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Unstructured.html

@@ -15210,17 +15210,17 @@ <h2 id="Loading-an-Unstructured-Mesh">Loading an Unstructured Mesh<a class="anch
 <span class="ansi-green-intense-fg ansi-bold">   1354</span>     results<span style="color: rgb(98,98,98)">.</span>append(f_output)
 <span class="ansi-green-intense-fg ansi-bold">   1355</span> <span class="ansi-bold" style="color: rgb(0,135,0)">if</span> <span style="color: rgb(0,135,0)">isinstance</span>(results[<span style="color: rgb(98,98,98)">0</span>], <span style="color: rgb(0,135,0)">tuple</span>):
 
-File <span class="ansi-green-fg">/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/phi/geom/_mesh.py:489</span>, in <span class="ansi-cyan-fg">load_su2</span><span class="ansi-blue-fg">(file_or_mesh, cell_dim, face_format)</span>
-<span class="ansi-green-intense-fg ansi-bold">    475</span> <span style="color: rgb(175,0,0)">&#34;&#34;&#34;</span>
-<span class="ansi-green-intense-fg ansi-bold">    476</span> <span style="color: rgb(175,0,0)">Load an unstructured mesh from a `.su2` file.</span>
-<span class="ansi-green-intense-fg ansi-bold">    477</span> 
+File <span class="ansi-green-fg">/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/phi/geom/_mesh.py:488</span>, in <span class="ansi-cyan-fg">load_su2</span><span class="ansi-blue-fg">(file_or_mesh, cell_dim, face_format)</span>
+<span class="ansi-green-intense-fg ansi-bold">    474</span> <span style="color: rgb(175,0,0)">&#34;&#34;&#34;</span>
+<span class="ansi-green-intense-fg ansi-bold">    475</span> <span style="color: rgb(175,0,0)">Load an unstructured mesh from a `.su2` file.</span>
+<span class="ansi-green-intense-fg ansi-bold">    476</span> 
 <span class="ansi-green-fg">   (...)</span>
-<span class="ansi-green-intense-fg ansi-bold">    486</span> <span style="color: rgb(175,0,0)">    `Mesh`</span>
-<span class="ansi-green-intense-fg ansi-bold">    487</span> <span style="color: rgb(175,0,0)">&#34;&#34;&#34;</span>
-<span class="ansi-green-intense-fg ansi-bold">    488</span> <span class="ansi-bold" style="color: rgb(0,135,0)">if</span> <span style="color: rgb(0,135,0)">isinstance</span>(file_or_mesh, <span style="color: rgb(0,135,0)">str</span>):
-<span class="ansi-green-fg">--&gt; 489</span>     <span class="ansi-bold" style="color: rgb(0,135,0)">from</span> <span class="ansi-bold" style="color: rgb(0,0,255)">ezmesh</span> <span class="ansi-bold" style="color: rgb(0,135,0)">import</span> import_from_file
-<span class="ansi-green-intense-fg ansi-bold">    490</span>     mesh <span style="color: rgb(98,98,98)">=</span> import_from_file(file_or_mesh)
-<span class="ansi-green-intense-fg ansi-bold">    491</span> <span class="ansi-bold" style="color: rgb(0,135,0)">else</span>:
+<span class="ansi-green-intense-fg ansi-bold">    485</span> <span style="color: rgb(175,0,0)">    `Mesh`</span>
+<span class="ansi-green-intense-fg ansi-bold">    486</span> <span style="color: rgb(175,0,0)">&#34;&#34;&#34;</span>
+<span class="ansi-green-intense-fg ansi-bold">    487</span> <span class="ansi-bold" style="color: rgb(0,135,0)">if</span> <span style="color: rgb(0,135,0)">isinstance</span>(file_or_mesh, <span style="color: rgb(0,135,0)">str</span>):
+<span class="ansi-green-fg">--&gt; 488</span>     <span class="ansi-bold" style="color: rgb(0,135,0)">from</span> <span class="ansi-bold" style="color: rgb(0,0,255)">ezmesh</span> <span class="ansi-bold" style="color: rgb(0,135,0)">import</span> import_from_file
+<span class="ansi-green-intense-fg ansi-bold">    489</span>     mesh <span style="color: rgb(98,98,98)">=</span> import_from_file(file_or_mesh)
+<span class="ansi-green-intense-fg ansi-bold">    490</span> <span class="ansi-bold" style="color: rgb(0,135,0)">else</span>:
 
 <span class="ansi-red-fg">ModuleNotFoundError</span>: No module named &#39;ezmesh&#39;</pre>
 </div>

data/sim_000000/description.json

@@ -10,10 +10,10 @@
       null
     ],
     "data": [
-      0.8061959147453308,
-      0.5076926350593567,
-      0.6010867357254028,
-      0.8142030835151672
+      0.2324673980474472,
+      0.016804978251457214,
+      0.7554008960723877,
+      0.01973273791372776
     ]
   },
   "__tensors__": [

data/sim_000001/description.json

@@ -1,3 +1,3 @@
 {
-  "smoothness": 0.8061959147453308
+  "smoothness": 0.2324673980474472
 }

data/sim_000002/description.json

@@ -1,3 +1,3 @@
 {
-  "smoothness": 0.5076926350593567
+  "smoothness": 0.016804978251457214
 }

data/sim_000003/description.json

@@ -1,3 +1,3 @@
 {
-  "smoothness": 0.6010867357254028
+  "smoothness": 0.7554008960723877
 }

data/sim_000004/description.json

@@ -1,3 +1,3 @@
 {
-  "smoothness": 0.8142030835151672
+  "smoothness": 0.01973273791372776
 }

phi/field/index.html

@@ -325,7 +325,7 @@ <h2 id="args">Args</h2>
 </dl></div>
 </dd>
 <dt id="phi.field.divergence"><code class="name flex">
-<span>def <span class="ident">divergence</span></span>(<span>field: phi.field._field.Field,<br>order=2,<br>implicit: phiml.math._optimize.Solve = None,<br>upwind: phi.field._field.Field = None,<br>implicitness: int = None) ‑> <function <a title="phi.field.CenteredGrid" href="#phi.field.CenteredGrid">CenteredGrid()</a> at 0x7f97b02a3380></span>
+<span>def <span class="ident">divergence</span></span>(<span>field: phi.field._field.Field,<br>order=2,<br>implicit: phiml.math._optimize.Solve = None,<br>upwind: phi.field._field.Field = None,<br>implicitness: int = None) ‑> <function <a title="phi.field.CenteredGrid" href="#phi.field.CenteredGrid">CenteredGrid()</a> at 0x7f1a98492700></span>
 </code></dt>
 <dd>
 <div class="desc"><p>Computes the divergence of a grid using finite differences.</p>

phi/geom/index.html

@@ -718,7 +718,7 @@ <h2 id="returns">Returns</h2>
 <p>Rotated <code><a title="phi.geom.Geometry" href="#phi.geom.Geometry">Geometry</a></code></p></div>
 </dd>
 <dt id="phi.geom.stack"><code class="name flex">
-<span>def <span class="ident">stack</span></span>(<span>values: Sequence[~PhiTreeNodeType] | Dict[str, ~PhiTreeNodeType],<br>dim: phiml.math._shape.Shape | str,<br>expand_values=False,<br>simplify=False,<br>**kwargs) ‑> ~PhiTreeNodeType</span>
+<span>def <span class="ident">stack</span></span>(<span>values: Sequence[~PhiTreeNodeType] | Dict[str, ~PhiTreeNodeType],<br>dim: phiml.math._shape.Shape | str,<br>expand_values=False,<br>simplify=False,<br>layout_non_matching=False,<br>**kwargs) ‑> ~PhiTreeNodeType</span>
 </code></dt>
 <dd>
 <div class="desc"><p>Stacks <code>values</code> along the new dimension <code>dim</code>.
@@ -742,6 +742,8 @@ <h2 id="args">Args</h2>
 If <code>False</code>, this may return a non-numeric object instead.</dd>
 <dt><strong><code>simplify</code></strong></dt>
 <dd>If <code>True</code> and all values are equal, returns one value without adding the dimension.</dd>
+<dt><strong><code>layout_non_matching</code></strong></dt>
+<dd>If non-matching values should be stacked using a Layout object, i.e. should be put into a named list instead.</dd>
 <dt><strong><code>**kwargs</code></strong></dt>
 <dd>Additional keyword arguments required by specific implementations.
 Adding spatial dimensions to fields requires the <code>bounds: Box</code> argument specifying the physical extent of the new dimensions.
@@ -948,6 +950,8 @@ <h2 class="section-title" id="header-classes">Classes</h2>
         max_sgn_dist = math.max(sgn_surf_delta, &#39;vector&#39;)
         normal_axis = max_sgn_dist == sgn_surf_delta  # ToDo only one if inside
         normal = math.vec_normalize(normal_axis * math.sign(loc_to_center))
+        if self.rotation_matrix is not None:
+            normal = rotate(normal, self.rotation_matrix)
         surf_to_center = math.where(normal_axis, math.sign(loc_to_center) * self.half_size, loc_to_center)
         closest_to_center = math.clip(surf_to_center, -self.half_size, self.half_size)
         surface_pos = self.local_to_global(closest_to_center, scale=False, origin=&#39;center&#39;)
@@ -1884,7 +1888,7 @@ <h2 id="args">Args</h2>
         if &#39;vector&#39; not in center.shape or center.shape.get_item_names(&#39;vector&#39;) is None:
             center = math.expand(center, channel(self._half_size))
         self._center = center
-        self._rotation_matrix = None if rotation is None else rotation_matrix(rotation)
+        self._rotation_matrix = None if rotation is None else rotation_matrix(rotation, matrix_dim=center.shape[&#39;vector&#39;])
         self._size_variable = size_variable
 
     def __repr__(self):
@@ -2285,7 +2289,7 @@ <h2 id="returns">Returns</h2>
         if self.rotation is not None:
             tip = abs(self.up) * .5 * self.depth
             return tip + self.radius * sqrt(maximum(epsilon, 1 - self.up**2))
-        return ncat([.5*self.depth, expand(self.radius, channel(vector=self.radial_axes))], self._center.shape[&#39;vector&#39;])
+        return ncat([.5*self.depth, expand(self.radius, channel(vector=self.radial_axes))], self._center.shape[&#39;vector&#39;], expand_values=True)
 
     def at(self, center: Tensor) -&gt; &#39;Geometry&#39;:
         return Cylinder(center, self.radius, self.depth, self.rotation, self.axis, self.variable_attrs, self.value_attrs)
@@ -5277,15 +5281,13 @@ <h2 id="args">Args</h2>
 
     @cached_property
     def _faces(self) -&gt; Dict[str, Any]:
-        if self.element_rank == 2:
-            centers, normals, areas, boundary_slices = build_faces(self.vertices.center, self.elements, self.boundaries, self.element_rank, self.periodic, self._vertex_mean, self.face_format)
-            return {
-                &#39;center&#39;: centers,
-                &#39;normal&#39;: normals,
-                &#39;area&#39;: areas,
-                &#39;boundary_slices&#39;: boundary_slices,
-            }
-        return None
+        centers, normals, areas, boundary_slices = build_faces(self.vertices.center, self.elements, self.boundaries, self.element_rank, self.periodic, self._vertex_mean, self.face_format)
+        return {
+            &#39;center&#39;: centers,
+            &#39;normal&#39;: normals,
+            &#39;area&#39;: areas,
+            &#39;boundary_slices&#39;: boundary_slices,
+        }
 
     @property
     def face_shape(self) -&gt; Shape:
@@ -5380,7 +5382,8 @@ <h2 id="args">Args</h2>
     @cached_property
     def _cell_deltas(self):
         bounds = bounding_box(self.vertices)
-        is_periodic = dim_mask(self.vector.item_names, self.periodic)
+        periodic = {dim[:-len(&#39;[::-1]&#39;)] if dim.endswith(&#39;[::-1]&#39;) else dim: dim.endswith(&#39;[::-1]&#39;) for dim in self.periodic}
+        is_periodic = dim_mask(self.vector.item_names, tuple(periodic))
         return pairwise_distances(self.center, format=self.cell_connectivity, periodic=is_periodic, domain=(bounds.lower, bounds.upper))
 
     @cached_property
@@ -5483,11 +5486,13 @@ <h2 id="args">Args</h2>
 
     @property
     def volume(self) -&gt; Tensor:
-        if isinstance(self.elements, CompactSparseTensor) and self.element_rank == 2:
-            if instance(self.vertices).volume &gt; 0:
-                A, B, C, *_ = unstack(self.vertices.center[self.elements._indices], dual)
-                cross_area = vec_length(cross(B - A, C - A))
-                fac = {3: 0.5, 4: 1}[dual(self.elements._indices).size]  # tri, quad, ...
+        if self.element_rank == 2:
+            if instance(self.elements).volume &gt; 0:
+                three_vertices = nonzero(self.elements, 3, list_dims=dual)
+                v1, v2, v3 = unstack(self.vertices.center[{instance: three_vertices}], dual)
+                cross_area = vec_length(cross(v2-v1, v3-v1))
+                vertex_count = math.sum(self.elements, dual)
+                fac = where(vertex_count == 3, 0.5, 1)  # tri, quad, ...
                 return fac * cross_area
             else:
                 return zeros(instance(self.vertices))  # empty mesh
@@ -5502,9 +5507,7 @@ <h2 id="args">Args</h2>
         &#34;&#34;&#34;Extrinsic element normal space. This is a 0D vector for solid elements and 1D for surface elements.&#34;&#34;&#34;
         if self.element_rank == 2:
             three_vertices = nonzero(self.elements, 3, list_dims=dual)
-            corners = self.vertices.center[{instance: three_vertices}]
-            assert dual(corners).size == 3, f&#34;signed distance currently only supports triangles&#34;
-            v1, v2, v3 = unstack(corners, dual)
+            v1, v2, v3 = unstack(self.vertices.center[{instance: three_vertices}], dual)
             return vec_normalize(cross(v2 - v1, v3 - v1))
         raise NotImplementedError
 
@@ -6206,9 +6209,7 @@ <h2 id="returns">Returns</h2>
     &#34;&#34;&#34;Extrinsic element normal space. This is a 0D vector for solid elements and 1D for surface elements.&#34;&#34;&#34;
     if self.element_rank == 2:
         three_vertices = nonzero(self.elements, 3, list_dims=dual)
-        corners = self.vertices.center[{instance: three_vertices}]
-        assert dual(corners).size == 3, f&#34;signed distance currently only supports triangles&#34;
-        v1, v2, v3 = unstack(corners, dual)
+        v1, v2, v3 = unstack(self.vertices.center[{instance: three_vertices}], dual)
         return vec_normalize(cross(v2 - v1, v3 - v1))
     raise NotImplementedError</code></pre>
 </details>
@@ -6405,11 +6406,13 @@ <h2 id="returns">Returns</h2>
 </summary>
 <pre><code class="python">@property
 def volume(self) -&gt; Tensor:
-    if isinstance(self.elements, CompactSparseTensor) and self.element_rank == 2:
-        if instance(self.vertices).volume &gt; 0:
-            A, B, C, *_ = unstack(self.vertices.center[self.elements._indices], dual)
-            cross_area = vec_length(cross(B - A, C - A))
-            fac = {3: 0.5, 4: 1}[dual(self.elements._indices).size]  # tri, quad, ...
+    if self.element_rank == 2:
+        if instance(self.elements).volume &gt; 0:
+            three_vertices = nonzero(self.elements, 3, list_dims=dual)
+            v1, v2, v3 = unstack(self.vertices.center[{instance: three_vertices}], dual)
+            cross_area = vec_length(cross(v2-v1, v3-v1))
+            vertex_count = math.sum(self.elements, dual)
+            fac = where(vertex_count == 3, 0.5, 1)  # tri, quad, ...
             return fac * cross_area
         else:
             return zeros(instance(self.vertices))  # empty mesh

phi/physics/fluid.html

@@ -52,7 +52,7 @@ <h2 id="returns">Returns</h2>
 <p>Velocity of same type as <code>velocity</code></p></div>
 </dd>
 <dt id="phi.physics.fluid.boundary_push"><code class="name flex">
-<span>def <span class="ident">boundary_push</span></span>(<span>particles: <function PointCloud at 0x7f97b032c540>,<br>obstacles: tuple,<br>separation: float = 0.5) ‑> <function PointCloud at 0x7f97b032c540></span>
+<span>def <span class="ident">boundary_push</span></span>(<span>particles: <function PointCloud at 0x7f1a98493880>,<br>obstacles: tuple,<br>separation: float = 0.5) ‑> <function PointCloud at 0x7f1a98493880></span>
 </code></dt>
 <dd>
 <div class="desc"><p>Enforces boundary conditions by correcting possible errors of the advection step and shifting particles out of
@@ -104,7 +104,7 @@ <h2 id="returns">Returns</h2>
 </dl></div>
 </dd>
 <dt id="phi.physics.fluid.make_incompressible"><code class="name flex">
-<span>def <span class="ident">make_incompressible</span></span>(<span>velocity: phi.field._field.Field,<br>obstacles: <a title="phi.physics.fluid.Obstacle" href="#phi.physics.fluid.Obstacle">Obstacle</a> = (),<br>solve: phiml.math._optimize.Solve = auto with tolerance None (rel), None (abs), max_iterations=1000,<br>active: <function CenteredGrid at 0x7f97b02a3380> = None,<br>order: int = 2,<br>correct_skew=False,<br>wide_stencil: bool = None) ‑> Tuple[phi.field._field.Field, phi.field._field.Field]</span>
+<span>def <span class="ident">make_incompressible</span></span>(<span>velocity: phi.field._field.Field,<br>obstacles: <a title="phi.physics.fluid.Obstacle" href="#phi.physics.fluid.Obstacle">Obstacle</a> = (),<br>solve: phiml.math._optimize.Solve = auto with tolerance None (rel), None (abs), max_iterations=1000,<br>active: <function CenteredGrid at 0x7f1a98492700> = None,<br>order: int = 2,<br>correct_skew=False,<br>wide_stencil: bool = None) ‑> Tuple[phi.field._field.Field, phi.field._field.Field]</span>
 </code></dt>
 <dd>
 <div class="desc"><p>Projects the given velocity field by solving for the pressure and subtracting its spatial_gradient.</p>