Fixes to key errors in examples jupyter notebook and plot proc

examples/examples.ipynb

@@ -33,7 +33,7 @@
     "PROJ_DIR = Path.cwd().parent\n",
     "\n",
     "\n",
-    "def copy_to_temp_dir(input_rel):\n",
+    "def copy_to_temp_dir(input_rel, config=None):\n",
     "    \"\"\"Copy an input file to a new temp dir and return its new path.\n",
     "\n",
     "    The new TemporaryDirectory object is returned to avoid destruction of the\n",
@@ -61,6 +61,19 @@
     "    copy(input_abs_path, temp_dir_path)\n",
     "    temp_input_path = temp_dir_path / input_abs_path.name\n",
     "\n",
+    "    if config is not None:\n",
+    "        config_rel_path = Path(config)\n",
+    "        config_abs_path = PROJ_DIR / config_rel_path\n",
+    "        try:\n",
+    "            assert config_abs_path.exists()\n",
+    "        except AssertionError as err:\n",
+    "            raise FileNotFoundError(\"Config file doesn't exist.\") from err\n",
+    "\n",
+    "        copy(config_abs_path, temp_dir_path)\n",
+    "        temp_config_path = temp_dir_path / config_abs_path.name\n",
+    "\n",
+    "        return temp_dir, temp_input_path, temp_config_path\n",
+    "\n",
     "    return temp_dir, temp_input_path"
    ]
   },
@@ -86,10 +99,19 @@
     "\n",
     "# Define input file name relative to project dir, then copy to temp dir\n",
     "script_dir = Path(\"__file__\").parent.resolve()\n",
+    "# standard run of conventional tokamak from data files\n",
     "input_rel = script_dir / \"data/large_tokamak_IN.DAT\"\n",
-    "\n",
     "temp_dir, temp_input_path = copy_to_temp_dir(input_rel)\n",
     "\n",
+    "# # alternative run of ST from regression files\n",
+    "# input_rel = script_dir / \"../tests/regression/input_files/st_regression.IN.DAT\"\n",
+    "# temp_dir, temp_input_path = copy_to_temp_dir(input_rel)\n",
+    "\n",
+    "# # alternative run of stellarator from regression files with associated config\n",
+    "# input_rel = script_dir / \"../tests/regression/input_files/stellarator_helias_eval.IN.DAT\"\n",
+    "# config = script_dir / \"../tests/regression/input_files/stellarator_helias_eval.stella_conf.json\"\n",
+    "# temp_dir, temp_input_path, temp_config = copy_to_temp_dir(input_rel, config)\n",
+    "\n",
     "# Run process on an input file in a temporary directory\n",
     "single_run = SingleRun(str(temp_input_path))\n",
     "single_run.run()"
@@ -253,7 +275,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "env",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -270,5 +292,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

process/build.py

@@ -802,7 +802,6 @@ def calculate_vertical_build(self, output: bool) -> None:
                 self.outfile,
                 "\n*Cryostat roof allowance includes uppermost PF coil and outer thermal shield.\n*Cryostat floor allowance includes lowermost PF coil, outer thermal shield and gravity support.",
             )
-
         # Output the cdivertor geometry
         divht = self.divgeom(output)
         # Issue #481 Remove build_variables.vgaptf
@@ -864,6 +863,14 @@ def divgeom(self, output: bool):
         TART option: Peng SOFT paper
         """
         if physics_variables.itart == 1:
+            if output:
+                po.ovarrf(
+                    self.outfile,
+                    "TF coil vertical offset (m)",
+                    "(dz_tf_plasma_centre_offset)",
+                    build_variables.dz_tf_plasma_centre_offset,
+                    "OP ",
+                )
             return 1.75e0 * physics_variables.rminor
         #  Conventional tokamak divertor model
         #  options for seperate upper and lower physics_variables.triangularity
@@ -985,7 +992,6 @@ def divgeom(self, output: bool):
         )
 
         divht = max(zplti, zplto) - min(zplbo, zplbi)
-
         if output:
             if physics_variables.n_divertors == 1:
                 po.oheadr(self.outfile, "Divertor build and plasma position")

process/geometry/pfcoil_geometry.py

@@ -12,9 +12,6 @@ def pfcoil_geometry(
     coils_z: list[float],
     coils_dr: list[float],
     coils_dz: list[float],
-    dr_bore: float,
-    dr_cs: float,
-    ohdz: float,
 ) -> tuple[np.ndarray, np.ndarray, RectangleGeometry]:
     """Calculates radial and vertical distances for the geometry of the pf coils and central coil
 
@@ -26,12 +23,6 @@ def pfcoil_geometry(
     :type coils_dr: List[float]
     :param coils_dz: list of pf coil vertical thicknesses
     :type coils_dz: List[float]
-    :param dr_bore: central solenoid inboard radius
-    :type dr_bore: float
-    :param dr_cs: central solenoid thickness
-    :type dr_cs: float
-    :param ohdz: central solenoid vertical thickness
-    :type ohdz: float
     :return: tuple containing radial and vertical coordinates for pf coils, and dataclass returning coordinates representing a rectangular geometry used to plot the central coil
     :rtype: Tuple[np.ndarray, np.ndarray, RectangleGeometry]
     """
@@ -44,9 +35,25 @@ def pfcoil_geometry(
         r_2 = float(coils_r[i]) + 0.5 * float(coils_dr[i])
         r_points.append([r_1, r_1, r_2, r_2, r_1])
         z_points.append([z_1, z_2, z_2, z_1, z_1])
+    return r_points, z_points
+
+
+def cs_geometry(
+    dr_bore: float,
+    dr_cs: float,
+    ohdz: float,
+) -> RectangleGeometry:
+    """Calculates radial and vertical distances for the geometry of the central coil
 
-    central_coil = RectangleGeometry(
+    :param dr_bore: central solenoid inboard radius
+    :type dr_bore: float
+    :param dr_cs: central solenoid thickness
+    :type dr_cs: float
+    :param ohdz: central solenoid vertical thickness
+    :type ohdz: float
+    :return: Dataclass returning coordinates representing a rectangular geometry used to plot the central coil
+    :rtype: RectangleGeometry
+    """
+    return RectangleGeometry(
         anchor_x=dr_bore, anchor_z=(-ohdz / 2), width=dr_cs, height=ohdz
     )
-
-    return r_points, z_points, central_coil