LBPM/IO/silo.h

#ifndef SILO_INTERFACE
#define SILO_INTERFACE

#include <array>
#include <string>
#include <vector>

#include "IO/Mesh.h"
#include "common/Array.h"
#include "common/Communication.h"
#include "common/MPI.h"


#ifdef USE_SILO
#include <silo.h>
#else
typedef int DBfile;
#endif


namespace IO {
namespace silo {


enum FileMode { READ, WRITE, CREATE };


/*!
 * @brief  Open silo file
 * @details  This function opens a silo file
 * @param[in] filename      File to open
 * @param[in] mode          Open the file for reading or writing
 * @return This function returns a handle to the file
 */
DBfile *open( const std::string &filename, FileMode mode );


/*!
 * @brief  Close silo file
 * @details  This function closes a silo file
 * @param[in] fid           Handle to the open file
 */
void close( DBfile *fid );


/*!
 * @brief  Get the variable type
 * @details  This function returns the type of variable data
 * @param[in] fid           Handle to the open file
 * @param[in] name          Name of variable
 */
DataType varDataType( DBfile *fid, const std::string &name );


/*!
 * @brief  Write data to silo
 * @details  This function writes an arbitrary array to silo
 * @param[in] fid           Handle to the open file
 * @param[in] varname       Variable name
 * @param[in] data          Data to write
 */
template<class TYPE>
void write( DBfile *fid, const std::string &varname, const std::vector<TYPE> &data );


/*!
 * @brief  Write data to silo
 * @details  This function writes an arbitrary array to silo
 * @param[in] fid           Handle to the open file
 * @param[in] varname       Variable name
 * @return                  Data read
 */
template<class TYPE>
std::vector<TYPE> read( DBfile *fid, const std::string &varname );


/*!
 * @brief  Write a uniform grid
 * @details  This function writes a uniform grid to silo as a Quadmesh
 * @param[in] fid           Handle to the open file
 * @param[in] meshname      Mesh name
 * @param[in] range         Range of mesh { xmin, xmax, ymin, ymax, zmin, zmax }
 * @param[in] N             Number of cells in each direction
 */
template<int NDIM>
void writeUniformMesh( DBfile *fid, const std::string &meshname,
    const std::array<double, 2 * NDIM> &range, const std::array<int, NDIM> &N );


/*!
 * @brief  Read a uniform grid
 * @details  This function reads a uniform grid from silo
 * @param[in] fid           Handle to the open file
 * @param[in] meshname      Mesh name
 * @param[out] range         Range of mesh { xmin, xmax, ymin, ymax, zmin, zmax }
 * @param[out] N             Number of cells in each direction
 */
void readUniformMesh(
    DBfile *fid, const std::string &meshname, std::vector<double> &range, std::vector<int> &N );


/*!
 * @brief  Write a uniform grid variable
 * @details  This function writes a uniform grid variable to silo as a Quadmesh
 * @param[in] fid           Handle to the open file
 * @param[in] meshname      Mesh name
 * @param[in] N             Number of cells in each direction
 * @param[in] varname       Variable name
 * @param[in] data          Variable data
 * @param[in] type          Variable type
 */
template<int NDIM, class TYPE>
void writeUniformMeshVariable( DBfile *fid, const std::string &meshname,
    const std::array<int, NDIM> &N, const std::string &varname, const Array<TYPE> &data,
    VariableType type );


/*!
 * @brief  Read a uniform mesh grid variable
 * @details  This function read a uniform mesh variable to silo
 * @param[in] fid           Handle to the open file
 * @param[in] varname       Variable name
 * @return                  Variable data
 */
template<class TYPE>
Array<TYPE> readUniformMeshVariable( DBfile *fid, const std::string &varname );


/*!
 * @brief  Write a pointmesh
 * @details  This function writes a pointmesh to silo
 * @param[in] fid           Handle to the open file
 * @param[in] meshname      Mesh name
 * @param[in] ndim          Number of dimensions
 * @param[in] N             Number of points
 * @param[in] coords        Coordinates of the points
 */
template<class TYPE>
void writePointMesh(
    DBfile *fid, const std::string &meshname, int ndim, int N, const TYPE *coords[] );


/*!
 * @brief  Read a pointmesh
 * @details  This function reads a pointmesh from silo
 * @param[in] fid           Handle to the open file
 * @param[in] meshname      Mesh name
 * @return                  Returns the coordinates as a N x ndim array
 */
template<class TYPE>
Array<TYPE> readPointMesh( DBfile *fid, const std::string &meshname );


/*!
 * @brief  Write a pointmesh grid variable
 * @details  This function writes a pointmesh variable to silo
 * @param[in] fid           Handle to the open file
 * @param[in] meshname      Mesh name
 * @param[in] varname       Variable name
 * @param[in] data          Variable data
 */
template<class TYPE>
void writePointMeshVariable(
    DBfile *fid, const std::string &meshname, const std::string &varname, const Array<TYPE> &data );


/*!
 * @brief  Read a pointmesh grid variable
 * @details  This function reads a pointmesh variable from silo
 * @param[in] fid           Handle to the open file
 * @param[in] varname       Variable name
 * @return                  Variable data
 */
template<class TYPE>
Array<TYPE> readPointMeshVariable( DBfile *fid, const std::string &varname );


/*!
 * @brief  Write a triangle mesh
 * @details  This function writes a triangle (or simplex) based mesh to silo
 * @param[in] fid           Handle to the open file
 * @param[in] meshname      Mesh name
 * @param[in] ndim          Number of dimensions for the coordinates
 * @param[in] ndim_tri      Number of dimensions for the triangles (2: surface, 3: volume)
 * @param[in] N             Number of points
 * @param[in] coords        Coordinates of the points
 * @param[in] N_tri         Number of triangles
 * @param[in] tri           Coordinates of the points
 */
template<class TYPE>
void writeTriMesh( DBfile *fid, const std::string &meshname, int ndim, int ndim_tri, int N,
    const TYPE *coords[], int N_tri, const int *tri[] );


/*!
 * @brief  Read a triangle mesh
 * @details  This function reads a triangle (or simplex) based mesh to silo
 * @param[in] fid           Handle to the open file
 * @param[in] meshname      Mesh name
 * @param[in] coords        Coordinates of the points
 * @param[in] tri           Coordinates of the points
 */
template<class TYPE>
void readTriMesh( DBfile *fid, const std::string &meshname, Array<TYPE> &coords, Array<int> &tri );


/*!
 * @brief  Write a triangle mesh grid variable
 * @details  This function writes a triangle mesh variable to silo
 * @param[in] fid           Handle to the open file
 * @param[in] ndim          Number of dimensions
 * @param[in] meshname      Mesh name
 * @param[in] varname       Variable name
 * @param[in] data          Variable data
 * @param[in] type          Variable type
 */
template<class TYPE>
void writeTriMeshVariable( DBfile *fid, int ndim, const std::string &meshname,
    const std::string &varname, const Array<TYPE> &data, VariableType type );


/*!
 * @brief  Read a triangle mesh grid variable
 * @details  This function read a triangle mesh variable to silo
 * @param[in] fid           Handle to the open file
 * @param[in] varname       Variable name
 * @return                  Variable data
 */
template<class TYPE>
Array<TYPE> readTriMeshVariable( DBfile *fid, const std::string &varname );


/*!
 * @brief  Write a multimesh
 * @details  This function writes a multimesh to silo
 * @param[in] fid           Handle to the open file
 * @param[in] meshname      Mesh name
 * @param[in] subMeshNames  Names of the sub meshes in the form "filename:meshname"
 * @param[in] subMeshTypes  Type of each submesh
 */
void writeMultiMesh( DBfile *fid, const std::string &meshname,
    const std::vector<std::string> &subMeshNames, const std::vector<int> &subMeshTypes );


/*!
 * @brief  Write a multivariable
 * @details  This function writes a multivariable to silo
 * @return This function returns a handle to the file
 * @param[in] fid           Handle to the open file
 * @param[in] varname       Mesh name
 * @param[in] subVarNames   Names of the sub meshes in the form "filename:meshname"
 * @param[in] subVarTypes   Type of each submesh
 */
void writeMultiVar( DBfile *fid, const std::string &varname,
    const std::vector<std::string> &subVarNames, const std::vector<int> &subVarTypes );


} // namespace silo
} // namespace IO

#endif

#include "IO/silo.hpp"