Feature puma patches [8/x] Batch processing of tree ref_coords [1/x] Interface

example/geometry/t8_example_geometries.cxx

@@ -90,12 +90,16 @@ class t8_geometry_sincos: public t8_geometry {
    * models the rectangle [0,2] x [0,1].
    * \param [in]  cmesh      The cmesh in which the point lies.
    * \param [in]  gtreeid    The global tree (of the cmesh) in which the reference point is.
-   * \param [in]  ref_coords Array of \a dimension many entries, specifying a point in \f$ [0,1]^2 \f$.
+   * \param [in]  ref_coords Array of \a dimension x \a num_coords many entries, specifying a point in \f$ [0,1]^2 \f$.
+   * \param [in]  num_coords Amount of points of /f$ \mathrm{dim} /f$ to map.
    * \param [out] out_coords The mapped coordinates in physical space of \a ref_coords.
    */
   void
-  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double out_coords[3]) const
+  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                    double out_coords[3]) const
   {
+    if (num_coords != 1)
+      SC_ABORT ("Error: Batch computation of geometry not yet supported.");
     double x = ref_coords[0];
     if (gtreeid == 1) {
       /* Translate ref coordinates by +1 in x direction for the second tree. */
@@ -108,7 +112,8 @@ class t8_geometry_sincos: public t8_geometry {
 
   /* Jacobian, not implemented. */
   void
-  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double *jacobian) const
+  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                             double *jacobian) const
   {
     SC_ABORT_NOT_REACHED ();
   }
@@ -139,12 +144,16 @@ class t8_geometry_moebius: public t8_geometry_with_vertices {
    * Map a point in a point in \f$ [0,1]^2 \f$ to the moebius band.
    * \param [in]  cmesh      The cmesh in which the point lies.
    * \param [in]  gtreeid    The global tree (of the cmesh) in which the reference point is.
-   * \param [in]  ref_coords Array of \a dimension many entries, specifying a point in \f$ [0,1]^2 \f$.
+   * \param [in]  ref_coords Array of \a dimension x \a num_coords many entries, specifying a point in \f$ [0,1]^2 \f$.
+   * \param [in]  num_coords Amount of points of /f$ \mathrm{dim} /f$ to map.
    * \param [out] out_coords The mapped coordinates in physical space of \a ref_coords.
    */
   void
-  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double out_coords[3]) const
+  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                    double out_coords[3]) const
   {
+    if (num_coords != 1)
+      SC_ABORT ("Error: Batch computation of geometry not yet supported.");
     double t;
     double phi;
 
@@ -165,7 +174,8 @@ class t8_geometry_moebius: public t8_geometry_with_vertices {
 
   /* Jacobian, not implemented. */
   void
-  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double *jacobian) const
+  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                             double *jacobian) const
   {
     SC_ABORT_NOT_REACHED ();
   }
@@ -189,20 +199,25 @@ class t8_geometry_cylinder: public t8_geometry {
    * Map a reference point in the unit square to a cylinder.
    * \param [in]  cmesh      The cmesh in which the point lies.
    * \param [in]  gtreeid    The global tree (of the cmesh) in which the reference point is.
-   * \param [in]  ref_coords Array of \a dimension many entries, specifying a point in \f$ [0,1]^\mathrm{dim} \f$.
+   * \param [in]  ref_coords Array of \a dimension x \a num_coords many entries, specifying a point in \f$ [0,1]^2 \f$.
+   * \param [in]  num_coords Amount of points of /f$ \mathrm{dim} /f$ to map.
    * \param [out] out_coords The mapped coordinates in physical space of \a ref_coords.
    */
   void
-  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double out_coords[3]) const
+  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                    double out_coords[3]) const
   {
+    if (num_coords != 1)
+      SC_ABORT ("Error: Batch computation of geometry not yet supported.");
     out_coords[0] = cos (ref_coords[0] * 2 * M_PI);
     out_coords[1] = ref_coords[1];
     out_coords[2] = sin (ref_coords[0] * 2 * M_PI);
   }
 
   /* Jacobian, not implemented. */
   void
-  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double *jacobian) const
+  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                             double *jacobian) const
   {
     SC_ABORT_NOT_REACHED ();
   }
@@ -235,12 +250,16 @@ class t8_geometry_circle: public t8_geometry_with_vertices {
    * Map a reference point in the unit square to a circle.
    * \param [in]  cmesh      The cmesh in which the point lies.
    * \param [in]  gtreeid    The global tree (of the cmesh) in which the reference point is.
-   * \param [in]  ref_coords Array of \a dimension many entries, specifying a point in \f$ [0,1]^2 \f$.
+   * \param [in]  ref_coords Array of \a dimension x \a num_coords many entries, specifying a point in \f$ [0,1]^2 \f$.
+   * \param [in]  num_coords Amount of points of /f$ \mathrm{dim} /f$ to map.
    * \param [out] out_coords The mapped coordinates in physical space of \a ref_coords.
    */
   void
-  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double out_coords[3]) const
+  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                    double out_coords[3]) const
   {
+    if (num_coords != 1)
+      SC_ABORT ("Error: Batch computation of geometry not yet supported.");
     double x;
     double y;
 
@@ -261,7 +280,8 @@ class t8_geometry_circle: public t8_geometry_with_vertices {
 
   /* Jacobian, not implemented. */
   void
-  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double *jacobian) const
+  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                             double *jacobian) const
   {
     SC_ABORT_NOT_REACHED ();
   }
@@ -290,12 +310,16 @@ class t8_geometry_moving: public t8_geometry {
    * Map a reference point in the unit square to a square distorted with time.
    * \param [in]  cmesh      The cmesh in which the point lies.
    * \param [in]  gtreeid    The global tree (of the cmesh) in which the reference point is.
-   * \param [in]  ref_coords Array of \a dimension many entries, specifying a point in \f$ [0,1]^2 \f$.
+   * \param [in]  ref_coords Array of \a dimension x \a num_coords many entries, specifying a point in \f$ [0,1]^2 \f$.
+   * \param [in]  num_coords Amount of points of /f$ \mathrm{dim} /f$ to map.
    * \param [out] out_coords The mapped coordinates in physical space of \a ref_coords.
    */
   void
-  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double out_coords[3]) const
+  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                    double out_coords[3]) const
   {
+    if (num_coords != 1)
+      SC_ABORT ("Error: Batch computation of geometry not yet supported.");
     double x = ref_coords[0] - .5;
     double y = ref_coords[1] - .5;
     const double time = *ptime;
@@ -319,7 +343,8 @@ class t8_geometry_moving: public t8_geometry {
 
   /* Jacobian, not implemented. */
   void
-  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double *jacobian) const
+  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                             double *jacobian) const
   {
     SC_ABORT_NOT_REACHED ();
   }
@@ -350,20 +375,25 @@ class t8_geometry_cube_zdistorted: public t8_geometry {
    * Map a reference point in the unit cube to a cube distorted in the z axis.
    * \param [in]  cmesh      The cmesh in which the point lies.
    * \param [in]  gtreeid    The global tree (of the cmesh) in which the reference point is.
-   * \param [in]  ref_coords Array of \a dimension many entries, specifying a point in \f$ [0,1]^3 \f$.
+   * \param [in]  ref_coords Array of \a dimension x \a num_coords many entries, specifying a point in \f$ [0,1]^2 \f$.
+   * \param [in]  num_coords Amount of points of /f$ \mathrm{dim} /f$ to map.
    * \param [out] out_coords The mapped coordinates in physical space of \a ref_coords.
    */
   void
-  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double out_coords[3]) const
+  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                    double out_coords[3]) const
   {
+    if (num_coords != 1)
+      SC_ABORT ("Error: Batch computation of geometry not yet supported.");
     out_coords[0] = ref_coords[0];
     out_coords[1] = ref_coords[1];
     out_coords[2] = ref_coords[2] * (0.8 + 0.2 * sin (ref_coords[0] * 2 * M_PI) * cos (ref_coords[1] * 2 * M_PI));
   }
 
   /* Jacobian, not implemented. */
   void
-  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double *jacobian) const
+  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                             double *jacobian) const
   {
     SC_ABORT_NOT_REACHED ();
   }

src/t8_forest/t8_forest_cxx.cxx

@@ -388,20 +388,21 @@ t8_forest_element_coordinate (t8_forest_t forest, t8_locidx_t ltree_id, const t8
   /* Get the cmesh */
   cmesh = t8_forest_get_cmesh (forest);
   /* Evaluate the geometry */
-  t8_geometry_evaluate (cmesh, gtreeid, vertex_coords, coordinates);
+  t8_geometry_evaluate (cmesh, gtreeid, vertex_coords, 1, coordinates);
 }
 
 void
 t8_forest_element_from_ref_coords (t8_forest_t forest, t8_locidx_t ltreeid, const t8_element_t *element,
-                                   const double *ref_coords, double *coords_out, sc_array_t *stretch_factors)
+                                   const double *ref_coords, const size_t num_coords, double *coords_out,
+                                   sc_array_t *stretch_factors)
 {
   double tree_ref_coords[3] = { 0 };
   const t8_eclass_t tree_class = t8_forest_get_tree_class (forest, ltreeid);
   const t8_eclass_scheme_c *scheme = t8_forest_get_eclass_scheme (forest, tree_class);
-  scheme->t8_element_reference_coords (element, ref_coords, 1, tree_ref_coords);
+  scheme->t8_element_reference_coords (element, ref_coords, num_coords, tree_ref_coords);
   const t8_cmesh_t cmesh = t8_forest_get_cmesh (forest);
   const t8_gloidx_t gtreeid = t8_forest_global_tree_id (forest, ltreeid);
-  t8_geometry_evaluate (cmesh, gtreeid, tree_ref_coords, coords_out);
+  t8_geometry_evaluate (cmesh, gtreeid, tree_ref_coords, num_coords, coords_out);
 }
 
 /* Compute the diameter of an element. */
@@ -459,7 +460,7 @@ t8_forest_element_centroid (t8_forest_t forest, t8_locidx_t ltreeid, const t8_el
   /* Get the element class and calculate the centroid using its element
    * reference coordinates */
   element_shape = t8_element_shape (ts, element);
-  t8_forest_element_from_ref_coords (forest, ltreeid, element, t8_element_centroid_ref_coords[element_shape],
+  t8_forest_element_from_ref_coords (forest, ltreeid, element, t8_element_centroid_ref_coords[element_shape], 1,
                                      coordinates, NULL);
 }
 

src/t8_forest/t8_forest_geometrical.h

@@ -57,6 +57,7 @@ t8_forest_element_coordinate (t8_forest_t forest, t8_locidx_t ltree_id, const t8
  * \param [in]      ltreeid           The forest local id of the tree in which the element is.
  * \param [in]      element           The element.
  * \param [in]      ref_coord         The reference coordinates of the point inside the element.
+ * \param [in]      num_coords        The number of coordinate sets in ref_coord (dimension x double).
  * \param [out]     coords_out        On input an allocated array to store 3 doubles, on output
  *                                    the x, y and z coordinates of the point inside the domain.
  * \param [in]      stretch_factors   An element-wise array with d (dimension) doubles per element, 
@@ -66,7 +67,8 @@ t8_forest_element_coordinate (t8_forest_t forest, t8_locidx_t ltree_id, const t8
  */
 void
 t8_forest_element_from_ref_coords (t8_forest_t forest, t8_locidx_t ltreeid, const t8_element_t *element,
-                                   const double *ref_coord, double *coords_out, sc_array_t *stretch_factors);
+                                   const double *ref_coord, const size_t num_coords, double *coords_out,
+                                   sc_array_t *stretch_factors);
 
 /** Compute the coordinates of the centroid of an element if a geometry
  * for this tree is registered in the forest's cmesh.

src/t8_forest/t8_forest_vtk.cxx

@@ -187,7 +187,7 @@ t8_forest_vtk_get_element_nodes (t8_forest_t forest, t8_locidx_t ltreeid, const
   const t8_eclass_scheme_c *scheme = t8_forest_get_eclass_scheme (forest, tree_class);
   const t8_element_shape_t element_shape = scheme->t8_element_shape (element);
   const double *ref_coords = t8_forest_vtk_point_to_element_ref_coords[element_shape][vertex];
-  t8_forest_element_from_ref_coords (forest, ltreeid, element, ref_coords, out_coords, stretch_factors);
+  t8_forest_element_from_ref_coords (forest, ltreeid, element, ref_coords, 1, out_coords, stretch_factors);
 }
 
 /**

src/t8_geometry/t8_geometry.cxx

@@ -288,7 +288,8 @@ t8_geom_handler_update_tree (t8_geometry_handler_t *geom_handler, t8_cmesh_t cme
 }
 
 void
-t8_geometry_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double *out_coords)
+t8_geometry_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                      double *out_coords)
 {
   double start_wtime = 0; /* Used for profiling. */
   /* The cmesh must be committed */
@@ -310,7 +311,8 @@ t8_geometry_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_c
   T8_ASSERT (geom_handler->active_geometry != NULL);
 
   /* Evaluate the geometry. */
-  geom_handler->active_geometry->t8_geom_evaluate (cmesh, geom_handler->active_tree, ref_coords, out_coords);
+  geom_handler->active_geometry->t8_geom_evaluate (cmesh, geom_handler->active_tree, ref_coords, num_coords,
+                                                   out_coords);
 
   if (cmesh->profile != NULL) {
     /* If profiling is enabled, add the runtime to the profiling
@@ -321,7 +323,8 @@ t8_geometry_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_c
 }
 
 void
-t8_geometry_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double *jacobian)
+t8_geometry_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const int num_coords,
+                      double *jacobian)
 {
   /* The cmesh must be committed */
   T8_ASSERT (t8_cmesh_is_committed (cmesh));
@@ -335,5 +338,8 @@ t8_geometry_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_c
   t8_geom_handler_update_tree (geom_handler, cmesh, gtreeid);
 
   /* Evaluate the jacobian. */
-  geom_handler->active_geometry->t8_geom_evaluate_jacobian (cmesh, geom_handler->active_tree, ref_coords, jacobian);
+  /* *INDENT-OFF* */
+  geom_handler->active_geometry->t8_geom_evaluate_jacobian (cmesh, geom_handler->active_tree, ref_coords, num_coords,
+                                                            jacobian);
+  /* *INDENT-ON* */
 }

src/t8_geometry/t8_geometry.h

@@ -139,10 +139,12 @@ t8_geometry_c *
 t8_geom_handler_find_geometry (const t8_geometry_handler_t *geom_handler, const char *name);
 
 void
-t8_geometry_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double *out_coords);
+t8_geometry_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                      double *out_coords);
 
 void
-t8_geometry_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double *jacobian);
+t8_geometry_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                      double *jacobian);
 
 T8_EXTERN_C_END ();
 

src/t8_geometry/t8_geometry_base.hxx

@@ -59,25 +59,29 @@ struct t8_geometry
 
   /**
    * Map a point in the reference space \f$ [0,1]^\mathrm{dim} \to \mathbb{R}^3 \f$.
-   * \param [in]  cmesh      The cmesh in which the point lies.
-   * \param [in]  gtreeid    The global tree (of the cmesh) in which the reference point is.
-   * \param [in]  ref_coords  Array of \a dimension many entries, specifying a point in \f$ [0,1]^\mathrm{dim} \f$.
+   * \param [in]  cmesh       The cmesh in which the point lies.
+   * \param [in]  gtreeid     The global tree (of the cmesh) in which the reference point is.
+   * \param [in]  ref_coords  Array of \a dimension x \a num_coords many entries, specifying points in \f$ [0,1]^\mathrm{dim} \f$.
+   * \param [in]  num_coords  Amount of points of /f$ \mathrm{dim} /f$ to map.
    * \param [out] out_coords  The mapped coordinates in physical space of \a ref_coords.
    */
   virtual void
-  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double out_coords[3]) const
+  t8_geom_evaluate (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                    double out_coords[3]) const
     = 0;
 
   /**
    * Compute the jacobian of the \a t8_geom_evaluate map at a point in the reference space \f$ [0,1]^\mathrm{dim} \f$.
    * \param [in]  cmesh      The cmesh in which the point lies.
    * \param [in]  glreeid    The global tree (of the cmesh) in which the reference point is.
-   * \param [in]  ref_coords  Array of \a dimension many entries, specifying a point in \f$ [0,1]^\mathrm{dim} \f$.
-   * \param [out] jacobian    The jacobian at \a ref_coords. Array of size \f$ \mathrm{dim} \cdot 3 \f$. Indices \f$ 3 \cdot i\f$ , \f$ 3 \cdot i+1 \f$ , \f$ 3 \cdot i+2 \f$
-   *                          correspond to the \f$ i \f$-th column of the jacobian (Entry \f$ 3 \cdot i + j \f$ is \f$ \frac{\partial f_j}{\partial x_i} \f$).
+   * \param [in]  ref_coords  Array of \a dimension x \a num_coords many entries, specifying points in \f$ [0,1]^\mathrm{dim} \f$.
+   * \param [in]  num_coords  Amount of points of /f$ \mathrm{dim} /f$ to map.
+   * \param [out] jacobian    The jacobian at \a ref_coords. Array of size \a num_coords x dimension x 3. Indices \f$ 3 \cdot i\f$ , \f$ 3 \cdot i+1 \f$ , \f$ 3 \cdot i+2 \f$
+   *                          correspond to the \f$ i \f$-th column of the jacobian  (Entry \f$ 3 \cdot i + j \f$ is \f$ \frac{\partial f_j}{\partial x_i} \f$).
    */
   virtual void
-  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, double *jacobian) const
+  t8_geom_evaluate_jacobian (t8_cmesh_t cmesh, t8_gloidx_t gtreeid, const double *ref_coords, const size_t num_coords,
+                             double *jacobian) const
     = 0;
 
   /** Update a possible internal data buffer for per tree data.