MFlowCode · sbryngelson · Feb 19, 2026 · Feb 19, 2026 · Feb 19, 2026 · Feb 19, 2026
@@ -24,4 +24,5 @@ exclude = [
     "https://mflowcode\\.github\\.io/sitemap\\.xml",  # Only exists after deployment
     "https://cpe\\.ext\\.hpe\\.com",                   # HPE Cray docs have broken SSL cert
     "https://sc22\\.supercomputing\\.org",              # Returns 415 to automated requests
+    "https://strawberryperl\\.com",                    # Frequently times out
 ]
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -806,6 +806,38 @@ if (MFC_DOCUMENTATION)
     GEN_DOCS(post_process  "MFC: Post-Process")
     GEN_DOCS(documentation "MFC")
 
+    # Generate API landing pages for pre_process, simulation, post_process.
+    # Scans src/{target}/*.fpp to produce module lists in docs/{target}/readme.md.
+    add_custom_command(
+        OUTPUT  "${CMAKE_CURRENT_BINARY_DIR}/gen-api-landing.stamp"
+        DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/gen_api_landing.py"
-        DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/gen_api_landing.py"
+                ${pre_process_FPPs}
+                ${simulation_FPPs}
+                ${post_process_FPPs}
-        DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/gen_api_landing.py"
+                ${pre_process_FPPs}
+                ${simulation_FPPs}
+                ${post_process_FPPs}
+        COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/docs/gen_api_landing.py"
+                "${CMAKE_CURRENT_SOURCE_DIR}"
+        COMMAND "${CMAKE_COMMAND}" -E touch "${CMAKE_CURRENT_BINARY_DIR}/gen-api-landing.stamp"
+        COMMENT "Generating API landing pages"
+        VERBATIM
+    )
+    add_custom_target(gen_api_landing DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gen-api-landing.stamp")
+    add_dependencies(pre_process_doxygen gen_api_landing)
+    add_dependencies(simulation_doxygen gen_api_landing)
+    add_dependencies(post_process_doxygen gen_api_landing)
+
+    # Fix @file/@brief headers to match actual module/program declarations.
+    # Handles mixed-case Fortran names and catches stale module renames.
+    add_custom_command(
+        OUTPUT  "${CMAKE_CURRENT_BINARY_DIR}/fix-file-briefs.stamp"
+        DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/fix_file_briefs.py"
+        COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/docs/fix_file_briefs.py"
-        COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/docs/fix_file_briefs.py"
+                ${pre_process_FPPs}
+                ${simulation_FPPs}
+                ${post_process_FPPs}
-        COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/docs/fix_file_briefs.py"
+                ${pre_process_FPPs}
+                ${simulation_FPPs}
+                ${post_process_FPPs}
+                "${CMAKE_CURRENT_SOURCE_DIR}"
+        COMMAND "${CMAKE_COMMAND}" -E touch "${CMAKE_CURRENT_BINARY_DIR}/fix-file-briefs.stamp"
+        COMMENT "Fixing @file brief headers"
+        VERBATIM
+    )
+    add_custom_target(fix_file_briefs DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/fix-file-briefs.stamp")
+    add_dependencies(pre_process_doxygen fix_file_briefs)
+    add_dependencies(simulation_doxygen fix_file_briefs)
+    add_dependencies(post_process_doxygen fix_file_briefs)
+
     # Inject per-page last-updated dates into documentation markdown files.
     # Runs after auto-generated .md files exist, before Doxygen processes them.
     # Uses a stamp file so it only runs once per build.

diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
@@ -983,7 +983,7 @@ USE_MDFILE_AS_MAINPAGE =
 # also VERBATIM_HEADERS is set to NO.
 # The default value is: NO.
 
-SOURCE_BROWSER         = NO
+SOURCE_BROWSER         = YES
 
 # Setting the INLINE_SOURCES tag to YES will include the body of functions,
 # classes and enums directly into the documentation.

diff --git a/docs/documentation/readme.md b/docs/documentation/readme.md
@@ -32,6 +32,9 @@ Welcome to the Multi-component Flow Code (MFC) documentation.
 ## Development
 
 - @ref contributing "Contributing" - Developer guide and coding standards
+- [Pre-Process API](../pre_process/index.html) - Source code reference for mesh generation and initial conditions
+- [Simulation API](../simulation/index.html) - Source code reference for the flow solver
+- [Post-Process API](../post_process/index.html) - Source code reference for data extraction and visualization
 
 ## About
 

diff --git a/docs/fix_file_briefs.py b/docs/fix_file_briefs.py
@@ -0,0 +1,103 @@
+#!/usr/bin/env python3
+"""Ensure @file/@brief headers match actual module/program declarations.
+
+Usage: python3 fix_file_briefs.py [source_dir]
+  source_dir defaults to current directory.
+
+For each .fpp/.f90 in src/{pre_process,simulation,post_process,common}:
+  1. Parses the first `module <name>` or `program <name>` declaration.
+  2. If no @file directive exists in the first 15 lines, prepends a header.
+  3. If a "Contains module/program ..." @brief exists, rewrites the name
+     to match the source, using @ref for mixed-case Fortran identifiers
+     (Doxygen lowercases Fortran namespaces).
+"""
+
+import re
+import sys
+from pathlib import Path
+
+src_dir = Path(sys.argv[1]) if len(sys.argv) > 1 else Path(".")
+
+DIRS = [
+    src_dir / "src" / "pre_process",
+    src_dir / "src" / "simulation",
+    src_dir / "src" / "post_process",
+    src_dir / "src" / "common",
+]
+
+# First `module X` or `program X` that isn't `end module/program`.
+DECL_RE = re.compile(
+    r"^\s*(module|program)\s+(\w+)\s*$", re.MULTILINE | re.IGNORECASE
-    r"^\s*(module|program)\s+(\w+)\s*$", re.MULTILINE | re.IGNORECASE
+    r"^\s*(module(?!\s+procedure)\b|program)\s+(\w+)\s*$",
+    re.MULTILINE | re.IGNORECASE,
-    r"^\s*(module|program)\s+(\w+)\s*$", re.MULTILINE | re.IGNORECASE
+    r"^\s*(module(?!\s+procedure)\b|program)\s+(\w+)\s*$",
+    re.MULTILINE | re.IGNORECASE,
+)
+
+# Any "Contains module/program <name>" in a Doxygen comment line.
+# Matches both `!! @brief Contains ...` and `!> @brief Contains ...`.
+BRIEF_CONTAINS_RE = re.compile(
+    r"^(!!|!>)\s*@brief\s+(Contains (?:module|program) )(.*)",
+    re.MULTILINE,
+)
+
+
+def find_entity(text: str) -> tuple[str, str] | None:
+    """Return (kind, name) of the first module/program declaration."""
+    for m in DECL_RE.finditer(text):
+        line_start = text.rfind("\n", 0, m.start()) + 1
+        line = text[line_start : m.end()].strip()
+        if line.lower().startswith("end"):
+            continue
+        return m.group(1).lower(), m.group(2)
+    return None
+
+
+def make_ref(name: str) -> str:
+    """Return @ref for mixed-case names, plain name for lowercase."""
+    lower = name.lower()
+    return f'@ref {lower} "{name}"' if lower != name else name
+
+
+def has_file_directive(text: str) -> bool:
+    """Check if @file appears in the first 15 lines."""
+    head = "\n".join(text.splitlines()[:15])
+    return bool(re.search(r"@file", head))
+
+
+fixed = 0
+for d in DIRS:
+    if not d.exists():
+        continue
+    for f in sorted(list(d.glob("*.fpp")) + list(d.glob("*.f90"))):
+        text = f.read_text()
+        entity = find_entity(text)
+        if entity is None:
+            continue
+        kind, name = entity
+        ref = make_ref(name)
+
+        if not has_file_directive(text):
+            # No @file at all — prepend a complete header.
+            header = f"!>\n!! @file\n!! @brief Contains {kind} {ref}\n\n"
+            text = header + text
+            f.write_text(text)
+            fixed += 1
+            print(f"Added  {f.relative_to(src_dir)}")
+            continue
+
+        # Has @file — check if there's a "Contains module/program" brief to fix.
+        m = BRIEF_CONTAINS_RE.search(text)
+        if m is None:
+            continue  # Has @file but no "Contains ..." brief — leave it alone
+
+        current_name = m.group(3).strip()
+        if current_name == ref:
+            continue  # Already correct
+
+        # Replace the name portion of the brief line.
+        new_line = f"{m.group(1)} @brief {m.group(2)}{ref}"
+        new_text = text[: m.start()] + new_line + text[m.end() :]
+
+        if new_text != text:
+            f.write_text(new_text)
-        text = f.read_text()
-        entity = find_entity(text)
-        if entity is None:
-            continue
-        kind, name = entity
-        ref = make_ref(name)
-
-        if not has_file_directive(text):
-            # No @file at all — prepend a complete header.
-            header = f"!>\n!! @file\n!! @brief Contains {kind} {ref}\n\n"
-            text = header + text
-            f.write_text(text)
-            fixed += 1
-            print(f"Added  {f.relative_to(src_dir)}")
-            continue
-
-        # Has @file — check if there's a "Contains module/program" brief to fix.
-        m = BRIEF_CONTAINS_RE.search(text)
-        if m is None:
-            continue  # Has @file but no "Contains ..." brief — leave it alone
-
-        current_name = m.group(3).strip()
-        if current_name == ref:
-            continue  # Already correct
-
-        # Replace the name portion of the brief line.
-        new_line = f"{m.group(1)} @brief {m.group(2)}{ref}"
-        new_text = text[: m.start()] + new_line + text[m.end() :]
-
-        if new_text != text:
-            f.write_text(new_text)
+        text = f.read_text(encoding="utf-8")
+        entity = find_entity(text)
+        if entity is None:
+            continue
+        kind, name = entity
+        ref = make_ref(name)
+
+        if not has_file_directive(text):
+            # No @file at all — prepend a complete header.
+            header = f"!>\n!! @file\n!! @brief Contains {kind} {ref}\n\n"
+            text = header + text
+            f.write_text(text, encoding="utf-8")
+            fixed += 1
+            print(f"Added  {f.relative_to(src_dir)}")
+            continue
+
+        # Has @file — check if there's a "Contains module/program" brief to fix.
+        m = BRIEF_CONTAINS_RE.search(text)
+        if m is None:
+            continue  # Has @file but no "Contains ..." brief — leave it alone
+
+        current_name = m.group(3).strip()
+        if current_name == ref:
+            continue  # Already correct
+
+        # Replace the name portion of the brief line.
+        new_line = f"{m.group(1)} @brief {m.group(2)}{ref}"
+        new_text = text[: m.start()] + new_line + text[m.end() :]
+
+        if new_text != text:
+            f.write_text(new_text, encoding="utf-8")
-        text = f.read_text()
-        entity = find_entity(text)
-        if entity is None:
-            continue
-        kind, name = entity
-        ref = make_ref(name)
-
-        if not has_file_directive(text):
-            # No @file at all — prepend a complete header.
-            header = f"!>\n!! @file\n!! @brief Contains {kind} {ref}\n\n"
-            text = header + text
-            f.write_text(text)
-            fixed += 1
-            print(f"Added  {f.relative_to(src_dir)}")
-            continue
-
-        # Has @file — check if there's a "Contains module/program" brief to fix.
-        m = BRIEF_CONTAINS_RE.search(text)
-        if m is None:
-            continue  # Has @file but no "Contains ..." brief — leave it alone
-
-        current_name = m.group(3).strip()
-        if current_name == ref:
-            continue  # Already correct
-
-        # Replace the name portion of the brief line.
-        new_line = f"{m.group(1)} @brief {m.group(2)}{ref}"
-        new_text = text[: m.start()] + new_line + text[m.end() :]
-
-        if new_text != text:
-            f.write_text(new_text)
+        text = f.read_text(encoding="utf-8")
+        entity = find_entity(text)
+        if entity is None:
+            continue
+        kind, name = entity
+        ref = make_ref(name)
+
+        if not has_file_directive(text):
+            # No @file at all — prepend a complete header.
+            header = f"!>\n!! @file\n!! @brief Contains {kind} {ref}\n\n"
+            text = header + text
+            f.write_text(text, encoding="utf-8")
+            fixed += 1
+            print(f"Added  {f.relative_to(src_dir)}")
+            continue
+
+        # Has @file — check if there's a "Contains module/program" brief to fix.
+        m = BRIEF_CONTAINS_RE.search(text)
+        if m is None:
+            continue  # Has @file but no "Contains ..." brief — leave it alone
+
+        current_name = m.group(3).strip()
+        if current_name == ref:
+            continue  # Already correct
+
+        # Replace the name portion of the brief line.
+        new_line = f"{m.group(1)} @brief {m.group(2)}{ref}"
+        new_text = text[: m.start()] + new_line + text[m.end() :]
+
+        if new_text != text:
+            f.write_text(new_text, encoding="utf-8")
+            fixed += 1
+            print(f"Fixed  {f.relative_to(src_dir)}: {current_name} -> {ref}")
+
+print(f"Done — {fixed} file(s) updated.")
diff --git a/docs/gen_api_landing.py b/docs/gen_api_landing.py
@@ -0,0 +1,92 @@
+#!/usr/bin/env python3
+"""Generate API landing pages for pre_process, simulation, and post_process.
+
+Usage: python3 gen_api_landing.py [source_dir]
+  source_dir defaults to current directory.
+
+Scans src/{target}/*.fpp and src/common/*.fpp to produce module tables
+in docs/{target}/readme.md. Intro text is defined below per target.
+"""
+
+import sys
+from pathlib import Path
+
-
+from typing import List
-
+from typing import List
+src_dir = Path(sys.argv[1]) if len(sys.argv) > 1 else Path(".")
+
+TARGETS = {
+    "pre_process": {
+        "title": "MFC Pre-Process",
+        "intro": (
+            "The pre-process component generates initial conditions and "
+            "computational meshes for MFC simulations. It supports patch-based "
+            "geometry construction, multi-component material initialization, "
+            "and immersed boundary geometry."
+        ),
+        "siblings": [("Simulation", "simulation"), ("Post-Process", "post_process")],
+    },
+    "simulation": {
+        "title": "MFC Simulation",
+        "intro": (
+            "The simulation component is the core flow solver. It advances the "
+            "governing equations in time using high-order finite-volume methods "
+            "on structured grids with GPU acceleration via OpenACC/OpenMP offloading."
+        ),
+        "siblings": [("Pre-Process", "pre_process"), ("Post-Process", "post_process")],
+    },
+    "post_process": {
+        "title": "MFC Post-Process",
+        "intro": (
+            "The post-process component reads raw simulation output and computes "
+            "derived quantities for visualization. It produces silo/HDF5 files "
+            "compatible with VisIt, ParaView, and other visualization tools."
+        ),
+        "siblings": [("Pre-Process", "pre_process"), ("Simulation", "simulation")],
+    },
+}
+
+
+def get_modules(directory: Path) -> list[str]:
-def get_modules(directory: Path) -> list[str]:
+def get_modules(directory: Path) -> List[str]:
-def get_modules(directory: Path) -> list[str]:
+def get_modules(directory: Path) -> List[str]:
+    """Return sorted list of module names (m_*) from .fpp files."""
+    return sorted(
+        f.stem for f in directory.glob("m_*.fpp")
+    )
-    """Return sorted list of module names (m_*) from .fpp files."""
-    return sorted(
-        f.stem for f in directory.glob("m_*.fpp")
-    )
+    """Return sorted list of module names (m_*) from .fpp and .f90 files."""
+    modules: set[str] = set()
+    for pattern in ("m_*.fpp", "m_*.f90"):
+        for f in directory.glob(pattern):
+            modules.add(f.stem)
+    return sorted(modules)
-    """Return sorted list of module names (m_*) from .fpp files."""
-    return sorted(
-        f.stem for f in directory.glob("m_*.fpp")
-    )
+    """Return sorted list of module names (m_*) from .fpp and .f90 files."""
+    modules: set[str] = set()
+    for pattern in ("m_*.fpp", "m_*.f90"):
+        for f in directory.glob(pattern):
+            modules.add(f.stem)
+    return sorted(modules)
+
+
+for target, info in TARGETS.items():
+    target_modules = get_modules(src_dir / "src" / target)
+    common_modules = get_modules(src_dir / "src" / "common")
+
+    out = src_dir / "docs" / target / "readme.md"
+
+    lines = [
+        f"@mainpage {info['title']}",
+        "",
+        info["intro"],
+        "",
+        "## Modules",
+        "",
+    ]
+
+    if target_modules:
+        lines.append(f"### {info['title'].split()[-1]}")
+        lines.append("")
+        for m in target_modules:
+            lines.append(f"- @ref {m.lower()} \"{m}\"")
+        lines.append("")
+
+    if common_modules:
+        lines.append("### Common (shared)")
+        lines.append("")
+        for m in common_modules:
+            lines.append(f"- @ref {m.lower()} \"{m}\"")
+        lines.append("")
+
+    lines.append("## See Also")
+    lines.append("")
+    lines.append("- [Home & User Guide](../documentation/index.html)")
+    for label, sib in info["siblings"]:
+        lines.append(f"- [{label} API](../{sib}/index.html)")
+    lines.append("")
+
+    out.write_text("\n".join(lines))
-    out.write_text("\n".join(lines))
+    out.parent.mkdir(parents=True, exist_ok=True)
-    out.write_text("\n".join(lines))
+    out.parent.mkdir(parents=True, exist_ok=True)
+    print(f"Generated {out}")
diff --git a/docs/index.html b/docs/index.html
@@ -172,7 +172,7 @@
                 </div>
             </div>
             <div class="flex mx-auto">
-                <div class="justify-center grid grid-cols-2 sm:grid-cols-3 lg:grid-cols-6 gap-x-4 md:gap-x-8 text-md md:text-xl text-center text-white font-medium">
+                <div class="justify-center grid grid-cols-2 sm:grid-cols-3 lg:grid-cols-7 gap-x-4 md:gap-x-8 text-md md:text-xl text-center text-white font-medium">
                     <a class="px-4 flex flex-row items-center py-4 border-b-2 hover:border-amber-400" href="https://github.com/MFlowCode/MFC">
                         <i class="pr-4 fa-brands fa-github"></i>
                         <span class="flex-1">GitHub</span>
@@ -192,6 +192,10 @@
                         <i class="pr-4 fa-solid fa-book"></i>
                         <span class="flex-1">Documentation</span>
                     </a>
+                    <a class="px-4 flex flex-row items-center py-4 border-b-2 hover:border-amber-400" href="simulation/index.html">
+                        <i class="pr-4 fa-solid fa-code"></i>
+                        <span class="flex-1">API</span>
+                    </a>
                     <a class="px-4 flex flex-row items-center py-4 border-b-2 hover:border-amber-400" href="documentation/papers.html">
                         <i class="pr-4 fa-solid fa-newspaper"></i>
                         <span class="flex-1">Papers</span>

diff --git a/docs/post_process/readme.md b/docs/post_process/readme.md
@@ -1,8 +1,35 @@
-# MFC Post-Process
+@mainpage MFC Post-Process
 
-This documentation page is for MFC Post-Process. You can also visit:
-- [Home & User Guide](../documentation/)
-- [Pre Process](../pre_process/)
-- [Simulation](../simulation/)
+The post-process component reads raw simulation output and computes derived quantities for visualization. It produces silo/HDF5 files compatible with VisIt, ParaView, and other visualization tools.
 
-If you are viewing this page Github, please visit [our website](https://mflowcode.github.io/post_process) for the doxygen-generated documentation of this code.
+## Modules
+
+### Post-Process
+
+- @ref m_checker "m_checker"
+- @ref m_data_output "m_data_output"
+- @ref m_derived_variables "m_derived_variables"
+- @ref m_global_parameters "m_global_parameters"
+- @ref m_mpi_proxy "m_mpi_proxy"
+- @ref m_start_up "m_start_up"
+
+### Common (shared)
+
+- @ref m_boundary_common "m_boundary_common"
+- @ref m_checker_common "m_checker_common"
+- @ref m_chemistry "m_chemistry"
+- @ref m_constants "m_constants"
+- @ref m_derived_types "m_derived_types"
+- @ref m_finite_differences "m_finite_differences"
+- @ref m_helper "m_helper"
+- @ref m_helper_basic "m_helper_basic"
+- @ref m_model "m_model"
+- @ref m_mpi_common "m_mpi_common"
+- @ref m_phase_change "m_phase_change"
+- @ref m_variables_conversion "m_variables_conversion"
+
+## See Also
+
+- [Home & User Guide](../documentation/index.html)
+- [Pre-Process API](../pre_process/index.html)
+- [Simulation API](../simulation/index.html)
diff --git a/docs/pre_process/readme.md b/docs/pre_process/readme.md
@@ -1,8 +1,42 @@
-# MFC Pre-Process
+@mainpage MFC Pre-Process
 
-This documentation page is for MFC Pre-Process. You can also visit:
-- [Home & User Guide](../documentation/)
-- [Simulation](../simulation/)
-- [Post Process](../post_process/)
+The pre-process component generates initial conditions and computational meshes for MFC simulations. It supports patch-based geometry construction, multi-component material initialization, and immersed boundary geometry.
 
-If you are viewing this page Github, please visit [our website](https://mflowcode.github.io/pre_process) for the doxygen-generated documentation of this code.
+## Modules
+
+### Pre-Process
+
+- @ref m_assign_variables "m_assign_variables"
+- @ref m_boundary_conditions "m_boundary_conditions"
+- @ref m_check_ib_patches "m_check_ib_patches"
+- @ref m_check_patches "m_check_patches"
+- @ref m_checker "m_checker"
+- @ref m_data_output "m_data_output"
+- @ref m_global_parameters "m_global_parameters"
+- @ref m_icpp_patches "m_icpp_patches"
+- @ref m_initial_condition "m_initial_condition"
+- @ref m_mpi_proxy "m_mpi_proxy"
+- @ref m_perturbation "m_perturbation"
+- @ref m_simplex_noise "m_simplex_noise"
+- @ref m_start_up "m_start_up"
+
+### Common (shared)
+
+- @ref m_boundary_common "m_boundary_common"
+- @ref m_checker_common "m_checker_common"
+- @ref m_chemistry "m_chemistry"
+- @ref m_constants "m_constants"
+- @ref m_derived_types "m_derived_types"
+- @ref m_finite_differences "m_finite_differences"
+- @ref m_helper "m_helper"
+- @ref m_helper_basic "m_helper_basic"
+- @ref m_model "m_model"
+- @ref m_mpi_common "m_mpi_common"
+- @ref m_phase_change "m_phase_change"
+- @ref m_variables_conversion "m_variables_conversion"
+
+## See Also
+
+- [Home & User Guide](../documentation/index.html)
+- [Simulation API](../simulation/index.html)
+- [Post-Process API](../post_process/index.html)