xslope 0.1.2__py3-none-any.whl

xslope/mesh.py

@@ -0,0 +1,2719 @@
+# Copyright 2025 Norman L. Jones
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import numpy as np
+from scipy.sparse import coo_matrix
+from scipy.sparse.csgraph import reverse_cuthill_mckee
+
+# Lazy import gmsh - only needed for mesh generation functions
+_gmsh = None
+def _get_gmsh():
+    global _gmsh
+    if _gmsh is None:
+        try:
+            import gmsh
+            _gmsh = gmsh
+        except (ImportError, OSError) as e:
+            raise ImportError(
+                "gmsh is required for mesh generation but could not be imported. "
+                "If you only need limit equilibrium analysis, you can ignore this. "
+                "To use FEM features, install gmsh: pip install gmsh\n"
+                f"Original error: {e}"
+            ) from e
+    return _gmsh
+
+
+
+def build_mesh_from_polygons(polygons, target_size, element_type='tri3', lines=None, debug=False, mesh_params=None, target_size_1d=None):
+    """
+    Build a finite element mesh with material regions using Gmsh.
+    Fixed version that properly handles shared boundaries between polygons.
+    
+    Parameters:
+        polygons     : List of lists of (x, y) tuples defining material boundaries
+        target_size  : Desired element size
+        element_type : 'tri3' (3-node triangles), 'tri6' (6-node triangles), 
+                      'quad4' (4-node quadrilaterals), 'quad8' (8-node quadrilaterals),
+                      'quad9' (9-node quadrilaterals)
+        lines        : Optional list of lines, each defined by list of (x, y) tuples for 1D elements
+        debug        : Enable debug output
+        mesh_params  : Optional dictionary of GMSH meshing parameters to override defaults
+        target_size_1d : Optional target size for 1D elements (default None, which is set to target_size if None)
+
+    Returns:
+        mesh dict containing:
+        nodes        : np.ndarray of node coordinates (n_nodes, 2)
+        elements     : np.ndarray of 2D element vertex indices (n_elements, 9) - unused nodes set to 0
+        element_types: np.ndarray indicating number of nodes per 2D element (3, 4, 6, 8, or 9)
+        element_materials: np.ndarray of material ID for each 2D element
+        
+        If lines is provided, also includes:
+        elements_1d  : np.ndarray of 1D element vertex indices (n_elements_1d, 3) - unused nodes set to 0
+        element_types_1d: np.ndarray indicating element type (2 for linear, 3 for quadratic)
+        element_materials_1d: np.ndarray of material ID for each 1D element (line index)
+    """
+    gmsh = _get_gmsh()
+    from collections import defaultdict
+
+    # Set default target_size_1d if None
+    if target_size_1d is None:
+        target_size_1d = target_size
+        if debug:
+            print(f"Using default target_size_1d = target_size = {target_size_1d}")
+
+    # build a list of region ids (list of material IDs - one per polygon)
+    region_ids = [i for i in range(len(polygons))]
+
+    if element_type not in ['tri3', 'tri6', 'quad4', 'quad8', 'quad9']:
+        raise ValueError("element_type must be 'tri3', 'tri6', 'quad4', 'quad8', or 'quad9'")
+
+    # Determine if we need quadratic elements - but always generate linear first
+    quadratic = element_type in ['tri6', 'quad8', 'quad9']
+    
+    # For quadratic elements, always start with linear base element
+    if quadratic:
+        if element_type == 'tri6':
+            base_element_type = 'tri3'
+        elif element_type in ['quad8', 'quad9']:
+            base_element_type = 'quad4'
+        if debug:
+            print(f"Quadratic element '{element_type}' requested: generating '{base_element_type}' first, then post-processing")
+    else:
+        base_element_type = element_type
+    
+    # Adjust target_size for quads to compensate for recombination creating finer meshes
+    if element_type.startswith('quad'):
+        # Different adjustment factors based on meshing parameters
+        if mesh_params and 'size_factor' in mesh_params:
+            size_factor = mesh_params['size_factor']
+        else:
+            # Default size factors for different approaches
+            if mesh_params and mesh_params.get("Mesh.RecombinationAlgorithm") == 0:
+                size_factor = 1.2  # Fast algorithm needs less adjustment
+            elif mesh_params and mesh_params.get("Mesh.RecombineOptimizeTopology", 0) > 50:
+                size_factor = 1.8  # High optimization creates more elements
+            else:
+                size_factor = 1.4  # Default
+        
+        adjusted_target_size = target_size * size_factor
+        if debug:
+            print(f"Adjusted target size for quads: {target_size} -> {adjusted_target_size} (factor: {size_factor})")
+    else:
+        adjusted_target_size = target_size
+
+    gmsh.initialize()
+    gmsh.option.setNumber("General.Verbosity", 4)  # Reduce verbosity
+    gmsh.model.add("multi_region_mesh")
+    
+    # Global point map to ensure shared boundaries use the same points
+    point_map = {}  # maps (x, y) to Gmsh point tag
+    
+    # Track all unique edges and their usage
+    edge_map = {}  # maps (pt1, pt2) tuple to line tag
+    edge_usage = defaultdict(list)  # maps edge to list of (region_id, orientation)
+    
+    def add_point(x, y, size_override=None):
+        key = (x, y)
+        if key not in point_map:
+            point_size = size_override if size_override is not None else adjusted_target_size
+            tag = gmsh.model.geo.addPoint(x, y, 0, point_size)
+            point_map[key] = tag
+        return point_map[key]
+
+    def get_edge_key(pt1, pt2):
+        """Get canonical edge key (always smaller point first)"""
+        return (min(pt1, pt2), max(pt1, pt2))
+
+    # First pass: Create all points and identify short edges
+    polygon_data = []
+    short_edge_points = set()  # Points that are endpoints of short edges
+    
+    # Pre-pass to identify short edges - improved logic
+    for idx, (poly_pts, region_id) in enumerate(zip(polygons, region_ids)):
+        poly_pts_clean = remove_duplicate_endpoint(list(poly_pts))
+        for i in range(len(poly_pts_clean)):
+            p1 = poly_pts_clean[i]
+            p2 = poly_pts_clean[(i + 1) % len(poly_pts_clean)]
+            edge_length = ((p2[0] - p1[0])**2 + (p2[1] - p1[1])**2)**0.5
+            
+            # Only mark as short edge if it's genuinely short AND not a major boundary
+            # Major boundaries should maintain consistent mesh sizing
+            is_major_boundary = False
+            
+            # Check if this edge is part of a major boundary (long horizontal or vertical edge)
+            if abs(p2[0] - p1[0]) > adjusted_target_size * 5:  # Long horizontal edge
+                is_major_boundary = True
+            elif abs(p2[1] - p1[1]) > adjusted_target_size * 5:  # Long vertical edge
+                is_major_boundary = True
+            
+            # Only apply short edge sizing if edge is genuinely short AND not a major boundary
+            if edge_length < adjusted_target_size and not is_major_boundary:
+                short_edge_points.add(p1)
+                short_edge_points.add(p2)
+                if debug:
+                    print(f"Short edge found: {p1} to {p2}, length={edge_length:.2f}")
+            elif debug and edge_length < adjusted_target_size:
+                print(f"Short edge ignored (major boundary): {p1} to {p2}, length={edge_length:.2f}")
+    
+    # Main pass: Create points with appropriate sizes
+    for idx, (poly_pts, region_id) in enumerate(zip(polygons, region_ids)):
+        poly_pts_clean = remove_duplicate_endpoint(list(poly_pts))  # make a copy
+        pt_tags = []
+        for x, y in poly_pts_clean:
+            # Use larger size for points on short edges to discourage subdivision
+            # But be more conservative about when to apply this
+            if (x, y) in short_edge_points:
+                point_size = adjusted_target_size * 2.0  # Reduced from 3.0 to 2.0
+                pt_tags.append(add_point(x, y, point_size))
+            else:
+                pt_tags.append(add_point(x, y))
+        
+        # Track edges for this polygon
+        edges = []
+        for i in range(len(pt_tags)):
+            pt1 = pt_tags[i]
+            pt2 = pt_tags[(i + 1) % len(pt_tags)]
+            
+            edge_key = get_edge_key(pt1, pt2)
+            
+            # Determine orientation: True if pt1 < pt2, False otherwise
+            forward = (pt1 < pt2)
+            
+            # Store edge usage
+            edge_usage[edge_key].append((region_id, forward))
+            edges.append((pt1, pt2, edge_key, forward))
+        
+        polygon_data.append({
+            'region_id': region_id,
+            'pt_tags': pt_tags,
+            'edges': edges
+        })
+
+    # Second pass: Create all unique lines and track short edges
+    short_edges = []  # Track short edges for later processing
+    for edge_key in edge_usage.keys():
+        pt1, pt2 = edge_key
+        line_tag = gmsh.model.geo.addLine(pt1, pt2)
+        edge_map[edge_key] = line_tag
+        
+        # Calculate edge length from point coordinates
+        pt1_coords = None
+        pt2_coords = None
+        for (x, y), tag in point_map.items():
+            if tag == pt1:
+                pt1_coords = (x, y)
+            if tag == pt2:
+                pt2_coords = (x, y)
+        
+        if pt1_coords and pt2_coords:
+            edge_length = ((pt2_coords[0] - pt1_coords[0])**2 + (pt2_coords[1] - pt1_coords[1])**2)**0.5
+            
+            # Add transfinite constraints for long boundary edges to ensure consistent mesh sizing
+            # This prevents the creation of overly coarse elements along major boundaries
+            if edge_length > adjusted_target_size * 3:  # Long edge
+                # Calculate how many elements should be along this edge
+                num_elements = max(3, int(edge_length / adjusted_target_size))
+                try:
+                    gmsh.model.geo.mesh.setTransfiniteCurve(line_tag, num_elements)
+                    if debug:
+                        print(f"Set transfinite constraint on long edge: {pt1_coords} to {pt2_coords}, length={edge_length:.2f}, num_elements={num_elements}")
+                except Exception as e:
+                    if debug:
+                        print(f"Warning: Could not set transfinite constraint on edge {pt1_coords} to {pt2_coords}: {e}")
+            
+            # Add transfinite constraints for short edges to prevent subdivision
+            # This forces GMSH to use exactly 2 nodes (start and end) for short edges
+            elif edge_length < adjusted_target_size:
+                try:
+                    gmsh.model.geo.mesh.setTransfiniteCurve(line_tag, 2)  # Exactly 2 nodes
+                    if debug:
+                        print(f"Set transfinite constraint on short edge: {pt1_coords} to {pt2_coords}, length={edge_length:.2f}, exactly 2 nodes")
+                except Exception as e:
+                    if debug:
+                        print(f"Warning: Could not set transfinite constraint on short edge {pt1_coords} to {pt2_coords}: {e}")
+            
+            # Short edges are now handled by point sizing, no need for transfinite curves
+
+    # Ensure all polygon points (including intersection points) are created as GMSH points
+    # The intersection points were already added to polygons in build_polygons(), 
+    # so we just need to ensure they exist as GMSH geometric entities
+    if lines is not None:
+        if debug:
+            print("Ensuring all polygon points (including intersections) are created as GMSH points...")
+        
+        # Collect all points from all polygons to ensure they exist in GMSH
+        all_polygon_points = set()
+        for poly_data in polygon_data:
+            pt_tags = poly_data['pt_tags']
+            for tag in pt_tags:
+                # Find the coordinates for this point tag
+                for (x, y), point_tag in point_map.items():
+                    if point_tag == tag:
+                        all_polygon_points.add((x, y))
+                        break
+        
+        # Create any missing GMSH points
+        for x, y in all_polygon_points:
+            key = (x, y)
+            if key not in point_map:
+                pt_tag = gmsh.model.geo.addPoint(x, y, 0.0, adjusted_target_size * 0.5)
+                point_map[key] = pt_tag
+                if debug:
+                    print(f"Created GMSH point for polygon vertex {key}: tag {pt_tag}")
+        
+        if debug:
+            print(f"Ensured {len(all_polygon_points)} polygon points exist as GMSH entities")
+        
+        # Create enhanced reinforcement lines that include intersection points from polygons
+        # This is essential for proper mesh generation with embedded 1D elements
+        enhanced_lines = []
+        for line_idx, line_pts in enumerate(lines):
+            line_pts_clean = remove_duplicate_endpoint(list(line_pts))
+            
+            # Collect all points for this line: original + intersection points from polygons
+            all_line_points = []
+            
+            # Add original line points
+            for x, y in line_pts_clean:
+                all_line_points.append((x, y, 'original'))
+            
+            # Add intersection points that are on this line (from polygon data)
+            for poly_data in polygon_data:
+                pt_tags = poly_data['pt_tags']
+                for tag in pt_tags:
+                    # Find the coordinates for this point tag
+                    for (x, y), point_tag in point_map.items():
+                        if point_tag == tag:
+                            # Check if this point is on the reinforcement line
+                            if is_point_on_line_segments((x, y), line_pts_clean, tolerance=1e-6):
+                                all_line_points.append((x, y, 'intersection'))
+                            break
+            
+            # Sort all points along the line to maintain proper order
+            if len(all_line_points) > 1:
+                all_line_points.sort(key=lambda p: line_segment_parameter((p[0], p[1]), line_pts_clean[0], line_pts_clean[-1]))
+            
+            # Remove duplicates (keep first occurrence)
+            unique_points = []
+            seen = set()
+            for x, y, point_type in all_line_points:
+                point_key = (round(x, 8), round(y, 8))  # Round to avoid floating point issues
+                if point_key not in seen:
+                    seen.add(point_key)
+                    unique_points.append((x, y, point_type))
+            
+            # Create the enhanced line
+            enhanced_line = [(x, y) for x, y, _ in unique_points]
+            enhanced_lines.append(enhanced_line)
+            
+            if debug:
+                print(f"Enhanced line {line_idx}: {len(line_pts_clean)} original points -> {len(enhanced_line)} total points")
+        
+        # Replace original lines with enhanced lines
+        lines = enhanced_lines
+
+    # Create reinforcement lines as geometric constraints to force 2D mesh edges
+    line_data = []
+    
+    if lines is not None:
+        for line_idx, line_pts in enumerate(lines):
+            # Use the enhanced line coordinates (which include intersection points)
+            line_pts_clean = remove_duplicate_endpoint(list(line_pts))
+            
+            # Create points for this reinforcement line
+            line_point_tags = []
+            
+            # Create all points for this line (original + intersection points)
+            for x, y in line_pts_clean:
+                key = (x, y)
+                if key in point_map:
+                    line_point_tags.append((x, y, point_map[key]))
+                else:
+                    # Create new point with small mesh size to ensure it's preserved
+                    pt_tag = gmsh.model.geo.addPoint(x, y, 0.0, adjusted_target_size * 0.5)
+                    point_map[key] = pt_tag
+                    line_point_tags.append((x, y, pt_tag))
+            
+            # Sort points along the line to maintain proper order
+            line_point_tags.sort(key=lambda p: line_segment_parameter((p[0], p[1]), line_pts_clean[0], line_pts_clean[-1]))
+            
+            # Extract just the point tags in order
+            pt_tags = [tag for _, _, tag in line_point_tags]
+            
+            if debug:
+                print(f"  Line {line_idx} points: {[(x, y) for x, y, _ in line_point_tags]}")
+            
+            # Create line segments as geometric constraints with controlled meshing
+            line_tags = []
+            for i in range(len(pt_tags) - 1):
+                pt1, pt2 = pt_tags[i], pt_tags[i + 1]
+                
+                # Calculate segment length to determine number of subdivisions
+                coord1 = None
+                coord2 = None
+                for (x, y), tag in point_map.items():
+                    if tag == pt1:
+                        coord1 = (x, y)
+                    if tag == pt2:
+                        coord2 = (x, y)
+                
+                if coord1 and coord2:
+                    segment_length = ((coord2[0] - coord1[0])**2 + (coord2[1] - coord1[1])**2)**0.5
+                    # Calculate number of elements needed to achieve target_size_1d
+                    # For segments longer than target_size_1d, we want multiple elements
+                    # For segments shorter than target_size_1d, we still want at least 2 elements
+                    if segment_length > target_size_1d:
+                        num_elements = max(3, int(round(segment_length / target_size_1d)))
+                    else:
+                        num_elements = 2
+                    
+                    if debug:
+                        print(f"  Segment {i}: length {segment_length:.2f}, creating {num_elements} elements")
+                    
+                    line_tag = gmsh.model.geo.addLine(pt1, pt2)
+                    line_tags.append(line_tag)
+                    
+                    # Set transfinite constraint to create appropriate number of nodes
+                    try:
+                        gmsh.model.geo.mesh.setTransfiniteCurve(line_tag, num_elements)
+                        if debug:
+                            print(f"  Set transfinite constraint on line segment {i}: {num_elements} nodes")
+                    except Exception as e:
+                        if debug:
+                            print(f"  Warning: Could not set transfinite constraint on segment {i}: {e}")
+                else:
+                    # Fallback: create line with default 2 nodes
+                    line_tag = gmsh.model.geo.addLine(pt1, pt2)
+                    line_tags.append(line_tag)
+                    
+                    try:
+                        gmsh.model.geo.mesh.setTransfiniteCurve(line_tag, 2)
+                        if debug:
+                            print(f"  Set transfinite constraint on line segment {i}: 2 nodes (fallback)")
+                    except Exception as e:
+                        if debug:
+                            print(f"  Warning: Could not set transfinite constraint on segment {i}: {e}")
+            
+            # Store line data for later 1D element extraction
+            # Use the enhanced line coordinates (which include intersection points)
+            line_data.append({
+                'line_idx': line_idx,
+                'line_tags': line_tags,
+                'point_coords': line_pts_clean  # This now contains the enhanced coordinates
+            })
+            
+            if debug:
+                print(f"Created reinforcement constraint line {line_idx} with {len(line_tags)} segments: {line_pts_clean}")
+
+    # Third pass: Create surfaces using the shared lines
+    surface_to_region = {}
+    
+    for poly_data in polygon_data:
+        region_id = poly_data['region_id']
+        edges = poly_data['edges']
+        
+        line_tags = []
+        for pt1, pt2, edge_key, forward in edges:
+            line_tag = edge_map[edge_key]
+            
+            # Use positive or negative line tag based on orientation
+            if forward:
+                line_tags.append(line_tag)
+            else:
+                line_tags.append(-line_tag)
+        
+        # Create curve loop and surface
+        try:
+            loop = gmsh.model.geo.addCurveLoop(line_tags)
+            surface = gmsh.model.geo.addPlaneSurface([loop])
+            surface_to_region[surface] = region_id
+        except Exception as e:
+            print(f"Warning: Could not create surface for region {region_id}: {e}")
+            continue
+
+    # Synchronize geometry
+    gmsh.model.geo.synchronize()
+    
+    # Force mesh edges along reinforcement lines by creating additional geometric constraints
+    if lines is not None:
+        for line_info in line_data:
+            line_idx = line_info['line_idx']
+            line_tags = line_info['line_tags']
+            line_pts = line_info['point_coords']
+            
+            # Set transfinite constraints to force mesh edges along each line segment
+            # REMOVED: This was conflicting with the target_size_1d calculations above
+            # for i, line_tag in enumerate(line_tags):
+            #     try:
+            #         # Force exactly 2 nodes (start and end) to prevent subdivision
+            #         gmsh.model.geo.mesh.setTransfiniteCurve(line_tag, 2)
+            #         if debug:
+            #             print(f"Set transfinite constraint on line {line_idx} segment {i}: exactly 2 nodes")
+            #     except Exception as e:
+            #         if debug:
+            #             print(f"Warning: Could not set transfinite constraint on line {line_idx} segment {i}: {e}")
+            
+            # Embed reinforcement lines in all surfaces to ensure they're part of the mesh
+            for surface in surface_to_region.keys():
+                try:
+                    # Embed all line segments of this reinforcement line
+                    gmsh.model.mesh.embed(1, line_tags, 2, surface)
+                    if debug:
+                        print(f"Embedded reinforcement line {line_idx} in surface {surface}")
+                except Exception as e:
+                    if debug:
+                        print(f"Could not embed line {line_idx} in surface {surface}: {e}")
+    
+    # CRITICAL: Set mesh coherence to ensure shared nodes along boundaries
+    # This forces Gmsh to use the same nodes for shared geometric entities
+    gmsh.model.mesh.removeDuplicateNodes()
+    
+    # Create physical groups for material regions (this helps with mesh consistency)
+    physical_surfaces = []
+    for surface, region_id in surface_to_region.items():
+        physical_tag = gmsh.model.addPhysicalGroup(2, [surface])
+        physical_surfaces.append((physical_tag, region_id))
+    
+    # Create physical groups for embedded reinforcement lines
+    physical_lines = []
+    if lines is not None:
+        for line_info in line_data:
+            line_idx = line_info['line_idx']
+            line_tags = line_info['line_tags']
+            physical_tag = gmsh.model.addPhysicalGroup(1, line_tags)
+            physical_lines.append((physical_tag, line_idx))
+    
+    # Check for potential quad4 + reinforcement line conflicts
+    has_reinforcement_lines = lines is not None and len(lines) > 0
+    wants_quads = base_element_type.startswith('quad')
+    
+    # Set mesh algorithm and recombination options BEFORE generating mesh
+    if base_element_type.startswith('quad'):
+        # Check if we need to use a more robust algorithm for reinforcement lines
+        if has_reinforcement_lines:
+            if debug:
+                print(f"Detected quad elements with reinforcement lines.")
+                print(f"Using robust recombination algorithm to handle embedded line constraints.")
+            
+            # Use 'fast' algorithm which is more robust with embedded constraints
+            default_params = {
+                "Mesh.Algorithm": 8,  # Frontal-Delaunay for quads
+                "Mesh.RecombineAll": 1,  # Recombine triangles into quads
+                "Mesh.RecombinationAlgorithm": 0,  # Standard (more robust than simple)
+                "Mesh.SubdivisionAlgorithm": 0,  # Mixed tri/quad where needed
+                "Mesh.RecombineOptimizeTopology": 0,  # Minimal optimization
+                "Mesh.RecombineNodeRepositioning": 1,  # Still reposition nodes
+                "Mesh.RecombineMinimumQuality": 0.01,  # Keep quality threshold
+                "Mesh.Smoothing": 5,  # Reduced smoothing
+                "Mesh.SmoothNormals": 1,  # Keep smooth normals
+                "Mesh.SmoothRatio": 1.8,  # Keep smoothing ratio
+            }
+        else:
+            # Standard quad meshing parameters for cases without reinforcement lines
+            default_params = {
+                "Mesh.Algorithm": 8,  # Frontal-Delaunay for quads (try 5, 6, 8)
+                "Mesh.RecombineAll": 1,  # Recombine triangles into quads
+                "Mesh.RecombinationAlgorithm": 1,  # Simple recombination (try 0, 1, 2, 3)
+                "Mesh.SubdivisionAlgorithm": 1,  # All quads (try 0, 1, 2)
+                "Mesh.RecombineOptimizeTopology": 5,  # Optimize topology (0-100)
+                "Mesh.RecombineNodeRepositioning": 1,  # Reposition nodes (0 or 1)
+                "Mesh.RecombineMinimumQuality": 0.01,  # Minimum quality threshold
+                "Mesh.Smoothing": 10,  # Number of smoothing steps (try 0-100)
+                "Mesh.SmoothNormals": 1,  # Smooth normals
+                "Mesh.SmoothRatio": 1.8,  # Smoothing ratio (1.0-3.0)
+            }
+        
+        # Override with user-provided parameters
+        if mesh_params:
+            default_params.update(mesh_params)
+        
+        # Apply all parameters (except our custom ones)
+        for param, value in default_params.items():
+            if param not in ['size_factor']:  # Skip our custom parameters
+                gmsh.option.setNumber(param, value)
+        
+        # Set recombination for each surface
+        for surface in surface_to_region.keys():
+            gmsh.model.mesh.setRecombine(2, surface)
+    else:
+        gmsh.option.setNumber("Mesh.Algorithm", 6)  # Frontal-Delaunay for triangles
+    
+    # Always generate linear elements first - quadratic conversion is done in post-processing
+    # This avoids gmsh issues with quadratic elements and embedded 1D lines
+    gmsh.option.setNumber("Mesh.ElementOrder", 1)
+    
+    # Force mesh coherence before generation
+    gmsh.option.setNumber("Mesh.ToleranceInitialDelaunay", 1e-12)
+    
+    # Short edge control is now handled by point sizing during geometry creation
+    
+    # Generate mesh
+    gmsh.model.mesh.generate(2)
+    
+    # Remove duplicate nodes again after mesh generation (belt and suspenders)
+    gmsh.model.mesh.removeDuplicateNodes()
+
+    # Get nodes
+    node_tags, coords, _ = gmsh.model.mesh.getNodes()
+    nodes = np.array(coords).reshape(-1, 3)[:, :2]
+    
+    # Create node tag to index mapping
+    node_tag_to_index = {tag: i for i, tag in enumerate(node_tags)}
+
+    elements = []
+    mat_ids = []
+    element_node_counts = []
+    
+    # For quad8: track center nodes to delete later
+    center_nodes_to_delete = set() if element_type == 'quad8' else None
+
+    # Extract elements using physical groups for better region identification
+    for physical_tag, region_id in physical_surfaces:
+        try:
+            # Get entities in this physical group
+            entities = gmsh.model.getEntitiesForPhysicalGroup(2, physical_tag)
+            
+            for entity in entities:
+                # Get all elements for this entity
+                elem_types, elem_tags_list, node_tags_list = gmsh.model.mesh.getElements(2, entity)
+                
+                for elem_type, elem_tags, node_tags in zip(elem_types, elem_tags_list, node_tags_list):
+                    # Gmsh element type mapping:
+                    # 2: 3-node triangle, 9: 6-node triangle
+                    # 3: 4-node quadrilateral, 10: 8-node quadrilateral
+                    if elem_type == 2:  # 3-node triangle
+                        elements_array = np.array(node_tags).reshape(-1, 3)
+                        for element in elements_array:
+                            idxs = [node_tag_to_index[tag] for tag in element]
+                            
+                            # GMSH returns clockwise triangles - reorder to counter-clockwise
+                            idxs[1], idxs[2] = idxs[2], idxs[1]
+                            
+                            # Pad to 9 columns with zeros
+                            padded_idxs = idxs + [0] * (9 - len(idxs))
+                            elements.append(padded_idxs)
+                            mat_ids.append(region_id)
+                            element_node_counts.append(3)
+                    elif elem_type == 9:  # 6-node triangle
+                        elements_array = np.array(node_tags).reshape(-1, 6)
+                        for element in elements_array:
+                            idxs = [node_tag_to_index[tag] for tag in element]
+                            
+                            # GMSH returns clockwise tri6 elements - reorder to counter-clockwise
+                            # Swap corner nodes 1 and 2
+                            idxs[1], idxs[2] = idxs[2], idxs[1]
+                            # Fix midpoint assignments after corner swap 1<->2:
+                            # GMSH gives: n3=edge(0-1), n4=edge(1-2), n5=edge(2-0)
+                            # After swap: n3=edge(0-2), n4=edge(2-1), n5=edge(1-0)
+                            # Standard requires: n3=edge(0-1), n4=edge(1-2), n5=edge(2-0)
+                            # So remap: new_n3=old_n5, new_n4=old_n4, new_n5=old_n3
+                            old_3, old_4, old_5 = idxs[3], idxs[4], idxs[5]
+                            idxs[3] = old_5  # standard edge(0-1) gets GMSH edge(2-0) midpoint
+                            idxs[4] = old_4  # standard edge(1-2) gets GMSH edge(1-2) midpoint  
+                            idxs[5] = old_3  # standard edge(2-0) gets GMSH edge(0-1) midpoint
+                            
+                            # Pad to 9 columns with zeros
+                            padded_idxs = idxs + [0] * (9 - len(idxs))
+                            elements.append(padded_idxs)
+                            mat_ids.append(region_id)
+                            element_node_counts.append(6)
+                    elif elem_type == 3:  # 4-node quadrilateral
+                        elements_array = np.array(node_tags).reshape(-1, 4)
+                        for element in elements_array:
+                            idxs = [node_tag_to_index[tag] for tag in element]
+                            # Fix node ordering for quadrilateral elements
+                            if element_type.startswith('quad'):
+                                idxs = idxs[::-1] # Simple reversal of node order
+                            # Pad to 9 columns with zeros
+                            padded_idxs = idxs + [0] * (9 - len(idxs))
+                            elements.append(padded_idxs)
+                            mat_ids.append(region_id)
+                            element_node_counts.append(4)
+                    elif elem_type == 10:  # Quadratic quadrilateral (gmsh generates 9-node Lagrange)
+                        # Gmsh always generates 9-node Lagrange quads for order 2
+                        elements_array = np.array(node_tags).reshape(-1, 9)
+                        for element in elements_array:
+                            idxs = [node_tag_to_index[tag] for tag in element]
+                            
+                            if element_type in ['quad8', 'quad9']:
+                                # Both quad8 and quad9 need CW to CCW conversion for first 8 nodes
+                                # Convert from Gmsh CW to CCW ordering for quadrilateral
+                                # Corner nodes: reverse order (0,1,2,3) -> (0,3,2,1)
+                                # Midpoint nodes need to be reordered accordingly:
+                                # GMSH: n4=edge(0-1), n5=edge(1-2), n6=edge(2-3), n7=edge(3-0)
+                                # After corner reversal: need n4=edge(0-3), n5=edge(3-2), n6=edge(2-1), n7=edge(1-0)
+                                # So: new_n4=old_n7, new_n5=old_n6, new_n6=old_n5, new_n7=old_n4
+                                reordered_first8 = [
+                                    idxs[0],  # corner 0 stays
+                                    idxs[3],  # corner 1 -> corner 3  
+                                    idxs[2],  # corner 2 stays
+                                    idxs[1],  # corner 3 -> corner 1
+                                    idxs[7],  # edge(0-1) -> edge(0-3) = old edge(3-0)
+                                    idxs[6],  # edge(1-2) -> edge(3-2) = old edge(2-3)  
+                                    idxs[5],  # edge(2-3) -> edge(2-1) = old edge(1-2)
+                                    idxs[4]   # edge(3-0) -> edge(1-0) = old edge(0-1)
+                                ]
+                                
+                                if element_type == 'quad8':
+                                    # For quad8, skip center node and mark for deletion
+                                    center_node_idx = idxs[8]  # Mark center node for deletion
+                                    center_nodes_to_delete.add(center_node_idx)
+                                    padded_idxs = reordered_first8 + [0]  # Skip center node, pad to 9
+                                    elements.append(padded_idxs)
+                                    mat_ids.append(region_id)
+                                    element_node_counts.append(8)
+                                else:  # quad9
+                                    # For quad9, keep center node (9th node unchanged)
+                                    full_idxs = reordered_first8 + [idxs[8]]  # Add center node
+                                    elements.append(full_idxs)
+                                    mat_ids.append(region_id)
+                                    element_node_counts.append(9)
+                            else:
+                                # This should never happen since element_type is validated earlier
+                                raise ValueError(f"Unexpected element_type '{element_type}' for Gmsh elem_type {elem_type}")
+        except Exception as e:
+            print(f"Warning: Could not extract elements for physical group {physical_tag} (region {region_id}): {e}")
+            continue
+
+    # Convert to numpy arrays
+    elements_array = np.array(elements, dtype=int)
+    element_types = np.array(element_node_counts, dtype=int)
+    element_materials = np.array(mat_ids, dtype=int)
+
+    # Extract 1D elements from Gmsh-generated 1D mesh along reinforcement lines
+    elements_1d = []
+    mat_ids_1d = []
+    element_node_counts_1d = []
+    
+    if lines is not None:
+        # Extract 1D elements from physical groups for each reinforcement line
+        for physical_tag, line_idx in physical_lines:
+            try:
+                # Get entities in this physical group
+                entities = gmsh.model.getEntitiesForPhysicalGroup(1, physical_tag)
+                
+                if debug:
+                    print(f"  Physical group {physical_tag} (line {line_idx}): found {len(entities)} entities")
+                
+                for entity in entities:
+                    # Get all 1D elements for this entity
+                    elem_types, elem_tags_list, node_tags_list = gmsh.model.mesh.getElements(1, entity)
+                    
+                    for elem_type, elem_tags, node_tags in zip(elem_types, elem_tags_list, node_tags_list):
+                        # Gmsh 1D element type mapping:
+                        # 1: 2-node line (linear), 8: 3-node line (quadratic)
+                        if elem_type == 1:  # Linear 1D elements (2 nodes)
+                            elements_array = np.array(node_tags).reshape(-1, 2)
+                            for element in elements_array:
+                                try:
+                                    # Convert numpy arrays to regular Python scalars
+                                    element_list = element.tolist()  # Convert to Python list
+                                    if len(element_list) >= 2:
+                                        tag1 = int(element_list[0])
+                                        tag2 = int(element_list[1])
+                                        
+                                        # Get node indices
+                                        idx1 = node_tag_to_index[tag1]
+                                        idx2 = node_tag_to_index[tag2]
+                                        
+                                        # Create 1D element
+                                        padded_idxs = [idx1, idx2, 0]
+                                        elements_1d.append(padded_idxs)
+                                        mat_ids_1d.append(line_idx)
+                                        element_node_counts_1d.append(2)
+                                        
+                                        if debug:
+                                            coord1 = nodes[idx1]
+                                            coord2 = nodes[idx2]
+                                            print(f"    Created 1D element: {coord1} -> {coord2}")
+                                except (KeyError, TypeError, ValueError, IndexError) as e:
+                                    if debug:
+                                        print(f"    Skipping 1D element due to error: {e}")
+                                    continue
+                        elif elem_type == 8:  # Quadratic 1D elements (3 nodes)
+                            elements_array = np.array(node_tags).reshape(-1, 3)
+                            for element in elements_array:
+                                try:
+                                    # Convert numpy arrays to regular Python scalars
+                                    element_list = element.tolist()  # Convert to Python list
+                                    if len(element_list) >= 3:
+                                        tag1 = int(element_list[0])
+                                        tag2 = int(element_list[1])
+                                        tag3 = int(element_list[2])
+                                        
+                                        # Get node indices
+                                        idx1 = node_tag_to_index[tag1]
+                                        idx2 = node_tag_to_index[tag2]
+                                        idx3 = node_tag_to_index[tag3]
+                                        
+                                        # Create 1D element
+                                        padded_idxs = [idx1, idx2, idx3]
+                                        elements_1d.append(padded_idxs)
+                                        mat_ids_1d.append(line_idx)
+                                        element_node_counts_1d.append(3)
+                                except (KeyError, TypeError, ValueError, IndexError) as e:
+                                    if debug:
+                                        print(f"    Skipping quadratic 1D element due to error: {e}")
+                                    continue
+            except Exception as e:
+                if debug:
+                    print(f"  Error extracting 1D elements for line {line_idx}: {e}")
+                continue
+
+    gmsh.finalize()
+
+    # Clean up center nodes for quad8 elements
+    if element_type == 'quad8' and center_nodes_to_delete:
+        print(f"Quad8 cleanup: removing {len(center_nodes_to_delete)} center nodes from {len(nodes)} total nodes")
+        
+        # c) Create array tracking original node numbering
+        original_node_count = len(nodes)
+        nodes_to_keep = [i for i in range(original_node_count) if i not in center_nodes_to_delete]
+        
+        # d) Delete center nodes - create new nodes array
+        new_nodes = nodes[nodes_to_keep]
+        
+        # e) Create mapping from old node indices to new node indices
+        old_to_new_mapping = {old_idx: new_idx for new_idx, old_idx in enumerate(nodes_to_keep)}
+        
+        # f) Update element topology to use new node numbering
+        new_elements = []
+        for element in elements_array:
+            new_element = []
+            for node_idx in element:
+                if node_idx == 0:  # Keep padding zeros
+                    new_element.append(0)
+                elif node_idx in center_nodes_to_delete:
+                    # This should not happen since we set center nodes to 0
+                    new_element.append(0)
+                else:
+                    # Map to new node index
+                    new_element.append(old_to_new_mapping[node_idx])
+            new_elements.append(new_element)
+        
+        # g) Replace arrays with consolidated versions
+        elements_array = np.array(new_elements, dtype=int)
+        nodes = new_nodes
+        
+        print(f"Quad8 cleanup complete: {len(nodes)} nodes, {len(elements_array)} elements")
+
+    # Convert lists to arrays
+    elements_array = np.array(elements, dtype=int)
+    element_types = np.array(element_node_counts, dtype=int)
+    element_materials = np.array(mat_ids, dtype=int) + 1  # Make 1-based
+
+    mesh = {
+        "nodes": nodes,
+        "elements": elements_array,
+        "element_types": element_types,
+        "element_materials": element_materials,
+    }
+
+    # Add 1D element data if lines were provided
+    if lines is not None and len(elements_1d) > 0:
+        elements_1d_array = np.array(elements_1d, dtype=int)
+        element_types_1d = np.array(element_node_counts_1d, dtype=int)
+        element_materials_1d = np.array(mat_ids_1d, dtype=int) + 1  # Make 1-based
+        
+        mesh["elements_1d"] = elements_1d_array
+        mesh["element_types_1d"] = element_types_1d
+        mesh["element_materials_1d"] = element_materials_1d
+
+    # Post-process to convert linear elements to quadratic if requested
+    if quadratic:
+        if debug:
+            print(f"Converting linear {base_element_type} mesh to quadratic {element_type}")
+        mesh = convert_linear_to_quadratic_mesh(mesh, element_type, debug=debug)
+
+    return mesh
+
+
+def convert_linear_to_quadratic_mesh(mesh, target_element_type, debug=False):
+    """
+    Convert a linear mesh (tri3/quad4) to quadratic (tri6/quad8/quad9) by adding midside nodes.
+    
+    This is much more robust than gmsh's built-in quadratic generation, especially 
+    when dealing with embedded 1D elements (reinforcement lines).
+    
+    Parameters:
+        mesh: Dictionary containing linear mesh data
+        target_element_type: 'tri6', 'quad8', or 'quad9'
+        debug: Enable debug output
+        
+    Returns:
+        Updated mesh dictionary with quadratic elements
+    """
+    if debug:
+        print(f"Converting to {target_element_type} elements...")
+    
+    nodes = mesh["nodes"].copy()
+    elements = mesh["elements"].copy()
+    element_types = mesh["element_types"].copy()
+    element_materials = mesh["element_materials"].copy()
+    
+    # Handle 1D elements if present
+    elements_1d = mesh.get("elements_1d")
+    element_types_1d = mesh.get("element_types_1d") 
+    element_materials_1d = mesh.get("element_materials_1d")
+    has_1d_elements = elements_1d is not None
+    
+    if has_1d_elements:
+        elements_1d = elements_1d.copy()
+        element_types_1d = element_types_1d.copy()
+        element_materials_1d = element_materials_1d.copy()
+    
+    # Dictionary to store midside nodes: (node1_idx, node2_idx) -> midside_node_idx
+    # Always store with node1_idx < node2_idx for consistency
+    midside_nodes = {}
+    next_node_idx = len(nodes)
+    
+    def get_or_create_midside_node(n1_idx, n2_idx):
+        """Get existing midside node or create new one between n1 and n2"""
+        nonlocal next_node_idx, nodes
+        
+        # Ensure consistent ordering
+        if n1_idx > n2_idx:
+            n1_idx, n2_idx = n2_idx, n1_idx
+            
+        edge_key = (n1_idx, n2_idx)
+        
+        if edge_key in midside_nodes:
+            return midside_nodes[edge_key]
+        
+        # Create new midside node at edge center
+        n1 = nodes[n1_idx]
+        n2 = nodes[n2_idx]
+        midside_coord = (n1 + n2) / 2.0
+        
+        # Add to nodes array
+        nodes_list = nodes.tolist()
+        nodes_list.append(midside_coord.tolist())
+        nodes = np.array(nodes_list)
+        
+        midside_idx = next_node_idx
+        midside_nodes[edge_key] = midside_idx
+        next_node_idx += 1
+        
+        if debug and len(midside_nodes) <= 10:  # Only print first few
+            print(f"  Created midside node {midside_idx} between {n1_idx}-{n2_idx} at {midside_coord}")
+        
+        return midside_idx
+    
+    # Convert 2D elements
+    new_elements = []
+    new_element_types = []
+    
+    for elem_idx, element in enumerate(elements):
+        elem_type = element_types[elem_idx]
+        
+        if target_element_type == 'tri6' and elem_type == 3:
+            # Convert tri3 to tri6
+            n0, n1, n2 = element[0], element[1], element[2]
+            
+            # Get/create midside nodes
+            n3 = get_or_create_midside_node(n0, n1)  # edge 0-1
+            n4 = get_or_create_midside_node(n1, n2)  # edge 1-2
+            n5 = get_or_create_midside_node(n2, n0)  # edge 2-0
+            
+            # tri6 node ordering: [corner_nodes, midside_nodes]
+            new_element = [n0, n1, n2, n3, n4, n5, 0, 0, 0]
+            new_elements.append(new_element)
+            new_element_types.append(6)
+            
+        elif target_element_type == 'quad8' and elem_type == 4:
+            # Convert quad4 to quad8
+            n0, n1, n2, n3 = element[0], element[1], element[2], element[3]
+            
+            # Get/create midside nodes on edges
+            n4 = get_or_create_midside_node(n0, n1)  # edge 0-1
+            n5 = get_or_create_midside_node(n1, n2)  # edge 1-2
+            n6 = get_or_create_midside_node(n2, n3)  # edge 2-3
+            n7 = get_or_create_midside_node(n3, n0)  # edge 3-0
+            
+            # quad8 node ordering: [corner_nodes, midside_nodes]
+            new_element = [n0, n1, n2, n3, n4, n5, n6, n7, 0]
+            new_elements.append(new_element)
+            new_element_types.append(8)
+            
+        elif target_element_type == 'quad9' and elem_type == 4:
+            # Convert quad4 to quad9
+            n0, n1, n2, n3 = element[0], element[1], element[2], element[3]
+            
+            # Get/create midside nodes on edges
+            n4 = get_or_create_midside_node(n0, n1)  # edge 0-1
+            n5 = get_or_create_midside_node(n1, n2)  # edge 1-2
+            n6 = get_or_create_midside_node(n2, n3)  # edge 2-3
+            n7 = get_or_create_midside_node(n3, n0)  # edge 3-0
+            
+            # Create center node
+            center_coord = (nodes[n0] + nodes[n1] + nodes[n2] + nodes[n3]) / 4.0
+            nodes_list = nodes.tolist()
+            nodes_list.append(center_coord.tolist())
+            nodes = np.array(nodes_list)
+            n8 = next_node_idx
+            next_node_idx += 1
+            
+            # quad9 node ordering: [corner_nodes, midside_nodes, center_node]
+            new_element = [n0, n1, n2, n3, n4, n5, n6, n7, n8]
+            new_elements.append(new_element)
+            new_element_types.append(9)
+            
+        else:
+            # Keep original element unchanged
+            new_elements.append(element.tolist())
+            new_element_types.append(elem_type)
+    
+    # Convert 1D elements to quadratic if present
+    new_elements_1d = []
+    new_element_types_1d = [] 
+    
+    if has_1d_elements:
+        for elem_idx, element in enumerate(elements_1d):
+            elem_type = element_types_1d[elem_idx]
+            
+            if elem_type == 2:  # Convert linear 1D to quadratic
+                n0, n1 = element[0], element[1]
+                
+                # Get/create midside node (reuse if already created for 2D elements)
+                n2 = get_or_create_midside_node(n0, n1)
+                
+                new_element = [n0, n1, n2]
+                new_elements_1d.append(new_element)
+                new_element_types_1d.append(3)  # quadratic 1D
+            else:
+                # Keep original element unchanged
+                new_elements_1d.append(element.tolist())
+                new_element_types_1d.append(elem_type)
+    
+    if debug:
+        print(f"  Added {len(midside_nodes)} midside nodes")
+        print(f"  Total nodes: {len(nodes)} (was {len(mesh['nodes'])})")
+    
+    # Create updated mesh
+    updated_mesh = {
+        "nodes": nodes,
+        "elements": np.array(new_elements, dtype=int),
+        "element_types": np.array(new_element_types, dtype=int),
+        "element_materials": element_materials
+    }
+    
+    if has_1d_elements:
+        updated_mesh["elements_1d"] = np.array(new_elements_1d, dtype=int)
+        updated_mesh["element_types_1d"] = np.array(new_element_types_1d, dtype=int)
+        updated_mesh["element_materials_1d"] = element_materials_1d
+    
+    return updated_mesh
+
+
+def line_segment_parameter(point, line_start, line_end):
+    """
+    Calculate the parameter t (0 to 1) of a point along a line segment.
+    Returns t where point = line_start + t * (line_end - line_start)
+    """
+    px, py = point
+    x1, y1 = line_start
+    x2, y2 = line_end
+    
+    # Calculate parameter t
+    dx = x2 - x1
+    dy = y2 - y1
+    
+    if abs(dx) > abs(dy):
+        t = (px - x1) / dx
+    else:
+        t = (py - y1) / dy
+    
+    return t
+
+
+def line_segment_intersection(p1, p2, p3, p4, tol=1e-8):
+    """
+    Find intersection point between two line segments.
+    Returns intersection point (x, y) if it exists, None otherwise.
+    """
+    x1, y1 = p1
+    x2, y2 = p2
+    x3, y3 = p3
+    x4, y4 = p4
+    
+    # Calculate direction vectors
+    d1x, d1y = x2 - x1, y2 - y1
+    d2x, d2y = x4 - x3, y4 - y3
+    
+    # Calculate determinant
+    det = d1x * d2y - d1y * d2x
+    
+    if abs(det) < tol:  # Lines are parallel
+        return None
+    
+    # Calculate parameters
+    t1 = ((x3 - x1) * d2y - (y3 - y1) * d2x) / det
+    t2 = ((x3 - x1) * d1y - (y3 - y1) * d1x) / det
+    
+    # Check if intersection is within both segments
+    if 0 <= t1 <= 1 and 0 <= t2 <= 1:
+        # Calculate intersection point
+        ix = x1 + t1 * d1x
+        iy = y1 + t1 * d1y
+        return (round(ix, 6), round(iy, 6))
+    
+    return None
+
+
+def point_near_existing(point, existing_points, tol=1e-8):
+    """Check if a point is near any existing points."""
+    px, py = point
+    for ex, ey in existing_points:
+        if abs(px - ex) < tol and abs(py - ey) < tol:
+            return True
+    return False
+
+
+def insert_point_into_polygon_edge(intersection, edge_start, edge_end, poly_data, point_map, target_size):
+    """Insert an intersection point into a polygon edge, updating the polygon's coordinate list."""
+    x, y = intersection
+    # Ensure the point exists in the point_map (for Gmsh)
+    if (x, y) not in point_map:
+        tag = len(point_map) + 1  # Simple tag assignment
+        point_map[(x, y)] = tag
+    
+    # Insert the intersection point into the polygon's coordinate list at the correct edge
+    # poly_data['pt_tags'] is a list of Gmsh point tags, but we need to update the coordinate list used to build the polygon
+    # We'll reconstruct the coordinate list from the tags and point_map
+    pt_tags = poly_data['pt_tags']
+    # Build coordinate list for the polygon
+    coords = []
+    tag_to_coord = {v: k for k, v in point_map.items()}
+    for tag in pt_tags:
+        if tag in tag_to_coord:
+            coords.append(tag_to_coord[tag])
+        else:
+            # Fallback: try to find the coordinate in point_map
+            found = False
+            for (cx, cy), t in point_map.items():
+                if t == tag:
+                    coords.append((cx, cy))
+                    found = True
+                    break
+            if not found:
+                coords.append((None, None))  # Should not happen
+    # Find the edge to insert after
+    insert_idx = None
+    for i in range(len(coords)):
+        a = coords[i]
+        b = coords[(i + 1) % len(coords)]
+        if (abs(a[0] - edge_start[0]) < 1e-8 and abs(a[1] - edge_start[1]) < 1e-8 and
+            abs(b[0] - edge_end[0]) < 1e-8 and abs(b[1] - edge_end[1]) < 1e-8):
+            insert_idx = i + 1
+            break
+        # Also check reversed edge
+        if (abs(a[0] - edge_end[0]) < 1e-8 and abs(a[1] - edge_end[1]) < 1e-8 and
+            abs(b[0] - edge_start[0]) < 1e-8 and abs(b[1] - edge_start[1]) < 1e-8):
+            insert_idx = i + 1
+            break
+    if insert_idx is not None:
+        # Insert the intersection point into the coordinate list
+        coords.insert(insert_idx, (x, y))
+        # Now update pt_tags to match
+        tag = point_map[(x, y)]
+        pt_tags.insert(insert_idx, tag)
+        # Update poly_data
+        poly_data['pt_tags'] = pt_tags
+    # If not found, do nothing (should not happen)
+
+
+def get_quad_mesh_presets():
+    """
+    Returns dictionary of preset quad meshing parameter combinations to try.
+    """
+    presets = {
+        'default': {
+            "Mesh.Algorithm": 8,
+            "Mesh.RecombinationAlgorithm": 1,
+            "Mesh.SubdivisionAlgorithm": 1,
+            "Mesh.RecombineOptimizeTopology": 5,
+            "Mesh.Smoothing": 10,
+            "size_factor": 1.4,  # Target size adjustment
+        },
+        'blossom': {
+            "Mesh.Algorithm": 6,
+            "Mesh.RecombinationAlgorithm": 2,  # Blossom
+            "Mesh.SubdivisionAlgorithm": 1,
+            "Mesh.RecombineOptimizeTopology": 20,
+            "Mesh.Smoothing": 20,
+            "size_factor": 1.6,  # Slightly larger for better recombination
+        },
+        'blossom_full': {
+            "Mesh.Algorithm": 5,
+            "Mesh.RecombinationAlgorithm": 3,  # Blossom full-quad
+            "Mesh.SubdivisionAlgorithm": 1,
+            "Mesh.RecombineOptimizeTopology": 50,
+            "Mesh.Smoothing": 30,
+            "size_factor": 1.7,  # Larger for complex recombination
+        },
+        'high_quality': {
+            "Mesh.Algorithm": 6,
+            "Mesh.RecombinationAlgorithm": 1,
+            "Mesh.SubdivisionAlgorithm": 1,
+            "Mesh.RecombineOptimizeTopology": 100,
+            "Mesh.RecombineNodeRepositioning": 1,
+            "Mesh.RecombineMinimumQuality": 0.1,
+            "Mesh.Smoothing": 50,
+            "Mesh.SmoothRatio": 2.0,
+            "size_factor": 2.0,  # Much larger due to heavy optimization
+        },
+        'fast': {
+            "Mesh.Algorithm": 8,
+            "Mesh.RecombinationAlgorithm": 0,  # Standard (fastest)
+            "Mesh.SubdivisionAlgorithm": 0,
+            "Mesh.RecombineOptimizeTopology": 0,
+            "Mesh.Smoothing": 5,
+            "size_factor": 0.7,  # Smaller adjustment = more elements
+        }
+    }
+    return presets
+
+
+
+def build_polygons(slope_data, reinf_lines=None, debug=False):
+    """
+    Build material zone polygons from slope_data.
+    
+    Extracts profile lines and max depth, then creates polygons for each material zone.
+    Also integrates distributed load points and reinforcement line endpoints that are
+    coincident with polygon edges.
+    
+    Parameters:
+        slope_data: Dictionary containing slope geometry data
+        
+    Returns:
+        List of polygons, each defined by (x,y) coordinate tuples
+    """
+    import numpy as np
+    import copy
+
+    # Extract profile lines and max depth from slope_data
+    profile_lines = slope_data.get('profile_lines', [])
+    max_depth = slope_data.get('max_depth', None)
+
+    if not profile_lines:
+        raise ValueError("Need at least 1 profile line to create material zones")
+    
+    # For single profile line, max_depth serves as the bottom boundary
+    if len(profile_lines) == 1:
+        if max_depth is None:
+            raise ValueError("When using only 1 profile line, max_depth must be specified")
+
+    def get_avg_y(line):
+        return sum(y for _, y in line) / len(line)
+
+    # Sort profile lines from top to bottom by average y
+    sorted_lines = sorted(profile_lines, key=get_avg_y, reverse=True)
+    n = len(sorted_lines)
+    # Deep copy so we can insert points
+    lines = [list(line) for line in copy.deepcopy(sorted_lines)]
+    tol = 1e-8
+
+    for i in range(n - 1):
+        top = lines[i]
+        for endpoint in [0, -1]:  # left and right
+            x_top, y_top = top[endpoint]
+            # Find the highest lower profile at this x
+            best_j = None
+            best_y = -np.inf
+            for j in range(i + 1, n):
+                lower = lines[j]
+                xs_lower = np.array([x for x, y in lower])
+                ys_lower = np.array([y for x, y in lower])
+                if xs_lower[0] - tol <= x_top <= xs_lower[-1] + tol:
+                    y_proj = np.interp(x_top, xs_lower, ys_lower)
+                    if y_proj > best_y:
+                        best_y = y_proj
+                        best_j = j
+            if best_j is not None:
+                lower = lines[best_j]
+                xs_lower = np.array([x for x, y in lower])
+                ys_lower = np.array([y for x, y in lower])
+                y_proj = np.interp(x_top, xs_lower, ys_lower)
+                # Check if lower profile already has a point at this x (within tol)
+                found = False
+                for (x_l, y_l) in lower:
+                    if abs(x_l - x_top) < tol:
+                        found = True
+                        break
+                if abs(y_proj - y_top) < tol:
+                    # Coincident: insert (x_top, y_top) if not present
+                    if not found:
+                        insert_idx = np.searchsorted(xs_lower, x_top)
+                        lower.insert(insert_idx, (round(x_top, 6), round(y_top, 6)))
+                else:
+                    # Not coincident: insert (x_top, y_proj) if not present
+                    if not found:
+                        insert_idx = np.searchsorted(xs_lower, x_top)
+                        lower.insert(insert_idx, (round(x_top, 6), round(y_proj, 6)))
+
+    def clean_polygon(poly, tol=1e-8):
+        # Remove consecutive duplicate points (except for closing point)
+        if not poly:
+            return poly
+        cleaned = [poly[0]]
+        for pt in poly[1:]:
+            if abs(pt[0] - cleaned[-1][0]) > tol or abs(pt[1] - cleaned[-1][1]) > tol:
+                cleaned.append(pt)
+        # Ensure closed
+        if abs(cleaned[0][0] - cleaned[-1][0]) > tol or abs(cleaned[0][1] - cleaned[-1][1]) > tol:
+            cleaned.append(cleaned[0])
+        return cleaned
+
+    # Now build polygons as before
+    polygons = []
+    for i, top_line in enumerate(lines):
+        xs_top, ys_top = zip(*top_line)
+        xs_top = np.array(xs_top)
+        ys_top = np.array(ys_top)
+        left_x, left_y = xs_top[0], ys_top[0]
+        right_x, right_y = xs_top[-1], ys_top[-1]
+
+        if i < n - 1:
+            lower_line = lines[i + 1]
+            xs_bot, ys_bot = zip(*lower_line)
+            xs_bot = np.array(xs_bot)
+            ys_bot = np.array(ys_bot)
+            # Project left and right endpoints vertically to lower profile
+            left_y_bot = np.interp(left_x, xs_bot, ys_bot)
+            right_y_bot = np.interp(right_x, xs_bot, ys_bot)
+            # Find all lower profile points between left_x and right_x (exclusive)
+            mask = (xs_bot > left_x) & (xs_bot < right_x)
+            xs_bot_in = xs_bot[mask]
+            ys_bot_in = ys_bot[mask]
+            # Build bottom boundary: right projection, lower profile points (right to left), left projection
+            bottom = []
+            bottom.append((right_x, right_y_bot))
+            for x, y in zip(xs_bot_in[::-1], ys_bot_in[::-1]):
+                bottom.append((x, y))
+            bottom.append((left_x, left_y_bot))
+        else:
+            # For the lowest polygon, bottom is at max_depth
+            # Only need endpoints - no intermediate points
+            bottom = []
+            bottom.append((right_x, max_depth))
+            bottom.append((left_x, max_depth))
+
+        # Build polygon: top left-to-right, bottom right-to-left
+        poly = []
+        for x, y in zip(xs_top, ys_top):
+            poly.append((round(x, 6), round(y, 6)))
+        for x, y in bottom:
+            poly.append((round(x, 6), round(y, 6)))
+        # Clean up polygon (should rarely do anything)
+        poly = clean_polygon(poly)
+        polygons.append(poly)
+    
+    # Add distributed load points to polygon edges if coincident
+    polygons = add_dload_points_to_polygons(polygons, slope_data)
+    
+    # Add intersection points with reinforcement lines if provided
+    if reinf_lines is not None:
+        polygons = add_intersection_points_to_polygons(polygons, reinf_lines, debug=debug)
+    
+    return polygons
+
+def add_dload_points_to_polygons(polygons, slope_data):
+    """
+    Add distributed load points to polygon edges if they are coincident with edges 
+    but not existing vertices.
+    
+    Parameters:
+        polygons: List of polygons (lists of (x,y) tuples)
+        slope_data: Dictionary containing slope data
+        
+    Returns:
+        Updated list of polygons with added points
+    """
+    import numpy as np
+    tol = 1e-8
+    
+    # Collect distributed load points to check
+    points_to_check = []
+    
+    # Add distributed load points
+    distributed_loads = slope_data.get('distributed_loads', [])
+    for load in distributed_loads:
+        if 'xy' in load:
+            for point in load['xy']:
+                points_to_check.append(point)
+    
+    if not points_to_check:
+        return polygons
+    
+    # Process each polygon
+    updated_polygons = []
+    for poly in polygons:
+        updated_poly = list(poly)  # Make a copy
+        
+        # Check each point against polygon edges
+        for check_point in points_to_check:
+            x_check, y_check = check_point
+            
+            # Check if point is already a vertex
+            is_vertex = False
+            for vertex in updated_poly:
+                if abs(vertex[0] - x_check) < tol and abs(vertex[1] - y_check) < tol:
+                    is_vertex = True
+                    break
+            
+            if is_vertex:
+                continue
+            
+            # Check if point lies on any edge
+            for i in range(len(updated_poly)):
+                x1, y1 = updated_poly[i]
+                x2, y2 = updated_poly[(i + 1) % len(updated_poly)]
+                
+                # Check if point lies on edge segment
+                if is_point_on_edge((x_check, y_check), (x1, y1), (x2, y2), tol):
+                    # Insert point after vertex i
+                    updated_poly.insert(i + 1, (round(x_check, 6), round(y_check, 6)))
+                    break  # Only insert once per point
+        
+        updated_polygons.append(updated_poly)
+    
+    return updated_polygons
+
+def is_point_on_edge(point, edge_start, edge_end, tol=1e-8):
+    """
+    Check if a point lies on a line segment (edge).
+    
+    Parameters:
+        point: (x, y) tuple of point to check
+        edge_start: (x, y) tuple of edge start
+        edge_end: (x, y) tuple of edge end
+        tol: Tolerance for coincidence
+        
+    Returns:
+        bool: True if point lies on edge segment
+    """
+    px, py = point
+    x1, y1 = edge_start
+    x2, y2 = edge_end
+    
+    # Check if point is within bounding box of edge
+    if not (min(x1, x2) - tol <= px <= max(x1, x2) + tol and
+            min(y1, y2) - tol <= py <= max(y1, y2) + tol):
+        return False
+    
+    # Check if point is collinear with edge
+    # Use cross product to check collinearity
+    cross_product = abs((py - y1) * (x2 - x1) - (px - x1) * (y2 - y1))
+    
+    # If cross product is close to zero, point is on the line
+    # Also check that it's within the segment bounds
+    if cross_product < tol:
+        # Check if point is between edge endpoints
+        dot_product = (px - x1) * (x2 - x1) + (py - y1) * (y2 - y1)
+        edge_length_sq = (x2 - x1) ** 2 + (y2 - y1) ** 2
+        
+        if edge_length_sq < tol:  # Edge is essentially a point
+            return abs(px - x1) < tol and abs(py - y1) < tol
+        
+        # Parameter t should be between 0 and 1 for point to be on segment
+        t = dot_product / edge_length_sq
+        return -tol <= t <= 1 + tol
+    
+    return False
+
+def print_polygon_summary(polygons):
+    """
+    Prints a summary of the generated polygons for diagnostic purposes.
+    
+    Parameters:
+        polygons: List of polygon coordinate lists
+    """
+    print("=== POLYGON SUMMARY ===")
+    print(f"Number of material zones: {len(polygons)}")
+    print()
+    
+    for i, polygon in enumerate(polygons):
+        print(f"Material Zone {i+1} (Material ID: {i}):")
+        print(f"  Number of vertices: {len(polygon)}")
+        
+        # Calculate area (simple shoelace formula)
+        area = 0
+        for j in range(len(polygon) - 1):
+            x1, y1 = polygon[j]
+            x2, y2 = polygon[j + 1]
+            area += (x2 - x1) * (y2 + y1) / 2
+        area = abs(area)
+        
+        print(f"  Approximate area: {area:.2f} square units")
+        
+        # Print bounding box
+        xs = [x for x, y in polygon]
+        ys = [y for x, y in polygon]
+        print(f"  Bounding box: x=[{min(xs):.2f}, {max(xs):.2f}], y=[{min(ys):.2f}, {max(ys):.2f}]")
+        print()
+
+
+
+
+def export_mesh_to_json(mesh, filename):
+    """Save mesh dictionary to JSON file."""
+    import json
+    import numpy as np
+    
+    # Convert numpy arrays to lists for JSON serialization
+    mesh_json = {}
+    for key, value in mesh.items():
+        if isinstance(value, np.ndarray):
+            mesh_json[key] = value.tolist()
+        else:
+            mesh_json[key] = value
+    
+    with open(filename, 'w') as f:
+        json.dump(mesh_json, f, indent=2)
+    
+    print(f"Mesh saved to {filename}")
+
+def import_mesh_from_json(filename):
+    """Load mesh dictionary from JSON file."""
+    import json
+    import numpy as np
+    
+    with open(filename, 'r') as f:
+        mesh_json = json.load(f)
+    
+    # Convert lists back to numpy arrays
+    mesh = {}
+    for key, value in mesh_json.items():
+        if isinstance(value, list):
+            mesh[key] = np.array(value)
+        else:
+            mesh[key] = value
+    
+    return mesh
+
+def remove_duplicate_endpoint(poly, tol=1e-8):
+    if len(poly) > 1 and abs(poly[0][0] - poly[-1][0]) < tol and abs(poly[0][1] - poly[-1][1]) < tol:
+        return poly[:-1]
+    return poly
+
+
+def extract_1d_elements_from_2d_edges(nodes, elements_2d, element_types_2d, lines, debug=False):
+    """
+    Extract 1D elements from 2D element edges that lie along reinforcement lines.
+    This ensures proper finite element integration where 1D elements are shared edges of 2D elements.
+    
+    Parameters:
+        nodes: np.ndarray of node coordinates (n_nodes, 2)
+        elements_2d: np.ndarray of 2D element vertex indices (n_elements, 9)
+        element_types_2d: np.ndarray indicating 2D element type (3, 4, 6, 8, or 9 nodes)
+        lines: List of reinforcement lines, each defined by list of (x, y) tuples
+        debug: Enable debug output
+        
+    Returns:
+        tuple: (elements_1d, mat_ids_1d, element_node_counts_1d)
+    """
+    import numpy as np
+    from collections import defaultdict
+    
+    elements_1d = []
+    mat_ids_1d = []
+    element_node_counts_1d = []
+    
+    # Build edge-to-element mapping from 2D elements
+    edge_to_element = defaultdict(list)  # edge (n1, n2) -> list of element indices
+    element_edges = {}  # element_idx -> list of edges
+    
+    for elem_idx, (element, elem_type) in enumerate(zip(elements_2d, element_types_2d)):
+        edges = []
+        
+        if elem_type in [3, 6]:  # Triangle
+            # Triangle edges: (0,1), (1,2), (2,0)
+            corner_nodes = [element[0], element[1], element[2]]
+            edge_pairs = [(0, 1), (1, 2), (2, 0)]
+            
+            for i, j in edge_pairs:
+                n1, n2 = corner_nodes[i], corner_nodes[j]
+                edge_key = (min(n1, n2), max(n1, n2))  # Canonical edge representation
+                edges.append(edge_key)
+                edge_to_element[edge_key].append(elem_idx)
+                
+        elif elem_type in [4, 8, 9]:  # Quadrilateral
+            # Quadrilateral edges: (0,1), (1,2), (2,3), (3,0)
+            corner_nodes = [element[0], element[1], element[2], element[3]]
+            edge_pairs = [(0, 1), (1, 2), (2, 3), (3, 0)]
+            
+            for i, j in edge_pairs:
+                n1, n2 = corner_nodes[i], corner_nodes[j]
+                edge_key = (min(n1, n2), max(n1, n2))  # Canonical edge representation
+                edges.append(edge_key)
+                edge_to_element[edge_key].append(elem_idx)
+        
+        element_edges[elem_idx] = edges
+    
+    if debug:
+        print(f"Built edge map with {len(edge_to_element)} unique edges from {len(elements_2d)} 2D elements")
+    
+    # For each reinforcement line, find 2D element edges that lie along it
+    for line_idx, line_pts in enumerate(lines):
+        line_pts_clean = remove_duplicate_endpoint(list(line_pts))
+        
+        if len(line_pts_clean) < 2:
+            continue
+            
+        if debug:
+            print(f"Processing reinforcement line {line_idx}: {line_pts_clean}")
+        
+        # Find all 2D element edges that lie along this reinforcement line
+        line_edges = []
+        
+        for edge_key, elem_indices in edge_to_element.items():
+            n1, n2 = edge_key
+            
+            # Get coordinates of edge endpoints
+            coord1 = nodes[n1]
+            coord2 = nodes[n2]
+            
+            # Check if this edge lies along the reinforcement line
+            if is_edge_on_reinforcement_line(coord1, coord2, line_pts_clean, tolerance=1e-6):
+                line_edges.append((n1, n2))
+                if debug:
+                    print(f"  Found edge ({n1}, {n2}) at coords {coord1} -> {coord2}")
+        
+        # Sort edges to form continuous 1D elements along the line
+        if line_edges:
+            sorted_edges = sort_edges_along_line(line_edges, nodes, line_pts_clean, debug)
+            
+            # Create 1D elements from sorted edges
+            for n1, n2 in sorted_edges:
+                # For linear elements, just use the two nodes
+                elements_1d.append([n1, n2, 0])  # Pad to 3 columns
+                mat_ids_1d.append(line_idx)
+                element_node_counts_1d.append(2)
+            
+            if debug:
+                print(f"  Created {len(sorted_edges)} 1D elements for line {line_idx}")
+    
+    if debug:
+        print(f"Total 1D elements extracted: {len(elements_1d)}")
+    
+    return elements_1d, mat_ids_1d, element_node_counts_1d
+
+
+def is_edge_on_reinforcement_line(coord1, coord2, line_pts, tolerance=1e-6):
+    """
+    Check if an edge lies along a reinforcement line.
+    
+    Parameters:
+        coord1, coord2: Edge endpoint coordinates (x, y)
+        line_pts: List of (x, y) points defining the reinforcement line
+        tolerance: Tolerance for coincidence checking
+        
+    Returns:
+        bool: True if edge lies along the reinforcement line
+    """
+    x1, y1 = coord1
+    x2, y2 = coord2
+    
+    # Check if both endpoints lie on the reinforcement line
+    point1_on_line = is_point_on_line_segments(coord1, line_pts, tolerance)
+    point2_on_line = is_point_on_line_segments(coord2, line_pts, tolerance)
+    
+    if not (point1_on_line and point2_on_line):
+        return False
+    
+    # Additional check: ensure edge direction is consistent with line direction
+    # This prevents selecting edges that cross the reinforcement line
+    edge_vector = np.array([x2 - x1, y2 - y1])
+    edge_length = np.linalg.norm(edge_vector)
+    
+    if edge_length < tolerance:
+        return False
+    
+    edge_unit = edge_vector / edge_length
+    
+    # Check alignment with any segment of the reinforcement line
+    # This allows edges to span multiple segments after intersection preprocessing
+    for i in range(len(line_pts) - 1):
+        seg_start = np.array(line_pts[i])
+        seg_end = np.array(line_pts[i + 1])
+        seg_vector = seg_end - seg_start
+        seg_length = np.linalg.norm(seg_vector)
+        
+        if seg_length < tolerance:
+            continue
+            
+        seg_unit = seg_vector / seg_length
+        
+        # Check if edge is aligned with this segment (or opposite direction)
+        dot_product = abs(np.dot(edge_unit, seg_unit))
+        if dot_product > 0.95:  # Nearly parallel (cos(18°) ≈ 0.95)
+            # More flexible check: edge should be collinear with the reinforcement line
+            # and both endpoints should lie on the line (but not necessarily on the same segment)
+            return True
+    
+    return False
+
+
+def is_point_on_line_segments(point, line_pts, tolerance=1e-6):
+    """
+    Check if a point lies on any segment of a multi-segment line.
+    
+    Parameters:
+        point: (x, y) coordinates of point to check
+        line_pts: List of (x, y) points defining the line segments
+        tolerance: Tolerance for coincidence checking
+        
+    Returns:
+        bool: True if point lies on any line segment
+    """
+    for i in range(len(line_pts) - 1):
+        if is_point_on_line_segment(point, line_pts[i], line_pts[i + 1], tolerance):
+            return True
+    return False
+
+
+def is_point_on_line_segment(point, seg_start, seg_end, tolerance=1e-6):
+    """
+    Check if a point lies on a line segment.
+    
+    Parameters:
+        point: (x, y) coordinates of point to check
+        seg_start: (x, y) coordinates of segment start
+        seg_end: (x, y) coordinates of segment end
+        tolerance: Tolerance for coincidence checking
+        
+    Returns:
+        bool: True if point lies on the line segment
+    """
+    px, py = point
+    x1, y1 = seg_start
+    x2, y2 = seg_end
+    
+    # Check if point is within bounding box of segment
+    if not (min(x1, x2) - tolerance <= px <= max(x1, x2) + tolerance and
+            min(y1, y2) - tolerance <= py <= max(y1, y2) + tolerance):
+        return False
+    
+    # Check collinearity using cross product
+    cross_product = abs((py - y1) * (x2 - x1) - (px - x1) * (y2 - y1))
+    
+    # Check if cross product is close to zero (collinear)
+    if cross_product < tolerance:
+        # Verify point is between segment endpoints using dot product
+        dot_product = (px - x1) * (x2 - x1) + (py - y1) * (y2 - y1)
+        segment_length_sq = (x2 - x1) ** 2 + (y2 - y1) ** 2
+        
+        if segment_length_sq < tolerance:  # Degenerate segment
+            return abs(px - x1) < tolerance and abs(py - y1) < tolerance
+        
+        # Parameter t should be between 0 and 1 for point to be on segment
+        t = dot_product / segment_length_sq
+        return -tolerance <= t <= 1 + tolerance
+    
+    return False
+
+
+def sort_edges_along_line(edges, nodes, line_pts, debug=False):
+    """
+    Sort edges to form a continuous sequence along a reinforcement line.
+    
+    Parameters:
+        edges: List of (n1, n2) edge tuples
+        nodes: Node coordinates array
+        line_pts: Reinforcement line points
+        debug: Enable debug output
+        
+    Returns:
+        list: Sorted list of (n1, n2) edge tuples
+    """
+    if not edges:
+        return []
+    
+    if len(edges) == 1:
+        return edges
+    
+    # Build connectivity graph
+    node_connections = defaultdict(list)
+    for n1, n2 in edges:
+        node_connections[n1].append(n2)
+        node_connections[n2].append(n1)
+    
+    # Find start node (should have only one connection, or be closest to line start)
+    line_start = np.array(line_pts[0])
+    line_end = np.array(line_pts[-1])
+    
+    start_candidates = []
+    for node in node_connections:
+        if len(node_connections[node]) == 1:  # End node
+            start_candidates.append(node)
+    
+    if not start_candidates:
+        # No clear end nodes, use node closest to line start
+        min_dist = float('inf')
+        start_node = list(node_connections.keys())[0]
+        for node in node_connections:
+            dist = np.linalg.norm(nodes[node] - line_start)
+            if dist < min_dist:
+                min_dist = dist
+                start_node = node
+    else:
+        # Choose end node closest to line start
+        min_dist = float('inf')
+        start_node = start_candidates[0]
+        for node in start_candidates:
+            dist = np.linalg.norm(nodes[node] - line_start)
+            if dist < min_dist:
+                min_dist = dist
+                start_node = node
+    
+    # Trace path from start node
+    sorted_edges = []
+    used_edges = set()
+    current_node = start_node
+    
+    while True:
+        # Find next unused edge from current node
+        next_node = None
+        for neighbor in node_connections[current_node]:
+            edge_key = (min(current_node, neighbor), max(current_node, neighbor))
+            if edge_key not in used_edges:
+                next_node = neighbor
+                used_edges.add(edge_key)
+                sorted_edges.append((current_node, next_node))
+                break
+        
+        if next_node is None:
+            break
+            
+        current_node = next_node
+    
+    if debug:
+        print(f"    Sorted {len(sorted_edges)} edges along line")
+    
+    return sorted_edges
+
+def verify_mesh_connectivity(mesh, tolerance=1e-8):
+    """
+    Verify that the mesh is properly connected by checking for duplicate nodes at shared boundaries.
+    
+    Parameters:
+        mesh: Mesh dictionary with 'nodes' and 'elements' keys
+        tolerance: Tolerance for considering nodes as duplicates
+    
+    Returns:
+        dict: Connectivity verification results
+    """
+    import numpy as np
+    from collections import defaultdict
+    
+    nodes = mesh["nodes"]
+    elements = mesh["elements"]
+    
+    # Find duplicate nodes (nodes at same location)
+    duplicate_groups = []
+    used_indices = set()
+    
+    for i in range(len(nodes)):
+        if i in used_indices:
+            continue
+            
+        duplicates = [i]
+        for j in range(i + 1, len(nodes)):
+            if j in used_indices:
+                continue
+                
+            if np.linalg.norm(nodes[i] - nodes[j]) < tolerance:
+                duplicates.append(j)
+                used_indices.add(j)
+        
+        if len(duplicates) > 1:
+            duplicate_groups.append(duplicates)
+            used_indices.add(i)
+    
+    # Check element connectivity
+    element_connectivity = defaultdict(set)
+    for elem_idx, element in enumerate(elements):
+        for node_idx in element:
+            element_connectivity[node_idx].add(elem_idx)
+    
+    # Find isolated nodes (nodes not used by any element)
+    isolated_nodes = []
+    for i in range(len(nodes)):
+        if i not in element_connectivity:
+            isolated_nodes.append(i)
+    
+    # Find elements with duplicate nodes
+    elements_with_duplicates = []
+    for elem_idx, element in enumerate(elements):
+        unique_nodes = set(element)
+        if len(unique_nodes) != len(element):
+            elements_with_duplicates.append(elem_idx)
+    
+    results = {
+        "total_nodes": len(nodes),
+        "total_elements": len(elements),
+        "duplicate_node_groups": duplicate_groups,
+        "isolated_nodes": isolated_nodes,
+        "elements_with_duplicates": elements_with_duplicates,
+        "is_connected": len(duplicate_groups) == 0 and len(isolated_nodes) == 0
+    }
+    
+    return results
+
+def print_mesh_connectivity_report(mesh, tolerance=1e-8):
+    """
+    Print a detailed report about mesh connectivity.
+    
+    Parameters:
+        mesh: Mesh dictionary
+        tolerance: Tolerance for considering nodes as duplicates
+    """
+    results = verify_mesh_connectivity(mesh, tolerance)
+    
+    print("=== MESH CONNECTIVITY REPORT ===")
+    print(f"Total nodes: {results['total_nodes']}")
+    print(f"Total elements: {results['total_elements']}")
+    print(f"Mesh is properly connected: {results['is_connected']}")
+    print()
+    
+    if results['duplicate_node_groups']:
+        print(f"WARNING: Found {len(results['duplicate_node_groups'])} groups of duplicate nodes:")
+        for i, group in enumerate(results['duplicate_node_groups']):
+            print(f"  Group {i+1}: Nodes {group} at position {mesh['nodes'][group[0]]}")
+        print()
+    
+    if results['isolated_nodes']:
+        print(f"WARNING: Found {len(results['isolated_nodes'])} isolated nodes:")
+        for node_idx in results['isolated_nodes']:
+            print(f"  Node {node_idx} at position {mesh['nodes'][node_idx]}")
+        print()
+    
+    if results['elements_with_duplicates']:
+        print(f"WARNING: Found {len(results['elements_with_duplicates'])} elements with duplicate nodes:")
+        for elem_idx in results['elements_with_duplicates']:
+            print(f"  Element {elem_idx}: {mesh['elements'][elem_idx]}")
+        print()
+    
+    if results['is_connected']:
+        print("✓ Mesh connectivity is good - no duplicate nodes or isolated nodes found.")
+    else:
+        print("✗ Mesh connectivity issues detected. Consider regenerating the mesh.")
+
+def find_element_containing_point(nodes, elements, element_types, point):
+    """
+    Find which element contains the given point using spatial indexing for efficiency.
+    
+    Parameters:
+        nodes: np.ndarray of node coordinates (n_nodes, 2)
+        elements: np.ndarray of element vertex indices (n_elements, 9) - unused nodes set to 0
+        element_types: np.ndarray indicating element type (3, 4, 6, 8, or 9 nodes)
+        point: tuple (x, y) coordinates of the point to find
+        
+    Returns:
+        int: Index of the element containing the point, or -1 if not found
+    """
+    x, y = point
+    
+    # Use spatial indexing to find candidate elements quickly
+    # Build spatial hash grid if not already built
+    if not hasattr(find_element_containing_point, '_spatial_grid'):
+        find_element_containing_point._spatial_grid = _build_spatial_grid(nodes, elements, element_types)
+    
+    spatial_grid = find_element_containing_point._spatial_grid
+    
+    # Find grid cell containing the point
+    grid_x = int((x - spatial_grid['x_min']) / spatial_grid['cell_size'])
+    grid_y = int((y - spatial_grid['y_min']) / spatial_grid['cell_size'])
+    
+    # Get candidate elements from this cell and neighboring cells
+    candidate_elements = set()
+    for dx in [-1, 0, 1]:
+        for dy in [-1, 0, 1]:
+            cell_key = (grid_x + dx, grid_y + dy)
+            if cell_key in spatial_grid['cells']:
+                candidate_elements.update(spatial_grid['cells'][cell_key])
+    
+    # Check only the candidate elements
+    for elem_idx in candidate_elements:
+        element = elements[elem_idx]
+        elem_type = element_types[elem_idx]
+        
+        if elem_type in [3, 6]:  # Triangle (linear or quadratic)
+            # For point-in-element testing, use only corner nodes
+            x1, y1 = nodes[element[0]]
+            x2, y2 = nodes[element[1]]
+            x3, y3 = nodes[element[2]]
+            
+            # Calculate barycentric coordinates
+            det = (y2 - y3) * (x1 - x3) + (x3 - x2) * (y1 - y3)
+            if abs(det) < 1e-12:  # Degenerate triangle
+                continue
+                
+            lambda1 = ((y2 - y3) * (x - x3) + (x3 - x2) * (y - y3)) / det
+            lambda2 = ((y3 - y1) * (x - x3) + (x1 - x3) * (y - y3)) / det
+            lambda3 = 1.0 - lambda1 - lambda2
+            
+            # Check if point is inside triangle (all barycentric coordinates >= 0)
+            if lambda1 >= -1e-12 and lambda2 >= -1e-12 and lambda3 >= -1e-12:
+                return elem_idx
+                
+        elif elem_type in [4, 8, 9]:  # Quadrilateral (linear or quadratic)
+            # For point-in-element testing, use only corner nodes
+            x1, y1 = nodes[element[0]]
+            x2, y2 = nodes[element[1]]
+            x3, y3 = nodes[element[2]]
+            x4, y4 = nodes[element[3]]
+            
+            # Use point-in-polygon test for quadrilaterals
+            # Check if point is inside by counting crossings
+            vertices = [(x1, y1), (x2, y2), (x3, y3), (x4, y4)]
+            inside = False
+            
+            for j in range(len(vertices)):
+                xi, yi = vertices[j]
+                xj, yj = vertices[(j + 1) % len(vertices)]
+                
+                if ((yi > y) != (yj > y)) and (x < (xj - xi) * (y - yi) / (yj - yi) + xi):
+                    inside = not inside
+            
+            if inside:
+                return elem_idx
+    
+    return -1  # Point not found in any element
+
+
+def _build_spatial_grid(nodes, elements, element_types):
+    """
+    Build a spatial hash grid for efficient element searching.
+    
+    Parameters:
+        nodes: np.ndarray of node coordinates (n_nodes, 2)
+        elements: np.ndarray of element vertex indices (n_elements, 8)
+        element_types: np.ndarray indicating element type (3, 4, 6, or 8 nodes)
+        
+    Returns:
+        dict: Spatial grid data structure
+    """
+    # Calculate bounding box
+    x_coords = nodes[:, 0]
+    y_coords = nodes[:, 1]
+    x_min, x_max = x_coords.min(), x_coords.max()
+    y_min, y_max = y_coords.min(), y_coords.max()
+    
+    # Determine optimal cell size based on average element size
+    total_area = 0
+    for i, (element, elem_type) in enumerate(zip(elements, element_types)):
+        if elem_type in [3, 6]:  # Triangle
+            x1, y1 = nodes[element[0]]
+            x2, y2 = nodes[element[1]]
+            x3, y3 = nodes[element[2]]
+            area = 0.5 * abs((x2 - x1) * (y3 - y1) - (x3 - x1) * (y2 - y1))
+        else:  # Quadrilateral (4 or 8 nodes)
+            x1, y1 = nodes[element[0]]
+            x2, y2 = nodes[element[1]]
+            x3, y3 = nodes[element[2]]
+            x4, y4 = nodes[element[3]]
+            area = 0.5 * abs((x2 - x1) * (y4 - y1) - (x4 - x1) * (y2 - y1))
+        total_area += area
+    
+    avg_element_area = total_area / len(elements)
+    # Cell size should be roughly 2-3 times the square root of average element area
+    cell_size = max(0.1, 2.5 * np.sqrt(avg_element_area))
+    
+    # Build grid
+    grid = {
+        'x_min': x_min,
+        'y_min': y_min,
+        'cell_size': cell_size,
+        'cells': {}
+    }
+    
+    # Assign elements to grid cells
+    for elem_idx, (element, elem_type) in enumerate(zip(elements, element_types)):
+        # Calculate element bounding box
+        if elem_type in [3, 6]:  # Triangle
+            x_coords = [nodes[element[0]][0], nodes[element[1]][0], nodes[element[2]][0]]
+            y_coords = [nodes[element[0]][1], nodes[element[1]][1], nodes[element[2]][1]]
+        else:  # Quadrilateral (4 or 8 nodes)
+            x_coords = [nodes[element[0]][0], nodes[element[1]][0], nodes[element[2]][0], nodes[element[3]][0]]
+            y_coords = [nodes[element[0]][1], nodes[element[1]][1], nodes[element[2]][1], nodes[element[3]][1]]
+        
+        elem_x_min, elem_x_max = min(x_coords), max(x_coords)
+        elem_y_min, elem_y_max = min(y_coords), max(y_coords)
+        
+        # Find grid cells that overlap with this element
+        start_x = int((elem_x_min - x_min) / cell_size)
+        end_x = int((elem_x_max - x_min) / cell_size) + 1
+        start_y = int((elem_y_min - y_min) / cell_size)
+        end_y = int((elem_y_max - y_min) / cell_size) + 1
+        
+        # Add element to all overlapping cells
+        for grid_x in range(start_x, end_x + 1):
+            for grid_y in range(start_y, end_y + 1):
+                cell_key = (grid_x, grid_y)
+                if cell_key not in grid['cells']:
+                    grid['cells'][cell_key] = set()
+                grid['cells'][cell_key].add(elem_idx)
+    
+    return grid
+
+
+def interpolate_at_point(nodes, elements, element_types, values, point):
+    """
+    Interpolate values at a given point using the mesh.
+    
+    Parameters:
+        nodes: np.ndarray of node coordinates (n_nodes, 2)
+        elements: np.ndarray of element vertex indices (n_elements, 8)
+        element_types: np.ndarray indicating element type (3, 4, 6, or 8 nodes)
+        values: np.ndarray of values at nodes (n_nodes,)
+        point: tuple (x, y) coordinates of the point to interpolate at
+        
+    Returns:
+        float: Interpolated value at the point, or 0.0 if point not found
+    """
+    # Find the element containing the point
+    element_idx = find_element_containing_point(nodes, elements, element_types, point)
+    
+    if element_idx == -1:
+        return 0.0  # Point not found in any element
+    
+    element = elements[element_idx]
+    elem_type = element_types[element_idx]
+    x, y = point
+    
+    if elem_type == 3:  # Linear triangle
+        # Get triangle vertices and values
+        x1, y1 = nodes[element[0]]
+        x2, y2 = nodes[element[1]]
+        x3, y3 = nodes[element[2]]
+        v1 = values[element[0]]
+        v2 = values[element[1]]
+        v3 = values[element[2]]
+        
+        # Calculate barycentric coordinates
+        det = (y2 - y3) * (x1 - x3) + (x3 - x2) * (y1 - y3)
+        lambda1 = ((y2 - y3) * (x - x3) + (x3 - x2) * (y - y3)) / det
+        lambda2 = ((y3 - y1) * (x - x3) + (x1 - x3) * (y - y3)) / det
+        lambda3 = 1.0 - lambda1 - lambda2
+        
+        # Interpolate using barycentric coordinates
+        interpolated_value = lambda1 * v1 + lambda2 * v2 + lambda3 * v3
+        
+    elif elem_type == 6:  # Quadratic triangle
+        # Get all 6 nodes: corners (0,1,2) and midpoints (3,4,5)
+        # Node ordering: 0-1-2 corners, 3 midpoint of 0-1, 4 midpoint of 1-2, 5 midpoint of 2-0
+        corner_nodes = [element[0], element[1], element[2]]
+        midpoint_nodes = [element[3], element[4], element[5]]
+        
+        # Get coordinates
+        x1, y1 = nodes[corner_nodes[0]]  # Node 0
+        x2, y2 = nodes[corner_nodes[1]]  # Node 1  
+        x3, y3 = nodes[corner_nodes[2]]  # Node 2
+        
+        # Calculate barycentric coordinates (L1, L2, L3)
+        det = (y2 - y3) * (x1 - x3) + (x3 - x2) * (y1 - y3)
+        L1 = ((y2 - y3) * (x - x3) + (x3 - x2) * (y - y3)) / det
+        L2 = ((y3 - y1) * (x - x3) + (x1 - x3) * (y - y3)) / det
+        L3 = 1.0 - L1 - L2
+        
+        # Quadratic shape functions for 6-node triangle
+        N = np.zeros(6)
+        N[0] = L1 * (2*L1 - 1)     # Corner node 0
+        N[1] = L2 * (2*L2 - 1)     # Corner node 1
+        N[2] = L3 * (2*L3 - 1)     # Corner node 2
+        N[3] = 4 * L1 * L2         # Midpoint node 0-1
+        N[4] = 4 * L2 * L3         # Midpoint node 1-2
+        N[5] = 4 * L3 * L1         # Midpoint node 2-0
+        
+        # Interpolate using quadratic shape functions
+        interpolated_value = 0.0
+        for i in range(6):
+            interpolated_value += N[i] * values[element[i]]
+        
+    elif elem_type == 4:  # Linear quadrilateral
+        # Get quadrilateral vertices and values
+        x1, y1 = nodes[element[0]]
+        x2, y2 = nodes[element[1]]
+        x3, y3 = nodes[element[2]]
+        x4, y4 = nodes[element[3]]
+        v1 = values[element[0]]
+        v2 = values[element[1]]
+        v3 = values[element[2]]
+        v4 = values[element[3]]
+        
+        # Use proper bilinear shape functions for quadrilaterals
+        # Map to natural coordinates (xi, eta) in [-1, 1] x [-1, 1]
+        
+        # For bilinear quad4, use iterative Newton-Raphson to find natural coordinates
+        # Initial guess at element center
+        xi, eta = 0.0, 0.0
+        
+        # Newton-Raphson iteration to find (xi, eta) such that physical coordinates match
+        for _ in range(10):  # Max 10 iterations
+            # Bilinear shape functions
+            N = np.array([
+                0.25 * (1-xi) * (1-eta),  # Node 0
+                0.25 * (1+xi) * (1-eta),  # Node 1
+                0.25 * (1+xi) * (1+eta),  # Node 2
+                0.25 * (1-xi) * (1+eta)   # Node 3
+            ])
+            
+            # Shape function derivatives
+            dN_dxi = np.array([
+                -0.25 * (1-eta),  # Node 0
+                 0.25 * (1-eta),  # Node 1
+                 0.25 * (1+eta),  # Node 2
+                -0.25 * (1+eta)   # Node 3
+            ])
+            
+            dN_deta = np.array([
+                -0.25 * (1-xi),   # Node 0
+                -0.25 * (1+xi),   # Node 1
+                 0.25 * (1+xi),   # Node 2
+                 0.25 * (1-xi)    # Node 3
+            ])
+            
+            # Current physical coordinates
+            x_curr = N[0]*x1 + N[1]*x2 + N[2]*x3 + N[3]*x4
+            y_curr = N[0]*y1 + N[1]*y2 + N[2]*y3 + N[3]*y4
+            
+            # Residual
+            fx = x_curr - x
+            fy = y_curr - y
+            
+            if abs(fx) < 1e-10 and abs(fy) < 1e-10:
+                break
+                
+            # Jacobian
+            dx_dxi = dN_dxi[0]*x1 + dN_dxi[1]*x2 + dN_dxi[2]*x3 + dN_dxi[3]*x4
+            dx_deta = dN_deta[0]*x1 + dN_deta[1]*x2 + dN_deta[2]*x3 + dN_deta[3]*x4
+            dy_dxi = dN_dxi[0]*y1 + dN_dxi[1]*y2 + dN_dxi[2]*y3 + dN_dxi[3]*y4
+            dy_deta = dN_deta[0]*y1 + dN_deta[1]*y2 + dN_deta[2]*y3 + dN_deta[3]*y4
+            
+            det_J = dx_dxi * dy_deta - dx_deta * dy_dxi
+            if abs(det_J) < 1e-12:
+                break
+            
+            # Newton-Raphson update
+            dxi = (dy_deta * fx - dx_deta * fy) / det_J
+            deta = (-dy_dxi * fx + dx_dxi * fy) / det_J
+            
+            xi -= dxi
+            eta -= deta
+            
+            # Clamp to [-1,1]
+            xi = max(-1, min(1, xi))
+            eta = max(-1, min(1, eta))
+        
+        # Final bilinear shape functions
+        N = np.array([
+            0.25 * (1-xi) * (1-eta),  # Node 0
+            0.25 * (1+xi) * (1-eta),  # Node 1
+            0.25 * (1+xi) * (1+eta),  # Node 2
+            0.25 * (1-xi) * (1+eta)   # Node 3
+        ])
+        
+        # Interpolate using bilinear shape functions
+        interpolated_value = N[0]*v1 + N[1]*v2 + N[2]*v3 + N[3]*v4
+        
+    elif elem_type == 8:  # Quadratic quadrilateral
+        # Get all 8 nodes: corners (0,1,2,3) and midpoints (4,5,6,7)
+        # Node ordering: 0-1-2-3 corners, 4 midpoint of 0-1, 5 midpoint of 1-2, 
+        #                6 midpoint of 2-3, 7 midpoint of 3-0
+        
+        # Get corner coordinates for mapping to natural coordinates
+        x1, y1 = nodes[element[0]]  # Node 0
+        x2, y2 = nodes[element[1]]  # Node 1
+        x3, y3 = nodes[element[2]]  # Node 2
+        x4, y4 = nodes[element[3]]  # Node 3
+        
+        # For quadratic quads, we need to map from physical (x,y) to natural coordinates (xi,eta)
+        # This is complex for general quadrilaterals, so use simplified approach:
+        # Map to unit square [-1,1] x [-1,1] using bilinear mapping of corners
+        
+        # Bilinear inverse mapping (approximate for general quads)
+        # Solve for natural coordinates xi, eta in [-1,1] x [-1,1]
+        
+        # For simplicity, use area coordinate method similar to linear quad
+        # but with quadratic shape functions
+        
+        # Calculate area coordinates (this is an approximation)
+        A_total = 0.5 * abs((x3-x1)*(y4-y2) - (x4-x2)*(y3-y1))
+        if A_total < 1e-12:
+            # Degenerate element, fall back to linear
+            A1 = abs((x - x1) * (y2 - y1) - (x2 - x1) * (y - y1)) / 2
+            A2 = abs((x - x2) * (y3 - y2) - (x3 - x2) * (y - y2)) / 2
+            A3 = abs((x - x3) * (y4 - y3) - (x4 - x3) * (y - y3)) / 2
+            A4 = abs((x - x4) * (y1 - y4) - (x1 - x4) * (y - y4)) / 2
+            A_sum = A1 + A2 + A3 + A4
+            if A_sum > 1e-12:
+                w1, w2, w3, w4 = A1/A_sum, A2/A_sum, A3/A_sum, A4/A_sum
+            else:
+                w1 = w2 = w3 = w4 = 0.25
+            
+            # Linear interpolation as fallback
+            interpolated_value = (w1 * values[element[0]] + w2 * values[element[1]] + 
+                                w3 * values[element[2]] + w4 * values[element[3]])
+        else:
+            # For proper quadratic interpolation, we need natural coordinates
+            # This is a simplified implementation - full implementation would solve
+            # the nonlinear system for xi,eta
+            
+            # Use parametric coordinates estimation
+            # Map point to approximate natural coordinates
+            xi_approx = 2 * (x - 0.5*(x1+x3)) / (x2+x3-x1-x4) if abs(x2+x3-x1-x4) > 1e-12 else 0
+            eta_approx = 2 * (y - 0.5*(y1+y3)) / (y2+y4-y1-y3) if abs(y2+y4-y1-y3) > 1e-12 else 0
+            
+            # Clamp to [-1,1]
+            xi = max(-1, min(1, xi_approx))
+            eta = max(-1, min(1, eta_approx))
+            
+            # Quadratic shape functions for 8-node quad in natural coordinates
+            N = np.zeros(8)
+            # Corner nodes
+            N[0] = 0.25 * (1-xi) * (1-eta) * (-xi-eta-1)   # Node 0
+            N[1] = 0.25 * (1+xi) * (1-eta) * (xi-eta-1)    # Node 1  
+            N[2] = 0.25 * (1+xi) * (1+eta) * (xi+eta-1)    # Node 2
+            N[3] = 0.25 * (1-xi) * (1+eta) * (-xi+eta-1)   # Node 3
+            # Midpoint nodes
+            N[4] = 0.5 * (1-xi*xi) * (1-eta)               # Node 4 (midpoint 0-1)
+            N[5] = 0.5 * (1+xi) * (1-eta*eta)              # Node 5 (midpoint 1-2)
+            N[6] = 0.5 * (1-xi*xi) * (1+eta)               # Node 6 (midpoint 2-3)
+            N[7] = 0.5 * (1-xi) * (1-eta*eta)              # Node 7 (midpoint 3-0)
+            
+            # Interpolate using quadratic shape functions
+            interpolated_value = 0.0
+            for i in range(8):
+                interpolated_value += N[i] * values[element[i]]
+    
+    elif elem_type == 9:  # Biquadratic quadrilateral (9-node Lagrange)
+        # Get all 9 nodes: corners (0,1,2,3), edges (4,5,6,7), and center (8)
+        # Node ordering: 0-1-2-3 corners, 4 midpoint of 0-1, 5 midpoint of 1-2,
+        #                6 midpoint of 2-3, 7 midpoint of 3-0, 8 center
+        
+        # Get corner coordinates for mapping to natural coordinates
+        x1, y1 = nodes[element[0]]  # Node 0
+        x2, y2 = nodes[element[1]]  # Node 1
+        x3, y3 = nodes[element[2]]  # Node 2
+        x4, y4 = nodes[element[3]]  # Node 3
+        
+        # Newton-Raphson iteration to find natural coordinates (xi, eta)
+        xi, eta = 0.0, 0.0  # Initial guess at element center
+        
+        for _ in range(10):  # Max 10 iterations
+            # Biquadratic Lagrange shape functions for all 9 nodes
+            N = np.zeros(9)
+            # Corner nodes
+            N[0] = 0.25 * xi * (xi-1) * eta * (eta-1)     # Node 0: (-1,-1)
+            N[1] = 0.25 * xi * (xi+1) * eta * (eta-1)     # Node 1: (1,-1)  
+            N[2] = 0.25 * xi * (xi+1) * eta * (eta+1)     # Node 2: (1,1)
+            N[3] = 0.25 * xi * (xi-1) * eta * (eta+1)     # Node 3: (-1,1)
+            # Edge nodes
+            N[4] = 0.5 * (1-xi*xi) * eta * (eta-1)        # Node 4: (0,-1)
+            N[5] = 0.5 * xi * (xi+1) * (1-eta*eta)        # Node 5: (1,0)
+            N[6] = 0.5 * (1-xi*xi) * eta * (eta+1)        # Node 6: (0,1)
+            N[7] = 0.5 * xi * (xi-1) * (1-eta*eta)        # Node 7: (-1,0)
+            # Center node
+            N[8] = (1-xi*xi) * (1-eta*eta)                # Node 8: (0,0)
+            
+            # Shape function derivatives w.r.t. xi
+            dN_dxi = np.zeros(9)
+            dN_dxi[0] = 0.25 * (2*xi-1) * eta * (eta-1)
+            dN_dxi[1] = 0.25 * (2*xi+1) * eta * (eta-1)
+            dN_dxi[2] = 0.25 * (2*xi+1) * eta * (eta+1)
+            dN_dxi[3] = 0.25 * (2*xi-1) * eta * (eta+1)
+            dN_dxi[4] = -xi * eta * (eta-1)
+            dN_dxi[5] = 0.5 * (2*xi+1) * (1-eta*eta)
+            dN_dxi[6] = -xi * eta * (eta+1)
+            dN_dxi[7] = 0.5 * (2*xi-1) * (1-eta*eta)
+            dN_dxi[8] = -2*xi * (1-eta*eta)
+            
+            # Shape function derivatives w.r.t. eta
+            dN_deta = np.zeros(9)
+            dN_deta[0] = 0.25 * xi * (xi-1) * (2*eta-1)
+            dN_deta[1] = 0.25 * xi * (xi+1) * (2*eta-1)
+            dN_deta[2] = 0.25 * xi * (xi+1) * (2*eta+1)
+            dN_deta[3] = 0.25 * xi * (xi-1) * (2*eta+1)
+            dN_deta[4] = 0.5 * (1-xi*xi) * (2*eta-1)
+            dN_deta[5] = -eta * xi * (xi+1)
+            dN_deta[6] = 0.5 * (1-xi*xi) * (2*eta+1)
+            dN_deta[7] = -eta * xi * (xi-1)
+            dN_deta[8] = -2*eta * (1-xi*xi)
+            
+            # Current physical coordinates using all 9 nodes
+            node_coords = nodes[element[:9]]
+            x_curr = np.sum(N * node_coords[:, 0])
+            y_curr = np.sum(N * node_coords[:, 1])
+            
+            # Residual
+            fx = x_curr - x
+            fy = y_curr - y
+            
+            if abs(fx) < 1e-10 and abs(fy) < 1e-10:
+                break
+                
+            # Jacobian
+            dx_dxi = np.sum(dN_dxi * node_coords[:, 0])
+            dx_deta = np.sum(dN_deta * node_coords[:, 0])
+            dy_dxi = np.sum(dN_dxi * node_coords[:, 1])
+            dy_deta = np.sum(dN_deta * node_coords[:, 1])
+            
+            det_J = dx_dxi * dy_deta - dx_deta * dy_dxi
+            if abs(det_J) < 1e-12:
+                break
+            
+            # Newton-Raphson update
+            dxi = (dy_deta * fx - dx_deta * fy) / det_J
+            deta = (-dy_dxi * fx + dx_dxi * fy) / det_J
+            
+            xi -= dxi
+            eta -= deta
+            
+            # Clamp to [-1,1]
+            xi = max(-1, min(1, xi))
+            eta = max(-1, min(1, eta))
+        
+        # Final biquadratic shape functions
+        N = np.zeros(9)
+        N[0] = 0.25 * xi * (xi-1) * eta * (eta-1)     # Node 0
+        N[1] = 0.25 * xi * (xi+1) * eta * (eta-1)     # Node 1
+        N[2] = 0.25 * xi * (xi+1) * eta * (eta+1)     # Node 2
+        N[3] = 0.25 * xi * (xi-1) * eta * (eta+1)     # Node 3
+        N[4] = 0.5 * (1-xi*xi) * eta * (eta-1)        # Node 4
+        N[5] = 0.5 * xi * (xi+1) * (1-eta*eta)        # Node 5
+        N[6] = 0.5 * (1-xi*xi) * eta * (eta+1)        # Node 6
+        N[7] = 0.5 * xi * (xi-1) * (1-eta*eta)        # Node 7
+        N[8] = (1-xi*xi) * (1-eta*eta)                # Node 8
+        
+        # Interpolate using biquadratic shape functions
+        interpolated_value = 0.0
+        for i in range(9):
+            interpolated_value += N[i] * values[element[i]]
+    
+    else:
+        return 0.0  # Unknown element type
+    
+    # Return zero if interpolated value is negative (pore pressure cannot be negative)
+    return max(0.0, interpolated_value)
+
+
+def test_1d_element_alignment(mesh, reinforcement_lines, tolerance=1e-6, debug=True):
+    """
+    Test that 1D elements correctly align with reinforcement lines.
+    
+    This function verifies that:
+    1. Each reinforcement line is represented by a sequence of 1D elements
+    2. The 1D elements form continuous paths along each reinforcement line
+    3. The element endpoints match the expected line segment endpoints
+    
+    Parameters:
+        mesh: Dictionary containing nodes and 1D element data
+        reinforcement_lines: List of reinforcement lines, each containing coordinate tuples
+        tolerance: Tolerance for coordinate comparison (default 1e-6)
+        debug: Enable detailed debug output
+        
+    Returns:
+        bool: True if all tests pass, False otherwise
+    """
+    if debug:
+        print("\n=== Testing 1D Element Alignment ===")
+    
+    if 'elements_1d' not in mesh:
+        print("ERROR: No 1D elements found in mesh")
+        return False
+        
+    elements_1d = mesh['elements_1d']
+    if elements_1d is None or len(elements_1d) == 0:
+        print("ERROR: No 1D elements found in mesh")
+        return False
+    
+    nodes = np.array(mesh['nodes'])
+    elements_1d = mesh['elements_1d']
+    
+    if debug:
+        print(f"Testing {len(reinforcement_lines)} reinforcement lines")
+        print(f"Found {len(elements_1d)} 1D elements")
+    
+    success = True
+    
+    for line_idx, line_pts in enumerate(reinforcement_lines):
+        if debug:
+            print(f"\nTesting line {line_idx}: {line_pts}")
+        
+        # Remove duplicate endpoints and get expected segments
+        line_pts_clean = remove_duplicate_endpoint(list(line_pts))
+        if len(line_pts_clean) < 2:
+            if debug:
+                print(f"  Skipping line {line_idx}: insufficient points")
+            continue
+        
+        # Expected segments for this line
+        expected_segments = []
+        for i in range(len(line_pts_clean) - 1):
+            expected_segments.append((line_pts_clean[i], line_pts_clean[i + 1]))
+        
+        if debug:
+            print(f"  Expected {len(expected_segments)} segments:")
+            for i, (start, end) in enumerate(expected_segments):
+                print(f"    Segment {i}: {start} -> {end}")
+        
+        # Find 1D elements that belong to this reinforcement line using material IDs
+        line_elements = []
+        if 'element_materials_1d' in mesh:
+            element_materials_1d = mesh['element_materials_1d']
+            for elem_idx, (element, material_id) in enumerate(zip(elements_1d, element_materials_1d)):
+                # Skip zero-padded elements
+                if len(element) < 2 or element[1] == 0:
+                    continue
+                    
+                # Check if this element belongs to the current line
+                if material_id == line_idx + 1:  # Material IDs are 1-based
+                    # Get element coordinates
+                    try:
+                        coord1 = nodes[element[0]]
+                        coord2 = nodes[element[1]]
+                    except IndexError:
+                        if debug:
+                            print(f"  WARNING: Element {elem_idx} has invalid node indices {element[0]}, {element[1]}")
+                        continue
+                    
+                    line_elements.append((elem_idx, coord1, coord2))
+        else:
+            # Fallback: use the old method if material IDs are not available
+            for elem_idx, element in enumerate(elements_1d):
+                # Skip zero-padded elements
+                if len(element) < 2 or element[1] == 0:
+                    continue
+                    
+                # Get element coordinates
+                try:
+                    coord1 = nodes[element[0]]
+                    coord2 = nodes[element[1]]
+                except IndexError:
+                    if debug:
+                        print(f"  WARNING: Element {elem_idx} has invalid node indices {element[0]}, {element[1]}")
+                    continue
+                
+                # Check if this element lies on the current reinforcement line
+                if is_edge_on_reinforcement_line(coord1, coord2, line_pts_clean, tolerance):
+                    line_elements.append((elem_idx, coord1, coord2))
+        
+        if debug:
+            print(f"  Found {len(line_elements)} 1D elements on this line:")
+            for elem_idx, coord1, coord2 in line_elements:
+                print(f"    Element {elem_idx}: {coord1} -> {coord2}")
+        
+        # Test 1: Check that we have at least some 1D elements for this line
+        if len(line_elements) == 0:
+            print(f"ERROR: Line {line_idx} has no 1D elements")
+            success = False
+            continue
+        
+        # Test 2: Check that we have reasonable number of elements
+        # After intersection preprocessing, we may have more elements than original segments
+        # But we should have at least some elements for each line
+        if len(line_elements) == 0:
+            print(f"ERROR: Line {line_idx} has no 1D elements")
+            success = False
+            continue
+        
+        # Test 2: Check if elements form continuous path
+        if len(line_elements) > 1:
+            # Sort elements to form continuous sequence
+            sorted_elements = []
+            remaining_elements = line_elements.copy()
+            
+            # Start with first element
+            current_elem = remaining_elements.pop(0)
+            sorted_elements.append(current_elem)
+            
+            # Build chain by finding connecting elements
+            while remaining_elements:
+                last_coord = sorted_elements[-1][2]  # End coordinate of last element
+                
+                # Find next element that starts where last one ended
+                found_next = False
+                for i, (elem_idx, coord1, coord2) in enumerate(remaining_elements):
+                    if np.linalg.norm(np.array(coord1) - np.array(last_coord)) < tolerance:
+                        sorted_elements.append((elem_idx, coord1, coord2))
+                        remaining_elements.pop(i)
+                        found_next = True
+                        break
+                    elif np.linalg.norm(np.array(coord2) - np.array(last_coord)) < tolerance:
+                        # Element is reversed, flip it
+                        sorted_elements.append((elem_idx, coord2, coord1))
+                        remaining_elements.pop(i)
+                        found_next = True
+                        break
+                
+                if not found_next:
+                    print(f"ERROR: Line {line_idx} elements do not form continuous path")
+                    print(f"  Cannot connect from {last_coord}")
+                    print(f"  Remaining elements: {remaining_elements}")
+                    success = False
+                    break
+            
+            line_elements = sorted_elements
+        
+        # Test 3: Check that the 1D elements cover the reinforcement line from start to end
+        if len(line_elements) > 0:
+            # Get the start and end points of the reinforcement line
+            line_start = line_pts_clean[0]
+            line_end = line_pts_clean[-1]
+            
+            # Find the first and last 1D elements
+            first_elem = line_elements[0]
+            last_elem = line_elements[-1]
+            
+            # Check if the first element starts near the line start
+            first_start_dist = np.linalg.norm(np.array(first_elem[1]) - np.array(line_start))
+            first_end_dist = np.linalg.norm(np.array(first_elem[2]) - np.array(line_start))
+            
+            # Check if the last element ends near the line end
+            last_start_dist = np.linalg.norm(np.array(last_elem[1]) - np.array(line_end))
+            last_end_dist = np.linalg.norm(np.array(last_elem[2]) - np.array(line_end))
+            
+            # The first element should start near the line start (either direction)
+            # Be more flexible due to intersection preprocessing
+            if first_start_dist > tolerance * 10 and first_end_dist > tolerance * 10:
+                print(f"WARNING: Line {line_idx} first element does not start at line start")
+                print(f"  Line start: {line_start}")
+                print(f"  First element: {first_elem[1]} -> {first_elem[2]}")
+                print(f"  Start distances: {first_start_dist:.2e}, {first_end_dist:.2e}")
+                # Don't fail the test for this - just warn
+            
+            # The last element should end near the line end (either direction)
+            # Be more flexible due to intersection preprocessing
+            if last_start_dist > tolerance * 10 and last_end_dist > tolerance * 10:
+                print(f"WARNING: Line {line_idx} last element does not end at line end")
+                print(f"  Line end: {line_end}")
+                print(f"  Last element: {last_elem[1]} -> {last_elem[2]}")
+                print(f"  End distances: {last_start_dist:.2e}, {last_end_dist:.2e}")
+                # Don't fail the test for this - just warn
+        
+        # Test 4: Check that line path is continuous
+        if len(line_elements) > 1:
+            for i in range(len(line_elements) - 1):
+                end_coord = line_elements[i][2]  # End of current element
+                start_coord = line_elements[i + 1][1]  # Start of next element
+                
+                gap = np.linalg.norm(np.array(end_coord) - np.array(start_coord))
+                if gap > tolerance:
+                    print(f"ERROR: Line {line_idx} has gap between elements {i} and {i+1}")
+                    print(f"  Gap size: {gap:.2e}")
+                    print(f"  Element {i} end: {end_coord}")
+                    print(f"  Element {i+1} start: {start_coord}")
+                    success = False
+        
+        if debug and success:
+            print(f"  ✓ Line {line_idx} passes all alignment tests")
+    
+    if debug:
+        if success:
+            print("\n=== All 1D Element Alignment Tests PASSED ===")
+        else:
+            print("\n=== 1D Element Alignment Tests FAILED ===")
+    
+    return success
+
+def add_intersection_points_to_polygons(polygons, lines, debug=False):
+    """
+    Add intersection points between reinforcement lines and polygon edges to the polygon vertex lists.
+    This ensures that polygons have vertices at all intersection points with reinforcement lines.
+    
+    Parameters:
+        polygons: List of polygons (lists of (x,y) tuples)
+        lines: List of reinforcement lines (lists of (x,y) tuples)
+        debug: Enable debug output
+        
+    Returns:
+        Updated list of polygons with intersection points added
+    """
+    if not lines:
+        return polygons
+        
+    if debug:
+        print("Adding intersection points to polygons...")
+    
+    # Make a copy of polygons to modify
+    updated_polygons = []
+    for poly in polygons:
+        updated_polygons.append(list(poly))  # Convert to list for modification
+    
+    # Find all intersections
+    for line_idx, line_pts in enumerate(lines):
+        line_pts_clean = remove_duplicate_endpoint(list(line_pts))
+        
+        if debug:
+            print(f"Processing line {line_idx}: {line_pts_clean}")
+        
+        # Check each segment of the reinforcement line
+        for i in range(len(line_pts_clean) - 1):
+            line_seg_start = line_pts_clean[i]
+            line_seg_end = line_pts_clean[i + 1]
+            
+            # Check intersection with each polygon
+            for poly_idx, poly in enumerate(updated_polygons):
+                # Check each edge of this polygon
+                for j in range(len(poly)):
+                    poly_edge_start = poly[j]
+                    poly_edge_end = poly[(j + 1) % len(poly)]
+                    
+                    # Find intersection point if it exists
+                    intersection = line_segment_intersection(
+                        line_seg_start, line_seg_end,
+                        poly_edge_start, poly_edge_end
+                    )
+                    
+                    if intersection:
+                        if debug:
+                            print(f"Found intersection {intersection} between line {line_idx} segment {i} and polygon {poly_idx} edge {j}")
+                        
+                        # Check if intersection point is already a vertex of this polygon
+                        is_vertex = False
+                        for vertex in poly:
+                            if abs(vertex[0] - intersection[0]) < 1e-8 and abs(vertex[1] - intersection[1]) < 1e-8:
+                                is_vertex = True
+                                break
+                        
+                        if not is_vertex:
+                            # Insert intersection point into polygon at the correct position
+                            # Insert after vertex j (which is the start of the edge)
+                            insert_idx = j + 1
+                            updated_polygons[poly_idx].insert(insert_idx, intersection)
+                            
+                            if debug:
+                                print(f"Added intersection point {intersection} to polygon {poly_idx} at position {insert_idx}")
+    
+    return updated_polygons
+
+def extract_reinforcement_line_geometry(slope_data):
+    """
+    Extract reinforcement line geometry from slope_data in the format needed for mesh generation.
+    
+    Parameters:
+        slope_data: Dictionary containing slope data with 'reinforce_lines' key
+        
+    Returns:
+        List of reinforcement lines, where each line is a list of (x, y) coordinate tuples
+    """
+    lines = []
+    if 'reinforce_lines' in slope_data and slope_data['reinforce_lines']:
+        for line in slope_data['reinforce_lines']:
+            # Convert from dict format to tuple format
+            line_coords = [(point['X'], point['Y']) for point in line]
+            lines.append(line_coords)
+    return lines