indexing, function calls)
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s/\([[:space:]]*([^,)[:space:]]+)[[:space:]]*,/(\1,/g # First argument
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s/,[[:space:]]*([^,)[:space:]]+)[[:space:]]*,/,\1,/g # Middle arguments
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s/,[[:space:]]*([^,)[:space:]]+)[[:space:]]*\)/,\1)/g # Last argument
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s/\([[:space:]]*([^,)[:space:]]+)[[:space:]]*\)/(\1)/g # Single argument
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# Remove spaces around brackets and parentheses
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s/\[[[:space:]]*/</g
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s/\[[[:space:]]*/>/g
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s/\[[[:space:]]*/</g
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s/[[:space:]]*\]/]/g
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s/\([[:space:]]*/(/g
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s/[[:space:]]*\)/)/g
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# Remove spaces around comparison operators
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s/[[:space:]]*<=[[:space:]]*/</g
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s/[[:space:]]*>=[[:space:]]*/>/g
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s/[[:space:]]*<[[:space:]]*/</g
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s/[[:space:]]*>[[:space:]]*/>/g
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s/[[:space:]]*==[[:space:]]*/==/g
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# Remove full-line comments
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/^\s*!/d
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/^[cC*dD]/d
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/^[ \t]*[cC*dD]/d
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/^[[:space:]]*$/d
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# Remove end-of-line comments, preserving quoted strings
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s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
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' "$file" > "$TMP_FILE"
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if cmp -s "$file" "$TMP_FILE"; then
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rm "$TMP_FILE"
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else
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# Overwrite the original file with the processed content
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mv "$TMP_FILE" "$file"
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fi
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done
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"${PMD_HOME}/bin/pmd" cpd \
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--dir src \
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--language fortran \
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--minimum-tokens=40
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--minimum-tokens=20 \
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--no-fail-on-violation \
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--no-fail-on-error

‎.pr_agent.toml‎

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# .pr_agent.toml
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[github_app]
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# Run these tools automatically on every new PR:
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pr_commands = ["/describe", "/review", "/improve"]
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[pr_reviewer] # (all fields optional)
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num_max_findings = 5 # how many items to surface
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require_tests_review = true
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extra_instructions = """
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Focus on duplicate code, the possibility of bugs, and if the PR added appropriate tests if it added a simulation feature.
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"""
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[pr_code_suggestions]
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commitable_code_suggestions = false # purely advisory, no write ops
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apply_suggestions_checkbox = false # hides the “Apply/Chat” boxes

‎docs/documentation/case.md‎

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Additional variables can be declared in `Hardcoded1[2,3]DVariables` and used in `hardcoded1[2,3]D`.
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As a convention, any hard coded patches that are part of the MFC master branch should be identified as 1[2,3]xx where the first digit indicates the number of dimensions.
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The code provides three pre-built patches for dimensional extrusion of initial conditions:
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- `case(170)`: Load 1D profile from data files
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- `case(270)`: Extrude 1D data to 2D domain
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- `case(370)`: Extrude 2D data to 3D domain
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Setup: Only requires specifying `init_dir` and filename pattern via `zeros_default`. Grid dimensions are automatically detected from the data files.
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Implementation: All variables and file handling are managed in `src/pre_process/include/ExtrusionHardcodedIC.fpp` with no manual grid configuration needed.
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Usage: Ideal for initializing simulations from lower-dimensional solutions, enabling users to add perturbations or modifications to the base extruded fields for flow instability studies.
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#### Parameter Descriptions
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- `num_patches` defines the total number of patches defined in the domain.

‎src/common/m_checker_common.fpp‎

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@:PROHIBIT(surface_tension .and. sigma < 0._wp, &
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"sigma must be greater than or equal to zero")
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337-
@:PROHIBIT(surface_tension .and. sigma == dflt_real, &
337+
@:PROHIBIT(surface_tension .and. f_approx_equal(sigma, dflt_real), &
338338
"sigma must be set if surface_tension is enabled")
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340340
@:PROHIBIT(.not. f_is_default(sigma) .and. .not. surface_tension, &
@@ -359,9 +359,12 @@ contains
359359
!! Called by s_check_inputs_common for all three stages
360360
impure subroutine s_check_inputs_moving_bc
361361
#:for X, VB2, VB3 in [('x', 'vb2', 'vb3'), ('y', 'vb3', 'vb1'), ('z', 'vb1', 'vb2')]
362-
if (any((/bc_${X}$%vb1, bc_${X}$%vb2, bc_${X}$%vb3/) /= 0._wp)) then
362+
if (.not. (f_approx_equal(bc_${X}$%vb1, 0._wp) .and. &
363+
f_approx_equal(bc_${X}$%vb2, 0._wp) .and. &
364+
f_approx_equal(bc_${X}$%vb3, 0._wp))) then
363365
if (bc_${X}$%beg == BC_SLIP_WALL) then
364-
if (any((/bc_${X}$%${VB2}$, bc_${X}$%${VB3}$/) /= 0._wp)) then
366+
if (.not. (f_approx_equal(bc_${X}$%${VB2}$, 0._wp) .and. &
367+
f_approx_equal(bc_${X}$%${VB3}$, 0._wp))) then
365368
call s_mpi_abort("bc_${X}$%beg must be -15 if "// &
366369
"bc_${X}$%${VB2}$ or bc_${X}$%${VB3}$ "// &
367370
"is set. Exiting.", CASE_FILE_ERROR_CODE)
@@ -374,9 +377,12 @@ contains
374377
#:endfor
375378

376379
#:for X, VE2, VE3 in [('x', 've2', 've3'), ('y', 've3', 've1'), ('z', 've1', 've2')]
377-
if (any((/bc_${X}$%ve1, bc_${X}$%ve2, bc_${X}$%ve3/) /= 0._wp)) then
380+
if (.not. (f_approx_equal(bc_${X}$%ve1, 0._wp) .and. &
381+
f_approx_equal(bc_${X}$%ve2, 0._wp) .and. &
382+
f_approx_equal(bc_${X}$%ve3, 0._wp))) then
378383
if (bc_${X}$%end == BC_SLIP_WALL) then
379-
if (any((/bc_${X}$%${VE2}$, bc_${X}$%${VE3}$/) /= 0._wp)) then
384+
if (.not. (f_approx_equal(bc_${X}$%${VE2}$, 0._wp) .and. &
385+
f_approx_equal(bc_${X}$%${VE3}$, 0._wp))) then
380386
call s_mpi_abort("bc_${X}$%end must be -15 if "// &
381387
"bc_${X}$%${VE2}$ or bc_${X}$%${VE3}$ "// &
382388
"is set. Exiting.", CASE_FILE_ERROR_CODE)

‎src/common/m_constants.fpp‎

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Original file line numberDiff line numberDiff line change
@@ -8,9 +8,9 @@ module m_constants
88

99
character, parameter :: dflt_char = ' ' !< Default string value
1010

11-
real(wp), parameter :: dflt_real = -1e6_wp !< Default real value
12-
real(wp), parameter :: sgm_eps = 1e-16_wp !< Segmentation tolerance
13-
real(wp), parameter :: small_alf = 1e-11_wp !< Small alf tolerance
11+
real(wp), parameter :: dflt_real = -1.e6_wp !< Default real value
12+
real(wp), parameter :: sgm_eps = 1.e-16_wp !< Segmentation tolerance
13+
real(wp), parameter :: small_alf = 1.e-11_wp !< Small alf tolerance
1414
real(wp), parameter :: pi = 3.141592653589793_wp !< Pi
1515
real(wp), parameter :: verysmall = 1.e-12_wp !< Very small number
1616

@@ -29,7 +29,7 @@ module m_constants
2929
integer, parameter :: dflt_num_igr_warm_start_iters = 50 !< default number of iterations for IGR elliptic solve
3030
real(wp), parameter :: dflt_alf_factor = 10._wp !< scaling factor for IGR alpha
3131
integer, parameter :: gp_layers = 3 !< Number of ghost point layers for IBM
32-
real(wp), parameter :: capillary_cutoff = 1e-6 !< color function gradient magnitude at which to apply the surface tension fluxes
32+
real(wp), parameter :: capillary_cutoff = 1.e-6 !< color function gradient magnitude at which to apply the surface tension fluxes
3333
real(wp), parameter :: acoustic_spatial_support_width = 2.5_wp !< Spatial support width of acoustic source, used in s_source_spatial
3434
real(wp), parameter :: dflt_vcfl_dt = 100._wp !< value of vcfl_dt when viscosity is off for computing adaptive timestep size
3535
real(wp), parameter :: broadband_spectral_level_constant = 20._wp !< The constant to scale the spectral level at the lower frequency bound
@@ -44,25 +44,25 @@ module m_constants
4444
integer, parameter :: Ifactor_bary_3D = 20 !< Multiple factor of the ratio (triangle area to cell face area) for interpolation on triangle facets for 3D models
4545
integer, parameter :: num_ray = 20 !< Default number of rays traced per cell
4646
real(wp), parameter :: ray_tracing_threshold = 0.9_wp !< Threshold above which the cell is marked as the model patch
47-
real(wp), parameter :: threshold_vector_zero = 1e-10 !< Threshold to treat the component of a vector to be zero
48-
real(wp), parameter :: threshold_edge_zero = 1e-10 !< Threshold to treat two edges to be overlapped
49-
real(wp), parameter :: threshold_bary = 1e-1 !< Threshold to interpolate a barycentric facet
50-
real(wp), parameter :: initial_distance_buffer = 1e12_wp !< Initialized levelset distance for the shortest path pair algorithm
47+
real(wp), parameter :: threshold_vector_zero = 1.e-10_wp !< Threshold to treat the component of a vector to be zero
48+
real(wp), parameter :: threshold_edge_zero = 1.e-10_wp !< Threshold to treat two edges to be overlapped
49+
real(wp), parameter :: threshold_bary = 1.e-1_wp !< Threshold to interpolate a barycentric facet
50+
real(wp), parameter :: initial_distance_buffer = 1.e12_wp !< Initialized levelset distance for the shortest path pair algorithm
5151

5252
! Lagrange bubbles constants
5353
integer, parameter :: mapCells = 3 !< Number of cells around the bubble where the smoothening function will have effect
5454
real(wp), parameter :: R_uni = 8314._wp ! Universal gas constant - J/kmol/K
5555

5656
! Strang Splitting constants
57-
real(wp), parameter :: dflt_adap_dt_tol = 1e-4_wp !< Default tolerance for adaptive step size
57+
real(wp), parameter :: dflt_adap_dt_tol = 1.e-4_wp !< Default tolerance for adaptive step size
5858
integer, parameter :: adap_dt_max_iters = 100 !< Maximum number of iterations
5959
! Constants of the algorithm described by Heirer, E. Hairer S.P.Nørsett G. Wanner, Solving Ordinary Differential Equations I, Chapter II.4
6060
! to choose the initial time step size for the adaptive time stepping routine
61-
real(wp), parameter :: threshold_first_guess = 1e-5_wp
62-
real(wp), parameter :: threshold_second_guess = 1e-15_wp
63-
real(wp), parameter :: scale_first_guess = 1e-3_wp
64-
real(wp), parameter :: scale_guess = 1e-2_wp
65-
real(wp), parameter :: small_guess = 1e-6_wp
61+
real(wp), parameter :: threshold_first_guess = 1.e-5_wp
62+
real(wp), parameter :: threshold_second_guess = 1.e-15_wp
63+
real(wp), parameter :: scale_first_guess = 1.e-3_wp
64+
real(wp), parameter :: scale_guess = 1.e-2_wp
65+
real(wp), parameter :: small_guess = 1.e-6_wp
6666

6767
! Relativity
6868
integer, parameter :: relativity_cons_to_prim_max_iter = 100

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