fix dropped 1D nodes for 3D sim

Author: adamchengtkc

warmth/build.py

@@ -716,6 +716,7 @@ def _create_nodes(self, all_sediments_grid: List[List[List]]):
                 for sed_grid in all_sediments_grid:
                     node_sed.append(sed_grid[index[0]][index[1]])
                 if all(node_sed) is False:
+                    self.nodes[index[0]][index[1]] = False
                     logger.warning(f"dropping node {index}. One of the layer has no depth value")
                 else:
                     top = np.empty(0)