aligned with the new material structure of libalea

Author: giovanni-mariano

csrc/libalea

@@ -641,21 +641,50 @@ static PyObject* AleaTHORSystem_get_surface_nodes(AleaTHORSystemObject* self, Py
 static PyObject* AleaTHORSystem_add_cell(AleaTHORSystemObject* self, PyObject* args, PyObject* kwds) {
     int cell_id;
     unsigned long root_node;
-    int material_id = 0;
+    int material_index = -1;  /* ALEA_MATERIAL_VOID */
     double density = 0.0;
     int universe_id = 0;
-    static char* kwlist[] = {"cell_id", "root_node", "material_id", "density", "universe_id", NULL};
+    static char* kwlist[] = {"cell_id", "root_node", "material_index", "density", "universe_id", NULL};
 
     if (!PyArg_ParseTupleAndKeywords(args, kwds, "ik|idi", kwlist,
-                                     &cell_id, &root_node, &material_id, &density, &universe_id)) {
+                                     &cell_id, &root_node, &material_index, &density, &universe_id)) {
         return NULL;
     }
     if (!self->sys) { PyErr_SetString(PyExc_RuntimeError, "System not initialized"); return NULL; }
 
-    int idx = alea_add_cell(self->sys, cell_id, (alea_node_id_t)root_node, material_id, density, universe_id);
+    int idx = alea_add_cell(self->sys, cell_id, (alea_node_id_t)root_node, material_index, density, universe_id);
     if (idx < 0) {
         PyErr_SetString(PyExc_RuntimeError, "Failed to add cell");
         return NULL;
     }
     return PyLong_FromLong(idx);
 }
+
+/* ============================================================================
+ * AleaTHORSystem Methods - Material Registration
+ * ============================================================================ */
+
+static PyObject* AleaTHORSystem_add_material(AleaTHORSystemObject* self, PyObject* args) {
+    int material_id;
+    if (!PyArg_ParseTuple(args, "i", &material_id)) return NULL;
+    if (!self->sys) { PyErr_SetString(PyExc_RuntimeError, "System not initialized"); return NULL; }
+
+    int idx = alea_add_material(self->sys, material_id);
+    if (idx < 0) {
+        PyErr_SetString(PyExc_RuntimeError, "Failed to add material");
+        return NULL;
+    }
+    return PyLong_FromLong(idx);
+}
+
+static PyObject* AleaTHORSystem_find_material_by_id(AleaTHORSystemObject* self, PyObject* args) {
+    int material_id;
+    if (!PyArg_ParseTuple(args, "i", &material_id)) return NULL;
+    if (!self->sys) { PyErr_SetString(PyExc_RuntimeError, "System not initialized"); return NULL; }
+
+    int idx = alea_find_material_by_id(self->sys, material_id);
+    if (idx < 0) {
+        Py_RETURN_NONE;
+    }
+    return PyLong_FromLong(idx);
+}

src/aleathor/_binding/_bind_geometry.c

@@ -358,7 +358,14 @@ static PyMethodDef AleaTHORSystem_methods[] = {
     /* Cell registration */
     {"add_cell", (PyCFunction)AleaTHORSystem_add_cell,
      METH_VARARGS | METH_KEYWORDS,
-     "add_cell(cell_id, root_node, material_id=0, density=0.0, universe_id=0) -> index"},
+     "add_cell(cell_id, root_node, material_index=-1, density=0.0, universe_id=0) -> index\n\n"
+     "Register a cell. material_index is a material index from add_material(), or -1 for void."},
+
+    /* Material registration */
+    {"add_material", (PyCFunction)AleaTHORSystem_add_material, METH_VARARGS,
+     "add_material(material_id) -> index\n\nRegister a material by MCNP ID. Returns material index."},
+    {"find_material_by_id", (PyCFunction)AleaTHORSystem_find_material_by_id, METH_VARARGS,
+     "find_material_by_id(material_id) -> index or None\n\nFind material index by MCNP ID."},
 
     /* Export */
     {"export_mcnp", (PyCFunction)AleaTHORSystem_export_mcnp,

src/aleathor/_binding/aleathor_binding.c

@@ -172,14 +172,22 @@ def _rebuild_if_needed(self):
         self._sys.reset()
         self._halfspace_node_cache.clear()
 
+        # Register materials in C system and build id→index map
+        material_index_map = {}  # MCNP material_id → C material_index
+        for cell in self._cells.values():
+            mat_id = cell.material
+            if mat_id != 0 and mat_id not in material_index_map:
+                material_index_map[mat_id] = self._sys.add_material(mat_id)
+
         # Build cells
         for cell in self._cells.values():
             node_id = cell.region._to_csg(self)
             # C expects signed density: negative = g/cm³, positive = atoms/b-cm
             signed_density = -cell.density if cell.density_unit == "g/cm3" else cell.density
+            mat_index = material_index_map.get(cell.material, -1)  # -1 = void
             self._sys.add_cell(
                 cell.id, node_id,
-                material_id=cell.material,
+                material_index=mat_index,
                 density=signed_density,
                 universe_id=cell.universe
             )