Working interpolation from CFD data

.gitignore

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+.libs
+*-opt
+*-dbg
+*.so
+*.so.*
+*.la
+*.lo
+# Editor junk
+*.swp
+*.lo.d

Makefile

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+###############################################################################
+################### MOOSE Application Standard Makefile #######################
+###############################################################################
+#
+# Optional Environment variables
+# MOOSE_DIR        - Root directory of the MOOSE project 
+#
+###############################################################################
+# Use the MOOSE submodule if it exists and MOOSE_DIR is not set
+MOOSE_SUBMODULE    := $(CURDIR)/moose
+ifneq ($(wildcard $(MOOSE_SUBMODULE)/framework/Makefile),)
+  MOOSE_DIR        ?= $(MOOSE_SUBMODULE)
+else
+  MOOSE_DIR        ?= $(shell dirname `pwd`)/moose
+endif
+
+# framework
+FRAMEWORK_DIR      := $(MOOSE_DIR)/framework
+include $(FRAMEWORK_DIR)/build.mk
+include $(FRAMEWORK_DIR)/moose.mk
+
+################################## MODULES ####################################
+# To use certain physics included with MOOSE, set variables below to
+# yes as needed.  Or set ALL_MODULES to yes to turn on everything (overrides
+# other set variables).
+
+ALL_MODULES         := no
+
+CHEMICAL_REACTIONS  := no
+CONTACT             := yes
+FLUID_PROPERTIES    := no
+HEAT_CONDUCTION     := yes
+MISC                := no
+NAVIER_STOKES       := no
+PHASE_FIELD         := no
+RDG                 := no
+RICHARDS            := no
+SOLID_MECHANICS     := no
+STOCHASTIC_TOOLS    := no
+TENSOR_MECHANICS    := yes
+WATER_STEAM_EOS     := no
+XFEM                := no
+POROUS_FLOW         := no
+
+include $(MOOSE_DIR)/modules/modules.mk
+###############################################################################
+
+# dep apps
+APPLICATION_DIR    := $(CURDIR)
+APPLICATION_NAME   := deer
+BUILD_EXEC         := yes
+DEP_APPS           := $(shell $(FRAMEWORK_DIR)/scripts/find_dep_apps.py $(APPLICATION_NAME))
+include            $(FRAMEWORK_DIR)/app.mk
+
+###############################################################################
+# Additional special case targets should be added here

README.md

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+Deer
+=====
+
+"Fork Deer" to create a new MOOSE-based application.
+
+For more information see: [http://mooseframework.org/create-an-app/](http://mooseframework.org/create-an-app/)

include/base/DeerApp.h

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+#ifndef DEERAPP_H
+#define DEERAPP_H
+
+#include "MooseApp.h"
+
+class DeerApp;
+
+template<>
+InputParameters validParams<DeerApp>();
+
+class DeerApp : public MooseApp
+{
+public:
+  DeerApp(InputParameters parameters);
+  virtual ~DeerApp();
+
+  static void registerApps();
+  static void registerObjects(Factory & factory);
+  static void associateSyntax(Syntax & syntax, ActionFactory & action_factory);
+};
+
+#endif /* DEERAPP_H */

include/base/DeerRevision.h

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+/* THIS FILE IS AUTOGENERATED - DO NOT EDIT */
+
+#ifndef DEER_REVISION_H
+#define DEER_REVISION_H
+
+#define DEER_REVISION "unknown"
+
+#endif // DEER_REVISION_H

include/functions/TimeNDInterp.h

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+#ifndef TIME2DINTERP_H
+#define TIME2DINTERP_H
+
+#include "Function.h"
+
+#include "nanoflann.hpp"
+#include "KDTreeVectorOfVectorsAdaptor.h"
+
+using namespace nanoflann;
+
+typedef KDTreeVectorOfVectorsAdaptor<std::vector<std::vector<Real>>, Real> kd_tree_t;
+
+class TimeNDInterp;
+
+template <>
+InputParameters validParams<TimeNDInterp>();
+
+class TimeNDInterp : public Function
+{
+ public:
+  TimeNDInterp(const InputParameters & parameters);
+
+  virtual Real value(Real t, const Point & p) override;
+
+ private:
+  /// Read in data from HDF5 file
+  void read_data();
+  /// Setup the KD Tree
+  void setup_kdtree();
+
+ protected:
+  size_t ntime_, npoints_, ndim_;
+  FileName fname_;
+  std::vector<std::vector<Real>> points_;
+  std::vector<Real> times_;
+  std::vector<std::vector<Real>> values_;
+  std::unique_ptr<kd_tree_t> kd_;
+};
+
+
+#endif // TIME2DINTERP_H

include/kd/KDTreeVectorOfVectorsAdaptor.h

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+/***********************************************************************
+ * Software License Agreement (BSD License)
+ *
+ * Copyright 2011-16 Jose Luis Blanco (joseluisblancoc@gmail.com).
+ *   All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
+ * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+ * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *************************************************************************/
+
+#pragma once
+
+#include <nanoflann.hpp>
+
+#include <vector>
+
+// ===== This example shows how to use nanoflann with these types of containers: =======
+//typedef std::vector<std::vector<double> > my_vector_of_vectors_t;
+//typedef std::vector<Eigen::VectorXd> my_vector_of_vectors_t;   // This requires #include <Eigen/Dense>
+// =====================================================================================
+
+
+/** A simple vector-of-vectors adaptor for nanoflann, without duplicating the storage.
+  *  The i'th vector represents a point in the state space.
+  *
+  *  \tparam DIM If set to >0, it specifies a compile-time fixed dimensionality for the points in the data set, allowing more compiler optimizations.
+  *  \tparam num_t The type of the point coordinates (typically, double or float).
+  *  \tparam Distance The distance metric to use: nanoflann::metric_L1, nanoflann::metric_L2, nanoflann::metric_L2_Simple, etc.
+  *  \tparam IndexType The type for indices in the KD-tree index (typically, size_t of int)
+  */
+template <class VectorOfVectorsType, typename num_t = double, int DIM = -1, class Distance = nanoflann::metric_L2, typename IndexType = size_t>
+struct KDTreeVectorOfVectorsAdaptor
+{
+	typedef KDTreeVectorOfVectorsAdaptor<VectorOfVectorsType,num_t,DIM,Distance> self_t;
+	typedef typename Distance::template traits<num_t,self_t>::distance_t metric_t;
+	typedef nanoflann::KDTreeSingleIndexAdaptor< metric_t,self_t,DIM,IndexType>  index_t;
+
+	index_t* index; //! The kd-tree index for the user to call its methods as usual with any other FLANN index.
+
+	/// Constructor: takes a const ref to the vector of vectors object with the data points
+	KDTreeVectorOfVectorsAdaptor(const int dimensionality, const VectorOfVectorsType &mat, const int leaf_max_size = 10) : m_data(mat)
+	{
+		assert(mat.size()!=0 && mat[0].size()!=0);
+		const size_t dims = mat[0].size();
+		if (DIM>0 && static_cast<int>(dims)!=DIM)
+			throw std::runtime_error("Data set dimensionality does not match the 'DIM' template argument");
+		index = new index_t( dims, *this /* adaptor */, nanoflann::KDTreeSingleIndexAdaptorParams(leaf_max_size ) );
+		index->buildIndex();
+	}
+
+	~KDTreeVectorOfVectorsAdaptor() {
+		delete index;
+	}
+
+	const VectorOfVectorsType &m_data;
+
+	/** Query for the \a num_closest closest points to a given point (entered as query_point[0:dim-1]).
+	  *  Note that this is a short-cut method for index->findNeighbors().
+	  *  The user can also call index->... methods as desired.
+	  * \note nChecks_IGNORED is ignored but kept for compatibility with the original FLANN interface.
+	  */
+	inline void query(const num_t *query_point, const size_t num_closest, IndexType *out_indices, num_t *out_distances_sq, const int nChecks_IGNORED = 10) const
+	{
+		nanoflann::KNNResultSet<num_t,IndexType> resultSet(num_closest);
+		resultSet.init(out_indices, out_distances_sq);
+		index->findNeighbors(resultSet, query_point, nanoflann::SearchParams());
+	}
+
+	/** @name Interface expected by KDTreeSingleIndexAdaptor
+	  * @{ */
+
+	const self_t & derived() const {
+		return *this;
+	}
+	self_t & derived()       {
+		return *this;
+	}
+
+	// Must return the number of data points
+	inline size_t kdtree_get_point_count() const {
+		return m_data.size();
+	}
+
+	// Returns the distance between the vector "p1[0:size-1]" and the data point with index "idx_p2" stored in the class:
+	inline num_t kdtree_distance(const num_t *p1, const size_t idx_p2,size_t size) const
+	{
+		num_t s=0;
+		for (size_t i=0; i<size; i++) {
+			const num_t d= p1[i]-m_data[idx_p2][i];
+			s+=d*d;
+		}
+		return s;
+	}
+
+	// Returns the dim'th component of the idx'th point in the class:
+	inline num_t kdtree_get_pt(const size_t idx, int dim) const {
+		return m_data[idx][dim];
+	}
+
+	// Optional bounding-box computation: return false to default to a standard bbox computation loop.
+	//   Return true if the BBOX was already computed by the class and returned in "bb" so it can be avoided to redo it again.
+	//   Look at bb.size() to find out the expected dimensionality (e.g. 2 or 3 for point clouds)
+	template <class BBOX>
+	bool kdtree_get_bbox(BBOX & /*bb*/) const {
+		return false;
+	}
+
+	/** @} */
+
+}; // end of KDTreeVectorOfVectorsAdaptor
+
+