dataexporter/src/FinleyMesh.h


/*******************************************************
*
* Copyright (c) 2003-2009 by University of Queensland
* Earth Systems Science Computational Center (ESSCC)
* http://www.uq.edu.au/esscc
*
* Primary Business: Queensland, Australia
* Licensed under the Open Software License version 3.0
* http://www.opensource.org/licenses/osl-3.0.php
*
*******************************************************/

#ifndef __FINLEYMESH_H__
#define __FINLEYMESH_H__

#include <escriptexport/escriptexport.h>
#include <escript/AbstractDomain.h>

class DBfile;
struct Finley_Mesh;

namespace escriptexport {

class ElementData;
class NodeData;

/// \brief Represents a full Finley domain including nodes and elements.
///
/// This class represents a Finley domain including nodes, cells, face elements
/// and contact elements. It provides functionality to read a domain from a
/// NetCDF file (generated by the domain's dump() method) or directly
/// through an instance of Finley_Mesh.
///
/// Once initialised, the domain can be saved in the Silo file format or
/// its nodes and elements accessed through the respective methods.
///
/// Note that this class is not MPI aware, that is if domain decomposition
/// was used only one 'chunk' of the domain can be read per instance of this
/// class. See MPDataSet for how to process full domains.
class FinleyMesh
{
public:
    /// \brief Default constructor.
    ESCRIPTEXPORT_DLL_API
    FinleyMesh();

    /// \brief Copy constructor.
    ESCRIPTEXPORT_DLL_API
    FinleyMesh(const FinleyMesh& m);
 
    /// \brief Virtual destructor.
    ESCRIPTEXPORT_DLL_API
    virtual ~FinleyMesh();

    /// \brief Initialises the mesh using an escript domain instance.
    /// \note Finley_Mesh is the only supported domain.
    ESCRIPTEXPORT_DLL_API
    bool initFromEscript(escript::const_Domain_ptr escriptDomain);

    /// \brief Reads the mesh from a NetCDF file
    ESCRIPTEXPORT_DLL_API
    bool initFromNetCDF(const std::string& filename);

    /// \brief Writes the mesh to a Silo file
    ESCRIPTEXPORT_DLL_API
    bool writeToSilo(DBfile* dbfile, const std::string& pathInSilo);

    /// \brief Reorders elements so that 'ghost' elements appear last
    ESCRIPTEXPORT_DLL_API
    void reorderGhostZones(int ownIndex);

    /// \brief Removes 'ghost' elements and nodes
    ESCRIPTEXPORT_DLL_API
    void removeGhostZones(int ownIndex);

    /// \brief Returns the names of all meshes
    ESCRIPTEXPORT_DLL_API
    StringVec getMeshNames() const;

    /// \brief Returns the names of all 'special' Finley mesh variables
    ESCRIPTEXPORT_DLL_API
    StringVec getVarNames() const;

    /// \brief Returns element data with given name
    ESCRIPTEXPORT_DLL_API
    ElementData_ptr getElementsByName(const std::string& name) const;

    /// \brief Returns node data with given name
    ESCRIPTEXPORT_DLL_API
    NodeData_ptr getMeshByName(const std::string& name) const;

    /// \brief Returns mesh variable data
    ESCRIPTEXPORT_DLL_API
    const IntVec& getVarDataByName(const std::string& name) const;

    /// \brief Returns the node mesh for given function space
    ESCRIPTEXPORT_DLL_API
    NodeData_ptr getMeshForFinleyFS(int functionSpace) const;

    /// \brief Returns the element data for given function space
    ESCRIPTEXPORT_DLL_API
    ElementData_ptr getElementsForFinleyFS(int functionSpace) const;

    /// \brief Returns a pointer to the nodes.
    ESCRIPTEXPORT_DLL_API
    NodeData_ptr getNodes() const { return nodes; }

    /// \brief Returns a pointer to the elements.
    ESCRIPTEXPORT_DLL_API
    ElementData_ptr getElements() { return cells; }

    /// \brief Returns a pointer to the face elements.
    ESCRIPTEXPORT_DLL_API
    ElementData_ptr getFaceElements() { return faces; }

    /// \brief Returns a pointer to the contact elements.
    ESCRIPTEXPORT_DLL_API
    ElementData_ptr getContactElements() { return contacts; }

    /// \brief Returns the absolute path within Silo file if writeToSilo()
    ///        or setSiloPath() was called before, the empty string otherwise.
    ESCRIPTEXPORT_DLL_API
    std::string getSiloPath() const { return siloPath; }

    /// \brief Sets the silo path to be used when saving to a Silo file.
    ESCRIPTEXPORT_DLL_API
    void setSiloPath(const std::string& path)  { siloPath = path; }

private:
    void cleanup();

    bool initialized;
    const Finley_Mesh* finleyMesh;
    NodeData_ptr    nodes;
    ElementData_ptr cells;
    ElementData_ptr faces;
    ElementData_ptr contacts;
    std::string siloPath;
};

} // namespace escriptexport

#endif // __FINLEYMESH_H__

1
2	/*******************************************************
3	*
4	* Copyright (c) 2003-2009 by University of Queensland
5	* Earth Systems Science Computational Center (ESSCC)
6	* http://www.uq.edu.au/esscc
7	*
8	* Primary Business: Queensland, Australia
9	* Licensed under the Open Software License version 3.0
10	* http://www.opensource.org/licenses/osl-3.0.php
11	*
12	*******************************************************/
13
14	#ifndef __FINLEYMESH_H__
15	#define __FINLEYMESH_H__
16
17	#include <escriptexport/escriptexport.h>
18	#include <escript/AbstractDomain.h>
19
20	class DBfile;
21	struct Finley_Mesh;
22
23	namespace escriptexport {
24
25	class ElementData;
26	class NodeData;
27
28	/// \brief Represents a full Finley domain including nodes and elements.
29	///
30	/// This class represents a Finley domain including nodes, cells, face elements
31	/// and contact elements. It provides functionality to read a domain from a
32	/// NetCDF file (generated by the domain's dump() method) or directly
33	/// through an instance of Finley_Mesh.
34	///
35	/// Once initialised, the domain can be saved in the Silo file format or
36	/// its nodes and elements accessed through the respective methods.
37	///
38	/// Note that this class is not MPI aware, that is if domain decomposition
39	/// was used only one 'chunk' of the domain can be read per instance of this
40	/// class. See MPDataSet for how to process full domains.
41	class FinleyMesh
42	{
43	public:
44	/// \brief Default constructor.
45	ESCRIPTEXPORT_DLL_API
46	FinleyMesh();
47
48	/// \brief Copy constructor.
49	ESCRIPTEXPORT_DLL_API
50	FinleyMesh(const FinleyMesh& m);
51
52	/// \brief Virtual destructor.
53	ESCRIPTEXPORT_DLL_API
54	virtual ~FinleyMesh();
55
56	/// \brief Initialises the mesh using an escript domain instance.
57	/// \note Finley_Mesh is the only supported domain.
58	ESCRIPTEXPORT_DLL_API
59	bool initFromEscript(escript::const_Domain_ptr escriptDomain);
60
61	/// \brief Reads the mesh from a NetCDF file
62	ESCRIPTEXPORT_DLL_API
63	bool initFromNetCDF(const std::string& filename);
64
65	/// \brief Writes the mesh to a Silo file
66	ESCRIPTEXPORT_DLL_API
67	bool writeToSilo(DBfile* dbfile, const std::string& pathInSilo);
68
69	/// \brief Reorders elements so that 'ghost' elements appear last
70	ESCRIPTEXPORT_DLL_API
71	void reorderGhostZones(int ownIndex);
72
73	/// \brief Removes 'ghost' elements and nodes
74	ESCRIPTEXPORT_DLL_API
75	void removeGhostZones(int ownIndex);
76
77	/// \brief Returns the names of all meshes
78	ESCRIPTEXPORT_DLL_API
79	StringVec getMeshNames() const;
80
81	/// \brief Returns the names of all 'special' Finley mesh variables
82	ESCRIPTEXPORT_DLL_API
83	StringVec getVarNames() const;
84
85	/// \brief Returns element data with given name
86	ESCRIPTEXPORT_DLL_API
87	ElementData_ptr getElementsByName(const std::string& name) const;
88
89	/// \brief Returns node data with given name
90	ESCRIPTEXPORT_DLL_API
91	NodeData_ptr getMeshByName(const std::string& name) const;
92
93	/// \brief Returns mesh variable data
94	ESCRIPTEXPORT_DLL_API
95	const IntVec& getVarDataByName(const std::string& name) const;
96
97	/// \brief Returns the node mesh for given function space
98	ESCRIPTEXPORT_DLL_API
99	NodeData_ptr getMeshForFinleyFS(int functionSpace) const;
100
101	/// \brief Returns the element data for given function space
102	ESCRIPTEXPORT_DLL_API
103	ElementData_ptr getElementsForFinleyFS(int functionSpace) const;
104
105	/// \brief Returns a pointer to the nodes.
106	ESCRIPTEXPORT_DLL_API
107	NodeData_ptr getNodes() const { return nodes; }
108
109	/// \brief Returns a pointer to the elements.
110	ESCRIPTEXPORT_DLL_API
111	ElementData_ptr getElements() { return cells; }
112
113	/// \brief Returns a pointer to the face elements.
114	ESCRIPTEXPORT_DLL_API
115	ElementData_ptr getFaceElements() { return faces; }
116
117	/// \brief Returns a pointer to the contact elements.
118	ESCRIPTEXPORT_DLL_API
119	ElementData_ptr getContactElements() { return contacts; }
120
121	/// \brief Returns the absolute path within Silo file if writeToSilo()
122	/// or setSiloPath() was called before, the empty string otherwise.
123	ESCRIPTEXPORT_DLL_API
124	std::string getSiloPath() const { return siloPath; }
125
126	/// \brief Sets the silo path to be used when saving to a Silo file.
127	ESCRIPTEXPORT_DLL_API
128	void setSiloPath(const std::string& path) { siloPath = path; }
129
130	private:
131	void cleanup();
132
133	bool initialized;
134	const Finley_Mesh* finleyMesh;
135	NodeData_ptr nodes;
136	ElementData_ptr cells;
137	ElementData_ptr faces;
138	ElementData_ptr contacts;
139	std::string siloPath;
140	};
141
142	} // namespace escriptexport
143
144	#endif // __FINLEYMESH_H__
145