Merge pull request #1167 from LLNL/feature/whitlock/conduit_tiled_exa…

…mple

Create tiled mesh example function.

CHANGELOG.md

@@ -10,10 +10,18 @@ and this project aspires to adhere to [Semantic Versioning](https://semver.org/s
 
 #### General
 - Added `conduit_json_external` protocol. Creates a json schema representation of a node that includes all addresses that the node is pointing to. Parsing this schema will create a node equivalent to `set_external()`.
+- Added a `conduit_generate_data` executable that can generate datasets using the `tiled()` and `braid()` functions and save the datasets to files.
 
 #### Relay
 - Added ability to read N-dimensional hyperslabs from HDF5 leaf arrays into linear memory arrays.
 
+#### Blueprint
+- Added a `conduit::blueprint::mesh::examples::tiled()` function that can generate meshes by repeating a tiled pattern.
+- Added a `conduit::blueprint::mpi::mesh::utils::adjset::compare_pointwise()` function that can compare adjsets for multi-domain meshes in parallel. The function is used to diagnose adjsets with points that are out of order on either side of the boundary. The comparison is done point by point within each group and it checks to ensure that the points reference the same spatial location.
+- Added a `conduit::blueprint::mesh::utils::reorder()` function that can accept a vector of element ids and create a reordered topology. The points and coordinates are re-ordered according to their first use in the new element ordering.
+- Added a `conduit::blueprint::mesh::utils::topology::spatial_ordering()` function that takes a topology and computes centroids for each element, passes them through a kdtree, and returns the new element ordering. The new ordering can be used with the `reorder()` function.
+- Added a `conduit::blueprint::mesh::utils::slice_array()` function that can slice Conduit nodes that contain arrays. A new node with the same type is created but it contains only the selected indices.
+- Added a `conduit::blueprint::mesh::utils::slice_field()` function. It is like `slice_array()` but it can handle the mcarray protocol. This functionality was generalized from the partitioner.
 
 ### Changed
 

src/CMakeLists.txt

@@ -15,7 +15,7 @@ endif()
 # Conduit
 ################################
 
-project(conduit VERSION "0.8.8")
+project(conduit VERSION "0.8.9")
 
 ################################ 
 # Build Options

src/docs/sphinx/blueprint_mesh.rst

@@ -1687,6 +1687,91 @@ equal to half the number of prisms.
 
 The resulting data is placed the Node ``res``, which is passed in via reference.
 
+
+tiled
++++++++++
+
+The ``tiled()`` function repeats a tile (given as a 2D Blueprint topology) into a larger mesh composed of
+a regular square tiling of the supplied tile. If no topology is given, a default pattern consisting of quads
+is used. The output mesh can be either 2D or 3D. For 3D, supply a ``nz`` parameter greater than zero. Note
+that the input tile must consist of a homogeneous set of triangles or quads to extrude the tile into 3D since
+polyhedral output is not yet supported. The ``tiled()`` function produces a single domain comprised of a
+main mesh, a boundary mesh, and adjacency sets if the output mesh is to be part of a multi-domain dataset.
+
+.. code:: cpp
+
+    conduit::blueprint::mesh::examples::tiled(index_t nx,                   // number of tiles along x
+                                              index_t ny,                   // number of tiles along y
+                                              index_t nz,                   // number of elements along z (0 for 2D)
+                                              conduit::Node &res,           // result container
+                                              const conduit::Node &options);// options node
+
+The ``tiled()`` function accepts a Conduit node containing options that influence how the mesh is generated.
+If the options contain a ``tile`` node that contains a 2D blueprint topology, the first supplied topology will
+be used to override the default tile pattern. The ``reorder`` option indicates the type of point and element
+reordering that will be done. Reordering can improve cache-friendliness. The default is to reorder points
+and elements, using "kdtree" method. Passing "none" or an empty string will prevent reordering.
+The name of the mesh can be given by passing a ``meshname`` option string. Likewise, the name of the boundary
+mesh can be supplied using the ``boundarymeshname`` option. The optional ``translate/x`` and ``translate/y``
+options determine the tile spacing. If the translation values are not given, they will be determined from
+the coordset extents. The output mesh topology will store its integer connectivity information as index_t
+by default. The precision of the integer output can turned to int32 by passing a ``datatype`` option containing
+the "int", "int32", "integer" strings.
+
+An important set of options define the left, right, bottom, and top sets of points within the supplied tile
+pattern. The values in the ``left`` option identify the list of points that define the left edge of the tile.
+These are indices into the coordset and the values should be in consecutive order along the edge. Opposite point
+sets must match. In other words, the left and right point sets must contain the same number of points and
+they need to proceed along their edges in the same order. The same is true of the bottom and top point sets.
+
+The ``tiled()`` function also accepts options that simplify the task of generating
+mesh domains for a multi-domain dataset. The coordinate extents of the current mesh domain are given using
+the ``extents`` option, which contains 6 double values: {xmin, xmax, ymin, ymax, zmin, zmax}. The ``domains``
+option contains a triple of {domainsI, domainsJ, domainsK} values that indicate how many divisions there are
+of the extents in the I,J,K dimensions. The product of these numbers determines the total number of domains.
+The ``domain`` option specifies a triple indicating the I,J,K domain id within the overall set of domains.
+This is used to help construct adjacency sets.
+
+.. code:: yaml
+
+    # Define the tile topology
+    tile:
+      coordsets:
+        coords:
+          type: explicit
+          values:
+            x: [0., 1., 2., 0., 1., 2., 0., 1., 2.]
+            y: [0., 0.5, 0., 1., 1.5, 1., 2., 2.5, 2.]
+      topologies:
+        tile:
+          type: unstructured
+          coordset: coords
+          elements:
+            shape: tri
+            connectivity: [0,1,4, 0,4,3, 1,2,5, 1,5,4, 3,4,7, 3,7,6, 4,5,8, 4,8,7]
+    # Set some options that aid tiling.
+    reorder: 1
+    left: [0,3,6]
+    right: [2,5,8]
+    bottom: [0,1,2]
+    top: [6,7,8]
+    translate:
+      x: 2.
+      y: 2.
+
+.. figure:: tiled_single.png
+    :width: 400px
+    :align: center
+
+    Pseudocolor plot of zoneid for default tile mesh that has been reordered.
+
+.. figure:: tiled.png
+    :width: 600px
+    :align: center
+
+    Subset plots of multi-domain datasets created using the ``tiled()`` function.
+
+
 miscellaneous
 ++++++++++++++
 

src/docs/sphinx/index.rst

@@ -115,7 +115,7 @@ Contributors
 - Mark Miller (LLNL)
 - Todd Gamblin (LLNL)
 - Kevin Huynh (LLNL)
-- Brad Whitlock (Intelligent Light)
+- Brad Whitlock (LLNL)
 - Chris Laganella (Intelligent Light)
 - George Aspesi (Harvey Mudd)
 - Justin Bai (Harvey Mudd)

src/executables/CMakeLists.txt

@@ -3,3 +3,4 @@
 # other details. No copyright assignment is required to contribute to Conduit.
 
 add_subdirectory(adjset_validate)
+add_subdirectory(generate_data)

src/executables/generate_data/CMakeLists.txt

@@ -0,0 +1,36 @@
+# Copyright (c) Lawrence Livermore National Security, LLC and other Conduit
+# Project developers. See top-level LICENSE AND COPYRIGHT files for dates and
+# other details. No copyright assignment is required to contribute to Conduit.
+
+if(ENABLE_UTILS)
+    blt_add_executable(
+        NAME        conduit_generate_data
+        SOURCES     conduit_generate_data.cpp
+        OUTPUT_DIR  ${CMAKE_CURRENT_BINARY_DIR}
+        DEPENDS_ON  conduit conduit_blueprint conduit_relay
+        FOLDER      utils
+        )
+
+    # add install target
+    install(TARGETS conduit_generate_data
+            RUNTIME DESTINATION bin)
+
+    ################################################################
+    # If we have mpi, add a parallel version.
+    ################################################################
+
+    if(MPI_FOUND)
+        blt_add_executable(
+            NAME        conduit_generate_data_mpi
+            SOURCES     conduit_generate_data.cpp
+            OUTPUT_DIR  ${CMAKE_CURRENT_BINARY_DIR}
+            DEFINES     CONDUIT_PARALLEL
+            DEPENDS_ON  conduit conduit_blueprint conduit_relay conduit_relay_mpi_io ${conduit_blt_mpi_deps}
+            FOLDER      utils
+            )
+
+        # add install target
+        install(TARGETS conduit_generate_data_mpi
+                RUNTIME DESTINATION bin)
+    endif()
+endif()