Add chemistry support to MFC with Spack compatibility

This commit enables thermochemistry in MFC via a new MFC_CHEMISTRY CMake
option and adds full Spack package support for the chemistry variant.

Changes:

CMake (CMakeLists.txt):
- Add MFC_CHEMISTRY option (default OFF) to enable chemistry
- Add MFC_MECH_FILE cache variable for specifying Cantera mechanism files
- Pass chemistry flag to Fypp preprocessor as -D chemistry=True/False
- Add Python3 requirement when MFC_CHEMISTRY=ON
- Generate m_thermochem.f90 via gen_thermochem.py during build

Python (toolchain/scripts/gen_thermochem.py):
- New script to generate Fortran chemistry module using Pyrometheus and Cantera
- Called by CMake when MFC_CHEMISTRY=ON
- Supports custom mechanism files via --mech argument

Fortran (src/common/m_derived_types.fpp):
- Guard m_thermochem import with #:if chemistry
- Move fallback num_species declaration after implicit none
- Fixes "IMPLICIT NONE after data declaration" error

Build system (toolchain/mfc/build.py):
- Auto-enable MFC_CHEMISTRY=ON when case requests chemistry
- Pass MFC_MECH_FILE when cantera_file is specified in case

Spack (packaging/spack/package.py):
- Add chemistry variant (default False)
- Add cantera+python dependency when +chemistry
- Vendor Pyrometheus 1.0.5 as a resource
- Pass MFC_CHEMISTRY to CMake via cmake_args
- Add Pyrometheus to PYTHONPATH in setup_build_environment

Documentation (packaging/spack/SPACK.md):
- Document chemistry variant and usage
- List chemistry dependencies

This preserves backward compatibility: existing builds work unchanged
(chemistry OFF by default), while enabling reproducible chemistry builds
via Spack with "spack install mfc+chemistry".

Author: sbryngelson

CMakeLists.txt

@@ -95,6 +95,11 @@ endif()
 
 find_program(FYPP_EXE fypp REQUIRED)
 
+# Python3 is required for chemistry code generation when MFC_CHEMISTRY is ON
+if (MFC_CHEMISTRY)
+    find_package(Python3 REQUIRED COMPONENTS Interpreter)
+endif()
+
 
 # Miscellaneous Configuration:
 # *  Explicitly link to -ldl (or system equivalent)
@@ -372,7 +377,7 @@ macro(HANDLE_SOURCES target useCommon)
                                  -D MFC_${${target}_UPPER}
                                  -D MFC_COMPILER="${CMAKE_Fortran_COMPILER_ID}"
                                  -D MFC_CASE_OPTIMIZATION=False
-                                 -D chemistry=False
+                                 -D chemistry=${_chem_str}
                                  --line-numbering
                                  --no-folding
 								 --line-length=999
@@ -385,6 +390,27 @@ macro(HANDLE_SOURCES target useCommon)
 
         list(APPEND ${target}_SRCs ${f90})
     endforeach()
+
+    # Generate m_thermochem.f90 when chemistry is enabled
+    if (MFC_CHEMISTRY)
+        file(MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/modules/${target}")
+
+        add_custom_command(
+            OUTPUT  "${CMAKE_BINARY_DIR}/modules/${target}/m_thermochem.f90"
+            COMMAND ${CMAKE_COMMAND} -E make_directory "${CMAKE_BINARY_DIR}/modules/${target}"
+            COMMAND ${Python3_EXECUTABLE}
+                    "${CMAKE_SOURCE_DIR}/toolchain/scripts/gen_thermochem.py"
+                    --module m_thermochem
+                    --out    "${CMAKE_BINARY_DIR}/modules/${target}/m_thermochem.f90"
+                    --mech   "${MFC_MECH_FILE}"
+            DEPENDS "${CMAKE_SOURCE_DIR}/toolchain/scripts/gen_thermochem.py"
+            COMMENT "Generating m_thermochem.f90 via Pyrometheus/Cantera for ${target}"
+            VERBATIM
+        )
+
+        list(APPEND ${target}_SRCs
+             "${CMAKE_BINARY_DIR}/modules/${target}/m_thermochem.f90")
+    endif()
 endmacro()
 
 

packaging/spack/SPACK.md

@@ -88,6 +88,12 @@ spack install mfc~post_process    # Skip post_process binary
 ```
 Controls whether the post-processing tool is built.
 
+#### Chemistry (default: disabled)
+```
+spack install mfc+chemistry
+```
+Enables thermochemistry support by generating the `m_thermochem.f90` module using Pyrometheus and Cantera during the build. When enabled, MFC can perform reactive flow simulations with detailed chemical kinetics. Requires `cantera+python` and vendors Pyrometheus automatically.
+
 ### Dependencies
 
 Build-time dependencies (required during compilation):
@@ -103,6 +109,8 @@ Optional dependencies (variant-controlled):
 - mpi - Message Passing Interface (when +mpi)
 - silo - Silo data format with HDF5 support (when +post_process)
 - hdf5 - HDF5 data format (transitive dependency via Silo when +post_process)
+- cantera+python - Thermochemical kinetics library (when +chemistry)
+- pyrometheus - Fortran code generator for chemistry (vendored automatically when +chemistry)
 - cuda - NVIDIA CUDA toolkit (when +openacc or +openmp with NVHPC)
 - hip - AMD ROCm HIP (when +openacc or +openmp with Cray)
 

packaging/spack/package.py

@@ -36,13 +36,24 @@ class Mfc(CMakePackage):
         description="Floating point precision",
     )
     variant("post_process", default=True, description="Build post-processing tool")
+    variant("chemistry", default=False, description="Enable thermochemistry via Pyrometheus/Cantera")
 
     # Required dependencies
     depends_on("cmake@3.20:", type="build")
     depends_on("py-fypp", type="build")
     depends_on("python@3:", type="build")
-    # Note: py-cantera is not yet available in Spack builtin repo
-    # Will add when chemistry variant is implemented
+
+    # Chemistry dependencies
+    depends_on("cantera+python", type="build", when="+chemistry")
+    # Note: py-pyrometheus may not be in Spack yet; will be added to PYTHONPATH via resource
+    resource(
+        name="pyrometheus",
+        url="https://files.pythonhosted.org/packages/21/77/1e48bef25dfef5d9e35c1ab3a3a2ea1c82adb59aceb82b18d13b3d6c8a2b/pyrometheus-1.0.5.tar.gz",
+        sha256="a572ab6db954f4a850d1292bb1ef6d6055916784a894d149d657996fa98d0367",
+        when="+chemistry",
+        placement="pydeps/pyrometheus",
+        expand=True
+    )
 
     # Runtime dependencies
     depends_on("fftw@3:", when="~mpi")
@@ -80,6 +91,7 @@ def cmake_args(self):
             self.define("MFC_PRE_PROCESS", True),
             self.define("MFC_SIMULATION", True),
             self.define_from_variant("MFC_POST_PROCESS", "post_process"),
+            self.define_from_variant("MFC_CHEMISTRY", "chemistry"),
         ]
 
         if self.spec.variants["precision"].value == "single":
@@ -90,3 +102,7 @@ def cmake_args(self):
     def setup_build_environment(self, env):
         # Fypp is required for preprocessing
         env.prepend_path("PATH", self.spec["py-fypp"].prefix.bin)
+        
+        # Make vendored Pyrometheus importable when chemistry is enabled
+        if "+chemistry" in self.spec:
+            env.prepend_path("PYTHONPATH", join_path(self.stage.source_path, "pydeps", "pyrometheus"))

src/common/m_derived_types.fpp

@@ -11,10 +11,16 @@ module m_derived_types
     use m_constants  !< Constants
 
     use m_precision_select
+#:if chemistry
     use m_thermochem, only: num_species
+#:endif
 
     implicit none
 
+#:if not chemistry
+    integer, parameter :: num_species = 1
+#:endif
+
     !> Derived type adding the field position (fp) as an attribute
     type field_position
         real(stp), allocatable, dimension(:, :, :) :: fp !< Field position

toolchain/mfc/build.py

@@ -154,6 +154,14 @@ def configure(self, case: Case):
             flags.append(f"-DMFC_Unified={'ON' if ARG('unified') else 'OFF'}")
             flags.append(f"-DMFC_Fastmath={'ON' if ARG('fastmath') else 'OFF'}")
 
+            # Enable chemistry flags when requested by the case
+            if case.params.get('chemistry', 'F') == 'T':
+                flags.append("-DMFC_CHEMISTRY=ON")
+                # Pass mechanism if provided; otherwise Cantera defaults (e.g., h2o2.yaml)
+                mech = case.params.get("cantera_file", "")
+                if mech:
+                    flags.append(f"-DMFC_MECH_FILE={mech}")
+
         command = ["cmake"] + flags + ["-S", cmake_dirpath, "-B", build_dirpath]
 
         delete_directory(build_dirpath)

toolchain/scripts/gen_thermochem.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+"""
+Generate m_thermochem.f90 module using Pyrometheus and Cantera.
+
+This script is called by CMake when MFC_CHEMISTRY=ON to generate
+the Fortran thermochemistry module from a Cantera mechanism file.
+"""
+import argparse
+import sys
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Generate Fortran thermochemistry module via Pyrometheus"
+    )
+    parser.add_argument("--module", required=True, help="Module name (e.g., m_thermochem)")
+    parser.add_argument("--out", required=True, help="Output Fortran file path")
+    parser.add_argument(
+        "--mech",
+        default="h2o2.yaml",
+        help="Cantera mechanism file (YAML). Defaults to h2o2.yaml"
+    )
+    args = parser.parse_args()
+
+    try:
+        import cantera as ct
+    except ImportError:
+        print("ERROR: cantera Python package is required for chemistry.", file=sys.stderr)
+        print("Install it with: pip install cantera", file=sys.stderr)
+        sys.exit(1)
+
+    try:
+        import pyrometheus as pyro
+    except ImportError:
+        print("ERROR: pyrometheus Python package is required for chemistry.", file=sys.stderr)
+        print("Install it with: pip install pyrometheus", file=sys.stderr)
+        sys.exit(1)
+
+    # Load the Cantera solution
+    # If no mechanism file is specified or it's empty, use Cantera's default h2o2.yaml
+    mech_file = args.mech if args.mech else "h2o2.yaml"
+    
+    try:
+        sol = ct.Solution(mech_file)
+    except Exception as e:
+        print(f"ERROR: Failed to load Cantera mechanism '{mech_file}': {e}", file=sys.stderr)
+        sys.exit(1)
+
+    # Generate Fortran code using Pyrometheus
+    try:
+        code = pyro.FortranCodeGenerator().generate(args.module, sol)
+    except Exception as e:
+        print(f"ERROR: Failed to generate Fortran code: {e}", file=sys.stderr)
+        sys.exit(1)
+
+    # Write to output file
+    try:
+        with open(args.out, 'w') as f:
+            f.write(code)
+        print(f"Successfully generated {args.out} from {mech_file}")
+    except Exception as e:
+        print(f"ERROR: Failed to write output file '{args.out}': {e}", file=sys.stderr)
+        sys.exit(1)
+
+if __name__ == "__main__":
+    main()
+